DOI: 10.5061/dryad.r4xgxd2qc
title: Data from: Seed dormancy explains plant response to mass mortality events

description: Mass mortality events (MMEs) are large-scale, rapid die-offs resulting in
 extreme inputs of carrion biomass. Recent work demonstrates the effects of
 increasing carrion biomass on plant communities modulated by vertebrate
 scavengers and herbivores. However, the mechanisms underlying plant
 response to MMEs remain unclear. We hypothesized that carrion
 decomposition would interact with vertebrate herbivory and scavenging to
 generate distinct ecological filters on plants grouped by three seed
 dormancy classes (no dormancy, physiological dormancy, and physical
 dormancy). We designed a replicated field experiment crossing two levels
 of carrion biomass (~30 kg and ~360 kg) with three levels of vertebrate
 exclusion (open/no exclusion, scavenger exclusion, and herbivore
 exclusion) to quantify plant extirpation and colonization, plant
 performance, and the response of simulated seed bank and seed rain. We
 measured carrion decomposition rate, plant tissue nutrients (N, P, and K),
 seed survival, plant height, flower production, and plant community
 changes over 3 years. Carrion biomass levels associated with mass
 mortality increased plant tissue nutrients and plant extirpation and
 decreased seed bank survival, likely promoting plant colonization from
 seed rain. Vertebrate exclusion determined colonization probability in
 different ways, depending on seed dormancy classes. Vertebrate scavenger
 exclusion delayed decomposition, and the resulting environment favored the
 colonization of plants with impermeable seed coats (physical dormancy). In
 contrast, vertebrate herbivore exclusion promoted rapid germinators (no
 dormancy) that arrived as seed rain and quickly capitalized on the
 nutrient-rich exposed soil. With both functional roles intact (open/no
 exclusion), vertebrate scavenging ameliorated the negative effects of
 decomposition on seeds and plants, and selective herbivory on
 nutrient-rich plant tissue reduced overall plant height and flower
 production. The activity of both functional roles favored plants of the
 dominant physiological seed dormancy class and those with physical
 dormancy. Our results suggest that seed response to carrion decomposition
 and vertebrate functional activity can inform plant community response to
 MMEs.
description: <strong>Materials
 and Methods</strong> <strong>Replication statement</strong> We conducted simulated mass mortality events of herbivores and scavengers by crossing exclusion and carrion biomass treatments. Several response variables related to vertebrate and vegetation response enabled measurement of these treatments. To facilitate the interpretation of replication and scale, we present these response variables in the context of scale of inference, scale of treatment, and number of appropriate replicates. Response variable Scale of inference Scale at which factor of interest is applied Number of replicates at the appropriate scale Response of vertebrate herbivores (# of observations) Plot (70 m<sup>2</sup>) Plot (70 m<sup>2</sup>) 4, 4 blocks with a 3x2 factorial design (n = 6) + 1 reference plot (6 treatment plots, 1 reference plot); block is the level of replication Response of vertebrate scavengers (# of observations) Carrion decomposition rate Plant colonization (binary 0/1) Plant extirpation (binary 0/1) Plant tissue nutrients (effect size) Seed survival (binary 0/1, effect size calculated by comparing to reference plot) Microsite Plot (70 m<sup>2</sup>) 4, 4 blocks with a 2x2 factorial design (n =4) nested within 3x2 factorial design (n = 24) + 2 packets per reference plot (6 treatment plots, 1 reference plot); block is the level of replication Plant reproduction (# of flowers) Plant Plot 13, 26 total plants (opportunistic design does not account for location of plants in different clusters/plots) Overview and Design <em>Location</em> We conducted this experiment on Oswalt Ranch, a managed rangeland (i.e., a mix of mostly native grasses, shrubs, and trees along riparian corridors) owned by Noble Research Institute (NRI) that is underlain by poorly drained and shallow soils (34°11'8.75" N, 