Testing a new SNP-chip on the Alpine and Apennine brown bear ( Ursus arctos ) populations using non-invasive samples
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METHODS AND RESOURCES ARTICLES
Testing a new SNP-chip on the Alpine and Apennine brown bear (Ursus arctos) populations using non-invasive samples Patrizia Giangregorio1,2 · Anita J. Norman3,4 · Francesca Davoli1 · Göran Spong4,5 Received: 20 June 2017 / Accepted: 23 February 2018 © Springer Science+Business Media B.V., part of Springer Nature 2018
Abstract Brown bears in Italy persist in two isolated populations, one in the Alpine and the other in the Apennine mountain range. Both are threatened and elusive. Non-invasive genetics provides a good way to monitor the populations. Microsatellites (STRs) have been the marker of choice for non-invasive genetic monitoring, but due to non-invasive bad quality samples, these analyses were plagued by low amplification rates and genotyping errors. Moreover, to compare microsatellite genotypes, allele calibration is needed between laboratories, leading to difficulties in individual identification. In contrast, SNP genotyping is directly comparable between laboratories, and more sensitive and accurate. Here we test a 96-marker SNP chip developed for the Scandinavian brown bear population on the Italian populations. A subset of these SNPs was found informative and could reliable confirm species, sex and, only in the Alpine population, distinguish individuals. A total of 51 informative SNPs provided better resolution power than 15 STRs, used in the routine monitoring of the Alpine population in Italy. In contrast, only 15 SNPs were found to be informative for the Apennine population, which did not have enough resolution to discriminate individuals and were less informative than 11 STRs. While highly useful in the Alpine population, additional SNP markers must be included to reach the same level of resolution in the Apennine population. Keywords SNP-chip · SNP resolution · Non-invasive genetics · Fingerprinting · Brown bear
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-018-1017-0) contains supplementary material, which is available to authorized users. * Patrizia Giangregorio [email protected] 1
ISPRA, Conservation Genetics Laboratory, Institute for Environmental Protection and Research, Via Cà Fornacetta 9, 40064 Bologna, Ozzano Dell’emilia, Italy
2
Department of Earth, Life and Environmental Sciences, University of Bologna, Piazza di Porta S. Donato 1, 40126 Bologna, Italy
3
Department of Life Sciences, San Diego Zoo Global, Box 120551, San Diego, CA 92112, USA
4
Department of Wildlife, Fish and Environmental Studies, Molecular Ecology Group, Swedish University of Agricultural Sciences, Skogsmarksgränd, 901 83 Umeå, Sweden
5
Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh 27695, USA
Elusive and rare species are difficult to monitor, therefore non-invasive genetics are commonly employed in carnivore management (Gervasi et al. 2008; Kindberg et al. 2011; Tsaparis et al. 2014). Non-invasive genetic sampling ena
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