I started a new job in January 2017, moving from a research-focused postdoc to a role with a mix of research and project management, coordinating the Oz Mammals Genomics Initiative. Getting stuck into this has given me less time to spend writing papers (and blogs…) than in previous years, so I’m pretty happy to have three papers with 2017 publication dates.
I was very excited to see my PhD student Elodie Modave’s first paper: “A single mini-barcode test to screen for Australian mammalian predators from environmental samples”, published in GigaScience. Elodie developed a DNA test that can be used in barcoding / metabarcoding studies to distinguish all of the larger Australian mammal predators. In previous work, we’ve screened scat DNA to detect introduced (fox, cat, dog) and native (devil, quoll) predators, but we have found it difficult to discriminate among quoll species. There are four species of quoll in Australia, all in the genus Dasyurus, but there is not much genetic variation within this genus at the genetic markers we’ve used before, so we couldn’t assign sequences from unknown samples to the species level. We could tell that a scat came from a quoll, but not which quoll… but now we can!
My second paper for 2017 was led by colleagues Dave Ramsey and Candida Barclay: “Detecting rare carnivores using scats: Implications for monitoring a fox incursion into Tasmania”, published in Ecology and Evolution. Some animals can be difficult to detect in the wild, and non-invasive sampling of scats can provide more information than relying upon captures and sightings alone. We evaluated how effective human and dog survey teams were at detecting known scats, using standardised field survey methods. The answer… not as effective as we might have hoped. But this is an important thing to understand: these results can be used to estimate how many animals could be present without being detected.
Finally -and this feels like cheating(!) – I’m going to remind you of a paper I mentioned in 2016’s “What We Wrote“. It was accepted in late 2016, but has a 2017 publication date, so why not… Also, I just really like this paper: “A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA”, in Molecular Ecology Resources.
What I wrote and what I published this year are vastly different things. *criesintohands* This year I published a fun side project on the geographic origins of lab rats, “Genomic analyses identify multiple Asian origins and deeply diverged mitochondrial clades in inbred brown rats (Rattus norvegicus).” There are over 500 strains of lab rats that have been inbred, many for specific disease models. One of the most storied strains is the Wistar rat which gave rise to many other lines. The Wistar Institute in Philadelphia, USA produced and maintained the original colony. Thus it has long been hypothesized that lab rats were from North America. My previous work on rat phylogeography identified global population structure, so my colleagues and I decided to test where lab rats came from geographically. We used the genomes of 25 strains and saw that the nuclear genome had a distinct western North America and eastern Asia signal. Our results show that much of the global diversity of rats is missing from contemporary medical models.