DOI: 10.5061/dryad.rn8pk0pn0
title: Data from: Increasing prevalence of plant-fungal symbiosis across two centuries of environmental change

description: Species' distributions and abundances are shifting in response to
 ongoing global climate change.  Mutualistic microbial symbionts
 can provide their hosts with protection from environmental stress that may
 contribute towards resilient responses to environmental change, however
 these changes may also disrupt species interactions and lead to declines
 in hosts and/or symbionts. Symbionts preserved within natural history
 specimens offer a unique opportunity to quantify changes in microbial
 symbiosis across broad temporal and spatial scales.  We asked how
 the prevalence of seed-transmitted fungal symbionts of grasses (Epichloë
 endophytes) have changed over time in response to climate change, and how
 these changes vary across host species' ranges. Specifically, we
 analyzed 2,346 herbarium specimens of three grass host species (Agrostis
 hyemalis, Agrostis perennans, Elymus virginicus) collected over the past
 two centuries (1824-2019) for the presence or absence of Epichloë
 symbiosis.  We found that endophytes increased in prevalence over
 the last two centuries from ca. 25% prevalence to ca. 75% prevalence, on
 average, across three host species. Changes in seasonal climate drivers
 were associated with increasing endophyte prevalence.  Notably,
 increasing precipitation during the peak growing season for Agrostis
 species and decreasing precipitation for E. virginicus were associated
 with increasing endophyte prevalence. Changes in the variability of
 precipitation and temperature during off-peak seasons were also important
 predictors of increasing endophyte prevalence. Our analysis performed
 favorably in an out-of-sample predictive test with contemporary survey
 data, a rare extra step in collections-based research. However, we
 identified greater local-scale variability in endophyte prevalence in
 contemporary data compared to model predictions based on historic data,
 suggesting new directions that could improve predictive accuracy. Our
 results provide novel evidence for a cryptic biological response to
 climate change that may contribute to the resilience of host-microbe
 symbiosis through context-dependent benefits that confer a fitness
 advantage to symbiotic hosts under environmental change.
description: Data includes presence/absence data of Epichloë fungal endophytes
 within grass host specimens collected from herbarium specimens. Specimens
 come from 9 herbaria, visited between 2019 and 2022, and were scored for
 endophyte presence by examing 5-10 seeds per specimen using 200-400X
 magnification and analine blue lactic acid stain. Collection locations
 were georeferenced using the ggmap package in R for the
 state/county/municpality centroid depending on the availability of that
 informatio to obtain Lat/Lon coordinates. Data presents the number of
 seeds scored as positive and negative for each specimen, as well as
 liberal and conservative scores denoting endophyte-free (0) and
 endophyte-positive (1) that consider a plant positive if at least one seed
 is endophyte-positive. Liberal and conservative scores may differ
 depending on the certainty of identifying endophytes within a sample (low
 uptake of stain, unusual morphology, etc.) Additional
 data on endophyte prevalence from contemporary population surveys come
 from collection trips between 2013 and 2020. Data from <em>Elymus
 virginicus</em> were compiled from Sneck et al. 2013, and data for
 Agrostis hyemalis come from surveys between 2015 and 2020. At each
 population, seeds from up to 30 plants were collected and scored using
 microscopy as above. Data presents the proportion of endophyte-positive
 plants for each sampled population. 
description: # Data from: Increasing prevalence of plant-fungal symbiosis across two
 centuries of environmental change
 [https://doi.org/10.5061/dryad.rn8pk0pn0](https://doi.org/10.5061/dryad.rn8pk0pn0) ## Description of the data and file structure This data was collected to examine historic changes in the prevalence of a common symbiosis between grasses and Epichloë fungal endophytes. Data includes scores for presence/absence of fungi within historic herbarium specimens collected across the eastern North America between 1824 and 2019. This data is used to examine spatially-varying trends in endophyte prevalence, and to examine how these trends are associated with changes in climate across time. We examined herbarium specimens from three host species (Agrostis hyemalis, Agrostis perennans, and Elymus virginicus). We acquired seed samples from 1135 A. hyemalis specimens collected between 1824 and 2019, 357 A. perennans specimens collected between 1863 and 2017, and 854 E. virginicus specimens collected between 1839 and 2019. Each specimen is associated with collection location and year information, taken from digitized herbarium records or transcribed at the time of seed collection. A secondary dataset records contemporary survey data used as out-of-sample test data to test the predictive ability of the model built on historic data. These contemporary surveys from 63 populations include up to 30 individuals per population for Agrostis hyemalis and Elymus virginicus. ### Files and variables #### File: contemp\_surveys.csv **Description:** Records population prevalence from population surveys of Epichloë endophyte host species (Agrostis hyemalis and Elymus virginicus) from 63 populations across the southeastern United States. Up to 30 individuals of each species were collected within each sampled location. This data compiles surveys from Sneck et al. 2013, and surveys from Fowler et al. between 2015 and 2019. Data is compiled in R and can be found at: ##### Variables * SiteID: unique id for each collection location * SpeciesID: denotes host species (AGHY: Agrostis hyemalis; ELVI: Elymus virginicus) * lat: Latitude in decimal degrees recorded with a handheld GPS unit * lon: Longitude in decimal degrees recorded with a handheld GPS unit * Year: year of survey * sample_size: number of individual plants sampled within the population * endo_prev: proportion of endophyte positive individuals within the scored individuals from the population (presented as a proportion on a scale of 0 to 1, indicating 0% prevalence to 100% prevalence respectively) #### File: endo\_herb\_georef.csv **Description:** Records presence/absence of Epichloë fungal endophytes within herbarium specimens. 