Microtus, Schrank, 1798

Jackson, Donavan J & Cook, Joseph A, 2020, A precarious future for distinctive peripheral populations of meadow voles (Microtus pennsylvanicus), Journal of Mammalogy 101 (1), pp. 36-51 : 38

Microtus Phylogeny Inferred from Cytochrome b

Sampling and phylogenetic reconstruction.— We inferred the phylogeny of species of Microtus , generally accepting the species designations of Musser and Carleton (2005). Cytochrome b (Cytb) sequences were downloaded for 110 individuals representing 62 species from GenBank (Supplementary Data SD1) with eight newly sequenced individuals (two represent the first sequences for M. breweri ; Supplementary Data SD2) for a total of 118 individuals and 64 species of Microtus , with two outgroup species ( Chionomys robertsi and C. nivalis ). Exceptions to Musser and Carleton (2005) include the formally unrecognized species M. gromovi ( Bannikova et al. 2010) , M. hartingi ( KryŠtufek et al. 2012) , M. atticus (Rovatsos and Giagia-Athanasopoulou 2012) , and two controversial species M. rossiaemeridionalis and M. obscurus ( Jaarola et al. 2004; Bannikova 2010; Tougard et al. 2013; Markova et al. 2014), which we treat as distinct species. In addition, we included a single randomly chosen individual from each of four independent mtDNA lineages identified in M. pennsylvanicus (this study). All sequences were aligned in Geneious v. 8.1.9 ( Kearse et al. 2012) using the MUSCLE ( Edgar 2004) algorithm and phylogenetic reconstruction was carried out in BEAST v1.10.4 ( Suchard et al. 2018) using the best-fit substitution model, GTR+I+G, from jModelTest with a uncorrelated relaxed lognormal clock prior. We used a Coalescent Constant Population tree prior and ran analyses for 40 million generations, sampling every 2,000 generations and excluding a 20% burn-in. Independent runs were assessed in TRACER v1.6.0 ( Rambaut et al. 2014) ensuring effective sample size (ESS) was above 200 for all parameters and that independent runs had converged.

Genetic distance between Microtus species. — Pairwise genetic distance (uncorrected p -distance and Kimura 2-parameter [K2P]) of Cytb sequences (excluding M. pennsylvanicus and its putative sister species M. montanus ) was computed using the program MEGA7 ( Kumar et al. 2016). All individuals were grouped by species if more than one individual was used in analyses and sister relationships were inferred from our Bayesian phylogeny. Mean between-group distance was computed under both uncorrelated p -distance and the K2P model; both were computed by bootstrapping with 1,000 replicates, with pairwise deletions for missing data.