DOI: 10.5061/dryad.v9s4mw75t
title: Serpentine plant community surveys (3 years) following a dispersal manipulation at McLaughlin Natural Reserve

description: While investigating how historical contingencies manifest in ecological
 communities is common, research has yet to uncover how species
 distributions and abundances may be impacted by ecological processes
 interacting across spatial and temporal scales. We assessed the influence
 of a historical dispersal event on community assembly by simulating five
 scales of dispersal for 240 serpentine annual plant communities that
 experienced a large shift from drought to high rainfall conditions over
 three years. We collected, aggregated, and redistributed the aboveground
 seed bank from 30 sites across five nested spatial scales (~1 m, 5 m, 100
 m, 5 km, and 10 km), and annually censused communities over a three-year
 period to identify change in community structure among dispersal scales
 and over time. We assessed the change in community composition and
 diversity that occurred over the study period by comparing contrasts of
 Bray-Curtis disimilarity and net changes in species richness between a
 baseline control plot and each experimental dispersal treatment plot. We
 also determined how species turnover through time was affected by
 dispersal scale, including how the number of established, sink, and
 intermittent species found in experimental plots were impacted by our past
 dispersal manipuation. Finally, we examined species’ differences in
 response to environmental fluctuations (i.e. stress-tolerant vs.
 stress-intolerant) and whether dispersal enhances these differences to
 increase turnover in dominant species groups. Our one-time dispersal
 manipulation diversified local seed banks, thereby providing insurance
 against temporal variability and supporting community re-assembly toward a
 new compositional state when drought was lifted. We also found evidence
 that various forms of temporal lags directed community responses to
 environmental fluctuations, preventing rare species extirpations and
 providing subordinate species discrete windows of time to supplement their
 seed banks. This experiment underscores the importance of dispersal and
 dormancy for diversity maintenance in the face of future climate where the
 degree and magnitude of fluctuations are uncertain.
description: # Serpentine plant community surveys (3 years) following a dispersal
 experiment at McLaughlin Natural Reserve We have submitted the raw
 (data_raw.zip) and clean (data_clean.zip) data files and R scripts
 (Rmarkdown files) needed to perform the analyses described in our article:
 'Experimentally enhancing dispersal reveals the outsized importance
 of transient dynamics in a fluctuating environment'. The article
 investigates the assembly trajectories of communities following a
 dispersal manipulation under the background of a changing climate (from
 drought to non-drought). ## Data collection In the summer of 2013, 30
 serpentine grassland sites were chosen from the northwestern and
 southeastern ends of McLaughlin Natural Reserve in northern California.
 Each site was then divided into eight 0.75 m x 0.75 m plots that were
 separated by 1 m of bare ground and arranged in a 2 x 4 block, for a total
 of 240 plots (8 plots x 30 sites). Sites were chosen such that they could
 be hierarchically grouped at five spatial scales: at the level of a single
 plot (1 m), a block of plots at a single site (5 m), a group of sites (100
 m), half of the reserve (5 km), and the whole reserve (10 km). After the
 winter species had senesced and most of the summer annuals had set seed,
 all standing vegetation and the loose layers of the seedbank were
 harvested using garden shears and a gas-powered leaf vacuum (Stihl BG86).
 Prior to processing, the collected material was left outdoors in paper
 bags to heat stratify for approximately six weeks. In late August of 2013,
 each of the eight plots per site were randomly assigned to receive one of
 five dispersal treatments or one of three control treatments. Treatments
 plots simulated different spatial scales of dispersal, corresponding to
 our nested plot design, by pooling, homogenizing, and redistributing the
 collected material at five scales: from a single plot (1 m), multiple
 plots at a single site (5 m), five sites in a group (100 m), 15 sites
 within half of the reserve (5 km), and all 30 sites from across the entire
 reserve (10 km). As a result of the pooling manipulation, the richness and
 composition of the species pool plots received differed across treatments
 as more species were introduced as dispersal scale increased, mimicking
 the effect of natural dispersal on species pools. Control plots were then
 created as follows: “C1” was vacuumed without replacement, to identify
 species that were left behind following vacuuming, “C2” was left unaltered
 to assess for unintended effects of the seed collection procedure on
 diversity, and “C3” was vacuumed, homogenized, and redistributed to
 examine effects caused by the vacuuming procedure itself (compared to
 “C1”). ## Description of the data & file structures The datasets
 included in this repository are as follows: ### Located in data_raw 1.
