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  5. 长期近亲繁殖动物的生存机制与案例研究

长期近亲繁殖动物的生存机制与案例研究

深度研究匿名用户发表于 2025年12月23日 15:292阅读
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1. 近亲繁殖的生物学基础与普遍灭绝风险

1.1 近亲繁殖的遗传效应解析

近亲繁殖（Inbreeding）是指亲缘关系较近的个体之间进行交配和繁殖的现象。其遗传本质在于导致后代基因组中纯合子（homozygosity）的比例增加，而杂合子（heterozygosity）的比例相应减少，即遗传多样性降低12。这种纯合度的增加，尤其是对于染色体上连续的纯合区域（Runs of Homozygosity, ROH）而言，是衡量近亲繁殖程度的重要指标345。

近亲繁殖最显著的负面后果是“近交衰退”（Inbreeding Depression），这是一种普遍存在的生物学现象，指的是亲缘关系较近个体繁殖的后代，其适应度（fitness）降低的表现。近交衰退的遗传学基础主要包括两个方面：

  1. 有害隐性等位基因的纯合化表达：每个个体基因组中都携带着一定数量的有害隐性突变。在随机交配的群体中，这些有害突变通常以杂合状态存在，其负面效应被显性正常等位基因所掩盖。然而，在近亲繁殖中，由于亲本共享祖先，后代从父母双方继承相同有害隐变基因的概率大大增加，导致这些隐性有害等位基因以纯合状态表达，从而引发各种生理缺陷、疾病易感性增加或发育异常1267。例如，在赛马中，近亲繁殖程度的增加与参赛概率降低有关，研究发现某个在软骨组织中高表达的基因的纯合性与赛马概率显著降低相关3；在家畜中，近交系数每增加1%，性状平均值会降低0.137%，其中生产性状的降低幅度更大（0.351%）8。在皮奥猪中，近交系数每增加1%导致平均断奶前日增重（ADG）减少0.005克9。人类的研究也表明，近亲繁殖系数（相当于表亲结婚的程度）与生育后代几率降低55%有关5。

  2. 适应性基因多样性丧失：近亲繁殖导致遗传多样性整体下降，这意味着群体在面对环境变化（如疾病、气候变化、资源匮乏）时，可供自然选择利用的遗传变异减少，从而降低了群体适应新环境或抵抗新威胁的能力1610。长期而言，这种适应性潜力的丧失可能会使种群在演化上陷入僵局，无法有效应对生存挑战。

近交衰退对个体的生存力、繁殖力和环境适应能力产生普遍的负面影响。例如，它可能导致后代出生体重下降、生长速度减缓、免疫力低下、疾病抵抗力差以及繁殖成功率降低（如生育力下降、后代存活率低）8911。研究表明，雌性个体可能比雄性个体遭受略高的近交衰退影响11。这些负面效应不仅在短期内削弱个体的健康和繁殖表现，长远来看也严重威胁了整个种群的存续。

1.2 近亲繁殖导致灭绝的典型路径

近亲繁殖与种群灭绝之间存在着密切的联系，其核心机制通常通过“灭绝漩涡”（Extinction Vortex）效应来体现 12。灭绝漩涡描述了一个恶性循环过程，其中种群的缩小与遗传、人口学和环境因素的负面影响相互作用，加速了种群走向灭绝的进程 1213。

灭绝漩涡的典型路径如下：

  1. 小种群规模：当种群数量减少到一定程度时，有效种群大小（Ne）也会随之减小。小种群面临更高的随机事件风险，如环境灾难、疾病爆发等，这些事件可能导致种群数量进一步骤降。
  2. 遗传多样性流失：小种群由于遗传漂变（genetic drift）效应增强，会迅速丢失遗传多样性 61214。遗传多样性的丧失意味着种群适应环境变化（如气候变化、新病原体出现）的潜力减弱 1。研究指出，即使是大型种群，在栖息地丧失和气候变化的背景下，也可能损失超过10%的遗传多样性 14。
  3. 近交衰退加剧：遗传多样性的减少直接导致近亲繁殖的发生率和程度增加 12。如前所述，近亲繁殖使得有害隐性等位基因纯合表达，严重降低个体的生存力、繁殖力，并可能导致多种健康问题和适应性缺陷 16。例如，在虎鲸种群中，近交衰退被证明强烈影响了其生存率，限制了种群增长，并预测若种群保持遗传隔离将进一步下降 15。此外，蜜蜂种群中近亲繁殖还会导致二倍体雄性产生，其后代不育，进一步加速种群的灭绝漩涡 16。
  4. 个体存活率与繁殖率下降：近交衰退导致的适应度下降，表现为个体寿命缩短、对疾病的抵抗力减弱、繁殖成功率降低（如产仔数减少、后代存活率低）612。这些直接影响种群的出生率和死亡率动态，使得种群无法有效补充或增长。例如，在寄生蜂中，近亲繁殖引起的二倍体雄性问题可导致灭绝风险增加 17。
  5. 种群进一步缩小：由于个体存活率和繁殖率的下降，种群数量将不可避免地进一步减少。这又回到了灭绝漩涡的起点，形成一个正反馈循环。
  6. 遗传压力循环增强：种群规模的持续缩小使得遗传漂变和近亲繁殖的负面影响愈发显著，遗传多样性持续丢失，有害突变积累，最终使得种群在遗传上变得“枯竭”，完全丧失适应和恢复的能力 12。

这个连锁反应最终导致种群无法维持最低生存阈值，从而走向灭绝 1。在许多濒危物种中，都可以观察到这种灭绝漩涡的迹象。例如，对已灭绝植物种群的分析显示，其遗传多样性在灭绝前显著下降，并表现出更高的近交衰退，这为灭绝漩涡理论提供了实证支持 18。

值得注意的是，性选择在一定程度上可以影响灭绝漩涡的进程。有研究表明，强性选择的种群在面对环境和遗传压力时，其适应度下降较慢，灭绝风险较低，这可能通过“清除有害基因”来缓解近交衰退的影响 19。然而，如果性选择因其他因素（如性食同类率过高）而导致生殖冲突，也可能进一步降低种群活力 20。

2. 长期近亲繁殖未灭绝的动物案例

2.1 岛屿特有种的极端近亲繁殖生存

岛屿生态系统因其独特的地理隔离特性，常常孕育出高度特有且长期处于近亲繁殖状态的物种。这些岛屿特有种在有限的栖息地内，种群规模相对较小，基因交流受到极大限制，按理说应更容易遭受近交衰退的负面影响而走向灭绝。然而，一些岛屿物种却表现出令人惊讶的长期近亲繁殖生存能力。

例如，夏威夷的吸蜜鸟（Hawaiian honeycreepers）面临着前所未有的灭绝危机，尽管它们的种群数量急剧下降，甚至有些物种已濒临灭绝，但出乎意料的是，这些鸟类，包括已灭绝的Po'ouli个体，仍然保持着较高的杂合度，这反映了它们历史上曾有较大的种群规模 21。尽管如此，高度近亲繁殖的‘Akikiki鸟种群中，个体表现出较低的生存率和繁殖成功率，这表明近交衰退对其产生了显著影响 21。

另一个案例是台湾的中华穿山甲（Manis pentadactyla pentadactyla）。作为一种极度濒危的岛屿特有亚种，其北部品系由于经历了更严重的种群瓶颈和隔离，导致遗传多样性较低，近亲繁殖程度较高，遗传负荷也更高 22。这意味着它们对气候变化等环境压力的抵抗力更弱，需要更高的种群增长率才能在未来100年内达到与非北部品系相同的演化潜力，因此其保护工作更具优先性 22。

在毛里求斯，特有物种Phelsuma guimbeaui（低地森林日行守宫）也面临着严重的近亲繁殖风险。由于栖息地碎片化和人类定居造成的隔离，该物种现在仅限于30个孤立的小型亚种群 23。微卫星数据显示，这些亚种群之间存在显著的种群结构，遗传多样性高，但遗传分化大，且大多数亚种群之间没有基因迁移 23。亚种群的有效种群规模很小，从44到167不等，模拟结果表明，如果缺乏迁移，部分亚种群在未来50年内生存和等位基因多样性将急剧下降 23。

塔斯马尼亚恶魔（Tasmanian devil）也提供了一个独特的案例。该物种正遭受毁灭性的传染性面部肿瘤病（DFTD）威胁，导致野生种群急剧下降，面临近交衰退的风险。为了保护该物种，研究人员建立了圈养“保险种群” 24。尽管圈养种群中个体的近亲繁殖程度存在显著差异，但研究并未发现近亲繁殖与六种适应性指标（如尺骨长度、断奶体重、睾丸体积、繁殖成功率和存活率）之间存在关联 24。这可能表明，在没有野生环境压力的圈养条件下，近交衰退的强度会降低 24。然而，对野生塔斯马尼亚恶魔的研究发现，其面临疾病导致的种群下降，虽然存在近亲繁殖，但在对DFTD易感性、体型大小等性状上并未发现近交衰退的证据，这可能与该物种对疾病的快速适应性演化潜力有关 2526。

这些案例共同揭示了岛屿特有种在长期近亲繁殖下生存的复杂性。它们能够长期存在而未灭绝，可能受到多种因素的支撑，包括：

  • 种群规模和历史：虽然目前种群可能很小，但历史上较大的种群规模为其积累了相对较高的遗传多样性，使得它们在一定程度上能承受后来的种群瓶颈和近亲繁殖压力 21。
  • 栖息地稳定性：在某些岛屿上，如果环境相对稳定，资源充足，且天敌较少，物种可能面临较低的选择压力，从而降低了近交衰退的负面影响。
  • 遗传负荷的清除：在长期小种群和近亲繁殖的环境下，有害隐性等位基因可能通过自然选择逐渐被清除，即“遗传净化”（genetic purging）过程。这使得种群能够适应高近亲繁殖水平。

然而，这些看似能够承受近亲繁殖的岛屿物种，一旦遭遇环境剧变，如气候变化、疾病爆发或栖息地丧失，其脆弱的平衡就可能被打破，使其面临更高的灭绝风险 2223。

2.2 实验室与人工管理种群的特殊案例

在实验室环境和人工管理下，一些动物种群长期进行着高度近亲繁殖，但并未灭绝，这主要得益于人类的严格控制和干预措施。这些案例为理解近亲繁殖的边界效应提供了宝贵的视角。

实验室小鼠是研究近亲繁殖的典型模型。为了实验的标准化和重复性，实验室通常会培育高度近交系的品系，例如，衰老加速小鼠（Senescence-Accelerated Mouse, SAM）就是通过对AKR/J品系小鼠进行选择性近亲繁殖而开发的，目前已有9个易衰老近交系（SAMP）和3个抗衰老近交系（SAMR），它们分别表现出加速衰老或抵抗衰老的特性 27。这些近交系小鼠在特定的研究背景下得以维持，但它们通常具有较低的遗传多样性，并可能表现出一些近交衰退的症状。例如，虽然异系繁殖小鼠在同种异体移植中表现出异质性的结果，部分移植早期失败，但总的来说，它们的“杂种优势”和遗传多样性并未对诱导免疫耐受形成普遍障碍 28。这表明，尽管近亲繁殖在某些方面降低了适应性，但在受控条件下，其负面影响可以被管理或利用。

家猫和家犬等伴侣动物的繁育也提供了大量人工管理下近亲繁殖的案例。为了保持特定的品种标准（如外貌、行为特征），育种者常常采用近亲繁殖或系内繁殖的策略 2930。然而，这种做法也导致了遗传多样性的丧失和近交衰退的风险增加。

  • 家猫：与狗的品种相比，猫的品种内个体数量通常较少，为了维持品种标准，一定程度的近亲繁殖是必要的 29。然而，当近亲繁殖达到一定阈值时，会导致生育力下降，表现为受孕失败、产仔数减少、新生儿疾病增加和死亡率上升 29。例如，对暹罗猫等纯种猫的研究表明，它们存在较高的近交水平，需要采取适当的育种实践，例如增加遗传多样性，以降低近交衰退和遗传疾病的风险 31。欧洲大陆的泰国猫（传统暹罗猫）种群通过优化贡献选择和限制与其他品种的杂交，可以显著改善其遗传多样性 32。对流浪猫和人工选育的暹罗猫及东方短毛猫的研究显示，人工选育的猫品种近亲繁殖系数显著高于流浪猫，且有效种群规模急剧缩小，基因组纯合片段（ROH）更长更频繁，这表明长期的人工选择导致了遗传多样性的快速流失 33。
  • 家犬：犬类同样面临近亲繁殖的挑战。许多纯种犬品系在建立过程中经历了严重的种群瓶颈和近亲繁殖，导致遗传多样性降低，并与各种健康问题和寿命缩短相关 3034。例如，与体型相匹配的混血犬相比，纯种犬的平均寿命短约1.2年 34。在一项针对9000多只金毛猎犬的研究中，个体层面的近亲繁殖系数确实对寿命产生了负面影响 34。瑞典的12个本土犬种的研究显示，在1980年至2012年间，平均近亲繁殖系数从0.03增加到0.07，创始人等位基因平均丧失了70% 35。这表明，即使是数量庞大的品种，如果育种实践不当，也可能迅速增加近亲繁殖水平。

然而，人工管理种群之所以能长期维持，主要在于：

  1. 选择性淘汰有害表型：育种者会主动淘汰表现出严重遗传缺陷或疾病的个体，从而在一定程度上清除群体中的有害隐性等位基因。
  2. 基因补充与育种管理：在某些情况下，育种者会引入外部血缘（outcross）以增加遗传多样性，缓解近交衰退。例如，一些保护项目会通过“遗传救援”来挽救濒危的近亲繁殖种群。此外，现代育种已开始利用基因组信息来计算近亲繁殖系数，并指导配对，以最大程度地保留遗传多样性 30。
  3. 受控环境：实验室和人工养殖环境通常提供稳定的食物、适宜的温度、医疗护理等，减少了自然选择的压力，使得一些在野外无法存活的近亲繁殖个体得以生存和繁衍。

这些案例表明，在人类的干预下，通过精心的育种策略、基因监测和环境控制，即使是高度近亲繁殖的种群也能在一定程度上规避灭绝的风险。然而，这并不能完全消除近亲繁殖带来的潜在危害，尤其是在遗传疾病和整体适应性方面。

2.3 自然种群的“抗性”案例

在自然界中，一些长期处于近亲繁殖状态的物种，通过其独特的生物学机制或环境因素，表现出对近交衰退的“抗性”，得以在遗传多样性较低的情况下存续。这些案例为理解近亲繁殖的复杂影响提供了重要的视角。

面粉甲虫（Tribolium castaneum） 的实验研究提供了一个在强性选择压力下，近亲繁殖种群通过清除有害突变维持生存的实证。在一个模拟严苛环境的实验中，研究人员观察了红面粉甲虫在不同移民率下的适应性变化。结果表明，在初始种群下降后，没有移民的种群比有移民的种群提前一代获得了更高的增长率，这说明了移民对适应的限制作用。然而，经过7代之后，无论移民率如何，所有种群都表现出了适应性的证据 36。这项研究揭示了即使在近亲繁殖加剧的条件下，强烈的自然选择或性选择也能驱动种群进化，清除有害突变，从而实现“遗传净化”，使种群得以适应。具体来说，当种群面临高压环境时，那些携带适应性基因的个体具有更强的生存和繁殖优势，有害突变携带者则被淘汰，从而在一定程度上缓解了近交衰退。

除了实验室模型，一些野生种群也展现出类似的“抗性”：

  • 野生绵羊（Soay sheep）：苏格兰圣基尔达岛的索艾羊是一个长期受到研究的孤立种群，其历史上的种群瓶颈和持续的近亲繁殖使其基因组中存在广泛的纯合区域（ROH） 3738。研究发现，长ROH（>12.5 cM）导致的第一年存活率降低幅度（12.4%）远高于中ROH（1.56-12.5 cM）的降低幅度（7.7%），而短ROH（<1.56 cM）对存活率没有影响 37。这与理论预测一致：相比短ROH，长ROH中通常包含更高密度的有害等位基因。然而，研究也表明，在较老的单倍型（通常对应于短ROH）中，突变负荷会随着时间推移而减少，这暗示了纯化选择（purifying selection）一直在清除有害突变 37。尽管存在持续的近交衰退，这个种群仍在自然环境中维持了数百年，这可能归因于长期的遗传净化过程，使得最严重的有害突变已被淘汰，种群对高近亲繁殖水平产生了某种程度的耐受性。
  • 阿纳托利亚盘羊和塞浦路斯盘羊（Anatolian and Cyprian mouflons）：这两种濒危的盘羊亚种在20世纪濒临灭绝，目前被IUCN列为濒危物种 39。对它们的全基因组测序分析显示，这两个亚种都具有相当多的短ROH片段，反映了小的有效种群大小。其中，塞浦路斯盘羊的有效种群大小和突变负荷估计值低于阿纳托利亚盘羊，这表明在塞浦路斯盘羊的长期小有效种群中，隐性有害变异可能被清除 39。这可能是由于奠基者效应、岛屿隔离、与家养血统的基因渗入或瓶颈动态差异等因素导致的。尽管面临严重的近亲繁殖，它们通过长期的遗传净化过程得以存续。
  • 斯堪的纳维亚狼（Scandinavian wolf）：这是一个隔离且高度近亲繁殖的种群。然而，研究发现，少量移民的引入（遗传救援）可以显著提高后代的配对和繁殖成功率 40。这表明，虽然该种群曾遭受严重的近交衰退，但在一定程度上通过基因流的引入获得了恢复力，并得以继续存在。
  • 条纹海豚（Striped dolphin）：对条纹海豚的研究发现，近亲繁殖程度与病原体负荷之间存在关联，但在雌性海豚中，杂合度较高的个体具有较低的肺部线虫感染率 41。这表明近交衰退通过降低免疫力来增加疾病易感性，但种群中仍存在较高杂合度的个体能够抵抗病原体，这可能反映了对某些特定基因座的强选择作用，从而维持了种群的生存。

这些案例表明，自然种群在面对近亲繁殖压力时，并非总是走向灭绝。通过遗传净化（即自然选择清除有害隐性突变）、环境缓冲（如稳定的资源、较低的竞争或捕食压力），以及性选择（通过偏好高适应性配偶来维持种群健康），一些物种能够发展出对近交衰退的抵抗机制，在严酷的遗传条件下长期存活。然而，这种“抗性”并非无限，环境的剧烈变化仍可能打破这种脆弱的平衡。

3. 长期近亲繁殖未灭绝的关键生存机制

3.1 遗传净化：有害突变的清除效应

“遗传净化”（Genetic purging）是指在长期近亲繁殖或种群规模持续较小的情况下，自然选择系统性地淘汰携带严重有害隐性突变的个体，从而减少群体中有害突变负荷（genetic load）的过程 742。这一机制是解释某些近亲繁殖种群为何能够持续生存而未灭绝的关键因素之一 743。

遗传净化的基本原理如下：在近亲繁殖过程中，原本以杂合状态存在而不表现有害效应的隐性突变，因纯合度增加而得以表达。一旦这些有害突变以纯合形式出现，携带者往往表现出较低的适应性，例如存活率下降、繁殖力降低或更易患病。自然选择随即对这些适应性低的个体进行淘汰，将其从基因库中清除。随着世代的推移，那些严重有害的隐性突变逐渐被清除，使得种群整体的遗传负荷降低，从而缓解近交衰退的强度 744。

然而，遗传净化并非对所有有害突变都有效。它主要针对那些效应较强、纯合后能显著降低个体适应性的隐性突变。对于那些效应微弱（微效有害突变）或部分显性的突变，由于其对适应性的影响不明显，自然选择的清除效率较低，因此这类突变在近亲繁殖种群中仍可能累积 4546。此外，遗传净化的效率还受到突变本身的显性程度、选择强度以及种群历史（如瓶颈强度和持续时间）的影响 742。

