Gene Expression and Tree Growth in the CTFS-ForestGEO Plot at Harvard Forest 2017-2019

<para>Major goals in ecosystem ecology have been to scale from leaves to canopies and to determine whether individual-level, intra-species and inter-specific variation is critical for models projecting ecosystem processes now and in the future. The project is important in that it examines these issues in detail considering genotypes and levels of gene expression all the way up to canopy level CO2 flux. Ecological genomics and transcriptomics are nascent fields that have been primarily restricted to model species in natural and (mostly) controlled environments. To date, we have very few studies of non-model organisms in nature and/or studies of functional genomics through space and time. The research is producing extraordinarily rich datasets regarding the gene expression of trees across populations, through space in each population, across the growing season and across years and linking this information to growth and gas exchange. It will, therefore, provide tremendous insights into how much variation exists in nature thereby guiding sampling designs in future ecological 'omics projects. More importantly, it will provide unusually detailed phenotypic information for important non-model species that have large impacts on the CO2 flux of eastern US forests. </para> </section> </abstract> <keywordSet> <keyword>demography</keyword> <keyword>dendrometers</keyword> <keyword>genomics</keyword> <keyword>population dynamics</keyword> <keyword>species diversity</keyword> <keywordThesaurus>LTER controlled vocabulary</keywordThesaurus> </keywordSet> <keywordSet> <keyword>primary production</keyword> <keyword>populations</keyword> <keywordThesaurus>LTER core area</keywordThesaurus> </keywordSet> <keywordSet> <keyword>Harvard Forest</keyword> <keyword>HFR</keyword> <keyword>LTER</keyword> <keyword>USA</keyword> <keywordThesaurus>HFR default</keywordThesaurus> </keywordSet> <intellectualRights> <section> <para>This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.</para> </section> </intellectualRights> <licensed> <licenseName>Creative Commons Zero v1.0 Universal</licenseName> <url>https://spdx.org/licenses/CC0-1.0.html</url> <identifier>CC0-1.0</identifier> </licensed> <distribution> <online> <url function="information">https://harvardforest.fas.harvard.edu/exist/apps/datasets/showData.html?id=hf342</url> </online> </distribution> <coverage> <geographicCoverage> <geographicDescription>Prospect Hill Tract (Harvard Forest). Coordinates based on WGS84 datum.</geographicDescription> <boundingCoordinates> <westBoundingCoordinate>-72.1755</westBoundingCoordinate> <eastBoundingCoordinate>-72.1755</eastBoundingCoordinate> <northBoundingCoordinate>+42.5388</northBoundingCoordinate> <southBoundingCoordinate>+42.5388</southBoundingCoordinate> <boundingAltitudes> <altitudeMinimum>350</altitudeMinimum> <altitudeMaximum>350</altitudeMaximum> <altitudeUnits>meter</altitudeUnits> </boundingAltitudes> </boundingCoordinates> </geographicCoverage> <temporalCoverage> <rangeOfDates> <beginDate> <calendarDate>2017</calendarDate> </beginDate> <endDate> <calendarDate>2019</calendarDate> </endDate> </rangeOfDates> </temporalCoverage> <taxonomicCoverage> <taxonomicClassification> <taxonRankName>genus</taxonRankName> <taxonRankValue>Acer</taxonRankValue> <taxonomicClassification> <taxonRankName>species</taxonRankName> <taxonRankValue>rubrum</taxonRankValue> <commonName>red maple</commonName> </taxonomicClassification> </taxonomicClassification> <taxonomicClassification> <taxonRankName>genus</taxonRankName> <taxonRankValue>Fagus</taxonRankValue> <taxonomicClassification> <taxonRankName>species</taxonRankName> <taxonRankValue>grandifolia</taxonRankValue> <commonName>American beech</commonName> </taxonomicClassification> </taxonomicClassification> <taxonomicClassification> <taxonRankName>genus</taxonRankName> <taxonRankValue>Fraxinus</taxonRankValue> <taxonomicClassification> <taxonRankName>species</taxonRankName> <taxonRankValue>americana</taxonRankValue> <commonName>white ash</commonName> </taxonomicClassification> </taxonomicClassification> <taxonomicClassification> <taxonRankName>genus</taxonRankName> <taxonRankValue>Prunus</taxonRankValue> <taxonomicClassification> <taxonRankName>species</taxonRankName> <taxonRankValue>serotina</taxonRankValue> <commonName>black cherry</commonName> </taxonomicClassification> </taxonomicClassification> <taxonomicClassification> <taxonRankName>genus</taxonRankName> <taxonRankValue>Quercus</taxonRankValue> <taxonomicClassification> <taxonRankName>species</taxonRankName> <taxonRankValue>rubra</taxonRankValue> <commonName>northern red oak</commonName> </taxonomicClassification> </taxonomicClassification> </taxonomicCoverage> </coverage> <maintenance> <description> <para>complete</para> </description> </maintenance> <contact scope="document"> <positionName>Information Manager</positionName> <organizationName>Harvard Forest</organizationName> <address scope="document"> <deliveryPoint>324 North Main Street</deliveryPoint> <city>Petersham</city> <administrativeArea>MA</administrativeArea> <postalCode>01366</postalCode> <country>USA</country> </address> <phone phonetype="voice">(978) 724-3302</phone> <electronicMailAddress>hf-im@lists.fas.harvard.edu</electronicMailAddress> </contact> <publisher scope="document"> <organizationName>Harvard Forest</organizationName> <address scope="document"> <deliveryPoint>324 North Main Street</deliveryPoint> <city>Petersham</city> <administrativeArea>MA</administrativeArea> <postalCode>01366</postalCode> <country>USA</country> </address> <phone phonetype="voice">(978) 724-3302</phone> <phone phonetype="fax">(978) 724-3595</phone> <onlineUrl>https://harvardforest.fas.harvard.edu</onlineUrl> </publisher> <methods> <methodStep> <description> <section> <title/> <para>We installed dendrometer bands on 250 trees in Harvard Forest and measured them every week over 2017 and 2018, and twice in 2019. We sampled leaf material from these same trees for RNAseq sequencing in the early summer of 2017. Additional leaf samples were taken from 20 trees five further times over 2017 and 2018. Libraries have been prepared. Sequencing is completed for Fagus in 2017 and 2018, but other species are still being processed.</para> </section> </description> </methodStep> </methods> <project> <title>Harvard Forest Long-Term Ecological Research Harvard Forest

