108 results on '"Sean R. Connolly"'
Search Results
2. The spatial footprint and patchiness of large‐scale disturbances on coral reefs
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Michael Bode, Andreas Dietzel, Terry P. Hughes, and Sean R. Connolly
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Global and Planetary Change ,geography ,geography.geographical_feature_category ,Ecology ,Coral Reefs ,Cyclonic Storms ,Coral bleaching ,Coral reef ,Anthozoa ,Spatial distribution ,Disturbance (ecology) ,Larva ,Animals ,Humans ,Environmental Chemistry ,Environmental science ,Biological dispersal ,Ecosystem ,Tropical cyclone ,Reef ,General Environmental Science - Abstract
Ecosystems have always been shaped by disturbances, but many of these events are becoming larger, more severe and more frequent. The recovery capacity of depleted populations depends on the frequency of disturbances, the spatial distribution of mortality and the scale of dispersal. Here, we show that four mass coral bleaching events on the Great Barrier Reef (in 1998, 2002, 2016 and 2017) each had markedly larger disturbance footprints and were less patchy than a severe category 5 tropical cyclone (Cyclone Yasi, 2011). Severely bleached reefs in 2016 and 2017 were isolated from the nearest lightly affected reefs by up to 146 and 200 km, respectively. In contrast, reefs damaged by Cyclone Yasi were on average 20 km away from relatively undisturbed reefs, well within the estimated range of larval dispersal for most corals. Based on these results, we present a model of coral reef disturbance and recovery to examine (1) how the spatial clustering of disturbances modifies large-scale recovery rates; and (2) how recovery rates are shaped by species' dispersal abilities. Our findings illustrate that the spatial footprint of the recent mass bleaching events poses an unprecedented threat to the resilience of coral species in human history, a threat that is even larger than the amount of mortality suggests.
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- 2021
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3. Human exploitation shapes productivity–biomass relationships on coral reefs
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Renato A. Morais, Sean R. Connolly, and David R. Bellwood
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0106 biological sciences ,Conservation of Natural Resources ,010504 meteorology & atmospheric sciences ,Coral reef fish ,Fishing ,Fisheries ,complex mixtures ,010603 evolutionary biology ,01 natural sciences ,Coral Triangle ,Animals ,Humans ,Environmental Chemistry ,Biomass ,Ecosystem ,0105 earth and related environmental sciences ,General Environmental Science ,Global and Planetary Change ,Biomass (ecology) ,geography ,geography.geographical_feature_category ,Ecology ,Overfishing ,Coral Reefs ,Fishes ,food and beverages ,Coral reef ,Anthozoa ,Fishery ,Overexploitation ,Productivity (ecology) ,Environmental science - Abstract
Coral reef fisheries support the livelihoods of millions of people in tropical countries, despite large-scale depletion of fish biomass. While human adaptability can help to explain the resistance of fisheries to biomass depletion, compensatory ecological mechanisms may also be involved. If this is the case, high productivity should coexist with low biomass under relatively high exploitation. Here we integrate large spatial scale empirical data analysis and a theory-driven modelling approach to unveil the effects of human exploitation on reef fish productivity-biomass relationships. We show that differences in how productivity and biomass respond to overexploitation can decouple their relationship. As size-selective exploitation depletes fish biomass, it triggers increased production per unit biomass, averting immediate productivity collapse in both the modelling and the empirical systems. This 'buffering productivity' exposes the danger of assuming resource production-biomass equivalence, but may help to explain why some biomass-depleted fish assemblages still provide ecosystem goods under continued global fishing exploitation.
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- 2020
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4. Reply to: Conclusions of low extinction risk for most species of reef-building corals are premature
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Andreas Dietzel, Michael Bode, Sean R. Connolly, and Terry P. Hughes
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Ecology ,Ecology, Evolution, Behavior and Systematics - Published
- 2022
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5. Global warming impairs stock–recruitment dynamics of corals
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Sean R. Connolly, Tory J. Chase, Ailsa P. Kerswell, Andrew H. Baird, Mia O. Hoogenboom, Tessa Hill, Morgan S. Pratchett, Terry P. Hughes, Andreas Dietzel, Allison S. Paley, Gergely Torda, James T. Kerry, Joshua S. Madin, Andrew S. Hoey, Rachael M. Woods, Abbie Mieog, and Mizue Jacobson
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0106 biological sciences ,geography ,Multidisciplinary ,geography.geographical_feature_category ,Coral bleaching ,Ecology ,010604 marine biology & hydrobiology ,fungi ,Global warming ,technology, industry, and agriculture ,Climate change ,Coral reef ,Biology ,010603 evolutionary biology ,01 natural sciences ,Brood ,Ecological collapse ,Biological dispersal ,Ecosystem - Abstract
Changes in disturbance regimes due to climate change are increasingly challenging the capacity of ecosystems to absorb recurrent shocks and reassemble afterwards, escalating the risk of widespread ecological collapse of current ecosystems and the emergence of novel assemblages1–3. In marine systems, the production of larvae and recruitment of functionally important species are fundamental processes for rebuilding depleted adult populations, maintaining resilience and avoiding regime shifts in the face of rising environmental pressures4,5. Here we document a regional-scale shift in stock–recruitment relationships of corals along the Great Barrier Reef—the world’s largest coral reef system—following unprecedented back-to-back mass bleaching events caused by global warming. As a consequence of mass mortality of adult brood stock in 2016 and 2017 owing to heat stress6, the amount of larval recruitment declined in 2018 by 89% compared to historical levels. For the first time, brooding pocilloporids replaced spawning acroporids as the dominant taxon in the depleted recruitment pool. The collapse in stock–recruitment relationships indicates that the low resistance of adult brood stocks to repeated episodes of coral bleaching is inexorably tied to an impaired capacity for recovery, which highlights the multifaceted processes that underlie the global decline of coral reefs. The extent to which the Great Barrier Reef will be able to recover from the collapse in stock–recruitment relationships remains uncertain, given the projected increased frequency of extreme climate events over the next two decades7. A regional-scale shift in the relationships between adult stock and recruitment of corals occurred along the Great Barrier Reef, following mass bleaching events in 2016 and 2017 caused by global warming.
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- 2019
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6. Coral adaptation to climate change: Meta-analysis reveals high heritability across multiple traits
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Madeleine J. H. van Oppen, Mia O. Hoogenboom, Sean R. Connolly, and Kevin R. Bairos-Novak
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0106 biological sciences ,Coral ,Acclimatization ,Climate Change ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Genetic variation ,Environmental Chemistry ,Animals ,14. Life underwater ,Stabilizing selection ,030304 developmental biology ,General Environmental Science ,0303 health sciences ,Global and Planetary Change ,Natural selection ,Ecology ,Coral Reefs ,Quantitative genetics ,Heritability ,Anthozoa ,Adaptation, Physiological ,13. Climate action ,Trait ,Adaptation - Abstract
Anthropogenic climate change is a rapidly intensifying selection pressure on biodiversity across the globe and, particularly, on the world's coral reefs. The rate of adaptation to climate change is proportional to the amount of phenotypic variation that can be inherited by subsequent generations (i.e., narrow-sense heritability, h2 ). Thus, traits that have higher heritability (e.g., h2 > 0.5) are likely to adapt to future conditions faster than traits with lower heritability (e.g., h2
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- 2021
7. Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution
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J. Emmett Duffy, Laetitia G. E. Wilkins, Sarah A. Gignoux-Wolfsohn, William T. Wcislo, W. Owen McMillan, Benedict Yuen, Melissa K. McCormick, Jonathan A. Eisen, Tiago José Pereira, Matthieu Leray, Elin Videvall, Friederike Clever, Sean R. Connolly, Aaron O'Dea, Edward Allen Herre, Mark E. Torchin, Amy Apprill, Jordan G. Kueneman, Jonathan Z. Kaye, David I. Kline, Leïla Ezzat, Jillian M. Petersen, Marina E. De León, Rebecca Vega Thurber, Daniel F. Petticord, and Holly M. Bik
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0106 biological sciences ,Aquatic Organisms ,Environmental change ,Acclimatization ,Marine and Aquatic Sciences ,Pathogenesis ,Pathology and Laboratory Medicine ,01 natural sciences ,Medical and Health Sciences ,Microbial ecology ,Medicine and Health Sciences ,Marine Fish ,Biology (General) ,0303 health sciences ,Ecology ,Microbial evolution ,General Neuroscience ,Microbiota ,Eukaryota ,Genomics ,Biological Sciences ,Biological Evolution ,Medical Microbiology ,Vertebrates ,General Agricultural and Biological Sciences ,Marine ecosystems ,Evolutionary Processes ,QH301-705.5 ,Essay ,Marine geology ,Marine Biology ,Microbial Genomics ,Biology ,010603 evolutionary biology ,Microbiology ,General Biochemistry, Genetics and Molecular Biology ,Natural (archaeology) ,Ecosystems ,Marine ecology ,03 medical and health sciences ,Evolutionary Adaptation ,Genetics ,Animals ,Humans ,Marine ecosystem ,14. Life underwater ,Microbiome ,Community ecology ,Symbiosis ,Ecosystem ,030304 developmental biology ,Evolutionary Biology ,General Immunology and Microbiology ,Community ,Agricultural and Veterinary Sciences ,Host-pathogen interactions ,Ecology and Environmental Sciences ,Organisms ,Biology and Life Sciences ,Organismal Evolution ,Multicellular organism ,Fish ,13. Climate action ,Earth Sciences ,Evolutionary ecology ,Zoology ,Developmental Biology - Abstract
Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions., This Essay argues that in order to truly understand how marine hosts benefit from the immense diversity of microbes, we need to expand towards long-term, multi-disciplinary research focussing on few areas of the world’s ocean that we refer to as “natural experiments,” where processes can be studied at scales that far exceed those captured in laboratory experiments.
