Landscape genetics gets existential

is-everything-even-anything

I had a lot of ideas for future posts, but “landscape genetics” keeps pulling me back.

Beyond the new methodology, reviews, and empirical findings, I suppose someone has to pump the brakes and get more existential. Rodney Dyer does just that in the upcoming Molecular Ecology opinion “Is there such a thing as landscape genetics?“, first seen on bioRxiv and Haldane’s Sieve.

Landscape genetics is sold as an integrative field, combining elements from landscape ecology and population genetics to answer all sorts of questions relating to the spatial arrangement of heterogeneity. Dyer attempts to match this integrative definition with the reality of what questions and methods are actually being used in landscape genetics literature.

According to a National Academies report entitled, Facilitating Interdisciplinary Research (2004), interdisciplinary research is “…a mode of research by teams or individuals that integrates information, data, techniques, tools, perspectives, concepts, and/or theories from two or more disciplines or bodies of specialized knowledge…” The purpose of these interactions are to either “…advance fundamental understanding or to solve problems whose solutions are beyond the scope of a single discipline or area of research practice.”

Put simply, a truly integrative field must:

  1. Have contributions from two or more disciplines
  2. Produce emergent insights possible only through those contributions

To test the literature for these characteristics, Dyer analyzed more than three hundred published papers that self-identified as landscape genetics (LG), landscape ecology (LE), and population genetics (PG). After mining and processing the text from introduction and methods sections of these papers, he using a discriminant analyses to measure the “fusion” of LE and PG in landscape genetics manuscripts. To look for emergent insights, overrepresented terms were identified in LG manuscripts in comparison to underrepresented (inferred as unappreciated or undeveloped) terms in the LE and PG literature.

The result: landscape genetics papers most-closely resemble population genetics papers in their questions/methodologies in comparison to landscape ecology papers.

Fig 2 from Dyer (2015) describes the discriminant scores across the three disciplines

Fig 2 from Dyer (2015) describes the discriminant scores across the three disciplines

Overall, both the discriminant analysis and term usage suggest that to a large degree landscape genetic studies resemble the kinds of questions and approaches commonly called population genetic prior to 2003. These data do suggest that there should be a discussion about the appropriateness of referring to landscape genetics as a unique endeavour versus a subdiscipline residing within population genetics.

However, there are certainly areas of advancement in the LG manuscripts. The most prominent of these is the use of distance matrices for both predictor and response variables at a ~50% increase in frequency compared to the two “parental” disciplines.

What I found most interesting is the contradiction between the similarity of LG papers to PG papers and the relative impact of LE on the LG papers. Dyer describes a highly skewed development of the two components (genetic distances and landscape/environmental distances). Where the characterization of ecological/physical distance between samples has been highly refined in the LE literature and then applied to landscape genetics, pairwise genetic structure has become increasingly aged in comparison.

It is time for the population geneticists to become more involved in landscape genetics. There is a real opportunity here to not only introduce existing tools that are not being utilized to their full potential, but also to push the envelope in how we characterize genetic data and how we connect landscape scale processes (both spatial and temporal) into the existing body of evolutionary theory.

In the end, I don’t think Dyer is making a semantics argument or condemnation of landscape genetics as a non-existent discipline. If anything, this is a unique and empirical way to look for future directions and areas for increased focus in this relatively new discipline. Combined other outlooks described in the links above, it could be just the beginning of where this this thing is headed next.

 

Dyer, RJ. 2015. Is there such a thing as Landscape Genetics? Molecular Ecology. DOI: 10.1111/mec.13249

National Academies. 2004. Facilitating interdisciplinary research. Committee on Facilitating Interdisciplinary Research. 332 pgs. National Academies Press. Washington DC.

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About Rob Denton

I'm a Postdoctoral Fellow in the Department of Molecular and Cell Biology at UConn. I'm most interested in understanding the evolutionary/ecological consequences of strange reproduction in salamanders (unisexual Ambystoma). Topics I'm likely to write about: population and landscape genetics, mitonuclear interactions, polyploidy, and reptiles/amphibians.
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