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De novo discovery of SNPs for genotyping endangered sun parakeets ( Aratinga solstitialis ) in Guyana
Conservation Genetics Resources ( IF 1.1 ) Pub Date : 2020-05-14 , DOI: 10.1007/s12686-020-01151-x
Robert Spitzer , Anita J. Norman , Helena Königsson , Bastian Schiffthaler , Göran Spong

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.



中文翻译:

从头开始发现在圭亚那对濒临灭绝的太阳鹦鹉(Aratinga solstitialis)进行基因分型的SNP

鹦鹉(Psittaciformes)是当今最濒危的鸟类之一,仍然受到栖息地丧失和活禽贸易剥削的威胁。在这种情况下,可靠和非侵入性的监测技术对于成功的保护措施至关重要。在这项研究中,我们开发了一组由86个高质量SNP组成的小组,用于对濒临灭绝的太阳鹦鹉(Aratinga solstitialis)进行基因分型)在圭亚那,这是该南美野生物种最后为人所知的繁殖种群之一。对不同类型的样本(血液,羽毛,粪便,喙和泄殖腔拭子)进行了基因分型测试。尽管血液表现最好,但羽毛和粪便也产生了可靠的结果,因此可以用作未来人口监测的DNA的非侵入性来源。对基因型的主要成分(DAPC)的判别分析显示,圭亚那太阳鹦鹉与其他鹦鹉螺物种以及被圈养种群的同种异种单独聚集。SNP专家组还充分检测到先验已知的一阶血族。使用一系列实验性污染,我们发现来自其他鹦鹉螺菌种的污染和同种菌的轻微污染(〜10%)并不能阻止成功的基因分型和个体识别。我们表明,通过提高杂合度水平可以检测到较高的特定污染(〜50%),这种杂合度落在未污染样品的分布范围之外。

更新日期:2020-05-14
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