Latest Scientific Papers:


Consistent multi-level trophic effects of marine reserve protection across northern New Zealand

PloS ONE (2017)

Reef Life Survey data are used to show complex but consistent responses to protection from fishing in well-enforced temperate New Zealand marine reserves.


Through systematic Reef Life Survey censuses of rocky reef fishes, invertebrates and macroalgae at eight marine reserves across northern New Zealand and the Kermadec Islands, we investigated whether a system of no-take marine reserves generates consistent biodiversity outcomes. Ecological responses of reef assemblages to protection from fishing, including potential trophic cascades, were assessed using a control-impact design for the six marine reserves studied with associated reference sites, and also by comparing observations at reserve sites with predictions from random forest models that assume reserve locations are fished. Reserve sites were characterised by higher abundance and biomass of large fishes than fished sites, most notably for snapper Chrysophrys auratus, with forty-fold higher observed biomass inside relative to out. In agreement with conceptual models, significant reserve effects not only reflected direct interactions between fishing and targeted species (higher large fish biomass; higher snapper and lobster abundance), but also second order interactions (lower urchin abundance), third order interactions (higher kelp cover), and fourth order interactions (lower understory algal cover). Unexpectedly, we also found: (i) a consistent trend for higher (~20%) Ecklonia cover across reserves relative to nearby fished sites regardless of lobster and urchin density, (ii) an inconsistent response of crustose coralline algae to urchin density, (iii) low cover of other understory algae in marine reserves with few urchins, and (iv) more variable fish and benthic invertebrate communities at reserve relative to fished locations. Overall, reef food webs showed complex but consistent responses to protection from fishing in well-enforced temperate New Zealand marine reserves. The small proportion of the northeastern New Zealand coastal zone located within marine reserves (~0.2%) encompassed a disproportionately large representation of the full range of fish and benthic invertebrate biodiversity within this region.

Assessing National Biodiversity Trends for Rocky and Coral Reefs through the Integration of Citizen Science and Scientific Monitoring Programs

Bioscience (2017)

RLS provides a valuable template for improving national-scale marine biodiversity reporting, revealing where marine heatwaves, fishing and invasive species are having greatest effects on reef communities around Australia over the last decade.


Reporting progress against targets for international biodiversity agreements is hindered by a shortage of suitable biodiversity data. We describe a cost-effective system involving Reef Life Survey citizen scientists in the systematic collection of quantitative data covering multiple phyla that can underpin numerous marine biodiversity indicators at high spatial and temporal resolution. We then summarize the findings of a continental- and decadal-scale State of the Environment assessment for rocky and coral reefs based on indicators of ecosystem state relating to fishing, ocean warming, and invasive species and describing the distribution of threatened species. Fishing impacts are widespread, whereas substantial warming-related change affected some regions between 2005 and 2015. Invasive species are concentrated near harbors in southeastern Australia, and the threatened-species index is highest for the Great Australian Bight and Tasman Sea. Our approach can be applied globally to improve reporting against biodiversity targets and enhance public and policymakers’ understanding of marine biodiversity trends. Keywords: Convention on Biological Diversity, state of the environment, ecological indicator, Marine Trophic Index, community temperature index.


Predicting the diet of coastal fishes at a continental scale based on taxonomy and body size

Journal of Experimental Marine Biology and Ecology (2016)

Ground-truthing dietary model predictions using stomach contents of Australian fish species. 


Predicting diet of animals in ecological communities is necessary for a better understanding of trophic links and piecing together food webs to inform ecosystem-based management. A dietary model, Consume, was recently developed to predict detailed dietary information for fishes on the basis of fish identity and size. This model was field-tested over a continental scale, predicting community-level consumption for other temperate marine fish communities that differed in species composition and size structure. Using local stomach contents data to field-test predictions, accurate performance of the model was found across 14 locations around southern Australia. Prey type and mean prey size were predicted for fishes at new locations with high accuracy (mean percentage overlap between predicted and actual prey types = 73%; r2 between predicted and observed mean prey size = 89%) when trained with stomach contents data from subsets of sampled fishes at all locations. Model accuracy dropped, but was still respectable, when using training data only from one location (prey type accuracy = 67%; mean prey size r2 = 56%). Prey type was more accurately predicted on the basis of consumer body size than species identity, while consumer family identity and size were needed for accurate prediction of mean prey size. The most important factors were evaluated by leaving out predictors (species, genus and family identity; size of consumer; habitat, location, ecoregion and biogeographic province). Exclusion of geographical location information resulted in little loss in accuracy. Our results highlight the need for consideration of consumer body size in trophic models, rather than binning species into functional groups solely on the basis of taxonomy. Application of Consume to situations where no dietary information exists, but at least fish family identity and size structure are known, will provide a novel mechanism for testing important ecological hypotheses and assessing trophic consequences of anthropogenically-induced changes in community structure.
© 2016 Elsevier B.V. All rights reserved

