Whole genome sequences from non-invasively collected samples

Abstract

Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to reconstruct high coverage whole genomes using standard laboratory techniques, therefore in a cost-effective and efficient way. We use wild collected faecal pellets collected from wild caribou (Rangifer tarandus), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome likely due to differences in endogenous DNA content, affecting overall coverage. One of our faecal genomes was only reconstructed at low coverage (1.6X), however the other three obtained between 7 and 15X, compared to 19 and 25X for the tissue samples. We successfully reconstructed high-quality whole genomes from faecal DNA and, to our knowledge, are the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species, representing an important advancement for non-invasive conservation genomics.

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

“…Additionally, they could be perceived as being more ethical if they do not require direct interaction with individuals of endangered animals (Solberg et al, 2006;Arandjelovic and Vigilant, 2018). Estimates derived from hair or fecal samples, for example, may require 2-3 times more samples than the expected number of animals in the population to arrive at acceptably precise estimates; however, the most recent technological developments may make it possible to even obtain whole-genome level coverage from these "poor-quality" samples (Taylor et al, 2020). In addition, the same fecal samples may be analyzed with metabarcoding methods to discover information about diet and roles of animals in ecological networks (Barba et al, 2014;Barnes and Turner, 2016).…”

Major diversification of caribou shaped by glacial cycles before the Last Glacial Maximum

“…We combined these with 15 new whole genome sequences, 12 of which were from tissue samples and 3 of which were from faecal samples ( Figure 1; Table 1). Two of the tissue and the three faecal genomes were used for a methods paper describing the success of reconstructing genomes using non-invasive samples (Taylor, Manseau, Redquest, & Wilson, 2020b). Tissue samples were extracted using a Qiagen DNAeasy tissue extraction kit following the manufacturer's instructions (Qiagen, Hilden, Germany).…”

“…Samples were run on a Qubit fluorometer (Thermo Fisher Scientific, MA, USA) using the High Sensitivity Assay Kit and normalized to 20ng/µl at a final volume of 50µl. The laboratory protocol for faecal samples is described in detail in Taylor et al (2020b) Laboratory protocols for the mitochondrial DNA control region sequencing analysis (mtDNA control region) are described in detail in Klütsch et al (2012;2016). 1,832 samples were included for the mtDNA analysis ( Figure 2; Table 2).…”

LI-Seq: A Cost-Effective, Low Input DNA method for Whole Genome Library Preparation

“…Such high quality and quantity DNA can be difficult to attain when working with threatened, endangered, or cryptic species, where ethical and logistical challenges are often prohibitive (Kohn et al 2006; Ouborg et al 2010). However, samples that yield low quality and quantity DNA have previously found limited use in whole genome studies unless potentially cost-prohibitive library preparation kits or methods are employed (Taylor et al 2020). Given the immense potential benefits of analyzing whole genomes for effective wildlife conservation and management efforts (Funk et al 2012; Ryder 2005; Russello et al 2015), there is an urgent need for a cost-effective method of preparing WGS libraries from low quality and quantity DNA samples.…”

“…In recent years, noninvasive and minimally invasive sampling methods have gained popularity, especially for use in monitoring threatened and endangered species (Lukacs and Burnham 2005; Fuentes-Pardo and Ruzzante 2017). However, noninvasively or minimally invasively collected samples typically yield lower concentrations of DNA which can limit their use in whole genome studies unless expensive library preparation kits or library preparation methods are employed (Taylor et al 2020). Given the immense potential benefits of analyzing whole genomes for effective wildlife conservation and management efforts (Funk et al 2012; Ryder 2005; Russello et al 2015), there is an urgent need for a cost-effective method of preparing WGS libraries from noninvasively or minimally invasively collected samples.…”