97°5'12.42" W). Oswalt Ranch is in a humid subtropical region of southcentral Oklahoma with average temperatures of ~17 C° and average rainfall of ~870 mm (1981–2010; Oklahoma Climatological Survey, 2022). Plants on site with no seed dormancy are often annual species; plants with physical dormancy include legumes (Fabaceae), bindweeds (Convolvulaceae), and animal-dispersed seeds that require gut scarification; and most of the remaining plant species, including native and improved pasture grasses (Poaceae), are often physiologically dormant (Supplemental materials 1). White-tailed deer (<em>Odocoileus virginianus</em>) are common herbivores. Black vultures (<em>Coragyps atratus</em>), turkey vultures (<em>Cathartes aura</em>), and coyotes (<em>Canis latrans</em>) are dominant scavengers. Non-native and domesticated vertebrates include wild pigs (<em>Sus scrofa</em>) and cattle (<em>Bos taurus</em>). Noble Research Institute staff culled wild pigs to protect native ecosystems and property (Gaskamp <em>et al.</em>, 2021). After a scheduled culling event, they deployed the resultant carcasses that we monitored for our experiment. Given that this culling event occurred distinct from our experiment, we did not require IACUC approval. In addition, we required no permit to conduct research on this private land. <em>Experimental design</em> NRI staff constructed four blocks (0.5 ha) spaced at least 750 m apart. Each block consisted of six plots randomly assigned a combined treatment based on two factors: biomass (single or mass mortality) and exclusion (open, scavenger, and herbivore; Figure 1A). Outside of each block, we also constructed a fenced reference plot (i.e., no carrion and no herbivory) for baseline plant tissue nutrient and seed survival measurements. We did not use netting to restrict avian access to reference plots. MME simulation plots contained ~12 times the biomass (~360 kg) as plots simulating background mortality (~30 kg). This biomass density does not approach that of some natural MMEs and experiments (e.g., 36 kg per m<sup>2</sup>; Steyaert <em>et al</em>., 2018; Baruzzi <em>et al.,</em> 2022<sup>a</sup>) and thus likely represents a conservative biomass density. However, we had almost 1,200 kg of biomass in each block with this density of biomass (~7 kg per m<sup>2</sup>, ~50 carcasses per block), which is difficult to accomplish with simulated MMEs (Lashley <em>et al.</em>, 2018; Fey <em>et al.</em>, 2019). We simulated MMEs of vertebrate herbivores and scavengers using carcasses with exclusion fencing and netting deployed in two phases, where each phase aligned with the period when the functional role exerts influence on the ecosystem. Beginning with carrion deployment (2019-04-15), we installed cages topped with netting around scavenger exclusion plots, leaving all other plots open. After active decomposition (2019-05-05), we removed the cages from the scavenger exclusion plots and established fencing in the herbivore exclusion plots to exclude vertebrate herbivores from the plots during plant recovery. The cages remained on herbivore exclusion plots for more than three years after carrion deployment until the conclusion of the sampling period (2021-07-18). Because this site actively grazes cattle in pastures, NRI employees also installed a two-strand polywire electric fence to exclude cattle from the entire block while still allowing vertebrate wildlife to enter the block (Figure 1A). <em>Software and analysis</em> All analyses conducted in R studio version 4.2 (R Core Team, 2023). We cleaned and visualized using the tidyverse package (Wickham <em>et al.