Humans and seasonal climate variability threaten large-bodied coral reef fish with small ranges

Nature (2016)

The most sensitive coral reef fish species are identified along with their thresholds for human and climate stressors.


Coral reefs are among the most species-rich and threatened ecosystems on Earth, yet the extent to which human stressors determine species occurrences, compared with biogeography or environmental conditions, remains largely unknown. With ever-increasing human-mediated disturbances on these ecosystems, an important question is not only how many species can inhabit local communities, but also which biological traits determine species that can persist (or not) above particular disturbance thresholds. Here we show that human pressure and seasonal climate variability are disproportionately and negatively associated with the occurrence of large-bodied and geographically small-ranging fishes within local coral reef communities. These species are 67% less likely to occur where human impact and temperature seasonality exceed critical thresholds, such as in the marine biodiversity hotspot: the Coral Triangle. Our results identify the most sensitive species and critical thresholds of human and climatic stressors, providing opportunity for targeted conservation intervention to prevent local extinctions.

New Approaches to Marine Conservation Through the Scaling Up of Ecological Data

Annual Review of Marine Science (2016)

Advances in statistical analysis and the systematic collection compilation of global marine data aid in the progress of improving conservation outcomes.


In an era of rapid global change, conservation managers urgently need improved tools to track and counter declining ecosystem conditions. This need is particularly acute in the marine realm, where threats are out of sight, inadequately mapped, cumulative, and often poorly understood, thereby generating impacts that are inefficiently managed. Recent advances in macroecology, statistical analysis, and the compilation of global data will play a central role in improving conservation outcomes, provided that global, regional, and local data streams can be integrated to produce locally relevant and interpretable outputs. Progress will be assisted by (a) expanded rollout of systematic surveys that quantify species patterns, including some carried out with help from citizen scientists; (b) coordinated experimental research networks that utilize large-scale manipulations to identify mechanisms underlying these patterns; (c) improved understanding of consequences of threats through the application of recently developed statistical techniques to analyze global species’ distributional data and associated environmental and socioeconomic factors; (d ) development of reliable ecological indicators for accurate and comprehensible tracking of threats; and (e) improved data-handling and communication tools.

New opportunities for conservation of handfishes (Family Brachionichthyidae) and other inconspicuous and threatened marine species through citizen science

Biological Conservation (2016)

The RLS survey program is a model for how skilled citizen scientists can enhance survey efforts of cryptic marine organisms, such as handfishes.


Volunteer divers participating in the Reef Life Survey (RLS) program actively assist species conservation efforts by generating data for threat assessments and population trend monitoring, through in-water restoration efforts, and through outreach of marine conservation messages. Up to 2014, standardised underwater visual survey data provided by RLS divers described densities of 495 cryptic fish species at over 1200 sites distributed around Australia. Each species was recorded on 34 separate transect blocks on average, allowing the first assessments of population trends for many species. These data highlight the threatened and data deficient status of endemic Australian handfish species. At least five shallow-water handfish species are potentially threatened, including the smooth handfish Sympterichthys unipennis, which has not been sighted for over 200 years, but is yet to be included on any threatened species list. RLS divers undertook directed searches at key historical locations for two handfish species, the red handfish Thymichthys politus, now only known from a single reef, and Ziebell’s handfish Brachiopsilus ziebelli, with no confirmed sighting for over a decade. From a total of 100 h of underwater search effort, only four red handfish were recorded, all at a site threatened by adjacent human activity. These and other handfish species should be considered for inclusion on the IUCN Red List given that populations are either very small or have vanished, spawning substrates have probably declined, and the species lack a larval dispersal stage. More importantly, the absence of information on the conservation status of the majority of marine species needs urgent attention, including through expanded citizen science efforts, if management intervention is to occur and extinctions minimised.

