DOI: 10.5061/dryad.bk3j9kdhv
title: Hierarchical drivers of cryptic biodiversity on coral reefs

description: Declines in habitat structural complexity have marked ecological outcomes,
 as currently observed in many of the world’s ecosystems. Coral reefs have
 provided a model for such changes in marine ecosystems, but our
 understanding has been centred on corals and fishes at broad spatial
 scales when metazoan diversity on coral reefs is dominated by small
 cryptic taxa (herein: ‘cryptofauna’). Given the paucity of studies and
 high taxonomic complexity of the cryptofauna, both of which limit a priori
 hypotheses, we asked whether hierarchical structuring theory provides a
 compelling framework to impose order and quantify pattern. In general
 terms, we explored whether cryptic communities are sufficiently described
 by broad seascape parameters or limited by a set of processes operating at
 their distinctly nested microhabitat scale. To address this theory and
 gaps in knowledge for the cryptofauna, we characterised community
 structure in coral rubble, an eroded coral condition where biodiversity
 proliferates. Rubble was sampled along a depth and exposure gradient at
 Heron Island on the Great Barrier Reef, Australia, to parameterise
 environmental and morphological indicators of sessile taxa and motile
 cryptofauna communities. We employed a hierarchical study framework from
 microhabitat to seascape scales, which were evaluated using non-structured
 multivariate analyses and Bayesian structural equation modelling. While
 the non-structured analyses showed the effects of seascape on the
 cryptobenthos and its community, this approach overlooked the finer
 hierarchical patterns in rubble ecology revealed only in the structured
 model. Seascape parameters (exposure and depth) influenced microhabitat
 complexity (i.e., rubble branchiness), which determined the cover of
 sessile organisms on rubble pieces, which shaped the motile cryptofauna
 community. Rubble is likely to be increasingly prevalent on coral reefs in
 the Anthropocene and is typically associated with low seascape-level
 complexity and reduced macrofaunal richness. Parallel with hierarchical
 structuring theory, we show a similar response operating at the
 microhabitat scale whereby low rubble complexity (i.e., branchiness)
 reduces cryptobenthic structure, diversity and size spectra. We expect
 there may be an initial increase in biodiversity and trophodynamic
 processes derived from branching rubble, but a delay in ecosystem-scale
 outcomes if coral, and thus rubble, generation and complexity cannot be
 sustained in a future ocean.
description: <strong>Overarching aim and design: </strong>This
 study was designed to investigate whether the theory of hierarchical
 structuring of ecological systems could explain resource aggregation in
 coral rubble where biodiversity proliferates. Data were analysed across
 multiple scales of ecological organisation; first at the level of seascape
 drivers and then at the level of microhabitat. At the
 seascape scale, water depth and hydrodynamic exposure represented
 higher-order environmental limits on rubble patches. Whether these
 seascape parameters sufficiently explained lower-level entities within
 rubble was assessed independently using permutational multivariate
 analysis of variance (PERMANOVA) on (1) rubble piece morphology, (2) the
 proportional cover of sessile taxa on rubble pieces, and motile
 cryptofauna (3) density, (4) diversity and (5) size spectra. Separate
 Excel spreadsheets are attached for each of these five datasets.
 To determine the applicability of hierarchical theory to rubble
 biomes more acutely, the relative influence of seascape drivers (wave
 exposure and depth) and lower-level microhabitat variables (rubble
 morphology, sessile taxa, and motile cryptofauna density, diversity and
 size spectra) on rubble community assembly were interrogated in a Bayesian
 SEM framework. Explicit consideration of this hierarchical study structure
 from seascape to microhabitat helped to disentangle the network of
 relationships that shape the complex rubble cryptobiome where tropical
 marine biodiversity proliferates and provides a model example of the
 utility of SEM approaches in ecological research.
 <strong>Data collection:</strong>
 Rubble patches were surveyed at Heron Island, situated in the
 Capricorn Bunker Group in the southern GBR, Australia (23˚26’31” S,
 151˚54’50” E), which predominantly experiences moderate south-east winds.
 Three sites were established along the south-west margin of Heron Reef,
 where prevailing winds result in a moderate exposure gradient. Six samples
 of rubble (~500 mL) were taken from two shallow (3–5 m) and two deep (7–11
 m) rubble patches at each site, resulting in a total of 72 samples of
 coral rubble to characterise morphological and biological features across
 scale. <strong>(1) Rubble piece
 morphology:</strong> Morphometric parameters predicted to be
 informative in defining rubble were measured for every rubble piece (n =
 6–35 per sample). Parameters of individual rubble pieces included (1)
 widest span (longest length in any direction), (2) mean thickness of
 primary branch (n = 3 measurements per piece), (3) mean secondary branch
 length (n = 0–3 measurements per piece; some pieces did not exhibit
 branching morphology), (4) number of secondary branches &gt; 1 cm
 (herein: ‘branchiness’), (5) wet and (6) dry weight, (7) wet volume (water
 displacement volume, mL), and (8) porosity.
 <strong>(2) Proportional cover of sessile taxa on
 rubble:</strong> Six rubble pieces were taken at random from each
 sample and photographed to quantify the relative cover of sessile taxa on
 rubble pieces. Each piece was photographed from two distinct perspectives,
 as community succession in rubble differs between surface (top) and
 subsurface (bottom) microhabitats. Proportional cover of major functional
 groups, including bare surface, encrusting calcifying algae (including
 crustose coralline algae (CCA) and <em>Peyssonnelia</em>),
 turf algae, macroalgae (including <em>Dictyota</em>,
 <em>Lobophora</em> and <em>Halimeda</em>), sponges
 and ascidians, and bryozoans (erect and encrusting), on each rubble piece
 was quantified using a gird overlay on each photo. The number of cells
 occupied by each substrate type was counted. Data attained from both
 surface and subsurface perspectives were combined to establish a
 whole-of-piece cover estimate. <strong>Motile
 cryptofauna (3) density, (4) diversity and (5) size
 spectra:</strong> Contents of each sample were poured into separate
 trays and conspicuous motile fauna were collected using forceps and
 spoons. Remaining cryptic fauna were dislodged from rubble pieces using a
 series of freshwater rinses (~ 1 min) and pressurised water over a 210 µm
 sieve. All motile organisms were grouped to represent one sample of
 cryptofauna per rubble sample, preserved in 70% ethanol for later
 identification. The size (mm), abundance and diversity of motile
 cryptofauna in each sample were determined. Cryptofauna were identified
 under a dissecting microscope primarily to the level of family and
 measured to the nearest 250 µm using a scored dish. Standard measurements
 for size were used; carapace width for crab-like crustaceans or length for
 shrimp-like crustaceans, shell length for molluscs (longest distance),
 diameter for echinoderms with radial symmetry, and length for all types of
 worms. Density was determined from abundance and the water displacement
 volume (mL) of each rubble sample. Size spectra were determined for each
 sample as the linear relationship between log-density and log-size of all
 individuals, resulting in intercept and slope coefficients for each rubble
 sample.
description: Microsoft Excel is required to open the data files. No novel code
 was used.