最近强有力的选择性扫描重塑了淡水双壳类Megalonaias nervosa的遗传多样性〈动〉性<动>
Strong, recent selective sweeps reshape genetic diversity in freshwater bivalve Megalonaias nervosa
摘要：
淡水蚌类双壳类最近面临着生态动荡，通过污染，传播障碍，人类收获，以及鱼类宿主流行的变化。目前，超过70%的物种受到威胁，濒危或灭绝。为了描述这些最近的选择压力的遗传反应，我们收集了一个成功的双壳类物种，Megalonaias nervosa的群体遗传数据。我们确定了在整个种群中几乎是单态的巨型区域，这是一个强烈的信号，最近的选择重塑了遗传多样性〈动〉性<动>。这些选择的签名包括总共73 Mb，比通常在群体遗传模型中看到的对选择的响应更大。我们观察到102个重复的基因与高dN/dS的末端分支之间的区域与扫描，表明基因重复是一个致病机制的最近适应M。神经。扫描中的基因反映了已知对Unionid生存重要的功能类别，包括对鱼类宿主寄生重要的抗凝基因、排毒基因、线粒体管理和壳形成。我们确定了选择性扫描区域没有已知的功能影响，适应机制，值得更多的关注，在未来的工作物种生存。相比之下，多态性转座因子插入似乎是有害的，并且在具有扫描的区域中代表性不足。TE站点频谱向单变量倾斜，并且具有扫描的区域之间的TE仅存在于低频率。我们的工作表明，重复基因是遗传新颖性的重要来源，帮助这个成功的物种在其他物种挣扎的环境中取得成功。这些结果表明，在非模式种群基因组学中，基因重复值得更多的关注，特别是在最近面临突发环境挑战的物种中。
英文摘要：
Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, human harvesting, and changes in fish-host prevalence. Currently, over 70% of species are threatened, endangered or extinct. To characterize the genetic response to these recent selective pressures, we collected population genetic data for one successful bivalve species, Megalonaias nervosa. We identify megabase sized regions that are nearly monomorphic across the population, a signal of strong, recent selection reshaping genetic diversity. These signatures of selection encompass a total of 73Mb, greater response to selection than is commonly seen in population genetic models. We observe 102 duplicate genes with high dN/dS on terminal branches among regions with sweeps, suggesting that gene duplication is a causative mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect functional classes known to be important for Unionid survival, including anticoagulation genes important for fish host parasitization, detox genes, mitochondria management, and shell formation. We identify selective sweeps in regions with no known functional impacts, suggesting mechanisms of adaptation that deserve greater attention in future work on species survival. In contrast, polymorphic transposable element insertions appear to be detrimental and underrepresented among regions with sweeps. TE site frequency spectra are skewed toward singleton variants, and TEs among regions with sweeps are present only at low frequency. Our work suggests that duplicate genes are an essential source of genetic novelty that has helped this successful species succeed in environments where others have struggled. These results suggest that gene duplications deserve greater attention in non-model population genomics, especially in species that have recently faced sudden environmental challenges.
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