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- 2021
8. Long-term shifts in the colony size structure of coral populations along the Great Barrier Reef
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Michael Bode, Terry P. Hughes, Andreas Dietzel, and Sean R. Connolly
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0106 biological sciences ,Coral bleaching ,Coral ,Population ,Biology ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Abundance (ecology) ,Animals ,14. Life underwater ,education ,Reef ,General Environmental Science ,education.field_of_study ,geography ,geography.geographical_feature_category ,General Immunology and Microbiology ,Ecology ,Coral Reefs ,Reproduction ,010604 marine biology & hydrobiology ,fungi ,Australia ,technology, industry, and agriculture ,General Medicine ,biochemical phenomena, metabolism, and nutrition ,Anthozoa ,Fertility ,Taxon ,Habitat ,Disturbance (ecology) ,population characteristics ,General Agricultural and Biological Sciences ,geographic locations - Abstract
The age or size structure of a population has a marked influence on its demography and reproductive capacity. While declines in coral cover are well documented, concomitant shifts in the size-frequency distribution of coral colonies are rarely measured at large spatial scales. Here, we document major shifts in the colony size structure of coral populations along the 2300 km length of the Great Barrier Reef relative to historical baselines (1995/1996). Coral colony abundances on reef crests and slopes have declined sharply across all colony size classes and in all coral taxa compared to historical baselines. Declines were particularly pronounced in the northern and central regions of the Great Barrier Reef, following mass coral bleaching in 2016 and 2017. The relative abundances of large colonies remained relatively stable, but this apparent stability masks steep declines in absolute abundance. The potential for recovery of older fecund corals is uncertain given the increasing frequency and intensity of disturbance events. The systematic decline in smaller colonies across regions, habitats and taxa, suggests that a decline in recruitment has further eroded the recovery potential and resilience of coral populations.
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- 2020
9. Disturbance-induced changes in size-structure promote coral biodiversity
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Maria Dornelas, Sean R. Connolly, Joshua S. Madin, Andrew H. Baird, and Mariana Álvarez-Noriega
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Coexistence theory ,Competition model ,Disturbance (geology) ,Population model ,Ecology ,Coral ,media_common.quotation_subject ,Biodiversity ,Biology ,Competitive exclusion ,Competition (biology) ,media_common - Abstract
Reef-building coral assemblages are typically species-rich, yet the processes maintaining coral biodiversity remain poorly understood. Disturbance has long been believed to promote coral species coexistence by reducing the strength of competition. However, such disturbance-induced effects have since been shown to be insufficient on their own to prevent competitive exclusion. Nevertheless, Modern Coexistence Theory has revealed other mechanisms by which disturbance and, more generally, environmental variation can favour coexistence. Here, we formulate, calibrate, and analyze a size-structured, stochastic coral competition model using field data from two common colony morphologies. These two coral morphologies, tabular and digitate, differ in their size-dependent vulnerability to dislodgement caused by wave action. We confirm that fluctuations in wave action can promote coral species coexistence. However, using a recently proposed partitioning framework, we show that, contrast to previous expectations, temporal variability in strength of competition did not promote coexistence. Instead, coexistence was enabled by differential fluctuations in size-dependent mortality among competitors. Frequent and intense disturbances resulted in monocultures of digitate corals, which are more robust to wave action than tabular corals. In contrast, infrequent or weak disturbances resulted in monocultures of tabular corals. Coexistence was only possible under intermediate levels of disturbance frequency and intensity. Given the sensitivity of coexistence to disturbance frequency and intensity, anthropogenic changes in disturbance regimes are likely to affect biodiversity in coral assemblages in ways that are not predictable from single population models.
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- 2020
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10. The population sizes and global extinction risk of reef-building coral species at biogeographic scales
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Michael Bode, Andreas Dietzel, Sean R. Connolly, and Terry P. Hughes
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0106 biological sciences ,Population ,Biodiversity ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Abundance (ecology) ,Animals ,natural sciences ,education ,Reef ,Ecology, Evolution, Behavior and Systematics ,Ecosystem ,030304 developmental biology ,Population Density ,0303 health sciences ,education.field_of_study ,Extinction ,geography.geographical_feature_category ,Pacific Ocean ,Ecology ,Amazon rainforest ,Coral Reefs ,fungi ,technology, industry, and agriculture ,social sciences ,Coral reef ,Anthozoa ,Geography ,Indonesia ,Coral species ,geographic locations - Abstract
Knowledge of a species’ abundance is critically important for assessing its risk of extinction, but for the vast majority of wild animal and plant species such data are scarce at biogeographic scales. Here, we estimate the total number of reef-building corals and the population sizes of more than 300 individual species on reefs spanning the Pacific Ocean biodiversity gradient, from Indonesia to French Polynesia. Our analysis suggests that approximately half a trillion corals (0.3 × 1012–0.8 × 1012) inhabit these coral reefs, similar to the number of trees in the Amazon. Two-thirds of the examined species have population sizes exceeding 100 million colonies, and one-fifth of the species even have population sizes greater than 1 billion colonies. Our findings suggest that, while local depletions pose imminent threats that can have ecologically devastating impacts to coral reefs, the global extinction risk of most coral species is lower than previously estimated. Approximately half a trillion reef-building corals live across the Pacific Ocean, based on estimates of the population sizes of more than 300 species.
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- 2020
11. Ecological memory modifies the cumulative impact of recurrent climate extremes
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C. Mark Eakin, Mizue Jacobson, Terry P. Hughes, Andrew S. Hoey, Andrew H. Baird, Scott F. Heron, James T. Kerry, Morgan S. Pratchett, Mia O. Hoogenboom, Gang Liu, Gergely Torda, Sean R. Connolly, and William J. Skirving
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0303 health sciences ,010504 meteorology & atmospheric sciences ,Severe weather ,Ecology ,Extreme events ,Climate change ,Environmental Science (miscellaneous) ,01 natural sciences ,Great barrier reef ,03 medical and health sciences ,Geography ,Disturbance (ecology) ,Spatial ecology ,Ecosystem ,Climate extremes ,Social Sciences (miscellaneous) ,030304 developmental biology ,0105 earth and related environmental sciences - Abstract
Climate change is radically altering the frequency, intensity and spatial scale of severe weather events, such as heatwaves, droughts, floods and fires1. As the time interval shrinks between recurrent shocks2–5, the responses of ecosystems to each new disturbance are increasingly likely to be contingent on the history of other recent extreme events. Ecological memory—defined as the ability of the past to influence the present trajectory of ecosystems6,7—is also critically important for understanding how species assemblages are responding to rapid changes in disturbance regimes due to anthropogenic climate change2,3,6–8. Here, we show the emergence of ecological memory during unprecedented back-to-back mass bleaching of corals along the 2,300 km length of the Great Barrier Reef in 2016, and again in 2017, whereby the impacts of the second severe heatwave, and its geographic footprint, were contingent on the first. Our results underscore the need to understand the strengthening interactions among sequences of climate-driven events, and highlight the accelerating and cumulative impacts of novel disturbance regimes on vulnerable ecosystems. The increasing frequency of marine heatwaves suggests that the impacts of successive events may be influenced by previous events. The extent of the 2016 and 2017 bleaching events on the Great Barrier Reef shows that ecological memory played a role in the impacts of the second heatwave.
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- 2018
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12. Effects of tropical storms on the demography of reef corals
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Maria Dornelas, Joshua S. Madin, Sean R. Connolly, Mariana Álvarez-Noriega, Andrew H. Baird, Vivian R. Cumbo, European Research Council, University of St Andrews. School of Biology, University of St Andrews. Centre for Biological Diversity, University of St Andrews. Fish Behaviour and Biodiversity Research Group, and University of St Andrews. Marine Alliance for Science & Technology Scotland
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0106 biological sciences ,Coral reefs ,Coral bleaching ,QH301 Biology ,NDAS ,Aquatic Science ,010603 evolutionary biology ,01 natural sciences ,QH301 ,Recovery ,SDG 13 - Climate Action ,Climate change ,Acropora ,Reef ,Ecology, Evolution, Behavior and Systematics ,Demography ,Poritidae ,geography ,geography.geographical_feature_category ,Ecology ,biology ,010604 marine biology & hydrobiology ,Disturbance ,Coral reef ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Goniastrea retiformis ,Cyclone ,Tropical cyclone - Abstract
Funding was provided by the Australian Research Council Centre of Excellence for Coral Reef Studies (CE140100020), a Future Fellowship (A.H.B.), an Australian Professorial Fellowship (S.R.C.) and the Templeton Foundation (grant no. 60501, ‘Putting the Extended Evolutionary Synthesis to the Test’). M.D. is grateful to the Scottish Funding Council (MASTS, grant reference HR09011) and the European Research Council (grant BioTIME). Disturbances, such as cyclones, have a major effect on the structure and dynamics of coral reef assemblages. However, the effect of cyclones on demographic traits, such as fecundity, has rarely been quantified, and direct estimates of mortality at the species level are rare. Here, we document the effect of Severe Tropical Cyclone Nathan on the demography of corals on the reef crest at Trimodal Reef in the northern Great Barrier Reef. Mortality rates based on tagged colonies were very high, ranging from 85.2% in Goniastrea retiformis to 100% in 6 Acropora species, 3 to 40 times higher than averages rates in the 5 yr preceding Cyclone Nathan. Fecundity was lower in 3 out of the 4 species examined following the cyclone, and egg carbon content was reduced by 58-63% in the 2 species examined. These results suggest that energy normally invested in reproduction was diverted to other processes such as injury repair and demonstrate that cyclones have important sub-lethal effects in addition to high rates of whole colony mortality. Coral cover was reduced from 34.9 ± 3.9% (mean ± SE) to 3.4 ± 1.5%, with reductions in the cover of all taxa except those with predominantly massive morphologies such as the Poritidae. A projected increase in the frequency of tropical storms as a result of global warming, combined with an increase in the frequency and scale of coral bleaching, suggest a fundamental shift in mortality regimes on reefs which has the potential to threaten their long-term persistence. Postprint
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- 2018
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13. Cumulative effects of cyclones and bleaching on coral cover and species richness at Lizard Island
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Andrew H. Baird, Joshua S. Madin, Kyle J. A. Zawada, Tom C. L. Bridge, Maria Dornelas, Sean R. Connolly, John Templeton Foundation, University of St Andrews. School of Biology, University of St Andrews. Centre for Biological Diversity, University of St Andrews. Fish Behaviour and Biodiversity Research Group, and University of St Andrews. Marine Alliance for Science & Technology Scotland
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0106 biological sciences ,Coral reefs ,QH301 Biology ,Coral ,NDAS ,Aquatic Science ,010603 evolutionary biology ,01 natural sciences ,QH301 ,Great Barrier Reef ,SDG 13 - Climate Action ,Climate change ,Community ecology ,Transect ,Reef ,Ecology, Evolution, Behavior and Systematics ,Diversity ,geography ,geography.geographical_feature_category ,Ecology ,Community ,010604 marine biology & hydrobiology ,Disturbance ,Coral reef ,Oceanography ,Disturbance (ecology) ,Spatial ecology ,Environmental science ,Species richness - Abstract
Funding was provided by the Australian Council Centre of Excellence for Coral Reef Studies (COE140100020) and the John Templeton Foundation (M.D., J.S.M. grant #60501 'Putting the Extended Evolutionary Synthesis to the Test’). Coral reefs are being subjected to an increase in the frequency and intensity of disturbance, such as bleaching and cyclones, and it is important to document the effects of such disturbance on reef coral assemblages. Between March 2014 and May 2017, the reefs of Lizard Island in the northern section of the Great Barrier Reef were affected by 4 consecutive disturbances: severe tropical cyclones Ita and Nathan in 2014 and 2015, and mass bleaching events in 2016 and 2017. Loss of coral cover following the cyclones was patchy and dependent on the direction of the waves generated. In contrast, loss of cover following bleaching was much more uniform. Overall, coral cover declined 5-fold from 36% pre-cyclone Ita to 7% post-bleaching in 2017, while mean species richness dropped from 10 to 4 species per transect. The spatial scale and magnitude of the loss of coral cover in the region suggests that it will be many years before these reefs recover. Postprint
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- 2018
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14. Emergent properties in the responses of tropical corals to recurrent climate extremes
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Joanne Moneghetti, Migdonio A. Gonzalez, Sean R. Connolly, Jorge G. Álvarez-Romero, Scott F. Heron, Terry P. Hughes, C. Mark Eakin, and James T. Kerry
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geography ,geography.geographical_feature_category ,Coral bleaching ,Ecology ,Global warming ,Climate change ,Coral reef ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Spatial heterogeneity ,Spatial ecology ,Climate model ,General Agricultural and Biological Sciences ,Reef - Abstract
The frequency, intensity, and spatial scale of climate extremes are changing rapidly due to anthropogenic global warming.1,2 A growing research challenge is to understand how multiple climate-driven disturbances interact with each other over multi-decadal time frames, generating combined effects that cannot be predicted from single events alone.3, 4, 5 Here we examine the emergent dynamics of five coral bleaching events along the 2,300 km length of the Great Barrier Reef that affected >98% of the Reef between 1998 and 2020. We show that the bleaching responses of corals to a given level of heat exposure differed in each event and were strongly influenced by contingency and the spatial overlap and strength of interactions between events. Naive regions that escaped bleaching for a decade or longer were the most susceptible to bouts of heat exposure. Conversely, when pairs of successive bleaching episodes were close together (1–3 years apart), the thermal threshold for severe bleaching increased because the earlier event hardened regions of the Great Barrier Reef to further impacts. In the near future, the biological responses to recurrent bleaching events may become stronger as the cumulative geographic footprint expands further, potentially impairing the stock-recruitment relationships among lightly and severely bleached reefs with diverse recent histories. Understanding the emergent properties and collective dynamics of recurrent disturbances will be critical for predicting spatial refuges and cumulative ecological responses, and for managing the longer-term impacts of anthropogenic climate change on ecosystems.