Bright spots among the world’s coral reefs

Nature (2016)

Learning from ‘outliers’ – What are some of the common elements in marine management and local culture that are associated with places where reef fish biomass is much greater or much worse than we might expect?


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Ongoing declines in the structure and function of the world’s coral reefs require novel approaches to sustain these ecosystems and the millions of people who depend on them. A presently unexplored approach that draws on theory and practice in human health and rural development is to systematically identify and learn from the ‘outliers’—places where ecosystems are substantially better (‘bright spots’) or worse (‘dark spots’) than expected, given the environmental conditions and socioeconomic drivers they are exposed to. Here we compile data from more than 2,500 reefs worldwide and develop a Bayesian hierarchical model to generate expectations of how standing stocks of reef fish biomass are related to 18 socioeconomic drivers and environmental conditions. We identify 15 bright spots and 35 dark spots among our global survey of coral reefs, defined as sites that have biomass levels more than two standard deviations from expectations. Importantly, bright spots are not simply comprised of remote areas with low fishing pressure; they include localities where human populations and use of ecosystem resources is high, potentially providing insights into how communities have successfully confronted strong drivers of change. Conversely, dark spots are not necessarily the sites with the lowest absolute biomass and even include some remote, uninhabited locations often considered near pristine. We surveyed local experts about social, institutional, and environmental conditions at these sites to reveal that bright spots are characterized by strong sociocultural institutions such as customary taboos and marine tenure, high levels of local engagement in management, high dependence on marine resources, and beneficial environmental conditions such as deep-water refuges. Alternatively, dark spots are characterized by intensive capture and storage technology and a recent history of environmental shocks. Our results suggest that investments in strengthening fisheries governance, particularly aspects such as participation and property rights, could facilitate innovative conservation actions that help communities defy expectations of global reef degradation.

Biodiversity enhances reef fish biomass and resistance to climate change

PNAS (2016)

More species = more fish biomass produced. Well-known from experiments, but RLS field data from around the world prove that biodiversity is critical to support fish production. Also, having more species even helps maintain fish production under ocean warming and increasing temperature extremes.


Fishes are the most diverse group of vertebrates, play key functionalBiodiv enhances biomass and resis to CC_Duffy 2016 roles in aquatic ecosystems, and provide protein for a billion people, especially in the developing world. Those functions are compromised by mounting pressures on marine biodiversity and ecosystems. Because of its economic and food value, fish biomass production provides an unusually direct link from biodiversity to critical ecosystem services. We used the Reef Life Survey’s global database of 4,556 standardized fish surveys to test the importance of biodiversity to fish production relative to 25 environmental drivers. Temperature, biodiversity, and human influence together explained 47% of the global variation in reef fish biomass among sites. Fish species richness and functional diversity were among the strongest predictors of fish biomass, particularly for the large-bodied species and carnivores preferred by fishers, and these biodiversity effects were robust to potentially confounding influences of sample abundance, scale, and environmental correlations. Warmer temperatures increased biomass directly, presumably by raising metabolism, and indirectly by increasing diversity, whereas temperature variability reduced biomass. Importantly, diversity and climate interact, with biomass of diverse communities less affected by rising and variable temperatures than species-poor communities. Biodiversity thus buffers global fish biomass from climate change, and conservation of marine biodiversity can stabilize fish production in a changing ocean.





Thermal biases and vulnerabilities to warming in the world’s marine fauna

Nature (2015)

The distribution (geographical range) of fish and invertebrate species on reefs around the world informs us of where the majority of species are already living close to their upper temperature limits, or where most species could actually thrive with further warming.


