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

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 non-significant 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 non-model species.

我们利用两种具有不同生活史特征的物种——美国龙虾（Homarus americanus）与北极红点鲑（Salvelinus alpinus）的大规模并行测序（massively parallel sequencing）数据，阐明了样本中失衡的性比例与少量性连锁标记，如何会导致种群结构解读出现偏差，进而导致潜在的错误管理建议。本研究通过多变量分析发现，两组遗传聚类仅依据样本性别进行区分，而非预期的空间差异：对美国龙虾而言为近岸与远岸采样点，对北极红点鲑而言则为东西部采样点。为进一步探究该现象，我们对近岸/远岸、东西部群组构建了多个人工调整性比例的子样本，随后证实：尽管美国龙虾种群存在泛交现象，仍可检测到显著的遗传分化；而北极红点鲑的固定指数（Fst，Fixation Index）值则被高估。该现象分别由12个与94个性连锁标记驱动，对应美国龙虾与北极红点鲑的遗传分化。移除性连锁标记后，美国龙虾的遗传结构不再显著，北极红点鲑的Fst值估算也更为准确。我们利用现有转录组与基因组数据，确定了这些标记的位置以及标记所在或邻近基因的推定身份，这为两个物种的性别决定机制提供了新的认识。鉴于迄今为止所有海洋/洄游种群基因组研究中，仅有9.6%报告了个体性别信息，我们呼吁研究者收集并重视个体性别数据。因此，性别信息不仅有助于规避性连锁标记带来的意外偏差，还能增进我们对非模式物种性别决定系统的认知。