What We Read: Favorite Papers of 2015

Part two of our Year in Review: we describe our favorite papers of 2015. 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.

I’m terrible at picking favourites, but after a fair amount of deliberation I’ve selected two papers as my highlights of 2015. The first “How will the ‘molecular revolution’ contribute to biological recording?” provides a great review of environmental DNA (eDNA), the benefits and limitations of eDNA studies, and how eDNA projects can encourage public engagement in biodiversity research. Case studies are provided to demonstrate the application of eDNA to biodiversity monitoring and detection of introduced species. This paper also raises an important point: we need to come up with better ways to manage molecular records and integrate eDNA data into existing records databases.

My second choice is “Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species”  I picked this paper because it really got me to think deeply about some new ideas. Invasive species can be incredibly successful in new habitats, despite low genetic diversity within introduced populations. If this seems counter-intuitive to you, you’re not alone: traditionally we think of populations with low genetic diversity as having an increased risk of extinction. This paper proposes a new hypothesis: the activity of transposable elements within the genomes of invasives may allow rapid adaptation to novel environmental conditions. Transposable elements are pieces of DNA that are able to move around within a genome. As they move, they can also move other DNA sequences around with them, leading to the deletion or duplication of existing genes, or changes in the way genes are regulated or expressed. In this paper, the authors hypothesise that the stress of exposure to a new environment changes the activity of transposable elements and rapidly generates new genetic diversity. It will be interesting to see how this idea develops over the next few years.

I chose “How Nature-Based Tourism Might Increase Prey Vulnerability to Predators.” This paper was my favorite of the year because I think it touches upon an interesting aspect of behavioral ecology that is often ignored, the human effect. While a lot of the literature is devoted to the negative effects of humans on species, nature-based tourism is typically thought of as a positive solution to solving conservation problems, especially in developing countries. This paper is not necessarily saying that nature-based tourism is bad, but that human presence will impact species, and will do so in an imbalanced way such that some species may benefit from human presence (prey), while others may suffer consequences. I do think the title of this paper is misleading, but I think the concepts, and extending this to understanding the overall presence of humans in the landscape (not just for nature-based tourism, but in their daily lives living in their homes, going to school, work, etc.), and their influence on species as a part of a community with dynamic interactions and relationships is an exciting topic for future research.

My top two papers of the year are not the type to make a usual “What We’re Reading” post, as these are closer to my specialty area. First up is, “Wildlife in a Politically Divided World: Insularism Inflates Estimates of Brown Bear Abundance.” The authors of this paper explain how sampling along political borders skew estimates of population size. The premise of this paper is so simple and something that anyone putting together a thoughtful sampling design already know. But the problem of sampling within political borders versus the range of a population is a persistent problem for conservation genetics. I like how both Bischof and colleagues and Meirmans (a 2015 honorable mention which discusses implications of this problem in data analysis) are acknowledging this aspect of experimental design and its downstream implications in conservation to the community.

My other favorite paper of the year was, “A Spatial Framework for Understanding Population Structure and Admixture.” While I have not played with SpaceMix yet, I can’t wait to check out how it identifies and displays admixture relationships between populations. I like this paper because this is what I think about, how populations diverge then come back together and how population genetics can understand those processes and what it means for genetic drift and adaptation.


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