DOI: 10.5061/dryad.gtht76hv1
title: Population genetics of caribou in the Alaska-Yukon border region: implications for designation of conservation units and small herd persistence

description: Better knowledge of genetic relationships between the Fortymile caribou
 herd and its neighbors is needed for conservation decision-making in
 Canada. Here, we contribute the first fine-scale analysis of genetic
 population structure in nine contiguous caribou herds at the geographic
 boundaries between Barren-ground and Northern Mountain caribou, and at the
 Alaska-Yukon border. Using pairwise differentiation metrics, STRUCTURE,
 and discriminant analysis of principal components (DAPC) to analyze 15
 microsatellite loci in 379 caribou, we found complex patterns of genetic
 differentiation. The Fortymile was the only herd assigned to more than one
 genetic cluster, indicative of its history as a larger herd whose range
 expansions and gene flow to other herds were likely important to
 maintaining diversity across a functioning genetic metapopulation. Some
 small herds (Chisana, Klaza, and White Mountains) were genetically
 distinct, while others (Hart River, Clear Creek, Mentasta) exhibited
 little differentiation from herds they occasionally overlap, including
 herds assigned to different conservation units (DUs). This genetic
 connectivity does not result from demographic connectivity, as episodic
 contact during rut, rather than herd switching, is the likely mechanism.
 Unusually, one small herd (White Mountains) maintained genetic
 differentiation despite rut overlap with Fortymile. Our data reveal that
 some herds with different ecological and behavioral attributes are
 demographically independent but nonetheless genetically connected. Thus,
 we suggest that managing caribou for an appropriate level of genetic
 connectivity, while also supporting herd persistence, will be essential to
 conserve caribou genetic diversity in the region.
description: Caribou whole blood, dried blood on filter paper, hair, and fecal
 samples were collected by the Yukon Department of Environment, Alaska
 Department of Fish and Game, and Bureau of Land Management. The herd
 identities of sampled caribou were determined by biologists in the natural
 resource agencies who sampled them, usually based on presence in known
 seasonal ranges and often confirmed with collar locations. Most samples
 were from adult females. See publication for detailed description of DNA
 extraction, PCR, genotyping, and error-checking protocols use to produce
 this dataset of genotypes of 379 individual caribou at 15 microsatellite
 loci. 
description: # AK-YT\_Caribou\_Msats
 [https://doi.org/10.5061/dryad.gtht76hv1](https://doi.org/10.5061/dryad.gtht76hv1) This dataset contains microsatellite genotypes for 379 caribou from the Alaska-Yukon border region. Samples were collected by biologists from the Yukon government, Alaska Dept of Fish and Game, and U.S. Bureau of Land Management who identified each individual's herd of origin based on presence in known seasonal ranges and/or collar location data. After DNA extraction, we used PCR to amplify data at 15 microsatellite loci using fluorescently-labeled primers, ran fragment analysis, and genotyped the data. See Mager et al. 2024 (Conservation Genetics) for detailed methods. ## Description of the data and file structure Microsatellite genotypes for 379 caribou used in this study. Columns contain variables including unique sample ID, herd, and diploid genotype (as fragment length) at each of 15 loci. Each row contains data for an individual caribou. “-9” indicates missing data.