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.