De novo discovery of SNPs for genotyping endangered sun parakeets (Aratinga solstitialis) in Guyana

• Published in: Conservation genetics resources 2020-12, Vol.12 (4), p.631-641
• Main Authors: Spitzer, Robert, Norman, Anita J., Königsson, Helena, Schiffthaler, Bastian, Spong, Göran
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Biodiversity; Biomedical and Life Sciences; Conservation; Conservation Biology/Ecology; Contamination; Ecology; Ekologi; Evolutionary Biology; Life Sciences; Methods and Resources Article; Non-invasive sampling; Plant Genetics and Genomics; Relatedness; SNP; Sun parakeet
• ISSN: 1877-7252; 1877-7260; 1877-7260
• DOI: 10.1007/s12686-020-01151-x

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.