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

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.

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

“…This result is consistent with previous reports that have stressed the importance of accounting for sex in reduced representation sequencing studies, where sex-linked variation can cause erroneous estimates of population genetic differentiation (Benestan et al, 2017;Catchen, 2017). We identified 92 outlier loci associated with sex (Table 5C).…”

“…In addition to neutral and adaptive genetic differences, it is important to consider genetic variation associated with sex (Grummer et al, 2019). Such variation and sex biases in sampling can lead to inaccurate interpretations of population genetic differentiation (Benestan et al, 2017), potentially leading to incorrect management decisions.…”

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

“…Because the sex ratio of the samples from two of the studied populations was not known, the SNP dataset was checked for the presence of sex-linked markers to avoid introducing bias into the analysis (Benestan et al, 2017…”

Widespread intersex differentiation across the stickleback genome – The signature of sexually antagonistic selection?

“…This has immediate implications to population genomics: in marker-based comparisons of populations, localized genome regions exhibiting high differentiation -often interpreted as hotspots harbouring polymorphisms targeted by divergent selection between the populations -may emerge simply because the population samples differ in their proportion of females and males, and hence in the proportion of the two sex chromosomes (Benestan et al, 2017). This has immediate implications to population genomics: in marker-based comparisons of populations, localized genome regions exhibiting high differentiation -often interpreted as hotspots harbouring polymorphisms targeted by divergent selection between the populations -may emerge simply because the population samples differ in their proportion of females and males, and hence in the proportion of the two sex chromosomes (Benestan et al, 2017).…”