多项基因组学研究为遗传净化现象提供了实证支持：

  • 野生绵羊与鹿类：对山羊（mountain goat）、白尾鹿（white-tailed deer）和驯鹿（caribou）等有蹄类动物的基因组研究显示，长期经历瓶颈效应和低有效种群大小的山羊，其基因组中纯合区域（ROH）的比例更高，但有害突变负荷（尤其是在高度受限的基因区域）反而更低 47。这表明在长期的小种群历史中，强烈的纯化选择有效地清除了大部分有害等位基因。与此相反，白尾鹿虽然种群正在扩张，但其有害突变负荷最高，这可能反映了有害突变在没有强净化选择压力下的累积 47。
  • 阿纳托利亚盘羊与塞浦路斯盘羊：对这两种濒危盘羊亚种的全基因组分析表明，塞浦路斯盘羊的有效种群大小和突变负荷估计值均低于阿纳托利亚盘羊 3948。这可能意味着塞浦路斯盘羊在长期的小种群隔离状态下，通过遗传净化过程，清除了其基因组中的隐性有害变异 39。
  • 印度虎：一项对57只印度虎的全基因组测序研究发现，小型孤立种群（平均基因组近亲繁殖系数F=0.57）虽然近亲繁殖水平显著高于大型连接种群，但其功能缺失突变（loss-of-function mutation）负荷最低 49。这强烈暗示了在小种群中，强烈的纯化选择导致了高度有害的隐性突变的清除，即遗传净化。尽管如此，该研究也指出，小种群中剩余的有害等位基因频率更高，纯合性也更高，这仍可能导致与近亲繁殖相关的适应性代价 49。
  • 树蕨：在高度近亲繁殖的树蕨（Alsophila spinulosa）中，基因组分析显示其有害突变总量有所减少 43。这表明长期近亲繁殖可能促使强烈有害突变被清除，从而延长了该物种的生存时间 43。
  • 罗德豪岛竹节虫：这种竹节虫在圈养繁殖过程中经历了极端的人口瓶颈。研究发现，在如此极端的瓶颈之后，致死突变（stop-codon mutations）在圈养个体中被优先清除，尤其是在纯合区域外检测到的有害突变更多，这说明近亲繁殖加速了有害突变的表达和清除 50。

这些研究共同揭示了遗传净化在长期近亲繁殖种群中维持生存能力的重要性。虽然近亲繁殖会带来短期内的适应度下降，但长期的近亲繁殖环境也可能为自然选择提供清除有害突变的机会，从而使种群对高近亲繁殖水平产生一定程度的耐受性。这种动态平衡是理解一些极端近亲繁殖物种能够持续存在而不灭绝的关键机制之一。然而，这并不意味着近亲繁殖是无害的，它始终伴随着遗传多样性降低和对环境变化适应能力减弱的风险。

3.2 性选择与繁殖策略的调节作用

性选择（Sexual selection）在长期近亲繁殖的种群中扮演着至关重要的角色，它可以通过“基因捕获”（genic capture）机制，有效地筛选出具有高适应性的个体，从而缓解近交衰退的负面影响，为种群的持续生存提供优势 51。基因捕获理论认为，如果繁殖成功与个体的整体状况（condition）相关，而个体状况又受到突变负荷（mutation load）的影响，那么性选择就能通过筛选高质量配偶来清除有害突变 51。

性选择的净化效应：面粉甲虫的实验证据

对面粉甲虫（Tribolium castaneum）的实验研究提供了性选择如何对抗近交衰退的有力证据。研究人员将面粉甲虫种群分别在强性选择和弱性选择条件下饲养了6至7年。强性选择组允许雄性之间进行激烈竞争，雌性有充分的配偶选择权；弱性选择组则限制了这种竞争和选择。随后，研究人员对来自这两个组的甲虫进行了近亲繁殖（兄妹交配）实验，以观察它们对近交衰退的抵抗力 51。

结果发现：

  • 强性选择背景下的种群：在长期经历强性选择的种群中，其后代在近亲繁殖条件下表现出更强的生命力和适应性，不易灭绝。即使经过20代的兄妹交配，一些家系仍能存活 51。这表明强烈的性选择有效地清除了种群中的突变负荷，使其对遗传压力（如近亲繁殖）具有更强的抵抗力。
  • 弱性选择背景下的种群：相比之下，那些经历弱性选择或没有性选择的种群，在近亲繁殖条件下迅速表现出适应性下降，在第10代后所有家系均已灭绝 51。

这一实验结果有力地支持了“性选择通过基因捕获机制清除有害突变，从而提高种群面对遗传压力的生存能力”的理论 51。性选择的作用在于，它不仅决定了哪些个体能够成功繁殖，更重要的是，它通过淘汰携带更多有害突变的低适应性个体，减少了有害基因在种群中的传播，从而降低了整体突变负荷。

繁殖策略的调节作用

除了性选择，不同的繁殖策略也可能在缓解近亲繁殖影响方面发挥作用：

  • 多配偶制（Polyandry）：指雌性与多个雄性交配的繁殖系统。在一些鸟类中，例如在某些岸鸟（shorebirds）中观察到的角色逆转的多配偶制，可能与更快的Z染色体进化速度相关 52。这可能表明，在强性选择作用于多配偶雌性的情况下，有利于隐性优势等位基因固定的选择压力更强 52。在存在配子选择（如精子竞争）的情况下，多配偶制可以增加后代的适应度，因为它为雌性提供了选择高质量配子的机会 53。通过这种机制，多配偶制可能有助于降低近交衰退的程度，甚至在一定程度上补偿近亲繁殖带来的不利影响。研究发现，在基因救援中，即使救援效果会随时间减弱，但高强度性选择背景下的救援者能更有效地改善种群生产力 54。
  • 雌雄同体与自交/异交并存（Facultative selfing in hermaphrodites）：一些雌雄同体的生物，如某些植物和淡水贻贝（如Anodonta cygnea），可以进行自交（self-fertilization）和异交（outcrossing）。自交虽然会导致近亲繁殖，但当种群密度极低或异交机会缺乏时，它能确保繁殖的成功。然而，自交通常会导致遗传多样性显著降低、近亲繁殖增加以及有效种群规模下降 55。尽管如此，在某些情况下，自交可以作为一种繁殖策略，允许有害突变更快地以纯合形式表达并被清除（遗传净化），从而减少近交衰退的长期影响 53。当然，这种策略的负面效应是短期的适应度损失和长期遗传适应性潜力的降低。
  • 顺序雌雄同体（Sequential hermaphroditism）：在鱼类等物种中，个体可以先以一种性别成熟，然后转变性别。这种策略可能通过增加有效种群大小或改变繁殖模式，间接影响近亲繁殖的程度和后果，但具体作用机制尚需进一步研究。

总而言之，性选择通过基因捕获机制，有效筛选并清除有害突变，尤其在强性选择环境下，能够显著增强种群对近亲繁殖的抵抗力 51。同时，某些繁殖策略，如多配偶制，也可能通过提高选择强度或促进异交，在一定程度上缓解近交衰退，帮助种群在遗传多样性受限的条件下得以存续。

3.3 环境稳定性与低选择压力的缓冲

在某些特定环境中，长期近亲繁殖的动物种群能够持续生存，其关键机制之一在于这些环境提供了高度的稳定性、充足的资源以及较低的选择压力。这种“缓冲效应”使得种群对遗传多样性的需求降低，从而能够承受较高水平的近亲繁殖而未灭绝。

稳定环境的特点通常包括：

  • 资源充足且可预测：食物来源稳定，不存在剧烈的季节性波动或突发性短缺。
  • 捕食者和竞争者稀少：天敌压力小，种内和种间竞争不激烈，个体存活率自然较高。
  • 物理环境稳定：气候、温度、湿度等环境因子变化不大，避免了极端气候事件或栖息地剧烈变化的挑战。

在这样的环境下，种群面临的适应性选择压力较弱。生物无需进行快速的适应性进化来应对生存威胁，因此，即使遗传多样性较低，个体也能在相对“安逸”的条件下存活和繁殖。近交衰退带来的负面效应（如免疫力下降、繁殖效率降低）可能被充足的资源和较低的生存挑战所抵消或掩盖。

洞穴生物是体现这一机制的典型案例。许多生活在恒温、黑暗、高湿度的地下洞穴中的物种，如盲鱼、洞穴 salamander和无脊椎动物，由于其栖息地的极端稳定性，往往表现出特化的形态特征（如眼睛退化、色素缺失）和极低的代谢率。这些环境通常资源有限，但同时也非常稳定，且几乎没有捕食者。例如，对洞穴鱼类（如墨西哥丽脂鲤 Astyanax mexicanus）的研究表明，它们在与地表鱼类隔离后，经历了长期的小种群历史和近亲繁殖。虽然其遗传多样性远低于地表种群，但由于其生活在高度稳定的洞穴环境中，外部环境压力极小，使得它们能够长期存续。在这种封闭且稳定的生态系统中，维持高遗传多样性的演化优势减弱。

岛屿小型哺乳动物也常表现出类似的特征。虽然岛屿环境可能面临风暴等随机事件，但在缺乏大型捕食者和竞争者的情况下，小型岛屿哺乳动物（例如某些啮齿类或食虫目动物）的种群可以相对稳定地增长，并能承受一定程度的近亲繁殖。这些物种往往由于地理隔离而形成小的创始种群，并在此基础上持续近亲繁殖。如果岛屿生态系统能提供稳定的食物来源和庇护所，那么近交衰退的负面影响可能不那么显著。例如，对澳洲虎蛇（Western tiger snake）的研究表明，在城市化造成的隔离“岛屿”生境中，随着地理隔离的增加，近亲繁殖和遗传漂变的信号越发明显。尽管如此，这些种群的有效种群规模（Ne）很小（<100），但它们仍然存活，这可能与栖息地提供的缓冲作用有关，因为Ne似乎更多地反映了可用栖息地的大小，而非城市化程度 56。

然而，这种基于环境稳定性的生存机制并非没有风险。一旦环境发生剧烈变化（如气候变化导致栖息地恶化、外来物种入侵带来新的捕食或竞争压力、疾病爆发），这些长期近亲繁殖的种群将因遗传多样性不足而缺乏适应能力，其脆弱性将迅速暴露，面临极高的灭绝风险 57。例如，斑马鱼（Danio rerio）的研究显示，近亲繁殖的种群在高温和内分泌干扰物（EDCs）的复合作用下，种群增长率急剧下降，灭绝风险远高于非近亲繁殖种群，尤其是在性别比例失衡的情况下 57。这表明，环境稳定性是近亲繁殖种群得以延续的重要保障，但一旦这种保障失效，其生存将面临严峻挑战。

4. 近亲繁殖生存的动态平衡与潜在风险

4.1 环境变化对近亲繁殖种群的冲击

尽管某些近亲繁殖的种群能够在特定条件下长期存续，但这种生存往往建立在一种脆弱的动态平衡之上。当环境发生剧烈变化时，这种平衡极易被打破，导致遗传多样性不足的种群因缺乏适应性而迅速走向衰退甚至灭绝。环境变化对近亲繁殖种群的冲击主要体现在以下几个方面：

  1. 气候变化与极端天气事件：
    气候变化是当前生物多样性面临的最大威胁之一。对于遗传多样性本就较低的近亲繁殖种群而言，气温升高、降水模式改变、极端天气事件（如干旱、洪灾、热浪）的频率和强度增加，都可能带来毁灭性的打击。缺乏足够的遗传变异，这些种群无法快速演化出适应新气候条件的能力。例如，有研究表明，气候变化与内分泌干扰物（EDCs）的复合作用会加速斑马鱼种群的衰退，而近亲繁殖的斑马鱼种群对此类影响的敏感性远高于非近亲繁殖种群 57。此外，北极地区是全球变暖最快的区域，冰层消融为虎鲸等亚北极物种打开了新的栖息地。对西北大西洋虎鲸的基因组分析显示，有两个遗传上高度独立的种群，它们的有效种群规模近期均有所下降，并表现出对近亲繁殖和适应性潜力降低的脆弱性。气候变化背景下北极环境的动态性，使得虎鲸的保护管理工作复杂化，对这些顶级捕食者及其北极猎物构成了双重挑战 58。

  2. 疾病入侵与病原体爆发：
    近亲繁殖会导致免疫系统相关基因的纯合性增加，降低种群对病原体的抵抗力，使其更容易受到疾病爆发的冲击。一旦新的或毒力更强的病原体入侵，近亲繁殖种群可能因缺乏具有抗病基因的个体而面临灭顶之灾。

    • 塔斯马尼亚恶魔面部肿瘤病 (DFTD)：这是最著名的案例之一。塔斯马尼亚恶魔因其历史上经历过种群瓶颈，遗传多样性极低，整个种群的MHC（主要组织相容性复合体）基因多样性很小，导致其对传染性面部肿瘤病（Devil Facial Tumour Disease, DFTD）的抵抗力普遍低下。DFTD是一种通过接触传播的克隆性癌症，导致了野生种群数量的急剧下降。其低遗传多样性使得种群对这种新型疾病的应对能力极为有限，极大地增加了其灭绝风险。保护工作包括引入外源个体来增加功能性遗传多样性，以增强其对疾病的抵抗力 59。
    • 其他病原体案例：豚鼠种群中爆发的肺炎球菌感染显示，不同豚鼠品系对疾病的感染率差异显著，有些近亲繁殖品系感染率高达75%，而另一些品系则完全没有被感染 60。这突显了遗传背景在疾病抵抗中的关键作用。此外，两栖动物壶菌病（Bd）也对两栖动物种群造成了严重的打击，Bd导致的成年存活率降低显著缩小了整合种群的生存空间，需要更高的景观连通性和招募率才能维持生存 61。

  3. 栖息地丧失与破碎化：
    人类活动导致的栖息地丧失、退化和破碎化，使得野生种群被分割成更小的、孤立的亚群。这些小亚群进一步加剧了近亲繁殖，降低了基因交流，使得它们更容易受到随机事件和近交衰退的负面影响。例如，西澳大利亚的虎蛇（Notechis scutatus occidentalis）在城市化导致的栖息地破碎化中，其种群隔离度越高，近亲繁殖和遗传漂变的信号越明显，有效种群规模（Ne）也越小 56。这些小而孤立的种群虽然可能暂时存活，但在面对任何新的环境压力时，都将面临巨大的挑战。

总而言之，环境变化对长期近亲繁殖种群的冲击是多方面的，它们打破了原有生态系统的平衡，使得这些本就脆弱的种群暴露在更高的风险之中。缺乏遗传“缓冲”，这些种群在应对新的生存挑战时往往力不从心，从而加速了灭绝的进程。

4.2 基因流动的“双刃剑”效应

基因流动（Gene flow），即不同种群之间基因的交换，对于近亲繁殖种群而言，无疑是一把“双刃剑”。它既可能通过引入新的遗传变异来“拯救”濒危种群，即“遗传救援”（Genetic Rescue），也可能因“杂交衰退”（Outbreeding Depression）而带来新的风险 62。

遗传救援：提升多样性的积极作用

遗传救援是指通过引入来自不同种群的个体，增加小而孤立种群的遗传多样性，从而缓解近交衰退，提高种群适应度和生存力的保护策略 6364。当一个种群长期处于小规模状态时，其遗传多样性会因遗传漂变和近亲繁殖而急剧下降，导致有害隐性等位基因纯合表达，严重影响个体的生存和繁殖。此时，引入外源基因流，可以带来以下积极影响：

  1. 恢复遗传多样性：外源基因的引入增加了种群内部的等位基因种类和频率，从而增强了种群的遗传多样性。更高的遗传多样性对于种群长期适应环境变化至关重要，因为它可以提供更丰富的基因库，允许种群在面对新的选择压力时进行适应性演化 65。
  2. 缓解近交衰退：新引入的基因可以掩盖本地种群中已经纯合的有害隐性等位基因，降低有害突变纯合表达的概率，从而改善个体的生存率、繁殖力和整体健康状况 6364。北极狐（Vulpes lagopus）的基因组研究显示，移民个体与本地个体杂交产生的F1代具有更高的杂合度，其第一年存活率也显著提高 66。
  3. 增强适应潜力：更高的遗传多样性意味着种群拥有更丰富的基因库，从而更有可能在面对新的环境挑战（如疾病、气候变化）时，通过自然选择快速演化出适应性特征 65。

杂交衰退：潜在的负面风险

然而，基因流动并非总是带来益处。在某些情况下，不适当的基因流动可能导致“杂交衰退”，即杂交后代的适应度低于亲本种群，这可能是由遗传不兼容性或本地适应性丧失引起的 6267。杂交衰退主要有两种表现形式：

  1. 遗传不兼容性（Genetic Incompatibility）：当两个种群长期地理隔离并适应了不同的环境时，它们之间可能积累了不同的基因组合，这些基因在各自的背景下协同工作，但在杂交后代中可能出现不协调，导致基因相互作用的破坏。例如，黑腹果蝇（Drosophila montana）的种群间杂交实验显示，F1代和F2代的鸣唱频率都出现了杂交衰退，这可能与有利的上位性基因组合被破坏有关 68。在拟南芥（Arabidopsis thaliana）的两个种群间的杂交也发现，杂交后代表现出负向显性效应导致的杂交衰退 67。
  2. 本地适应性丧失（Loss of Local Adaptation）：如果引入的基因来自适应了不同环境条件的种群，那么杂交后代可能会失去对本地环境的适应性优势。一项关于基因流如何影响适应性的研究指出，在面对环境梯度时，基因流可能导致适应性丧失，特别是在物种分布的边缘区域，这表明外源基因的引入可能稀释了对本地环境特有的适应性基因，导致后代在本地环境中表现不佳 69。一项关于大西洋鲑鱼（Salmo salar）在圈养繁殖项目中的研究发现，杂交衰退的后果难以预测，但在某些年份，杂交个体表现出较低的适应度 70。

风险评估与管理

为了最大化遗传救援的益处，同时规避杂交衰退的风险，管理者需要进行细致的风险评估。关键考虑因素包括：

  • 种群间的遗传距离和隔离时间：长期隔离且遗传分化显著的种群，其杂交衰退的风险更高 71。然而，即使在较大地理距离的种群间进行杂交，也并非总会导致负面结果。例如，在澳大利亚高山地区的一种触发植物（Stylidium armeria）中，仅在较远的地理距离下观测到种子产量方面的杂交衰退，而在萌发率和植物表现上未见不利影响 69。
  • 环境差异：如果源种群和受体种群所处的环境差异较大，则引入基因导致本地适应性丧失的风险会增加 71。
  • 杂交策略：一次性大规模引入（“洪水式”救援）可能比逐步引入带来更大的杂交衰退风险。
  • 监测与评估：在进行遗传救援后，必须对杂交后代的适应度进行长期监测，以及时发现并纠正可能出现的问题 72。

总之，基因流动在挽救近亲繁殖种群方面具有巨大潜力，但其应用需要审慎。保护生物学家正致力于通过基因组学工具，更准确地预测杂交衰退的风险，并优化遗传救援策略，以实现濒危物种的有效保护 73。

4.3 近亲繁殖生存的动态平衡与潜在风险

在自然界中，长期近亲繁殖的种群得以存续，往往是遗传因素、环境条件和选择压力之间复杂动态平衡的结果。这种平衡并非一成不变，而是充满了潜在的风险。

首先，遗传净化在一定程度上帮助近亲繁殖种群清除了有害隐性突变，但这往往是一个缓慢而代价高昂的过程，需要足够的时间和强度才能有效作用。在此过程中，种群可能经历严重的适应性下降。其次，环境的稳定性为低遗传多样性的种群提供了缓冲，使其在无需快速适应新挑战的情况下得以生存。然而，这种稳定性是有限的，一旦环境发生剧烈变化，如气候变暖、栖息地退化或疾病暴发，这些种群将迅速暴露其遗传多样性不足的脆弱性。

最后，性选择虽然能通过基因捕获机制筛选高适应性个体，但其效率也受到多种因素的影响，如种群规模、繁殖系统和环境压力。在极端近亲繁殖条件下，能够参与繁殖的个体数量锐减，性选择的作用也可能受限。

