Phylogeography of the western jumping mouse (<i>Zapus princeps</i>) detects deep and persistent allopatry with expansion

Malaney, Jason L.; Conroy, Chris J.; Moffitt, Lena A.; Spoonhunter, Harmony D.; Patton, James L.; Cook, Joseph A.

doi:10.1644/12-mamm-a-006.1

Cited by 17 publications

(15 citation statements)

References 149 publications

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“…(). A phylogenetic break between the Sierra Nevada and Rocky Mountains, which are physically separated by the Great Basin (NV), is commonly observed in forest‐dwelling vertebrates (Malaney et al., ; Manthey, Klicka, & Spellman, ; Spellman & Klicka, ) and plants (Gugger, Sugita, & Cavender‐Bares, ; Potter et al., ). MPB from sites in the Great Basin form a lineage unique from MPB in both the Sierra Nevada and Rocky Mountain ranges, similar to what has been found in woodpeckers, which are also a forest‐associated species (Klicka, Spellman, Winker, Chua, & Smith, ).…”

Section: Discussionmentioning

confidence: 99%

Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

et al. 2017

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Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo-Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.

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Section: Discussionmentioning

confidence: 99%

Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

et al. 2017

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“…Pleistocene climatic fluctuations influenced the diversification of the North American biota because of the repeated segregation of species into refugial populations (Hewitt, 1996), and this cyclic history is reflected in substantial phylogeographical structure in wide ranging species (Malaney et al, 2013). Late Pleistocene glacial cycling, in particular, shaped diversification within north-western Peromyscus, with multilocus tests supporting the presence of three distinctive deermice near the extreme north-western boundary of their range.…”

Section: Discussionmentioning

confidence: 99%

Diversification of deermice (Rodentia: genus Peromyscus) at their north‐western range limit: genetic consequences of refugial and island isolation

Sawyer

Flamme

Jung

et al. 2017

Journal of Biogeography

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Aim We surveyed the genetic variability of deermice (genus Peromyscus) at the north‐western edge of their range to test for occupancy in multiple, hypothesized ice‐free regions during the late Pleistocene and explore post‐glacial dynamics. Location North‐western North America. Methods We used sequences from four independent nuclear and mitochondrial loci from 341 specimens of Peromyscus maniculatus, Peromyscus keeni and Peromyscus sp. (Yukon) to assess species limits, population structure, and demographical change as a result of historical climate change, using a Bayesian approach. Species distribution models were built in MaxEnt to explore the niche overlap amongst genetically distinct species. Results Divergence amongst three lineages began before the last interglacial, and each shows signs of post‐glacial expansion. Multilocus species trees strongly support P. keeni and Peromyscus sp. (Yukon) as independent from P. maniculatus. Substantial substructure was observed for P. keeni across the fragmented Alexander Archipelago. Northern lineages or clades (Peromyscus sp. and P. keeni) differed in potential ecological distributions. Main conclusions At the extreme north‐western range of deermice in North America, three distinct lineages persist reflecting divergence in at least three ice‐free regions [Beringia, Coastal (near Southeast Alaska) and Southern Continental] throughout the latest Pleistocene glacial cycles. Although spatially proximate in Yukon, no locations were identified where these lineages are in contact. Further, west along the Pacific Coast, P. keeni is widespread across the complex landscape of Southeast Alaska, yet there is limited contemporary gene flow amongst island populations, a finding consistent with the barriers produced by rising sea levels at the end of the Last Glacial Maximum.

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“…These changes, combined with lower elevational peaks in the northern Sierra Nevada vs. much higher peaks in the southern portion of the range, resulted in distinctive climatic conditions for this region during the late Pleistocene (675-500 ka) (Mulch et al 2008). Ecological and climatic changes brought on by the geographic differences have also been attributed to diversification in mountain kingsnakes (Myers et al 2013), woodrats (Matocq et al 2012) and jumping mice (Moritz et al 2008;Malaney et al 2013). The San Joaquin River basin was historically distinctive from the Sacramento River basin, having been influenced by an inland sea over 16 Ma (Howard 1979;Dupr e 1990).…”

Section: Divergence Of Inland C Gulosus and C Pitensismentioning

confidence: 99%

Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus)

et al. 2014

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Species ranges that span different geographic landscapes frequently contain cryptic species- or population-level structure. Identifying these possible diversification factors can often be accomplished under a comparative phylogeographic framework. However, comparisons suffer if previous studies are limited to a particular group or habitat type. In California, a complex landscape has led to several phylogeographic breaks, primarily in terrestrial species. However, two sister taxa of freshwater fish, riffle sculpin (Cottus gulosus) and Pit sculpin (Cottus pitensis), display ranges based on morphological identifications that do not coincide with these breaks. Using a comprehensive sampling and nuclear, mitochondrial and microsatellite markers, we hypothesized that proposed species ranges are erroneous based on potential hybridization/gene flow between species. Results identified a phylogeographic signature consistent with this hypothesis, with breaks at the Coast Range Mountains and Sacramento/San Joaquin River confluence. Coastal locations of C. gulosus represent a unique lineage, and 'true' C. gulosus were limited to the San Joaquin basin, both regions under strong anthropogenic influence and potential conservation targets. C. pitensis limits extended historically throughout the Sacramento/Pit River basin but currently are restricted to the Pit River. Interestingly, locations in the Sacramento River contained low levels of ancestral hybridization and gene flow from C. gulosus but now appear to be a distinct population. The remaining population structure was strongly correlated with Sierra Nevada presence (high) or absence (low). This study stresses the importance of testing phylogeographic breaks across multiple taxa/habitats before conservation decisions are made, but also the potential impact of different geographic landscapes on evolutionary diversification.

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Phylogeography of the western jumping mouse (Zapus princeps) detects deep and persistent allopatry with expansion

Cited by 17 publications

References 149 publications

Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Diversification of deermice (Rodentia: genus Peromyscus) at their north‐western range limit: genetic consequences of refugial and island isolation

Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus)

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