Patterns of genetic partitioning and gene flow in the endangered San Bernardino kangaroo rat ( Dipodomys merriami parvus
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RESEARCH ARTICLE
Patterns of genetic partitioning and gene flow in the endangered San Bernardino kangaroo rat (Dipodomys merriami parvus) and implications for conservation management Sarah Hendricks1 · Asako Y. Navarro1 · Thea Wang1 · Aryn Wilder1 · Oliver A. Ryder1 · Debra M. Shier1 Received: 3 March 2020 / Accepted: 23 June 2020 © Springer Nature B.V. 2020
Abstract San Bernardino kangaroo rat (Dipodomys merriami parvus; SBKR), an endangered subspecies, faces ongoing anthropogenic threats such as habitat loss. Their habitat has undergone strong human-mediated fragmentation, resulting in extinction of some local populations and dramatic size reduction of the remaining populations. We examined the genetic diversity, population structure, and phylogeography of this subspecies using partial mitochrondrial DNA sequencing and microsatellite genotyping. Our study indicates that currently, the three remaining populations seem to be highly fragmented. Clear population structure and low level of haplotype sharing suggests that there has been no recent gene flow among populations, except in the case of human mediated gene flow as a result of a single translocation event. Diversity levels are on par with other species with fragmented distributions. Further, shallow phylogenetic divergence suggests the populations have not been diverged long enough to detect phylogenetic structure and separation is likely recent. Given the limited gene flow, low numbers of SBKR as evident by low return on trapping efforts, and low effective population size, habitat restoration and translocations may be warranted to maintain levels of diversity in a declining metapopulation. Keywords Dipodomys merriami · Gene flow · Genetic diversity · Microsatellites · mtDNA · Population structure
Introduction Destruction and degradation of natural ecosystems continue to alter landscapes at unprecedented rates. Anthropogenic fragmentation of habitat, the fracturing of habitat into smaller and more isolated patches disjointed by unfavorable habitat due to human impact, is one cause of widespread biodiversity loss (Schipper et al. 2008; Ceballos et al. 2017). Species occurring in areas with more fragmentation are at elevated risk of extinction due to having smaller ranges, Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10592-020-01289-z) contains supplementary material, which is available to authorized users. * Sarah Hendricks [email protected] * Debra M. Shier [email protected] 1
San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA
a lower proportion of high-suitability habitat within their range, and high-suitability habitat outside of their protected areas, which increases their exposure to anthropogenic threats (Crooks et al. 2017). The processes of fragmented populations are complex (Young and Clarke 2000) and can lead to detrimental effects as a result of a reduced gene flow between populations. Gene flow is an
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