这种动态平衡的潜在风险在于：

  • 累积微效有害突变：即使强效应有害突变被清除，但大量微效有害突变仍可能在近亲繁殖种群中累积。这些突变单独作用不明显，但累积起来可能对种群适应度产生显著的负面影响，尤其是在环境压力增加时。
  • 适应性潜力的丧失：长期近亲繁殖导致整体遗传多样性大幅降低，使得种群丧失了应对未来不可预测环境变化的潜力。这意味着，即使当前种群处于一个相对稳定的环境中，一旦新的病原体出现或气候条件改变，它们可能无法演化出必要的适应性特征，从而面临灭绝。
  • 灭绝漩涡的临界点：近亲繁殖种群始终游走在灭绝漩涡的边缘。一旦某种环境变化超出其承受范围，或内部遗传负荷达到临界点，种群可能迅速陷入不可逆转的衰退，并加速走向灭绝。例如，在加利福尼亚的海岸红杉（Sequoia sempervirens）中，长期的近亲繁殖导致了自交衰退，表现为幼苗成活率低和生长缓慢，这可能是其种群萎缩的原因之一 。

因此，尽管一些动物能在长期近亲繁殖中存活下来，但这并非普遍规律，而是特殊条件下的脆弱平衡。这种平衡极易被打破，尤其是在全球环境变化加剧的今天，任何外部扰动都可能将这些“幸运”的种群推向灭绝的深渊。

5. 保护启示与未来研究方向

5.1 近亲繁殖管理的保护策略

面对近亲繁殖对濒危物种生存的威胁，保护生物学领域已经发展出多种策略，旨在缓解近交衰退、提升遗传多样性，并最终增强种群的长期生存能力。这些策略主要包括基因救助和选择性繁殖管理 74。

  1. 基因救助（Genetic Rescue）：
    基因救助是指通过从遗传多样性更高的源种群引入少量个体到目标种群中，以增加目标种群的遗传多样性并缓解近交衰退的策略 637576。这一方法已被证明能有效提升种群的适应度，例如提高繁殖成功率和存活率。

    • 实施案例：
      • 塔斯马尼亚恶魔补充计划：塔斯马尼亚恶魔（Sarcophilus harrisii）由于面临毁灭性的面部肿瘤病（DFTD），其野生种群遗传多样性极低。为了对抗疾病并保持遗传多样性，保护项目建立了“保险种群”进行圈养繁殖 77。虽然圈养个体中近亲繁殖程度与适应性指标之间并未发现显著关联，但这并不意味着遗传多样性不重要。相反，通过精心设计的圈养繁殖计划，包括管理繁殖配对以维持遗传多样性，是长期保护的关键。当野生种群遭遇疾病打击而导致基因库进一步萎缩时，适时将圈养种群中具有更高遗传多样性的个体引入野生种群，可以被视为一种潜在的遗传救援措施，以增强野生种群对疾病的抵抗力。
      • 野生狐狸的遗传救援：北美山区赤狐（Vulpes vulpes）的种群面临高度近亲繁殖和有害等位基因纯合性的问题，尤其是在隔离的喀斯喀特山脉和内华达山脉种群中 78。基因组学研究表明，引入外部个体进行异地迁徙是有效的遗传救援策略，能够通过掩盖有害隐性等位基因来提高种群增长率，从而对抗近交衰退 78。
      • 第纳尔山猞猁种群的强化：第纳尔山脉的欧亚猞猁（Lynx lynx）种群面临严重的近亲繁殖威胁，有效近交系数在2019年高达0.316 79。为扭转这一局面，从2019年至2023年，保护人员将12只来自喀尔巴阡山脉的个体引入第纳尔山脉。尽管模型预测，即使经过强化，近亲繁殖水平仍可能在45年内恢复到临界水平，但这强调了遗传救援只是第一步，长期遗传管理不可或缺 79。
    • 注意事项：基因救助并非没有风险，不当的基因引入可能导致“杂交衰退”，即杂交后代的适应度低于亲本种群 63。因此，在实施基因救助前，需要通过基因组学工具（如ROH分析）评估种群间的遗传距离和本地适应性，以最大化益处并规避风险 738081。

  2. 选择性繁殖（Selective Breeding）：
    选择性繁殖主要应用于圈养种群和人工管理种群，旨在通过控制繁殖配对来管理近亲繁殖水平和遗传多样性。

    • 避免高近交系数配对：在圈养繁殖计划中，通过谱系追踪和基因组学数据（如Run of Homozygosity, ROH），可以精确计算每个个体的近交系数 82。管理人员可以有意识地选择亲缘关系较远、近交系数较低的个体进行配对，以最大程度地减少后代的近亲繁殖程度，并保留遗传多样性。例如，许多动物园的物种生存计划（SSP）都采用这种方法来管理濒危物种的圈养种群。
    • 优化遗传多样性贡献：在有限的圈养种群中，确保每个创始个体的基因都能得到有效传递至关重要。通过“平均亲缘关系”（Mean Kinship）管理，可以优先选择那些亲缘关系较低、对种群遗传多样性贡献最大的个体进行繁殖，从而维持种群的整体遗传健康。
    • 选择性淘汰：在人工管理的种群中，可以通过选择性淘汰那些表现出明显近交衰退症状（如严重的遗传疾病、繁殖力低下）的个体，在一定程度上清除有害等位基因。然而，这种方法必须谨慎，因为过度淘汰可能进一步缩小基因库。
    • 利用基因组信息进行育种：现代育种已开始利用基因组信息来预测个体携带的有害突变负荷，指导配对选择，以最大程度地降低近交衰退的影响，并提高育种效率 83。
    • 选择性避孕：在某些圈养繁殖计划中，为了更好地管理繁殖贡献和基因多样性，可以通过选择性避孕来控制特定个体的繁殖。例如，对于塔斯马尼亚恶魔、黑侧岩袋鼠和穴居袋狸，选择性避孕可以优化圈养繁殖计划的遗传多样性和行为完整性 77。

通过这些综合性的保护策略，保护生物学家和管理者可以更有效地应对近亲繁殖对濒危物种造成的挑战，努力确保这些物种在不断变化的环境中得以存续。

5.2 未解问题与研究展望

尽管在近亲繁殖及其生存机制方面已取得了显著进展，但仍有诸多未解问题和挑战，为未来的研究指明了方向。深入探索这些领域，将有助于我们更全面地理解近亲繁殖的生物学后果，并为濒危物种的保护提供更精细的策略。

  1. 长期近亲繁殖的遗传代价：累积微效有害突变
    遗传净化主要针对那些效应显著的有害隐性突变，能够将其从种群中清除。然而，对于效应微弱、对适应度影响不大的“微效有害突变”（mildly deleterious mutations）而言，自然选择的清除效率较低。在长期近亲繁殖的种群中，这些微效有害突变可能持续累积，形成“突变负荷”（mutation load）。尽管单个微效突变的影响微乎其微，但它们的累积效应可能在未来环境变化或种群面临新压力时，突然爆发，导致种群适应度下降，甚至加速灭绝 8485。

    • 研究展望：未来的研究需要开发更灵敏的基因组学工具和计算方法，以识别和量化微效有害突变。通过对长期近亲繁殖种群的纵向基因组研究，追踪这些突变的累积模式及其对适应度的长期影响。此外，需要更深入地理解不同物种基因组中微效有害突变负荷的差异及其演化轨迹。

  2. 不同物种的抗性差异机制
    并非所有物种对近亲繁殖的耐受性都相同。有些物种在经历高度近亲繁殖后仍能存活，而另一些则迅速灭绝。这种差异可能源于多种内在机制：

    • 性染色体系统：有研究表明，近交衰退可能存在性别差异，雌性可能比雄性遭受略高的近交衰退 11。在某些物种中，性染色体上的基因（如X染色体或Z染色体）可能在近交衰退中扮演重要角色。例如，在褐鳟（Salmo trutta）中，雌性幼鱼在近亲繁殖程度增加时体型更小，而雄性则没有这种关联 86。此外，人类研究也发现，男性老年患者中近亲繁殖对COVID-19住院和严重程度的影响更强 87。
    • 繁殖模式：不同的繁殖模式，如自交、多配偶制、单配偶制等，可能影响种群中近亲繁殖的发生率和遗传净化的效率。自交植物可以在一定程度上清除有害突变，但代价是遗传多样性的丧失 88。猪的繁殖研究也表明，近亲繁殖对精子质量、窝产仔数等繁殖性状有不利影响 8990。
    • 物种特异性遗传架构：不同物种基因组的结构、基因调控网络和基因间相互作用（上位性）可能影响近交衰退的表达和遗传净化的效率。一些物种可能天生就具有较低的遗传负荷，或者其基因组能够更好地缓冲近亲繁殖带来的负面效应。
    • 研究展望：通过比较基因组学和实验进化研究，可以探究不同性染色体系统、繁殖策略和基因组特征如何影响物种对近亲繁殖的抗性。例如，可以关注那些长期在极端隔离环境下生存的物种（如岛屿特有种、洞穴生物），分析其基因组特征，以揭示其特有的耐受机制。

  3. 基因组学技术在近亲繁殖研究中的应用前景
    随着高通量测序技术的发展和生物信息学工具的进步，基因组学已成为研究近亲繁殖及其后果的强大工具，并将在未来的研究和保护实践中发挥越来越重要的作用 91。

    • ROH（Runs of Homozygosity）分析：ROH是基因组中连续的纯合区域，是衡量个体近亲繁殖程度和历史的直接指标 35。未来的研究可以利用ROH分析更精确地估算种群的有效大小、近亲繁殖系数，并追溯近亲繁殖事件发生的时间。通过将ROH与表型数据相结合，可以识别与近交衰退相关的基因组区域，甚至定位特定的有害突变。
    • 适应性基因定位：基因组学可以帮助我们识别与适应性相关的功能基因（如免疫基因、环境适应基因），从而评估近亲繁殖对这些关键基因多样性的影响。通过全基因组关联分析（GWAS），有望定位出影响近交衰退性状（如生育力、存活率、抗病性）的基因或基因组区域。
    • 基因组预测与育种管理：在圈养繁殖计划中，基因组数据可以用于预测个体的近亲繁殖系数和遗传负荷，从而指导配对选择，最大化遗传多样性，并最小化近交衰退的风险 92。例如，基于基因组的近交系数（genomic inbreeding coefficients）比基于谱系的近交系数更精确，可以更好地评估近亲繁殖对性状的影响 89。
    • 遗传救援的精确评估与规划：基因组学工具可以帮助我们更准确地评估潜在源种群和受体种群之间的遗传距离和遗传负荷，从而预测遗传救援的成功率和杂交衰退的风险 63。
    • 研究展望：未来将更多地利用全基因组测序数据，结合复杂的生物信息学算法，构建物种的“近亲繁殖图谱”和“遗传负荷图谱”。通过结合环境数据，深入解析基因型-环境相互作用对近交衰退的影响。同时，发展更精确的遗传模型，预测在不同近亲繁殖水平下，种群的长期生存概率和演化潜力。

总之，对长期近亲繁殖动物生存机制的研究，不仅揭示了生命演化的复杂性，也为濒危物种的保护提供了宝贵的理论依据和技术支持。未来的研究应继续整合多学科方法，尤其是基因组学和生态学，以应对近亲繁殖这一全球性保护挑战。

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参考文献

1Conservation and Genetics.PubMed

Charles B Fenster, Jonathan D Ballou, Michele R Dudash, et al.
Yale J Biol Med. 2018 Dec 21;91(4):491-501. eCollection 2018 Dec.
Humans are responsible for a cataclysm of species extinction that will change the world as we see it, and will adversely affect human health and wellbeing. We need to understand at individual and societal levels why species conservation is important. Accepting the premise that species have value, we need to next consider the mechanisms underlying species extinction and what we can do to reverse the process. One of the last stages of species extinction is the reduction of a species to a few populations of relatively few individuals, a scenario that leads invariably to inbreeding and its adverse consequences, inbreeding depression. Inbreeding depression can be so severe that populations become at risk of extinction not only because of the expression of harmful recessive alleles (alleles having no phenotypic effect when in the heterozygous condition, ., Aa, where is the recessive allele), but also because of their inability to respond genetically with sufficient speed to adapt to changing environmental conditions. However, new conservation approaches based on foundational quantitative and population genetic theory advocate for active genetic management of fragmented populations by facilitating gene movements between populations, ., admixture, or genetic rescue. Why species conservation is critical, the genetic consequences of small population size that often lead to extinction, and possible solutions to the problem of small population size are discussed and presented.

2Genetics of consanguinity and inbreeding in health and disease.PubMed

Mohd Fareed, Mohammad Afzal
Ann Hum Biol. 2017 Mar;44(2):99-107. doi: 10.1080/03014460.2016.1265148. Epub 2016 Dec 14.
CONTEXT: Inbreeding increases the level of homozygotes for autosomal recessive disorders and is the major objective in clinical studies. The prevalence of consanguinity and the degree of inbreeding vary from one population to another depending on ethnicity, religion, culture and geography. Global epidemiological studies have revealed that consanguineous unions have been significantly associated with increased susceptibility to various forms of inherited diseases. OBJECTIVE: The study aimed to determine the role of consanguinity in human health and to highlight the associated risks for various diseases or disorders. METHODS: PubMed and Google Scholar search engines were used to explore the published literature on consanguinity and its associated risks using the key words "consanguinity", "prevalence", "inbreeding depression", "coefficient of inbreeding", "child health", "mortality", "human health", "homozygosity" and "complex diseases" in different combinations. The studies were screened for eligibility on the basis of their epidemiological relevance. RESULTS: This comprehensive assessment highlights the deleterious consequences in populations with a higher prevalence of consanguinity among different countries worldwide. CONCLUSIONS: To avoid the inbreeding load there is the need to improve socioeconomic and educational status and to increase public awareness of reproductive health and anticipated deleterious effects. Pre-marital and pre-conception counselling of consanguineous populations should be an integral part of health policy to train people and make people aware of its harmful consequences. Furthermore, runs of homozygosity (ROH) and whole-exome sequencing (WES) are useful tools in exploring new genomic signatures for the cause of inbreeding depression.

3Inbreeding depression and the probability of racing in the Thoroughbred horse.PubMed

Emmeline W Hill, Martin A Stoffel, Beatrice A McGivney, et al.
Proc Biol Sci. 2022 Jun 29;289(1977):20220487. doi: 10.1098/rspb.2022.0487.
Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increase in inbreeding () is associated with a 7% lower probability of ever racing. Moreover, a ROH-based genome-wide association study identified a haplotype on ECA14 which, in its homozygous state, is linked to a 32.1% lower predicted probability of ever racing, independent of . The haplotype overlaps a candidate gene, , that is highly expressed in cartilage tissue, which when damaged is one of the most common causes of catastrophic musculoskeletal injury in racehorses. Genomics-informed breeding aiming to reduce inbreeding depression and avoid damaging haplotype carrier matings will improve population health and racehorse welfare.

4Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal.PubMed

M A Stoffel, S E Johnston, J G Pilkington, et al.
Nat Commun. 2021 May 20;12(1):2972. doi: 10.1038/s41467-021-23222-9.
Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding F is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.

5Associations of autozygosity with a broad range of human phenotypes.PubMed

David W Clark, Yukinori Okada, Kristjan H S Moore, et al.
Nat Commun. 2019 Oct 31;10(1):4957. doi: 10.1038/s41467-019-12283-6.
In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (F) for >1.4 million individuals, we show that F is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: F equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44-66%] in the odds of having children. Finally, the effects of F are confirmed within full-sibling pairs, where the variation in F is independent of all environmental confounding.

6Conservation genetics.PubMed

R Frankham
Annu Rev Genet. 1995;29:305-27. doi: 10.1146/annurev.ge.29.120195.001513.
Inbreeding depression, accumulation and loss of deleterious mutations, loss of genetic variation in small populations, genetic adaptation to captivity and its effect on reintroduction success, and outbreeding depression are reviewed. The impact of genetic factors in endangerment and extinction has been underestimated in some recent publications. Inbreeding depression in wildlife and in the field has been clearly established, while its impact has been greatly underestimated. The size of populations where genetic factors become important is higher than previously recognized, as Ne/N ratios average 0.11. Purging effects have been overestimated as a mechanism for eliminating deleterious alleles in small populations. The impact of loss of genetic variation in increasing the susceptibility of populations to environmental stochasticity and catastrophes has generally been ignored. Consequently, extinctions are often attributed to "nongenetic" factors when these may have interacted with genetic factors to cause extinction.

7Understanding Inbreeding Depression, Purging, and Genetic Rescue.PubMed

Philip W Hedrick, Aurora Garcia-Dorado
Trends Ecol Evol. 2016 Dec;31(12):940-952. doi: 10.1016/j.tree.2016.09.005. Epub 2016 Oct 12.
Inbreeding depression, the reduction of fitness caused by inbreeding, is a nearly universal phenomenon that depends on past mutation, selection, and genetic drift. Recent estimates suggest that its impact on individual fitness is even greater than previously thought. Genomic information is contributing to its detection and can enlighten important aspects of its genetic architecture. In natural populations, purging and genetic rescue mitigate fitness decline during inbreeding periods, and might be critical to population survival, thus, both mechanisms should be considered when assessing extinction risks. However, deliberate purging and genetic rescue involve considerable risk in the short and medium term, so that neither appears to be a panacea against high inbreeding depression.

8Inbreeding depression in livestock species: review and meta-analysis.PubMed

G Leroy
Anim Genet. 2014 Oct;45(5):618-28. doi: 10.1111/age.12178. Epub 2014 Jun 28.
Inbreeding, by virtue of its consequence on traits of interest, is a topic of major interest for geneticists and animal breeders. Based on meta-analysis conducted on 57 studies and seven livestock species considering a wide variety of selected traits, it was estimated that inbreeding depression corresponds to on average a decrease of 0.137 percent of the mean of a trait per 1 percent of inbreeding. The decrease was larger for production traits (reduction of 0.351%) than for other trait categories. For populations raised as purebreds, inbreeding depression may impact the economic income of breeders. There is a need for studies assessing the existence of an inbreeding purge phenomenon as well as the impact of inbreeding on adaptation capacities of livestock species. Promises brought by the development of dense genotyping as well as functional genomics will increase the capacities to improve our understanding and management of the phenomenon.

9Estimation of genetic parameters and inbreeding depression in Piau pig breed.PubMed

Letícia Fernanda de Oliveira, Paulo Sávio Lopes, Layla Cristien Cássia Miranda Dias, et al.
Trop Anim Health Prod. 2022 Dec 20;55(1):14. doi: 10.1007/s11250-022-03428-9.
This study is aimed at estimating genetic parameters, effective population size, inbreeding, and inbreeding depression for birth weight, weaning weight, and average pre-weaning daily weight gain (ADG) in Piau pigs. We used information from 3841 Piau pigs, and four linear models were fitted in single-trait analyses, including or excluding maternal genetic effect, common litter effect, or a combination. The adjustments of the models were compared using the likelihood ratio test, in which the model that presented the best fit for each trait was used to estimate the (co)variance components. The inbreeding depression effect was evaluated using a linear model that included the fixed effects of sex, parity order, contemporary group, and inbreeding coefficient as a fixed covariate. The weights at birth and weaning showed low direct heritabilities (0.08 and 0.05, respectively), while the ADG showed moderate heritability (0.20). The weight at birth showed high genetic correlations with the weight at weaning (0.90) and the ADG (0.82). The weight at weaning and the ADG also showed a high genetic correlation (0.99). There was an inbreeding increase over the generations and a reduction in the effective population size. In the last generation evaluated, all the animals were inbred, the average inbreeding coefficient was 0.07, and the effective population size was 20.8. A significant inbreeding effect on ADG was observed, where an increase of 1% in the inbreeding coefficient resulted in a decrease of 0.005 g in the ADG. Thus, increasing effective population size is mandatory for controlling inbreeding and reducing the loss of variability in this Piau pig population.

10Stress and adaptation in conservation genetics.PubMed

R Frankham
J Evol Biol. 2005 Jul;18(4):750-5. doi: 10.1111/j.1420-9101.2005.00885.x.
Stress, adaptation and evolution are major concerns in conservation biology. Stresses from pollution, climatic changes, disease etc. may affect population persistence. Further, stress typically occurs when species are placed in captivity. Threatened species are usually managed to conserve their ability to adapt to environmental changes, whilst species in captivity undergo adaptations that are deleterious upon reintroduction into the wild. In model studies using Drosophila melanogaster, we have found that; (a) inbreeding and loss of genetic variation reduced resistance to the stress of disease, (b) extinction rates under inbreeding are elevated by stress, (c) adaptive evolutionary potential in an increasingly stressful environment is reduced in small population, (d) rates of inbreeding are elevated under stressful conditions, (e) genetic adaptation to captivity reduces fitness when populations are reintroduced into the 'wild', and (f) the deleterious effects of adaptation on reintroduction success can be reduced by population fragmentation.

