Fellow's research: Shed hair are the best non-invasive samples for sequencing whole genomes


26 Jun 2020

Fellow's research: Shed hair are the best non-invasive samples for sequencing whole genomes

Uma Ramakrishnan, Senior Fellow, NCBS, Bengaluru

In our latest publication, we have shown with studies on wild tigers that shed hair is an ideal non-invasive resource for genetic profiling of endangered species.

Population genomic studies on endangered large carnivores are limited by the number of high-quality invasive samples that can be collected over a short time period, since such samples tend to rare. In our recently published study, we investigated the optimal non-invasive biological material for sequencing whole genomes of wild tigers. We find that shed hair can be collected from several individuals in a short span of time compared to fecal, blood and carcass samples. We find that the genome sequences from shed hair are free of biases and provide reliable population genetics information and the ability to estimate relationships in the wild. A pilot study with shed hair genomes allowed us to uncover the unknown ancestry of three tigers.

Whole genome sequencing requires good quality DNA. Such DNA is mostly obtained from biological material such as blood and other tissues, which have to be collected invasively from tranquilized animals or from carcasses thus making them challenging. As a result, population genomic studies on wild endangered carnivores are often limited by low sample sizes. We set out to discover the best non-invasive biological sample that can be collected in short span of time, yields DNA that be used of whole genome sequencing and investigated whether whole genome sequences from such samples can be used for population genomic analysis for large endangered wild carnivores.

We followed identified individual tigers in Ranthambore Tiger Reserve and collected all potential sample types (hair, scat, carcass) deposited by them. We extracted DNA from such samples and sequenced whole genomes. The whole genome sequences were analyzed for errors and holistic biases by comparing to high quality genomes from the same individuals and assessing population genetic and relatedness patterns.

We find that shed hair are the most commonly encountered samples in the wild. DNA sequences obtained from 8-10 whole hair is free of holistic biases and has the least amount of mismatch with DNA sequences from blood samples. Using DNA sequences from whole shed hair we identified at least two new matrilines in Ranthambore Tiger Reserve.

Our findings provide a fast and reliable way for scaling up population genomic studies of wild endangered large carnivores. Our approach can be used to reconstruct pedigrees in wild populations, and potentially initiate genome-wide association studies in the wild for unique phenotypes or diseases. Overall, our results suggest that genome sequencing can be applied to various species and samples, and help gain better understanding of species ecology, evolution and conservation in the wild.

Reference:

Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild? Anubhab Khan, Kaushalkumar Patel, Subhadeep Bhattacharjee, Sudarshan Sharma, Anup N. Chugani, Karthikeyan Sivaraman, Vinayak Hosawad, Yogesh Kumar Sahu, Goddilla V. Reddy, and Uma Ramakrishnan. Ecology and Evolution (2020)

Suggested reading:

Secrets of Wild Tigers - Visual Abstract