Biology ETDs

Publication Date

Summer 7-17-2023


Museum collections provide essential biodiversity sampling needed to understand the species limits, phylogeny, and biogeographic history of mammals, all key features of the foundation for comparative analyses in ecology and evolution. We add to this framework a diverse assemblage of species of leaf-eared mice (genus Phyllotis) in South America and then focus on the Phyllotis xanthopygus complex by combining available mitochondrial sequence (cytochrome b; cytb) data (351 GenBank samples) with 52 newly sequenced museum samples from the northern extent of this complex’s range (51 from Bolivia and 1 from northern Chile) to reconstruct evolutionary relationships using maximum likelihood and Bayesian methods. Taxonomic limits within the P. xanthopygus complex have remained uncertain due to cryptic diversity contributing to a clouded interpretation of their history. Determining phylogeographic structure is an important first step for assessing species limits. Consequently, we reconstruct demographic history and apply species delimitation methods across distinct lineages of the P. xanthopygus complex. The number of delimited species varied between 11 and 20 using different methods. Applying the Generalized Mixed Yule Coalescent (GMYC) model, for example, we identified 18 lineages that included P. xanthopygus, P. limatus, four lineages within P. vaccarum, a new lineage sister to P. caprinus, P. caprinus, three lineages within P. pehuenche, P. camiari, P. bonariensis, and five lineages in P. rupestris including one new lineage. The fossil-calibrated tree revealed diversification of this species complex initiated ca. 150,000 ya, with pulses of diversification ca. 65,000 ya, and 25,000 ya corresponding to the Santa Maria (Casma) and Llanquihue glacial cycles, respectively. Three clades (P. pehuenche, P. rupestris, and P. xanthopygus) showed consistent evidence of expansion across three tests (Tajima’s D, Fu’s Fs, andRamos-Onsins and Roza’s R2), while other lineages had mixed signatures of expansion. Newly added samples provide novel insights into the dynamic diversification history of the P. xanthopygus complex near their northern extent, in addition to alternative perspectives on their systematics. More broadly, this study serves as a foundation for future investigations of phylogeographic variation that can lead to key insights for physiological adaptations associated with high-elevation mammals.

Project Sponsors

National Science Foundation




Phylogeography, Evolution, Mammals, Phyllotis

Document Type


Degree Name


Level of Degree


Department Name

UNM Biology Department

First Committee Member (Chair)

Joseph Cook

Second Committee Member

Jason Malaney

Third Committee Member

Lisa Barrow