Progress 06/29/15 to 06/17/20
Outputs
Target Audience: The target audiences for this project has been academic scientists working to understand the effects of climate on forest tree biology, and hence the impacts that climate change may have on forest ecosystems and the services they provide. Throughout this project, we have engaged multiple scientists in collaboration related to our red spruce research, including both academics and government scientists working at the USDA Forest Service. In addition, we greatly expanded our sharing of results and collaboration with NGO conservationists and restoration ecologists working with the Naure Conservancy and other agencies to restore red spruce forests where they have been decimated, primarily in the Central Appalachian region. In addition, another importat target audience during this project has been students interested in oursuing careers in plant science and conservation biology.During this project, I have supported one graduate student (Brittany Verrico) who is developing her PhD research around the response of forest trees, and red spruce in particular, to climate gradients through space (elevation gradients) and time (climate change). Brittany and i have also mentored undergraduate student researchers on this project, including Jeremy Weiland (Biology and Computer Science major), Katie Bardsley (Plant Biology major); Noah Kaufman (Plant Biology major) and Helena Munson (Biology and Environmental Science major). Additionally, this project has supported 2 recent UVM graduates as research technicians (Ethan Thibaut and Helena Munson). Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has supported the development of a diverse group of yound plant scientists. This included:1 PhD student (1 female), 4 undergraduate students (2 females), and 4 research technicians (2 females, 1 student from the LGBTQ community). It also kick-started an important collaboration between Keller's lab and the US Forest Service, particularly with John Butnor (USFS Plant Physiologist), who recently received promotion in part attributable to productivity associated with this project. In addition to providing mentoring in experimental design, data collection, lab and field techniques, and manuscript preparaton, this project has supported professional development though giving conference and symposium talks and sharing their research with diverse stakeholders. How have the results been disseminated to communities of interest?We have presented numerous research updates and seminars to diverse communities of interest. These include: One seminar eachyear given to the UVM Department of Plant Biology 1-2 seminars per year given at the Forest Ecosystem Monitoring Cooperative annual conference 1-2 seminars per year given at scientific conferences (e.g., Society for the Study of Evolution; American Genetics Association) Seminars given to local community groups or NGOs (e.g., Central Appalachian Spruce Restoration Initiative, CASRI) Another major avenue for communication of results has been via scholarly publications in peer-reviewed journals Lastly, we have written several articles on our spruce research geared towards the general public, including a publiushed article in the Burlington Conservation Newsletter (written by Sonia DeYoung, 2018) and another in press at Northern Woodlands magazine (DeYoung 2020) for the winter 2020 issue. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Across the history of the project, we met or exceeded each of our major goals as outlined in the proposal. Specifically: Goal 1:Determine historical and recent patterns of red spruce gene flow in relation to upslope migration of the BDE along an elevational transect in the Green Mountains. We surveyed and reinventoried all trees >2 cm dbh within the 85 plots of the historic Siccama transect on Camels Hump, VT. This latest survey data gave us a 50 dataset which we used to analyze long-term trends in change in forest community composition and shifting elevational distributions. We analyzed these data using new sophisticated multivariate matrix regression models to test the associations of community shifts in response to different anthropognic stressors (temperature change, atmospheric pollution). We publiushed our paper (Verricho et al. 2020)in Diversity and Distributions (IF=4.092). We sequenced reduced representation libraries from the genomes of >800 red spruce individuals along elevational transects on two mountains (Camels Hump and Mansfield, VT), and analyzed the resulting polymrophism data for signatures of gene flow. We found slight but significant divergence between the mountains, suggesting spatially restricted gene flow at the level of 10s of kilometers. However, gene flow was extremely high across the elevational transects within each mountain, showiung a complete homogenization of diversity between low and high elevation stands. These findings are part of a manuscript in draft by Verrico, to be submitted in 2021. Goal 2:Determine levels of standing