Ranking ecological contingencies from high-order factorial data demonstrate tidy control of biodiversity from facilitation cascades in estuaries on the South Island of New Zealand
Data files
Feb 08, 2025 version files 62.56 KB
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data_and_code.zip
37.27 KB
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README.md
25.29 KB
Abstract
Community ecology has been described as a ‘mess’ because ecological processes vary in space, time, and across species traits, resulting in myriads of ecological contingencies and low scientific predictability. Here we aimed to identify and rank ecological contingencies and improve predictability, using fully crossed high-order factorial mensurative and manipulative experiments across axes of spatiotemporal variability that may influence the strength of facilitation cascades on the South Island of New Zealand. Facilitation cascades, arising from chains of positive interactions, are prevalent in intertidal sedimentary estuaries, where biogenic habitat-formers, like bivalves and attached seaweed, provide hard substrates, food, hiding places, and reduce environmental stress for small animals. Specifically, we measured facilitation of >65,000 small mobile invertebrates across eight archetypical contingencies, i.e., within and between seasons, latitudes, sites with different distances to the open ocean, vertical intertidal elevations, wider habitat matrix (bare sediment vs. seagrass beds), and between small-scale habitat-forming species (the endemic cockle Austrovenus and attached cosmopolitan seaweeds, Ulva and Gracilaria spp.) and their sizes. Overall, our multifactorial tests revealed that most higher-order interactions (three-way or more) were not important ecologically, and that many important lower-order interactions (two-way) were ‘simple’, demonstrating that facilitation can increase when and where the baseline biodiversity is higher. Furthermore, most of the main test factors were significant and ecologically important, suggesting that facilitation of animals, generally and across other factors, were strongest on large and morphologically complex seaweeds, at near-ocean sites and deeper intertidal elevations, and in warmer summer months. Our case study highlights a relatively tidy – not messy – control of biodiversity of intertidal epifauna, and that high-order factorial sampling can help unravel and rank co-occurring spatiotemporal drivers to better understand ecological contingencies. Finally, our results may also inform management of habitat-forming species to preserve estuarine biodiversity and maintain their secondary production.
https://doi.org/10.5061/dryad.v9s4mw746
This upload contains all the data and code necessary to reproduce the analyses and visualizations associated with the following publication:
Clemente, K. J. E., & Thomsen, M. S. (2025). Ranking ecological contingencies from high-order factorial data demonstrate tidy control of biodiversity from facilitation cascades in estuaries on the South Island of New Zealand. Ecography (accepted). https://doi.org/10.1111/ecog.07488
For any questions, please contact Ken Clemente at kenjoseph.clemente@gmail.com
Note: A small subset of this dataset contains data from an already published dataset in Dryad: https://doi.org/10.5061/dryad.dr7sqvb5t. This subset is part of the authors’ previously published work in Ecosphere. The current dataset associated with the Ecography paper is significantly larger, containing extensive data collected beyond the scope of the previous study.
Description of the data and file structure
In the ‘data_and_code.zip’ folder, there are two datasets in .csv format containing community data from field surveys and experiments. The filenames for both datasets are the same as those used in the R code to facilitate re-running. The accompanying code consists of four R scripts that can be used for the following purposes: (1) univariate factorial permutation ANOVA, (2) multivariate factorial PERMANOVA, (3) means plots for surveys and experiments, and (4) nMDS plots for multivariate data. These scripts can be used in conjunction with the datasets to perform the statistical analysis and generate statistical results and visualizations.
The data files include:
data_survey.csv
This file contains community data from field surveys. KJEC collected all data under the supervision of MST.
variable | units | description |
---|---|---|
sample_id | number | numerical identifier for samples |
latitude | categorical | “southern” = colder latitude site in the central region of New Zealand’s South Island; “northern” = warmer latitude site in the northern region of New Zealand’s South Island |
estuary | categorical | “ahe_causeway” = colder latitude site along the causeway of Avon Heathcote Estuary; “ahe_spit” = colder latitude site along the Brighton spit of Avon Heathcote Estuary; “del”= warmer latitude site in Delaware Inlet; “nel”= warmer latitude site in Nelson Haven |
site | categorical | “far-mouth” = site far from ocean opening; “near-mouth”= site near from ocean opening or estuary mouth |
site_specific | nominal | specific names assigned to sampled sites |
elevation | categorical | “high”=shallow mid-intertidal zone; “low” = deeper low-intertidal zone |
date | date | date of field collection |
season | categorical | winter or summer |
intraseason | categorical | colder or warmer month within a season |
hf1 | nominal | the primary foundation species (i.e., Austrovenus) |
hf_species | nominal | secondary foundation species attached to the primary foundation species (i.e., seaweeds) |
hf1_length_cm | cm | Austrovenus shell length |
hf1_biomass_g | g | Austrovenus shell dry biomass |
hf2_biomass_g | g | seaweed dry biomass |
hf_amount | categorical | small or large seaweed size |
copepod | count | number of copepods |
amphipod | count | number of amphipods |
isopod | count | number of isopods |
halicarcinus | count | number of Halicarcinus sp.crabs |
juvenile_gastropods | count | number of juvenile gastropods |
