标题： 强而近期的定向选择扫荡重塑了淡水双壳类Megalonaias nervosa的遗传多样性 显示英文标题

标题： Strong, recent selective sweeps reshape genetic diversity in freshwater bivalve Megalonaias nervosa

摘要： 淡水联合双壳类最近由于污染、扩散障碍、人类采集以及鱼类宿主流行率的变化而面临生态动荡。目前，超过70%的物种受到威胁、濒危或灭绝。为了描述这些近期选择压力的遗传反应，我们收集了一种成功的双壳类物种Megalonaias nervosa的群体遗传数据。我们识别出在种群中几乎单态的大规模区域，这是强烈近期选择重塑遗传多样性的信号。这些选择的迹象总共涵盖了73Mb，比在群体遗传模型中通常看到的选择响应更大。我们在具有扫掠区域的末端分支上观察到102个具有高dN/dS的重复基因，这表明基因重复是M. nervosa近期适应的一个因果机制。扫掠中的基因反映了对联合双壳类生存重要的功能类别，包括对鱼类宿主寄生重要的抗凝血基因、解毒基因、线粒体管理以及贝壳形成。我们在没有已知功能影响的区域中发现了选择扫掠，这表明适应机制值得在未来的研究中给予更多关注。相反，多态性转座子插入似乎是有害的，并且在具有扫掠的区域中代表性不足。TE位点频率光谱偏向单一变异，而在具有扫掠的区域中的TE仅以低频率存在。我们的工作表明，重复基因是遗传新颖性的关键来源，帮助这一成功物种在其他物种挣扎的环境中取得成功。这些结果表明，在非模式群体基因组学中，基因重复值得更多关注，特别是在最近面临突然环境挑战的物种中。 显示英文摘要

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.