</em>, 2019). Linear model structures are guided by experimental design and hypotheses rather than model selection. In some cases, complexity was reduced for model convergence. We visualized the distributions of data prior to selecting a distribution and assessed model assumptions using statistical tests and visualizations of normality, outliers, independence, and homoscedasticity using the DHARMa package (Hartig, 2021). Unless otherwise noted, we present estimated marginal means and effect sizes from emmeans, which corrects for multiple comparisons using the Tukey method (Lenth, 2022). For models with interaction terms, we conducted type 3 analyses using the Anova function from the car package (Fox & Weisberg, 2019) Measuring Ecosystem Response to Carrion  1.1 Measuring response of vertebrate functional roles We measured vertebrate activity in the plots to (1) determine the effect of carrion biomass on herbivore and scavenger activity and (2) ensure the efficacy of the exclusion efforts on functional role suppression. At each plot, we mounted a camera (Bushnell Trophy Cam HD; Bushnell Outdoor Products, Overland Park, KS) ~1 m from the plot edge facing the same cardinal direction (Figure 1B) with the following settings: high sensitivity, 5-minute delay, 15-second video. We deployed cameras 3 days prior to carrion deployment and retrieved them after the first year of the experiment. Our measure of activity results from counting all individual vertebrates in each video (i.e., the same individual animal in consecutive videos would count as two observations. 1.2 <em>Response of vertebrate functional roles analysis</em> After processing the camera trap data, we grouped vertebrate observations (counts) into scavengers (obligate and facultative), herbivores, and other animals. Then, we analyzed total scavenger and herbivore observations during active decomposition (2019-04-15–2019-05-05) and plant recovery (2019-05-05–2019-10-06). We used the MASS package to conduct a generalized linear model with a negative binomial distribution for total scavenger observations during the active decomposition period (Venables & Ripley, 2002) and base R to conduct Poisson regression for total herbivore observations during the plant recovery period (R Core Team, 2023). These models would not converge with any degree of complexity. Both models thus include only treatment (carrion biomass and vertebrate exclusion combined) and site as predictor variables. <em>2.1 Measuring carrion decomposition rate</em> We photographed carcasses each day in the week following deployment, for another three times in 3-day intervals, and once more 7 weeks later (n = 11). In MME treatments, we randomly selected three carcasses during each sampling event. We analyzed pictures using the Total Body Score method (<em>sensu</em> Keough <em>et al</em>., 2017). <em>2.2 Carrion decomposition rate analysis</em> We used the glmer function from the lme4 package to conduct two general mixed effects models evaluating the number of days elapsed before a carcass entered advanced and skeletal decomposition stage (Bates <em>et al.</em>, 2015). We used biomass and functional impairment as fixed effects and block as a random effect (i.e., intercept). <em>3.1 Nested seed survival experiment</em> We crossed timing of seed arrival (seed bank or seed rain) with location (carrion contact or 0.5 m from carrion) by placing a single sealed pouch in each position (10 x 10 cm, 1 mm mesh screening). We placed pouches simulating seed rain on top of carrion or on top of the soil and simulated seed bank pouches beneath the soil (Figure 1C). In both cases, we affixed a metal wire to the pouch and a pole at the center of the plot to prevent removal and enable rediscovery. Having no carrion, the reference plot did not need the distance comparison used in single carrion and MME plots and received only two pouches (seed rain and seed bank). Each block received a unique set of random species belonging to one of three functional roles (Table 1), and the number of seeds inside the pouch varied by species due to seed size and availability (Figure 1D).    <strong>Table 1. Simplified classes reflect the commonly encountered types of seed dormancy.