Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels

Abstract

Structured populations, and replicated zones of contact between species, are an ideal opportunity to study regions of the genome with unusual levels of differentiation; and these can illuminate the genomic architecture of species isolation, and the spread of adaptive alleles across species ranges. Here, we investigated the effects of gene flow on divergence and adaptation in the Mytilus complex of species, including replicated parental populations in quite distant geographical locations. We used target enrichment sequencing of 1269 contigs of a few kb each, including some genes of known function, to infer gene genealogies at a small chromosomal scale. We show that geography is an important determinant of the genomewide patterns of introgression in Mytilus and that gene flow between different species, with contiguous ranges, explained up to half of the intraspecific outliers. This suggests that local introgression is both widespread and tends to affect larger chromosomal regions than purely intraspecific processes. We argue that this situation might be common, and this implies that genome scans should always consider the possibility of introgression from sister species, unsampled differentiated backgrounds, or even extinct relatives, for example Neanderthals in humans. The hypothesis that reticulate evolution over long periods of time contributes widely to adaptation, and to the spatial and genomic reorganization of genetic backgrounds, needs to be more widely considered to make better sense of genome scans.

Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns

“…2016a). To test for this, we genotyped 129 pure‐species individuals, and repeated our analyses with a subset of 33 markers that were strongly differentiated between the pure species (see Methods, Fig.…”

Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

“…2014), and targeted enrichment sequencing (Fraïsse et al. 2015). However, with declining costs of sequencing technology (Liu et al.…”

“…2011) and introgression (Fraïsse et al. 2015). Mytilus species are prone to produce hybrid in geographical areas where two sibling species coexist (Daguin et al.…”

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

“…This may cause rapid drift of some alleles at the expanding edge and high differentiation in allele frequencies over the landscape for some loci, even in the absence of selection. Another demographic process that can lead to idiosyncratic effects at individual loci is hybridization and introgression from related taxa (e.g., Geraldes et al 2014; Fraïsse et al 2016), which could confound genetic-environment associations and differentiation outlier methods focusedononespecies(Kane et al 2009; Nachman and Payseur 2012; Brandvain et al 2014; Bragg et al 2015). …”

“…Some of the issues in multiple comparisons, particularly that of nonindependence among linked SNPs, may be alleviated by using genome window-based methods (Kelly et al 2013; Amorim et al 2015; Wright et al 2015; Fraïsse et al 2016). These methods calculate summary statistics, such as F ST , across a set of adjacent markers for defined windows across the genome and can greatly improve results of outlier analyses.…”