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性别在大规模平行测序中很重要:遗传参数估计中的偏倚证据和性别决定系统的研究。

Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems.

机构信息

Département de Biologie, Université Laval, Québec, QC, Canada.

Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.

出版信息

Mol Ecol. 2017 Dec;26(24):6767-6783. doi: 10.1111/mec.14217. Epub 2017 Jul 24.

Abstract

Using massively parallel sequencing data from two species with different life history traits, American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus), we highlight how an unbalanced sex ratio in the samples and a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Here, multivariate analyses revealed two genetic clusters separating samples by sex instead of by expected spatial variation: inshore and offshore locations in lobster, or east and west locations in Arctic Char. To further investigate this, we created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups and then demonstrated that significant genetic differentiation could be observed despite panmixia in lobster, and that F values were overestimated in Arctic Char. This pattern was due to 12 and 94 sex-linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex-linked markers led to nonsignificant genetic structure in lobster and a more accurate estimation of F in Arctic Char. The locations of these markers and putative identities of genes containing or nearby the markers were determined using available transcriptomic and genomic data, and this provided new information related to sex determination in both species. Given that only 9.6% of all marine/diadromous population genomic studies to date have reported sex information, we urge researchers to collect and consider individual sex information. Sex information is therefore relevant for avoiding unexpected biases due to sex-linked markers as well as for improving our knowledge of sex determination systems in nonmodel species.

摘要

利用来自两种具有不同生活史特征的物种——美洲螯龙虾(Homarus americanus)和北极鳕鱼(Salvelinus alpinus)的大规模平行测序数据,我们强调了样本中不平衡的性别比例和少数性连锁标记如何导致对种群结构的错误解释,从而可能导致潜在的错误管理建议。在这里,多元分析揭示了两个遗传聚类,这些聚类通过性别而不是预期的空间变化来分离样本:在龙虾中是近岸和远岸位置,在北极鳕鱼中是东、西部位置。为了进一步研究这一点,我们人为地改变了近岸/远岸和东/西部群体中的性别比例,创建了几个亚样本,然后证明尽管在龙虾中存在混合群体,但仍可以观察到显著的遗传分化,并且在北极鳕鱼中 F 值被高估了。这种模式是由于 12 个和 94 个性连锁标记分别驱动了龙虾和北极鳕鱼的分化。去除性连锁标记导致龙虾的遗传结构不再显著,并且更准确地估计了北极鳕鱼的 F 值。这些标记的位置以及包含或附近标记的基因的假定身份是使用可用的转录组和基因组数据确定的,这为这两个物种的性别决定提供了新的信息。鉴于迄今为止所有海洋/洄游种群基因组研究中只有 9.6%报告了性别信息,我们敦促研究人员收集和考虑个体性别信息。因此,性别信息对于避免由于性连锁标记引起的意外偏差以及提高我们对非模式物种性别决定系统的认识都是相关的。

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