11Sex-specific inbreeding depression: A meta-analysis.PubMed

Regina Vega-Trejo, Raïssa A de Boer, John L Fitzpatrick, et al.
Ecol Lett. 2022 Apr;25(4):1009-1026. doi: 10.1111/ele.13961. Epub 2022 Jan 21.
Inbreeding depression, the reduced fitness of the offspring of related individuals, can affect males and females differently. Although a comprehensive theoretical framework describing the causes of sex-specific inbreeding depression is lacking, empirical evidence suggests that often one sex tends to be more vulnerable than the other. However, the generality, direction, and degree of sex-specific difference in inbreeding depression remains enigmatic as studies on this topic have reported conflicting results. Here, we conduct a meta-analysis to test for sex-specific differences in the magnitude of inbreeding depression. We synthetised 321 effect sizes of experimental studies across 47 species and found a small difference in inbreeding depression between the sexes: females suffered slightly higher inbreeding depression than males. Furthermore, a higher inbreeding coefficient was correlated with higher inbreeding depression. However, there was a large amount of heterogeneity that remained unexplained, even when considering different factors that could affect inbreeding between the sexes, such as sexual size dimorphism, heterogamety, the type of trait measured and whether animals were tested in a stressful environment. As such, we highlight the need to further explore inbreeding depression across different species to determine the occurrence and causes of sex differences to increase our understanding of the evolutionary consequences of sex-specific inbreeding depression.

12How density dependence, genetic erosion and the extinction vortex impact evolutionary rescue.PubMed

Scott W Nordstrom, Ruth A Hufbauer, Laure Olazcuaga, et al.
Proc Biol Sci. 2023 Nov 29;290(2011):20231228. doi: 10.1098/rspb.2023.1228. Epub 2023 Nov 22.
Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity and the fixation of maladaptive alleles, hindered adaptation and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.

13Conservation: Corals in an extinction vortex.PubMed

Zoe T Richards
Curr Biol. 2024 Nov 4;34(21):R1090-R1093. doi: 10.1016/j.cub.2024.09.081.
Population declines threaten many marine ecosystems, but their genetic consequences remain largely unknown. A new study shows how a Caribbean coral finds itself trapped in an extinction vortex and vulnerable to the interplay of climate change, habitat degradation, small population size, low genetic diversity and reduced dispersal.

14Genetic diversity loss in the Anthropocene.PubMed

Moises Exposito-Alonso, Tom R Booker, Lucas Czech, et al.
Science. 2022 Sep 23;377(6613):1431-1435. doi: 10.1126/science.abn5642. Epub 2022 Sep 22.
Anthropogenic habitat loss and climate change are reducing species' geographic ranges, increasing extinction risk and losses of species' genetic diversity. Although preserving genetic diversity is key to maintaining species' adaptability, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. We introduce a mathematical framework that bridges biodiversity theory and population genetics to understand the loss of naturally occurring DNA mutations with decreasing habitat. By analyzing genomic variation of 10,095 georeferenced individuals from 20 plant and animal species, we show that genome-wide diversity follows a mutations-area relationship power law with geographic area, which can predict genetic diversity loss from local population extinctions. We estimate that more than 10% of genetic diversity may already be lost for many threatened and nonthreatened species, surpassing the United Nations' post-2020 targets for genetic preservation.

15Inbreeding depression explains killer whale population dynamics.PubMed

Marty Kardos, Yaolei Zhang, Kim M Parsons, et al.
Nat Ecol Evol. 2023 May;7(5):675-686. doi: 10.1038/s41559-023-01995-0. Epub 2023 Mar 20.
Understanding the factors that cause endangered populations to either grow or decline is crucial for preserving biodiversity. Conservation efforts often address extrinsic threats, such as environmental degradation and overexploitation, that can limit the recovery of endangered populations. Genetic factors such as inbreeding depression can also affect population dynamics but these effects are rarely measured in the wild and thus often neglected in conservation efforts. Here we show that inbreeding depression strongly influences the population dynamics of an endangered killer whale population, despite genomic signatures of purging of deleterious alleles via natural selection. We find that the 'Southern Residents', which are currently endangered despite nearly 50 years of conservation efforts, exhibit strong inbreeding depression for survival. Our population models suggest that this inbreeding depression limits population growth and predict further decline if the population remains genetically isolated and typical environmental conditions continue. The Southern Residents also had more inferred homozygous deleterious alleles than three other, growing, populations, further suggesting that inbreeding depression affects population fitness. These results demonstrate that inbreeding depression can substantially limit the recovery of endangered populations. Conservation actions focused only on extrinsic threats may therefore fail to account for key intrinsic genetic factors that also limit population growth.

16Chemical reproductive traits of diploid Bombus terrestris males: Consequences on bumblebee conservation.PubMed

Thomas Lecocq, Maxence Gérard, Kevin Maebe, et al.
Insect Sci. 2017 Aug;24(4):623-630. doi: 10.1111/1744-7917.12332. Epub 2016 Jun 7.
The current bumblebee decline leads to inbreeding in populations that fosters a loss of allelic diversity and diploid male production. As diploid males are viable and their offspring are sterile, bumblebee populations can quickly fall in a vortex of extinction. In this article, we investigate for the first time a potential premating mechanism through a major chemical reproductive trait (male cephalic labial gland secretions) that could prevent monandrous virgin queens from mating with diploid males. We focus our study on the cephalic labial gland secretions of diploid and haploid males of Bombus terrestris (L.). Contrary to initial expectations, our results do not show any significant differentiation of cephalic labial gland secretions between diploid and haploid specimens. Queens seem therefore to be unable to avoid mating with diploid males based on their compositions of cephalic labial gland secretions. This suggests that the vortex of extinction of diploid males could not be stopped through premating avoidance based on the cephalic labial gland secretions but other mechanisms could avoid mating between diploid males and queens.

17The effects of functional response and host abundance fluctuations on genetic rescue in parasitoids with single-locus sex determination.PubMed

Etsuko Nonaka, Veijo Kaitala
Ecol Evol. 2020 Oct 14;10(23):13030-13043. doi: 10.1002/ece3.6889. eCollection 2020 Dec.
Many parasitoids have single-locus complementary sex determination (sl-CSD), which produces sterile or inviable males when homozygous at the sex determining locus. A previous study theoretically showed that small populations have elevated risks of extinction due to the positive feedback between inbreeding and small population size, referred to as the diploid male vortex. A few modeling studies have suggested that the diploid male vortex may not be as common because balancing selection at sex determining loci tends to maintain high allelic diversity in spatially structured populations. However, the generality of the conclusion is yet uncertain, as they were drawn either from models developed for particular systems or from a general-purpose competition model. To attest the conclusion, we study several well-studied host-parasitoid models that incorporate functional response specifying the number of attacked hosts given a host density and derive the conditions for a diploid male vortex in a single population. Then, we develop spatially structured individual-based versions of the models to include female behavior, diploid male fertility, and temporal fluctuations. The results show that producing a handful of successful offspring per female parasitoid could enable parasitoid persistence when a typical number of CSD alleles are present. The effect of functional response depends on the levels of fluctuations in host abundance, and inviable or partially fertile diploid males and a small increase in dispersal can alleviate the risk of a diploid male vortex. Our work supports the generality of effective genetic rescue in spatially connected parasitoid populations with sl-CSD. However, under more variable climate, the efficacy of the CSD mechanism may substantially decline.

18Tracking population genetic signatures of local extinction with herbarium specimens.PubMed

Christoph Rosche, Annett Baasch, Karen Runge, et al.
Ann Bot. 2022 Jul 18;129(7):857-868. doi: 10.1093/aob/mcac061.
BACKGROUND AND AIMS: Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness, which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management. METHODS: We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as a surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. KEY RESULTS: Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both the spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as a powerful predictor of functional connectivity which may promote decision-making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. CONCLUSIONS: Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex situ population and a germination trial underlines the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.

19Mating patterns influence vulnerability to the extinction vortex.PubMed

Joanne L Godwin, Alyson J Lumley, Łukasz Michalczyk, et al.
Glob Chang Biol. 2020 Aug;26(8):4226-4239. doi: 10.1111/gcb.15186. Epub 2020 Jun 19.
Earth's biodiversity is undergoing mass extinction due to anthropogenic compounding of environmental, demographic and genetic stresses. These different stresses can trap populations within a reinforcing feedback loop known as the extinction vortex, in which synergistic pressures build upon one another through time, driving down population viability. Sexual selection, the widespread evolutionary force arising from competition, choice and reproductive variance within animal mating patterns could have vital consequences for population viability and the extinction vortex: (a) if sexual selection reinforces natural selection to fix 'good genes' and purge 'bad genes', then mating patterns encouraging competition and choice may help protect populations from extinction; (b) by contrast, if mating patterns create load through evolutionary or ecological conflict, then population viability could be further reduced by sexual selection. We test between these opposing theories using replicate populations of the model insect Tribolium castaneum exposed to over 10 years of experimental evolution under monogamous versus polyandrous mating patterns. After a 95-generation history of divergence in sexual selection, we compared fitness and extinction of monogamous versus polyandrous populations through an experimental extinction vortex comprising 15 generations of cycling environmental and genetic stresses. Results showed that lineages from monogamous evolutionary backgrounds, with limited opportunities for sexual selection, showed rapid declines in fitness and complete extinction through the vortex. By contrast, fitness of populations from the history of polyandry, with stronger opportunities for sexual selection, declined slowly, with 60% of populations surviving by the study end. The three vortex stresses of (a) nutritional deprivation, (b) thermal stress and (c) genetic bottlenecking had similar impacts on fitness declines and extinction risk, with an overall sigmoid decline in survival through time. We therefore reveal sexual selection as an important force behind lineages facing extinction threats, identifying the relevance of natural mating patterns for conservation management.

20Sexual cannibalism and population viability.PubMed

Adam M Fisher, Stephen J Cornell, Gregory I Holwell, et al.
Ecol Evol. 2018 Jun 24;8(13):6663-6670. doi: 10.1002/ece3.4155. eCollection 2018 Jul.
Some behaviours that typically increase fitness at the individual level may reduce population persistence, particularly in the face of environmental changes. Sexual cannibalism is an extreme mating behaviour which typically involves a male being devoured by the female immediately before, during or after copulation, and is widespread amongst predatory invertebrates. Although the individual-level effects of sexual cannibalism are reasonably well understood, very little is known about the population-level effects. We constructed both a mathematical model and an individual-based model to predict how sexual cannibalism might affect population growth rate and extinction risk. We found that in the absence of any cannibalism-derived fecundity benefit, sexual cannibalism is always detrimental to population growth rate and leads to a higher population extinction risk. Increasing the fecundity benefits of sexual cannibalism leads to a consistently higher population growth rate and likely a lower extinction risk. However, even if cannibalism-derived fecundity benefits are large, very high rates of sexual cannibalism (>70%) can still drive the population to negative growth and potential extinction. Pre-copulatory cannibalism was particularly damaging for population growth rates and was the main predictor of growth declining below the replacement rate. Surprisingly, post-copulatory cannibalism had a largely positive effect on population growth rate when fecundity benefits were present. This study is the first to formally estimate the population-level effects of sexual cannibalism. We highlight the detrimental effect sexual cannibalism may have on population viability if (1) cannibalism rates become high, and/or (2) cannibalism-derived fecundity benefits become low. Decreased food availability could plausibly both increase the frequency of cannibalism, and reduce the fecundity benefit of cannibalism, suggesting that sexual cannibalism may increase the risk of population collapse in the face of environmental change.

21Population genomics of recovery and extinction in Hawaiian honeycreepers.PubMed

Christopher C Kyriazis, Madhvi Venkatraman, Bryce Masuda, et al.
Curr Biol. 2025 Jun 9;35(11):2697-2708.e4. doi: 10.1016/j.cub.2025.04.078. Epub 2025 May 29.
Native Hawaiian forest birds are experiencing an unprecedented extinction crisis. In particular, the iconic Hawaiian honeycreeper radiation has declined to just 17 out of ∼60 species remaining, most threatened with extinction due to avian malaria. Here, we investigate the genomic signatures of these declines in three honeycreeper species: the critically endangered 'akikiki (Oreomystis bairdi) and 'akeke'e (Loxops caeruleirostris) and the extinct po'ouli (Melamprosops phaeosoma). Surprisingly, we find that Hawaiian honeycreepers, even the last known po'ouli individual, maintain high heterozygosity compared with other island birds, reflecting historically large population sizes. This high heterozygosity may contribute to an elevated impact of inbreeding depression, as evidenced by reduced survival and reproductive success among highly inbred 'akikiki. Demographic analysis revealed that recent precipitous declines in 'akikiki and 'akeke'e coincide with the spread of avian malaria in the late 20 century, consistent with malaria being the primary driver of population collapse. Using predictive population viability modeling, we explore potential recovery scenarios for 'akeke'e, which has recently declined below 100 individuals in the wild. Our models predict that, under current conditions, 'akeke'e is likely to go extinct in the near future. However, if mosquito control campaigns are effective at reducing malaria, recovery can still occur. These findings emphasize the urgency of ongoing mosquito control efforts, demonstrating hope for a species nearing the brink of extinction. More broadly, our study provides a detailed examination of genomic diversity, inbreeding depression, and extinction risk in a collapsing adaptive radiation, with implications for conservation of other endangered island species.

22Population genomic landscapes and insights for conservation of the critically endangered island-endemic Chinese pangolin in Taiwan.PubMed

Tianya Zhai, Jichao Wang, Guangquan Zhan, et al.
Sci China Life Sci. 2025 Sep;68(9):2768-2783. doi: 10.1007/s11427-024-2904-6. Epub 2025 Jul 11.
Island species/populations are characterized by evolutionary uniqueness and a high degree of endemism and extinction. The conservation and restoration of island species/populations have become the most challenging and urgent issues in biodiversity conservation. Chinese pangolin in Taiwan island (Manis pentadactyla pentadactyla) is a well-known, critically endangered, and island-endemic Chinese pangolin subspecies, which has been the focus of conservation concern. Here, we first generated large-scale population genomics data for the Chinese pangolin in Taiwan to address its population structure, demographic history, the genomic consequences of population declines, and survival potential. We revealed that the Chinese pangolin in Taiwan originated in southeast China and was differentiated into Northern and non-Northern populations due to the isolation of the Xueshan and Central Mountain Ranges, proposing to treat them as separate conservation units. The southeast of Taiwan island acted as a refuge for this Chinese pangolin subspecies during the Last Glacial Maximum. The Northern population had experienced a more severe bottleneck and isolation than the non-Northern population, which corresponded to the estimated current lower genetic diversity, higher inbreeding, and genetic load of the Northern population. The modeling results revealed that the Northern population is more seriously affected by climate change than the non-Northern population, which highlights that climate change poses a substantial threat to island biodiversity. The simulation results indicate that the Northern population needs a higher population growth rate to achieve evolutionary potential equal to the non-Northern population over the next 100 years, deserving conservation prioritization. This study enhances the understanding of genetic background, conservation status, and future prospects for Chinese pangolin in Taiwan, as well as the genetic consequences of a small and isolated island population.

23High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.PubMed

Steeves Buckland, Nik C Cole, Jim J Groombridge, et al.
PLoS One. 2014 Jun 25;9(6):e93387. doi: 10.1371/journal.pone.0093387. eCollection 2014.
Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations.

24No evidence of inbreeding depression in a Tasmanian devil insurance population despite significant variation in inbreeding.PubMed

Rebecca Gooley, Carolyn J Hogg, Katherine Belov, et al.
Sci Rep. 2017 May 12;7(1):1830. doi: 10.1038/s41598-017-02000-y.
Inbreeding depression occurs when inbred individuals experience reduced fitness as a result of reduced genome-wide heterozygosity. The Tasmanian devil faces extinction due to a contagious cancer, devil facial tumour disease (DFTD). An insurance metapopulation was established in 2006 to ensure the survival of the species and to be used as a source population for re-wilding and genetic rescue. The emergence of DFTD and the rapid decline of wild devil populations have rendered the species at risk of inbreeding depression. We used 33 microsatellite loci to (1) reconstruct a pedigree for the insurance population and (2) estimate genome-wide heterozygosity for 200 individuals. Using heterozygosity-fitness correlations, we investigated the effect of heterozygosity on six diverse fitness measures (ulna length, asymmetry, weight-at-weaning, testes volume, reproductive success and survival). Despite statistically significant evidence of variation in individual inbreeding in this population, we found no associations between inbreeding and any of our six fitness measurements. We propose that the benign environment in captivity may decrease the intensity of inbreeding depression, relative to the stressful conditions in the wild. Future work will need to measure fitness of released animals to facilitate translation of this data to the broader conservation management of the species in its native range.

25Adaptive potential in the face of a transmissible cancer in Tasmanian devils.PubMed

Kasha Strickland, Menna E Jones, Andrew Storfer, et al.
Mol Ecol. 2024 Nov;33(21):e17531. doi: 10.1111/mec.17531. Epub 2024 Sep 28.
Emerging infectious diseases (EIDs) not only cause catastrophic declines in wildlife populations but also generate selective pressures that may result in rapid evolutionary responses. One such EID is devil facial tumour disease (DFTD) in the Tasmanian devil. DFTD is almost always fatal and has reduced the average lifespan of individuals by around 2 years, likely causing strong selection for traits that reduce susceptibility to the disease, but population decline has also left Tasmanian devils vulnerable to inbreeding depression. We analysed 22 years of data from an ongoing study of a population of Tasmanian devils on Freycinet Peninsula, Tasmania, to (1) identify whether DFTD may be causing selection on body size, by estimating phenotypic and genetic correlations between DFTD and size traits, (2) estimate the additive genetic variance of susceptibility to DFTD, and (3) investigate whether size traits or susceptibility to DFTD were under inbreeding depression. We found a positive phenotypic relationship between head width and susceptibility to DFTD, but this was not underpinned by a genetic correlation. Conversely, we found a negative phenotypic relationship between body weight and susceptibility to DFTD, and there was evidence for a negative genetic correlation between susceptibility to DFTD and body weight. There was additive genetic variance in susceptibility to DFTD, head width and body weight, but there was no evidence for inbreeding depression in any of these traits. These results suggest that Tasmanian devils have the potential to respond adaptively to DFTD, although the realised evolutionary response will critically further depend on the evolution of DFTD itself.

26Life-history trade-offs and reproductive strategies in Tasmanian devils following disease-induced population decline.PubMed

Kasha Strickland, Menna Jones, Shelly Lachish, et al.
Proc Biol Sci. 2025 May;292(2047):20250697. doi: 10.1098/rspb.2025.0697. Epub 2025 May 21.
Life-history trade-offs can mediate population declines following perturbations, and early reproduction should be favoured when adult survival is impacted more than juvenile survival. In Tasmanian devils (), following the emergence of a transmissible cancer that caused steep population declines, females started to breed precocially (i.e. at age 1 instead of 2 years old). Here, using 18 years of mark-recapture data from a site where the disease was present (Freycinet Peninsula, Tasmania, Australia), we tested whether: (i) the probability of 1-yea-old females breeding continued to increase over time; (ii) there was a relationship between body size and breeding success for either 1-year-old or adult females; and (iii) there was inbreeding depression in breeding success for either age category. We show that the probability of 1-year-old females breeding did not increase between 2003 and 2021, and that the proportion of precocially breeding females remains at around 40%. We also show that there was no effect of skeletal body size on the probability of breeding, but heavier females were always more likely to breed. Finally, we found no evidence for inbreeding depression in breeding success. We discuss our results in the context of possible constraints by way of limitations to growth in the offspring of precocially breeding females.

