Whole genome sequences from non-invasively collected caribou faecal samples

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 re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from 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 due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics.

Dietary specialisation in a Critically Endangered pipefish revealed by faecal eDNA metabarcoding

The estuarine pipefish, Syngnathus watermeyeri, is one of the rarest animals in Africa and occurs in only two South African estuaries. The species was declared provisionally extinct in 1994, but was later rediscovered and is currently listed by the IUCN as Critically Endangered. A conservation programme was launched in 2017, with the re-introduction of captive-bred individuals into estuaries where this species was recorded historically was the main aims. Successful captive breeding requires knowledge of the species’ dietary requirements. In the present study, we used metabarcoding of faecal DNA to identify prey species consumed by wild-captured S. watermeyeri from one of the two surviving populations. We compared the diet of the estuarine pipefish with that of the longsnout pipefish, S. temminckii, in the same estuary, to determine whether these two species compete for the same prey items. Both species occupy similar estuarine habitats, but S. temminckii has a much wider distribution and also occurs in the marine environment. Our results show that even though both pipefish species prey on three major invertebrate classes (Gastropoda, Malacostraca and Maxillopoda), the relative proportions differ. Syngnathus watermeyeri primarily targets Maxillopoda, with a single species of calanoid copepod constituting >95% of the Amplicon Sequence Variants (ASVs) identified from its faecal DNA, whereas the diet of S. temminckii mostly comprises snail and decapod crustacean larvae. Our finding supports the hypothesis that population declines and localised extirpations of S. watermeyeri during previous decades may have been the result of reductions in the abundance of calanoid copepods. Calanoids rely on freshwater pulses to thrive, but such events have become rare in the two estuaries inhabited by S. watermeyeri due to excessive freshwater abstraction for urban and agricultural use.

Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species

A significant number of Southeast Asian mammal species described in the 19th and 20th century were subsequently synonymized and are now considered subspecies. Many are affected by rapid habitat loss and there is thus an urgent need to re-assess the conservation status based on species boundaries established with molecular data. However, such data are lacking for many populations and subspecies. We document via a literature survey and empirical study how shotgun sequencing of faecal DNA is a still underutilized but powerful tool for accelerating such evaluations. We obtain 11 mitochondrial genomes for three subspecies in the langur genus Presbytis through shotgun sequencing of faecal DNA (P. femoralis femoralis, P. f. percura, P. siamensis cf. cana). The genomes support the resurrection of all three subspecies to species based on multiple species delimitation algorithms (PTP, ABGD, Objective Clustering) applied to a dataset covering 40 species and 43 subspecies of Asian colobines. For two of the newly recognized species (P. femoralis, P. percura), the results lead to an immediate change in the IUCN status to Critically Endangered due to small population estimates and fragmented habitat. We conclude that faecal DNA should be more widely used for clarifying species boundaries in endangered mammals.