EE BIOL 194B - Research Group or Internship Seminars: Ecology and Evolutionary Biology
EE BIOL 146/246 - Conservation Genomics
EE BIOL 154 - Ecosystems of California
Conservation Biology, Ecology, Evolutionary Biology, Plant Biology, Tropical Biology
My research program examines the evolution of tree populations to their local environment as the outcome of gene flow, natural selection and their demographic history. I have selected trees as a focus of my research for many reasons?they are key determinants of their ecosystem; their long lifespan and typically high population sizes provides an interesting context for studying evolution; and their conservation not only preserves the tree species of interest by multiple trophic levels of biodiversity from the soil microbiome to the wildlife that feed on their fruit. Oaks (Quercus) in general, and valley oak (Quercus lobata Née) in particular, are an excellent study system for investigating the molecular basis of local adaptation of trees. The genus Quercus has many species through the Northern Hemisphere that are important economically and ecologically; in North American oaks have more biomass and species than pine.
Our lab has long used genetic markers as a valuable tool for studying gene flow and demographic history and in the last five years we have switched our emphasis to genomic tools for studying adaptive genetic variation. With that transition, we have increasingly focused on oaks as a model system, in particular valley oak (Quercus lobata). Below are some topics currently under investigation:
1) Valley oak as an emerging model system. To support research on valley oak, we have created a high quality, well annotated genome of valley oak and two common gardens containing over 600 families derived from throughout the species range. The genome provides an essential too
2) Evolution of local adaptation. For this research theme, we are conducting studies on landscape and ecological genomics of trees, transcriptomic studies of gene expression in response to water stress, and epigenetic studies of DNA methylation patterns across environments.
3) Molecular ecology of pollen- and seed-mediate gene movement. For many years, our lab has used genetic markers to study pollen and seed dispersal to understand how these processes affect genetic diversity within populations and and connectivity among populations. With new genomic tools, we can now study how these processes affects patterns of adaptive genetic variation that may be critical for survival.
4) Phylogeography and geographic patterns of genetic variation. Phylogeography is the study of geographic patterns of genetic lineages with the goal of understanding how the physical landscape (e.g. mountains, valleys, water bodies) and climate cycles shape the evolutionary history of species, the emergence of new species, and the extinction of others.
5) Hybridization and introgression. Interspecific gene flow is a potential source of genetic variation, including favorable variants that may allow plants to survive better locally. My research program explores hybridization and ancient introgression in California oaks from a population and phylogenetic perspective.
6) Conservation science of trees. Through the integration of genomic studies and the analysis of phenotypic variation observed in the two common gardens, we are developing models of how valley oak will respond to climate change. Such information will be critical in developing specific management strategies for this species, and rules of thumb for tree species in general.
In all these topics, my research integrates genetic patterns across scales that range from a single nucleotide base in a DNA sequence of plant to the landscape to the species' range. This work addresses fundamental questions about the evolutionary ecology of tree species and utilizes that information to inform policies about reserve networks that will optimize their survival in constantly changing landscapes and rapidly changing environment.
Sork VL*, SJ Cokus*, ST Fitz-Gibbon*, AV Zimin, D Puiu, JA Garcia, PF Gugger, C Henriquez, Y Zhen, KE Lohmueller, M Pellegrini, SL Salzberg. 2022. High-quality genome and methylomes illustrate features underlying the evolutionary success of oaks. *equal co-authors. Nature Communications 13:1-15. https://doi.org/10.1038/s41467-022-29584-y
Hvilsom, C, G Segelbacher, R Ekblom, MC Fischer, L Laikre, K Leus, D O´Brien, R Shaw, V Sork. 2022.Selecting species and populations for monitoring of genetic diversity. Gland, Switzerland: IUCN. https://doi.org/10.2305/IUCN.CH.2022.07.en
Shaffer, HB, E Toffelmier, RB Corbett-Detig, M Escalona, B Erickson, P Fiedler, M Gold, RJ Harrigan, S Hodges, TK Luckau, C Miller, DR Oliveira, KE Shaffer, B Shapiro, VL Sork, and IJ Wang. 2022. Landscape genomics to enable conservation actions: The California Conservation Genomics Project. J. Heredity. DOI: 10.1093/jhered/esac020
O’Donnell, S, ST Fitz-Gibbon, and VL Sork 2021. Ancient introgression between distantly related white oaks (Quercus sect Quercus) shows evidence of climate-associated asymmetric gene exchange. J. Heredity 112: 663-670
Sork, VL, and JW Wright. 2021. Replanting oaks? New research in valley oak may help inform seed sourcing decisions. Artemesia 8 (2): 13-18.
Browne, L, B MacDonald, S Fitz-Gibbon, JW Wright, and VL Sork. 2021. Genome-wide variation in DNA methylation predicts variation in leaf traits in an ecosystem-foundational oak species. Forests 12: 569.https://doi.org/10.3390/f12050569
Gugger PF, ST Fitz-Gibbon, A Albarrán-Lara, JW Wright, VL Sork. 2021. Landscape genomics of Quercus lobata reveals genes involved in local climate adaptation at multiple spatial scales. Molecular Ecology 30: 406-423. https://doi.org/10.1111/mec.15731
Browne L, A Mead, C Horn, K Chang, Z Celikkol, C Henriquez, F Ma, E Beraut, R Meyer, VL Sork. 2020. Experimental DNA demethylation affects phenotype and gene expression of tree seedlings. G3: Genes|Genomes|Genetics 10:1019-1028 doi.org/10.1534/g3.119.400770
Browne L, JW Wright, ST Fitz-Gibbon, PF Gugger, VL Sork. 2019. Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow. Proceedings of the National Academy of Sciences 116(50): 25179-25185 https://doi.org/10.1073/pnas.1908771116
Mead A, J Peñaloza Ramirez, MK Bartlett, JW Wright, L Sack, VL Sork. 2019. Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations. Molecular Ecology 23: 5248-5264 https://doi.org/10.1111/mec.15289
Kim B, X Wei, ST Fitz-Gibbon, KE Lohmueller, J Ortego, PF Gugger, VL Sork. 2018. RADseq data reveal ancient, but not pervasive, introgression among Californian tree and scrub oak species (Quercus: Fagaceae). Molecular Ecology, 27: 4556-4571. DOI: 10.1111/mec.14869.
Martins, K, PF Gugger, J Llanderal-Mendoza, A González-Rodríguez, ST Fitz-Gibbon, J-L Zhao, K Oyama, VL Sork. 2018. Landscape genomics provides evidence of climate-associated adaptive genetic variation in Mexican populations of Quercus rugosa. Evolutionary Applications 11: 1842-1858. DOI:10.1111/eva.12684.
Browne L, K Ottewell, VL Sork, J Karubian. 2018. The relative contributions of seed and pollen dispersal to gene flow and genetic diversity in seedlings of a tropical palm. Molecular Ecology 27:3159–3173.
Sork VL. 2018. Genomic studies of local adaptation in natural plant populations. Journal of Heredity. 109:3–15. DOI: 10.1093/jhered/esx091.
Ortego J, PF Gugger, VL Sork. 2018. Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus). New Phytologist 218:804–818. DOI: 10.1111/nph. 14951