27Senescence-accelerated mouse (SAM): a novel murine model of senescence.PubMed

T Takeda, M Hosokawa, K Higuchi
Exp Gerontol. 1997 Jan-Apr;32(1-2):105-9. doi: 10.1016/s0531-5565(96)00036-8.
The Senescence-Accelerated Mouse (SAM) has been under development by our research team at Kyoto University since 1970 through the selective inbreeding of the AKR/J strain of mice donated by the Jackson Laboratory in 1968, based on a graded score for senescence, life span, and pathologic phenotype. At present, there are 12 lines of SAM: nine senescence-prone inbred strains (SAMP) including SAMP1, SAMP2, SAMP3, SAMP6, SAMP7, SAMP8, SAMP9, SAMP10, and SAMP11; and three senescence-resistant inbred strains (SAMR) including SAMR1, SAMR4, and SAMR5. Data from survival curves, Gompertzian function, and grading score of senescence, together with growth patterns of body weight of these SAMP and SAMR, revealed that the characteristic feature of aging common to all SAMP mice is "accelerated senescence;" early onset and irreversible advance of senescence manifested by several signs and gross lesions such as the loss of normal behavior, various skin lesions, increased lordokyphosis, etc., after a period of normal development. In the course of SAM development, it became evident that SAMP strains manifest various pathologic phenotypes that are characteristic enough to differentiate the SAM strains. The genetic background and significance of SAM development are discussed.

28Allograft outcomes in outbred mice.PubMed

D K Reichenbach, Q Li, R A Hoffman, et al.
Am J Transplant. 2013 Mar;13(3):580-8. doi: 10.1111/ajt.12056. Epub 2013 Jan 11.
Inbreeding depression and lack of genetic diversity in inbred mice could mask unappreciated causes of graft failure or remove barriers to tolerance induction. To test these possibilities, we performed heart transplantation between outbred or inbred mice. Unlike untreated inbred mice in which all allografts were rejected acutely (6-16 days posttransplantation), untreated outbred mice had heterogeneous outcomes, with grafts failing early (<4 days posttransplantation), acutely (6-24 days) or undergoing chronic rejection (>75 days). Blocking T cell costimulation induced long-term graft acceptance in both inbred and outbred mice, but did not prevent the early graft failure observed in the latter. Further investigation of this early phenotype established that it is dependent on the donor, and not the recipient, being outbred and that it is characterized by hemorrhagic necrosis and neutrophilic vasculitis in the graft without preformed, high titer antidonor antibodies in the recipient. Complement or neutrophil depletion prevented early failure of outbred grafts, whereas transplanting CD73-deficient inbred hearts, which are highly susceptible to ischemia-reperfusion injury, recapitulated the early phenotype. Therefore, outbred mice could provide broader insight into donor and recipient determinants of allograft outcomes but their hybrid vigor and genetic diversity do not constitute a uniform barrier to tolerance induction.

29Feline Fertility: Consequences of inbreeding and implications for reproductive fitness.PubMed

Margret L Casal
J Feline Med Surg. 2022 Sep;24(9):847-852. doi: 10.1177/1098612X221118755.
PRACTICAL RELEVANCE: When compared with the number of individuals that make up a dog breed, the population within a given cat breed is very small. Therefore, to maintain a breed standard, a certain degree of inbreeding is necessary. However, when inbreeding reaches a certain threshold, it can lead to decreased fertility, which manifests as failure to conceive, smaller litter size, increased neonatal illness and neonatal mortality. Breeders should be encouraged to keep comprehensive records on breeding outcomes, including number of kittens born, neonatal vitality, daily kitten weights and kitten health at weaning. Commercially available DNA panels are available to inform and facilitate excellent breeding choices and can estimate the coefficient of inbreeding. Clinicians should include a review of the degree of inbreeding in the work-up for any cattery or cat colony experiencing decreased fertility. AIM: The objective of this article is to provide clinicians, especially those working with cat breeders, with an easy-to-understand guide to genetics and to demonstrate how inbreeding influences fertility and neonatal survival. EQUIPMENT AND TECHNICAL SKILLS: Medical records and the pedigree of the cats in question are required to investigate cases of infertility that may be related to inbreeding. A DNA analysis kit that measures genetic diversity and health parameters can also be helpful; those that have been developed by geneticists and veterinarians at universities are preferable, as they include access to highly skilled genetic counselors and researchers who are open to working up newly discovered genetic diseases. EVIDENCE BASE: The material provided is based on current literature and the author's own studies examining outcomes in a closed cattery.

30Canine fertility: The consequences of selection for special traits.PubMed

Stefano P Marelli, Michela Beccaglia, Alessandro Bagnato, et al.
Reprod Domest Anim. 2020 Jul;55 Suppl 2:4-9. doi: 10.1111/rda.13586. Epub 2020 Jan 8.
Pedigree dogs and cats are bred aiming to conform breed standards with very poor consideration for breeding stock fertility. At the same time, the genetic asset underlining reproductive traits could be effectively analysed like in other species under selection. The definition of selection targets is very important in breeding protocols determination. The aim of the present work is to present an overview of the different correlations between reproduction and genetics, starting from selection procedure and inbreeding coefficient moving to genomic and the application of SNPs and GWAS on population study and identification of genes involved in phenotypical variation of reproductive traits in dogs. Particular relevance has been given to the concept of inbreeding which effects on canine reproduction have been presented. The use of genomic information in inbreeding coefficient calculation can be considered an improved effective procedure in the evaluation of the genetic variability loss in canine population and its negative effects on reproductive traits.

31Genetic relationships and inbreeding levels among geographically distant populations of Felis catus from Japan and the United States.PubMed

Yuki Matsumoto, Napat Ruamrungsri, Minori Arahori, et al.
Genomics. 2021 Jan;113(1 Pt 1):104-110. doi: 10.1016/j.ygeno.2020.11.018. Epub 2020 Nov 25.
Pedigreed cats have traditionally been mated with close relatives, which increases the risks for inbreeding depression and genetic disorders. We evaluated the genome-wide population structure and the degree of inbreeding of 1022 cats, including 13 pedigreed and two random bred populations from Japan and the USA, using single nucleotide polymorphism array-based data. Ancestry structure analysis revealed Japan's American Curl, Norwegian Forest, and Siamese cat populations were genetically distinct from their American counterparts. Furthermore, we found an ancestral genetic component shared between five pedigreed and random bred Japanese cats, suggesting the breeds were admixed with Japanese cats or cats of east Asian origin. Between-country differences in inbreeding estimates based on runs of homozygosity were found for Maine Coon, Siamese, and random bred cats. To reduce the risks of inbreeding depression and genetic disorders, particularly for highly inbred breeds, such as Abyssinian cats, as well as Russian Blue and Siamese cats in the USA, appropriate breeding practices must be observed, including mating practices that increase the genetic diversity.

32Statistical analysis in support of maintaining a healthy traditional Siamese cat population.PubMed

Arthur M A Pistorius, Ineke Blokker
Genet Sel Evol. 2021 Jan 6;53(1):6. doi: 10.1186/s12711-020-00596-w.
BACKGROUND: For many years, breeders of companion animals have applied inbreeding or line breeding to transfer desirable genetic traits from parents to their offspring. Simultaneously, this resulted in a considerable spread of hereditary diseases and phenomena associated with inbreeding depression. RESULTS: Our cluster analysis of kinship and inbreeding coefficients suggests that the Thai or traditional Siamese cat could be considered as a subpopulation of the Siamese cat, which shares common ancestors, although they are considered as separate breeds. In addition, model-based cluster analysis could detect regional differences between Thai subpopulations. We show that by applying optimal contribution selection and simultaneously limiting the contributions by other breeds, the genetic diversity within subpopulations can be improved. CONCLUSION: In principle, the European mainland Thai cat population can achieve a genetic diversity of about 26 founder genome equivalents, a value that could potentially sustain a genetically diverse population. However, reaching such a target will be difficult in the absence of a supervised breeding program. Suboptimal solutions can be obtained by minimisation of kinships within regional subpopulations. Exchanging animals between different regions on a small scale might be already quite useful to reduce the kinship, by achieving a potential diversity of 23 founder genome equivalents. However, contributions by other breeds should be minimised to preserve the original Siamese gene pool.

33Tracking footprints of artificial and natural selection signatures in breeding and non-breeding cats.PubMed

Xuying Zhang, Kokila Jamwal, Ottmar Distl
Sci Rep. 2022 Oct 27;12(1):18061. doi: 10.1038/s41598-022-22155-7.
Stray non-breeding cats (stray) represent the largest heterogeneous cat population subject to natural selection, while populations of the Siamese (SIAM) and Oriental Shorthair (OSH) breeds developed through intensive artificial selection for aesthetic traits. Runs of homozygosity (ROH) and demographic measures are useful tools to discover chromosomal regions of recent selection and to characterize genetic diversity in domestic cat populations. To achieve this, we genotyped 150 stray and 26 household non-breeding cats (household) on the Illumina feline 63 K SNP BeadChip and compared them to SIAM and OSH. The 50% decay value of squared correlation coefficients (r) in stray (0.23), household (0.25), OSH (0.24) and SIAM (0.25) corresponded to a mean marker distance of 1.12 Kb, 4.55 Kb, 62.50 Kb and 175.07 Kb, respectively. The effective population size (N) decreased in the current generation to 55 in stray, 11 in household, 9 in OSH and 7 in SIAM. In the recent generation, the increase in inbreeding per generation (ΔF) reached its maximum values of 0.0090, 0.0443, 0.0561 and 0.0710 in stray, household, OSH and SIAM, respectively. The genomic inbreeding coefficient (F) based on ROH was calculated for three length categories. The F was between 0.014 (F) and 0.020 (F) for stray, between 0.018 (F) and 0.024 (F) for household, between 0.048 (F) and 0.069 (F) for OSH and between 0.053 (F) and 0.073 (F) for SIAM. We identified nine unique selective regions for stray through genome-wide analyses for regions with reduced heterozygosity based on F statistics. Genes in these regions have previously been associated with reproduction (BUB1B), motor/neurological behavior (GPHN, GABRB3), cold-induced thermogenesis (DIO2, TSHR), immune system development (TSHR), viral carcinogenesis (GTF2A1), host immune response against bacteria, viruses, chemoattractant and cancer cells (PLCB2, BAHD1, TIGAR), and lifespan and aging (BUB1B, FGF23). In addition, we identified twelve unique selective regions for OSH containing candidate genes for a wide range of coat colors and patterns (ADAMTS20, KITLG, TYR, TYRO3-a MITF regulator, GPNMB, FGF7, RAB38) as well as congenital heart defects (PDE4D, PKP2) and gastrointestinal disorders (NLGN1, ALDH1B1). Genes in stray that represent unique selective events indicate, at least in part, natural selection for environmental adaptation and resistance to infectious disease, and should be the subject of future research. Stray cats represent an important genetic resource and have the potential to become a research model for disease resistance and longevity, which is why we recommend preserving semen before neutering.

34Body size, inbreeding, and lifespan in domestic dogs.PubMed

Jennifer Yordy, Cornelia Kraus, Jessica J Hayward, et al.
Conserv Genet. 2020 Feb;21(1):137-148. doi: 10.1007/s10592-019-01240-x. Epub 2019 Dec 5.
Inbreeding poses a real or potential threat to nearly every species of conservation concern. Inbreeding leads to loss of diversity at the individual level, which can cause inbreeding depression, and at the population level, which can hinder ability to respond to a changing environment. In closed populations such as endangered species and ex situ breeding programs, some degree of inbreeding is inevitable. It is therefore vital to understand how different patterns of breeding and inbreeding can affect fitness in real animals. Domestic dogs provide an excellent model, showing dramatic variation in degree of inbreeding and in lifespan, an important aspect of fitness that is known to be impacted by inbreeding in other species. There is a strong negative correlation between body size and lifespan in dogs, but it is unknown whether the higher rate of aging in large dogs is due to body size per se or some other factor associated with large size. We used dense genome-wide SNP array data to calculate average inbreeding for over 100 dog breeds based on autozygous segment length and found that large breeds tend to have higher coefficients of inbreeding than small breeds. We then used data from the Veterinary medical Database and other published sources to estimate life expectancies for pure and mixed breed dogs. When controlling for size, variation in inbreeding was not associated with life expectancy across breeds. When comparing mixed versus purebred dogs, however, mixed breed dogs lived about 1.2 years longer on average than size-matched purebred dogs. Furthermore, individual pedigree coefficients of inbreeding and lifespans for over 9000 golden retrievers showed that inbreeding does negatively impact lifespan at the individual level. Registration data from the American Kennel Club suggest that the molecular inbreeding patterns observed in purebred dogs result from specific breeding practices and/or founder effects and not the current population size. Our results suggest that recent inbreeding, as reflected in variation within a breed, is more likely to affect fitness than historic inbreeding, as reflected in variation among breeds. Our results also indicate that occasional outcrosses, as in mixed breed dogs, can have a substantial positive effect on fitness.

35Pedigree data indicate rapid inbreeding and loss of genetic diversity within populations of native, traditional dog breeds of conservation concern.PubMed

Mija Jansson, Linda Laikre
PLoS One. 2018 Sep 12;13(9):e0202849. doi: 10.1371/journal.pone.0202849. eCollection 2018.
Increasing concern is directed towards genetic diversity of domestic animal populations because strong selective breeding can rapidly deplete genetic diversity of socio-economically valuable animals. International conservation policy identifies minimizing genetic erosion of domesticated animals as a key biodiversity target. We used breeding records to assess potential indications of inbreeding and loss of founder allelic diversity in 12 native Swedish dog breeds, traditional to the country, ten of which have been identified by authorities as of conservation concern. The pedigrees dated back to the mid-1900, comprising 5-11 generations and 350-66,500 individuals per pedigree. We assessed rates of inbreeding and potential indications of loss of genetic variation by measuring inbreeding coefficients and remaining number of founder alleles at five points in time during 1980-2012. We found average inbreeding coefficients among breeds to double-from an average of 0.03 in 1980 to 0.07 in 2012 -in spite of the majority of breeds being numerically large with pedigrees comprising thousands of individuals indicating that such rapid increase of inbreeding should have been possible to avoid. We also found indications of extensive loss of intra-breed variation; on average 70 percent of founder alleles are lost during 1980-2012. Explicit conservation goals for these breeds were not reflected in pedigree based conservation genetic measures; breeding needs to focus more on retaining genetic variation, and supplementary genomic analyses of these breeds are highly warranted in order to find out the extent to which the trends indicated here are reflected over the genomes of these breeds.

36Immigration delays but does not prevent adaptation following environmental change: experimental evidence.PubMed

Lily F Durkee, Laure Olazcuaga, Brett A Melbourne, et al.
J Evol Biol. 2024 Jun 28;37(6):665-676. doi: 10.1093/jeb/voae031.
In today's rapidly changing world, it is critical to examine how animal populations will respond to severe environmental change. Following events such as pollution or deforestation that cause populations to decline, extinction will occur unless populations can adapt in response to natural selection, a process called evolutionary rescue. Theory predicts that immigration can delay extinction and provide novel genetic material that can prevent inbreeding depression and facilitate adaptation. However, when potential source populations have not experienced the new environment before (i.e., are naive), immigration can counteract selection and constrain adaptation. This study evaluated the effects of immigration of naive individuals on evolutionary rescue using the red flour beetle, Tribolium castaneum, as a model system. Small populations were exposed to a challenging environment, and 3 immigration rates (0, 1, or 5 migrants per generation) were implemented with migrants from a benign environment. Following an initial decline in population size across all treatments, populations receiving no immigration gained a higher growth rate one generation earlier than those with immigration, illustrating the constraining effects of immigration on adaptation. After 7 generations, a reciprocal transplant experiment found evidence for adaptation regardless of immigration rate. Thus, while the immigration of naive individuals briefly delayed adaptation, it did not increase extinction risk or prevent adaptation following environmental change.

37Mutation load decreases with haplotype age in wild Soay sheep.PubMed

Martin A Stoffel, Susan E Johnston, Jill G Pilkington, et al.
Evol Lett. 2021 May 17;5(3):187-195. doi: 10.1002/evl3.229. eCollection 2021 Jun.
Runs of homozygosity (ROH) are pervasive in diploid genomes and expose the effects of deleterious recessive mutations, but how exactly these regions contribute to variation in fitness remains unclear. Here, we combined empirical analyses and simulations to explore the deleterious effects of ROH with varying genetic map lengths in wild Soay sheep. Using a long-term dataset of 4879 individuals genotyped at 417K SNPs, we found that inbreeding depression increases with ROH length. A 1% genomic increase in long ROH (>12.5 cM) reduced the odds of first-year survival by 12.4% compared to only 7.7% for medium ROH (1.56-12.5 cM), whereas short ROH (<1.56 cM) had no effect on survival. We show by forward genetic simulations that this is predicted: compared to shorter ROH, long ROH will have higher densities of deleterious alleles, with larger average effects on fitness and lower population frequencies. Taken together, our results are consistent with the idea that the mutation load decreases in older haplotypes underlying shorter ROH, where purifying selection has had more time to purge deleterious mutations. Finally, our study demonstrates that strong inbreeding depression can persist despite ongoing purging in a historically small population.

38Inbreeding depression by environment interactions in a free-living mammal population.PubMed

J M Pemberton, P E Ellis, J G Pilkington, et al.
Heredity (Edinb). 2017 Jan;118(1):64-77. doi: 10.1038/hdy.2016.100. Epub 2016 Nov 23.
Experimental studies often find that inbreeding depression is more severe in harsh environments, but the few studies of in situ wild populations available to date rarely find strong support for this effect. We investigated evidence for inbreeding depression by environment interactions in nine traits in the individually monitored Soay sheep population of St Kilda, using genomic inbreeding coefficients based on 37 037 single-nucleotide polymorphism loci, and population density as an axis of environmental variation. All traits showed variation with population density and all traits showed some evidence for depression because of either an individual's own inbreeding or maternal inbreeding. However, only six traits showed evidence for an interaction in the expected direction, and only two interactions were statistically significant. We identify three possible reasons why wild population studies may generally fail to find strong support for interactions between inbreeding depression and environmental variation compared with experimental studies. First, for species with biparental inbreeding only, the amount of observed inbreeding in natural populations is generally low compared with that used in experimental studies. Second, it is possible that experimental studies sometimes actually impose higher levels of stress than organisms experience in the wild. Third, some purging of the deleterious recessive alleles that underpin interaction effects may occur in the wild.

39Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages.PubMed

Gözde Atağ, Damla Kaptan, Eren Yüncü, et al.
Genome Biol Evol. 2024 May 2;16(5). doi: 10.1093/gbe/evae090.
Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.

40Genetic rescue in a severely inbred wolf population.PubMed

Mikael Åkesson, Olof Liberg, Håkan Sand, et al.
Mol Ecol. 2016 Oct;25(19):4745-56. doi: 10.1111/mec.13797. Epub 2016 Sep 6.
Natural populations are becoming increasingly fragmented which is expected to affect their viability due to inbreeding depression, reduced genetic diversity and increased sensitivity to demographic and environmental stochasticity. In small and highly inbred populations, the introduction of only a few immigrants may increase vital rates significantly. However, very few studies have quantified the long-term success of immigrants and inbred individuals in natural populations. Following an episode of natural immigration to the isolated, severely inbred Scandinavian wolf (Canis lupus) population, we demonstrate significantly higher pairing and breeding success for offspring to immigrants compared to offspring from native, inbred pairs. We argue that inbreeding depression is the underlying mechanism for the profound difference in breeding success. Highly inbred wolves may have lower survival during natal dispersal as well as competitive disadvantage to find a partner. Our study is one of the first to quantify and compare the reproductive success of first-generation offspring from migrants vs. native, inbred individuals in a natural population. Indeed, our data demonstrate the profound impact single immigrants can have in small, inbred populations, and represent one of very few documented cases of genetic rescue in a population of large carnivores.