genetic variation and local adaptation for tolerance to freezing injury - a key abiotic factor determining productivity and survival of spruce growing across different elevations We collected seed from mother trees across the elevational gradients on 2 mountains, germinated and grew their seed in common garden conditions of the greenhouse, and then measured pehnotypic traits related to their timing of seasonal dormancy (bud set and bud flush) to avoid frost injury. We also measured their colkd tolerance using electrolyte leakage assays in controlled temperature chambers. The results show significant genetically-based trait divergence in bud set and cold tolerance between seedlings sourced from high vs. low elevation mother trees, suggesting local adaptation. These results have been published in one paper already (Butnor et al. 2019) and another in preparation. Goal 3:Use ecological genomic techniques to identify regions of the genome associated with cold tolerance, and determine if recruitment of spruce forests at high and low elevations contains genetic variants needed to maintain or increase productivity under future climate We sequenced genotype-by-sequencing libraries from >800 spruce trees to discover single nucleotide polymorphisms for testing the genetic basis of climate adaptation between high and low elevations. While this effort has yielded the largest dataset to date of fine-scale genomic variation in a forest tree, the extremely large genome of spruce resulted in the the polymorphism being too spread out within the genonme to effieciently test for selection. Instead, we used these data in an appropriate set of analyses to understand gene flow and gene structure across the gradient (see Goal 1), and instead used an alternative approach to target genomic regions that are likely to contribute to adaptive variation using the approach of exome-capture sequencing. These results have been published in Capblancq et al. (2020). In addition, we established 3 common gardens of spruce trees sourced fron a wide range of climatic environments to test for local adaptation to climate. These gardens are located at high, mid, and low elevations along Mount Mansfield, VT. Data from these gardens are part of B. Verrico's PhD thesis, and the data show strong signals of trait plasticity and local adaptation. Manuscripts will be prepared for submission in 2021. Goal 4:Characterize the gene expression networks involved in spruce stress responses, and determine the overlap in gene pathways between different types of stressors relevant to spruce climate adaptation We accomplished this goal by using the seed we collected to germinate and grow seedlings under controlled conditions in growth chambers. At 12 weeks of age, we began stress treatments of heat and drought stress, and harvested leaf tissue fr RNA extraction. RNA was used to build transcriptomic libraries and sequenced to determine gene expression differences. PI Keller used these data with graduate course in Ecological Genbomics at UVM (PBIO381) to analyze for differential gene expression in response to multiple stressors and to teach the next generation of graduate students cutting edge techniques in plant science and genomics (Spring 2020). The results showed minimal impact of heat stress alone, but compounding stressors of heat + drought elicited strong gene expression responses, and revealed candidate genes in the protein phosphatate pathway, heat shock proteins, and other molecular chaperones. These data are currently in prep. for a manuscript to be subnmitted in 2021.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Capblancq, T., Fitzpatrick, M.C., Bay, R.A., Exposito-Alonso, M. and Keller, S.R., 2020. Genomic prediction of (mal) adaptation across current and future climatic landscapes. Annual Review of Ecology, Evolution, and Systematics, 51.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Capblancq, T., Butnor, J.R., Deyoung, S., Thibault, E., Munson, H., Nelson, D.M., Fitzpatrick, M.C. and Keller, S.R., 2020. Whole?exome sequencing reveals a long?term decline in effective population size of red spruce (Picea rubens). Evolutionary Applications.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Verrico, B.M., Weiland, J., Perkins, T.D., Beckage, B. and Keller, S.R., 2020. Long?term monitoring reveals forest tree community change driven by atmospheric sulphate pollution and contemporary climate change. Diversity and Distributions, 26(3), pp.270-283.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Butnor, J.R., Verrico, B.M., Johnsen, K.H., Maier, C.A., Vankus, V. and Keller, S.R., 2019. Phenotypic Variation in Climate-Associated Traits of Red Spruce (Picea rubens Sarg.) along Elevation Gradients in the Southern Appalachian Mountains. Castanea, 84(2), pp.128-143.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Butnor, J.R., Verrico, B.M., Vankus, V. and Keller, S.R., 2018. Ethanol exposure can inhibit red spruce (Picea rubens) seed germination. Seed Science and Technology, 46(2).