</strong> <strong>Physical dormancy</strong> <strong>Physiological dormancy</strong> <strong>No dormancy</strong> <em>Malva sylvestris</em>  <em>Triticum aestivum</em> <em>Sinapsis alba</em> <em>Rhus glabra</em> <em>Syringa</em> spp. <em>Beta vulgaris</em> <em>Bixa orella</em> <em>Hordeum vulgare</em> <em>Pisum sativum</em> <em>Glycine max</em> <em>Capsicum annum</em> <em>Pinus sylvestris</em>  We deployed 2,258 seeds from 12 distinct species 1 day after carrion deployment. Then, we collected the pouches 21 days after deployment and recorded the number of seeds recovered, perished, and survived (including living germinated seeds). We recovered 84% of the seeds. After this initial assessment, we attempted to germinate any remaining uncategorized seeds (70% of recovered seeds) to evaluate viability (e.g., perished or surviving). Seeds with no dormancy germinated with moisture exposure; seeds with physiological dormancy required stratification before moisture exposure; and seeds with physical dormancy required scarification and stratification before moisture exposure (Baskin & Baskin, 2004). We repeated this process three times on the remaining potentially dormant seeds. A small subset of seeds remained undetermined (~1%). <em>3.1 Nested Seed Survival Experiment analysis</em> We constructed a binomial generalized linear model with a binomial distribution using the number of surviving or perished seeds out of total seeds in each packet as a response variable (i.e., the number of successes and failures out of total trials) with the glmer function from the lme4 package (Bates <em>et al.</em>, 2015). The predictor variables for the model included carrion biomass, exclusion treatment, timing (seed bank or seed rain), location (carrion contact or 1 m from carrion), and seed dormancy class, with block as a random effect. Our observations (n = 276) did not permit a full interactive model, so we included the interactions that best represented our hypotheses regarding the differential responses of seed dormancy classes to MMEs and the response of seed banks and seed rain to carrion decomposition. Seed survival ~ Carrion biomass * Exclusion treatment * Dormancy class + Dormancy class * Timing * Carrion biomass + Location + (1| Block) We did not include reference plots in this model but separately estimated the MLE of survival probability as a baseline to visualize the results. Then, we calculated the difference in survival compared to the baseline at each block and summarized the mean odds ratio for each treatment. Then, we further summarized these means across groupings of treatments (i.e., mean for all seed bank treatments): <em>4.1 Measuring extirpation and colonization of seed dormancy classes</em> We sampled vegetation before carrion deployment (2019-03-17), each month during the initial growing season (2019-04-21, 2019-05-05, 2019-06-02, 2019-07-21), and once in each of the following 2 years (2020-07-20, 2021-07-18) using the point-intercept method at 1 m intervals for 4 m in each cardinal direction. At each point, we marked the presence of species (i.e., multiple species may occur at each point but not multiple individuals belonging to a single species). We also recorded bare ground, litter, dead plants, and carrion. For each plot and sampling date, we calculated the cover value in the resulting community matrix for each species by dividing the number of observed points by the total possible points (16 total points per plot). Then, we classified the surveyed plants according to seed dormancy using Baskin & Baskin’s (1998) seed dormancy database and published literature (Supplemental materials 1). <em>4.1 Extirpation and colonization of seed dormancy classes analysis</em> We converted the plant community time series into two datasets describing the probability that individual plants belonging to seed dormancy classes (1) vanished from transect points after the initial surveys or (2) colonized transect points after the experiment. Colonization or extirpation thus refers to an individual point, and we make no effort to confirm absence or presence across the transect or plot. This approach also makes a key assumption that whether we detected a species indicates the actual presence or absence of a species at the transect point. For the extirpation model, we subsetted the data into transect points with species belonging to physiological dormancy in the survey before carrion decomposition. Then, we determined whether absences of physiological dormancy occurred at that point to represent extirpation. We only used physiological dormancy for this model because nearly all individuals present during the initial pre-treatment survey (2019-03-17) belonged to this dormancy class. For the colonization model, we tracked each transect point and recorded any time a dormancy class absent during the initial pre-treatment