41Sex-specific impact of inbreeding on pathogen load in the striped dolphin.PubMed

Georgios A Gkafas, Menno de Jong, Athanasios Exadactylos, et al.
Proc Biol Sci. 2020 Mar 11;287(1922):20200195. doi: 10.1098/rspb.2020.0195.
The impact of inbreeding on fitness has been widely studied and provides consequential inference about adaptive potential and the impact on survival for reduced and fragmented natural populations. Correlations between heterozygosity and fitness are common in the literature, but they rarely inform about the likely mechanisms. Here, we investigate a pathology with a clear impact on health in striped dolphin hosts (a nematode infection that compromises lung function). Dolphins varied with respect to their parasite burden of this highly pathogenic lung nematode (). Genetic diversity revealed by high-resolution restriction-associated DNA (43 018 RADseq single nucleotide polymorphisms) analyses showed a clear association between heterozygosity and pathogen load, but only for female dolphins, for which the more heterozygous individuals had lower burden. One locus identified by RADseq was a strong outlier in association with parasite load (heterozygous in all uninfected females, homozygous for 94% of infected females), found in an intron of the citron rho-interacting serine/threonine kinase locus (associated with milk production in mammals). Allelic variation at the Class II major histocompatability complex DQB locus was also assessed and found to be associated with both regional variation and with pathogen load. Both sex specificity and the identification of associating functional loci provide insight into the mechanisms by which more inbred individuals may be more susceptible to the infection of this parasite. This provides important insight towards our understanding of the impact of inbreeding in natural populations, relevant to both evolutionary and practical conservation considerations.

42Purging and accumulation of genetic load in conservation.PubMed

Nicolas Dussex, Hernán E Morales, Christine Grossen, et al.
Trends Ecol Evol. 2023 Oct;38(10):961-969. doi: 10.1016/j.tree.2023.05.008. Epub 2023 Jun 19.
Our ability to assess the threat posed by the genetic load to small and declining populations has been greatly improved by advances in genome sequencing and computational approaches. Yet, considerable confusion remains around the definitions of the genetic load and its dynamics, and how they impact individual fitness and population viability. We illustrate how both selective purging and drift affect the distribution of deleterious mutations during population size decline and recovery. We show how this impacts the composition of the genetic load, and how this affects the extinction risk and recovery potential of populations. We propose a framework to examine load dynamics and advocate for the introduction of load estimates in the management of endangered populations.

43Genomic signatures of inbreeding and mutation load in tree ferns.PubMed

Huiqin Yi, Jing Wang, Shiyong Dong, et al.
Plant J. 2024 Nov;120(4):1522-1535. doi: 10.1111/tpj.17064. Epub 2024 Oct 10.
Ferns (Pteridophyta), as the second largest group of vascular plants, play important roles in ecosystem functioning. Homosporous ferns exhibit a remarkable range of mating systems, from extreme inbreeding to obligate outcrossing, which may have significant evolutionary and ecological implications. Despite their significance, the impact of genome-wide inbreeding on genetic diversity and mutation load within the fern lineage remain largely unexplored. In this study, we utilized whole-genome sequencing to investigate the genomic signatures of inbreeding and genetic load in three Alsophila tree fern species. Our analysis revealed extremely high inbreeding in A. spinulosa, in contrast to the predominantly outcrossing observed in A. costularis and A. latebrosa. This difference likely reflects divergent mating systems and demographic histories. Consistent with its extreme inbreeding propensity, A. spinulosa exhibits reduced genetic diversity and a pronounced decline in effective population size. Comparison of genetic load revealed an overall reduction in deleterious mutations in the highly inbred A. spinulosa, highlighting that long-term inbreeding may have contributed to the purging of strongly deleterious mutations, thereby prolonging the survival of A. spinulosa. Despite this, however, A. spinulosa carries a substantive realized genetic load that may potentially instigate future fitness decline. Our findings illuminate the complex evolutionary interplay between inbreeding and mutation load in homosporous ferns, yielding insights with important implications for the conservation and management of these species.

44Inferring purging from pedigree data.PubMed

Davorka Gulisija, James F Crow
Evolution. 2007 May;61(5):1043-51. doi: 10.1111/j.1558-5646.2007.00088.x.
The harmful effects of inbreeding can be reduced if deleterious recessive alleles were removed (purged) by selection against homozygotes in earlier generations. If only a few generations are involved, purging is due almost entirely to recessive alleles that reduce fitness to near zero. In this case the amount of purging and allele frequency change can be inferred approximately from pedigree data alone and are independent of the allele frequency. We examined pedigrees of 59,778 U.S. Jersey cows. Most of the pedigrees were for six generations, but a few went back slightly farther. Assuming recessive homozygotes have fitness 0, the reduction of total genetic load due to purging is estimated at 17%, but most of this is not expressed, being concealed by dominant alleles. Considering those alleles that are currently expressed due to inbreeding, the estimated amount of purging is such as to reduce the expressed load (inbreeding depression) in the current generation by 12.6%. That the reduction is not greater is due mainly to (1) generally low inbreeding levels because breeders in the past have tended to avoid consanguineous matings, and (2) there is essentially no information more than six generations back. The methods used here should be applicable to other populations for which there is pedigree information.

45The efficacy of selection may increase or decrease with selfing depending upon the recombination environment.PubMed

Shelley A Sianta, Stephan Peischl, David A Moeller, et al.
Evolution. 2023 Feb 4;77(2):394-408. doi: 10.1093/evolut/qpac013.
Much theory has focused on how a population's selfing rate affects the ability of natural selection to remove deleterious mutations from a population. However, most such theory has focused on mutations of a given dominance and fitness effect in isolation. It remains unclear how selfing affects the purging of deleterious mutations in a genome-wide context where mutations with different selection and dominance coefficients co-segregate. Here, we use individual-based forward simulations and analytical models to investigate how mutation, selection and recombination interact with selfing rate to shape genome-wide patterns of mutation accumulation and fitness. In addition to recovering previously described results for how selfing affects the efficacy of selection against mutations of a given dominance class, we find that the interaction of purifying selection against mutations of different dominance classes changes with selfing and recombination rates. In particular, when recombination is low and recessive deleterious mutations are common, outcrossing populations transition from purifying selection to pseudo-overdominance, dramatically reducing the efficacy of selection. At these parameter combinations, the efficacy of selection remains low until populations hit a threshold selfing rate, above which it increases. In contrast, selection is more effective in outcrossing than (partial) selfing populations when recombination rates are moderate to high and recessive deleterious mutations are rare.

46The Genetic Cost of Neanderthal Introgression.PubMed

Kelley Harris, Rasmus Nielsen
Genetics. 2016 Jun;203(2):881-91. doi: 10.1534/genetics.116.186890. Epub 2016 Apr 2.
Approximately 2-4% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis. We also predict a residual Neanderthal mutational load in non-Africans, leading to a fitness reduction of at least 0.5%. This effect of Neanderthal admixture has been left out of previous debate on mutation load differences between Africans and non-Africans. We also show that if many deleterious mutations are recessive, the Neanderthal admixture fraction could increase over time due to the protective effect of Neanderthal haplotypes against deleterious alleles that arose recently in the human population. This might partially explain why so many organisms retain gene flow from other species and appear to derive adaptive benefits from introgression.

47Genomic health is dependent on long-term population demographic history.PubMed

Eric Wootton, Claude Robert, Joëlle Taillon, et al.
Mol Ecol. 2023 Apr;32(8):1943-1954. doi: 10.1111/mec.16863. Epub 2023 Feb 8.
Current genetic methods of population assessment in conservation biology have been challenged by genome-scale analyses due to their quantitatively novel insights. These analyses include assessments of runs-of-homozygosity (ROH), genomic evolutionary rate profiling (GERP), and mutational load. Here, we aim to elucidate the relationships between these measures using three divergent ungulates: white-tailed deer, caribou, and mountain goat. The white-tailed deer is currently expanding, while caribou are in the midst of a significant decline. Mountain goats remain stable, having suffered a large historical bottleneck. We assessed genome-wide signatures of inbreeding using the inbreeding coefficient F and %ROH (F ) and identified evolutionarily constrained regions with GERP. Mutational load was estimated by identifying mutations in highly constrained elements (CEs) and sorting intolerant from tolerant (SIFT) mutations. Our results showed that F and F are higher in mountain goats than in caribou and white-tailed deer. Given the extended bottleneck and low N of the mountain goat, this supports the idea that the genome-wide effects of demographic change take time to accrue. Similarly, we found that mountain goats possess more highly constrained CEs and the lowest dN/dS values, both of which are indicative of greater purifying selection; this is also reflected by fewer mutations in CEs and deleterious mutations identified by SIFT. In contrast, white-tailed deer presented the highest mutational load with both metrics, in addition to dN/dS, while caribou were intermediate. Our results demonstrate that extended bottlenecks may lead to reduced diversity and increased F in ungulates, but not necessarily an increase in mutational load, probably due to the purging of deleterious alleles in small populations.

48Impacts of Population Size and Domestication Process on Genetic Diversity and Genetic Load in Genus .PubMed

Dongfeng Wang, Hosein Salehian-Dehkordi, Langda Suo, et al.
Genes (Basel). 2023 Oct 23;14(10):1977. doi: 10.3390/genes14101977.
In theoretical biology, a prevailing hypothesis posits a profound interconnection between effective population size (), genetic diversity, inbreeding, and genetic load. The domestication and improvement processes are believed to be pivotal in diminishing genetic diversity while elevating levels of inbreeding and increasing genetic load. In this study, we performed a whole genome analysis to quantity genetic diversity, inbreeding, and genetic load across seven wild species and five domesticated sheep breeds. Our research demonstrates that the genetic load and diversity of species in the genus have no discernible impact on recent , and three species within the subgenus tend to carry a higher genetic load and lower genetic diversity patterns. The results coincide with these species' dramatic decline in population sizes within the subgenus ~80-250 thousand years ago. European mouflon presented with the lowest , lower genetic diversity, and higher individual inbreeding coefficient but a lower genetic load (missense and LoF). This suggests that the small of European mouflon could reduce harmful mutations compared to other species within the genus . We showed lower genetic diversity in domesticated sheep than in Asiatic mouflon, but counterintuitive patterns of genetic load, i.e., lower weak genetic load (missense mutation) and no significant difference in strong genetic load (LoF mutation) between domestic sheep and Asiatic mouflon. These findings reveal that the "cost of domestication" during domestication and improvement processes reduced genetic diversity and purified weak genetic load more efficiently than wild species.

49Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers.PubMed

Anubhab Khan, Kaushalkumar Patel, Harsh Shukla, et al.
Proc Natl Acad Sci U S A. 2021 Dec 7;118(49). doi: 10.1073/pnas.2023018118.
Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding ( = 0.57) than the large-connected ( = 0.35 and = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

50Purging of Highly Deleterious Mutations Through an Extreme Bottleneck.PubMed

Oliver P Stuart, Rohan Cleave, Kate Pearce, et al.
Mol Biol Evol. 2025 Apr 1;42(4). doi: 10.1093/molbev/msaf079.
Transitions to captivity often produce population bottlenecks. On the one hand, bottlenecks increase inbreeding and decrease effective population size, thus increasing extinction risk. On the other hand, elevated homozygosity associated with inbreeding may purge deleterious mutations. Previous empirical studies of purging in captive breeding programs have focused on phenotypic measurements. We test natural selection's ability to purge deleterious mutations following an extreme population bottleneck by analyzing patterns of genetic diversity in wild and captive-bred individuals of the Lord Howe Island stick insect, Dryococelus australis. Dryococelus australis has been bred in captivity for two decades, having passed through an extreme bottleneck-only two mating pairs with few new additions since then. The magnitude of the bottleneck together with high female fecundity but low offspring recruitment set up nearly ideal conditions for the purging of deleterious mutations. As expected, captive-bred individuals had a greater number of long runs of homozygosity compared with wild individuals, implying strong inbreeding in captivity which would facilitate purging in homozygous regions. Stop-codon mutations were preferentially depleted in captivity compared with other mutations in coding and noncoding regions. The more deleterious a mutation was predicted to be, the more likely it was found outside of runs of homozygosity, implying that inbreeding facilitates the expression and thus removal of deleterious mutations, even after such an extreme bottleneck and under the benign conditions of captivity. These data implicate inbreeding and recessive deleterious mutation load in fitness variation among captive and wild D. australis.

51Sexual selection protects against extinction.PubMed

Alyson J Lumley, Łukasz Michalczyk, James J N Kitson, et al.
Nature. 2015 Jun 25;522(7557):470-3. doi: 10.1038/nature14419. Epub 2015 May 18.
Reproduction through sex carries substantial costs, mainly because only half of sexual adults produce offspring. It has been theorized that these costs could be countered if sex allows sexual selection to clear the universal fitness constraint of mutation load. Under sexual selection, competition between (usually) males and mate choice by (usually) females create important intraspecific filters for reproductive success, so that only a subset of males gains paternity. If reproductive success under sexual selection is dependent on individual condition, which is contingent to mutation load, then sexually selected filtering through 'genic capture' could offset the costs of sex because it provides genetic benefits to populations. Here we test this theory experimentally by comparing whether populations with histories of strong versus weak sexual selection purge mutation load and resist extinction differently. After evolving replicate populations of the flour beetle Tribolium castaneum for 6 to 7 years under conditions that differed solely in the strengths of sexual selection, we revealed mutation load using inbreeding. Lineages from populations that had previously experienced strong sexual selection were resilient to extinction and maintained fitness under inbreeding, with some families continuing to survive after 20 generations of sib × sib mating. By contrast, lineages derived from populations that experienced weak or non-existent sexual selection showed rapid fitness declines under inbreeding, and all were extinct after generation 10. Multiple mutations across the genome with individually small effects can be difficult to clear, yet sum to a significant fitness load; our findings reveal that sexual selection reduces this load, improving population viability in the face of genetic stress.

52Role-reversed polyandry is associated with faster fast-Z in shorebirds.PubMed

Kees Wanders, Guangji Chen, Shaohong Feng, et al.
Proc Biol Sci. 2024 Jun;291(2024):20240397. doi: 10.1098/rspb.2024.0397. Epub 2024 Jun 12.
In birds, males are homogametic and carry two copies of the Z chromosome ('ZZ'), while females are heterogametic and exhibit a 'ZW' genotype. The Z chromosome evolves at a faster rate than similarly sized autosomes, a phenomenon termed 'fast-Z evolution'. This is thought to be caused by two independent processes-greater Z chromosome genetic drift owing to a reduced effective population size, and stronger Z chromosome positive selection owing to the exposure of partially recessive alleles to selection. Here, we investigate the relative contributions of these processes by considering the effect of role-reversed polyandry on fast-Z in shorebirds, a paraphyletic group of wading birds that exhibit unusually diverse mating systems. We find stronger fast-Z effects under role-reversed polyandry, which is consistent with particularly strong selection on polyandrous females driving the fixation of recessive beneficial alleles. This result contrasts with previous research in birds, which has tended to implicate a primary role of genetic drift in driving fast-Z variation. We suggest that this discrepancy can be interpreted in two ways-stronger sexual selection acting on polyandrous females overwhelms an otherwise central role of genetic drift, and/or sexual antagonism is also contributing significantly to fast-Z and is exacerbated in sexually dimorphic species.

53Gametic selection favours polyandry and selfing.PubMed

Michael Francis Scott, Carl Mackintosh, Simone Immler
PLoS Genet. 2024 Feb 16;20(2):e1010660. doi: 10.1371/journal.pgen.1010660. eCollection 2024 Feb.
Competition among pollen or sperm (gametic selection) can cause evolution. Mating systems shape the intensity of gametic selection by determining the competitors involved, which can in turn cause the mating system itself to evolve. We model the bidirectional relationship between gametic selection and mating systems, focusing on variation in female mating frequency (monandry-polyandry) and self-fertilisation (selfing-outcrossing). First, we find that monandry and selfing both reduce the efficiency of gametic selection in removing deleterious alleles. This means that selfing can increase mutation load, in contrast to cases without gametic selection where selfing purges deleterious mutations and decreases mutation load. Second, we explore how mating systems evolve via their effect on gametic selection. By manipulating gametic selection, polyandry can evolve to increase the fitness of the offspring produced. However, this indirect advantage of post-copulatory sexual selection is weak and is likely to be overwhelmed by any direct fitness effects of mating systems. Nevertheless, gametic selection can be potentially decisive for selfing evolution because it significantly reduces inbreeding depression, which favours selfing. Thus, the presence of gametic selection could be a key factor driving selfing evolution.

54Sexual selection matters in genetic rescue, but productivity benefits fade over time: a multi-generation experiment to inform conservation.PubMed

George West, Michael Pointer, Will Nash, et al.
Proc Biol Sci. 2025 Jan;292(2039):20242374. doi: 10.1098/rspb.2024.2374. Epub 2025 Jan 29.
Globally, many species are threatened by population decline because of anthropogenic changes leading to population fragmentation, genetic isolation and inbreeding depression. Genetic rescue, the controlled introduction of genetic variation, is a method used to relieve such effects in small populations. However, without understanding how the characteristics of rescuers impact rescue attempts interventions run the risk of being sub-optimal, or even counterproductive. We use the red flour beetle () to test the impact of rescuer sex, and sexual selection background, on population productivity. We record the impact of genetic rescue on population productivity in 24 and 36 replicated populations for ten generations following intervention. We find little or no impact of rescuer sex on the efficacy of rescue but show that a background of elevated sexual selection makes individuals more effective rescuers. In both experiments, rescue effects diminish 6-10 generations after the rescue. Our results confirm that the efficacy of genetic rescue can be influenced by characteristics of the rescuers and that the level of sexual selection in the rescuing population is an important factor. We show that any increase in fitness associated with rescue may last for a limited number of generations, suggesting implications for conservation policy and practice.

55Beyond Genetic Indicators: How Reproductive Mode and Hybridisation Challenge Freshwater Mussel Conservation.PubMed

Ellika Faust, Julie Conrads, Marco Giulio, et al.
Mol Ecol. 2025 Nov;34(21):e70066. doi: 10.1111/mec.70066. Epub 2025 Aug 11.
Genetic diversity is a fundamental aspect of biodiversity, yet it is rarely assessed and monitored in conservation practice. Unionid freshwater mussels exemplify the dramatic loss of biodiversity in freshwater ecosystems, yet genomic data for these ecologically important species remain scarce. Here, we conducted a high-resolution population genomics study of all Anodonta species in Switzerland, with a focus on two species with contrasting reproductive strategies. After generating draft genomes of the hermaphroditic Anodonta cygnea and the gonochoric Anodonta anatina, we performed whole-genome resequencing of 421 individuals collected in 31 localities. While A. anatina populations followed a metapopulation structure shaped by catchment areas, genetic diversity correlated positively with waterbody size, suggesting greater vulnerability in small ponds compared with large lakes. Inbreeding levels were low; however, effective population sizes were consistently below 100, indicating serious extinction risks. Strong divergence between A. anatina populations north and south of the Alps suggests a putative undescribed Anodonta species in the Ticino area. Furthermore, we detected hybridisation between A. cygnea and A. exulcerata, indicating genomic permeability between these species. In addition, genomic data suggested facultative selfing in A. cygnea, leading to a marked reduction in genetic diversity, increased population structure and inbreeding and a decline in effective population size compared to the outcrossing A. anatina. Our study underscores that reproductive strategy fundamentally shapes genetic indicators of biodiversity and influences extinction risk; conservation targets should therefore be adapted to the biology of the species of interest. To conclude, we advocate for integrating reproductive mode and genomic data into conservation planning to more accurately assess vulnerability and guide effective action.

56Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow.PubMed

Damian C Lettoof, Vicki A Thomson, Jari Cornelis, et al.
PLoS One. 2021 Oct 29;16(10):e0259124. doi: 10.1371/journal.pone.0259124. eCollection 2021.
Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant 'islands'. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which 'islands' of habitat are most in need of management and protection.