 *2014_survey_RMG.csv, 2015_survey_RMG.csv, 2016_survey_RMG.csv*: community
 survey data for 2014, 2015, 2016 (including both annual and perennial
 species) 2. *species_info.csv*: list of known species that exist in the
 area and information about their growth forms, native status, and life
 history strategy.  3. *clim_decade.csv*: monthly climate data for the
 years 2014-2016 4. *disp_mode_RMG.csv*: database of species habitat
 affinities in McLaughlin Natural Reserve from *Szojka and Germain 2024.
 Dispersing across habitat boundaries: Uncovering the demographic fates of
 populations in unsuitable habitat. Ecosphere 15:e4814.*
 *[https://doi.org/10.1002/ecs2.4814](https://doi.org/10.1002/ecs2.4814)*
 ### Located in data_clean 1. *affinities_vis.csv*, *beta_vis.csv,
 c2_cover_vis.csv, count_cld.csv, count_vis.csv, cover_vis.csv,
 decomp_vis.csv, jacc_beta_vis.csv, net_rich_vis.csv, pred_burn_vis.csv,
 rate_cld.csv, rate_vis.csv, rich_cld_yr.csv, rich_cld.csv,
 rich_vis_yr.csv, rich_vis.csv, temp_beta_vis.csv,*: model outputs
 generated in *03stats.Rmd* that were used for plotting in
 *02data_vis.Rmd*, where "_*cld"* indicates dataset contains
 statistical significance letters, and *"_vis*" indicates dataset
 contains model outputs for plotting. All of these data frames can be
 generated using *03stats.Rmd*, but are included here for ease of use. ###
 Scripts *01data_clean.Rmd, 02data_vis.Rmd,* & *03stats.Rmd*: R
 markdown documents containing script for data cleaning and wrangling
 (01data_clean), figure creation (02data_vis), and statistical analyses
 (03stats) for our article. *01data_clean.Rmd* creates the primary data
 frames needed to run the statistical analyses in *03stats.Rmd* and should
 always be run first (either manually or using the source_rmd function
 found in *02data_vis.Rmd* and *03stats.Rmd*).  ## Survey Data ### Dataset
 overview: The survey data was collected twice in 2014, 2015, and 2016 at
 McLaughlin Natural Reserve in northern California, once in early spring
 (April/May) and again in late summer (August) to confirm species
 identities. Surveys were conducted at the plot level and species % cover
 recorded. Species were categorized as either edge species (negative %
 cover values) or not (positive % cover values). Each plot can be
 identified by its site location (site 1-30) and dispersal
 distance/treatment, which were originally recorded according to the
 colour-coded organization system outlined below: Dispersal treatment
 codes: Black = C1 (vacuum w/out replacement); Pink = C2 (unaltered); Blue
 = C3 (vacuum w/out movement); Green = 1m; Yellow = 5m; Orange = 100m;
 Purple = 5km; Red = 10km #### Data description: 2014_survey_RMG.csv. The
 csv file contains the following columns: **site**: identification number
 of experimental sites (1-30); **plot**: identification number of
 experimental plots located within sites (1-8); **treatment**: dispersal
 treatment assigned to plots (see colour code above); **species**:
 abbreviated code representing identified species (see 'Species
 data' for codes); **cover**: percentage of plot occupied by species
 (negative values = edge species, see above description) #### Data
 description: 2015_survey_RMG.csv. The csv file contains the following
 columns: **site**: identification number of experimental sites (1-30);
 **plot**: identification number of experimental plots located within sites
 (1-8); **treatment**: dispersal treatment assigned to plots (see colour
 code above); **species**: abbreviated code representing identified species
 (see 'Species data' for codes); **cover**: percentage of plot
 occupied by species (negative values = edge species, see above
 description); \ **dataset**: the time of year species were identified (see
 above description) #### Data description: 2016_survey_RMG.csv. The csv
 file contains the following columns: **site**: identification number of