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- 2021
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15. Process, Mechanism, and Modeling in Macroecology
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Robert K. Colwell, Carsten Rahbek, Sean R. Connolly, and Sally A. Keith
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0106 biological sciences ,0301 basic medicine ,Ecology ,Geography ,Process (engineering) ,Ecology (disciplines) ,Models, Theoretical ,Biology ,010603 evolutionary biology ,01 natural sciences ,Data science ,03 medical and health sciences ,030104 developmental biology ,Process mechanism ,Ecology, Evolution, Behavior and Systematics ,Macroecology - Abstract
Macroecology has traditionally relied on descriptive characterization of large-scale ecological patterns to offer narrative explanations for the origin and maintenance of those patterns. Only recently have macroecologists begun to employ models termed ‘process-based’ and ‘mechanistic’, in contrast to other areas of ecology, where such models have a longer history. Here, we define and differentiate between process-based and mechanistic features of models, and we identify and discuss important advantages of working with models possessing such features. We describe some of the risks associated with process-based and mechanistic model-centered research programs, and we propose ways to mitigate these risks. Giving process-based and mechanistic models a more central role in research programs can reinvigorate macroecology by strengthening the link between theory and data.
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- 2017
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16. A unified model explains commonness and rarity on coral reefs
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David R. Bellwood, Terry P. Hughes, and Sean R. Connolly
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0106 biological sciences ,0301 basic medicine ,Metacommunity ,Biodiversity ,Biology ,Models, Biological ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Ecological relationship ,Abundance (ecology) ,Animals ,14. Life underwater ,Ecology, Evolution, Behavior and Systematics ,Macroecology ,Relative abundance distribution ,Population Density ,geography ,Pacific Ocean ,geography.geographical_feature_category ,Coral Reefs ,Ecology ,Fishes ,Coral reef ,15. Life on land ,Anthozoa ,030104 developmental biology ,Species richness - Abstract
Abundance patterns in ecological communities have important implications for biodiversity maintenance and ecosystem functioning. However, ecological theory has been largely unsuccessful at capturing multiple macroecological abundance patterns simultaneously. Here, we propose a parsimonious model that unifies widespread ecological relationships involving local aggregation, species-abundance distributions, and species associations, and we test this model against the metacommunity structure of reef-building corals and coral reef fishes across the western and central Pacific. For both corals and fishes, the unified model simultaneously captures extremely well local species-abundance distributions, interspecific variation in the strength of spatial aggregation, patterns of community similarity, species accumulation, and regional species richness, performing far better than alternative models also examined here and in previous work on coral reefs. Our approach contributes to the development of synthetic theory for large-scale patterns of community structure in nature, and to addressing ongoing challenges in biodiversity conservation at macroecological scales.
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- 2017
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17. The molecular biogeography of the Indo-Pacific
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Jeff A. Eble, Eric A. Treml, Maria Beger, Shang-Yin Vanson Liu, Hawis Madduppa, Joseph D. DiBattista, Christopher E. Bird, Harilaos A. Lessios, William B. Ludt, Sharon F. Magnuson, John B. Horne, Eric D. Crandall, Marc Kochzius, Paul H. Barber, John M. Pandolfi, Robert J. Toonen, Libby Liggins, Michelle R. Gaither, Peter F. Cowman, Cynthia Riginos, Sean R. Connolly, Biology, and Ecology and Systematics
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0106 biological sciences ,comparative phylogeography ,Population ,Biology ,biogeographic provinces ,010603 evolutionary biology ,01 natural sciences ,Coalescent theory ,Genetic drift ,Effective population size ,analysis of molecular variance ,Vicariance ,discordance ,education ,dispersal ,Ecology, Evolution, Behavior and Systematics ,education.field_of_study ,Global and Planetary Change ,Ecology ,Null model ,010604 marine biology & hydrobiology ,Phylogeography ,biogeographic realms ,ecology ,distance-based redundancy analysis ,Indo-Pacific - Abstract
Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo-Pacific Ocean. Time period: Pliocene through the Holocene. Major taxa studied: Fifty-six marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise ΦST with a distance-based redundancy analysis (dbRDA). Results: We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographic or environmental barriers other than distance. Main conclusions: Although there is support for three previously described barriers, phylogeographic discordance in the Indo-Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo-Pacific species, even hard vicariance for tens of thousands of years can yield ΦSTvalues that range from 0 to nearly 0.5.
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- 2019
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18. Marine reserves stabilize fish populations and fisheries yields in disturbed coral reef systems
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Jess K. Hopf, Geoffrey P. Jones, David H. Williamson, and Sean R. Connolly
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0106 biological sciences ,Conservation of Natural Resources ,Population ,Fisheries ,Metapopulation ,010603 evolutionary biology ,01 natural sciences ,Animals ,education ,Ecosystem ,geography ,education.field_of_study ,geography.geographical_feature_category ,Ecology ,biology ,Coral Reefs ,010604 marine biology & hydrobiology ,fungi ,Marine reserve ,Australia ,Fishes ,Coral reef ,biology.organism_classification ,Fishery ,Reserve design ,Environmental science ,Marine protected area ,Fisheries management ,Coral trout - Abstract
Marine reserve networks are increasingly implemented to conserve biodiversity and enhance the persistence and resilience of exploited species and ecosystems. However, the efficacy of marine reserve networks in frequently disturbed systems, such as coral reefs, has rarely been evaluated. Here we analyze a well-mixed larval pool model and a spatially explicit model based on a well-documented coral trout (Plectropomus spp.) metapopulation in the Great Barrier Reef Marine Park, Australia, to determine the effects of marine reserve coverage and placement (in relation to larval connectivity and disturbance heterogeneity) on the temporal stability of fisheries yields and population biomass in environmentally disturbed systems. We show that marine reserves can contribute to stabilizing fishery yield while increasing metapopulation persistence, irrespective of whether reserves enhance or diminish average fishery yields. However, reserve placement and the level of larval connectivity among subpopulations were important factors affecting the stability and sustainability of fisheries and fish metapopulations. Protecting a mix of disturbed and non-disturbed reefs, rather than focusing on the least-disturbed habitats, was the most consistently beneficial approach across a range of dispersal and reserve coverage scenarios. Placing reserves only in non-disturbed areas was the most beneficial for biomass enhancement, but had variable results for fisheries and could potentially destabilize yields in systems with well-mixed larval or those that are moderately fished. We also found that focusing protection on highly disturbed areas could actually increase variability in yields and biomass, especially when degraded reef reserves were distant and poorly connected to the meta-population. Our findings have implications for the design and implementation of reserve networks in the presence of stochastic, patchy environmental disturbances.
- Published
- 2019
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19. Author Correction: The population sizes and global extinction risk of reef-building coral species at biogeographic scales
- Author
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Terry P. Hughes, Andreas Dietzel, Michael Bode, and Sean R. Connolly
- Subjects
geography ,education.field_of_study ,geography.geographical_feature_category ,Extinction ,Ecology ,Population ,Coral species ,education ,Reef ,Ecology, Evolution, Behavior and Systematics - Published
- 2021
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20. Prevalence of multimodal species abundance distributions is linked to spatial and taxonomic breadth
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Amadeu M.V.M. Soares, Sean R. Connolly, Maria Dornelas, Laura H. Antão, and Anne E. Magurran
- Subjects
0106 biological sciences ,Global and Planetary Change ,Ecology ,010604 marine biology & hydrobiology ,Biology ,010603 evolutionary biology ,01 natural sciences ,Ecology, Evolution, Behavior and Systematics - Abstract
We thank the University of St Andrews MHD Cluster and the Bioinformatics Unit (Wellcome Trust ISSF grant 105621/Z/14/Z). L.H.A. was supported by Fundacao para a Ciencia e Tecnologia, Portugal (POPH/FSE SFRH/BD/90469/2012). A.E.M. acknowledges the ERC (BioTIME 250189). M.D. acknowledges funding from the Marine Alliance for Science and Technology Scotland (MASTS), funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.
