Extending trait dispersion across trophic levels: predator assemblages act as top-down filters on prey communities
Data files
Apr 02, 2024 version files 49.32 KB
-
Gross___Stachowicz.zip
36.36 KB
-
README.md
12.96 KB
Apr 22, 2024 version files 2.62 MB
-
Gross___Stachowicz.zip
2.60 MB
-
README.md
14.91 KB
Abstract
Studies of community assembly typically focus on the effects of abiotic environmental filters and stabilizing competition on functional trait dispersion within single trophic levels. Predation is a well-known driver of community diversity and composition, yet the role of functionally diverse predator communities in filtering prey community traits has received less attention. We examined functionally diverse communities of predators (fishes) and prey (epifaunal crustaceans) in eelgrass (Zostera marina) beds in two Northern California estuaries to evaluate the filtering effects of predator traits on community assembly, and how filters acting on predators influence their ability to mediate prey community assembly. Fish traits related to bottom orientation selected for more clustered epifauna communities, and epifauna were generally overdispersed while fishes were clustered, suggesting that prey may be pushed to disparate areas of trait space to avoid capture by benthic sit-and-wait predators. We also found correlations between the trait dispersions of predator and prey communities that strengthened after accounting for the effects of habitat filters on predator dispersion, suggesting that habitat filtering effects on predator species pools may hinder their ability to affect prey community assembly. Our results present compelling observational evidence that specific predator traits have measurable impacts on the community assembly of prey, inviting experimental tests of predator trait means on community assembly, and explicit comparisons of how the relative effects of habitat filters and intraguild competition on predators impact their ability to affect prey community assembly. Integrating our understanding of traits at multiple trophic levels can help us better predict the impacts of community composition on food web dynamics as regional species pools shift with climate change and anthropogenic introductions.
README: Extending trait dispersion across trophic levels: predator assemblages act as top-down filters on prey communities
Description of the data and file structure
Environmental and species abundance data collected in summer (June-August) 2019 and 2021 from eelgrass beds in Northern California.
NOTE: Version created Apr 2024 added file #7.
This dataset consists of 7 data files:
- Epifauna.list.csv, created July 19, 2023. Invertebrates collected from grab samples of eelgrass (Zostera marina) from 8 sites across the two sampling years (only 6 sites were used in analyses).
- Sample: The code used to identify an individual grab sample, read as: subsite_tidal height, transect number_sample along transect_year
- Bay: The estuary where the samples were collected (BH = Bodega Harbor, DE = Drakes Estero, TB = Tomales Bay)
- Subsite: The site code used to define a community of epifauna (BL = Blake's Landing, CC = Campbell Cove, MM = Mason's Marina, MP = Millerton Point, NC = Nick's Cove, SB = Schooner Bay, SL = Sacramento Landing, WP = Westside Park)
- Year: Year sampled (2019 or 2021)
- Date: Date sampled (m/dd/yy)
- Tidal height: Height of transect relative to tidal regime; "upper" = intertidal transects 1-3 that were fully emersed, "lower" = subtidal transects 4-6 that were always immersed.
- Grab bag: The individual grab sample. U = upper, L = lower. First number refers to the transect, second refers to 1 of 2 samples along the transect.
- Species: Finest taxonomic resolution available for an organism observed in samples
- Count: The number of individuals of each species
- Epifaunal: Does the animal live on eelgrass blades or was it incidentally collected from the sediment?
- Mobile: Is the animal mobile or sessile?
- Peracarid: Is the animal an amphipod, isopod, or tanaid?
- Fish.list.csv, created July 19, 2023. Fishes collected from seine sets in eelgrass from 8 sites across the two sampling years (only 6 sites were used in analyses).
- Sample: The code used to identify an individual seine sample, read as: subsite_seine_year
- Bay: The estuary where the samples were collected (BH = Bodega Harbor, DE = Drakes Estero, TB = Tomales Bay)
- Subsite: The site code used to define a community of epifauna (BL = Blake's Landing, CC = Campbell Cove, MM = Mason's Marina, MP = Millerton Point, NC = Nick's Cove, SB = Schooner Bay, SL = Sacramento Landing, WP = Westside Park)
- Date: Date sampled (m/dd/yy)
- Time: Time (24 hr) when the seine was set.
- Species: Common name of species in seine
- Length: Standard length in millimeters measured in situ
- Count: Number of individuals of a species with a given standard length
- Size: For species with discrete size cohorts, is it larger or smaller?
- Fish.traits.csv, created June 1, 2023. Mean traits collected from individual fishes collected in the field and from published literature. Morphometric measurements are shown in Figure S1 of Appendix S1.