57Climate change and pollution speed declines in zebrafish populations.PubMed

A Ross Brown, Stewart F Owen, James Peters, et al.
Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):E1237-46. doi: 10.1073/pnas.1416269112. Epub 2015 Mar 2.
Endocrine disrupting chemicals (EDCs) are potent environmental contaminants, and their effects on wildlife populations could be exacerbated by climate change, especially in species with environmental sex determination. Endangered species may be particularly at risk because inbreeding depression and stochastic fluctuations in male and female numbers are often observed in the small populations that typify these taxa. Here, we assessed the interactive effects of water temperature and EDC exposure on sexual development and population viability of inbred and outbred zebrafish (Danio rerio). Water temperatures adopted were 28 °C (current ambient mean spawning temperature) and 33 °C (projected for the year 2100). The EDC selected was clotrimazole (at 2 μg/L and 10 μg/L), a widely used antifungal chemical that inhibits a key steroidogenic enzyme [cytochrome P450(CYP19) aromatase] required for estrogen synthesis in vertebrates. Elevated water temperature and clotrimazole exposure independently induced male-skewed sex ratios, and the effects of clotrimazole were greater at the higher temperature. Male sex ratio skews also occurred for the lower clotrimazole exposure concentration at the higher water temperature in inbred fish but not in outbred fish. Population viability analysis showed that population growth rates declined sharply in response to male skews and declines for inbred populations occurred at lower male skews than for outbred populations. These results indicate that elevated temperature associated with climate change can amplify the effects of EDCs and these effects are likely to be most acute in small, inbred populations exhibiting environmental sex determination and/or differentiation.

58Climate change introduces threatened killer whale populations and conservation challenges to the Arctic.PubMed

Colin J Garroway, Evelien de Greef, Kyle J Lefort, et al.
Glob Chang Biol. 2024 Jun;30(6):e17352. doi: 10.1111/gcb.17352.
The Arctic is the fastest-warming region on the planet, and the lengthening ice-free season is opening Arctic waters to sub-Arctic species such as the killer whale (Orcinus orca). As apex predators, killer whales can cause significant ecosystem-scale changes. Setting conservation priorities for killer whales and their Arctic prey species requires knowledge of their evolutionary history and demographic trajectory. Using whole-genome resequencing of 24 killer whales sampled in the northwest Atlantic, we first explored the population structure and demographic history of Arctic killer whales. To better understand the broader geographic relationship of these Arctic killer whales to other populations, we compared them to a globally sampled dataset. Finally, we assessed threats to Arctic killer whales due to anthropogenic harvest by reviewing the peer-reviewed and gray literature. We found that there are two highly genetically distinct, non-interbreeding populations of killer whales using the eastern Canadian Arctic. These populations appear to be as genetically different from each other as are ecotypes described elsewhere in the killer whale range; however, our data cannot speak to ecological differences between these populations. One population is newly identified as globally genetically distinct, and the second is genetically similar to individuals sampled from Greenland. The effective sizes of both populations recently declined, and both appear vulnerable to inbreeding and reduced adaptive potential. Our survey of human-caused mortalities suggests that harvest poses an ongoing threat to both populations. The dynamic Arctic environment complicates conservation and management efforts, with killer whales adding top-down pressure on Arctic food webs crucial to northern communities' social and economic well-being. While killer whales represent a conservation priority, they also complicate decisions surrounding wildlife conservation and resource management in the Arctic amid the effects of climate change.

59Boost or Bust? The Impact of Supplementation on Functional Genetic Diversity and Selective Processes in Tasmanian Devils.PubMed

Andrea L Schraven, Katherine A Farquharson, Kimberley C Batley, et al.
Mol Ecol. 2025 Dec;34(24):e70188. doi: 10.1111/mec.70188. Epub 2025 Nov 21.
Translocating individuals into existing populations of conspecifics can support threatened species by increasing population size, maintaining genetic diversity and reducing the risk of inbreeding. However, for species whose adaptive potential is compromised due to ongoing threats, like disease, the outcome of such management interventions becomes more complex. The Tasmanian devil (Sarcophilus harrisii) is a prime example, where the emergence of Devil Facial Tumour Disease (DFTD) has led to significant population declines, raising concerns about their long-term survival. It is therefore critical to understand if the introduction of new functional genetic variants through supplementation actions enhances, or potentially hinders, their long-term persistence. We investigated changes in functional gene diversity at both the population- and individual-levels, pre- and post-supplementation, across multiple wild devil sites (four supplemented and four not supplemented). We found that functional diversity increased post-supplementation. Though the magnitude of change was varied among sites, a similar site-specific pattern was also evident in genome-wide diversity. Importantly, we saw no evidence of swamping of local alleles or those putatively associated with DFTD regressions. This is likely due to the source population representing the broad wild genetic diversity and supplementations facilitating gene flow across the current fragmented landscape. Continued and long-term monitoring at multiple wild sites will be necessary to determine whether future generations retain this introduced genetic variation.

60An epizootic of pneumococcal infection occurred in inbred guinea pig colonies.PubMed

M Saito, T Muto, S Haruzono, et al.
Jikken Dobutsu. 1983 Jan;32(1):29-37. doi: 10.1538/expanim1978.32.1_29.
Epizootiological observations were made on an outbreak of pneumococcal infection occurred in 14 inbred guinea pig colonies during January to October, 1981. Monthly incidences of diseased animals ranged from 16.6 to 0%, showing the highest rate in the first month of the occurrence. Affection rates were remarkably different according to guinea pig strains, being 75% in JY-1 but 0% in JYG and Strain 2. Affected animals showed ruffled fur, dry-dirty noses, emaciated abdomen and dyspnea, and some of them were resulted in death. At necropsy, the fibrinopurulent pneumonia, pleuropneumonia and pleuritis were found as the major pathological features, and in addition, the fibrinopurulent pericarditis and peritonitis with a large amount of exudate were also observed in some cases. Streptococcus pneumoniae was isolated from nearly all the affected organs, and also from the external nares and trachea. Isolation rate from the external nares was especially high, thus 97.1% of infected guinea pigs including healthy carriers were detected by cultivation of nasal swab samples. Carrier rates of healthy animals were gradually increased from 17.2% in April to 36.5% in October, but the organism was not detected from JYG strain at all. During the observation period, vaccination, advance of weaning age of animals and administration of high vitamin C dose were taken as preventive measures of the epizootic, but no remarkable effect was obtained. The same diseased conditions were successfully produced in Hartley guinea pigs by experimental nasal infection of a pneumococcal strain isolated from this epizootic.

61Age truncation due to disease shrinks metapopulation viability for amphibians.PubMed

Geoffrey W Heard, Michael P Scroggie, Matthijs Hollanders, et al.
J Anim Ecol. 2024 Nov;93(11):1670-1683. doi: 10.1111/1365-2656.14177. Epub 2024 Sep 17.
Metapopulations often exist in a fragile balance between local extinctions and (re)colonisations, in which case emerging threats that alter species vital rates may drastically increase metapopulation extinction risk. We combined empirical data with metapopulation simulations to examine how demographic shifts associated with amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd) have altered metapopulation viability for threatened amphibians in Australia. Comparing the ages of museum specimens collected before Bd emerged in Australia with individuals from geographically matched remnant populations revealed significant truncation of age structures post-Bd, with a halving of annual adult survival probabilities. Spatially realistic metapopulation modelling demonstrated that reduced adult survival led to major reductions in the parameter space over which persistence was possible for the focal species, with contractions to landscapes with higher landscape connectivity, lower environmental stochasticity and considerably higher recruitment rates. Metapopulation persistence post-Bd required greater landscape connectivity than pre-Bd. This arises from a landscape-level analogue of compensatory recruitment at the population level, in which higher (re)colonisation rates can offset more frequent local extinctions, enabling persistence of amphibians susceptible to Bd. Interactions between recruitment rate, environmental stochasticity and landscape connectivity were also more important for metapopulation persistence post-Bd. Higher recruitment was required to mitigate the impacts of environmental stochasticity, and higher landscape connectivity was required to mitigate the impacts of environmental stochasticity and poor recruitment. Increased reliance on these interdependencies shrunk the parameter space over which metapopulations could persist post-Bd. Our study demonstrates that emerging threats that alter species vital rates can drastically reduce the capacity of certain environments to support metapopulations. For our focal species, reductions in adult survival rates due to Bd produced major reductions in the conditions under which persistence was possible, providing a mechanistic insight into the processes underpinning observed range and niche contractions of amphibians impacted by this pathogen. More broadly, our study illustrates how environmentally mediated host resilience can enable persistence following the emergence of novel pathogens. This pathway to persistence is worthy of greater attention on both conceptual and applied grounds.

62Hybridization and extinction.PubMed

Marco Todesco, Mariana A Pascual, Gregory L Owens, et al.
Evol Appl. 2016 Feb 22;9(7):892-908. doi: 10.1111/eva.12367. eCollection 2016 Aug.
Hybridization may drive rare taxa to extinction through genetic swamping, where the rare form is replaced by hybrids, or by demographic swamping, where population growth rates are reduced due to the wasteful production of maladaptive hybrids. Conversely, hybridization may rescue the viability of small, inbred populations. Understanding the factors that contribute to destructive versus constructive outcomes of hybridization is key to managing conservation concerns. Here, we survey the literature for studies of hybridization and extinction to identify the ecological, evolutionary, and genetic factors that critically affect extinction risk through hybridization. We find that while extinction risk is highly situation dependent, genetic swamping is much more frequent than demographic swamping. In addition, human involvement is associated with increased risk and high reproductive isolation with reduced risk. Although climate change is predicted to increase the risk of hybridization-induced extinction, we find little empirical support for this prediction. Similarly, theoretical and experimental studies imply that genetic rescue through hybridization may be equally or more probable than demographic swamping, but our literature survey failed to support this claim. We conclude that halting the introduction of hybridization-prone exotics and restoring mature and diverse habitats that are resistant to hybrid establishment should be management priorities.

63The Exciting Potential and Remaining Uncertainties of Genetic Rescue.PubMed

Donovan A Bell, Zachary L Robinson, W Chris Funk, et al.
Trends Ecol Evol. 2019 Dec;34(12):1070-1079. doi: 10.1016/j.tree.2019.06.006. Epub 2019 Jul 8.
Restoring gene flow into small, isolated populations can alleviate genetic load and decrease extinction risk (i.e., genetic rescue), yet gene flow is rarely augmented as a conservation strategy. Due to this discrepancy between opportunity and action, a recent call was made for widespread genetic rescue attempts. However, several aspects of augmenting gene flow are poorly understood, including the magnitude and duration of beneficial effects and when deleterious effects are likely to occur. We discuss the remaining uncertainties of genetic rescue in order to promote and direct future research and to hasten progress toward implementing this potentially powerful conservation strategy on a broader scale.

64Genetic rescue to the rescue.PubMed

Andrew R Whiteley, Sarah W Fitzpatrick, W Chris Funk, et al.
Trends Ecol Evol. 2015 Jan;30(1):42-9. doi: 10.1016/j.tree.2014.10.009. Epub 2014 Nov 27.
Genetic rescue can increase the fitness of small, imperiled populations via immigration. A suite of studies from the past decade highlights the value of genetic rescue in increasing population fitness. Nonetheless, genetic rescue has not been widely applied to conserve many of the threatened populations that it could benefit. In this review, we highlight recent studies of genetic rescue and place it in the larger context of theoretical and empirical developments in evolutionary and conservation biology. We also propose directions to help shape future research on genetic rescue. Genetic rescue is a tool that can stem biodiversity loss more than has been appreciated, provides population resilience, and will become increasingly useful if integrated with molecular advances in population genomics.

65Evolvability and evolutionary rescue.PubMed

Nathalie Feiner, Miguel Brun-Usan, Tobias Uller
Evol Dev. 2021 Jul;23(4):308-319. doi: 10.1111/ede.12374. Epub 2021 Feb 2.
The survival prospects of threatened species or populations can sometimes be improved by adaptive change. Such evolutionary rescue is particularly relevant when the threat comes from changing environments, or when long-term population persistence requires range expansion into new habitats. Conservation biologists are therefore often interested in whether or not populations or lineages show a disposition for adaptive evolution, that is, if they are evolvable. Here, we discuss four alternative perspectives that target different causes of evolvability and outline some of the key challenges those perspectives are designed to address. Standing genetic variation provides one familiar estimate of evolvability. Yet, the mere presence of genetic variation is often insufficient to predict if a population will adapt, or how it will adapt. The reason is that adaptive change not only depends on genetic variation, but also on the extent to which this genetic variation can be realized as adaptive phenotypic variation. This requires attention to developmental systems and how plasticity influences evolutionary potential. Finally, we discuss how a better understanding of the different factors that contribute to evolvability can be exploited in conservation practice.

66Genomic and fitness consequences of inbreeding in an endangered carnivore.PubMed

Malin Hasselgren, Nicolas Dussex, Johanna von Seth, et al.
Mol Ecol. 2021 Jun;30(12):2790-2799. doi: 10.1111/mec.15943. Epub 2021 May 20.
Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and resequencing complete genomes of 23 additional foxes born before and after a well-documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome-wide diversity, with 18% higher heterozygosity and 81% lower F in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach.

67Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana.PubMed

C G Oakley, J Ågren, D W Schemske
Heredity (Edinb). 2015 Jul;115(1):73-82. doi: 10.1038/hdy.2015.18. Epub 2015 Mar 18.
Understanding the causes and architecture of genetic differentiation between natural populations is of central importance in evolutionary biology. Crosses between natural populations can result in heterosis if recessive or nearly recessive deleterious mutations have become fixed within populations because of genetic drift. Divergence between populations can also result in outbreeding depression because of genetic incompatibilities. The net fitness consequences of between-population crosses will be a balance between heterosis and outbreeding depression. We estimated the magnitude of heterosis and outbreeding depression in the highly selfing model plant Arabidopsis thaliana, by crossing replicate line pairs from two sets of natural populations (C↔R, B↔S) separated by similar geographic distances (Italy↔Sweden). We examined the contribution of different modes of gene action to overall differences in estimates of lifetime fitness and fitness components using joint scaling tests with parental, reciprocal F1 and F2, and backcross lines. One of these population pairs (C↔R) was previously demonstrated to be locally adapted, but locally maladaptive quantitative trait loci were also found, suggesting a role for genetic drift in shaping adaptive variation. We found markedly different genetic architectures for fitness and fitness components in the two sets of populations. In one (C↔R), there were consistently positive effects of dominance, indicating the masking of recessive or nearly recessive deleterious mutations that had become fixed by genetic drift. The other set (B↔S) exhibited outbreeding depression because of negative dominance effects. Additional studies are needed to explore the molecular genetic basis of heterosis and outbreeding depression, and how their magnitudes vary across environments.

68Inbreeding and outbreeding depression in male courtship song characters in Drosophila montana.PubMed

J Aspi
Heredity (Edinb). 2000 Mar;84 ( Pt 3):273-82. doi: 10.1046/j.1365-2540.2000.00655.x.
In Drosophila montana, male courtship song frequency is closely associated with male courtship success and offspring survival. Other pulse characters (pulse length and cycle number) may also affect female mate choice, whereas pulse train characters (interpulse interval, pulse number and pulse train length) are not associated with these male fitness components. Inbreeding depression in these song characters was investigated by comparing the songs of inbred and outbred fly strains. The average change in most song characters as a result of inbreeding was only a few percent. However, in male song frequency the average inbreeding depression was about 14%, suggesting that this song character is associated with fitness. Outbreeding depression and the genetic architecture of song characters were investigated with interpopulation crosses and joint scaling tests. For pulse train characters the generation means show only evidence of additivity, and the existence of dominance or epistasis in these characters was strongly rejected in each case. In pulse characters the means of the F1 males were lower than the average of the parental generations. In pulse length and cycle number this difference was attributable to dominance alone. In frequency there was outbreeding depression also in the F2 generation, suggesting a break-up of favourable epistatic gene combinations. The outbreeding depression in this character in the F1 generation was caused by dominance, and in the F2 also by duplicate epistasis between dominant decreasers. The possible role of outbreeding depression and epistasis in speciation is discussed.

69Patterns and effects of gene flow on adaptation across spatial scales: implications for management.PubMed

Jason P Sexton, Molly Clemens, Nicholas Bell, et al.
J Evol Biol. 2024 Jun 28;37(6):732-745. doi: 10.1093/jeb/voae064.
Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.

70Risk assessment of inbreeding and outbreeding depression in a captive-breeding program.PubMed

Njal Rollinson, Dave M Keith, Aimee Lee S Houde, et al.
Conserv Biol. 2014 Apr;28(2):529-40. doi: 10.1111/cobi.12188. Epub 2014 Jan 29.
Captive-breeding programs can be implemented to preserve the genetic diversity of endangered populations such that the controlled release of captive-bred individuals into the wild may promote recovery. A common difficulty, however, is that programs are founded with limited wild broodstock, and inbreeding can become increasingly difficult to avoid with successive generations in captivity. Program managers must choose between maintaining the genetic purity of populations, at the risk of inbreeding depression, or interbreeding populations, at the risk of outbreeding depression. We evaluate these relative risks in a captive-breeding program for 3 endangered populations of Atlantic salmon (Salmo salar). In each of 2 years, we released juvenile F(1) and F(2) interpopulation hybrids, backcrosses, as well as inbred and noninbred within-population crosstypes into 9 wild streams. Juvenile size and survival was quantified in each year. Few crosstype effects were observed, but interestingly, the relative fitness consequences of inbreeding and outbreeding varied from year to year. Temporal variation in environmental quality might have driven some of these annual differences, by exacerbating the importance of maternal effects on juvenile fitness in a year of low environmental quality and by affecting the severity of inbreeding depression differently in different years. Nonetheless, inbreeding was more consistently associated with a negative effect on fitness, whereas the consequences of outbreeding were less predictable. Considering the challenges associated with a sound risk assessment in the wild and given that the effect of inbreeding on fitness is relatively predictable, we suggest that risk can be weighted more strongly in terms of the probable outcome of outbreeding. Factors such as genetic similarities between populations and the number of generations in isolation can sometimes be used to assess outbreeding risk, in lieu of experimentation.

71Predicting the probability of outbreeding depression.PubMed

Richard Frankham, Jonathan D Ballou, Mark D B Eldridge, et al.
Conserv Biol. 2011 Jun;25(3):465-75. doi: 10.1111/j.1523-1739.2011.01662.x. Epub 2011 Apr 12.
Fragmentation of animal and plant populations typically leads to genetic erosion and increased probability of extirpation. Although these effects can usually be reversed by re-establishing gene flow between population fragments, managers sometimes fail to do so due to fears of outbreeding depression (OD). Rapid development of OD is due primarily to adaptive differentiation from selection or fixation of chromosomal variants. Fixed chromosomal variants can be detected empirically. We used an extended form of the breeders' equation to predict the probability of OD due to adaptive differentiation between recently isolated population fragments as a function of intensity of selection, genetic diversity, effective population sizes, and generations of isolation. Empirical data indicated that populations in similar environments had not developed OD even after thousands of generations of isolation. To predict the probability of OD, we developed a decision tree that was based on the four variables from the breeders' equation, taxonomic status, and gene flow within the last 500 years. The predicted probability of OD in crosses between two populations is elevated when the populations have at least one of the following characteristics: are distinct species, have fixed chromosomal differences, exchanged no genes in the last 500 years, or inhabit different environments. Conversely, the predicted probability of OD in crosses between two populations of the same species is low for populations with the same karyotype, isolated for <500 years, and that occupy similar environments. In the former case, we recommend crossing be avoided or tried on a limited, experimental basis. In the latter case, crossing can be carried out with low probability of OD. We used crosses with known results to test the decision tree and found that it correctly identified cases where OD occurred. Current concerns about OD in recently fragmented populations are almost certainly excessive.

72Guidelines for genetic monitoring of translocated plant populations.PubMed

Fabienne Van Rossum, Olivier J Hardy
Conserv Biol. 2022 Feb;36(1):e13670. doi: 10.1111/cobi.13670. Epub 2021 Feb 16.
Plant translocation is a useful tool for implementing assisted gene flow in recovery plans of critically endangered plant species. Although it helps to restore genetically viable populations, it is not devoid of genetic risks, such as poor adaptation of transplants and outbreeding depression in the hybrid progeny, which may have negative consequences in terms of demographic growth and plant fitness. Hence, a follow-up genetic monitoring should evaluate whether the translocated populations are genetically viable and self-sustaining in the short and long term. The causes of failure to adjust management responses also need to be identified. Molecular markers and fitness-related quantitative traits can be used to determine whether a plant translocation enhanced genetic diversity, increased fitness, and improved the probability of long-term survival. We devised guidelines and illustrated them with studies from the literature to help practitioners determine the appropriate genetic survey methods so that management practices can better integrate evolutionary processes. These guidelines include methods for sampling and for assessing changes in genetic diversity and differentiation, contemporary gene flow, mode of local recruitment, admixture level, the effects of genetic rescue, inbreeding or outbreeding depression and local adaptation on plant fitness, and long-term genetic changes.

