Studying endangered species without disturbing animals or their habitats can be difficult, but scientists at Cardiff University have successfully reconstructed genetic information about otters using samples of only their poo.
The team, from the Cardiff University Otter Project , combined techniques from the fields of metagenomics (genetic material obtained from environmental samples) and ancient DNA (genetic material recovered from historical specimens), to create a novel approach to study the elusive species.
Using a method called shotgun sequencing, which can obtain the entire DNA sequence of an organism's genome by sequencing small random fragments, and then assembling them using computer algorithms, the team were able to successfully reconstruct whole mitogenome sequences from otter poo – known as spraint.
Mitogenomes provide insights into areas including population genetics, diversity and evolutionary history, which are all important for conservation efforts. The team say their results are the first known evidence that shotgun sequencing is able to recreate entire DNA from otter spraint alone.
Otters are a protected and much-loved species, so not only is it important that we collect data and information on the species to safeguard them for the future, but also when we do undertake otter research that we do it in a way that generates the least disruption possible.
27 otter droppings were collected by the team along the River Usk in south Wales. Using their new approach, the researchers were able to recover the complete set of genetic information encoded in mitochondrial DNA from 20 out of the 27 droppings analysed.
"Reassuringly, this is a high success rate compared with other genetic monitoring tools widely used for the species", said Dr Elizabeth Chadwick, Cardiff University Otter Project.
Among the 20 screened samples, the researchers observed three inherited genetic variants, known as haplotypes, that matched those reported in earlier studies of otters from Wales, which had instead analysed tissue samples.
"The three recovered haplotypes in these samples were identical to sequences previously documented in high-quality DNA from muscle tissue samples of otters from Wales, validating our approach," added Dr Sarah Du Plessis, Cardiff University Otter Project.
Our analyses of otter spraint also allowed us to identify genetic information from other species which Eurasian otters are known to eat. Identifying genetic information from both otters and their diet at the same time without having to invasively capture otters, their prey, or collect tissue samples is an exciting development, which could be applied to other species of conservation importance.
Cardiff University Otter Project has collected otters found dead from across England, Wales and Scotland since 1994. Using samples and data collected during post mortem examination, the project runs a broad research program on otters, a widely appreciated indicator species that helps monitor changes in chemical pollution of freshwater ecosystems.
The research, Recovering whole mitogenome sequences from Eurasian otter (Lutra lutra) spraint samples: a metagenomic approach , was published in Royal Society Open Science.