A critical assumption underlying projections of biodiversity change associated with global warming is that ecological communities comprise balanced mixes of warm-affinity and cool-affinity species which, on average, approximate local environmental temperatures. Nevertheless, here we find that most shallow water marine species occupy broad thermal distributions that are aggregated in either temperate or tropical realms. These distributional trends result in oceanscale spatial thermal biases, where communities are dominated by species with warmer or cooler affinity than local environmental temperatures. We use community-level thermal deviations from local temperatures as a form of sensitivity to warming, and combine these with projected ocean warming data to predict warming-related loss of species from present-day communities over the next century. Large changes in local species composition appear likely, and proximity to thermal limits, as inferred from present-day species’ distributional ranges, outweighs spatial variation in warming rates in contributing to predicted rates of local species loss.



Reef fishes at all trophic levels respond positively to effective marine protected areas

PLoS One (2015)

A global comparison of fish feeding groups inside and outside MPAs shows that it is not just the predators (higher trophic levels) that have been overfished – but fishing has affected the larger members of all groups.


Marine Protected Areas (MPAs) offer a unique opportunity to test the assumption that fishing pressure affects some trophic groups more than others. Removal of larger predators through fishing is often suggested to have positive flow-on effects for some lower trophic groups, in which case protection from fishing should result in suppression of lower trophic groups as predator populations recover. We tested this by assessing differences in the trophic structure of reef fish communities associated with 79 MPAs and open-access sites worldwide, using a standardised quantitative dataset on reef fish community structure. The biomass of all major trophic groups (higher carnivores, benthic carnivores, planktivores and herbivores) was significantly greater (by 40% – 200%) in effective no-take MPAs relative to fished open-access areas. This effect was most pronounced for individuals in large size classes, but with no size class of any trophic group showing signs of depressed biomass in MPAs, as predicted from higher predator abundance. Thus, greater biomass in effective MPAs implies that exploitation on shallow rocky and coral reefs negatively affects biomass of all fish trophic groups and size classes. These direct effects of fishing on trophic structure appear stronger than any top down effects on lower trophic levels that would be imposed by intact predator populations. We propose that exploitation affects fish assemblages at all trophic levels, and that local ecosystem function is generally modified by fishing.



A standardised vocabulary for identifying benthic biota and substrata from underwater imagery: the CATAMI Classification Scheme.

PLoS ONE (2015)

The description of a new standard set of categories for scoring the cover of seaweeds and corals in photoquadrats (and video).


Imagery collected by still and video cameras is an increasingly important tool for minimal impact, repeatable observations in the marine environment. Data generated from imagery includes identification, annotation and quantification of biological subjects and environmental features within an image. To be long-lived and useful beyond their project-specific initial purpose, and to maximize their utility across studies and disciplines, marine imagery data should use a standardised vocabulary of defined terms. This would enable the compilation of regional, national and/or global data sets from multiple sources, contributing to broadscale management studies and development of automated annotation algorithms. The classification scheme developed under the Collaborative and Automated Tools for Analysis of Marine Imagery (CATAMI) project provides such a vocabulary. The CATAMI classification scheme introduces Australian-wide acknowledged, standardised terminology for annotating benthic substrates and biota in marine imagery. It combines coarse-level taxonomy and morphology, and is a flexible, hierarchical classification that bridges the gap between habitat/biotope characterisation and taxonomy, acknowledging limitations when describing biological taxa through imagery. It is fully described, documented, and maintained through curated online databases, and can be applied across benthic image collection methods, annotation platforms and scoring methods. Following release in 2013, the CATAMI classification scheme was taken up by a wide variety of users, including government, academia and industry. This rapid acceptance highlights the scheme’s utility and the potential to facilitate broad-scale multidisciplinary studies of marine ecosystems when applied globally. Here we present the CATAMI classification scheme, describe its conception and features, and discuss its utility and the opportunities as well as challenges arising from its use.


Species traits and climate velocity explain geographic range shifts in an ocean warming hotspot.

Ecology Letters (2015)

Common characteristics of fish and invertebrate species that are extending further south with warming waters.


