Dudaniec Rachael Y, Yadav Sonu, Catchen Julian, Kleindorfer Sonia
School of Natural Sciences Macquarie University Sydney New South Wales Australia.
Biosecurity and Animal Welfare Northern Territory Government Darwin Northwest Territories Australia.
Evol Appl. 2025 Jan 2;18(1):e70066. doi: 10.1111/eva.70066. eCollection 2025 Jan.
Natural hybridisation among rare or endangered species and stable congenerics is increasingly topical for the conservation of species-level diversity under anthropogenic impacts. Evidence for beneficial genes being introgressed into or selected for in hybrids raises concurrent questions about its evolutionary significance. In Darwin's tree finches on the island of Floreana (Galapagos Islands, Ecuador), the Critically Endangered medium tree finch () undergoes introgression with the stable small tree finch (), and hybrids regularly backcross with Earlier studies in 2005-2013 documented an increase in the frequency of hybridisation on Floreana using field-based and microsatellite data. With single nucleotide polymorphism (SNP) data from the same Floreana tree finches sampled in 2005 and 2013 ( = 95), we examine genome-wide divergence across parental and hybrid birds and evidence for selection in hybrids. We found that just 18% of previously assigned hybrid birds based on microsatellites could be assigned to hybrids using SNPs. Over half of the previously assigned hybrids (63%) were reassigned to though parental species showed concordance with prior assignments. Of 4869 private alleles found in hybrid birds, 348 were at a high frequency (≥ 0.30) that exceeded their parental species of origin 89%-96% of the time. For private alleles detected in both years ( = 536) between 11%-76% of alleles underwent a frequency increase and 13%-61% a frequency decrease between 2005 and 2013, which was sensitive to sampling effort. We identified 28 private alleles that were candidates under selection via local PCA and outlier tests. Alleles were annotated to genes associated with inflammation, immunity, brain function and development. We provide evidence that introgression among a critically endangered and stable species of Darwin's tree finch across years may aid in the retention of adaptive alleles and genetic diversity in birds threatened with extinction.
在人为影响下，珍稀或濒危物种与稳定的同属物种之间的自然杂交对于物种水平多样性的保护而言，愈发成为热门话题。有益基因渗入杂种或在杂种中被选择的证据，引发了关于其进化意义的一系列问题。在弗洛雷阿纳岛（厄瓜多尔加拉帕戈斯群岛）上的达尔文树雀中，极度濒危的中型树雀（ ）与稳定的小型树雀（ ）发生基因渗入，且杂种经常与 回交。2005 - 2013年的早期研究利用实地调查和微卫星数据记录了弗洛雷阿纳岛上 杂交频率的增加。借助2005年和2013年对同一批弗洛雷阿纳树雀（ = 95）采样获得的单核苷酸多态性（SNP）数据，我们研究了亲代鸟和杂种鸟的全基因组差异以及杂种中选择的证据。我们发现，基于微卫星先前认定的杂种鸟中，仅有18%能够通过SNP被认定为杂种。超过一半（63%）先前认定的杂种被重新认定为 ，尽管亲代物种与先前的认定结果一致。在杂种鸟中发现的4869个私有等位基因里，有348个高频等位基因（≥ 0.30），其在89% - 96%的时间里超过了其亲代物种的频率。对于在两年中均检测到的私有等位基因（ = 536），在2005年至2013年间，11% - 76%的等位基因频率增加，13% - 61%的等位基因频率下降，这对采样力度较为敏感。我们通过局部主成分分析和异常值检验确定了28个可能受到选择的私有等位基因。这些等位基因被注释到与炎症、免疫、脑功能和发育相关的基因上。我们提供的证据表明，多年来达尔文树雀的极度濒危物种与稳定物种之间的基因渗入可能有助于在面临灭绝威胁的鸟类中保留适应性等位基因和遗传多样性。
