It's Hard to Get Genome Data from an Elusive Species

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This adorable little creature is an American pika (Ochotona princeps), a furry mammal about eight inches long that lives in alpine areas in North America.

It's the subject of a new study that uses next-generation sequencing to try to find out genome-wide data on the elusive species.

Genetics has recently come to the fore as a tool in conservation; this kind of analysis can tell us a lot about a species' diversity. But new technologies are going beyond focusing on individual genes to look at the genome—information on all the genes and how they work together.

Getting a sufficient DNA sample for genomic sequencing when you're working with elusive species can be difficult, however. If you're interested in an animal specifically because it's hard to find, swiping a blood sample or saliva swab is going to be a challenge.

But the new study published in open-access journal PeerJ suggests this may not be necessary. Researchers at the University of British Columbia and genotyping company SNPsaurus managed to get some genome-wide data about the American pika from a less invasively sourced sample: a bit of snagged hair.

While the American pika is not super endangered yet (unlike some other pika), it's of particular interest to conservationists because it's very sensitive to climate—the American pika can't live for long above 25.5 Celsius (77.9 Farenheit)—which means it could be particularly threatened by climate change.

The researchers used tape to snare strands of pika hair, ending up with enough to collect some genomic data from 67 animals. They used a type of sequencing developed by SNPsaurus to collect data on SNPs (single nucleotide polymorphisms), parts of DNA that vary between individuals.

Their results gave some information on the pika, such as that animals at lower habitats at less diversity, suggesting more inbreeding in their populations.

But more broadly, the study aimed to show that it is possible to get some data on the genomic level from samples collected in non-invasive ways, which could be applicable to other species of interest to conservation scientists.

It's not perfect—the authors note that it's easy for the samples to get contaminated with those of other species, and they also relied on a reference genome for the pika that might not be available for other species—but the researchers write that, "Overall, NGS (next-generation sequencing) data and population genomic analyses hold great promise for informing conservation-related studies."

"Here, we have shown that with careful consideration, genomic data collection is compatible with the non-invasive sampling required in practice for many conservation-related studies," they concluded.