DOI: 10.5061/dryad.6q573n67v
title: Data and code for: Moisture and competition constrain ephemeral resource quality for burying beetle reproduction

description: Shifts in abiotic factors such as temperature and moisture can change the
 availability of resources, especially under climate change. Both abiotic
 and biotic drivers can have profound, rapid effects on species
 distribution, survival, and reproduction. Little is known about how
 abiotic factors affect the availability of ephemeral resources. Burying
 beetles (Nicrophorus spp.) are specialist users of ephemeral resources, as
 their reproduction requires locating, defending, and burying a small
 carcass. Environmental moisture, such as coastal fog, could change how
 quickly carcasses dry out. We tested the role of carcass moisture and
 interspecific competition with a generalist scavenger, Heterosilpha spp.,
 on reproduction by placing pairs of Nicrophorus guttula in field chambers
 with control and experimentally dehydrated mouse carcasses. Pairs that
 were given control of mouse carcasses were more likely to carry out
 reproductive behaviors and produce viable offspring than pairs that were
 given a partially dehydrated mouse. For those pairs that reproduced,
 competition limited the number of offspring. These results indicate that
 shifts in abiotic factors under climate change, along with biotic factors
 like competition, can reduce the availability of ephemeral resource
 patches for consumers.
description: <em>Site</em>.<strong> </strong>We
 conducted this experiment at the Bodega Marine Reserve in Bodega Bay,
 California (38.319061, -123.072443) between June and September 2022. The
 site is composed of coastal prairie, dunes, and rocky intertidal habitat.
 Summers are mild (average daily minimum temperatures are 9-14 degrees C,
 with average daily maximum temperatures 15-20 degrees C), with fog often
 present early in the mornings (mean relative humidity is 85-100%) (WRCC
 2024). The coastal prairie is primarily composed of species such as bush
 lupine (<em>Lupinus arboreus</em>), seaside daisy
 (<em>Erigeron glaucus</em>), woolly sunflower
 (<em>Eriophyllum</em> spp.), and ice plant
 (<em>Carpobrotus</em> spp.) (Barbour et al. 1973).
 <em>Trapping beetles. </em>We set up pitfall traps
 baited with mouse carcasses in the coastal prairie to collect <em>N.
 guttula</em> and <em>Heterosilpha </em>spp. for
 experiments (Figure 1B, Figure 1C, Appendix S1: Section S1). <em>N.
 guttula</em> is our focal species (Appendix S1: Section S1), a
 burying beetle that requires a small carcass that it buries belowground in
 order to reproduce. The <em>Heterosilpha </em>beetles are our
 competitors, as they will feed from carrion and other detritus, but do not
 bury carcasses. Most of the <em>Heterosilpha</em> beetles were
 likely to be <em>H. ramosa</em>, as <em>H. aenescens
 </em>is rare at this site. We will refer to
 “<em>Heterosilpha</em> spp.” as just
 “<em>Heterosilpha</em>” in the remaining text. We caught most
 of the beetles used in this experiment along a transect of 13 traps
 installed 12.5 meters apart on the coast bluffs, approximately 600m south
 of the Bodega Marine Lab. When collecting <em>N. guttula</em>,
 we sexed them, counted the number of phoretic mites currently attached,
 and took photographs to measure size in ImageJ. We usually visited traps
 in the mornings to collect the beetles that would then be placed into
 experimental chambers later that day. <em>Mouse
 carcass preparation. </em>We purchased large frozen mice (mean = 21
 g, range = 17-26 g, SD = 2 g) (Appendix S1: Section S2) from a commercial
 source (Gourmet Rodent via Petco.com). We dried half of the mice in a food
 dehydrator for 5-6 hours at 45 °C. On average, dried mice lost 25% (SD =
 4%) of their weight in water. This corresponds to between 20 and 72 hours
 of mouse carcasses naturally drying out and decomposing at the site during
 the month of July (Appendix S1: Figure S1, Appendix S1: Section S3). Mice
 carcasses also tend to lose more water weight (dry out faster) during less
 humid and less foggy periods at the Bodega Marine Reserve (Appendix S1:
 Figure S2, Appendix S1: Section S3). While making these measurements of
 mouse carcasses naturally drying out at the site, we observed burial
 behaviors by <em>Nicrophorus </em>spp., fly presence, and
 evidence of vertebrate scavengers between 28 and 77 hours since the
 carcass became available (Appendix S1: Table S1). The overlapping
 timelines of these observations indicate that our 25% partially dehydrated
 treatment represents realistic conditions that burying beetles might
 experience at the Bodega Marine Reserve. All mice used in the experiment
 (partially dried and control) were refrozen after weighing to minimize
 further changes until they were placed into experimental chambers, where
 they thawed rapidly. <em>Setting up experimental
