Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench.
Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench.
复制标题
巨大的有效种群规模掩盖了最深的海洋生态系统马里亚纳海沟内的喜龙蝶片足类动物的种群遗传结构。
DOI：
10.1111/mec.16887
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发表时间：
2023
影响因子：
4.9
通讯作者：
Piertney SB
中科院分区：
文献类型：
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作者：
Piertney SB
对深海深渊带遗传结构的研究重点关注构造海沟之间的分歧，以了解环境和地理如何驱动物种分歧并促进特有现象。很少有人尝试检查沟渠内的局部遗传结构，部分原因是与适当规模采样相关的后勤挑战，并且可以充分采样的物种的有效种群规模很大，可能会掩盖潜在的遗传结构。在这里，我们检查了马里亚纳海沟深度 8126-10,545 米的超级丰富的片脚类 Hirondellea gigas 的遗传结构。在严格修剪基因座以防止旁系同源多拷贝基因组区域被错误合并后，使用 RAD 测序鉴定了个体中包含 43,408 个单核苷酸多态性 (SNP) 的 3182 个基因座。 SNP 基因型的主成分分析未解析采样地点之间的遗传结构，这与 panmixia 的特征一致。然而，对主成分的判别分析发现，所有位点之间的差异是由 169 个位点的 301 个异常 SNP 驱动的，并且与纬度和深度显着相关。位点的功能注释确定了分析中使用的单例位点与从数据集中修剪的旁系同源位点之间的差异，以及异常值和非异常值位点之间的差异，所有这些都与解释转座元件驱动基因组动力学的作用的假设一致。这项研究挑战了传统观点，即海沟内高度丰富的片脚类动物形成单一的恐慌种群。我们讨论了与深海生态进化和个体发生过程相关的发现，并强调了与具有固有的大有效种群规模和基因组的非模型系统中种群遗传分析相关的关键挑战。
The examination of genetic structure in the deep‐ocean hadal zone has focused on divergence between tectonic trenches to understand how environment and geography may drive species divergence and promote endemism. There has been little attempt to examine localized genetic structure within trenches, partly because of logistical challenges associated with sampling at an appropriate scale, and the large effective population sizes of species that can be sampled adequately may mask underlying genetic structure. Here we examine genetic structure in the superabundant amphipodHirondellea gigasin the Mariana Trench at depths of 8126–10,545 m. RAD sequencing was used to identify 3182 loci containing 43,408 single nucleotide polymorphisms (SNPs) across individuals after stringent pruning of loci to prevent paralogous multicopy genomic regions being erroneously merged. Principal components analysis of SNP genotypes resolved no genetic structure between sampling locations, consistent with a signature of panmixia. However, discriminant analysis of principal components identified divergence between all sites driven by 301 outlier SNPs in 169 loci and significantly associated with latitude and depth. Functional annotation of loci identified differences between singleton loci used in analysis and paralogous loci pruned from the data set and also between outlier and nonoutlier loci, all consistent with hypotheses explaining the role of transposable elements driving genome dynamics. This study challenges the traditional perspective that highly abundant amphipods within a trench form a single panmictic population. We discuss the findings in relation to eco‐evolutionary and ontogenetic processes operating in the deep sea, and highlight key challenges associated with population genetic analysis in nonmodel systems with inherent large effective population sizes and genomes.