- Published
- 2016
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21. A test of trophic cascade theory: fish and benthic assemblages across a predator density gradient on coral reefs
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Simon J. Brandl, Justin R. Rizzari, Ashley J. Frisch, Jordan M. Casey, Christopher E. Mirbach, Sean R. Connolly, Mia O. Hoogenboom, and Andrew H. Baird
- Subjects
0106 biological sciences ,geography ,geography.geographical_feature_category ,Coral Reefs ,Ecology ,010604 marine biology & hydrobiology ,fungi ,Fishes ,Nutritional Status ,Coral reef ,Biology ,010603 evolutionary biology ,01 natural sciences ,Predation ,Fishery ,Mesopredator release hypothesis ,Benthic zone ,Animals ,Herbivory ,Trophic cascade ,Reef ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,Apex predator ,Trophic level - Abstract
Removal of predators is often hypothesized to alter community structure through trophic cascades. However, despite recent advances in our understanding of trophic cascades, evidence is often circumstantial on coral reefs because fishing pressure frequently co-varies with other anthropogenic effects, such as fishing for herbivorous fishes and changes in water quality due to pollution. Australia's outer Great Barrier Reef (GBR) has experienced fishing-induced declines of apex predators and mesopredators, but pollution and targeting of herbivorous fishes are minimal. Here, we quantify fish and benthic assemblages across a fishing-induced predator density gradient on the outer GBR, including apex predators and mesopredators to herbivores and benthic assemblages, to test for evidence of trophic cascades and alternative hypotheses to trophic cascade theory. Using structural equation models, we found no cascading effects from apex predators to lower trophic levels: a loss of apex predators did not lead to higher levels of mesopredators, and this did not suppress mobile herbivores and drive algal proliferation. Likewise, we found no effects of mesopredators on lower trophic levels: a decline of mesopredators was not associated with higher abundances of algae-farming damselfishes and algae-dominated reefs. These findings indicate that top-down forces on coral reefs are weak, at least on the outer GBR. We conclude that predator-mediated trophic cascades are probably the exception rather than the rule in complex ecosystems such as the outer GBR.
- Published
- 2016
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22. Uncoupling temperature-dependent mortality from lipid depletion for scleractinian coral larvae
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Erin Graham, Bette L. Willis, Andrew H. Baird, Sean R. Connolly, and Mary A. Sewell
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0106 biological sciences ,Larva ,geography ,geography.geographical_feature_category ,ved/biology ,Ecology ,010604 marine biology & hydrobiology ,Coral ,fungi ,ved/biology.organism_classification_rank.species ,Climate change ,Coral reef ,Aquatic Science ,Biology ,010603 evolutionary biology ,01 natural sciences ,Abundance (ecology) ,Biological dispersal ,Acropora tenuis ,Reef - Abstract
Predicted increases in sea-surface temperatures due to climate change are likely to alter the physiology of marine organisms and ultimately influence the distribution and abundance of their populations. The consequences of increased temperatures for marine species, including decreased survival and altered rates of development, growth and settlement, are well known and often attributed to imbalances between energy supply and demand. To test this hypothesis, we calibrated the effect of temperature on rates of survival and lipid depletion for larvae of the common stony coral Acropora tenuis over a 7 °C temperature range. Temperature had a pronounced, linearly increasing effect on larval mortality, with a sixfold decrease in median survival time. Contrary to expectation, however, temperature had a quasi-parabolic effect on lipid use; rates declined as temperatures either increased above or decreased below the ambient temperature at the time of spawning. This contrasts with previous work suggesting that increased energy depletion is the cause of larval mortality at higher temperatures. Our results highlight the sensitivity of coral larvae to temperature and have implications for dispersal potential because fewer larvae will survive to disperse. Such projected declines in connectivity among coral populations are likely to undermine reef resilience.
- Published
- 2016
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23. Improving dynamic phytoplankton reserve-utilization models with an indirect proxy for internal nitrogen
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Kirsten Heimann, Martino E. Malerba, and Sean R. Connolly
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0106 biological sciences ,Statistics and Probability ,Time Factors ,Nitrogen ,Stochastic modelling ,chemistry.chemical_element ,Biology ,Models, Biological ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Proxy (climate) ,Nutrient ,Phytoplankton ,Computer Simulation ,General Immunology and Microbiology ,Ecology ,010604 marine biology & hydrobiology ,Applied Mathematics ,Limiting nutrient ,General Medicine ,Population model ,chemistry ,Modeling and Simulation ,Allometry ,General Agricultural and Biological Sciences ,Biological system - Abstract
Ecologists have often used indirect proxies to represent variables that are difficult or impossible to measure directly. In phytoplankton, the internal concentration of the most limiting nutrient in a cell determines its growth rate. However, directly measuring the concentration of nutrients within cells is inaccurate, expensive, destructive, and time-consuming, substantially impairing our ability to model growth rates in nutrient-limited phytoplankton populations. The red chlorophyll autofluorescence (hereafter "red fluorescence") signal emitted by a cell is highly correlated with nitrogen quota in nitrogen-limited phytoplankton species. The aim of this study was to evaluate the reliability of including flow cytometric red fluorescence as a proxy for internal nitrogen status to model phytoplankton growth rates. To this end, we used the classic Quota model and designed three approaches to calibrate its model parameters to data: where empirical observations on cell internal nitrogen quota were used to fit the model ("Nitrogen-Quota approach"), where quota dynamics were inferred only from changes in medium nutrient depletion and population density ("Virtual-Quota approach"), or where red fluorescence emission of a cell was used as an indirect proxy for its internal nitrogen quota ("Fluorescence-Quota approach"). Two separate analyses were carried out. In the first analysis, stochastic model simulations were parameterized from published empirical relationships and used to generate dynamics of phytoplankton communities reared under nitrogen-limited conditions. Quota models were fitted to the dynamics of each simulated species with the three different approaches and the performance of each model was compared. In the second analysis, we fit Quota models to laboratory time-series and we calculate the ability of each calibration approach to describe the observed trajectories of internal nitrogen quota in the culture. Results from both analyses concluded that the Fluorescence-Quota approach including per-cell red fluorescence as a proxy of internal nitrogen substantially improved the ability of Quota models to describe phytoplankton dynamics, while still accounting for the biologically important process of cell nitrogen storage. More broadly, many population models in ecology implicitly recognize the importance of accounting for storage mechanisms to describe the dynamics of individual organisms. Hence, the approach documented here with phytoplankton dynamics may also be useful for evaluating the potential of indirect proxies in other ecological systems.
- Published
- 2016
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24. A Trait-Based Approach to Advance Coral Reef Science
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Sean R. Connolly, Mia O. Hoogenboom, John M. Pandolfi, Hollie M. Putnam, Emily S. Darling, Daniel S. Falster, Andrew H. Baird, Joshua S. Madin, Danwei Huang, Sally A. Keith, and Toni Mizerek
- Subjects
0106 biological sciences ,geography ,Functional ecology ,geography.geographical_feature_category ,Ecology ,Coral Reefs ,Range (biology) ,010604 marine biology & hydrobiology ,Ecology (disciplines) ,Coral ,Coral reef ,Population biology ,Biology ,Anthozoa ,010603 evolutionary biology ,01 natural sciences ,Phenotype ,Threatened species ,Trait ,Animals ,Ecosystem ,Ecology, Evolution, Behavior and Systematics - Abstract
Coral reefs are biologically diverse and ecologically complex ecosystems constructed by stony corals. Despite decades of research, basic coral population biology and community ecology questions remain. Quantifying trait variation among species can help resolve these questions, but progress has been hampered by a paucity of trait data for the many, often rare, species and by a reliance on nonquantitative approaches. Therefore, we propose filling data gaps by prioritizing traits that are easy to measure, estimating key traits for species with missing data, and identifying 'supertraits' that capture a large amount of variation for a range of biological and ecological processes. Such an approach can accelerate our understanding of coral ecology and our ability to protect critically threatened global ecosystems.
- Published
- 2016
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25. Synergistic Effects of Marine Reserves and Harvest Controls on the Abundance and Catch Dynamics of a Coral Reef Fishery
- Author
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Jess K. Hopf, Geoffrey P. Jones, Sean R. Connolly, and David H. Williamson
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0106 biological sciences ,Conservation of Natural Resources ,Population ,Fishing ,Fisheries ,Fish stock ,Models, Biological ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Animals ,education ,education.field_of_study ,geography ,geography.geographical_feature_category ,biology ,Coral Reefs ,Ecology ,Plectropomus ,010604 marine biology & hydrobiology ,Marine reserve ,Australia ,Coral reef ,Catch per unit effort ,biology.organism_classification ,Perciformes ,Fishery ,General Agricultural and Biological Sciences ,Coral trout - Abstract
Marine no-take reserves, where fishing and other extractive activities are prohibited, have well-established conservation benefits [1], yet their impacts on fisheries remains contentious [2-4]. For fishery species, reserves are often implemented alongside more conventional harvest strategies, including catch and size limits [2, 5]. However, catch and fish abundances observed post-intervention are often attributed to reserves, without explicitly estimating the potential contribution of concurrent management interventions [2, 3, 6-9]. Here we test a metapopulation model against observed fishery [10] and population [11] data for an important coral reef fishery (coral trout; Plectropomus spp.) in Australia's Great Barrier Reef Marine Park (GBRMP) to evaluate how the combined increase in reserve area [12] and reduction in fishing effort [13, 14] in 2004 influenced changes in fish stocks and the commercial fishery. We found that declines in catch, increases in catch rates, and increases in biomass since 2004 were substantially attributable to the integration of direct effort controls with the rezoning, rather than the rezoning alone. The combined management approach was estimated to have been more productive for fish and fisheries than if the rezoning had occurred alone and comparable to what would have been obtained with effort controls alone. Sensitivity analyses indicate that the direct effort controls prevented initial decreases in catch per unit effort that would have otherwise occurred with the rezoning. Our findings demonstrate that by concurrently restructuring the fishery, the conservation benefits of reserves were enhanced and the fishery cost of rezoning the reserve network was socialized, mitigating negative impacts on individual fishers.
