Phylogeography of a widespread small carnivore, the western spotted skunk (Spilogale gracilis) reveals temporally variable signatures of isolation across western North America

Abstract

We analyzed phylogeographic patterns in the western spotted skunk, Spilogale gracilis Merriam, 1890 (Carnivora: Mephitidae) in relation to historical events associated with Pre‐Pleistocene Divergence (PPD) and Quaternary climate change (QCC) using mitochondrial DNA from 97 individuals distributed across Western North America. Divergence times were generated using BEAST to estimate when isolation in putative refugia occurred. Patterns and timing of demographic expansion was performed using Bayesian skyline plot. Putative climatic refugia resulting from Quaternary climate change were identified using paleoecological niche modeling and divergence dates compared to major vicariant events associated with Pre‐Pleistocene conditions. We recovered three major mitochondrial clades corresponding to western North America (California, Baja, and across the Great Basin), east‐central North America (Texas, central Mexico, New Mexico), and southwestern Arizona/northwestern Mexico. Time to most recent common ancestor for S. gracilis occurred ~1.36 Ma. Divergence times for each major clade occurred between 0.25 and 0.12 Ma, with signature of population expansion occurring 0.15 and 0.10 Ma. Ecological niche models identified three potential climatic refugia during the Last Interglacial, (1) west coast of California and Oregon, (2) northwestern Mexico, and (3) southern Texas/northeastern Mexico as well as two refugia during the Last Glacial Maximum, (1) western USA and (2) southern Texas/northeastern Mexico. This study supports PPD in shaping species‐level diversity compared to QCC‐driven changes at the intraspecific level for Spilogale, similar to the patterns reported for other small mammals (e.g., rodents and bats). Phylogeographic patterns also appear to have been shaped by both habitat and river vicariance, especially across the desert southwest. Further, continuing climate change during the Holocene coupled with anthropogenic modifications during the Anthropocene appears to be removing both of these barriers to current dispersal of western spotted skunks.

Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone

“…Neither a pattern of declining diversity with increasing latitude, nor isolation by distance, was seen in the West. Such results may be indicative of a more complex scenario of multiple glacial refugia in the western United States, as indicated in studies of other carnivore taxa (Harding and Dragoo, 2012;Ferguson et al, 2017). To provide a more comprehensive view of the biogeography of Urocyon, additional sampling to cover the full range (e.g., from Mexico and Central and South America) of gray foxes will be needed, and ecological niche modeling could help reconstruct the locations of glacial refugia and recolonization routes (Puckett et al, 2015;Ferguson et al, 2017).…”

“…Although debate has centered on whether this species-level diversification resulted primarily from Pleistocene vicariance (Johnson and Cicero, 2004;Weir and Schluter, 2004) or much earlier Pliocene events (Klicka and Zink, 1997;Zink et al, 2004;Barnosky, 2005), mounting evidence supports a role for Pleistocene events causing species-level divergence in many cases (Lovette, 2005;Peterson and Ammann, 2013;McDonough et al, 2020). A leading hypothesis for east-west divergences is that populations were separated into two or more disjunct Pleistocene forest refugia south of the glacial extent, an idea supported by climatic modeling of ecoregions (Hargrove and Hoffman, 2005) and ecological niche modeling of historical species distributions (Peterson and Ammann, 2013;Puckett et al, 2015;Loveless et al, 2016;Ferguson et al, 2017). These populations then diverged in allopatry, potentially with the eastern counterpart adapting to wetter and cooler environments and the western to drier and warmer environments (Rising, 1970(Rising, , 1983Webb and Bartlein, 1992;Swenson, 2006).…”