Khan Anubhab, Patel Kaushalkumar, Bhattacharjee Subhadeep, Sharma Sudarshan, Chugani Anup N, Sivaraman Karthikeyan, Hosawad Vinayak, Sahu Yogesh Kumar, Reddy Goddilla V, Ramakrishnan Uma
National Centre for Biological Sciences TIFR Bangalore India.
Rajasthan Forest Department Jaipur India.
Ecol Evol. 2020 May 18;10(11):4583-4594. doi: 10.1002/ece3.6157. eCollection 2020 Jun.
Knowledge of relationships in wild populations is critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, study genetic connectivity, study genotype-phenotype associations, trace individuals, or track wildlife trade, many identified individuals need to be genotyped at thousands of loci, mostly from noninvasive samples. This requires us to (a) identify the most common noninvasive sample available from identified individuals, (b) assess the ability to acquire genome-wide data from such samples, and (c) evaluate the quality of such genome-wide data, and its ability to reconstruct relationships between animals within a population.We followed identified individuals from a wild endangered tiger population and found that shed hair samples were the most common compared to scat samples, opportunistically found carcasses, and opportunistic invasive samples. We extracted DNA from these samples, prepared whole genome sequencing libraries, and sequenced genomes from these.Whole genome sequencing methods resulted in between 25%-98% of the genome sequenced for five such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages in accordance with long-term monitoring data. Even with just five samples, we were able to uncover the matrilineage for three individuals with unknown ancestry.In summary, we demonstrated that noninvasive shed hair samples yield adequate quality and quantity of DNA in conjunction with sensitive library preparation methods, and provide reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair an ideal noninvasive resource for studying individual-based genetics of elusive endangered species in the wild.
了解野生种群中的亲缘关系对于更好地理解交配系统和近亲繁殖情况至关重要，可为濒危物种的保护策略提供依据。为了描绘野生种群的谱系、研究遗传连通性、研究基因型与表型的关联、追踪个体或监测野生动物贸易，许多已识别的个体需要在数千个位点进行基因分型，这些位点大多来自非侵入性样本。这就要求我们：（a）确定已识别个体中最常见的非侵入性样本；（b）评估从此类样本中获取全基因组数据的能力；（c）评估此类全基因组数据的质量及其重建种群内动物之间亲缘关系的能力。我们追踪了一个野生濒危老虎种群中的已识别个体，发现与粪便样本、偶然发现的尸体以及偶然的侵入性样本相比，脱落毛发样本最为常见。我们从这些样本中提取DNA，制备全基因组测序文库，并对其进行基因组测序。全基因组测序方法使五个此类样本的基因组测序覆盖率达到25%至98%。探索性群体遗传分析表明，这些数据没有整体偏差，能够恢复预期的种群结构和亲缘关系。线粒体基因组根据长期监测数据恢复了母系谱系。即使只有五个样本，我们也能够揭示三个祖先未知个体的母系谱系。总之，我们证明，结合灵敏的文库制备方法，非侵入性脱落毛发样本能产生足够质量和数量的DNA，并提供来自全基因组数十万个单核苷酸多态性的可靠数据。这使得脱落毛发成为研究野生珍稀濒危物种个体遗传学的理想非侵入性资源。
