# Additional Complexity in Historic and Contemporary Gene Flow Among Hoary, Vancouver Island, and Olympic Marmots Revealed by Microsatellites and Ultraconserved Elements

## TL;DR

This study explores genetic mixing among three marmot species in the Pacific Northwest and finds complex patterns of historical and current gene flow, which may be influenced by climate change.

## Contribution

The study reveals new insights into historic and contemporary gene flow using microsatellites and UCEs, resolving mito-nuclear discordance in marmots.

## Key findings

- Microsatellite data show no current gene flow between hoary and Vancouver Island marmots.
- UCE data reveal historic gene flow between hoary and Vancouver Island marmots.
- Mito-nuclear discordance is driven by mitochondrial introgression and male-biased dispersal.

## Abstract

Alpine species are inordinately threatened by habitat loss and precipitation changes resulting from climate change. In North America's Pacific Northwest (PNW), three closely related alpine mammal species—hoary, Olympic, and Vancouver Island marmots—may face greater negative impacts of climate change relative to species found at lower elevations. Phylogenetic studies have found these three species form a monophyletic complex; however, discordant evolutionary histories between mitochondrial and nuclear genes suggest that gene flow may have occurred between these marmot species. Furthermore, mitochondrial data find two reciprocally monophyletic mitochondrial clades (haploclades) of hoary marmots. Nuclear data do not recover this pattern, and interspecific relationships among the markers are not consistent. We used nine microsatellite loci and ultraconserved elements (UCEs) to explore patterns of nuclear gene flow among marmot species in the PNW. Analyses of microsatellite data indicate no current gene flow between hoary and Vancouver Island marmots or between hoary and Olympic marmots but do reveal nuclear gene flow among hoary marmot haploclades. Additionally, UCE data reveal historic gene flow between hoary and Vancouver Island marmots. Overall, our results suggest that historic mitochondrial introgression between hoary and Vancouver Island marmots, as well as male‐biased dispersal, are driving mito‐nuclear discordance in this species complex.

This study examines gene flow among three alpine marmot species in the Pacific Northwest, focusing on the hoary, Olympic, and Vancouver Island marmots, which are highly threatened by climate change. Using microsatellite loci and ultraconserved elements, the research finds no current gene flow between hoary and Vancouver Island marmots but reveals complex patterns of historical and ongoing nuclear gene flow among hoary marmot populations. The findings suggest mitochondrial introgression and male‐biased dispersal as key factors contributing to genetic discordance, highlighting the need for further investigation to understand how these patterns may shift with climate change.