- Published
- 2016
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26. Nutrient utilization traits vary systematically with intraspecific cell size plasticity
- Author
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Martino E. Malerba, Kirsten Heimann, and Sean R. Connolly
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0106 biological sciences ,Nitrate uptake ,Ecology ,Cooperative research ,010604 marine biology & hydrobiology ,Ecological modelling ,Library science ,Uptake kinetics ,Biology ,010603 evolutionary biology ,01 natural sciences ,Cell size ,Advice (programming) ,Process noise ,Life history ,Ecology, Evolution, Behavior and Systematics - Abstract
We are grateful to the North Queensland Algal Identification and Culturing Facility (NQAIF), in particular Stan Hudson and Florian Berner. We are grateful to the Ecological Modelling Research Group at James Cook University, especially Dr Loic Thibaut for comments on modelling techniques and R codes. Also, thanks to the High Performance Computing team at James Cook University. We thank Dr Lyndon Llewellyn, Dr Christian Lonborg and Dr Catia Carreira for helpful advice. Finally, we thank A/Prof A. Martiny and an anonymous reviewer for detailed and constructive comments on the manuscript. This research was supported by AIMS@JCU (aims.jcu.edu.au), the Australian Institute of Marine Science (www.aims.gov.au), the Advanced Manufacturing Cooperative Research Centre (Project 2.3.4) and James Cook University (www.jcu.edu.au). The authors declare no conflict of interest.
- Published
- 2016
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27. Fishery consequences of marine reserves: short-term pain for longer-term gain
- Author
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David H. Williamson, Jess K. Hopf, Sean R. Connolly, and Geoffrey P. Jones
- Subjects
0106 biological sciences ,Conservation of Natural Resources ,Time Factors ,Population Dynamics ,Fishing ,Fisheries ,Metapopulation ,Models, Biological ,010603 evolutionary biology ,01 natural sciences ,Animals ,Ecology ,biology ,Coral Reefs ,Plectropomus ,010604 marine biology & hydrobiology ,Marine reserve ,biology.organism_classification ,Perciformes ,Fishery ,Reserve design ,Larva ,Marine protected area ,Fisheries management ,Animal Distribution ,Coral trout - Abstract
Marine reserves are often established in areas that support fisheries. Larval export from reserves is argued to help compensate for the loss of fishable habitat; however, previous modeling studies have focused on long-term equilibrium outcomes. We examined the transient consequences of reserve establishment for fished metapopulations, considering both a well-mixed larval pool and a spatially explicit model based on a coral trout (Plectropomus spp.) metapopulation. When fishing pressure was reallocated relative to the area protected, yields decreased initially, then recovered, and ultimately exceeded pre-reserve levels. However, recovery time was on the order of several years to decades. If fishing pressure intensified to maintain pre-reserve yields, reserves were sometimes unable to support the increased mortality and the metapopulation collapsed. This was more likely when reserves were small, or located peripherally within the metapopulation. Overall, reserves can achieve positive conservation and fishery benefits, but fisheries management complementary to reserve implementation is essential.
- Published
- 2016
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28. High-frequency sampling and piecewise models reshape dispersal kernels of a common reef coral
- Author
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Sean R. Connolly, Andrew H. Baird, Joanne Moneghetti, and Joana Figueiredo
- Subjects
0106 biological sciences ,geography ,geography.geographical_feature_category ,Ecology ,Coral Reefs ,010604 marine biology & hydrobiology ,Coral ,media_common.quotation_subject ,Metamorphosis, Biological ,Biology ,Anthozoa ,010603 evolutionary biology ,01 natural sciences ,High frequency sampling ,Survivorship curve ,Larva ,Piecewise ,Biological dispersal ,Animals ,Metamorphosis ,Vital rates ,Reef ,Ecology, Evolution, Behavior and Systematics ,media_common ,Demography - Abstract
Models of dispersal potential are required to predict connectivity between populations of sessile organisms. However, to date, such models do not allow for time-varying rates of acquisition and loss of competence to settle and metamorphose, and permit only a limited range of possible survivorship curves. We collect high-resolution observations of coral larval survival and metamorphosis, and apply a piecewise modeling approach that incorporates a broad range of temporally varying rates of mortality and loss of competence. Our analysis identified marked changes in competence loss and mortality rates, the timing of which implicates developmental failure and depletion of energy reserves. Asymmetric demographic rates suggest more intermediate-range dispersal, less local retention, and less long-distance dispersal than predicted by previously employed non-piecewise models. Because vital rates are likely temporally asymmetric, at least for nonfeeding broadcast-spawned larvae, piecewise analysis of demographic rates will likely yield more reliable predictions of dispersal potential.
- Published
- 2018
29. Hierarchical modeling strengthens evidence for density dependence in observational time series of population dynamics
- Author
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Sean R. Connolly and Loïc M. Thibaut
- Subjects
0106 biological sciences ,Population Density ,education.field_of_study ,Hierarchical modeling ,Ecology ,010604 marine biology & hydrobiology ,Gompertz function ,Population ,Population Dynamics ,Fishes ,010603 evolutionary biology ,01 natural sciences ,Models, Biological ,Hierarchical database model ,Birds ,Global population ,Density dependence ,Econometrics ,Leverage (statistics) ,Animals ,Observational study ,education ,Ecology, Evolution, Behavior and Systematics ,Mathematics - Abstract
The extent to which populations in nature are regulated by density-dependent processes is unresolved. While experiments increasingly find evidence of strong density dependence, unmanipulated population time series yield much more ambiguous evidence of regulation, especially when accounting for effects of observation error. Here, we reexamine the evidence for density dependence in time series of population sizes in nature, by conducting an aggregate analysis of the populations in the Global Population Dynamics Database (GPDD). First, following the conventional approach, we fit a density-dependent and a density-independent variant of the Gompertz state-space model to each time series. Then, we conduct an aggregate analysis of the entire database by considering two random-effects density-dependent models that leverage information across data sets. When individual time series are tested independently, we find very little evidence for density dependence. However, in the aggregate, we find very strong evidence for density dependence, even though, paradoxically, estimated strengths of density dependence for individual time series tend to be weaker than when each individual time series is analyzed independently. Furthermore, a hierarchical model that accounts for taxonomic variation in the strength of density dependence reveals that density dependence is consistently stronger in insects and fish than in birds and mammals. Our findings resolve apparent inconsistencies between observational and experimental studies of density dependence by revealing that the observational record does indeed contain strong support for the hypothesis that density dependence is widespread in nature.
- Published
- 2018
30. Standard flow cytometry as a rapid and non-destructive proxy for cell nitrogen quota
- Author
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Martino E. Malerba, Kirsten Heimann, and Sean R. Connolly
- Subjects
0301 basic medicine ,03 medical and health sciences ,030104 developmental biology ,Cooperative research ,Ecology ,Non destructive ,Library science ,Plant Science ,Sociology ,Aquatic Science - Abstract
We are grateful to the North Queensland Algal Identification and Culturing Facility (NQAIF), in particular Stan Hudson and Florian Berner. We also thank A/Prof Bruce Bowden and Prof James Burnell for the assistance in laboratory protocols. Finally, we thank Dr Lyndon Llewellyn, Dr Christian Lonborg, Dr Murray Logan, and Dr Catia Carreira for the helpful advice. This research was supported by AIMS@JCU (aims.jcu.edu.au), the Australian Institute of Marine Science (www.aims.gov.au), the Advanced Manufacturing Cooperative Research Centre (Project 2.3.4), and James Cook University (www.jcu.edu.au). We also thank the reviewers, whose comments and suggestions helped improve the manuscript.
- Published
- 2015
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31. Node self-connections and metapopulation persistence: reply to Saura (2018)
- Author
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Garry R. Russ, Rene A. Abesamis, Jessica Zamborain-Mason, Abner A. Bucol, and Sean R. Connolly
- Subjects
0106 biological sciences ,Persistence (psychology) ,Conservation planning ,Theoretical computer science ,010504 meteorology & atmospheric sciences ,Ecology ,Computer science ,Node (networking) ,Population Dynamics ,Metapopulation ,Network theory ,Metrics ,010603 evolutionary biology ,01 natural sciences ,Key terms ,Metric (mathematics) ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Probability - Abstract
Saura () claims that studies using the Probability of Connectivity metric (PC) had already demonstrated the importance of including node self-connections in network metrics. As originally defined and used, PC cannot test the importance of self-connections. However, with key terms redefined, PC could be a useful tool in future work.