Species’ ranges are shifting globally in response to climate warming, with substantial variability among taxa, even within regions. Relationships between range dynamics and intrinsic species traits may be particularly apparent in the ocean, where temperature more directly shapes species’ distributions. Here, we test for a role of species traits and climate velocity in driving range extensions in the ocean-warming hotspot of southeast Australia. Climate velocity explained some variation in range shifts, however, including species traits more than doubled the variation explained. Swimming ability, omnivory and latitudinal range size all had positive relationships with range extension rate, supporting hypotheses that increased dispersal capacity and ecological generalism promote extensions. We find independent support for the hypothesis that species with narrow latitudinal ranges are limited by factors other than climate. Our findings suggest that small-ranging species are in double jeopardy, with limited ability to escape warming and greater intrinsic vulnerability to stochastic disturbances.


Benthic invertebrates, climate change, climate response, fishes, functional traits, invasion, range expansion, range shifts, range size.

Ecology Letters (2015)

Broad-scale impacts of salmon farms on temperate macroalgal assemblages on rocky reefs.

Marine Pollution Bulletin (2015)

Photoquadrat data show increased cover of fast-growing, opportunistic algae on reefs closer to Atlantic Salmon farms in Tasmania.


Intensive fish culture in open sea pens delivers large amounts of nutrients to coastal environments. Relative to particulate waste impacts, the ecological impacts of dissolved wastes are poorly known despite their potential to substantially affect nutrient-assimilating components of surrounding ecosystems. Broad-scale enrichment effects of salmonid farms on Tasmanian reef communities were assessed by comparing macroalgal cover at four fixed distances from active fish farm leases across 44 sites. Macroalgal assemblages differed significantly between sites immediately adjacent (100 m) to fish farms and reference sites at 5 km distance, while sites at 400 m and 1 km exhibited intermediate characteristics. Epiphyte cover varied consistently with fish farm impacts in both sheltered and exposed locations. The green algae Chaetomorpha spp. predominated near fish farms at swell-exposed sites, whereas filamentous green algae showed elevated densities near sheltered farms. Cover of canopy-forming perennial algae appeared unaffected by fish farm impacts.



Loss of native rocky reef biodiversity in Australian metropolitan embayments.

Marine Pollution Bulletin (2015)

RLS surveys around major cities show trends in marine life related to major pollution sources, and numerous introduced species in Hobart.

Urbanisation of the coastal zone represents a key threat to marine biodiversity, including rocky reef communities which often possess disproportionate ecological, recreational and commercial importance. The nature and magnitude of local urban impacts on reef biodiversity near three Australian capital cities were quantified using visual census methods. The most impacted reefs in urbanised embayments were consistently characterised by smaller, faster growing species, reduced fish biomass and richness, and reduced mobile invertebrate abundance and richness. Reef faunal distribution varied significantly with heavy metals, local population density, and proximity to city ports, while native fish and invertebrate communities were most depauperate in locations where invasive species were abundant. Our study adds impetus for improved urban planning and pollution management practises, while also highlighting the potential for skilled volunteers to improve the tracking of changes in marine biodiversity values and the effectiveness of management intervention.

Functional traits reveal early responses in marine reserves following protection from fishing

Diversity and Distributions (2015)

A combination of RLS surveys and baited video undertaken by NSW marine parks staff show some responses of fish life to MPA protection evident in some younger MPAs


Sci-Paper---Functional-traits-reveal-early-responsesAim  Evaluating the effectiveness of marine reserves in achieving conservation goals is challenged by the decadal scales over which biological systems respond following protection. Given that trophic interactions underpin community responses following protection and that complex ecological interactions make responses difficult to identify, quantifying changes in species traits may provide detail missed by traditional diversity measures, including information relevant to ecosystem functioning. We determine whether this is the case by comparing community metrics based on functional traits to taxonomic diversity measures associated with ‘no take’ marine reserves and partially protected, fished areas along eight degrees of latitude.

Location  Eighteen ‘no take’ marine reserves and 14 partially protected, fished areas along the east coast of Australia.

Method  We use two independent datasets from shallow and deep coastal rocky reefs to analyse trait-based metrics and taxonomic diversity from sites inside reserves to sites in partially protected, fished areas.

Results  Taxonomic diversity (species diversity and richness) and trait-based multimetrics (functional richness and dispersion) showed no difference with level of protection. Total fish abundance responded positively to protection, but only on shallow reefs. Comparing values of individual functional traits implied a return of larger bodied species of fish in protected areas and an increase in trophic level. The latter was significant on deeper reefs and was strongly correlated with age of protected area. Thus, recovery responses were largely associated with community mean functional trait values, highlighting the value of trait-based approaches for detecting change, when no differences in traditional taxonomic diversity measures were apparent.