survey colonized by the final sampling period (2021-07-18), again resulting in a binary response variable for colonization. We used the glm function to conduct binomial generalized linear models analyzing extirpation with treatment as a predictor and colonization with dormancy class and treatment as interactive predictors (R Core Team, 2023). We did not include further complexity, including block as a predictor, due to convergence issues. <em>5.1 Plant tissue sampling</em> We randomly collected aboveground tissues from similar plant morphotypes in each block to meet biomass requirements. The Mississippi State University Soil Laboratory (Starkville, MS, USA) conducted plant tissue analysis. We focused on three essential plant macronutrients that (A) leach from carcasses and (B) may affect plant selection in white-tailed deer: nitrogen, phosphorous, and potassium (Barton <em>et al</em>., 2013a; Dykes <em>et al</em>., 2018). <em>5.2 Plant tissue analysis</em> We analyzed plant tissue nutrients using the adonis function from the vegan package to conduct a permutation-based multivariate ANOVA (Oksanen <em>et al.</em>, 2022). The model included treatment and date as interactive predictor variables, block as a random effect, and Hellinger-transformed (e.g., standardized) macronutrient values for the response variable. To visualize the effects of biomass and exclusion on nutrients, we calculated the log ratio of treatments compared to reference plots as an effect size: <em>6.1 Opportunistic Plant Fitness Sampling</em> We developed an opportunistic sampling regime (stratified random selection) upon visually observing dramatic increases in plant fitness correlates in simulated herbivore MMEs (Younginger <em>et al.</em>, 2017). During the final year of the experiment (2021-07-18), we measured the height and inflorescences of a dominant annual or biennial plant (<em>Lactuca serriola</em>) on individuals evenly distributed within and outside herbivore MME plots (n = 26). To analyze the opportunistic measurement of plant performance metrics, we conducted separate Welch’s t-tests using base R to determine the effects of treatment on height and inflorescences (R Core Team, 2023).
description: # Data from: Seed dormancy explains plant response to mass mortality
 events **Authors**: David S. Mason, Abby K. Jones, Brandon T. Barton, Mike
 Proctor, Stephen L. Webb, & Marcus A. Lashley **Corresponding
 Author**: [David Mason;
 [david.mason@jonesctr.org](mailto:david.mason@jonesctr.org)] **Manuscript
 Status**: In Press --- ## Description This data package accompanies the
 manuscript *Seed dormancy explains plant response to mass mortality
 events*, which investigates how seed traits mediate plant community
 responses following vertebrate mass mortality events. The study integrates
 data on plant traits and fitness, seed survival, and vertebrate herbivory,
 scavenging to understand indirect effects of carrion on plant communities.
 **Keywords**: carrion, decomposition, seed bank, seed rain, scavengers,
 herbivores, indirect effects, disturbance, community assembly --- ## Clean
 Data Files | File Name | Description | | :------------------------------ |
 :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Camera-traps.csv | Data from game camera videos of vertebrate scavengers and herbivores (detections) | | Carrion-decay-rate.csv | Time series of carrion decomposition stage assessed via photography  | | Dormancy-class-colonization.csv | Colonization probability for dormancy classes | | Dormancy-class-extirpation.csv | Extirpation probability for dominant physiological dormancy class | | Plant-fitness-indicators.csv | Indicators of plant fitness (height, inflorescences) | | Plant-tissue-nutrients.csv | Nutrient concentrations in plant tissue samples | | Seed-dormancy-db.csv | Seed dormancy classifications derived from the [database](https://docs.google.com/spreadsheets/d/e/2PACX-1vQT6PoytQP3NP5RyoMb3zSXxoMmNj6rdkkyTv5CjE-jdqeovJJcEVr8OGND_L9P0nvYgdcepDACL8HX/pubhtml) associated with Baskin, C. C., & Baskin, J. M. (2014). *Seeds: Ecology, Biogeography, and Evolution of Dormancy and Germination* (2nd ed.). Academic Press | | Seed-survival.csv | Results from the nested seed survival experiment  | 
 
