Like most fields in biology, experimental studies in model systems have helped to further mechanistic understanding of evolution. The first eukaryotic genome sequences and annotations were completed in experimentally tractable systems such as Arabidopsis thaliana and Drosophila melanogaster. Laboratory model species provide the perfect system to conduct experiments, which manipulate genes and/or environmental conditions. Genome-scale data derived from model species erect a framework with which to study the functional biology behind complex, ecologically important traits. Although its importance is irrefutable, functional genomic information from model systems alone does not suffice to understand ecology and evolution in nature. To bridge the gap between the evolution of wild species and the base knowledge gained from laboratory model species, many researchers have looked to related species.
Emerging ‘ecological model systems’ [i.e. Tautz et al. (2010)] have genomic resources from their close relatives in the laboratory, but represent biodiversity and well-documented ecological patterns. Using ecological model systems, it is possible to assess the ecological impacts of patterns and processes discovered in the laboratory.
Studies of ecological model systems seek to better understand the processes of evolution by connecting functional and neutral genetic variation to ecological patterns. There have been major steps towards the achievement of this lofty goal; however, progress is limited primarily by the astounding complexity and multiple scales of the required research. To fully understand evolution using the biodiversity of ecological model systems, three disciplines need to be integrated: systematics, ecology and genomics. Small-scale, system-specific meetings facilitate collaboration that bridges disciplines and advances the utility of ecological model systems.
Here, we discuss such a meeting of biologists studying an ecological model system: the genus Boechera (Brassicaceae). Boechera, as discussed at length elsewhere in this edition (Rushworth et al. 2011), is quickly emerging as a model system to study speciation, adaptation and development. Boechera’s greatest advantage is its close phylogenetic relationship with Arabidopsis and the resulting high degree of sequence conservation between species (Windsor et al. 2006; Schranz et al. 2007). This recent common ancestry with the premier system for functional genomics in plants provides a wealth of a priori hypotheses about genotype-to-phenotype processes and their potential role in adaptation.
Boechera species exhibit a tremendous amount of genetic and ecological diversity. Nearly all semi-arid, alpine and forested environments in western North America are inhabited by Boechera (Rushworth et al. 2011). Although some species inhabit a wide range of environments, speciation and a high degree of specialization account for much of this ecological diversity. Reticulate evolution and cladogenesis have driven the divergence of over 100 species from a relatively recent common ancestor (Al-Shehbaz 2003; Beck et al. 2011).
Grant-funded collaborations within and between laboratories have permitted the development of many useful tools specific to Boechera: (i) the phylogeny is nearly complete, (ii) fingerprinting techniques permit species identification via microsatellite genotyping, (iii) recombinant inbred lines have been generated from ecologically divergent populations, (iv) comparative genomics and functional genetics research programmes are highly advanced and (v) JGI is sequencing three genomes from two species (B. stricta; B. holboellii sensu lato) with more in the pipeline. In the light of these independent but globally useful developments, several laboratories committed to meet in a common environment with the goal of disseminating and discussing the current state of research on Boechera.
In June 2011, 20 researchers, united by their focus on species of the genus Boechera, gathered at the University of Colorado Mountain Research Station near Nederland, CO. The small number of attendees promoted lengthy discussions and the development of a Boechera community. Researchers were allotted an equal amount of time for presentations and discussion. Research spanning systematics, genomics and ecology was presented, covering the full spectrum of studies conducted on this ecological model system. Complete authorship and titles can be found in Table S1 (Supporting information).
The conference began with an overview of Boechera systematics. Michael Windham (Duke University) and his research group discussed the state of the molecular phylogeny. James Beck (University of Wisconsin, Milwaukee) described the phylogenetic patterns of apomixis across the entire genus, and Patrick Alexander (New Mexico State University) explained the patterns of reticulate evolution in New Mexico Boechera populations.
Many molecular resources utilized in Boechera systematics were derived from Arabidopsis methods; SSR markers were originally developed in Arabidopsis and translated to Boechera (Clauss et al. 2002). Several researchers discussed the methods to transfer genomic information to Boechera from other Brassicaceae species. John McKay (Colorado State University) explained how comparative genomic methods can be used to analyse drought adaptation in the context of the three fully sequenced genomes in the Brassicaceae. These techniques will become increasingly important as genomic sequencing projects currently underway across the Brassicaceae are completed. Eric Schranz (University of Amsterdam) further compared the genome structure of Boechera to other Brassicaceae. Timothy Sharbel (IPK Gatersleben) described his work using comparative genomics approaches to assess the functional genetics and developmental biology of apomixis across Boechera.
Several other talks connected this molecular work to ecology. Thomas Mitchell-Olds and his laboratory (Duke University) discussed diverse projects assessing adaptation in nature (described in detail elsewhere in this edition). Catherine Rushworth (Duke University) presented work on the microevolution of apomixis in two sympatric species. Others discussed the ecological patterns of species distribution (John Lovell, Colorado State University), local range limits (David Siemens, Black Hills State University) and pseudo-flowering forming fungus interactions (Riston Haugen, BHSU).
Several new results were presented that are broadly useful to the community. A large collaborative systematics project has advanced the molecular tools available in Boechera. Patrick Alexander and James Beck described how all sexual species can be delimited by 13 SSR markers, even though the phylogeny results in several polytomies. Using these methods, work is continuing to identify the parentage of apomictic hybrid lineages. Macro-evolutionary inference of apomictic species was largely made via morphological appearance until now. These molecular methods will encourage detailed and insightful studies of the evolution of apomixis. Micro-evolutionary work in the Mitchell-Olds laboratory has led to the development of several QTL analytical techniques. Cheng Ruei Lee (Duke University) and Thomas Mitchell-Olds demonstrated how mixed model approaches can be used to graphically present genotype-by-environment interactions, a novel and easily interpretable approach.
In addition to the sharing of ideas, this meeting set the stage for further development of genus-wide tools, available to the entire community. Thomas Mitchell-Olds and others are planning an association panel in Boechera stricta. Patrick Alexander has developed a forum for the exchange of information: Boechera.com/forum. Donovan Bailey (NMSU) and John Lovell have started ‘Boechera seed resources’ as a way to store and exchange validated seeds between collectors and laboratories, which are distant from collection sites. Over 200 accessions from Utah, Wyoming, Colorado and New Mexico are already included. Thanks to the work of Patrick Alexander, John Carman (Utah State University) and Michael Windham, and several hundred additional accessions will be added by the end of 2011. The development of these resources and collaborations are a direct result of the Boechera Summit 2011. Because of the need to connect these future developments, biennial future meetings for 2013 and beyond are planned. The Boechera Summit 2013 will be held in the Rocky Mountain west; contact J.T. Lovell for more information.
Collaboration between laboratories studying a common ecological model system is essential. The complete array of resources for ecological model systems can only be developed and utilized through the combined and integrative efforts of multiple and diverse research groups. The researchers at the Boechera Summit 2011 represented a wide array of goals and methods utilized, as well as a broad scale of enquiry. Laboratories rarely work at multiple scales and even more rarely utilize the diverse techniques that allow for each scale to be fully understood. As scales and techniques are structured between laboratories, small, integrative meetings like the Boechera Summit 2011 are necessary for the progression of research, especially in ecological model systems.