General lack of phylogeographic structure in two sympatric, forest obligate squirrels (Sciurus nigerandS. carolinensis)

Population genomic structure of a widespread, urban-dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)

Urbanization is a persistent and widespread driver of global environmental change, potentially shaping evolutionary processes due to genetic drift and reduced gene flow in cities induced by habitat fragmentation and small population sizes. We tested this prediction for the eastern grey squirrel (Sciurus carolinensis), a common and conspicuous forest-dwelling rodent, by obtaining 44K SNPs using reduced representation sequencing (ddRAD) for 403 individuals sampled across the species' native range in eastern North America. We observed moderate levels of genetic diversity, low levels of inbreeding, and only a modest signal of isolation-by-distance. Clustering and migration analyses show that estimated levels of migration and genetic connectivity were higher than expected across cities and forested areas, specifically within the eastern portion of the species' range dominated by urbanization, and genetic connectivity was less than expected within the western range where the landscape is fragmented by agriculture. Landscape genetic methods revealed greater gene flow among individual squirrels in forested regions, which likely provide abundant food and shelter for squirrels. Although gene flow appears to be higher in areas with more tree cover, only slight discontinuities in gene flow suggest eastern grey squirrels have maintained connected populations across urban areas in all but the most heavily fragmented agricultural landscapes. Our results suggest urbanization shapes biological evolution in wildlife species depending strongly on the composition and habitability of the landscape matrix surrounding urban areas.

Multiple origins of melanism in two species of North American tree squirrel (Sciurus)

BACKGROUND

While our understanding of the genetic basis of convergent evolution has improved there are still many uncertainties. Here we investigate the repeated evolution of dark colouration (melanism) in eastern fox squirrels (Sciurus niger; hereafter "fox squirrels") and eastern gray squirrels (S. carolinensis; hereafter "gray squirrels").

RESULTS

We show that convergent evolution of melanism has arisen by independent genetic mechanisms in two populations of the fox squirrel. In a western population, melanism is associated with a 24 bp deletion in the melanocortin-1-receptor gene (MC1RΔ24 allele), whereas in a south-eastern population, melanism is associated with a point substitution in the agouti signalling protein gene causing a Gly121Cys mutation. The MC1R∆24 allele is also associated with melanism in gray squirrels, and, remarkably, all the MC1R∆24 haplotypes are identical in the two species. Evolutionary analyses show that the MC1R∆24 haplotype is more closely related to other MC1R haplotypes in the fox squirrel than in the gray squirrel. Modelling supports the possibility of gene flow between the two species.

CONCLUSIONS

The presence of the MC1R∆24 allele and melanism in gray squirrels is likely due to introgression from fox squirrels, although we cannot completely rule out alternative hypotheses including introgression from gray squirrels to fox squirrels, or an ancestral polymorphism. Convergent melanism in these two species of tree squirrels has evolved by at least two and probably three different evolutionary routes.

Multiple introductions of the eastern fox squirrel (Sciurus niger) in California

Eastern fox squirrels (Sciurus niger) have been introduced into California within the past 130 years. Recently, their range has been expanding at an alarming rate. Genetic diversity was assessed in 101 control region sequences of eastern fox squirrels from three geographic regions within California (Los Angeles County, Alameda and Contra Costa counties and Sacramento County) to determine if a single or multiple introductions occurred within California, as indicated by the detection of multiple haplotypes. A total of 11 haplotypes were discovered, with haplotypes rarely shared among geographic regions and no clustering by region in a haplotype network. This suggests that the introduction to different regions within California came from different source populations within the native range of the species. Haplotype diversity was highest in Los Angeles County. Due to a lack of phylogeographic structure in fox squirrels in their native range, it is difficult to identify the sources of all introductions.