- Species: Fish common name and size class (if applicable)
- Standard_Length_mm: Length in mm from the tip of the snout to the end of the caudal peduncle
- Mouth_Height: Distance in mm from distal tip of the premaxilla to the distal tip of the dentary with the jaws fully extended, divided by standard length.
- Mouth_protrusion: Length in mm from distal tip of the premaxilla to the eye pupil with jaws fully extended, divided by head length.
- Dorsal_fin_length: Straight length in mm from the anterior to posterior end of the dorsal fin (summed where dorsal fins were discontinuous), divided by standard length.
- Pectoral_fin_length: Length in mm from base to the tip of the longest pectoral ray, divided by standard length.
- Eye_position: Vertical distance in mm from the pupil to the top of the head, divided by head depth.
- Snout_length: Distance in mm from eye pupil to distal tip of the premaxilla, with the mouth closed, divided by head length.
- Head_depth: Vertical distance in mm from the top of the head to the bottom of the head, passing through the eye pupil, divided by body depth.
- Eye_diameter: Horizontal distance in mm across the eye passing through the pupil, divided by head length.
- Head_length: Distance in mm from posterior margin of the operculum to the distal tip of the premaxilla with the jaws closed, divided by standard length.
- BDBM: Greatest vertical distance in mm below a horizontal line drawn from the tip of the snout to the end of the caudal peduncle, divided by body depth.
- Body_depth: Greatest vertical distance in mm from the top of the fish to the bottom, divided by standard length.
- Anal_fin: Straight length in mm from the anterior to posterior end of the anal fin, divided by standard length.
- Caupe_L: Horizontal distance in mm from the end of the caudal peduncle to the end of the anal fin, divided by standard length
- Caupe_D: Vertical distance in mm across the narrowest portion of the caudal peduncle, divided by body depth.
- CauF_L: Straight distance in mm from the end of the caudal peduncle to the distal tip of the longest caudal fin ray, divided by standard length.
- pursuit_predator: Suite of behaviors associated with feeding and foraging. Fuzzy-coded across 5 levels.
- benthic_browser: Suite of behaviors associated with feeding and foraging. Fuzzy-coded across 5 levels.
- epifaunal_browser: Suite of behaviors associated with feeding and foraging. Fuzzy-coded across 5 levels.
- planktivore: Suite of behaviors associated with feeding and foraging. Fuzzy-coded across 5 levels.
- sit_and_wait: Suite of behaviors associated with feeding and foraging. Fuzzy-coded across 5 levels.
- benthic: The orientation of the fish in the water column. Fuzzy-coded across three levels.
- pelagic: The orientation of the fish in the water column. Fuzzy-coded across three levels.
- benthopelagic: The orientation of the fish in the water column. Fuzzy-coded across three levels.
- Trophic_level: The average trophic level of the species, estimated from food items.
- Peracarid.traits.csv, created October 5, 2022. Mean traits collected from individual peracarids collected in the field and from published literature. Morphometric measurements are shown in Figure S3 of Appendix S1.
- Species: The binomial name of the peracarid species.
- Perc_swimming: Percentage of total video frames during which pleopod- driven locomotion occurred.
- Perc_walking: Percentage of total video frames during which pereopod-driven locomotion in contact with the cup surface occurred.
- Perc_still: Percentage of total video frames during which no forward locomotion occurred.
- Eye_diameter: Diameter in mm of a circle with an area equal to that of the eye (eyes are often irregurlarly-shaped), divided by body length.
- Antenna_length_1: Distance in mm from the base to the distal tip of antenna 1, divided by body length.
- Antenna_length_2: Distance in mm from the base to the distal tip of antenna 2, divided by body length.
- Tube_fidelity: The degree of association with constructed silk tubes.
- Body_size_observed: Body length in mm measured from the tip of the rostrum to the tip of the telson across individuals collected during sampling.
- Body_size_literature: Body length in mm measured from the tip of the rostrum to the tip of the telson as described in Carlton (2007).
- Shape: Overall body shape.
- Living_habit: Mode of contact with habitat substrate (eelgrass).
- Peracarid.tree.txt, created July 19, 2023. Ultrametric phylogeny of peracarid species observed in our grab samples, based on the Ashford et al. 2018 peracarid supertree (doi: 10.1098/rspb.2018.0923). Some of our species were not included in the supertree, so we made the following substitutions: Amphilochus tenuimanus --> Apolochus barnardi, Paracorophiini spp. --> Paracorophium sp., Ericthonius sp.--> Ericthonius brasiliensis, Photis sp. --> Photis brevipes, Leptochelia dubia --> Leptochelia sp., Sphaeroma quoianum --> Gnorimosphaeroma sp., Munnidae spp. --> Uromunna ubiquita, Corophium sp. --> Americorophium spinicorne, Lembos spp. --> Paramicrodeutopus schmitti
- Site.data.csv, created July 19, 2023. Environmental data collected from sites in 2019 and 2021.
