Admixture on the northern front: population genomics of range expansion in the white-footed mouse (Peromyscus leucopus) and secondary contact with the deer mouse (Peromyscus maniculatus)

Abstract

Range expansion has genetic consequences expected to result in differentiated wave-front populations with low genetic variation and potentially introgression from a local species. The northern expansion of Peromyscus leucopus in southern Quebec provides an opportunity to test these predictions using population genomic tools. Our results show evidence of recent and post-glacial expansion. Genome-wide variation in P. leucopus indicates two post-glacial lineages are separated by the St. Lawrence River, with a more recent divergence of populations isolated by the Richelieu River. In two of three transects we documented northern populations with low diversity in at least one genetic measure, although most relationships were not significant. Consistent with bottlenecks and allele surfing during northward expansion, we document a northern-most population with low nucleotide diversity, divergent allele frequencies and the most private alleles, and observed heterozygosity indicates outcrossing. Ancestry proportions revealed putative hybrids of P. leucopus and P. maniculatus. A formal test for gene flow confirmed secondary contact, showing that a reticulate population phylogeny between P. maniculatus and P. leucopus was a better fit to the data than a bifurcating model without gene flow. Thus, we provide the first genomic evidence of gene flow between this pair of species in natural populations. Understanding the evolutionary consequences of secondary contact is an important conservation concern as climate-induced range expansions are expected to result in new hybrid zones between closely related species.

Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon

“…Pleistocene glaciations and interglacial periods drove range contractions and expansions that have greatly influenced the genomes of many northern species (Bernatchez & Wilson, ; Garcia‐Elfring et al, ; Hewitt, ; Sim et al, ; Wares & Cunningham, ). As glaciers retreated ~10,000 bp , several marine species exhibited post‐glacial range expansions from Europe into North America (Wares & Cunningham, ) and signatures of historical trans‐Atlantic gene flow have been documented in species, such as Atlantic cod ( Gadus morhua ) (Bradbury et al, ), North Atlantic wolfish ( Anarhichas spp.)…”

“…Pleistocene glaciations and interglacial periods drove range contractions and expansions that have greatly influenced the genomes of many northern species (Bernatchez & Wilson, 1998;Garcia-Elfring et al, 2017;Hewitt, 2000;Sim et al, 2016;Wares & Cunningham, 2001). As glaciers retreated ~10,000 bp, * western and eastern Atlantic refugia (King et al, 2007), leading to secondary contact in some regions.…”

Climate change vulnerability assessment of species

“…SNP markers provide a more detailed and accurate picture of population processes (Çilingir et al, 2017; Younger et al, ), including the way in which populations have expanded and shrunk historically, and their interactions with other populations. Molecular markers indicate whether ongoing exchange of genes across populations or species has occurred which may bolster the species' adaptive capacity (Garcia‐Elfring et al, ).…”

Chromosome polymorphisms track trans-Atlantic divergence, admixture and adaptive evolution in salmon

“…When ice sheets retreated following glacial maxima, colonization of newly available habitats enabled secondary contact between allopatric lineages from different refugia (1, 3,4). Secondary contact between divergent lineages can have significant evolutionary consequences (5)(6)(7)(8)(9)(10), and the genetic legacy of these post-glacial admixture and range expansion events are present in modern genomes of many northern species (1, 3,[11][12][13].…”