 ### Data specific information for: | Camera-traps.csv | |
 :--------------- | | 
 
 | | **Variable** | Values | Units | Explanation | | :----------- |
 :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------------------- | :--------------------------------------------------------------------------------------------------------------------------------- | | DATE | 4/12/2019–10/24/2019 | Date, Month/Day/Year | 
 
 | | TIME | 0:00–23:56 | 24-hour time, HH:MM | 
 
 | | SITE | OS, GG, DF, WP | Categorical | Experimental blocks | |
 TREATMENT | CO, CH, CS, MO, MH, MS | Categorical | 2 x 3 factorial
 treatment combining carrion biomass (Control/Low, Mass/High) and
 vertebrate exclusion (Open, Herbivore, Scavenger) | | GROUP.SIZE | 1–21 |
 Numeric | Indicates the total number of individuals belonging to the
 vertebrate species in the game camera video | | INDIVIDUAL | 1–21 |
 Numeric | Differentiates individuals within a group of a single vertebrae
 species in the game camera video | | BIOMASS | Single carcass, MME |
 Categorical | Carrion biomass treatment: single carcass is\~30 kg, MME is
 multiple carcasses (\~360 kg) | | EXCLUSION | Open, Herbivore, Scavenger |
 Categorical | Vertebrate exclusion treatment | | COMMON.NAME | American
 crow, Belted Kingfisher, Black vulture, Bobcat, Cattle, Cottontail rabbit,
 Coyote, Dog, Greater roadrunner, Nine-banded armadillo, Raccoon,
 Researcher, Scissor-tailed flycatcher, Striped skunk, Turkey vulture,
 Unknown animal, Unknown bird, Unknown hawk, Unknown hummingbird, Unknown
 mammal, Unknown raptor, Unknown rodent, Unknown songbird, Unknown sparrow,
 Unknown vulture, Virginia opossum, White-tailed deer, Wild pig, Wild
 turkey | Categorical | Common name vertebrates observed in game camera
 videos | | FUNCTIONAL | Open, Herbivore, Scavenger | Categorical |
 Vertebrate exclusion treatment | | NOTE | Any additional notes regarding
 the observation | 
 
 | 
 
 | ### Data specific information for: | **Carrion-decay-rate.csv** | |
 :------------------------- | | 
 
 | | **Variable** | Values | Units | Explanation | | :----------- |
 :------------------------- | :---------- |
 :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | SITE | OS, GG, DF, WP | Categorical | Experimental blocks | | TREATMENT | CO, CH, CS, MO, MH, MS | Categorical | 2 x 3 factorial treatment combining carrion biomass (Control/Low, Mass/High) and vertebrate exclusion (Open, Herbivore, Scavenger) | | BIOMASS | Single carcass, MME | Categorical | Carrion biomass treatment: single carcass is\~30 kg, MME is multiple carcasses (\~360 kg) | | EXCLUSION | Open, Herbivore, Scavenger | Categorical | Vertebrate exclusion treatment | | DECAY.STAGE | Early, Advanced, Skeletal | Categorical | Carcass decay stage as described in: Keough, N., Myburgh, J. & Steyn, M. 2017. Scoring of decomposition: a proposed amendment to the method when using a pig model for human studies. *Journal of Forensic Sciences* ***62***(4): 986–993. | | MEAN.TBS | 4–35 | Numeric | Total body score of carcass decay as described in: Keough, N., Myburgh, J. & Steyn, M. 2017. Scoring of decomposition: a proposed amendment to the method when using a pig model for human studies. *Journal of Forensic Sciences* ***62***(4): 986–993. | | DAY.REACHED | 1–47 | Numeric | Days since carcass deployment | 
 
 ### Data specific information for: | Dormancy-class-colonization.csv | |
 :------------------------------ | | 
 
 | | **Variable** | Values | Units | Explanation | |
 :-------------------------------------------------------------------------
 | :------------------------- | :---------- |
 :--------------------------------------------------------------------------------------------------------------------------------- | | SITE | OS, GG, DF, WP | Categorical | Experimental blocks | | TREATMENT | CO, CH, CS, MO, MH, MS | Categorical | 2 x 3 factorial treatment combining carrion biomass (Control/Low, Mass/High) and vertebrate exclusion (Open, Herbivore, Scavenger) | | BIOMASS | Single carcass, MME | Categorical | Carrion biomass treatment: single carcass is\~30 kg, MME is multiple carcasses (\~360 kg) | | EXCLUSION | Open, Herbivore, Scavenger | Categorical | Vertebrate exclusion treatment | | TRANSECT | N, E, S, W | Categorical | Identifiers four vegetation transects in cardinal directions | | DISTANCE | 1-4 | Numeric | Identifiers individual 1 m transect point in each transect | | DORMANCY.CLASS | ND, PY, PD | Categorical | Simplified seed dormancy classification with no dormancy (ND), physical dormancy (PY), and physiological dormancy (PD) | | EXTIRPATED.EVER | 0,1 | Binary | Indicates whether that dormancy class was present at the transect point at the conclusion of the experiment | | 03/10/2019, 4/21/2019, 5/5/2019, 6/2/2019, 7/21/2019, 7/19/2020, 7/18/2021 | 0,1 | Binary | Indicates whether that dormancy class was present at the point at each time step | 
 