- Published
- 2018
32. Negligible effect of competition on coral colony growth
- Author
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Mariana Álvarez-Noriega, Andrew H. Baird, Joshua S. Madin, Maria Dornelas, Sean R. Connolly, European Research Council, University of St Andrews. School of Biology, University of St Andrews. Fish Behaviour and Biodiversity Research Group, University of St Andrews. Marine Alliance for Science & Technology Scotland, and University of St Andrews. Centre for Biological Diversity
- Subjects
Morphology ,0106 biological sciences ,Demographic rates ,food.ingredient ,QH301 Biology ,Coral ,media_common.quotation_subject ,Population ,NDAS ,Growth ,010603 evolutionary biology ,01 natural sciences ,Competition (biology) ,Intraspecific competition ,Aggregation ,QH301 ,food ,Acropora ,Animals ,14. Life underwater ,education ,Ecology, Evolution, Behavior and Systematics ,media_common ,education.field_of_study ,Competition ,biology ,Ecology ,Coral Reefs ,Tradeoff ,010604 marine biology & hydrobiology ,Interspecific competition ,biology.organism_classification ,Fecundity ,Anthozoa ,Goniastrea - Abstract
MD was supported by the ERC (BioTIME 250189) and the Scottish Funding Council (MASTS –HR09011). JM, AB and SC were supported by fellowships from the Australian Research Council (FT110100609, FT0990652 and DP0880544, respectively). Competition is an important determinant of assemblage structure and population regulation, often resulting in decreased growth, fecundity or survival. In corals, most studies testing for an effect of competition on demographic traits, such as growth, have been experimental and often impose very high levels of competition upon colonies. To more realistically assess the role of competition on coral traits, multispecies studies in the wild are required. Here, we use 5 yr of data that includes 11 coral species on the reef crest at Lizard Island on the Great Barrier Reef to quantify the effect of competition on growth. Additionally, we test whether species differ in their susceptibility to direct‐contact (overgrowth and digestion) and overtopping competition, and whether species from some morphological groups are more likely to compete with one another than with species from other morphological groups. We also investigate the relationships between competitive ability and three key traits: growth rate, mechanical stability and fecundity. In contrast to most previous work using field manipulations of competition, we found a negligible effect of competition on growth. Acropora species consistently won overtopping encounters but lost in direct‐contact encounters, and these results were consistent among the four Acropora morphological groups. In contrast, the massive Goniastrea spp. were poor at overtopping but generally won direct‐contact encounters. Only tabular colonies were disproportionally more likely to compete against one another than with other morphologies. This propensity increases intraspecific relative to interspecific competition, a phenomenon that can promote coexistence when it is present among dominant competitors. Good competitors grew more quickly and had higher fecundity but were less mechanically stable, implying a tradeoff between performance during disturbance vs. performance in the absence of disturbance. We conclude that competition among adults is less likely to influence community dynamics than previously thought. If competition does have an effect, it is more likely to occur at life‐stages other than adults. Publisher PDF
- Published
- 2017
33. Global warming transforms coral reef assemblages
- Author
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James T. Kerry, Andrew H. Baird, C. Mark Eakin, Mike McWilliam, Sean R. Connolly, Mia O. Hoogenboom, Jessica Stella, Gang Liu, Andrew S. Hoey, Andreas Dietzel, Terry P. Hughes, Rachel Pears, Morgan S. Pratchett, Gergely Torda, William J. Skirving, and Scott F. Heron
- Subjects
0106 biological sciences ,Marine biology ,geography ,Multidisciplinary ,geography.geographical_feature_category ,Hot Temperature ,Ecology ,Coral Reefs ,010604 marine biology & hydrobiology ,Coral ,Global warming ,Population Dynamics ,Australia ,Climate change ,Coral reef ,Anthozoa ,010603 evolutionary biology ,01 natural sciences ,Global Warming ,Disturbance (ecology) ,Animals ,Ecosystem ,Reef - Abstract
Global warming is rapidly emerging as a universal threat to ecological integrity and function, highlighting the urgent need for a better understanding of the impact of heat exposure on the resilience of ecosystems and the people who depend on them 1 . Here we show that in the aftermath of the record-breaking marine heatwave on the Great Barrier Reef in 2016 2 , corals began to die immediately on reefs where the accumulated heat exposure exceeded a critical threshold of degree heating weeks, which was 3–4 °C-weeks. After eight months, an exposure of 6 °C-weeks or more drove an unprecedented, regional-scale shift in the composition of coral assemblages, reflecting markedly divergent responses to heat stress by different taxa. Fast-growing staghorn and tabular corals suffered a catastrophic die-off, transforming the three-dimensionality and ecological functioning of 29% of the 3,863 reefs comprising the world’s largest coral reef system. Our study bridges the gap between the theory and practice of assessing the risk of ecosystem collapse, under the emerging framework for the International Union for Conservation of Nature (IUCN) Red List of Ecosystems 3 , by rigorously defining both the initial and collapsed states, identifying the major driver of change, and establishing quantitative collapse thresholds. The increasing prevalence of post-bleaching mass mortality of corals represents a radical shift in the disturbance regimes of tropical reefs, both adding to and far exceeding the influence of recurrent cyclones and other local pulse events, presenting a fundamental challenge to the long-term future of these iconic ecosystems.
- Published
- 2017
34. Corrigendum: Flow and Coral Morphology Control Coral Surface pH: Implications for the Effects of Ocean Acidification
- Author
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Neil C. S. Chan, Daniel Wangpraseurt, Michael Kühl, and Sean R. Connolly
- Subjects
Global and Planetary Change ,diffusive boundary layer ,lcsh:QH1-199.5 ,Ecology ,Coral ,carbonate chemistry ,Climate change ,Ocean acidification ,Ocean Engineering ,Biology ,Aquatic Science ,lcsh:General. Including nature conservation, geographical distribution ,Oceanography ,Surface ph ,Morphology control ,calcification ,climate change ,Marine Science ,lcsh:Q ,lcsh:Science ,Water Science and Technology - Published
- 2017
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35. Network theory and metapopulation persistence: incorporating node self-connections
- Author
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Rene A. Abesamis, Abner A. Bucol, Jessica Zamborain-Mason, Garry R. Russ, and Sean R. Connolly
- Subjects
0106 biological sciences ,Conservation planning ,Aquatic Organisms ,Ecology ,Computer science ,010604 marine biology & hydrobiology ,Population Dynamics ,Metapopulation ,Network theory ,Metrics ,010603 evolutionary biology ,01 natural sciences ,Models, Biological ,Robustness (computer science) ,Ecology, Evolution, Behavior and Systematics ,Ecosystem ,Network analysis - Abstract
Network analysis is gaining increasing importance in conservation planning. However, which network metrics are the best predictors of metapopulation persistence is still unresolved. Here, we identify a critical limitation of graph theory-derived network metrics that have been proposed for this purpose: their omission of node self-connections. We resolve this by presenting modifications of existing network metrics, and developing entirely new metrics, that account for node self-connections. Then, we illustrate the performance of these new and modified metrics with an age-structured metapopulation model for a real-world marine reserve network case study, and we evaluate the robustness of our findings by systematically varying particular features of that network. Our new and modified metrics predict metapopulation persistence much better than existing metrics do, even when self-connections are weak. Existing metrics become good predictors of persistence only when self-connections are entirely absent, an unrealistic scenario in the overwhelming majority of metapopulation applications. Our study provides a set of novel tools that can substantially enhance the extent to which network metrics can be employed to understand, and manage for, metapopulation persistence.
- Published
- 2017
36. Partitioning colony size variation into growth and partial mortality
- Author
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Maria Dornelas, Andrew H. Baird, Sean R. Connolly, Marissa L. Baskett, Joshua S. Madin, John Templeton Foundation, University of St Andrews. School of Biology, University of St Andrews. Centre for Biological Diversity, University of St Andrews. Fish Behaviour and Biodiversity Research Group, and University of St Andrews. Marine Alliance for Science & Technology Scotland
- Subjects
0106 biological sciences ,demography ,QH301 Biology ,Coral ,Body size ,Biology ,010603 evolutionary biology ,01 natural sciences ,life-histories ,partial mortality ,Predation ,QH301 ,Animals ,Body Size ,Demography ,Evolutionary Biology ,Agricultural and Biological Sciences(all) ,Ecology ,010604 marine biology & hydrobiology ,Trade offs ,DAS ,Biological Sciences ,Anthozoa ,Agricultural and Biological Sciences (miscellaneous) ,trade-offs ,Good Health and Well Being ,Trait ,colonial organism ,Population Ecology ,Allometry ,General Agricultural and Biological Sciences - Abstract
We thank the Australian Research Council for fellowship and research support. M.A.D. is funded by a Leverhulme Fellowship and by the John Templeton Foundation grant no. 60501. Body size is a trait that broadly influences the demography and ecology of organisms. In unitary organisms, body size tends to increase with age. In modular organisms, body size can either increase or decrease with age, with size changes being the net difference between modules added through growth and modules lost through partial mortality. Rates of colony extension are independent of body size, but net growth is allometric, suggesting a significant role of size-dependent mortality. In this study, we develop a generalizable model of partitioned growth and partial mortality and apply it to data from 11 species of reef-building coral. We show that corals generally grow at constant radial increments that are size independent, and that partial mortality acts more strongly on small colonies. We also show a clear life-history trade-off between growth and partial mortality that is governed by growth form. This decomposition of net growth can provide mechanistic insights into the relative demographic effects of the intrinsic factors (e.g. acquisition of food and life-history strategy), which tend to affect growth, and extrinsic factors (e.g. physical damage, and predation), which tend to affect mortality. Postprint Postprint
- Published
- 2020
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37. Double Jeopardy and Global Extinction Risk in Corals and Reef Fishes
- Author
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David R. Bellwood, Terry P. Hughes, Howard V. Cornell, Ronald H. Karlson, and Sean R. Connolly
- Subjects
Conservation of Natural Resources ,Rare species ,Biodiversity ,Biology ,Extinction, Biological ,Risk Assessment ,General Biochemistry, Genetics and Molecular Biology ,Coral Triangle ,Animals ,Macroecology ,geography ,Pacific Ocean ,geography.geographical_feature_category ,Extinction ,Agricultural and Biological Sciences(all) ,Biochemistry, Genetics and Molecular Biology(all) ,Coral Reefs ,Ecology ,Fishes ,Coral reef ,Anthozoa ,Threatened species ,Species richness ,General Agricultural and Biological Sciences ,Animal Distribution - Abstract
SummaryCoral reefs are critically important ecosystems that support the food security and livelihoods of hundreds of millions of people in maritime tropical countries, yet they are increasingly threatened by overfishing, coastal pollution, climate change, and other anthropogenic impacts, leading to concerns that some species may be threatened with local or even global extinction [1–7]. The concept of double jeopardy proposes that the risk of species extinction is elevated if species that are endemic (small range) are also scarce (low local abundance) [8]. Traditionally, marine macroecology has been founded on patterns of species richness and presence-absence data [9–11], which provide no information on species abundances or on the prevalence of double jeopardy. Here we quantify the abundances of >400 species of corals and fishes along one of the world’s major marine biodiversity gradients, from the Coral Triangle hotspot to French Polynesia, a distance of approximately 10,000 km. In contrast to classical terrestrial studies [12], we find that the abundance of these species bears no relationship to the size of their geographic ranges. Consequently, double jeopardy is uncommon because endemics are often locally abundant, and conversely many pandemics are rare. The Coral Triangle hotspot has more numerically rare species (both endemic and pandemic) but also encompasses more species with intermediate and higher abundances. We conclude that conservation efforts in the sea should focus less on extinction risk and more on maintaining and rebuilding key ecological functions that are highly vulnerable to human pressures, even if species can avoid extinction.