 chambers. </em>We set up 63 experimental chambers (Figure 1D)
 between June 22 and August 10, 2022. We used 5-liter buckets (16 cm tall
 by 22 cm diameter) with modified lids that had a layer of wire mesh with
 quarter-inch openings and a layer of fine mesh to prevent beetles from
 getting in or out. A cinder block was placed over each chamber to prevent
 vertebrate disturbances (Figure 1E). Each bucket was filled with local
 soil and plants and buried to a depth of 8 cm. We placed experimental
 chambers along a series of transects (running approximately parallel to
 the shoreline) in the coastal prairie, approximately 25 meters apart. At
 each transect point, we haphazardly placed experimental chambers by
 throwing a small object into the air and digging a hole wherever the
 object landed. Each experimental chamber received a male-female
 <em>N. guttula</em> pair (Appendix S1: Section S4). We
 randomly assigned chambers to receive one of four treatments: (1) 14
 received a control carcass and no <em>Heterosilpha</em>
 beetles, (2) 16 received a control carcass and a male-female pair of
 <em>Heterosilpha</em>, (3) 16 received a partially dried
 carcass and no <em>Heterosilpha</em> beetles, and (4) 17
 received a partially dried carcass with a male-female pair of
 <em>Heterosilpha</em>. <em>Measuring
 reproductive output. </em>We checked each chamber after about 39
 days (range = 35-42 days, SD = 2), between August 6, 2022, and September
 19, 2022, when the adult beetles that we started the experiment with had
 sufficient time to reproduce. We counted all larvae and pupae (Figure 1F).
 We also noted if the carcass was buried, even if there were no larvae or
 pupae present. <em>Analysis</em>. We tested
 two univariate models to analyze these data. First, we analyzed the role
 of carcass dryness and competition from <em>Heterosilpha</em>
 on binomial reproductive success with a binomial generalized linear model
 (GLM) using the R packages lme4 and jtools (Long 2023, Bates et al. 2023).
 We also included the initial undried mass of the carcass, day of year,
 female size, male size, and total number of mites on adults as covariate
 predictors. The initial undried mass of the carcass was included to
 control for initial variation in carcass size. The day of the year that
 the experimental chamber was set up was included to control for
 seasonality. Female and male sizes were included to account for the
 effects of size on fecundity and/or competition between mates during the
 reproductive process. The total number of mites on adults was included to
 account for the effects of the mites as either competitors or mutualists.
 Second, we made another GLM with a Poisson distribution and a smaller
 dataset that only included experimental chambers that had successful
 reproduction. The model had a number of offspring as the response
 variable, with the same predictors as the previously mentioned
 model.
description: # Data and code for: Moisture and competition constrain ephemeral resource
 quality for burying beetle reproduction
 [https://doi.org/10.5061/dryad.6q573n67v](https://doi.org/10.5061/dryad.6q573n67v) ## Description of the data and file structure These data involve an experiment completed in 2022 on burying beetle reproduction, and also a supplementary project in 2024 to confirm the treatment realism of the 2022 experiment.  ### Files and variables #### File: filled\_nicrocosms.csv **Description:** Data on the setup of experimental chambers and the male and female N. guttula pair placed within. ##### Variables * date_nicrocosm_complete: date the experimental chamber was set up with treatments and N. guttula pair - **NOTE: if a row has an empty cell for this date column, that entire row can be disregarded. No experimental chamber was set up, and these lines are removed in the script.**  * time_nicrocosm_complete: time the experimental chamber was set up with treatments and N. guttula pair - if time is blank but other columns are filled for a row, time was not recorded * fem_beetleID: beetle ID of female * fem_trapID: trap ID where the female was caught * fem_numMites: number of mites on this female * fem_photo: check if a photo was taken for size measurements * fem_dtCollect: date the female was collected from a trap * fem_timeCollect: time the female was collected from a trap * fem_dtPlaced: date the female was placed in the experimental chamber * fem_timePlaced: time the female was placed in the experimental chamber * mal_beetleID: beetle ID of male * mal_trapID: trap ID the male was caught * mal_numMites: number of mites on this male * mal_photo: check if a photo was taken for size measurements * mal_dtCollect: date the male was collected from a trap * mal_timeCollect: time the male was collected from a trap * mal_dtPlaced: date the male was placed in the experimental chamber * mal_timePlaced: time the male was