Data for: Additional complexity in historic and contemporary gene flow among hoary, Vancouver Island, and Olympic marmots revealed by microsatellites and ultraconserved elements

Alpine species are inordinately threatened by habitat loss and precipitation changes resulting from climate change. In North America’s Pacific Northwest, 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 cu..., DNA extraction and loci amplification
We amplified 15 microsatellite loci previously developed for use in marmots and closely related species (Supplementary Table S1). Amplification of microsatellite loci followed Schuelke (2000). For fragment analyses, reactions were combined by using 1.5 μL from each of three PCR reactions of independent loci (with different fluorescent dyes) for the same individual and brought to a final volume of 10 μL with 5.5 μL Hi-Di Formamide (Applied Biosystems, Foster City, CA). Microsatellite loci were analyzed at the DNA Facility on Science Hill at Yale University using a Liz-500 size standard (Applied Biosystems, Foster City, California). Alleles were scored using GeneMarker v. 2.6.0 (SoftGenetics, State College, PA). 
To further delimit the distribution of hoary marmot mtDNA clades, we also extracted DNA from dried study skins or adventitious tissue removed from skeletal material from 138 museum specimens for which archived fresh tissues were not avai..., , # Data for: Additional complexity in historic and contemporary gene flow among hoary, Vancouver Island, and Olympic marmots revealed by microsatellites and ultraconserved elements

[https://doi.org/10.5061/dryad.tb2rbp0bc](https://doi.org/10.5061/dryad.tb2rbp0bc)

## Description of the data and file structure

This dataset accompanies the publication: 
Additional complexity in historic and contemporary gene flow among hoary, Vancouver Island, and Olympic marmots revealed by microsatellites and ultraconserved elements. Natalie M. Hamilton, Nicholas J. Kerhoulas, Kathryn M. Everson, Aren M. Gunderson, and Link E. Olson

### Files and variables

#### File: Supplementary_Table_S4_UCE.xlsx

**Description:** This file contains metadata for UCE reads, supplementary table from publication

##### Variables

* Species name abbreviations: *M. caligata* = *Marmota caligata*, *M. flaviventris* = *Marmota flaviventris*, *M. olympus* = *Marmota olympus*, *M. vancouverensis* = *Marmota vancouverensis*
..., ,