5-10 seeds were collected from specimens and then scored under a microscope. Collections focused primarily on three host species (Agrostis hyemalis, Agrostis perennans, and Elymus virginicus), but early collection efforts also included Lolium perenne, Poa autumnalis, and Elymus texensis. For some specimens, additional stem samples were taken, however these were not included. Stem samples from previous survey by J.F. White were marked on herbarium sheets and were included in these scores. Within the dataset, missing values are recorded as "N/A", most commonly for specimens which were scored for their endophyte status, but for which location or collector information were unavailable upon searching online databases. ##### Variables * Sample_id: Unique id for each sampled specimen, assigned during collection. * Institution_specimen_id: Unique id for each herbarium specimen, recorded as the id assigned by the herbarium collection, or when not available as the collector name and number. * Spp_code: denotes host species (AGHY: Agrostis hyemalis; AGPE: Agrostis perennans; ELVI: Elymus virginicus; LOPE: Lolium perenne; POAU: Poa autumnalis; ELTE: Elymus texensis) * new_id: an id modified from the Institution_specimen_id to facilitate merging with online digitized herbarium records. * primary_collector: name of the primary collector recorded for each specimen. some specimens record multiple collectors, and here only the first is used. * collector_lastname: last name of the primary collector * collector_firstname: first name of the primary collector. * collector_full_string: simplified string recording the name of the collector * collector_string: simplified string recording the collectors first initial and last name. * location_string: search string used in ggmap georeferencing function; combines municipality, state, country information * Country: Country of collection location * State: State of collection location * County: County of collection location * Municipality: city or munipality of collection location * Locality: other locality information recorded on the herbarium sheet * hand_georef_lat: precise latitude recorded on herbarium sheet, if recorded * hand_georef_lon: precise longitude recorded on herbarium sheet, if recorded * year: year of collection * month: month of collection * day: day of collection * tissue_type: whether sample taken from herbarium specimen was seed or stem tissue * seed_scored: the total number of seeds scored from herbarium specimen * seed_eplus: the number of seeds scored as endophyte-positive from herbarium specimen * Endo_status_liberal: recorded as endophyte-positive if at least one seed is scored as endophyte-postive. To capture uncertainty in the scoring process, when we identified potential endophytes with unusual morphology, low uptake of stain, or a small amount of fungal hyphae across the scored seeds, we recorded a positive liberal status (more likely to be endophyte-positive) and a negative conservative status (less likely to be endophyte-positive). * Endo_status_conservative: recorded as endophyte-positive if at least one seed is scored as endophyte-postive. To capture uncertainty in the scoring process, when we identified potential endophytes with unusual morphology, low uptake of stain, or a small amount of fungal hyphae across the scored seeds, we recorded a positive liberal status (more likely to be endophyte-positive) and a negative conservative status (less likely to be endophyte-positive). * Date_scored: date of seed scoring * scorer_id: string recording the name of the researcher who scored specimen for endophyte presence * score_number: id recording separate scores for each specimen performed by different researchers. Seeds from a subset of specimens were scored separately by different scorers. * scorer_factor: unique id recording each scorer * collector_factor: unique id recording each collector * lat: georeferenced latitude in decimal degrees * lon: georeferenced longitude in decimal degrees ## Code/software Herbarium data deposited here are compiled from endophyte scoring data for each specimen, along with data available through online portals (Symbiota, KU Botany search) and records from individual herbaria that record collection information about each specimen. Compilation was performed in R and can be found at the following script: [https://github.com/joshuacfowler/EndoHerbarium/blob/master/Analyses/endo_herbarium_records_merge.R](https://github.com/joshuacfowler/EndoHerbarium/blob/master/Analyses/endo_herbarium_records_merge.R) Contemporary survey data deposited here are compiled from endophyte scoring data for contemporary population surveys, along with data available from the supplement of Sneck et al. 2013, *Microbial Ecology,* and new population surveys between 2015 and 2019. Compilation was performed in R and can be found at the following script: [https://github.com/joshuacfowler/EndoHerbarium/blob/master/Analyses/ecolab_validation_data_prep.R](https://github.com/joshuacfowler/EndoHerbarium/blob/master/Analyses/ecolab_validation_data_prep.R) ## Access information Data was derived from the following additional sources: * Sneck, M.E., Rudgers, J.A., Young, C.A. *et al.* Variation in the Prevalence and Transmission of Heritable Symbionts Across Host Populations in Heterogeneous Environments. *Microb Ecol* **74**, 640–653 (2017). [https://doi.org/10.1007/s00248-017-0964-4](https://doi.org/10.1007/s00248-017-0964-4) * Location and collector information was downloaded from the following open access portals: * [https://portal.torcherbaria.org/portal/collections/index.php](https://portal.torcherbaria.org/portal/collections/index.php) * [https://biodiversity.ku.edu/botany/vascular-plant-collection](https://biodiversity.ku.edu/botany/vascular-plant-collection)