Maas Diede L, Prost Stefan, de Leeuw Christiaan A, Bi Ke, Smith Lydia L, Purwanto Purwanto, Aji Ludi P, Tapilatu Ricardo F, Gillespie Rosemary G, Becking Leontine E
Marine Animal Ecology Wageningen University & Research Wageningen The Netherlands.
LOEWE Centre for Translational Biodiversity Genomics Senckenberg Natural History Museum Frankfurt am Main Germany.
Ecol Evol. 2023 Apr 13;13(4):e9945. doi: 10.1002/ece3.9945. eCollection 2023 Apr.
The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge ( = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.
地理、洋流和环境对固着海洋物种基因流动的相对影响仍是一个悬而未决的问题。由于有效种群规模大、遗传标记普遍缺乏分辨率，以及扩散障碍往往难以捉摸，在底栖生物种群中检测小尺度上的细微遗传分化具有挑战性。海湖可以通过提供离散且可重复的生态系统来规避混杂因素。利用高分辨率双酶切限制性位点关联DNA测序（4826个单核苷酸多态性，SNPs），我们对海绵种群（=125）进行基因分型，以测试空间尺度（1 - 1400千米）、当地环境条件和海景屏障通透性在塑造种群基因组结构中的相对重要性。通过SNPs数据集，我们展示了强烈的谱系内种群结构，即使在小于10千米的尺度上（平均 = 0.63），这是之前使用单一标记未检测到的。大多数变异可由种群间的分化解释（AMOVA：48.8%），每个湖泊都有种群数量下降和瓶颈的特征。尽管种群结构强烈，但我们未检测到地理距离、当地环境或与海洋连接程度对种群结构有显著影响，这表明诸如奠基者事件及后续优先效应等机制可能在起作用。我们表明，纳入可通过COI标记检测到的形态学上隐秘的谱系可使获得的SNP集减少约90%。未来关于海绵基因组学的工作应确认仅包含一个谱系。我们的结果呼吁重新评估先前基于低分辨率标记被认为高度连通的扩散能力差的底栖生物。