- Type:
Other
Status:
Published
Year Published:
2018
Citation:
Sonia DeYoung. "20,000 Years of Climate Change: Red Spruce Tells the Story." September 11, 2018. Burlington VT Conservation Newsletter (https://enjoyburlington.com/red-spruce/)
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:The target audiences for this project have been University students studying in Plant Biology, Biology, and Environmental Science. During this period, I have supported one graduate student (Brittany Verrico) who is developing her PhD research around the response of forest trees, and red spruce in particular, to climate gradients through space (elevation gradients) and time (climate change). Brittany and i have also mentored undergraduate student researchers on this project, including Jeremy Weiland (Biology and Computer Science major). Lastly, an additional target audience is the public sector of forest conervation professionals, including the USDA-Forest Service whom we've been interacting closely with regarding our findings and research agenda (J. Butnor, K. Johnsen, P. Schalberg), as well as state conservationists (Jim Duncan) and NGO's (Deborah Landau fro the Nature Conservancy), all of whom are interested in spruce conservation and restoration. Changes/Problems:We encountered a problem with our initial attempt atgrowing seedlings for the common garden work we had planned oroginally. Seeds were processed from cones by a certified USDA seed processing facility, using a protocol specific to conifers. Unfrotunately, a step in this processsing proved detrimental to seed germination, and we encountered significant losses of seed viability. Our contigency for this plan is several-fold: First, we have isolated the cause of the loss in seed viability, and determined it to be ethanol exposure used to separate filled vs. unfilled seed. We have done a series of experiments to verify this finding, and have prepared a manuscript for submission on the topic. We have collected a new set of seed from red spruce that we are now preparing for germination, and which we have processed without ethanol flotation. Thus the common garden experiment will take place, but is now planned for a start during summer 2018. What opportunities for training and professional development has the project provided?This project has supported the research development of a PhD-level graduate student, Brittany Verrico. Verrico's main research thrust is investigating cliate change adaptation and migration capacity of red spruce along elevational gradients in Vermont's forests. In addition, this project has supported the independent research of UVM undergraduate student, Jeremy Weiland. Weiland is a biological science major, and has conducted research on the germination physiology of red spruce, and also the variation in cold tolerance among seedlings derived from cones collected across a range of elevations. How have the results been disseminated to communities of interest?We have shared our findings with the broader scientific and public communities in a variety of ways: Seminars: Verrico has presented her research on this project during 2 seminars in the Plant Biology Marvin seminar series. Keller has presented research findings during an invited seminar to the UVM Rubsentstein School othe Environmenta and Natural Resources. Conferences: Verrico presented research from this project at the following conferences: American Genetics Association (Asilomar, CA) Conference for theSociety for the Study of Evolution (Portland, OR) Meeting of the Southern and Central AppalachianSpruce Restoration Initiative (SASRI and CASRI) What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we will be analyzing the genetic SNP data to create models of population structure, diversity, and gene flow of red spruce along the elevational gradients. We also plan to publish a manuscript on the Camels Hump 50-year forest inventory plot data showing the influence of temporal trends on forest community composition across elevation gradients. Lastly, we will begin work towards establishing an experimental common garden pot on Mount Mansfied to test the history of local adaptation along the elevation gradient.
Impacts
What was accomplished under these goals?
We have conducted data collection on forest inventory plots on Camel's Hump mountain, adding to a 50 year monitoring record documenting change in forest composition with elevation. Data analyses are applying Generalized Dissimilarity Modeling (GDM) to assess the change in forest community composition driven by changes in the underlying environmental gradients. Results currently suggest climate warming over the latter half of the 20th century has resulted in an upslope movement of the boreal spruce-fir forest, but also a surprising return of young spruce seedlings to lower elevations, possibly reflecting a fading history of land use. We also collected genetic samples from 540 trees plus several hundred seedlings on 2 mountains: Camel's Hump and Mt Mansfield, for the purpose of testing the genetic distinctiveness of high, mid, and low altitude populations and their adaptability. DNA has been extracted from all these samples, and genome-wide sequencing is finished. We now have estimates of genetic diversity for over 800 red spruce from these two Vermont mountains. Results indicate very high levels of gene flow and connectivity of spruce across the landscape, both across elevations on the same mountain, as well as across mountains. Lastly, we are coordinating with the USDA Forest Service to collect and process red spruce seed from mature cone-bearing trees in our 2 focal mountains in Vermont, and elsewhere throughout the northeast. These seeds have been germinated and grown at the UVM greenhouse, extracted for DNA to determine the dispersal dynamics between high and low elevation populations, and are currently targeted for experimental work in climate-controlled growth chambers to determine physiological responses to mid-winter warming. This has resulted in a refinement to our germination protocol and a technical note nearing submission for peer review.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2015
Citation:
Verrico, B., S.R. Keller T. Perkins, and B. Beckage. 50 years of forest community change along an elevation gradient on Camels Hump Mountain, Vermont. Vermont Monitoring Cooperative Annual Meeting .
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2017
Citation:
Verrico, B.V. and S.R. Keller Analysis of historical and contemporary microgeographical gene flow in a boreal forest tree species, Picea rubens. Presentation at the Society for the Study of Evolution conference; Portland, OR.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2016
Citation:
Verrico, B. and S.R. Keller. 2016 Microgeogaphic analysis of local adaptation and gene flow across an elevational gradient in northeastern red spruce forests. Invited presentation at the American Genetics Association President's Symposium.
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