placed in the experimental chamber * nicrocosmID: experimental chamber ID * compTreat: competition treatment (yes or no) * mouseTreat: mouse treatment (fresh vs dried = control vs partially dried) * mouseID: ID of mouse carcass (to connect to weight) - mouseID unknown if cell is empty * hetPairFrom: what trap area is the Heterosilpha pair collected from - no competition was added if the cell is empty * iButton: iButton ID if one was placed at this experimental chamber - no iButton was placed if the cell is empty * notes: any notes - no relevant notes if the cell is empty * newSoil: notes about soil being added to experimental chamber - no relevant soil notes if cell is empty #### File: parent\_checking.csv **Description:** double-checking the sex of parents to see if some pairs/experimental chambers need to be removed ##### Variables * nicrocosmID: experimental chamber ID * notes: any notes, no relevant notes if cell is blank * code: either 1, 2, or 3. Codes for each nicrocosm - 1 is good to go (1 of each sex), 2 is maybe good to go (some uncertainty about beetle sex or one was too messed up to identify), and 3 is unusable (two of one sex, or there were 1 or 3 beetles total). See script.  #### File: checking\_nicrocosms\_for\_repro.csv **Description:** Data table used when checking experimental chambers for reproduction.  ##### Variables * nicrocosmID: experimental chamber ID * date: date experimental chamber checked * time: time experimental chamber checked * female_status: female dead? alive? position within experimental chamber? * male_status: male dead? alive? position within experimental chamber? * num_pupae: count of pupae present * num_larvae: count of larvae present * num_int: count of intermediate prepupae present * mouse_notes: notes on mouse carcass remains - no relevant notes if cell is empty * het_notes: notes on Heterosilpha competition if present - no relevant notes if cell is empty * misc_notes: any notes - no relevant notes if cell is empty #### File: measuring\_parents\_imagej.csv **Description:** Output when measuring parent size (pronotum width) in ImageJ. A lot of extra measurements were taken here that were not used.  ##### Variables * beetleID: beetle ID * pro_length: pronotum length (mm) * pro_width: pronotum width (mm) * elytra_length: elytra length (mm) * elytra_width: elytra length (mm) * body_length_head: length including head (mm) * body_length_pro: length from top of pronotum to last segment (mm) * notes: any notes, no relevant notes if the cell is empty #### File: repro\_weights.csv **Description:** Weights of offspring collected (ended up not using this in the manuscript) ##### Variables * offspringID: offspring ID * stage: stage (larva vs pupa vs intermediate) * weight: weight (g) * numMites: number of mites on offspring * notes: any notes, no relevant notes if the cell is empty * dateWeighed: date weighed #### File: mouse\_weight.csv **Description:** Weight of mice carcasses used in the experiment.  ##### Variables * mouseID: mouse ID * wetWeight_g: weight of mouse when fresh/unthawed/undried (g) * driedWeight_g: weight of mouse when/if dried (g) #### File: BML\_fog\_202407.csv **Description:** Fog data ##### Variables * time: time * pulse_counts_1: number of pulse counts (bucket tips) for fog collector 1 * max_pulse_rate_1: max pulse rate over 15 min interval (pulse/h) for fog collector 1 * pulse_counts_2: number of pulse counts (bucket tips) for fog collector 2 * max_pulse_rate_2: max pulse rate over 15 min interval (pulse/h) for fog collector 2 * battery_percent: battery percent remaining * battery_voltage: battery voltage (mV) * ref_pressure: reference pressure (kPa) * logger_temp_C: logger temperature (C) * trialint: trial interval (used to link with mouse carcass weights, see carcass_weight_loss.R script) #### File: temp\_humidity\_edit.csv **Description:** Temperature and humidity data taken from the Bodega Marine Lab weather station.  ##### Variables * time_endLST: hour of day ending at L.S.T. * solar_rad: total solar radiation (KW-hr/m^2) * date: date * air_temp_mean: air temperature mean (C) * soil_temp_mean: soil temperature mean (C) * rel_humid_mean: relative humidity mean percent * trial: trial A or B * int_num: interval number (ID) * hr_count: number of hours within an interval #### File: carcass\_weighing\_2024\_1.csv **Description:** Carcass weighing data - Trial A ##### Variables * location_id: location ID * date: date * time: time * weight: weight of carcass (g) #### File: carcass\_weighing\_2024\_2.csv **Description:** Carcass weighing data - Trial B ##### Variables * location_id: location ID * date: date * time: time * weight: weight of carcass (g) ## Code/software #### File: carcass\_weight\_loss.R **Description:** Script that uses carcass weight measurements from field carcasses in 2024 to look at shifts over time and compare to fog and humidity measurements at the site.