Year in Review: What We Wrote 2016


I feel as though 2016 has been a slow year for papers for me, with a number of works in progress taking longer than I thought they would. However, I am ending the year with a handful of papers either in review or almost ready to submit, so I hope that 2017 will be much better.

The output I’m most proud of this year is “A framework for developing and validating taxon-specific primers for specimen identification from environmental DNA“, currently published as an early view article at Molecular Ecology Resources. There are two aspects to this work: a how-to guide for the development of species-specific DNA tests and a case study using bandicoots. I discussed these in more detail in this WildlifeSNPits blog post. A bit like Emily’s paper below, it actually took a few years to get this published, but in my case that was more because we changed the scope of the article during the writing process. Originally our plan was to focus on our bandicoot DNA test as a new tool for conservation. As we progressed we realised there was an opportunity to write more broadly about the way that DNA tests should be developed for trace samples, and how researchers need to be able to demonstrate that these tests do actually perform as expected.

Another paper published in 2016 was derived from my student Em Carlson’s Honours research, asking “How many conservation units are there for the endangered grassland earless dragons?” In this work we used population genetics to identify three distinct genetic lineages of this local threatened reptile. We recommended that each of these populations should be managed separately, to conserve as much genetic diversity as possible within the species. Again, I wrote a WildlifeSNPits post about this research, which you can read here.

Finally, I’d like to give an “honourable mention” to a report I contributed to, “The taxonomic status of populations of southern brown bandicoots, Isoodon obesulus, from eastern and southern Australia based on mitochondrial and nuclear gene analyses“, which we published online in late December 2015. This work has not yet been peer-reviewed (we’re still working on analyses for a broader paper) but some of our results had immediate relevance to conservation of threatened bandicoot populations, so we wanted to make the information available to managers as soon as possible.


The paper I’m most proud of is excited to see published this year is “Deer on the Lookout: how hunting, hiking and coyotes affect white-tailed deer vigilance.” This was my first first author paper from my work with eMammal and this paper is special because it contradicts a large body of literature which mostly supports that deer increase vigilance in response to hunters and coyotes (although studies on coyotes in the east are few). Since apex predators like cougars and gray wolves no longer live in the Eastern US, a lot of people assume that hunters and now coyotes can replace their role. But apex predators do more than just kill prey, they exert indirect effects, namely behavioral changes in prey that cause prey to be more cautious and take less risks, and which ultimately affects the ecosystem as non-fearful deer can freely browse the landscape. In the case of vigilance, white-tailed deer had similar vigilance levels across areas that were hunted and not hunted and with high and low levels of coyotes. Rather, deer habituated to human hikers, and were less vigilant in areas with high levels of recreation. This is the first study to evaluate vigilance at such a large scale – over six states in the Eastern US with thousands of camera trap sites rather than one site or a few sites that most studies try to tackle. I never want to look at a deer photo again! For the blog post version, click here.

Deer not afraid of the presence of apex predators will spend more time with their heads down foraging than scanning the landscape for signs of predators. 

I also co-authored on a paper of a similar theme, looking at how human hikers with their best friends influence wildlife when walking in parks: The ecological impact of humans and dogs on wildlife in protected areas in eastern North America (blog post version here). Using a similar large scale camera trap data set across six states in the Eastern US, we evaluated if wildlife temporally and spatially avoided dogs. Dogs were prolific throughout the parks, but well-mannered. They stuck to the trails with their owners, even if their owners broke the law by letting them off-leash. There wasn’t much spatial avoidance with wildlife in relation to dogs or changes in vigilance, but this paper developed a new technique called the Avoidance-Attraction Ratio, and found that there was some temporal avoidance. Given that there are a lot of dogs in parks, it appears that wildlife are aware of where they are and avoid the area temporarily until they are gone.

Dogs were frequently captured on camera traps, but rarely off-trail. 

2017 is already shaping up to be a great year for publishing. I have one education-based manuscript already accepted to be published in Science Scope in spring. I have four papers well underway, and it will be a matter of how fast I can write/analyze data to get them all done (plus even more that are ready to go)! Look out for my research on the attitudes of kids towards wildlife, schools as a unique urban habitat for wildlife, a review paper on elephant sociality, and an essay on the extinction of experience.


My favorite of the three papers I wrote this year was, “Taxonomic class, petitioning agency, and lawsuits affect time spent awaiting listing under the Endangered Species Act.”  Although to say my colleagues and I wrote it in 2016 is horribly disingenuous, as it took us 3 years to publish.  The time to publication was all the more ironic given that the paper is about long delays for species listings under the US Endangered Species Act (WildlifeSNPits blog post here).  But discussing endangered species policy is fraught and each reviewer wanted their perspective recognized in some way, which added many rounds of review and kept upping the peer review process time.  We identified multiple factors (taxa, who petitioned a listing, and lawsuits) that affected the process time of species listing, where the average was 12.1 years.

I wrote my second phylogeography paper, this one on the global range expansion of brown rats, ” Global population divergence and admixture of the brown rat (Rattus norvegicus).”  Brown rats are native to modern day China and Mongolia but these days you can see them scurrying around most major cities all over the world.  We identified five routes of range expansion that were mediated by human trade and increasing connectivity between human societies.  We also observed that the spatial scale of populations is very small, often the size of the city or island sampled.  Thus, we think there may be low gene flow in rats around the world, which would be great news for understanding disease transmission to humans.

Finally, I wrote a paper about genotyping costs, “Variability in total project and per sample genotyping costs under varying study designs including with microsatellites or SNPs to answer conservation genetic questions.”  I’m not a 100% sure why I wrote this, except I do hyperventilate a little when I see someone online state that a RADseq library costs $2 per sample.  Nope!  The AMPure bead clean-up alone costs $2 a sample, so try again.  Mostly I’m concerned with how conservation genetic studies will be funded and evaluated into the future as genomics becomes more common.  There’s a narrative that genomics is cheap; while that is true on a per marker basis, it’s not necessarily true on a per sample (or per project) basis.  Yet looking at projects from only a cost perspective ignores increasing evidence that genomic scale datasets increase accuracy (see Table 1 and associated discussion in the paper).  Thus conservation geneticists must start weighing these factors early in the study design process.


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