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.