Conservation Genetics

, Volume 19, Issue 2, pp 383–395 | Cite as

Conservation genomics of desert dwelling California voles (Microtus californicus) and implications for management of endangered Amargosa voles (Microtus californicus scirpensis)

  • Alexander R. Krohn
  • Chris J. Conroy
  • Risa Pesapane
  • Ke Bi
  • Janet E. Foley
  • Erica Bree Rosenblum
Research Article

Abstract

Understanding population genetic structure and levels of genetic variation is critical for the conservation and management of imperiled populations, especially when reintroductions are planned. We used restriction-site associated DNA (RAD) sequencing to study the genetic diversity and evolutionary relationships of the endangered Amargosa vole and other closely related desert-dwelling California voles. Specifically, we sought to determine how Amargosa voles are related to other California voles, how genetic variation is partitioned among subpopulations in wild Amargosa voles, and how much genetic variation is captured within a captive insurance colony of Amargosa voles. Our multilocus nuclear dataset provides strong evidence that Amargosa voles are part of a northern clade of California voles. Amargosa voles have highly reduced genetic variation relative to other California voles, but do exhibit some sub-structure among sampled marshes. Captive Amargosa voles capture approximately half of the total genetic variation present in the wild Amargosa vole populations. We discuss the management implications of our findings in light of reintroductions planned for Amargosa voles. Our study highlights the utility of reduced representation genomic approaches, like RADseq, to resolve relationships among small populations that are difficult to study with traditional markers due to low genetic variation and few individuals left in the wild.

Keywords

Captive breeding programs Endangered species Population structure RADseq 

Notes

Acknowledgements

Funding was provided by the Bureau of Land Management (SPO Number 201223906). We thank Andrew DeWoody, and the DeWoody lab at Purdue University for access to a draft Amargosa vole genome. We thank the Museum of Vertebrate Zoology (UC Berkeley) for access to tissues of California voles, and Jim Patton for capturing and giving insight on Microtus generally. We thank two anonymous reviewers and Rosemary Gillespie for their helpful feedback on this manuscript. This work was approved by the UC Davis IACUC (Permit Numbers 19741 and 18179).

Supplementary material

10592_2017_1010_MOESM1_ESM.pdf (204 kb)
Supplementary material 1—Museum of Vertebrate Zoology (MVZ) specimens used for this study (PDF 204 KB)
10592_2017_1010_MOESM2_ESM.eps (1.4 mb)
Supplementary material 2—NGSadmix analyses for other K values for California voles, including Amargosa voles. Admixture is shown on the y-axis and each major grouping of voles, from the northern, southern or Amargosa clade, is shown on the x-axis. Dashed black lines separate geographic sampling locations for the NGSadmix plots, while dashed white lines separate the groupings of each K. (EPS 1464 KB)
10592_2017_1010_MOESM3_ESM.eps (1.3 mb)
Supplementary material 3—NGSadmix analyses for other K values for wild Amargosa voles. Admixture is on the y-axis and marshes sampled is on the x-axis. Dashed white lines separate marshes sampled in this study. (EPS 1377 KB)
10592_2017_1010_MOESM4_ESM.eps (1.5 mb)
Supplementary material 4—NGSadmix analyses for other K values for wild and captive Amargosa voles. Admixture is on the y-axis and marshes or captive colony generation sampled is on the x-axis. Dashed white lines separate marshes or captive colony generation sampled in this study. (EPS 1538 KB)

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Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  1. 1.Department of Environmental, Science, Policy and ManagementUniversity of California, BerkeleyBerkeleyUSA
  2. 2.Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyUSA
  3. 3.Department of Medicine and Epidemiology, School of Veterinary MedicineUniversity of California, DavisDavisUSA
  4. 4.Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3)University of California, BerkeleyBerkeleyUSA

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