The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies

Abstract

Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the coding joint site frequency spectrum (jSFS), in an approximate Bayesian computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and classes in the jSFS), and show that the number of individuals and loci have little effect on model selection. In contrast, different decompositions of the joint site frequency spectrum strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of the ABC to compare more realistic models of speciation including variation in migration rates through time (i.e. periodic connectivity) and across genes (i.e. genome-wide heterogeneity in migration rates). We show that these models consistently outperform the simpler alternatives. This argues that methods that are restricted to simpler models may fail to reconstruct the true speciation history.

Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels

“…Naturally admixed Atl. M. galloprovincialis combine an old history of introgression during glacial oscillation periods (Fraïsse, Roux, et al, ; Roux et al, ) with ongoing local introgression from the native M. edulis populations in direct contact within the mosaic hybrid zone observed today (Fraïsse et al, ; Simon et al, ).…”

Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia

“…thousands of independent genealogies), model‐based inferences of isolation and migration are robust to small sample sizes (i.e. n = 5–10) (Fraïsse, Roux, et al, ; Robinson, Bunnefeld, Hearn, Stone, & Hickerson, ). Details relating to (a) the filtering of empirical genetic data sets, (b) parameterizing and generating coalescent simulations of genetic data under separate demographic models, (c) demographic model selection, (d) model validation, (e) incorporating parameter heterogeneity and (f) demographic parameter estimation are outlined in the Appendix .…”

“…Japan, Brannock, Wethey, & Hilbish, ; California, Rawson, Agrawal, & Hilbish, ; Saarman & Pogson, ). There is also strong evidence for differential introgression with sister species, Mytilus edulis, in some parts of its present day native range across mosaic hybrid zones in Europe (Bierne, Borsa, et al, ; Fraïsse et al, ; Fraïsse, Roux, et al, ; Gosset & Bierne, ; Rawson & Hilbish, ; Roux et al, ). Interspecific admixture with M. edulis has subsequently led to pronounced genetic differentiation between M. galloprovincialis lineages from the Mediterranean Sea and Atlantic Europe (Fraïsse et al, ; Quesada, Wenne, & Skibinski, ).…”

Fine-grained habitat-associated genetic connectivity in an admixed population of mussels in the small isolated Kerguelen Islands

“…The reason for this low rate of resolved relationship is twofold: (i) ongoing sorting of shared ancestral polymorphism, and (ii) introgression. In the Northern Hemisphere introgression has been shown to be the main process thanks to model fitting (Fraïsse et al 2018) and using comparison of introgression differential between populations within species (Fraïsse et al 2016). It is more difficult to tell apart ancestral shared polymorphism from introgression for the single Kerguelen population.…”

“…In the North, M. edulis and M. galloprovincialis are closely-related species which started to diverge about 2.5 mya (Roux et al 2014), while M. trossulus is an outgroup to them with a divergence dated at 3.5 mya (Rawson & Hilbish 1995). The three species have experienced a complex history of divergence punctuated by periods of gene flow (Roux et al 2014;Fraïsse et al 2018); and nowadays they display hybrid zones where their ranges overlap (Skibinski et al 1983;Väinölä & Hvilsom 1991;Bierne et al 2003). In the South, a reevaluation of allozyme data and a review of the results obtained with mtDNA and two nuclear DNA markers (Borsa et al 2012) encouraged to group Southern mussels in two different taxa, namely M. platensis for those related to M. edulis (the South American and Kerguelen mussels), and M. planulatus for those related to M. galloprovincialis (the Australasian mussels).…”