 ### Data specific information for: | Dormancy-class-extirpation.csv | |
 :----------------------------- | | 
 
 | | **Variable** | Values | Units | Explanation | |
 :-------------------------------------------------------------------------
 | :------------------------- | :---------- |
 :------------------------------------------------------------------------------------------------------------------------------------------------------------ | | SITE | OS, GG, DF, WP | Categorical | Experimental blocks | | TREATMENT | CO, CH, CS, MO, MH, MS | Categorical | 2 x 3 factorial treatment combining carrion biomass (Control/Low, Mass/High) and vertebrate exclusion (Open, Herbivore, Scavenger) | | BIOMASS | Single carcass, MME | Categorical | Carrion biomass treatment: single carcass is\~30 kg, MME is multiple carcasses (\~360 kg) | | EXCLUSION | Open, Herbivore, Scavenger | Categorical | Vertebrate exclusion treatment | | TRANSECT | N, E, S, W | Categorical | Identifiers four vegetation transects in cardinal directions | | DISTANCE | 1-4 | Numeric | Identifiers individual 1 m transect point in each transect | | DORMANCY.CLASS | PD | Categorical | Simplified seed dormancy classification with physiological dormancy (PD). Only one dormancy class was present enough at the first sampling event for analysis | | EXTIRPATED.EVER | 0,1 | Binary | Indicates whether PD was ever absent at the transect point during the experiment | | 03/10/2019, 4/21/2019, 5/5/2019, 6/2/2019, 7/21/2019, 7/19/2020, 7/18/2021 | 0,1 | Binary | Indicates whether that dormancy class was present at the point at each time step | ### Data specific information for: | **Plant-fitness.csv** | | :-------------------- | | 
 
 | | **Variable** | Values | Units | Explanation | | :----------- |
 :------------------------------------------- | :---------- |
 :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | SITE | WP-MH, OS-MH, GG-CS, GG, GG-MS, GG-MH, Gate  | Categorical | Sampling location. Most samples occurred in a block (first two letters; WP, OS, GG) and treatment (second two letters; Carrion = Control/Low, Mass/High, Vertebrate exclusion = Herbivore, Scavenger). Some samples were collected outside the blocks (gate). | | TREATMENT | Y/N | Binary | Samples were either taken from a simulated herbivore mass mortality (MH; Y) or any other location (N) | | HEIGHT | 46.4–171.8 | Numeric, cm | Height of plant measured from the soil surface to the highest point of an individual plant | | INFLOR | 33–715 | Numeric | Number of inflorescences counted on an individual plant | | NOTE | 
 
 | 
 
 | Includes an additional warning regarding the location of some
 individuals not being inside of experimental units. | ### Data specific
 information for: | Plant-tissue-nutrients.csv | |
 :------------------------- | | 
 
 | | **Variable** | Values | Units | Explanation | | :----------- |
 :----------------------------- | :------------------- |
 :---------------------------------------------------------------------------------------------------------------------------------------------- | | DATE | 8/1/2020, 5/4/2021 | Date, Month/Day/Year | 
 
 | | SITE | OS, GG, DF, WP | Categorical | Experimental blocks | | BIOMASS
 | Single carcass, MME, reference | Categorical | Carrion biomass
 treatment: single carcass is\~30 kg, MME is multiple carcasses (\~360 kg),
 reference is a no carcass plot outside of each block | | EXCLUSION | Open,
 Herbivore, Scavenger | Categorical | Vertebrate exclusion treatment | | N
 | 0.8–2.4 | Numeric | Percent of dry weight | | Ca | 0.3–3.4 | Numeric |
 Percent of dry weight | | K | 0.6–2.7 | Numeric | Percent of dry weight |
 | Mg | 0.1–0.5 | Numeric | Percent of dry weight | | P | 0.1–0.4 | Numeric
 | Percent of dry weight | | S | 0.0–0.5 | Numeric | Percent of dry weight
 | | Cu | 1.8–9.2 | Numeric | Percent of dry weight | | Zn | 16.4–55.4 |
 Numeric | Parts per million (ppm) | | Mn | 25.4–174.9 | Numeric | Parts
 per million (ppm) | | Fe | 40.9–82.9 | Numeric | Parts per million (ppm) |
 | B | 4.9–88.8 | Numeric | Parts per million (ppm) | ### Data specific
 information for: | Seed-dormancy-db.csv | | :------------------- | | 
 
