Assessing genetic diversity and connectivity in a tule elk (Cervus canadensis nannodes) metapopulation in Northern California

Abstract

The tule elk (Cervus canadensis nannodes) is a California endemic subspecies that experienced an extreme bottleneck (potentially two individuals) in the mid-1800s. Through active management, including reintroductions, the subspecies has grown to approximately 6000 individuals spread across 22 recognized populations. The populations tend to be localized and separated by unoccupied intervening habitat, prompting targeted translocations to ensure gene flow. However, little is known about the genetic status or connectivity among adjacent populations in the absence of active translocations. We used 19 microsatellites and a sex marker to obtain baseline data on the genetic effective population sizes and functional genetic connectivity of four of these populations, three of which were established since the 1980s and one of which was established ~ 100 years ago. A Bayesian assignment approach suggested the presence of 5 discrete genetic clusters, which corresponded to the four primary populations and two subpopulations within the oldest of them. Effective population sizes ranged from 15 (95% CI 10–22) to 51 (95% CI 32–88). We detected little or no evidence of gene flow among most populations. Exceptions were a signature of unidirectional gene flow to one population founded by emigrants of the other 30 years earlier, and bidirectional gene flow between subpopulations within the oldest population. We propose that social cohesion more than landscape characteristics explained population structure, which developed over many generations corresponding to population expansion. Whether or which populations can grow and reach sufficient effective population sizes on their own or require translocations to maintain genetic diversity and population growth is unclear. In the future, we recommend pairing genetic with demographic monitoring of these and other reintroduced elk populations, including targeted monitoring following translocations to evaluate their effects and necessity.

Noninvasive genetic sampling with a spatial capture‐recapture analysis to estimate abundance of Roosevelt elk

“…The University of California, Davis Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory processed fecal pellets for microsatellite markers to determine individual identity and sex using a process described in Lounsberry et al (2015) and Batter et al (2021). Researchers washed fecal pellets with an ATL (Qiagen, Valencia, CA, USA) buffer to create a solution of suspended epithelial cells.…”

“…Researchers washed fecal pellets with an ATL (Qiagen, Valencia, CA, USA) buffer to create a solution of suspended epithelial cells. They then extracted DNA using the Qiagen DNeasy Blood and Tissue Kit according to the manufacturers protocols from the resulting solution and amplified the microsatellite markers using a Qiagen multiplex polymerase chain reaction (PCR) kit (Lounsberry et al 2015, Furnas et al 2018, Batter et al 2021). They used 12 microsatellites and a sex marker developed for tule elk ( C. c. nannodes ), a closely related subspecies, for individual genetic profiles and sex determination (Sacks et al 2016).…”

Genetic structure of California's elk: a legacy of extirpations, reintroductions, population expansions, and admixture

“…Tissue and blood samples consisted of muscle or skin and were stored in desiccant after collection during 1995-2022. Genotypes for fecal samples had been analyzed as part of prior research projects conducted during 2017-2019, allowing us to select only a single genotype per individual for this study (Batter et al 2021(Batter et al , 2022Sacks et al 2022), which was described in detail for the same 427 fecal samples by Batter et al (2021). Specifically, only fecal DNA genotypes with ≥18 of the 20 loci were retained (Batter et al 2021) and genotype error rates for those genotypes were estimated at 0.011 allelic dropout and <0.001 false alleles (Batter et al 2022).…”

Mitigating anthropogenic barriers to facilitate distributional shifts helps reduce vulnerability of a large herbivore to climate change

“…Genetic diversity is low among tule elk, owing to a severe genetic bottleneck in the late 1800s, when as few as 2–10 individuals remained (McCullough, 1969; Williams et al., 2004; Meredith et al., 2007; Sacks et al., 2016). Additionally, connectivity among populations is low, owing to high levels of habitat fragmentation (California Department of Fish and Wildlife, 2018), barriers to movement (Batter et al., 2021) and a lack of seasonal migration (California Department of Fish and Wildlife, 2018). Tule elk also may be at risk of contracting various zoonotic diseases and come into conflict with private landowners (Cook et al., 1997; Munk et al., 2020; Denryter & Heeren, 2021).…”