Abstract

Noninvasive genetic studies of wild animals enable the recovery of information infeasible to obtain using other means. However, the low quantity and quality of noninvasively collected DNA often challenge the retrieval of reliable genotypes, which may cause biases in downstream analyses. In this study, we optimized SNP (single nucleotide polymorphism) genotyping of fecal samples from moose (Alces alces) with the main purpose of exploring the potential of using noninvasively retrieved genotypes for individual- and sex identification. Fecal pellets were collected during the late winter of 2016 on the Swedish island of oland in the Baltic Sea and DNA was extracted and genotyped using 86 autosomal, six sex-specific and five species diagnostic SNPs. The SNP error rate of the quality filtered dataset was 0.06 and the probability of identity for siblings below 0.001. Following a thorough quality filtering process, 182 reliable genotypes were obtained, corresponding to 100 unique individuals (37 males, 63 females), with an estimated male proportion of 37% (+/- 9%). The population size, estimated using two different capture-mark-recapture approaches, was found to be in the range of 115-156 individuals (95% CI). Furthermore, moose on oland showed significantly lower heterozygosity levels (z(Hexp) = -5.51, N = 69, p(Hexp) = 3.56 center dot 10(-8), z(Hobs) = -3.58, N = 69, p(Hobs) = 3.38 center dot 10(-4)) and appeared genetically differentiated from moose on the Swedish mainland. Thus, we show that quality controlled noninvasively derived SNP genotypes can be highly informative for individual and population monitoring in a large ungulate.

Keywords

Alces alces; Noninvasive sampling; SNP genotyping; Wildlife monitoring; Population genetics; Capture-mark-recapture

Published in

European Journal of Wildlife Research
2019, Volume: 65, number: 6, article number: 96
Publisher: SPRINGER

SLU Authors

• Blåhed, Ida-Maria

  • Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences
    

• Ericsson, Göran

  • Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences
    

• Spong, Göran

  • Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences
    
  • North Carolina State University (NC State)

UKÄ Subject classification

Zoology
Genetics
Ecology


Publication identifier

DOI: https://doi.org/10.1007/s10344-019-1337-8

Permanent link to this page (URI)

https://res.slu.se/id/publ/103481