What We Read: Favorite Papers of 2016

Part two of our Year in Review: we describe our favorite papers of 2016. These papers did not necessarily have to have been part of our Friday link dump series, What We’re Reading, which focuses on the WildlifeSNPits theme of the intersection between evolution and conservation.

So this year, after much deliberation, I’ve selected three favourite papers. The first is about methods for environmental DNA analysis in aquatic systems: “Critical considerations for the application of environmental DNA methods to detect aquatic species“. This is a really useful paper that provides guidelines on experimental design, implementation and interpretation of eDNA data. While the focus is on detection of aquatic macro-organisms, many of the points raised are valid to eDNA studies more broadly.

The second paper I chose, “Hybridization and endangered species protection in the molecular era“, tackles what can be a fairly controversial issue, how to deal with hybrids in conservation. Should hybrids of threatened species be protected, or culled? The answer, of course, is context-dependent, and this paper discusses the different circumstances that can influence management decisions relating to hybrids. An important aspect of this work is the aim of bridging the gap between research and policy, by providing a decision-tree framework that managers can use to evaluate whether or not particular hybrids should be protected.

My third choice, “Selection on mitochondrial variants occurs between and within individuals in an expanding invasion” is a really interesting study that explores rapid mitochondrial DNA evolution in an invasive starling population in Australia. The authors found that the best explanation for the rapid spread of a new haplotype in a population on the invasion front involved selection both among individuals and within individuals. This is because quite a lot of the starlings sampled displayed heteroplasmy, i.e. their cells carried mitochondria with the new haplotype and mitochondria with the ancestral haplotype. Understanding how organisms can quickly adapt to novel or changing environments is a fairly hot topic at the moment (no climate change pun intended) and this work highlights one possible mechanism.

Finally, I couldn’t resist giving a quick mention to three other papers I particularly liked:

This year, I’ve been thinking about, reading, and writing on topics beyond the traditional ecological and behavioral approaches I’ve used in my research before: a trifecta of citizen science, the extinction of experience, and social science research. Building upon a theme I raised in “When More Science Isn’t Better,” I chose two papers where the study subjects were people, not animals. Advocates of citizen science research (and I am one) say that citizen science can increase the knowledge of the participant, change attitudes, create a stronger sense of place, and can even alter behaviors. These are large and bold claims, and while easily tossed around, they are largely anecdotal and unsubstantiated in formal studies. Although citizen science has a wide breadth and broad scope, there are literally only dozens of studies that formally study the attitudes, knowledge, and behaviors of participants. Therefore, my favorite papers from this year are those that did this and found evidence of change: “Place-based and data-rich citizen science as a precursor for conservation action” and from my own eMammal team “Creating advocates for mammal conservation through citizen science.” Both of these studies showed an increase and knowledge and science skills among participants, and the former study also showed a stronger connection to place, community, and attitude and behavioral changes from volunteers. While the eMammal study did not show changes in attitudes, largely because participants were already dedicated to environmental issues, they did show that participants became more likely to spread messages of mammal conservation, thus creating conservation advocates. This issue of self-selection is rampant through citizen science. Are the changes observed in participants there because citizen science attracts members of society that are already highly engaged and caring? These are some of the questions that I will be pondering in 2017 and addressing using a rare dataset of participants that have not volunteered to do citizen science – kids doing it as part of their school day.

Word cloud from Forrester et al. 2016 that summarizes the “best part” about participating in eMammal citizen science research.

I’ve got two favorite papers this year.  I love reading about the evolutionary history of my favorite foods, so no surprise that I chose, “Domestication selected for deceleration of the circadian clock in cultivated tomato.”  This paper compared circadian movement of leaves with time sampled transcriptomes between domesticated tomatoes (Solanum lycopersicum) and their wild ancestor (S. pimpinellifolium).  They observed that gene expression was different between the species and that domesticated tomatoes had slower daily leaf movement.  The authors identified a hard sweep around the EID1 gene.  Not only did leaves move slower in plants with the domesticated EID1 alleles, but they were shorter and had more chlorophyll.  The authors hypothesize that this genotype was selected for after plants were brought to Europe from native Ecuador, where slowing down the time-sensing machinery allowed the crops to take advantage of long summer days.

My second pick is, “Getting a head in hard soils: Convergent skull evolution and divergent allometric patterns explain shape variation in a highly diverse genus of pocket gophers (Thomomys).”  I think I’ve read the methods of this ~30 times because I’m desperately trying to copy such a well designed study.  But once I get past the methods, I’m always struck by what an interesting question the authors tackle.  Pocket gophers can dig tunnels and burrows with both their teeth and their claws; thus, how does body shape of heads and forearms differ between species that live in soils of different hardness?  Soil hardness being the selection pressure for evolutionary change.   They observed multiple morphological pathways for species to transition from claw digging (often in soft soil) to tooth digging (in harder soils), and the change was not always associated with an increase in body size which had previously been hypothesized due to allometries associated with large body size.


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