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.本研究以两种生活史特征迥异的物种——美洲螯龙虾（American lobster, *Homarus americanus*）与北极红点鲑（Arctic Char, *Salvelinus alpinus*）的大规模并行测序数据为材料，阐明了样本性比例失衡与少量性连锁标记（sex-linked markers）如何引发种群结构解读失真，进而推导出存在偏差的种群管理建议。本研究通过多变量分析（multivariate analyses）发现，两组样本被划分为两个遗传簇（genetic clusters）的依据并非预期的空间变异：对于美洲螯龙虾而言是近岸与离岸生境，对于北极红点鲑而言则是东西部分布区域，而是样本自身的性别。为进一步验证该现象，我们针对近岸/离岸组与东西部组人工构建了多组性比例各异的子样本（subsamples），结果证实：即便美洲螯龙虾种群存在随机交配（panmixia），仍可观测到显著的遗传分化；而北极红点鲑的Fst群体分化系数则被高估。该现象的成因分别为美洲螯龙虾的12个与北极红点鲑的94个性连锁标记驱动了遗传分化。移除性连锁标记后，美洲螯龙虾的遗传结构不再显著，北极红点鲑的Fst值估算也更为精准。研究人员借助现有转录组学（transcriptomic）与基因组学（genomic）数据，确定了这些标记的基因组位置以及标记所在或邻近基因的推定功能，为两个物种的性别决定机制研究提供了新见解。鉴于目前已发表的海洋/溯河洄游（marine/diadromous）种群基因组学研究中，仅有9.6%报道了样本的性别信息，我们呼吁科研工作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非预期偏差，还能提升我们对非模式生物（non-model species）性别决定系统的认知水平。