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- 2014
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38. Coupled dynamics of territorial damselfishes and juvenile corals on the reef crest
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Sean R. Connolly, Jordan M. Casey, and John Howard Choat
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geography ,geography.geographical_feature_category ,biology ,Ecology ,Coral ,Pomacentridae ,Coral reef ,Aquatic Science ,biology.organism_classification ,Fishery ,Habitat ,Benthic zone ,Juvenile ,Damselfish ,Reef - Abstract
Territories of grazing fishes in the family Pomacentridae have been documented to cover a sub- stantial proportion of shallow, exposed coral reef fronts, and these fishes can have profound effects on benthic community composition, including the recruitment and post-settlement survival of scleractinian corals. However, current studies of territorial grazer effects on corals have focused on back-reef habitats. Territorial damselfishes occur in distinct behavioural guilds ranging from indeter- minate territorial grazers with thin algal turfs and low rates of territorial aggression to intensive territorial grazers with thick turfs and high rates of aggression. To determine the impact of territorial grazers on the establishment of juve- nile corals, we surveyed the reef crest habitat of Lizard Island, Great Barrier Reef, using fixed transects to assess the effects of indeterminate and intensive territorial grazers on juvenile coral abundance and taxonomic composition. In addition, the turnover of territorial pomacentrids was monitored as well as the effects of turnover on juvenile coral assemblages. Intensive territorial grazers were asso- ciated with a significantly lower juvenile coral abundance (34 % decrease), but neither intensive nor indeterminate grazer territories impacted juvenile coral taxonomic com- position. Over the course of 1 yr, there was a high rate of territorial turnover (39.7 %). Turnover from control plots to intensive damselfish territories was accompanied by a 44 % decrease in juvenile corals; conversely, turnover from intensive damselfish territories to control plots coin- cided with a 48 % increase in juvenile corals. These find- ings reveal two main conclusions. Firstly, the association between damselfish territories and the abundance and spatial turnover of juvenile corals strongly implies that territorial grazers have a negative effect on juvenile coral populations. Secondly, the unexpectedly high temporal turnover of damselfish territories indicates that damselfish- coral-algae linkages are highly dynamic, may be exten- sively influenced by local-scale effects, and have the potential to impact the structure of coral assemblages on coral reef fronts.
- Published
- 2014
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39. How robust are estimates of coral reef shark depletion?
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Ashley J. Frisch, Justin R. Rizzari, and Sean R. Connolly
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geography.geographical_feature_category ,Ecology ,Marine reserve ,chemical and pharmacologic phenomena ,Coral reef ,Illegal fishing ,Fishery ,Survey methodology ,Geography ,Management zones ,Abundance (ecology) ,human activities ,Reef ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation ,Apex predator - Abstract
On coral reefs, diver-surveys of shark abundance indicate that populations are severely depleted, even in no-take zones with low-levels of illegal fishing, but are protected by strictly enforced no-entry zones. These findings have been questioned, on the grounds that diver-surveys overestimate shark abundance. We evaluated whether divers encounter sharks at higher rates when they first enter the water, and whether these effects vary among reefs that are subject to different levels of human interaction due to management zoning. We also examined the consistency of abundance estimates derived from multiple survey methods. For timed-swim, towed-diver, and baited-remote-underwater-video (BRUV) surveys, encounter rates were constant over time. For audible-stationary-count (ASC) surveys, encounter rates were elevated initially, then decreased rapidly, but the extent of upward bias did not differ between management zones. Timed-swim, BRUV, and ASC surveys produced comparable estimates of shark density, however, towed-diver-surveys produced significantly lower estimates of shark density. Our findings provide no evidence for biases in diver-surveys: encounter rates with sharks were not elevated when divers first entered the water; behavioural responses of sharks were consistent across management zones; and diver-surveys yielded abundance estimates comparable to other stationary methods. Previous studies using underwater counts have concluded that sharks are vulnerable to low levels of illegal fishing in no-take management zones, and that additional measures are needed to protect species, which, like sharks, have demographic characteristics that make them vulnerable to low levels of exploitation. Our results support the robustness of the abundance estimates on which those conclusions have been based.
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- 2014
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40. Increased local retention of reef coral larvae as a result of ocean warming
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Sean R. Connolly, Saki Harii, Joana Figueiredo, and Andrew H. Baird
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Marine biology ,Larva ,geography ,animal structures ,geography.geographical_feature_category ,Ecology ,Effects of global warming on oceans ,Coral ,fungi ,Environmental Science (miscellaneous) ,Biology ,parasitic diseases ,Biological dispersal ,Local population ,Reef ,Social Sciences (miscellaneous) - Abstract
The impact of ocean warming on coral larvae survival and dispersal is investigated using a dynamic model. The authors find that globally most reefs will experience large increases in the local retention of larvae, which make populations more responsive to local conservation efforts. However, increased larvae retention will also weaken connectivity between populations, which may affect recovery if a local population is severely disturbed.
- Published
- 2014
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41. Evidence for multiple stressor interactions and effects on coral reefs
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Sean R. Connolly, Stephen S. Ban, and Nicholas A. J. Graham
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endocrine system ,Global and Planetary Change ,geography ,geography.geographical_feature_category ,Ecology ,Coral Reefs ,Global climate ,Coral bleaching ,Climate Change ,Qualitative evidence ,Coral ,Stressor ,Coral reef ,Biology ,Anthozoa ,behavioral disciplines and activities ,Stress, Physiological ,Water temperature ,Animals ,Environmental Chemistry ,Ecosystem ,psychological phenomena and processes ,General Environmental Science - Abstract
Concern is growing about the potential effects of interacting multiple stressors, especially as the global climate changes. We provide a comprehensive review of multiple stressor interactions in coral reef ecosystems, which are widely considered to be one of the most sensitive ecosystems to global change. First, we synthesized coral reef studies that examined interactions of two or more stressors, highlighting stressor interactions (where one stressor directly influences another) and potentially synergistic effects on response variables (where two stressors interact to produce an effect that is greater than purely additive). For stressor-stressor interactions, we found 176 studies that examined at least 2 of the 13 stressors of interest. Applying network analysis to analyze relationships between stressors, we found that pathogens were exacerbated by more costressors than any other stressor, with ca. 78% of studies reporting an enhancing effect by another stressor. Sedimentation, storms, and water temperature directly affected the largest number of other stressors. Pathogens, nutrients, and crown-of-thorns starfish were the most-influenced stressors. We found 187 studies that examined the effects of two or more stressors on a third dependent variable. The interaction of irradiance and temperature on corals has been the subject of more research (62 studies, 33% of the total) than any other combination of stressors, with many studies reporting a synergistic effect on coral symbiont photosynthetic performance (n = 19). Second, we performed a quantitative meta-analysis of existing literature on this most-studied interaction (irradiance and temperature). We found that the mean effect size of combined treatments was statistically indistinguishable from a purely additive interaction, although it should be noted that the sample size was relatively small (n = 26). Overall, although in aggregate a large body of literature examines stressor effects on coral reefs and coral organisms, considerable gaps remain for numerous stressor interactions and effects, and insufficient quantitative evidence exists to suggest that the prevailing type of stressor interaction is synergistic.
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- 2014
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42. Global diversity of marine macroalgae: environmental conditions explain less variation in the tropics
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Sally A. Keith, Sean R. Connolly, and Ailsa P. Kerswell
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Global and Planetary Change ,Herbivore ,Ecology ,media_common.quotation_subject ,Tropics ,Regression analysis ,Biology ,Competition (biology) ,Latitude ,Sea surface temperature ,Species richness ,Ecology, Evolution, Behavior and Systematics ,Macroecology ,media_common - Abstract
Aim Marine macroalgae provide an excellent opportunity to test hypotheses about latitudinal diversity gradients because macroalgal richness decreases towards the tropics, contrary to classic patterns, and because three evolutionarily distinct macroalgal clades (Rhodophyta, Chlorophyta, Phaeophyceae) have converged ecologically. Specifically, we determine the extent to which environmental conditions can predict genus richness in macroalgae. We also evaluate whether the magnitude or direction of the effect of environmental factors, or their ability to explain variation in macroalgal diversity, varies geographically. Location Global oceans. Methods We formulated and fitted global spatial regression models and geographically weighted regression (GWR) models to determine the extent to which environmental conditions could predict genus richness in macroalgae. GWR allowed us to determine how the role of environmental conditions varied amongst geographical regions. Results The global regression model showed that sea surface temperature and nutrients were important predictors of macroalgal genus richness at a global scale. However, GWR revealed that environmental factors explained less variability in richness in the tropics than elsewhere. Main conclusions Our results show that whilst environmental conditions influence marine macroalgal diversity, the strength of this influence shows considerable geographical variation. In particular, environmental conditions explain more of the observed variation in diversity at high latitudes than at low latitudes. This finding is consistent with the hypothesis that environmental tolerances influence species distributions more strongly at high latitudes, whereas other factors, such as biotic interactions, play a more prominent role in the tropics.
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- 2013
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43. Effects of delayed settlement on post-settlement growth and survival of scleractinian coral larvae
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Erin Graham, Bette L. Willis, Andrew H. Baird, and Sean R. Connolly
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Coral ,Longevity ,Population Dynamics ,ved/biology.organism_classification_rank.species ,Population ,Biology ,parasitic diseases ,Animals ,education ,Acropora tenuis ,Ecology, Evolution, Behavior and Systematics ,geography ,education.field_of_study ,geography.geographical_feature_category ,Coral Reefs ,ved/biology ,Settlement (structural) ,Ecology ,fungi ,technology, industry, and agriculture ,Pelagic zone ,social sciences ,Coral reef ,Anthozoa ,Larva ,Zooxanthellae ,population characteristics ,Biological dispersal ,Queensland - Abstract
Demographic connectivity requires both the dispersal of individuals between sub-populations, and their subsequent contribution to population dynamics. For planktonic, non-feeding marine larvae, the capacity to delay settlement enables greater dispersal distances, but the energetic cost of delayed settlement has been shown to adversely impact post-settlement fitness in several taxa. Here, we assess whether delayed settlement influences mortality rates or growth rates for the first 6 weeks following settlement of the scleractinian coral, Acropora tenuis. Coral larvae that were settled at 2, 4, and 6 weeks after spawning, and then deployed in the field, showed negligible effects of delayed settlement on post-settlement survival and time to initial budding for colony formation. Between-cohort differences in budding rate appeared to be explained by temporal variation in the post-settlement acquisition of zooxanthellae. The potential for coral larvae to remain in the pelagic zone for increased periods of time with little to no effect on post-settlement survival and growth suggests that the capacity for delayed settlement is likely to have meaningful demographic consequences for broadcast-spawning reef-building corals, and that the predicted trade-off between delayed settlement and post-settlement fitness is less applicable to reef-building scleractinian corals than other taxa with non-feeding larvae.