 experimental sites (1-30); **plot**: identification number of experimental
 plots located within sites (1-8); **treatment**: dispersal treatment
 assigned to plots (see colour code above); **species**: abbreviated code
 representing identified species (see 'Species data' for codes);
 **cover**: percentage of plot occupied by species (negative values = edge
 species, see above description) ## Species Data ### Dataset overview: The
 species list was collated from a local ID book based on those observed to
 be inhabiting the reserve over the study period. Information regarding
 growth form, regional status, and family were compiled using CalFlora
 Plant Database ([www.calflora.org](http://www.calflora.org)). #### Data
 description: species_info.csv. The csv file contains the following
 columns: **colnames(species.df.pa)**: abbreviated code representing
 identified species; **growth.form**: plant life history strategy where A =
 annual & P = perennial; **latin.name**: species latin name;
 **status**: regional species status where n = native & e = exotic; \
 **family:** general plant classification where g = grass & f = forb ##
 Climate Data ### Dataset overview: Climate data was retrieved from the
 Western Regional Climate Center online database
 ([https://wrcc.dri.edu](https://wrcc.dri.edu)), accessed through the UC
 Davis natural reserves website. The climate data was collected at the RAWS
 Knoxville Creek Weather Station near the McLaughlin field station. The
 data was generated in a monthly summary time series report from January
 2012 to December 2022. #### Data description: clim_decade.csv. The csv
 file contains the following columns: **year**: calendar year; **month**:
 calendar month encoded numerically (i.e, 1 = January);
 **av_dailymax_temp_F**: average maximum daily air temperature (degrees
 Fahrenheit); **av_dailymin_temp_F**: average minimum daily air temperature
 (degrees Fahrenheit); **dailyav_temp_F**: average daily air temperature
 (degrees Fahrenheit); **precip_in**: total monthly precipitation (in) ##
 Habitat affinities ### Dataset overview: Species habitat affinities were
 assigned by Szojka and Germain (2024) using a 7-year historical dataset of
 species' cover in serpentine and non-serpentine sites at McLaughlin
 Natural Reserve (80 sites total, courtesy of S. Harrison). For more
 information on how habitat affinities were assigned, see 'Assignment
 of species affinities' in the Supplementary Information associated
 with our article. Please contact S. Harrison with inquires about the raw
 dataset that was used to construct species habitat affinities.  #### Data
 description: disp_mode_RMG.csv. The csv file contains the following
 columns: **species**: abbreviated code representing identified species; \
 **status_sh**: habitat assignment where m = matrix (non-serpentine), p =
 patch (serpentine), g = generalist (both serpentine & non-serpentine),
 and r = rare (habitat unassigned) --- The raw data files have all been
 cleaned and wrangled to create the data frames used for generating the
 figures and statistical analyses in our article 'Experimentally
 enhancing dispersal reveals the outsized importance of transient dynamics
 in a fluctuating environment' (see *01data_clean.Rmd*). All figures
 for publication can be found in *02data_vis.Rmd*, which requires all raw
 data files, cleaned data files, and 01data_clean to run successfully.
 Note: all plots generated for publication in 02data_vis were tidied for
 visual clarity and aesthetics **only** (e.g., orientation and placement of
 plots/legends/statistical significance indicators, addition of cartoon
 icons, etc.) using Affinity Designer. Full descriptions of data frame
 structures for those used in each analysis are given in *03stats.Rmd*. To
 run the code in *03stats.Rmd*, all raw data files and *01data_clean.Rmd*
 are required.