324 North Main Street Petersham MA 01366 USA

(978) 724-3302 (978) 724-3595 https://harvardforest.fas.harvard.edu https://ror.org/059cpzx98 pointOfContact The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210. hf342-01-dendrometer.csv dendrometer data hf342-01-dendrometer.csv 609684 f2059f4db6a525722958b54a9882a38c 1 \r\n column , https://harvardforest.fas.harvard.edu/data/p34/hf342/hf342-01-dendrometer.csv site Harvard Forest LTER/ForestGEO plot Harvard Forest LTER/ForestGEO plot NA missing value tree.id physical tag number of the tree physical tag number of the tree Na missing value band.number number of the dendrometer band; greater than 1 if more than one band was installed/used during the study number of the dendrometer band; greater than 1 if more than one band was installed/used during the study NA missing value species USDA code for the species of each tree (plants.usda.gov) USDA code for the species of each tree (plants.usda.gov) NA missing value orig.dbh diameter at breast height of each tree from the first census data of the plot centimeter 0.1 real NA missing value gap.width dendrometer band gap width measured in mm using calipers millimeter 0.01 real NA missing value doy numerical day of the year the measurement was taken; starting at 1 on January 1st of each year nominalDay 1 natural NA missing value year year in which the measurement was taken YYYY 1 year NA missing value date date on which the measurement was taken YYYY-MM-DD 1 day NA missing value 12786 informatics atmosphere community regional short-term measurement modeling https://harvardforest.fas.harvard.edu/exist/apps/datasets/showData.html?id=hf253 https://forestgeo.si.edu/