Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis)

Kimberley G Barrett; Geneviève Amaral; Melanie Elphinstone; Malcolm L McAdie; Corey S Davis; Jasmine K Janes; John Carnio; Axel Moehrenschlager; Jamieson C Gorrell

doi:10.1007/s10592-022-01429-7

Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis)

Conserv Genet. 2022;23(2):417-428. doi: 10.1007/s10592-022-01429-7. Epub 2022 Jan 16.

Authors

Kimberley G Barrett^{1

2}, Geneviève Amaral^{1

3}, Melanie Elphinstone¹, Malcolm L McAdie⁴, Corey S Davis², Jasmine K Janes^{1

5}, John Carnio⁴, Axel Moehrenschlager^{6

7}, Jamieson C Gorrell¹

Affiliations

¹ Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada.
² Present Address: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3 Canada.
³ Present Address: Island Medical Program, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2 Canada.
⁴ Marmot Recovery Foundation, Nanaimo, BC V9R 6X9 Canada.
⁵ School of Environmental and Rural Science, University of New England, Armidale, NSW 2351 Australia.
⁶ Wilder Institute Calgary Zoo, Calgary, AB T2E 7V6 Canada.
⁷ IUCN Species Survival Commission, Conservation Translocation Specialist Group, Calgary, AB Canada.

Abstract

Captive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.

Supplementary information: The online version contains supplementary material available at 10.1007/s10592-022-01429-7.

Keywords: Captive-breeding; Conservation translocation; Genetic diversity; High-throughput amplicon sequencing; Relatedness; Studbook.