DOI: 10.5061/dryad.z8w9ghxmk
title: Return of diversity: wetland plant community recovery following purple loosestrife biocontrol

description: Spread of non-native species can be important drivers of widespread
 biodiversity declines, which often leads to precautionary management based
 on assumptions that (1) introduced biota have negative impacts and are
 therefore “guilty” of causing harm, and (2) reducing an introduced
 species’ abundance will reduce these negative impacts, in turn, benefiting
 native species. However, we frequently lack data to gauge both the
 negative impacts of introduced species and the success or failure of
 chosen management interventions. Addressing these knowledge gaps is
 critical to improving management outcomes for native species while
 maintaining public trust to sustain funding of management activities.
 Here, we investigated the response of Lythrum salicaria (purple
 loosestrife) and associated plant communities to the implementation of
 biological control in more than 10 wetland sites in New York State for up
 to 28 years. Introduced to North America from Europe in the 1800s, L.
 salicaria is a prime example of an introduced species with a
 continent-wide distribution that could not be suppressed by mechanical and
 chemical treatments. In the 1980s, waterfowl biologists, wetland managers,
 and conservationists alike worried about the loss of diverse wetland plant
 communities associated with the rapid expansion of L. salicaria.
 In response, after careful assessments of safety and potential costs and
 benefits, four highly host-specific insect herbivores were released in
 North America in the early 1990s to reduce L. salicaria abundance and its
 negative ecological impacts. In a companion paper (Blossey et al. 2024),
 we documented reduced L. salicaria occupancy and stem densities following
 insect releases over time (i.e., biological success), irrespective of
 site-specific differences in starting plant communities or L. salicaria
 abundance. Here, we show that reduced abundance of L. salicaria
 leads to the ultimate goal of introduced plant management: increased
 cover, abundance, and diversity of species, often of native species (i.e.,
 ecological success). We also conduct analyses to provide inference about
 which plant species are most sensitive to L. salicaria, including changes
 in L. salicaria stem density. Overall, we provide an important
 conservation success story: our findings emphasize that biocontrol of
 introduced plants can be effective and safe, allowing native species to
 recover as a dominant non-native species gradually declines.
description: Data collection methods are described in the main text of our
 associated manuscript. They were entered and formatted in Excel, as well
 as using RStudio.
description: # Return of diversity: Wetland plant community recovery following purple
 loosestrife biocontrol
 [https://doi.org/10.5061/dryad.z8w9ghxmk](https://doi.org/10.5061/dryad.z8w9ghxmk) Here, we investigated the response of *Lythrum salicaria* (purple loosestrife) and associated plant communities to the implementation of biological control in more than 10 wetland sites in New York State for up to 28 years. We initially visited 33 sites annually in early September to record *L. salicaria* stem density and cover (%). We also recorded presence and estimated cover (%) for all co-occurring plant species in each quadrat in 16 cover categories (midpoints: 0.01, 0.5, 1, 3, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 95, and 100%) at all Hudson River Valley, Eastern Lake Ontario and Western New York sites (n=14) in all years and at Montezuma sites (n=19) in 2019 only. The same individual (VN) recorded all vegetation data at all sites and years. Depending on insect releases, we repeated data collection for variable time periods at each site between 1996 and 2009 and again at all 33 sites in August and September 2019. ## Description of the data and file structure Data are uploaded as csv files. The associated R script files explain how to use this data to reproduce results within our associated publication. Some additional notes: * The rbDBA.visualization also includes code using the mvabund, as described in the main text * Two data files are syntheses of model outputs used for downstream analyses (subset.cover.measures.csv and cooccur_2019_top_invaders.csv); Although the code is provided for extracting these values, it also involves some post-processing checking and formatting in Excel * Additional codes and synthesis data files from the supplement can be made available upon request ## Column Descriptions by csv File ### final.diversity.metrics.csv * area - region of state where site was located (overall, we sampled four regions: 'hudson' [Hudson River Valley, NY], 'mont' [Montezuma, NY], 'tnc' [Western New York sites under stewardship of The Nature Conservancy], and 'west' [Western Lake Ontario sites in NY]; this subset dataset only does not include data from Montezuma, NY, as we only collected plant community data in 2019 at Montezuma—not through time) * site - name of sampled site (i.e., unique site identifier) * trt - which insects were intentionally released as part of the purple loosestrife biocontrol program (four treatments: control = no insects were released, gal = only *Galerucella* sp. were released, gal.hyl = both *Galerucella* sp. and *Hylobius transversovittatus* were released, gal.hyl.nan = *Galerucella* sp., *Hylobius transversovittatus*, and *Nanophyes marmoratus* were all released [note: this only applies to one site], hyl = only *Hylobius