Special Feature: Transcriptomic and Genomic Analyses of Communities

The latest issue of Journal of Ecology (105.3) includes a Special Feature on the latest ‘omics technologies and how they can serve community ecology. Below, guest editors, Nate Swenson and Andy Jones, tell us more about their Special Feature…

As many US-based ecologists will remember, in 2010, the US National Science Foundation’s Division of Environmental Biology announced a new call for proposals under the theme of “Dimensions of Biodiversity”. The stated goal of the 10-year program was to fund studies that would integrate an understanding of the genetic, taxonomic/phylogenetic, and functional dimensions of biological diversity.

The program, seemingly by design, necessitated collaborations between ecologists, evolutionary biologists, physiologists, and geneticists, among other disciplines to answer fundamental questions regarding how these different dimensions interact and shape each other and the role they play in the origin and maintenance of biological diversity.

Among the proposals that were funded in the first competition was a US-China International Research Coordination Network (IRCN) proposal that we were involved in writing.  The proposal: “Diversity and Forest Change: Characterizing functional, phylogenetic and genetic contributions to diversity gradients and dynamics in tree communities” was to run a variety of workshops to examine the three dimensions of biodiversity using data collected from the Smithsonian’s ForestGEO network of forest dynamics plots, which consists of 63 plots with > 6 million stems of > 10,000 tree species with standardized census approaches and data structures.


Photo credit: Keping Ma, doi.org/10.1111/1365-2745.12760

In most ways, the ForestGEO network is an ideal system to examine the dimensions of biological diversity on a global scale across tropical, temperate, and boreal forests. Since its founding, a fundamental goal of the network is to understand the mechanisms responsible for the coexistence of tree species on small spatial scales by using a standardized design and regular censuses. Aside from spatial and demographic data, these plots had begun to standardize the measurement of leaf and stem functional traits and generate community phylogenies using DNA barcoding approaches. So, the ForestGEO plot network and the affiliated researchers had strengths in taxonomic/phylogenetic and functional dimensions.

What we lacked, however, was a deep understanding of the genetic dimensions. Although many studies within ForestGEO plots had performed population genetic analyses on a handful of tree species, no studies had integrated genetic data for the entire community. Moreover, barcoding didn’t really satisfy the genetic component of diversity as the main goal was really inferring evolutionary relationships among species, not exploring functional genetic variation.

One of the goals during the summer workshops was to further develop a plan to integrate the genetic dimension into the ForestGEO network, beginning conversations between workshop participants about how one might use genomic approaches to address fundamental questions in community ecology.

We quickly realized, given the expense and time required to sequence entire genomes, let alone the complexity and size of some tree genomes, that doing comparative genomics for entire tree communities was out of the question (however, this is unlikely to be the case in the near future). We realized that incorporating transcriptomics and metagenomics was the more viable option.

Three of the papers presented in the Special Feature (Zambrano et al., Schappe et al., and Han et al.) were a direct result of these workshops and discussions. The Zambrano and Han papers are the result of an additional US-China Dimensions of Biodiversity collaborative pilot-project between one of us (Swenson) and Keping Ma proposing a functional phylogenomic approach to community ecology. The nexus of the proposal was a ForestGeo workshop held in Changbaishan in northeast China near the border of North Korea. The Schappe et al. paper is partially supported by another Dimensions project.

Over the course of the intervening 6 years, we have explored how ‘omics approaches could be integrated into ecology with increasing vigor. Our focus has been on addressing fundamental ecological questions using approaches that could be applied to non-model organisms. Around the time when we were obtaining our first important results and writing them up during the spring of 2016, the US National Science Foundation held a “Dimensions of Biodiversity” meeting. It was there that we realized there were multiple groups pursuing similar questions, using similar approaches and yielding exciting results!

Brad Cardinale, in particular, presented a fascinating piece of work on the gene expression response to competitors varying in their degree of phylogenetic relatedness (DEB-1046121). Seeing Cardinale’s presentation and hearing about the transcriptomic work emerging from the labs of Maren Friesen and Sharon Strauss (DEB-1342793) sparked the idea to compile this and other work into a Special Feature.

Coincidentally, it was at this time that Journal of Ecology was doing an inventory of the ‘omics type papers we have published over the last several years with the idea of generating a Virtual Issue. Executive Editor David Gibson had recognized that a significant integration of ‘omics and ecology was on the horizon and the Journal could be an important outlet for such work in the future. From this confluence of events, a Special Feature was born.

The work presented in the Special Feature represents important steps forward, and we expect a significant acceleration of the integration and complexity of ‘omics approaches in community ecology. We hope that the work presented will stimulate ecologists currently not working with ‘omics approaches to consider how they may enrich their research programs and we hope that those working with ‘omics may increasingly consider how to integrate their approaches to address the questions motivating community ecologists. Finally, we hope that the Special Feature will attract more submissions to the Journal that integrate ‘omics and ecology broadly.

It is an exciting time to be ecologists as we begin to take advantage of the amazing methodological, informatics and conceptual advances taking place in the world of ‘omics.

Andy Jones (Oregon State University) and Nate Swenson (University of Maryland)


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