73Conservation Genomics-Making a Difference.PubMed

Michael M Hansen, Christine Edwards, Christine Grossen, et al.
Mol Ecol. 2025 Dec;34(23):e70191. doi: 10.1111/mec.70191. Epub 2025 Nov 27.
Conservation genomics has increasingly transitioned from a promising concept to a science that integrates a range of advanced analytical approaches, providing new insights into inbreeding, genetic load, demographic history and adaptive divergence in species of conservation concern. Yet, questions remain about how effectively these advances translate into practical conservation action. This Special Issue, Conservation Genomics-Making a Difference, brings together 37 papers that collectively assess how genomic data are contributing to conservation science and management. The contributions encompass empirical studies, reviews, and perspectives that together demonstrate how genomic tools are now used to identify management units, quantify inbreeding, analyse inbreeding depression, reveal adaptive variation, forecast genomic vulnerability under climate change, and guide genetic rescue and assisted migration. Several papers show direct integration of genomics into conservation planning, including fisheries management, guiding restoration of endangered or habitat-forming species, and monitoring of genetic indicators under the Convention on Biological Diversity. Others highlight emerging questions in conservation, such as the significance of structural variation, and the genomic basis of invasiveness. However, persistent challenges remain, notably in bridging the gap between research and policy, uneven global distribution of genomic resources, and translating complex analyses into practical management advice. Nevertheless, the advances presented in the 37 papers show that conservation genomics is moving beyond its early theoretical and technical focus towards real-world applications. The field is maturing and is increasingly fulfilling its promise to make a real difference for populations, species, and ecosystems.

74Quantitative genetics in conservation biology.PubMed

R Frankham
Genet Res. 1999 Dec;74(3):237-44. doi: 10.1017/s001667239900405x.
Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.

75Transforming Ocean Conservation: Applying the Genetic Rescue Toolkit.PubMed

Ben J Novak, Devaughn Fraser, Thomas H Maloney
Genes (Basel). 2020 Feb 18;11(2):209. doi: 10.3390/genes11020209.
Although oceans provide critical ecosystem services and support the most abundant populations on earth, the extent of damage impacting oceans and the diversity of strategies to protect them is disconcertingly, and disproportionately, understudied. While conventional modes of conservation have made strides in mitigating impacts of human activities on ocean ecosystems, those strategies alone cannot completely stem the tide of mounting threats. Biotechnology and genomic research should be harnessed and developed within conservation frameworks to foster the persistence of viable ocean ecosystems. This document distills the results of a targeted survey, the Ocean Genomics Horizon Scan, which assessed opportunities to bring novel genetic rescue tools to marine conservation. From this Horizon Scan, we have identified how novel approaches from synthetic biology and genomics can alleviate major marine threats. While ethical frameworks for biotechnological interventions are necessary for effective and responsible practice, here we primarily assessed technological and social factors directly affecting technical development and deployment of biotechnology interventions for marine conservation. Genetic insight can greatly enhance established conservation methods, but the severity of many threats may demand genomic intervention. While intervention is controversial, for many marine areas the cost of inaction is too high to allow controversy to be a barrier to conserving viable ecosystems. Here, we offer a set of recommendations for engagement and program development to deploy genetic rescue safely and responsibly.

76Genetic conservation and management of the California endemic, Torrey pine ( Parry): Implications of genetic rescue in a genetically depauperate species.PubMed

Jill A Hamilton, Raphaël Royauté, Jessica W Wright, et al.
Ecol Evol. 2017 Aug 9;7(18):7370-7381. doi: 10.1002/ece3.3306. eCollection 2017 Sep.
Rare species present a challenge under changing environmental conditions as the genetic consequences of rarity may limit species ability to adapt to environmental change. To evaluate the evolutionary potential of a rare species, we assessed variation in traits important to plant fitness using multigenerational common garden experiments. Torrey pine, Parry, is one of the rarest pines in the world, restricted to one mainland and one island population. Morphological differentiation between island and mainland populations suggests adaptation to local environments may have contributed to trait variation. The distribution of phenotypic variances within the common garden suggests distinct population-specific growth trajectories underlay genetic differences, with the island population exhibiting substantially reduced genetic variance for growth relative to the mainland population. Furthermore, F1 hybrids, representing a cross between mainland and island trees, exhibit increased height accumulation and fecundity relative to mainland and island parents. This may indicate genetic rescue via intraspecific hybridization could provide the necessary genetic variation to persist in environments modified as a result of climate change. Long-term common garden experiments, such as these, provide invaluable resources to assess the distribution of genetic variance that may inform conservation strategies to preserve evolutionary potential of rare species, including genetic rescue.

77A role for selective contraception of individuals in conservation.PubMed

Holly R Cope, Carolyn J Hogg, Peter J White, et al.
Conserv Biol. 2018 Jun;32(3):546-558. doi: 10.1111/cobi.13042. Epub 2018 Mar 10.
Contraception has an established role in managing overabundant populations and preventing undesirable breeding in zoos. We propose that it can also be used strategically and selectively in conservation to increase the genetic and behavioral quality of the animals. In captive breeding programs, it is becoming increasingly important to maximize the retention of genetic diversity by managing the reproductive contribution of each individual and preventing genetically suboptimal breeding through the use of selective contraception. Reproductive suppression of selected individuals in conservation programs has further benefits of allowing animals to be housed as a group in extensive enclosures without interfering with breeding recommendations, which reduces adaptation to captivity and facilitates the expression of wild behaviors and social structures. Before selective contraception can be incorporated into a breeding program, the most suitable method of fertility control must be selected, and this can be influenced by factors such as species life history, age, ease of treatment, potential for reversibility, and desired management outcome for the individual or population. Contraception should then be implemented in the population following a step-by-step process. In this way, it can provide crucial, flexible control over breeding to promote the physical and genetic health and sustainability of a conservation dependent species held in captivity. For Tasmanian devils (Sarcophilus harrisii), black-flanked rock wallabies (Petrogale lateralis), and burrowing bettongs (Bettongia lesueur), contraception can benefit their conservation by maximizing genetic diversity and behavioral integrity in the captive breeding program, or, in the case of the wallabies and bettongs, by reducing populations to a sustainable size when they become locally overabundant. In these examples, contraceptive duration relative to reproductive life, reversibility, and predictability of the contraceptive agent being used are important to ensure the potential for individuals to reproduce following cessation of contraception, as exemplified by the wallabies when their population crashed and needed females to resume breeding.

78Whole Genomes Inform Genetic Rescue Strategy for Montane Red Foxes in North America.PubMed

Cate B Quinn, Sophie Preckler-Quisquater, Michael R Buchalski, et al.
Mol Biol Evol. 2024 Sep 4;41(9). doi: 10.1093/molbev/msae193.
A few iconic examples have proven the value of facilitated gene flow for counteracting inbreeding depression and staving off extinction; yet, the practice is often not implemented for fear of causing outbreeding depression. Using genomic sequencing, climatic niche modeling, and demographic reconstruction, we sought to assess the risks and benefits of using translocations as a tool for recovery of endangered montane red fox (Vulpes vulpes) populations in the western United States. We demonstrated elevated inbreeding and homozygosity of deleterious alleles across all populations, but especially those isolated in the Cascade and Sierra Nevada ranges. Consequently, translocations would be expected to increase population growth by masking deleterious recessive alleles. Demographic reconstructions further indicated shallow divergences of less than a few thousand years among montane populations, suggesting low risk of outbreeding depression. These genomic-guided findings set the stage for future management, the documentation of which will provide a roadmap for recovery of other data-deficient taxa.

79Genetic Rescue of the Dinaric Lynx Population: Insights for Conservation From Genetic Monitoring and Individual-Based Modelling.PubMed

Elena Pazhenkova, Matej Bartol, Barbara Boljte, et al.
Evol Appl. 2025 Jan 10;18(1):e70045. doi: 10.1111/eva.70045. eCollection 2025 Jan.
Inbreeding depression poses a severe threat to small populations, leading to the fixation of deleterious mutations and decreased survival probability. While the establishment of natural gene flow between populations is an ideal long-term solution, its practical implementation is often challenging. Reinforcement of populations by translocating individuals from larger populations is a viable strategy for reducing inbreeding, increasing genetic diversity and potentially saving populations from extinction. The Dinaric population of Eurasian lynx () has faced high inbreeding levels, with effective inbreeding reaching 0.316 in 2019, endangering the population's survival. To counteract this, population reinforcement was implemented between 2019 and 2023, involving the translocation of 12 individuals from the Carpathian Mountains to the Dinaric Mountains of Slovenia and Croatia. We conducted comprehensive genetic monitoring in this area, gathering 588 non-invasive and tissue samples, which were used for individual identification and estimation of population genetic parameters. We used stochastic modelling to assess the long-term viability of the Dinaric lynx population post-translocation and formulate effective conservation strategies. The model predicts that, despite significant improvement of genetic diversity after translocations, inbreeding will return to critical levels within 45 years. Our results highlight the fact that reinforcement is just the first step and that long-term genetic management is needed to keep the population from sliding back towards extinction. The Dinaric lynx population serves as a compelling example of genetic rescue. The lessons learnt here will be essential for ensuring the viability of the Dinaric lynx in the future and also provide a useful template for conservation of other populations and species facing similar threats.

80Conservation genomics of threatened animal species.PubMed

Cynthia C Steiner, Andrea S Putnam, Paquita E A Hoeck, et al.
Annu Rev Anim Biosci. 2013 Jan;1:261-81. doi: 10.1146/annurev-animal-031412-103636. Epub 2013 Jan 3.
The genomics era has opened up exciting possibilities in the field of conservation biology by enabling genomic analyses of threatened species that previously were limited to model organisms. Next-generation sequencing (NGS) and the collection of genome-wide data allow for more robust studies of the demographic history of populations and adaptive variation associated with fitness and local adaptation. Genomic analyses can also advance management efforts for threatened wild and captive populations by identifying loci contributing to inbreeding depression and disease susceptibility, and predicting fitness consequences of introgression. However, the development of genomic tools in wild species still carries multiple challenges, particularly those associated with computational and sampling constraints. This review provides an overview of the most significant applications of NGS and the implications and limitations of genomic studies in conservation.

81Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project.PubMed

H Bradley Shaffer, Erin Toffelmier, Russ B Corbett-Detig, et al.
J Hered. 2022 Nov 30;113(6):577-588. doi: 10.1093/jhered/esac020.
The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California's marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.

82Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding.PubMed

Jonathan D'Ambrosio, Florence Phocas, Pierrick Haffray, et al.
Genet Sel Evol. 2019 Jun 6;51(1):26. doi: 10.1186/s12711-019-0468-4.
BACKGROUND: Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout (Oncorhynchus mykiss) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fixation index (F), linkage disequilibrium (LD), effective population size (N) and inbreeding coefficient derived from runs of homozygosity (ROH). RESULTS: Our results showed a moderate level of genetic differentiation between selected lines (F ranging from 0.08 to 0.15). LD declined rapidly over the first 100 kb, but then remained quite high at long distances, leading to low estimates of N in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to differences in local rates of recombination or due to key genes that tended to have fixed favorable alleles for domestication or production. CONCLUSIONS: This is the first report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder effects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fish genome.

83Selective Breeding for Genetic Improvement of ( Linnaeus, 1758) in Uganda: Current Status, Challenges, and Future Perspectives.PubMed

Ivan Abaho, Gerald Kwikiriza, Faith Atukwatse, et al.
Animals (Basel). 2025 Jan 9;15(2):142. doi: 10.3390/ani15020142.
() aquaculture continues to significantly contribute to the growth of the aquaculture sector in Uganda. However, its production is beset by erratic and unreliable seed supply. Also, most hatcheries practice inbreeding of broodstock, resulting in inferior seed characterized by low growth rates. As such, a selective breeding program is necessary to readily avail fast-growing seed that respond to farmers' needs. The present review consolidates available information on developing a breeding program in Uganda. The article discusses the significance of genetic improvement, drawing lessons from successful selective breeding programs in other countries. From a literature review, no systematic selective breeding program was traceable in Uganda. Scanty information on the selective breeding efforts of the species was available, with little evidence of selection for improved performance. Overall, the national capacity for aquaculture research and development, including fish breeding and strain improvement, was weak and poorly funded. The review recommends purposive support for developing a systematic strain improvement breeding program, which will be a source of improved broodstock and seed for hatcheries and farmers, respectively. The program would guide the formulation of standard operating procedures for quality seed production towards ensuring sustainable aquaculture growth in Uganda.

84Mutational load, inbreeding depression and heterosis in subdivided populations.PubMed

Brian Charlesworth
Mol Ecol. 2018 Dec;27(24):4991-5003. doi: 10.1111/mec.14933. Epub 2018 Dec 18.
This paper examines the extent to which empirical estimates of inbreeding depression and interpopulation heterosis in subdivided populations, as well as the effects of local population size on mean fitness, can be explained in terms of current estimates of mutation rates, and the distribution of selection coefficients against deleterious mutations provided by population genomics data. Using population genetics models, numerical predictions of the genetic load, inbreeding depression and heterosis were obtained for a broad range of selection coefficients and mutation rates. The models allowed for the possibility of very high mutation rates per nucleotide site, as is sometimes observed for epiallelic mutations in plants. There was fairly good quantitative agreement between the theoretical predictions and empirical estimates of heterosis and the effects of population size on genetic load, on the assumption that the deleterious mutation rate per individual per generation is approximately one, but there was less good agreement for inbreeding depression. Weak selection, of the order of magnitude suggested by population genomic data, is required to explain the observed patterns. Possible caveats concerning the applicability of the models are discussed.

85Deleterious Variation in Natural Populations and Implications for Conservation Genetics.PubMed

Jacqueline Robinson, Christopher C Kyriazis, Stella C Yuan, et al.
Annu Rev Anim Biosci. 2023 Feb 15;11:93-114. doi: 10.1146/annurev-animal-080522-093311. Epub 2022 Nov 4.
Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.

86Sex-specific effects of inbreeding in juvenile brown trout.PubMed

Jonas Bylemans, Lucas Marques da Cunha, Sonia Sarmiento Cabello, et al.
Mol Ecol. 2024 Mar;33(6):e17298. doi: 10.1111/mec.17298. Epub 2024 Feb 15.
Inbreeding depression, that is, the reduction of health and vigour in individuals with high inbreeding coefficients, is expected to increase with environmental, social, or physiological stress. It has therefore been predicted that sexual selection and the associated stress usually lead to higher inbreeding depression in males than in females. However, sex-specific differences in life history may reverse that pattern during certain developmental stages. In some salmonids, for example, female juveniles start developing their gonads earlier than males who instead grow faster. We tested whether the sexes are differently affected by inbreeding during that time. To study the effects of inbreeding coefficients that may be typical for natural populations of brown trout (Salmo trutta), and also to control for potentially confounding maternal or paternal effects, we sampled males and females from the wild, used their gametes in a block-wise full-factorial breeding design to produce 60 full-sib families, released the offspring as yolk-sac larvae into the wild, sampled them 6 months later, identified their genetic sex, and used microsatellites to assign them to their parents. We used whole-genome resequencing to calculate the kinship coefficients for each breeding pair and hence the expected average inbreeding coefficient per family. Juvenile growth could be predicted from these expected inbreeding coefficients and the genetic sex: Females reached lower body sizes with increasing inbreeding coefficient, while no such link could be found in males. This sex-specific inbreeding depression led to the overall pattern that females were on average smaller than males by the end of their first summer.

87Novel genes and sex differences in COVID-19 severity.PubMed

Raquel Cruz, Silvia Diz-de Almeida, Miguel López de Heredia, et al.
Hum Mol Genet. 2022 Nov 10;31(22):3789-3806. doi: 10.1093/hmg/ddac132.
Here, we describe the results of a genome-wide study conducted in 11 939 coronavirus disease 2019 (COVID-19) positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (P < 5 × 10-8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (P = 1.3 × 10-22 and P = 8.1 × 10-12, respectively), and for variants in 9q21.32 near TLE1 only among females (P = 4.4 × 10-8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (P = 2.7 × 10-8) and ARHGAP33 (P = 1.3 × 10-8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative (HGI) confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, P = 4.1 × 10-8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.

88Self-incompatibility and the genetic architecture of inbreeding depression.PubMed

Daniel J Schoen, Sarah J Baldwin
New Phytol. 2023 Feb;237(3):1040-1049. doi: 10.1111/nph.18550. Epub 2022 Nov 22.
Inbreeding depression plays a fundamental role in evolution. To help detect and characterize the loci that underlie inbreeding depression, we used bud pollination and salt treatments to circumvent self-incompatibility (SI) in plants from populations of Leavenworthia alabamica and produced families of progeny that were then genotyped at genetically mapped single-nucleotide polymorphism (SNP) loci. Using Bayesian inference, the segregation patterns for each SNP were used to explore support for different dominance and selection coefficients at linked viability loci in different genomic regions. There was support for several partially recessive viability loci in one of the populations, and one such locus mapped to the genomic region of the novel SI locus in L. alabamica. These results are consistent with earlier findings that showed purging of inbreeding depression for germination rate in L. alabamica. They are also consistent with expectations from evolutionary genetic theory that recessive, deleterious alleles linked to loci under balancing selection can be sheltered from selection.

89Inbreeding depression and its effect on sperm quality traits in Pietrain pigs.PubMed

Gyembo Tsheten, Birgit Fuerst-Waltl, Christina Pfeiffer, et al.
J Anim Breed Genet. 2023 Nov;140(6):653-662. doi: 10.1111/jbg.12816. Epub 2023 Jul 6.
In most cases, inbreeding is expected to have unfavourable effects on traits in livestock. The consequences of inbreeding depression could be substantial, primarily in reproductive and sperm quality traits, and thus lead to decreased fertility. Therefore, the objectives of this study were (i) to compute inbreeding coefficients using pedigree (F ) and genomic data based on runs of homozygosity (ROH) in the genome (F ) of Austrian Pietrain pigs, and (ii) to assess inbreeding depression on four sperm quality traits. In total, 74,734 ejaculate records from 1034 Pietrain boars were used for inbreeding depression analyses. Traits were regressed on inbreeding coefficients using repeatability animal models. Pedigree-based inbreeding coefficients were lower than ROH-based inbreeding values. The correlations between pedigree and ROH-based inbreeding coefficients ranged from 0.186 to 0.357. Pedigree-based inbreeding affected only sperm motility while ROH-based inbreeding affected semen volume, number of spermatozoa, and motility. For example, a 1% increase in pedigree inbreeding considering 10 ancestor generations (F ) was significantly (p < 0.05) associated with a 0.231% decrease in sperm motility. Almost all estimated effects of inbreeding on the traits studied were unfavourable. It is advisable to properly manage the level of inbreeding to avoid high inbreeding depression in the future. Further, analysis of effects of inbreeding depression for other traits, including growth and litter size for the Austrian Pietrain population is strongly advised.

90Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs.PubMed

Carlos Hervás-Rivero, Houssemeddine Srihi, David López-Carbonell, et al.
Genes (Basel). 2023 Oct 15;14(10):1941. doi: 10.3390/genes14101941.
Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120.

91Population genomics for wildlife conservation and management.PubMed

Paul A Hohenlohe, W Chris Funk, Om P Rajora
Mol Ecol. 2021 Jan;30(1):62-82. doi: 10.1111/mec.15720. Epub 2020 Nov 18.
Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.

92Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations.PubMed

Samuel A Speak, Thomas Birley, Chiara Bortoluzzi, et al.
Mol Ecol Resour. 2024 Oct;24(7):e13967. doi: 10.1111/1755-0998.13967. Epub 2024 May 10.
Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long-term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (Nesoenas mayeri). We lifted the mutation-impact scores that had been calculated for the chicken (Gallus gallus) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics-informed conservation can reduce the genetic load whilst reducing the loss of genome-wide diversity. Genomics-informed management is likely to become instrumental in maintaining the long-term viability of zoo populations.