transversovittatus* were released) * quad - unique, within-in site identifier for each permanent 1 m^2 quadrat * year - year data was collected - year.of.release - year insects were first released at the site * num.years.after.release - number of years at time of data collection after the first insects were released at the site (referred to as 'time' within the manuscript) * Columns 8 through 240 (H through IF when opened in Excel) represent the percent cover of specific species (0%, 0.01%, 0.2%, 0.3%, 0.5%, 1%, 2%, 3%, 5%, and then 5% increments thereafter). Note: the column names for each of these columns are the abbreviated species codes for the species in question. The key to each of the species’ codes (which also includes more information about each species) can be found in the “Species_List” Excel file. * sum.total – sum of each percent cover within individual 1 m^2-quadrats estimated for each plant species, excluding *Lythrum salicaria* (note: sum may exceed 100) * sum.nat - sum of each percent cover estimated within individual 1 m^2-quadrats for each native plant species (note: sum may exceed 100) * sum.no.invas - sum of each percent cover estimated within individual 1 m^2-quadrats for all species except for invasive plant species (notes: sum may exceed 100; did not use in analyses) * sum.forb - sum of each percent cover estimated within individual 1 m^2-quadrats for each forb species, excluding *Lythrum salicaria* (notes: sum may exceed 100; did not use in analyses) * sum.gram - sum of each percent cover estimated within individual 1 m^2-quadrats for each graminoid species (notes: sum may exceed 100; did not use in analyses) * sum.woody - sum of each percent cover estimated within individual 1 m^2-quadrats for each woody species (notes: sum may exceed 100; did not use in analyses) * sum.perennial - sum of each percent cover estimated within individual 1 m^2-quadrats for each perennial species, excluding *L. salicaria* (notes: sum may exceed 100; did not use in analyses) * mean.total - mean of each percent cover estimated within individual 1 m^2-quadrats for each plant species, excluding *Lythrum salicaria* (notes: sum may exceed 100; did not use in analyses) * mean.nat - mean of each percent cover estimated within individual 1 m^2-quadrats for each native plant species (notes: sum may exceed 100; did not use in analyses) * mean.no.invas - mean of each percent cover estimated within individual 1 m^2-quadrats for all species except for invasive plant species (notes: sum may exceed 100; did not use in analyses) * mean.forb - mean of each percent cover estimated within individual 1 m^2-quadrats for each forb species, excluding *Lythrum salicaria* (notes: sum may exceed 100; did not use in analyses) * mean.gram - mean of each percent cover estimated within individual 1 m^2-quadrats for each graminoid species (notes: sum may exceed 100; did not use in analyses) * mean.woody - mean of each percent cover estimated within individual 1 m^2-quadrats for each woody species (notes: sum may exceed 100; did not use in analyses) * mean.perennial - mean of each percent cover estimated within individual 1 m^2-quadrats for each perennial species, excluding *L. salicaria* (notes: sum may exceed 100; did not use in analyses) * rich.nat - # of native plant species within each 1 m^2-quadrat * rich.no.invas - # of plant species within each 1 m^2-quadrat, excluding invasive species (note: did not use in the analyses) * rich.total - # of all plant species within each 1 m^2-quadrat * rich.forb - # of forb species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in the analyses) * rich.gram - # of graminoid species within each 1 m^2-quadrat (note: did not use in the analyses) * rich.woody - # of woody species within each 1 m^2-quadrat (note: did not use in the analyses) * rich.annual - # of annual species within each 1 m^2-quadrat (note: did not use in the analyses) * rich.perennial - # of perennial species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in the analyses) * shannon.nat – Shannon diversity index of only native plant species within each 1 m^2-quadrat * shannon.no.invas - Shannon diversity index of all plant species excluding invasive species within each 1 m^2-quadrat (note: did not use in analyses) * shannon.total - Shannon diversity index of all plant species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * shannon.forb - Shannon diversity index of all forb species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * shannon.gram - Shannon diversity index of all graminoid species within each 1 m^2-quadrat (note: did not use in analyses) * shannon.woody - Shannon diversity index of all woody species within each 1 m^2-quadrat (note: did not use in analyses) * shannon.annual - Shannon diversity index of all annual species within each 1 m^2-quadrat (note: did not use in analyses) * shannon.perennial - Shannon diversity index of all perennial species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * simpson.nat - Simpson diversity index of only native plant species within each 1 m^2-quadrat (note: did not use in analyses) * simpson.no.invas - Simpson diversity index of all plant species excluding invasive species within each 1 m^2-quadrat (note: did not use in analyses) * simpson.total - Simpson diversity index of all plant species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * simpson.forb - Simpson diversity index of all forb species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * simpson.gram - Simpson diversity index of all graminoid species within each 1 m^2-quadrat (note: did not use in