Differential introgression from a sister species explains highF_SToutlier loci within a mussel species

Abstract

Scanning genomes for loci with high levels of population differentiation has become a standard of population genetics. F ST outlier loci are most often interpreted as signatures of local selection, but outliers might arise for many other reasons too often left unexplored. Here, we tried to identify further the history and genetic basis underlying strong differentiation at F ST outlier loci in a marine mussel. A genome scan of genetic differentiation has been conducted between Atlantic and Mediterranean populations of Mytilus galloprovincialis. The differentiation was low overall (F ST = 0.03), but seven loci (2%) were strong F ST outliers. We then analysed DNA sequence polymorphism at two outlier loci. The genetic structure proved to be the consequence of differential introgression of alleles from the sister-hybridizing species Mytilus edulis. Surprisingly, the Mediterranean population was the most introgressed at these two loci, although the contact zone between the two species is nowadays localized along the Atlantic coasts of France and the British Isles. A historical contact between M. edulis and Mediterranean M. galloprovincialis should have happened during glacial periods. It proved difficult to disentangle two hypotheses: (i) introgression was adaptive, implying edulis alleles have been favoured in Mediterranean populations, or (ii) the genetic architecture of the barrier to edulis gene flow is different between the two M. galloprovincialis backgrounds. Five of the seven outliers between M. galloprovincialis populations were also outliers between M. edulis and Atlantic M. galloprovincialis, which would support the latter hypothesis. Differential introgression across semi-permeable barriers to gene flow is a neglected scenario to interpret outlying loci that may prove more widespread than anticipated.

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

“…2013; Lotterhos and Whitlock 2014). In our study, some F ST outlier SNPs may be interpreted as genetic variation in response to adaptation to local environmental conditions (Beaumont 2005), but other alternative explanations are also possible (Gosset and Bierne 2013) such as the examples of different cohorts described above or other endogenous barriers (Bierne et al. 2011) and introgression (Fraïsse et al.…”

“…2004a), given the opportunity to introgress alleles from one species into the other, producing higher F ST when these loci are evaluated in the genome of the recipient species. Such processes have been shown to cause signals of outlier F ST in two length polymorphism loci between Atlantic and Mediterranean populations of M. galloprovincialis (Gosset and Bierne 2013). Very large F ST values ≥0.5 can be found when different species of Mytilus and their hybrids are compared, even when outlier loci are removed (Zbawicka et al.…”

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

“…All outlier locus detection analyses used the reduced dataset that omitted any individual identified by STRUCTURE as having European ancestry as this might have affected which outlier loci were detected (Gosset & Bierne, 2013). We used four different methods of comparing the TOB_WILD population with the AQUA populations to find regions of the genome with differences in SNP allele frequencies that were greater than would be expected due to genetic drift alone.…”

A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks

“…Moreover, the range-wide sampling strategy implemented in our study, including different environments and forest structures (Supplementary File 1), was designed to enhance the detection of globally divergent genes, while losing power to reveal within-species variation. Thus, our sampling strategy should avoid complications derived both from the coupling hypothesis and from differential introgression with other species of the same evolutionary radiation (Gosset and Bierne, 2013).…”