De novo discovery of SNPs for genotyping endangered sun parakeets ( Aratinga solstitialis ) in Guyana
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METHODS AND RESOURCES ARTICLE
De novo discovery of SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana Robert Spitzer1 · Anita J. Norman2 · Helena Königsson2 · Bastian Schiffthaler3 · Göran Spong2,4 Received: 28 January 2020 / Accepted: 8 May 2020 © The Author(s) 2020
Abstract Parrots (Psittaciformes) are among the most endangered groups of birds today and remain threatened by habitat loss and exploitation for the live bird trade. Under such conditions, reliable and non-invasive monitoring techniques are crucial for successful conservation measures. In this study, we developed a panel of 86 high quality SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana, which form one of the last known breeding populations of this South American species in the wild. Genotyping was tested on different types of samples (blood, feathers, feces, beak and cloacal swabs). While blood performed best, feathers and feces also yielded reliable results and could thus be used as non-invasive sources of DNA for future population monitoring. Discriminant Analysis of Principal Components (DAPC) on genotypes revealed that Guyanese sun parakeets clustered separately from other psittacine species as well as conspecifics from a captive population. A priori known first-order kinships were also adequately detected by the SNP panel. Using a series of experimental contaminations, we found that contamination from other psittacine species and slight contamination (~ 10%) from conspecifics did not prevent successful genotyping and recognition of individuals. We show that instances of higher conspecific contamination (~ 50%) can be detected through an increased level of heterozygosity that falls outside the distribution of uncontaminated samples. Keywords SNP · Sun parakeet · Conservation · Relatedness · Non-invasive sampling · Contamination
Introduction Robert Spitzer and Anita J. Norman have contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-020-01151-x) contains supplementary material, which is available to authorized users. * Robert Spitzer [email protected] 1
Department of Wildlife, Fish, and Environmental Studies, Wildlife Ecology Group, Swedish University of Agricultural Sciences (SLU), 901 83 Umeå, Sweden
2
Department of Wildlife, Fish, and Environmental Studies, Molecular Ecology Group, Swedish University of Agricultural Sciences (SLU), 901 83 Umeå, Sweden
3
Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, SE‑901 87, Umeå, Sweden
4
Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, NC 27695, USA
Effective conservation and management of wild animal species often relies on trustworthy estimates of population size and trends (Newson et al. 2008; Marques et al. 2013), which also form vital elements of the IUCN Red List assessment protocol (IUCN 2019). Particularly in the case of rare and threat
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