Main conclusions  We empirically demonstrate that functional traits can eluci-date early conservation outcomes, when traditional multimetric diversity indi-ces do not distinguish protected and fished communities. Ecologically relevant but sensitive metrics are fundamental to allow information to be incorporated into adaptive management strategies, which often occur on political rather than biological time-scales.



Distinguishing geographic range shifts from artefacts of detectability and sampling effort.

Diversity and Distributions 21:13-22 (2014)

New statistical approaches to help identify shifts in the range edges of species.



The redistribution of species with climate change is well documented.

Even so, the relative contribution of species detectability to the variation in

measured range shift rates among species is poorly understood. How can true

range shifts be discerned from sampling artefacts? Location Australia.


We simulate range shifts for species which differ in their abundance for comparison to patterns derived from empirical range shift data from two regional-scale (100s km) empirical studies. We demonstrate the use of spatial occupancy data in a distance-to-edge (DTE) model to assess changes in geographical range edges of fish species within a temperate reef fish community.


Simulations identified how sampling design can produce relatively larger error in range shift estimates in less abundant species, patterns that correspond with those observed in real data. Application of the DTE model allowed us to estimate the location of the true range edge with high accuracy in common species. In addition, upper confidence bounds for range edge estimates identified species with range edges that have likely shifted in location.


Simulation and modelling approaches used to quantify the level of confidence that can be placed in observed range shifts are particularly valuable for studies of marine species, where observations are typically few and patchy. Given the observed variability in range shift estimates, the inclusion of confidence bounds on estimates of geographical range edges will advance our capacity to disentangle true distributional change from artefacts of sampling design.


Climate warming, extreme value statistics, range edge estimation, sampling methodology.


Systematic global assessment of reef fish communities by the Reef Life Survey program.

Scientific Data 1: 140007 (2014)

Describes the Method 1 fish data in the RLS database, including collection methods and utility.


The assessment of patterns in macroecology, including those most relevant to global biodiversity conservation, has been hampered by a lack of quantitative data collected in a consistent manner over the global scale. Global analyses of species’ abundance data typically rely on records aggregated from multiple studies where different sampling methods and varying levels of taxonomic and spatial resolution have been applied. Here we describe the Reef Life Survey (RLS) reef fish dataset, which contains 134,759 abundance records, of 2,367 fish taxa, from 1,879 sites in coral and rocky reefs distributed worldwide. Data were systematically collected using standardized methods, offering new opportunities to assess broad-scale spatial patterns in community structure. The development of such a large dataset was made possible through contributions of investigators associated with science and conservation agencies worldwide, and the assistance of a team of over 100 recreational SCUBA divers, who undertook training in scientific techniques for underwater surveys and voluntarily contributed skills, expertise and their time to data collection.


Global conservation outcomes depend on marine protected areas with five key features.

Nature 506: 216-220 (2014)

Identifies the design and management factors common among the most effective MPAs in the world.


In line with global targets agreed under the Convention on Biological Diversity, the number of marine protected areas (MPAs) is increasing rapidly, yet socio-economic benefits generated by MPAs remain difficult to predict and under debate1,2.MPAs often fail to reach their full potential as a consequence of factors such as illegal harvesting, regulations that legally allow detrimental harvesting, or emigration of animals outside boundaries because of continuous habitat or inadequate size of reserve3–5. Here we show that the conservation benefits of 87 MPAs investigated worldwide increase exponentially with the accumulation of five key features: no take, well enforced, old (.10 years), large (.100km2), and isolated by deep water or sand. Using effective MPAs with four or five key features as an unfished standard, comparisons of underwater survey data from effectiveMPAs with predictions based on survey data from fished coasts indicate that total fish biomass has declined about two-thirds from historical baselines as a result of fishing. Effective MPAs also had twice as many large (.250mm total length) fish species per transect, five times more large fish biomass, and fourteen times more shark biomass than fished areas. Most (59%) of the MPAs studied had only one or two key features and were not ecologically distinguishable from fished sites. Our results show that global conservation targets based on area alone will not optimize protection of marine biodiversity.More emphasis is needed on better MPA design, durable management and compliance to ensure thatMPAs achieve their desired conservation value.