 | | **Variable** | Values | Units | Explanation | | :------------- |
 :-------------------------------------- | :---------- |
 :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | GENUS.SPECIES | Species listed in binomial nomenclature | Categorical | List of 14,243 species in the Baskins & Baskins database (2014) | | DORMANCY.CLASS | ND, PD, MPD, PY, MD, PYPD | Categorical | Plant dormancy classification with no dormancy (ND), physiological dormancy (PD), morphophysiological dormancy, physical dormancy (PY), morphological dormancy (MD), and combination physical and physiological dormancy (PYPD) | ### Data specific information for: | **Seed-survival.csv** | | :-------------------- | | 
 
 | | **Variable** | Values | Units | Explanation | | :------------- |
 :--------------------------------------------------------------------------- | :---------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | SITE | OS, GG, DF, WP | Categorical | Experimental blocks | | BIOMASS | Single, MME, reference | Categorical | Carrion biomass treatment: single carcass is\~30 kg, MME is multiple carcasses (\~360 kg), reference is a no carcass plot outside of each block | | EXCLUSION | Open, Herbivore, Scavenger | Categorical | Vertebrate exclusion treatment | | PACKET | BA, BU, AA, AT | Categorical | Location of the packet simulating seed bank underneath the soil surface (first letter B) and seed rain above the soil surface (first letter A). Second letters indicate whether packet is under (U) or on top (T) of the carcasses or 1 m adjacent (A) | | DORMANCY.CLASS | ND, PY, PD | Categorical | Simplified seed dormancy classification with no dormancy (ND), physical dormancy (PY), and physiological dormancy (PD) | | SPECIES | MASY, TRAE, SIALD, RHGL, SYRIN, PISY, GLMA4, CAAN4, PISA6, BIOR, HOVU, BEVU2 | Categorical | MASY = *Malva sylvestris*, TRAE = *Triticum aestivum*, SIALD = *Sinapsis alba*, RHGL = *Rhus glabra*, SYRIN = *Syringa* sp., PISY = *Pinus sylvestris*, GLMA4 = *Glycine max*, CAAN4 = *Capsicum annum*, PISA6 = *Pisum sativum*, BIOR = *Bixa orella*, HOVU = *Hordeum vulgare*, BEVU2 = *Beta vulgaris* | | ID | 1–10 | Numeric | Unique identifier for multiple seeds of a single species in the same packet | | FINAL.STATUS | 0,1 | Binary | Indicates whether the seed ever germinated (at time of retrieval or after germination test) | ## Associated Code Repository All analyses and figure generation are reproducible using the R scripts available at: [GitHub Repository: Seed Dormancy and Mass Mortality](https://github.com/masond-UF/Seed-dormancy-explains-plant-response-to-mass-mortality-events.git) --- ## Study Design Summary * **Location**: Oswalt Ranch (Noble Research Institute), Ardmore, Oklahoma, USA. * **Duration**: April 2019 – October 2021 * **Design**: Field experiment testing the ecological consequences of vertebrate mass mortality events (MMEs) via simulated carrion addition. Response variables include vegetation cover, seed survival, scavenger/herbivore detections, and nutrient cycling --- ## Citation Please cite the manuscript when using these data: &gt; *Seed dormancy explains plant response to mass mortality events.* (in press). [Functional Ecology] (Full citation and DOI will be updated upon publication.) --- ## Licensing These data are released under the default Dryad open license (CC0). No restrictions on use. ---