Two of my 2015 papers tackle aspects of the same question: how reliable are genetic tests to detect wildlife from trace DNA samples? It’s great to be able to use DNA to work out which species of mammal has been pooping in the woods, or to confirm the identification of a museum sample or roadkill of uncertain origin. But there are various possible sources of error that could cause misleading results. By identifying the likely sources of error for each study, we may be able to take additional measures to minimise these risks. This is especially true when the results of our DNA tests directly inform management decision-making and resource allocation.
In “An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: the case of the red fox in Tasmania“, we used blind trials to evaluate the errors associated with sample handling and laboratory analysis (including PCR and DNA sequencing), when we screen scats for fox detection in Australia. If this sounds familiar, it might be because you’ve read the WildlifeSNPits post I wrote on this paper earlier in 2015.
In “Species assignment from trace DNA sequences: an in silico assessment of the test used to survey for foxes in Tasmania“, we used a bioinformatic approach to evaluate the risks of erroneous species identifications caused by unrecognised sequence similarities among different mammal species. Genetic markers for DNA barcoding and specimen identification are chosen because it is possible to discriminate among different species on the basis of these DNA sequences. However, closely related species often have very similar gene sequences, so it is important to demonstrate the limitations of different primer sets. Happily, in this case, we found no other Australian mammal that was likely to be mis-identified as a red fox on the basis of the short cytochrome b sequence used in our DNA test. NB, for those who are interested, I also wrote a blog post about this paper, for The Applied Ecologist’s blog.
Finally, last but not least, I also published “The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)“. The Pygopodidae are legless lizards that are only found in the Australo-Papuan region. They are closely related to geckos, but are often mistaken for snakes by people who have never heard of them. Aprasia parapulchella, the pink-tailed worm-lizard, is found in south eastern Australia, including around Canberra, and is threatened by urban development and habitat loss. Few genomic resources are available for this fascinating group of reptiles, but a mitochondrial genome is a good start!
Next year, look out for work on earless dragons, bandicoots, sugar gliders, #SpeciesFromFaeces and more about evaluating DNA tests from environmental DNA.
This year marks my debut in publishing on non-elephant mammals: raccoons! Having worked on elusive and endangered forest elephants for my dissertation, it was super exciting to work on a common species with a large data set. “The interplay between clumped resources, social aggregation, and genetic relatedness in the raccoon” is the last publication in a series of papers on an experimental study that manipulated resources (dog food) to understand raccoon behavior and disease ecology. This paper looks at how the distribution of resources affects genetic relationships within raccoons. We found raccoons likely change the structure of their home range (but not the size) to allow for the addition of new resources, which weakens patterns of relatedness found in female raccoons (but not males) when food is more dispersed and even. This provides evidence to support the resource dispersion hypothesis, which argues that individuals become social because of how resources are distributed, and not necessarily that they accrue benefits.
For 2016 look for my adventures into deer, results from the eMammal middle school data, and hopefully more elephants!
Oh academia, I spent the whole year writing and all I have to show for the effort is a dissertation and one journal article. At least I’m set up for a productive 2016 with more phylogeography, variation in black bears, and the US ESA.
Jokes aside, I’m really proud of my paper, “Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture.” I observed a previously undescribed phylogeographic pattern in North America, namely that black bears in Alaska were genetically more similar to bears in the eastern part of the continent than to the geographically closer west. I also inferred the locations of Pleistocene refugia (the focus of my WildlifeSNPits post) and patterns of range expansion to the contemporary extent. The paper has implications on the level of genomic diversity needed to describe populations as a subspecies, as the genomics did not support the current designations of 16 subspecies.