Statistical solutions for error and bias in global citizen science datasets.

Biological Conservation 173: 144-154 (2014)

Provides guidance on statistical methods for analyzing large scale datasets, including the RLS data


Networks of citizen scientists (CS) have the potential to observe biodiversity and species distributions atglobal scales. Yet the adoption of such datasets in conservation science may be hindered by a perception that the data are of low quality. This perception likely stems from the propensity of data generated by CS to contain greater levels of variability (e.g., measurement error) or bias (e.g., spatio-temporal clustering) in comparison to data collected by scientists or instruments. Modern analytical approaches can account for many types of error and bias typical of CS datasets. It is possible to (1) describe how pseudo-replication in sampling influences the overall variability in response data using mixed-effects modeling, (2) integrate data to explicitly model the sampling process and account for bias using a hierarchical modeling framework, and (3) examine the relative influence of many different or related explanatory factors using machine learning tools. Information from these modeling approaches can be used to predict species distributions and to estimate biodiversity. Even so, achieving the full potential from CS projects requires meta-data describing the sampling process, reference data to allow for standardization, and insightful modeling suitable to the question of interest

Resilience and signatures of tropicalization in protected reef fish communities.

Nature Climate Change 4: 62-67 (2014)

Demonstrates that more in-tact fish communities in an effective MPA can help resist colonization by new warmer water species.


Habitat reserves can promote ecological resilience to climate variability by supporting intact trophic webs and large bodied individuals1–3. Protection may also alter community responses to long-term climate change by offering habitat for range-shifting species4. Here we analyse the species richness, diversity and functional traits of temperate reef fish communities over 20 years in a global warming hotspot and compare patterns in a marine reserve with nearby sites open to fishing. Species richness and diversity oscillated strongly on the decadal scale. Long-term warming signatures were also present as increasing functional trait richness and functional diversity, driven in part by a general increase in herbivores. Nevertheless, reserve sites were distinguished from fished sites by displaying: greater stability in some aspects of biodiversity; recovery of large-bodied temperate species; resistance to colonization by subtropical vagrants; and less pronounced increases in the community-averaged temperature affinity. We empirically demonstrate that protection from fishing has buffered fluctuations in biodiversity and provided resistance to the initial stages of tropicalization.


Integrating abundance and functional traits reveals new global hotspots of fish diversity.

Nature 501: 539-542 (2013)

Adds an additional layer to understanding of the world’s fish diversity, showing patterns in abundance and characteristics of species that differ from patterns in species richness.


Species richness has dominated our view of global biodiversity patterns for centuries1,2. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broadscale diversity patterns and as a biological basis for management3,4. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling)5. Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao’s Q6), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only7,8. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites (‘community evenness’), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness2,4. Our findings suggest that the contribution of species diversity to a range of ecosystem functions varies over large scales, and imply that in tropical regions, which have higher numbers of species, each species contributes proportionally less to community-level ecological processes on average than species in temperate regions. Metrics of ecological function usefully complement metrics of species diversity in conservation management, including when identifying planning priorities and when tracking changes to biodiversity values.


Pre 2013

Global human footprint on the linkage between biodiversity and ecosystem functioning in reef fishes.

PLoS Biology 9: e1000606 (2011)

Explores the relationships between the number of species and the total biomass of reef fishes.


Difficulties in scaling up theoretical and experimental results have raised controversy over the consequences of biodiversity loss for the functioning of natural ecosystems. Using a global survey of reef fish assemblages, we show that in contrast to previous theoretical and experimental studies, ecosystem functioning (as measured by standing biomass) scales in a non-saturating manner with biodiversity (as measured by species and functional richness) in this ecosystem. Our field study also shows a significant and negative interaction between human population density and biodiversity on ecosystem functioning (i.e., for the same human density there were larger reductions in standing biomass at more diverse reefs). Human effects were found to be related to fishing, coastal development, and land use stressors, and currently affect over 75% of the world’s coral reefs. Our results indicate that the consequences of biodiversity loss in coral reefs have been considerably underestimated based on existing knowledge and that reef fish assemblages, particularly the most diverse, are greatly vulnerable to the expansion and intensity of anthropogenic stressors in coastal areas.