notoacmea | count | number of Notoacmea sp. |
juvenile_trochids | count | number of juvenile trochid snails |
juvenile_bivalve | count | number of juvenile bivalve shells |
micrelenchus | count | number of Micrelenchus sp. |
diloma | count | number of Diloma sp. |
nematode | count | number of nematodes |
polychaete | count | number of polychaetes |
ostracod | count | number of ostracods |
anemone | count | number of anemone |
juvenile_crab | count | number of juvenile crabs (<500 µm) |
perna_morph1 | count | number of Perna morphospecies (<1000 µm) |
barnacle | count | number of barnacles |
risellopsis | count | number of Risellopsis sp. |
tubeworm | count | number of tubeworms |
protothaca_crassicosta | count | number of Protothaca crassicosta shells |
ruditapes | count | number of Ruditapes sp. |
fanworm_sabellids | count | number of sabellid fanworms |
helice_crassa | count | number of Helice crassa crabs |
macrophthalmus | count | number of Macrophthalmus sp. crabs |
hemigrapsus | count | number of Hemigrapsus sp. crabs |
zeacumantus | count | number of Zeacumantus sp. shells |
cominella | count | number of Cominella sp. shells |
microcrustacean_morph1 | count | number of microcrustacean morphospecies |
nodilittorina | count | number of Nodilittorina sp. shells |
juvenile_batillariidae | count | number of Batillariidae juvenile shells |
potamopyrgus | count | number of Potamopyrgus sp. shells |
perna_morph2 | count | number of Perna morphospecies (0.5-1cm) |
chiton | count | number of Chiton shells |
acanthochitona | count | number of Acanthochitona sp. shells |
juvenile_amphibola | count | number of Amphibola sp. juvenile shells |
bulla | count | number of Bulla sp. |
bryozoa | count | number of bryozoan occurences |
paphies | count | number of Paphies sp. shells |
data_experiment.csv
This file contains community data from field experiments. KJEC collected all data under the supervision of MST.
variable | units | description |
---|---|---|
sample_id | number | numerical identifier for samples |
tag | categorical | “alive”= sample was alive during laboratory processing; “nsordead” = sample was missing or shell was dead |
site | categorical | “river” = site near river and far from the open ocean; “ocean”= site near from ocean opening or estuary mouth |
date started | date | start date of field experiment |
date collected | date | end date of field experiment and when samples were collected |
elevation | categorical | “high”=shallow mid-intertidal zone; “low” = deeper low-intertidal zone |
season | categorical | warm or cold |
hf1 | nominal | the primary foundation species (i.e., Austrovenus) |
hf_species | nominal | secondary foundation species attached to the primary foundation species (i.e., seaweeds Ulva or Gracilaria) |
hf1_length_cm | cm | Austrovenus shell length |
hf1_biomass_g | g | Austrovenus shell dry biomass |
hf2_biomass_g | g | seaweed dry biomass |
hf_amount | categorical | small or large seaweed size |
copepod | count | number of copepods |
amphipod | count | number of amphipods |
isopod | count | number of isopods |
halicarcinus | count | number of Halicarcinus sp.crabs |
juvenile_gastropods | count | number of juvenile gastropods |
notoacmea | count | number of Notoacmea sp. |
juvenile_trochids | count | number of juvenile trochids |
juvenile_bivalve | count | number of juvenile bivalves |
micrelenchus | count | number of Micrelenchus sp. |
diloma | count | number of Diloma sp. |
nematode | count | number of nematodes |
polychaete | count | number of polychaetes |
ostracod | count | number of ostracods |
anemone | count | number of anemone |
juvenile_crab | count | number of juvenile crabs (<500 µm) |
perna_morph1 | count | number of Perna morphospecies (<1000 µm) |
barnacle | count | number of barnacles |
helice_crassa | count | number of Helice crassa crabs |
macrophthalmus | count | number of Macrophthalmus sp. crabs |
zeacumantus | count | number of Zeacumantus sp. shells |
cominella | count | number of Cominella sp. shells |
juvenile_batillariidae | count | number of Batillariidae juvenile shells |
potamopyrgus | count | number of Potamopyrgus sp. shells |
chiton | count | number of Chiton shells |
This dataset was collected through high-order crossed-factorial field surveys and field experiments conducted in estuaries accross the South Island of New Zealand to measure biodiversity responses of small mobile invertebrates associated with co-occurring cockles and seaweeds. Individual cockles (Austrovenus stutchburyi) were collected with or without (controls) attached seaweeds (Ulva or Gracilaria). Labeled samples were transported chilled and stored frozen at -20 ºC. In the laboratory, samples were thawed and rinsed with freshwater in a 250 µm sieve. Detached inhabitants were transferred into a counting chamber (Bogorov 1927) and identified to lowest taxonomic level possible, and counted under a stereomicroscope with up to 40x magnification. All samples were stored in vials with 70% ethanol solution and labeled accordingly for preservation. The cockles and separated seaweed were weighed after oven-drying at 55 ºC for 72 h. Small and large Gracilaria were ≤0.6 and >0.6 gDW, whereas small and large Ulva (with a lower DW:WW ratio) were ≤0.35 and >0.35 gDW, respectively. Comprehensive data recording was maintained throughout the data processing workflow by systematically logging all relevant information in a dedicated spreadsheet. This included (1) background data such as sample ID, spatial, temporal, and habitat factors, (2) dry weights of cockles and seaweeds, and (3) individual counts of identified invertebrates.
Note: A small subset of this dataset contains data from an already published dataset in Dryad: https://doi.org/10.5061/dryad.dr7sqvb5t. This subset is part of the authors' previously published work in Ecosphere. The current dataset associated with the Ecography paper is significantly larger, containing extensive data collected beyond the scope of the previous study.