Browsing by Author "Excoffier, Laurent"
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- Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance sticklebackPublication . Marques, David A.; Lucek, Kay; Sousa, Vitor C; Excoffier, Laurent; Seehausen, OleEcological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation.
- Killer whale genomes reveal a complex history of recurrent admixture and vicariancePublication . Foote, Andrew D.; Martin, Michael D.; Louis, Marie; Pacheco, George; Robertson, Kelly M.; Sinding, Mikkel‐Holger S.; Amaral, Ana Rita; Baird, Robin W.; Baker, Charles Scott; Ballance, Lisa; Barlow, Jay; Brownlow, Andrew; Collins, Tim; Constantine, Rochelle; Dabin, Willy; Dalla Rosa, Luciano; Davison, Nicholas J.; Durban, John W.; Esteban, Ruth; Ferguson, Steven H.; Gerrodette, Tim; Guinet, Christophe; Hanson, M. Bradley; Hoggard, Wayne; Matthews, Cory J. D.; Samarra, Filipa I. P.; de Stephanis, Renaud; Tavares, Sara B.; Tixier, Paul; Totterdell, John A.; Wade, Paul; Excoffier, Laurent; Gilbert, M. Thomas P.; Wolf, Jochen B. W.; Morin, Phillip A.Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
- Reply to "Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin"Publication . Berner, Daniel; Lucek, Kay; Sousa, Vitor C; Excoffier, Laurent; Seehausen, OleA Matters Arising article1 raised concerns about the interpretation of our findings reported in our recent publication on admixture-facilitated ecological speciation in Lake Constance stickleback2. After careful consideration of the criticism, including additional analyses testing the proposed alternative hypotheses, we can confirm our confidence in the inference of secondary contact between a West European and an East European stickleback lineage in the catchment of Lake Constance, and that this admixture facilitated the ecological divergence between lake and stream ecotypes within Lake Constance2. In particular, Berner1 (i) questioned whether West and East European stickleback populations should be considered as divergent lineages, (ii) suggested that Lake Constance stickleback originated from the upper Danube instead of East Europe, (iii) questioned the suitability of our demographic modelling approach to reject an ‘ecological vicariance’ scenario, (iv) proposed that divergent selection within Lake Constance biased our inference of a secondary contact and admixture scenario, and (v) criticized our conclusion on admixture-facilitation of ecological speciation as premature. We address each of these concerns in this sequence.
- The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene FlowPublication . Pfeifer, Susanne P; Laurent, Stefan; Sousa, Vitor C; Linnen, Catherine R; Foll, Matthieu; Excoffier, Laurent; Hoekstra, Hopi E; Jensen, Jeffrey DThe interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, and fitness. Here, we examine the demographic and selective history of deer mice in and around the Nebraska Sand Hills, a system in which variation at the Agouti locus affects cryptic coloration that in turn affects the survival of mice in their local habitat. We first genotyped 250 individuals from 11 sites along a transect spanning the Sand Hills at 660,000 single nucleotide polymorphisms across the genome. Using these genomic data, we found that deer mice first colonized the Sand Hills following the last glacial period. Subsequent high rates of gene flow have served to homogenize the majority of the genome between populations on and off the Sand Hills, with the exception of the Agouti pigmentation locus. Furthermore, mutations at this locus are strongly associated with the pigment traits that are strongly correlated with local soil coloration and thus responsible for cryptic coloration.