Research challenges to improve the management and conservation of subtropical reefs to tackle climate change threats.

Ecological Management and Restoration 12:e7 -e10 (2011)

A summary from a workshop of scientists and managers who work with reef communities in dynamic subtropical zones


This paper reports on a workshop conducted in Australia in 2010, entitled ‘Management, Conservation, and Scientific Challenges on Subtropical Reefs under Climate Change’. The workshop brought together 26 experts actively involved in the science and management of subtropical reefs. Its primary aim was to identify the areas of research that need to be most urgently addressed to improve the decision-making framework for managers of subtropical reefs. The main findings of the workshop were a sustainable subtropical reefs declaration that highlights seven research priorities for subtropical reefs. These are to (i) conduct research and management activities across local government, state and bioregion borders; (ii) understand natural variability of environmental conditions; (iii) quantify socio-economic factors and ecosystem services; (iv) benchmark cross-realm connectivity; (v) know marine population connectivity; (vi) habitat mapping and ecological research; and (v) determine refugia. These findings are hoped to form a basis for focussing research efforts, leveraging funds and assisting managers with allocation of resources.

Exploited reefs protected from fishing transform over decades into conservation features otherwise absent from seascapes

Ecological Applications 19: 1967-1974 (2009)

Fish biomass recovery in MPAs of different ages demonstrates the long timeframes needed for fish communities to return to a more natural state.


Tasmanian reef communities within ‘‘no-take’’ marine protected areas (MPAs) exhibited direct and indirect ecological changes that increasingly manifested over 16 years, eventually transforming into communities not otherwise present in the regional seascape. Data from 14 temperate and subtropical Australian MPAs further demonstrated that ecological changes continue to develop in MPAs over at least two decades, probably much longer. The continent-scale study additionally showed recently established MPAs to be consistently located at sites with low resource value relative to adjacent fished reference areas. This outcome was presumably generated by sociopolitical pressures and planning processes that aim to systematically avoid locations with valuable resources, potentially compromising biodiversity conservation goals. Locations that were formerly highly fished are needed within MPA networks if the networks are to achieve conservation aims associated with (1) safeguarding all regional habitat types, (2) protecting threatened habitats and species, and (3) providing appropriate reference benchmarks for assessing impacts of fishing. Because of long time lags, the ubiquity of fishing impacts, and the relatively recent establishment of MPAs, the full impact of fishing on coastal reefs has yet to be empirically assessed.

Ecological effects of marine protected areas on rocky reef communities: a continental-scale analysis

Marine Ecology Press Series 388: 51-62 (2009)

The first analysis of RLS data, including comparison of data quality from trainees vs scientists


Data compiled by volunteer divers were utilised in a continental-scale investigation of ecological differences between reefs in no-take sanctuary zones in marine protected areas (MPAs) and adjacent fished zones. In a validation analysis, volunteer-generated data were found to be comparable to data obtained by scientific dive teams for all metrics investigated: estimated total number of species, total faunal abundance, mean fish size, and faunal composition of species sighted along transects. Variation between individual divers within volunteer and professional groups also contributed little to total estimated variance between transects compared to residual variation between replicate transects, variation between sites, and variation between regions studied. Sites in 11 MPAs distributed around 5000 km of the Australian coastline had significantly more large (>30 cm) fishes and total fish biomass than nearby fished reference sites. For the older MPAs, fishes belonging to the largest size class (80 cm) were observed approximately 10 times more often in sanctuary zones than in fished zones, while fishes in the smallest size class (2.5 cm) occurred at densities approximately 4 times higher in fished zones than in sanctuary zones. Results of our empirical field surveys contrast in several respects with outcomes of published meta-analyses. No overall differences in fish densities were evident between sanctuary zones and fished zones. The response of fish species richness to protection varied significantly between different MPAs, while invertebrate density and species richness were both significantly lower in sanctuary zones than in fished zones.

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