- Bay: The estuary where the samples were collected (BH = Bodega Harbor, DE = Drakes Estero, TB = Tomales Bay)
- Subsite: The site code used to define a community of epifauna (BL = Blake's Landing, CC = Campbell Cove, MM = Mason's Marina, MP = Millerton Point, NC = Nick's Cove, SB = Schooner Bay, SL = Sacramento Landing, WP = Westside Park)
- Year: Year sampled (2019 or 2021)
- Site.Year: Unique site-by-year combination.
- Eelgrass.wet.g: Wet weight (g) of eelgrass collected in epifauna grab sampling
- Algal.wet.g: Wet weight (g) of macroalgae collected in epifauna grab sampling
- Macrophyte.wet.g: sum of eelgrass and macroalgal weight (g) from epifauna grab samples
- Salinity.psu: In-situ refractometer measurements of salinity (psu)
- Mean.shoots.m2: The mean number of total eelgrass shoots per square meter at each site.
- Mean.flowering.m2: The mean number of flowering eelgrass shoots per square meter from 24 quadrats at each site.
- Mean.perc.cover.grass: The average percent cover of eelgrass from 24 0.25 square meter quadrats at each site.
- Mean.perc.cover.macroalgae: The average percent cover of macroalgae from 24 0.25 square meter quadrats at each site.
- Mean.perc.cover.bare: The average percent cover of unvegetated sediment from 24 0.25 square meter quadrats at each site.
- Mean.canopy.height.cm: The average length of the longest eelgrass blade from 30 shoots at each site.
- Mean.epiphyte.g.cm2: The average dry weight of epiphytes per square centimeter of eelgrass blade, calculated from 30 3rd-rank blades per site.
- Mean.summer.temp.C: The average summer temperature measured across the season from pendant Hobo loggers at upper intertidal transects.
- Supplementary Tables 1-3.xlsx, created Jul 24, 2023. Effect sizes of fish community-weighted mean traits and trait dispersion on peracarid trait and phylogenetic dispersion. Three data tabs:
- Table S1. Effect sizes of community-weighted mean fish traits on peracarid community trait and phylogenetic dispersion. Bolded cells indicate values significant at the alpha level indicated; the first 103 rows are models for which results are presented in the main text. Italicized rows represent posthoc tests of individual peracarid community response traits. Rows are colored according to the direction and magnitude of the effect size; red indicates a negative effect while blue indicates a positive effect, and color saturation is proportional to R2.
- Table S2. Effect sizes of fish community trait dispersion on residual peracarid community trait and phylogenetic dispersion, not accounting for the effects of habitat filters on fish dispersion. Bolded cells indicate values significant at the specified alpha level; the first 30 rows are effects for which results are presented in the main text. F statistics are on 1 and 10 degrees of freedom. Rows are colored according to the direction and magnitude of the effect size; red indicates a negative effect while blue indicates a positive effect, and color saturation is proportional to R2.
- Table S3. Effect sizes of fish community trait dispersion on residual peracarid community trait and phylogenetic dispersion, controlling for the effects of habitat filters on fish dispersion. Bolded cells indicate values significant at the specified alpha level; the first 30 rows are effects for which results are presented in the main text. Rows are colored according to the direction and magnitude of the effect size; red indicates a negative effect while blue indicates a positive effect, and color saturation is proportional to R2.
Sharing/Access information
- Data was derived from the following sources: Species abundance and environmental parameters were collected according to protocols described in Gross & Stachowicz in prep. for Ecology and Aoki et al. 2022 (doi: 10.1002/lno.12152). Trait data was compiled from literature and measured individuals as described and cited in the Appendix of Gross & Stachowicz in prep. Phylogenetic tree was subsetted from the Ashford et al. 2018 peracarid supertree (doi: 10.1098/rspb.2018.0923)
Code/Software
Gross.Stachowicz.R is a script containing all of the analyses conducted in the manuscript. A brief outline is as follows:
Load packages tidyverse, ggfortify, ggvegan, vegan, picante, and FD. Packages tidyselect, gawdis, ggpointdensity, and gridExtra are used incidentally and are called using the double colon (::) in context.
- Load data on traits and communities, calcluate distances and community weighted means
- Load environmental data
- Load epifaunal data
- Peracarid trait data
- Peracarid trait distances
- Peracarid community-weighted means D. Load fish data E. Fish trait data
- Fish community-weighted means
- Fish PCA
- Fish trait distances
- Calculate standard effect sizes for fish and peracarid communities
- Calculate peracarid dispersion for each SES, permutation algorithm, and trait.
