Species‐wide phylogeography of North American mule deer (Odocoileus hemionus): cryptic glacial refugia and postglacial recolonization

Abstract

Quaternary climatic oscillations greatly influenced the present-day population genetic structure of animals and plants. For species with high dispersal and reproductive potential, phylogeographic patterns resulting from historical processes can be cryptic, overshadowed by contemporary processes. Here we report a study of the phylogeography of Odocoileus hemionus, a large, vagile ungulate common throughout western North America. We examined sequence variation of mitochondrial DNA (control region and cytochrome b) within and among 70 natural populations across the entire range of the species. Among the 1766 individual animals surveyed, we recovered 496 haplotypes. Although fine-scale phylogenetic structure was weakly resolved using phylogenetic methods, network analysis clearly revealed the presence of 12 distinct haplogroups. The spatial distribution of haplogroups showed a strong genetic discontinuity between the two morphological types of O. hemionus, mule deer and black-tailed deer, east and west of the Cascade Mountains in the Pacific Northwest. Within the mule deer lineage, we identified several haplogroups that expanded before or during the Last Glacial Maximum, suggesting that mule deer persisted in multiple refugia south of the ice sheets. Patterns of genetic diversity within the black-tailed deer lineage suggest a single refugium along the Pacific Northwest coast, and refute the hypothesis that black-tailed deer persisted in one or more northern refugia. Our data suggest that black-tailed deer recolonized areas in accordance with the pattern of glacial retreat, with initial recolonization northward along a coastal route and secondary recolonization inland.

Population genetic structure of raccoons (Procyon lotor) inhabiting a highly fragmented landscape

“…hance our understanding of how ecological and evolutionary factors act in concert to shape genetic structure of populations (Beaumont 2005). Although many investigations utilizing molecular markers focus on changes occurring over evolutionary time scales, such as speciation events (Hodgson et al 2009;Latch et al 2009), the use of rapidly evolving portions of the genome now allow researchers to investigate genetic change over more proximate time scales, such as Table 1). …”

Genetic interrelationships of North American populations of giant liver fluke Fascioloides magna

“…Alternatively, the apparent western and eastern F. magna population structure may be a result of the lack of suitable cervid hosts following widespread extirpation of ungulate populations in eastern and central NA following European colonization that may also reduce the opportunity for genetic admixing among local F. magna populations [6]. The effect on population segregation has been documented by studies of mtDNA phylogeography in white-tailed deer [30, 33] as well as two other hosts of F. magna , the black-tailed deer [34] and caribou [35]. However, we find the historical separation more probable.…”

Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

“…Morphological [51], [52] and genetic studies [26], [28], [53], [54], however, strongly support the separation of this species into two highly distinct lineages that diverged in allopatry during the last glacial maximum. Black-tailed deer include subspecies O. h. columbianus and sitkensis and are found throughout the Pacific Northwest, west of the Cascade Mountains and north to Alaska along the Pacific Coast.…”

“…White-tailed deer can be subdivided into as many as 38 subspecies [45], [55], [56]. All three types of deer within this species complex show extensive local adaptation and population structuring [53], [57], [58], yet all have a conserved karyotype of 2n = 70 chromosomes [44] and are capable of extensive hybridization and introgression in regions of sympatry [26], [28], [40], . Notably, all three lineages overlap within our study area in western Oregon, making this region a natural experiment for testing specific hypotheses about such evolutionary processes as hybridization, local adaptation, and reproductive isolation.…”

“…D provides an unbiased quantification of differences in allele frequencies between populations without being affected by levels of genetic diversity and heterozygosity the way F ST and its analogues are [83]. D m performs well in recently diverged lineages and when mutation rate is low [37], and is therefore well suited for SNP data (low mutation rates and numbers of alleles [86]) and the study system (recently diverged lineages [53]). …”