DOI: 10.5061/dryad.v9s4mw746
title: 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

description: 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 &gt;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.
description: 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 (<em>Austrovenus stutchburyi</em>) were
 collected with or without (controls) attached seaweeds (<em>Ulva
 </em>or <em>Gracilaria</em>). 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 <em>Gracilaria</em> were ≤0.6 and
 &gt;0.6 gDW, whereas small and large <em>Ulva</em> (with a
 lower DW:WW ratio) were ≤0.35 and &gt;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. <br><br>
 <strong>Note:</strong> 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 <em>Ecosphere</em>. The current dataset associated with the <em>Ecography</em> paper is significantly larger, containing extensive data collected beyond the scope of the previous study.
description: # Ranking ecological contingencies from high-order factorial data
 demonstrate tidy control of biodiversity from estuarine facilitation
 cascades on the South Island of New Zealand
 [https://doi.org/10.5061/dryad.v9s4mw746](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](https://doi.org/10.1111/ecog.07488) For any questions, please contact Ken Clemente at [kenjoseph.clemente@gmail.com](mailto: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](https://doi.org/10.5061/dryad.dr7sqvb5t). This subset is part of the authors' previously published work in *[Ecosphere](https://doi.org/10.1002/ecs2.4834)*. 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 (&lt;500 µm) | | perna\_morph1 | count | number of *Perna* morphospecies (&lt;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 (&lt;500 µm) | | perna\_morph1 | count | number of *Perna* morphospecies (&lt;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 |