Biology ETDs

Publication Date

Summer 5-26-2022


Persistently low population sizes, when coupled with reduced interpopulation connectivity, can impede the long-term viability of species in fragmented landscapes. Riparian-associated species in the arid American Southwest now face a series of threats due to fragmented populations and changing environmental conditions. During the last century, riparian habitats have deteriorated due to the synergistic effects of livestock grazing, increasing incidence of fire, and other anthropogenic impacts potentially have made local populations smaller, less demographically stable, and susceptible to the negative impacts of genetic drift and stochastic events. We evaluated genomic variation within and across geographic areas (i.e., mountain ranges and river systems) in the federally endangered New Mexico meadow jumping mouse (Zapus luteus luteus) using neutral and outlier loci to test whether observed genomic variation was influenced by 1) historical allopatric divergence, 2) recent anthropogenic fragmentation, or 3) both of these factors. We sampled 145 specimens from across the range of Z. l. luteus and 44 samples of co-distributed, closely related taxa and obtained over 8,800 single nucleotide polymorphisms. Combining insights from population genomics and phylogenomics, we found that eight geographic areas that are significantly differentiated from one another and have exceptionally low variability and low effective population sizes (fewer than 50 effective individuals in most cases). These lineages, however, reflect a biogeographic history that is mismatched with hypothesized riparian connectivity, but instead point to possible mitonuclear discordance. Additionally, each lineage has genomic variation consistent with expectations of adaptation to local conditions. Combined, these results suggest that there may be insufficient genomic variation in these distinctive jumping mice populations necessary to sustain viable populations without active management efforts. This improved understanding of how drift and selection have likely shaped the genomic structure of this endangered mammal provides a foundation to develop thoughtful management decisions.




conservation genomics, genomic drift, genotype-environment associations, local adaptation, meadow jumping mouse, population divergence, Zapus luteus.

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Degree Name


Level of Degree


Department Name

UNM Biology Department

First Committee Member (Chair)

Joseph A. Cook

Second Committee Member

Jason A. Malaney

Third Committee Member

Lisa N.Barrow