Genetic variation and population structure in a threatened species, the Utah prairie dog Cynomys parvidens: the use of genetic data to inform conservation actions

• Published in: Ecology and evolution Vol. 6; no. 2; pp. 426 - 446
• Main Authors: Brown, Nathanael L., Peacock, Mary M., Ritchie, Mark E.
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.01.2016; John Wiley and Sons Inc
• Subjects: Anthropogenic factors; Bayesian genotype clustering analysis; Biodiversity; Biological evolution; Colonies; Corridors; Cynomys parvidens; Data recovery; Endangered & extinct species; Endangered species; Environmental degradation; Evolution; Gene flow; Genetic diversity; Genetic structure; Genotypes; Habitat loss; Original Research; Outbreaks; Plague; Population genetics; Population structure; Populations; Prairie dogs; Subpopulations; Sylvatic plague; threatened; Threatened species; Translocation; Utah prairie dog; Viability; Wildlife conservation; United States > US; Utah; USA, Utah; genetic diversity; genetic structure; threatened; Utah prairie dog; Bayesian genotype clustering analysis
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.1874

The Utah prairie dog (Cynomys parvidens), listed as threatened under the United States Endangered Species Act, was the subject of an extensive eradication program throughout its range during the 20th century. Eradication campaigns, habitat destruction/fragmentation/conversion, and epizootic outbreaks (e.g., sylvatic plague) have reduced prairie dog numbers from an estimated 95,000 individuals in the 1920s to approximately 14,000 (estimated adult spring count) today. As a result of these anthropogenic actions, the species is now found in small isolated sets of subpopulations. We characterized the levels of genetic diversity and population genetic structure using 10 neutral nuclear microsatellite loci for twelve populations (native and transplanted) representative of the three management designated “recovery units,” found in three distinct biogeographic regions, sampled across the species' range. The results indicate (1) low levels of genetic diversity within colonies (He = 0.109–0.357; Ho = 0.106‐ 0.313), (2) high levels of genetic differentiation among colonies (global FST = 0.296), (3) very small genetic effective population sizes, and (4) evidence of genetic bottlenecks. The genetic data reveal additional subdivision such that colonies within recovery units do not form single genotype clusters consistent with recovery unit boundaries. Genotype cluster membership support historical gene flow among colonies in the easternmost West Desert Recovery Unit with the westernmost Pausaugunt colonies and among the eastern Pausaugunt colonies and the Awapa Recovery unit to the north. In order to maintain the long‐term viability of the species, there needs to be an increased focus on maintaining suitable habitat between groups of existing populations that can act as connective corridors. The location of future translocation sites should be located in areas that will maximize connectivity, leading to maintenance of genetic variation and evolutionary potential. The Utah prairie dog underwent significant declines due to a particularly draconian pest control regime during the 20th century. We characterized the levels of genetic diversity and population genetic structure using 10 neutral nuclear microsatellite loci for twelve populations (native and transplanted) representative of the three management designated “recovery units,” found in three distinct biogeographic regions, sampled across the species' range. The results indicate (1) low levels of genetic diversity within colonies (He = 0.109–0.357; Ho = 0.106‐ 0.313), (2) high levels of genetic differentiation among colonies (global FST = 0.296), (3) very small genetic effective population sizes, and (4) evidence of genetic bottlenecks.