analyses) * simpson.woody - Simpson diversity index of all woody species within each 1 m^2-quadrat (note: did not use in analyses) * simpson.annual - Simpson diversity index of all annual species within each 1 m^2-quadrat (note: did not use in analyses) * simpson.perennial - Simpson diversity index of all perennial species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * pl.cover – estimated percent cover of *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * pl.density - # of *L. salicaria* stems within each 1 m^2-quadrat * latitude - latitude of site in decimal degrees * longitude – longitude of site in decimal degrees ### subset.cover.measures.csv Note: this file has many shared column names and descriptions with final.diversity.metrics.csv—the difference is that this dataset is reduced to include only the first and last sampling period for sites used in the manyglm models. Please see above for more information about shared column descriptions. Column names that differ are described in more detail below. * time.diff - # of years between first and last sampling time at each site * Columns 9 through 247 (I through IM when opened in Excel) represent the percent cover of specific species (0%, 0.01%, 0.2%, 0.3%, 0.5%, 1%, 2%, 3%, 5%, and then 5% increments thereafter). Note: the column names for each of these columns are the abbreviated species codes for the species in question. The key to each of the species’ codes (which also includes more information about each species) can be found in the “Species_List” Excel file. * piel.nat – Pielou index of only native plant species within each 1 m^2-quadrat (note: did not use in analyses) * piel.total - Pielou index of all plant species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * piel.forb - Pielou index of all forb species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * piel.gram - Pielou index of all graminoid species within each 1 m^2-quadrat (note: did not use in analyses) * peil.woody - Pielou index of all woody species within each 1 m^2-quadrat (note: did not use in analyses) * peil.annual - Pielou index of all annual species within each 1 m^2-quadrat (note: did not use in analyses) * piel.perennial - Pielou index of all perennial species excluding *L. salicaria* within each 1 m^2-quadrat (note: did not use in analyses) * LYTSAL – same as pl.cover column ### Cooccur\_2019\_top\_invaders.csv * row – the species code for one of the top three common invasive plant species found across our sites (three levels: LYTSAL [code for “*Lythrum salicaria*”], PHAARU [code for “*Phalaris arundinacea*”], and TYPANG [code for “*Typha angustifolia*”]) * col – the species code for the species ‘pair’ that the invasive plant in the ‘row’ column is being compared to. The key to each of the species’ codes (which also includes more information about each species) can be found in the “Species_List” Excel file. * value – standardized effect size of the pairwise interaction between the species listed in the ‘row’ and the ‘col’ columns when data are fit to a probabilistic model of species co-occurrence using the cooccur package in R (see associated manuscript for more detail) * site - name of sampled site (i.e., unique site identifier) * year - year data was collected * col.species.native – the status of the species in the ‘col’ column (0=non-native, 1=native, blank means that the status was unknown) * area - region of state where site was located (overall, we sampled four regions: 'hudson' [Hudson River Valley, NY], 'mont' [Montezuma, NY], 'tnc' [Western New York sites under stewardship of The Nature Conservancy], and 'west' [Western Lake Ontario sites in NY]) * trt - which insects were intentionally released as part of the purple loosestrife biocontrol program (four treatments: control = no insects were released, gal = only *Galerucella* sp. were released, gal.hyl = both *Galerucella* sp. and *Hylobius transversovittatus* were released, gal.hyl.nan = *Galerucella* sp., *Hylobius transversovittatus*, and *Nanophyes marmoratus* were all released [note: this only applies to one site], hyl = only *Hylobius transversovittatus* were released) * num.years.after.release - number of years at time of data collection after the first insects were released at the site (referred to as 'time' within the manuscript) * latitude - latitude of site in decimal degrees * longitude – longitude of site in decimal degrees * mean(pl.density) – the mean density of *L. salicaria* within the site ### formatted.quadxsp.final.csv * original.row.num – the original order of the data in the associated original unformatted csv file * area - region of state where site was located (overall, we sampled four regions: 'hudson' [Hudson River Valley, NY], 'mont' [Montezuma, NY], 'tnc' [Western New York sites under stewardship of The Nature Conservancy], and 'west' [Western Lake Ontario sites in NY]) * site - name of sampled site (i.e., unique site identifier) * trt - which insects were intentionally released as part of the purple loosestrife biocontrol program (four treatments: control = no insects were released, gal = only *Galerucella* sp. were released, gal.hyl = both *Galerucella* sp. and *Hylobius transversovittatus* were released, gal.hyl.nan = *Galerucella* sp., *Hylobius transversovittatus*, and *Nanophyes marmoratus* were all released [note: this only applies to one site], hyl = only *Hylobius transversovittatus* were released) * quad - unique, within-in site identifier for each permanent 1 m^2 quadrat * year - year data was collected * year.of.release - year insects were first released at the site - num.years.after.release - number of years at time of data collection after the first insects were released at the site (referred to as 'time' within the manuscript) - Columns 9 through 242 (I through IH when opened in Excel) represent the percent cover of specific species (0%, 0.01%, 0.2%, 0.3%, 0.5%, 1%, 2%, 3%, 5%, and then 5% increments thereafter). Note: the column names for each of these columns are the abbreviated species codes for the species in question. The key to each of the species’ codes (which also includes more information about each species) can be found in the “Species_List” Excel file ### manyglm\_test\_statistics\_output.csv * species.id - the unique species code for the species in question. The key to each of the species’ codes (which also includes more information about each species) can be found in the “Species_List” Excel file * log.pl.density – the log-transformed stem density of *L. salicaria* within 1 m^2-quadrats that was used as a predictor variable within the final manyglm model. * %.dev.density - the percent of the deviance for just the predictor of *L. salicaria* stem density in the final manyglm model that was explained by the species listed in this row for ‘species.id’. Note: sum of all %.dev.density values are ~100. * time – the number of years at the time of data collection after the first insects were released at the site (note: this was used as a predictor variable within the final manyglm model) * %.dev.time - the percent of the deviance for just the predictor of time in the final manyglm model that was explained by the species listed in this row for ‘species.id’. Note: sum of all %.dev.time values are ~100. * time.diff - # of years between first and last sampling time at each site (note: this was used as a predictor variable within the final manyglm model) * %.dev.time.diff - the percent of the deviance for just the predictor of “time.diff” in the final manyglm model that was explained by the species listed in this row for ‘species.id’. Note: sum of all %.dev.time.diff values is ~100. * site - name of sampled site (i.e., unique site identifier) * %.dev.site - the percent of the deviance for just the predictor of “site” in the final manyglm model that was explained by the species listed in this row for ‘species.id’. Note: sum of all %.dev.site values are ~100. * time:time.diff – the interaction between time and time.diff (note: this was used as a predictor variable within the final manyglm model). * %.dev.time:time.dev - the percent of the deviance for just the predictor of the interactive effect of “time:time.diff” in the final manyglm model that was explained by the species listed in this row for ‘species.id’. Note: sum of all %.dev.time:time.dev values are ~100. * total.deviance - the deviance for the entire univariate model for the species listed in this row for “species.id”. * %.total.deviance – the percent of the total multivariate model deviance (~100%—calculated as the percentage of the sum of all model deviances across all univariate species models) for the species listed in this row for “species.id” * species.name – full genus and species * native – binary variable describing whether the species is native (“1”) or non-native (“0”); was left blank when we were unsure of the species status * lifeform –notes on whether the plant was a forb or a graminoid (note: this was not used in the analysis) * annual – whether the plant was annual or perennial; left blank if unsure (note: this was not used in the analysis) * state.rank – State conservation status ranks (S ranks) communicate the rarity of the species in the state using a numeric index (1-5), where 1 denotes species that are exceptionally rare (note: this was not used in the analysis). Full explanations of the legal ranks can be found at [http://explorer.natureserve.org/](http://explorer.natureserve.org/) * global.rank - Global conservation status ranks (S ranks) communicate the rarity of the species throughout its global range using a numeric index (1-5), where 1 denotes species that are exceptionally rare (note: this was not used in the analysis). Full explanations of the legal ranks can be found at [http://explorer.natureserve.org/](http://explorer.natureserve.org/) * cleaned.species.name – shortened species names to improve readability for graphing ### Species\_List.xlsx * species.name - full genus and species * species.id - unique species code for the species * native – binary variable describing whether the species is native (“1”) or non-native (“0”); was left blank when we were unsure of the species status * lifeform –notes on whether the plant was a forb or a graminoid (note: this was not used in the analysis) * lifecycle - whether the plant was annual or perennial; left blank if unsure (note: this was not used in the analysis) * state.rank – State conservation status ranks (S ranks) communicate the rarity of the species in the state using a numeric index (1-5), where 1 denotes species that are exceptionally rare (note: this was not used in the analysis). Full explanations of the legal ranks can be found at [http://explorer.natureserve.org/](http://explorer.natureserve.org/) * global.rank - Global conservation status ranks (S ranks) communicate the rarity of the species throughout its global range using a numeric index (1-5), where 1 denotes species that are exceptionally rare (note: this was not used in the analysis). Full explanations of the legal ranks can be found at [http://explorer.natureserve.org/](http://explorer.natureserve.org/) ## Code/Software We used Excel and RStudio to enter, process, and visualize our results.