Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems
Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems
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DOI：
10.1111/mec.14217
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发表时间：
2017-12-01
影响因子：
4.9
通讯作者：
Bernatchez, Louis
中科院分区：
文献类型：
--
作者：
Benestan, Laura;Moore, Jean-Sebastien;Bernatchez, Louis
利用美国龙虾（Homarus americanus）和北极鲑（Salvelinus alpinus）这两个具有不同生活历史特征的物种的大量平行测序数据，我们强调了样本中不平衡的性别比例和一些性别连锁标记如何导致对种群结构的错误解释，从而可能导致错误的管理建议。在这里，多变量分析揭示了两个遗传集群按性别而不是按预期的空间变化将样本分开：龙虾的近海和近海位置，或北极Char的东部和西部位置。为了进一步研究这一点，我们人为地改变了近岸/近海和东/西群体的性别比例，然后证明了在虾群中可以观察到显著的遗传分化，并且在北极Char中FST值被高估了。这种模式是由于12个和94个性别连锁标记分别驱动龙虾和北极鲑的分化。去除性别连锁标记导致龙虾的遗传结构不显著，并更准确地估计了北极Char的FST。利用现有的转录组学和基因组学数据确定了这些标记的位置以及包含或邻近标记的基因的假定身份，这为两种物种的性别决定提供了新的信息。鉴于迄今为止只有9.6%的海洋/双生种群基因组研究报告了性别信息，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别连锁标记而产生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是相关的。
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 FST 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 FST 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.