Gugger Lab

   Ecological Genomics

Ecological genomics of local adaptation in oaks


How are long-lived trees adapted to environmental variation across their distributions, and what are the implications for responses to 21st Century environmental change? Through an NSF-funded project in collaboration with Victoria Sork and Matteo Pellegrini at UCLA and Steve Salzberg at Johns Hopkins, we are developing genomic resources and sampling natural populations of valley oak (Quercus lobata) to understand the genetic basis of local adaptation to climate. Oaks are ecologically and economically important trees in the northern temperature zone. Valley oak is a California endemic species with some convenient features that lend itself to studying local adaptation, such as having stably occupied a heterogeneous landscape for a relatively long period (Gugger et al. 2013 Mol Ecol; Sork et al. 2016 PNAS). We have also established a large common garden from 95 seed sources throughout its distribution to facilitate experimental research (Delfino-Mix et al. 2015). With our recently completed first draft genome sequence based on Illumina sequence data (Sork et al. 2016 G3), we can now map whole-genome sequences from throughout the entire distribution to build on our earlier work that used genotyping-by-sequencing (Gugger et al. in prep.), transcriptome sequencing (Cokus et al. 2015 BMC Genom; Gugger et al. 2016 TGG), and candidate gene approaches (Sork et al. 2016 AJB). The results of this project will lead to an enhanced understanding of adaptation in long-lived species, as well as information that can be used to predict responses to future environmental change. Learn more about this project or download data at the Valley Oak Genome Project website.




Epigenomics of local adaptation


Trees may be especially vulnerable to rapid environmental change because they cannot move and because they slowly develop to reproductive maturity. As a result, we are exploring, non-genetic mechanisms that may allow short-term response to environmental change. One intriguing potential mechanism is DNA (cytosine) methylation, an epigenetic mechanism. DNA methylation mutates quickly relative to DNA sequence, can be inherited across generations, varies among individuals and populations, and is thought to affect gene expression and thus phenotype. Thus, there is potential for methylation to be involved in evolutionary response to environmental change. We have found in oaks that CpG methylation variation is highly differentiated among populations and linked to putatively locally adaptive genomic regions (Platt et al. 2015 Mol Ecol). Furthermore, we have shown that CpG methylation can be especially strongly associated with climate on the landscape, suggesting that it may be involved in climate response (Gugger et al. 2016 Mol Ecol). Potential next steps are to evaluate the heritability of methylation in oaks, determine whether methylation acts independently or is simply controlled by the underlying genetics, and to what degree methylation variation arises randomly and is selected upon or arises by environmental induction. There remains considerable debate about the role of methylation in evolution and phenotypic plasticity.








Inferring responses to climate change:  integrating genetic, fossil, and climate data


Periods of past climate change offer us opportunities to investigate actual responses of organisms that can inform predictions of future responses. Three complementary approaches to inferring past responses are phylogeography, paleoecology, and ecological niche modeling (Gavin et al. 2014 New Phytol). We are particularly interested in bringing the latest genomic tools, large fossil databases, and increasingly fine-scale climate data together to infer demographic and adaptive evolutionary responses to changing environments since the last Ice Age. In earlier work, we have combined fossil (Gugger & Sugita 2010 QSR) and genetic data (Gugger et al. 2010 Mol Ecol, 2011 New Phytol) to infer responses of Douglas-fir (Pseudotsuga meziesii) to glacial-interglacial climate cycles and ancient geological change. We have also combined genetic data with niche models in California oaks to understand how past and present climates have influenced genetic diversity (Gugger et al. 2013 Mol Ecol; Ortego et al. 2012 Mol Ecol; Riordan et al. 2016 AJB) and speciation (Ortego et al. 2015 Mol Ecol).





Hybridization and adaptation in oaks


Interbreeding among species (hybridization) is an important mechanism for evolution in many plant taxa. Oaks have long been recognized for their propensity to hybridize, yet maintain distinct ecological and morphological species. This paradox raises the question of how these species can maintain distinctiveness despite successful mixing. One hypothesis is that strong divergent natural selection on ecologically relevant genes maintains differences (Gugger et al. 2015 BMC Genom). However, this raises the question of why complete reproductive barriers have not evolved. One possibility is that it depends on the strength of selection, the number of traits or genes involved, the functions of those genes, and the environmental context. A complementary hypothesis is that hybridization can be beneficial by facilitating occasional introgression of adaptive alleles from other species. We are exploring these forces across the genome and in relation to ecological function in natural systems to build on past work that considered only a small number of molecular markers in the absence of genomic information (Ortego et al. 2014 J Biogeog, in press New Phytol).



Conservation genomics of Acacia koa in Hawaii


Koa (Acacia koa) is a dominant tree species that is endemic to Hawaii. Because of its economic value, as well as human development, this species has declined considerably and is now the target of restoration and management efforts to ensure its future. In collaboration with Jessica Wright  and Christina Liang  at the US Forest Service, we are using genomic tools to assess population structure and local adaptation in koa. Results from our work will help inform seed planting guidelines and potential vulnerabilities to future environmental change.









Conservation genomics of bats


Bats are threatened by wind turbine development and an invasive fungus leading to white nose syndrome. In collaboration with Dave Nelson  and Ed Gates, we are assessing resulting changes in genetic diversity and inferring migration routes to better understand the resilience of bat populations and guide management decisions. Funding is provided by the Maryland Department of Natural Resources and the US Fish and Wildlife Service.




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Frostburg, Maryland 21532