- Calculate residual peracarid dispersion for SES_MNTD_ts
- Calculate residual peracarid dispersion for SES_MNTD_is
- Calculate residual peracarid dispersion for SES_MPD_ts
- Calculate residual peracarid dispersion for SES_MPD_is
- Calculate fish dispersion for each SES, permutation algorithm, and trait.
- Calculate total fish dispersion for SES_MNTD_ts
- Calculate total fish dispersion for SES_MNTD_is
- Calculate total fish dispersion for SES_MPD_ts
- Calculate total fish dispersion for SES_MPD_is
- Calculate residual fish dispersion for each SES, permutation algorithm, and trait.
- Calculate residual fish dispersion for SES_MNTD_ts
- Calculate residual fish dispersion for SES_MNTD_is
- Calculate residual fish dispersion for SES_MPD_ts
- Calculate residual fish dispersion for SES_MPD_is
- Calculate peracarid dispersion for each SES, permutation algorithm, and trait.
- Model peracarid dispersion as a function of fish dispersion and community-weighted means
- make.models() function
- Model residual peracarid dispersion as a function of fish community-weighted means
- Model residual peracarid dispersion as a function of total fish dispersion D. Model residual peracarid dispersion as a function of residual fish dispersion.
Methods
We sampled fish and epifaunal communities in 6 eelgrass beds in Bodega Harbor and Tomales Bay in the summers of 2019 and 2021. We sampled fishes in 6 sets of a custom beach seine net when the water level was at or below 1 m above the seafloor. The seine sampled a circular area of 11 m2. We counted, identified to the lowest possible taxonomic level (typically species), and released animals retained in the seine.
We sampled epifauna at 12 locations within each site separated by at least 10m and spanning a depth gradient of intertidal to shallow subtidal. We collected each sample by everting an open-mouth drawstring mesh bag (500 µm mesh size) over a clump of shoots in the eelgrass bed so that the mouth of the bag was flush with the sediment surface, cutting the shoots, and closing the drawstring to capture shoots, macroalgae, and associated animals. We transferred the shoots to the laboratory on ice, rinsed, and hand-inspected them to dislodge the epifauna, which we then passed through a 500 µm sieve and ultimately transferred into 70% ethanol. We then identified epifauna to the lowest possible taxonomic level (typically species). We also quantified the biomass of macroalgae in each epifaunal sample. We also measured water temperature, total eelgrass shoot density m-2, flowering shoot density m-2, percent cover, canopy height, and epiphyte dry weight mm-2 eelgrass as described by Aoki et al. (2022).
For the 23 most abundant species of peracarids in our surveys, we assigned values for 11 traits putatively related to predator avoidance and microhabitat niche. We collected three of these traits (maximum body size, shape, and living habit) from the literature. We determined the tube fidelity for each species according to observations of living and preserved specimens along a four-point ordered scale as follows: none (species lacks silk glands to build tubes), low (species has silk glands but was never observed in a tube alive or preserved in ethanol), medium (species has silk glands and was observed in tubes when alive but readily flees tube when exposed to ethanol), and high (species has silk glands, is tubicolous when alive, and is regularly found inside tubes after preservation in ethanol). We measured mean body size (length from rostrum to telson), relative eye diameter, and relative antenna lengths from 10-20 preserved individuals collected across sites and years. We measured activity levels as fractions of time spent swimming, walking, and still (unmoving) from one-minute video recordings of 10-20 live individuals per species across sites and years. We log-transformed peracarid traits where appropriate to conform to a normal distribution.
We assigned two categorical (vertical position and foraging mode) and one continuous trait (trophic level) to the 16 most abundant fishes based on the literature. We fuzzy-coded vertical position and foraging mode among 5 and 3 levels, respectively, to accommodate species that could be classified among multiple levels. We collected linear morphometric measurements of fishes (body and head dimensions, fin lengths, eye size and position, and mouth height and protrusion) from 2-26 specimens per species and size class collected from seines, and standardized them for ease of comparison across species.
This dataset includes average trait data for both peracarids and fishes.
To address the potential effects of evolutionary history on peracarid community responses to predators, we built a phylogeny of our species by subsetting from the ultrametric peracarid supertree published by Ashford et al. (2018). For species in our dataset that were not included in the supertree we substituted congeners or confamilials as needed.
Tables S1-S3 (on Zenodo) show modeled responses of residual peracarid community trait and phylogenetic dispersion to fish community-weighted mean trait values (Table S1), total fish community trait dispersion (Table S2) and residual fish community trait dispersion after accounting for habitat filters (Table S3).
Usage notes
Code file is written in R; data files are .csv files that can be opened and viewed with Microsoft Excel; phylogeny is a .txt that can be opened in a text editor and manipulated and analyzed in R. Supplementary Tables 1-3 are an .xlsx file viewable in Microsoft Excel.