Four Lineages in Peromyscus leucopus
In all analyses, the most divergent lineage was the Southwest lineage, a group found in Mexico, New Mexico, Texas, and southern Oklahoma. Multiple lines of evidence support divergence of the Southwest lineage, namely the highest estimated divergence time in BEAST (~25kya) and Fst values among all between lineage comparisons. Furthermore, the Southwest lineage roughly correspond to the previously defined western chromosomal race as identified in Baker et al. (1983). Baker et al. (1983) found that the chromosomal races meet at an ecotone transition between the Great Plains and eastern temperate forests (Strangl 1986) in Oklahoma, Kansas, and northern Texas. Our analysis extends the contact zone beyond Oklahoma to include eastern Texas and New Mexico, boundaries largely coincident with habitat transitions between grassland/desert and forests. A similar pattern of divergence is observed in the more cosmopolitan Peromyscus maniculatus where habitat is thought to reinforce divergence between putative species and lineages (Kalvik et al. 2012). Indeed, most lineages associated with forest and grassland habitats were once allopatric during the Pleistocene (Kalvik et al. 2012). Contact zones also occurred at habitat transitions, much like the breaks between the Southwest lineage and the remaining groups.
We believe the contact zone between the Southwest and the other lineages identified here exists in the southern Great Plains as observed in Strangl et al. (1986) where eastern deciduous forests transition into grassland habitats (i.e., eastern Oklahoma, Kansas, and Texas). This habitat transition acts as a contact zone between eastern and western lineages in both birds (Rising 1983) and mammals that were isolated during the Pleistocene (Reding et al. 2012, Kierepka et al. 2023), but levels of differentiation vary greatly across taxa. While our analysis presents evidence for fairly strong differentiation of southwesternP. leucopus , further study is needed to clarify this relationship. Mitochondrial DNA does not provide the full picture of evolutionary history due to its maternal inheritance and differing evolutionary rates. Reclassification has occurred in otherPeromyscus species including P. maniculatus , which was separated into six species based on numerous genetic, ecological, and morphological studies (e.g., Dragoo et al. 2006, Kalvik et al. 2012, Greenbaum et al. 2019). The Southwest lineage could be a cryptic species as observed in the P. maniculatus species group (P. maniculatus and. P. sonoriensis ), but nuclear DNA should confirm differentiation and patterns of hybridization within the contact zone.
Unlike the Southwest lineage, the East and Midwest lineages are primarily found in forested habitats. Splits between these lineages were aged at ~20,000 years ago during the Last Glacial Maximum (LGM) and received strong support in the haplotype network, PCoA, and Fst analyses. We acknowledge these estimates may be underestimations based on previous estimates (e.g. Moscarella et al. 2019, Prado et al. 2019). However, our TMRCA remained in the Pleistocene, which supports previous findings of two Pleistocene lineages separated by the Great Lakes and the St. Lawrence River (Rowe et al. 2006, Fiset et al. 2015, Baumgartner and Hoffman 2019, Moscarella et al. 2019, Prado et al. 2022). Beyond the Great Lakes and northeastern United States/Canada, East has the largest geographic distribution of P. leucopus’ lineages, extending along the entire eastern coast and Appalachians into western Tennessee, Alabama, and Louisiana. We also recorded East individuals in Wisconsin and Illinois whereas the Midwest lineage was largely confined to northern Midwest states including Minnesota, Illinois, the Upper Peninsula of Michigan, Wisconsin, Nebraska, and North Dakota. These areas largely correspond with the different hypothesized colonization routes taken following the LGM in the East and Midwest lineages and large water barriers that existed prior to the LGM (Rowe et al. 2006, Fiset et al. 2015, Moscarella et al. 2019, Prado et al. 2022). With the greater coverage of the reduced dataset, we found that East and Midwest co-occur in Indiana and Illinois along with the Central lineage. All three lineages crossed the Mississippi River, so we did not find evidence for it as a barrier.
While Southwest, East, and Midwest were highly supported in every analysis, the Central lineage is the least distinct. Central did not receive high support in the BEAST analysis, had the youngest divergence time, and was in the middle of the haplotype network and PCoA. Fst metrics were also smallest in Central comparisons. Interestingly, Central was placed sister to East in the phylogenetic tree, but was the least differentiated from Southwest in the PCoA and haplotype network. Rowe et al. (2006)’s dataset placed Central sister to the Midwest lineage, but also did not receive high support in the phylogeny. Fst values were the smallest between Central and Southwest, which appears to support that Central is more closely related to Southwest. Central also does not occur east of Indiana and primarily occurs in Missouri, east Texas, Louisiana, Illinois, Indiana, and northern New Mexico. All these areas are largely forested, which may indicate habitat-based differentiation between Southwest and Central or a separate refugium like the Ozarks. The hypothesized refugium for the Midwest lineage occurred in Illinois (Rowe et al. 2006), so another isolated refugium within a southern area is most likely for Central. We cannot discount that these results could be due to low sample sizes of Central or homoplasy. Much of our eastern Central individuals were from Genbank, and therefore, only had control region sequences, a marker more susceptible to homoplasy than slower evolving regions. This lineage was also detected in Herrera (2021), which used cytochrome b, so homoplasy in two markers is unlikely for the Central lineage. Consequently, more data is needed to elucidate the evolutionary relationship of Central to the other lineages.