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- 2013
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44. Effects of diversity-dependent colonization-extinction dynamics on the mid-domain effect
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Sean R. Connolly and Sal Keith
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Global and Planetary Change ,Extinction ,Ecology ,Occupancy ,Range (biology) ,Local extinction ,Species distribution ,Colonization ,Species richness ,Body size and species richness ,Biology ,Ecology, Evolution, Behavior and Systematics - Abstract
Aim We incorporate diversity-dependent colonization and extinction rates into process-based models of species geographic range dynamics to explore their effects on species richness gradients, and on extent and occupancy of species ranges. In particular, we investigate whether diversity dependence promotes or inhibits the emergence of mid-domain effects (MDEs) in homogeneous environments. Location A theoretical one-dimensional domain. Methods We formulated diversity-independent (DI) and diversity-dependent (DD) models that simulated colonization, local extinction and speciation within a homogenous domain. In the DD model, colonization and extinction probabilities were functions of diversity, whereas in the DI model, they were constants. For a wide range of parameter values, we examined local and regional species richness gradients and species range size frequency distributions (RSFDs). Results In contrast to the DI model, for which MDEs only occurred in a very narrow parameter range, the DD model generated a MDE in regional richness (range overlap) that was robust to colonization and extinction parameters, over a broad range of speciation rates. However, neither model could produce gradients in local richness (patch occupancy). The DD model also produced more realistic RSFDs than the DI model. In the latter, all species generally either became highly pandemic or went globally extinct, depending on the balance of colonization and extinction probabilities. Main conclusions Diversity-dependent colonization and extinction rates can have strong effects on species richness gradients and distributions of range extent and occupancy. Models with such diversity dependence amplify MDEs in regional richness, but largely eliminate MDEs in local richness, relative to DI models. DD models also generate more realistic RSFDs. These findings suggest that diffuse species interactions can strongly influence patterns of range size and overlap, but also that environmental gradients are likely to be necessary to explain many species richness patterns in nature, which exhibit both local and regional diversity gradients.
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- 2013
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45. Rapid declines in metabolism explain extended coral larval longevity
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Sean R. Connolly, Erin Graham, Mary A. Sewell, Bette L. Willis, and Andrew H. Baird
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Larva ,education.field_of_study ,Ecology ,Coral ,media_common.quotation_subject ,Marine larval ecology ,fungi ,Population ,Longevity ,Pelagic zone ,Marine invertebrates ,Aquatic Science ,Biology ,Biological dispersal ,education ,media_common - Abstract
Lecithotrophic, or non-feeding, marine invertebrate larvae generally have shorter pelagic larval durations (PLDs) than planktotrophic larvae. However, non-feeding larvae of scleractinian corals have PLDs far exceeding those of feeding larvae of other organisms and predictions of PLD based on energy reserves and metabolic rates, raising questions about how such longevity is achieved. Here, we measured temporal changes in metabolic rates and total lipid content of non-feeding larvae of four species of reef corals to determine whether changes in energy utilization through time contribute to extended larval durations. The temporal dynamics of both metabolic rates and lipid content were highly consistent among species. Prior to fertilization, metabolic rates were low (2.73–8.63 nmol O2 larva−1 h−1) before rapidly increasing to a peak during embryogenesis and early development 1–2 days after spawning. Metabolic rates remained high until shortly after larvae first became competent to metamorphose and then declined by up to two orders of magnitude to levels at or below rates seen in unfertilized eggs over the following week. Larvae remained in this state of low metabolic activity for up to 2 months. Consistent with temporal patterns in metabolic rates, depletion of lipids was extremely rapid during early development and then slowed dramatically from 1 week onward. Despite the very low metabolic rates in these species, larvae continued to swim and retained competence for at least 2 months. The capacity of non-feeding coral larvae to enter a state of low metabolism soon after becoming competent to metamorphose significantly extends dispersal potential, thereby accruing advantages typically associated with planktotrophy, notably enhanced population connectivity.
- Published
- 2013
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46. Aggression, interference, and the functional response of coral-feeding butterflyfishes
- Author
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Shane A. Blowes, Morgan S. Pratchett, and Sean R. Connolly
- Subjects
0106 biological sciences ,media_common.quotation_subject ,Foraging ,Functional response ,Biology ,010603 evolutionary biology ,01 natural sciences ,Competition (biology) ,medicine ,Animals ,Chaetodon trifascialis ,Ecology, Evolution, Behavior and Systematics ,Ecosystem ,media_common ,Chaetodon ,Ecology ,Aggression ,010604 marine biology & hydrobiology ,Fishes ,Interspecific competition ,biology.organism_classification ,Anthozoa ,Diet ,Perciformes ,Chaetodon baronessa ,medicine.symptom - Abstract
Functional responses describing how foraging rates change with respect to resource density are central to our understanding of interspecific interactions. Competitive interactions are an important determinant of foraging rates; however, the relationship between the exploitation and interference components of competition has received little empirical or theoretical consideration. Moreover, little is known about the relationship between aggressive behavioural interactions and interference competition. Using a natural gradient of consumer and resource densities, we empirically examine how aggressiveness relates to consumer-consumer encounter rates and foraging for four species of Chaetodon reef fish spanning a range of dietary niche breadths. The probability of aggression was most strongly associated with both total consumer and resource densities. In contrast, total encounter rates were best predicted by conspecific consumer density, and were highest for the most specialised consumer (Chaetodon trifascialis), not the most aggressive (Chaetodon baronessa). The most specialised consumer, not the most aggressive, also exhibited the largest reduction in foraging rates with increasing consumer density. Our results support the idea of a positive link between the exploitation and interference components of competition for the most specialised consumer. Moreover, our results caution against inferring the presence of ecological interactions (competition) from observations of behaviour (aggression and agonism) alone.
- Published
- 2016
47. A critique of claims for negative impacts of Marine Protected Areas on fisheries
- Author
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John Tanzer, Geoffrey P. Jones, Sean R. Connolly, Jon C. Day, Laurence J. McCook, Matthew A. Young, Robert L. Pressey, Terry P. Hughes, Darren S. Cameron, Peter J. Mumby, Andrew J. Tobin, Garry R. Russ, Rachel Pears, P McGinnity, and Andrew Chin
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0106 biological sciences ,geography ,geography.geographical_feature_category ,Ecology ,Coral Reefs ,010604 marine biology & hydrobiology ,Fishing ,Critical question ,Biodiversity ,Fisheries ,Fishes ,Coral reef ,010603 evolutionary biology ,01 natural sciences ,Great barrier reef ,Fishery ,Animals ,Ecosystem ,Marine protected area - Abstract
[Extract] To the Editor: Establishing Marine Protected Areas (MPAs), often including zones that are closed to fishing, is an effective approach to maintaining biodiversity and rebuilding ecosystem function (e.g. McCook et al. 2010). However, MPAs are frequently opposed by fishers and by some fisheries managers, because of the potential for displacing fishing activity and reducing catches (Caveen et al. 2015). How much catch is lost due to spatial closures in both the short and long term is a critical question, even where the objective of establishing MPAs is to conserve biodiversity rather than to regulate fisheries.
- Published
- 2016
48. The Coral Trait Database, a curated database of trait information for coral species from the global oceans
- Author
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Emily S. Darling, Hollie M. Putnam, Matthew A. Kosnik, T. Edward Roberts, Elizabeth Widman, Andrew H. Baird, Morgan S. Pratchett, Julieta C. Martinelli, Xavier Pochon, Janice M. Lough, Osmar J. Luiz, Danwei Huang, Carden C. Wallace, Michael Stat, Ruth D. Gates, Toni Mizerek, Magnus Heide Andreasen, Sean R. Connolly, Mia O. Hoogenboom, Chao-Yang Kuo, Stephen D. Cairns, Catherine E. Lovelock, Erik C. Franklin, Kristen G. Anderson, Sally A. Keith, Marcela Diaz, Tom C. L. Bridge, Joshua S. Madin, John M. Pandolfi, and Daniel S. Falster
- Subjects
0106 biological sciences ,Data descriptor ,Statistics and Probability ,Data Descriptor ,Coral reefs ,Environmental change ,Coral ,Montastraea annularis ,Library and Information Sciences ,computer.software_genre ,010603 evolutionary biology ,01 natural sciences ,Education ,Anthozoa ,Community ecology ,Organism ,Marine biology ,geography ,geography.geographical_feature_category ,biology ,Database ,Ecology ,010604 marine biology & hydrobiology ,Biodiversity ,Coral reef ,biology.organism_classification ,Computer Science Applications ,Biogeography ,Trait ,Statistics, Probability and Uncertainty ,computer ,Information Systems - Abstract
Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.
- Published
- 2016
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49. Fecundity and the demographic strategies of coral morphologies
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Maria Dornelas, Joshua S. Madin, Sean R. Connolly, Mariana Álvarez-Noriega, Andrew H. Baird, Vivian R. Cumbo, European Research Council, University of St Andrews. School of Biology, University of St Andrews. Fish Behaviour and Biodiversity Research Group, University of St Andrews. Marine Alliance for Science & Technology Scotland, and University of St Andrews. Centre for Biological Diversity
- Subjects
0106 biological sciences ,Morphology ,Ecology ,Coral Reefs ,010604 marine biology & hydrobiology ,Coral ,Tradeoff ,QH301 Biology ,Population Dynamics ,Colony morphology ,Biology ,Fecundity ,Trade-off ,Anthozoa ,010603 evolutionary biology ,01 natural sciences ,QH301 ,Fertility ,Community dynamics ,Reef coral ,Animals ,Demographic strategies ,14. Life underwater ,Ecology, Evolution, Behavior and Systematics - Abstract
JM, AB and SC were supported by fellowships from the Australian Research Council (FT110100609, FT0990652 and DP0880544 respectively). MD was supported by the ERC (BioTIME 250189) and the Scottish Funding Council (MASTS - HR09011). Understanding species differences in demographic strategies is a fundamental goal of ecology. In scleractinian corals, colony morphology is tightly linked with many demographic traits, such as size-specific growth and morality. Here, we test how well morphology predicts the colony size-fecundity relationship in eight species of broadcast-spawning corals. Variation in colony fecundity is greater among morphologies than between species with a similar morphology, demonstrating that colony morphology can be used as a quantitative proxy for demographic strategies. Additionally, we examine the relationship between size-specific colony fecundity and mechanical vulnerability (i.e. vulnerability to colony dislodgment). Interestingly, the relationship between size-specific fecundity and mechanical vulnerability varied among morphologies. For tabular species, the most fecund colonies are the most mechanically vulnerable, while the opposite is true for massive species. For corymbose and digitate colonies, mechanical vulnerability remains relatively constant as fecundity increases. These results reveal strong differences in the demographic trade-offs among species of different morphologies. Using colony morphology as a quantitative proxy for demographic strategies can help predict coral community dynamics and responses to anthropogenic change. Publisher PDF
- Published
- 2016
50. Dispersal-mediated coexistence under recruitment limitation and displacement competition
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Sean R. Connolly and Joana Figueiredo
- Subjects
Coexistence theory ,Ecology ,Ecological Modeling ,media_common.quotation_subject ,Survival strategy ,Biodiversity ,Biological dispersal ,Storage effect ,Biology ,Scramble competition ,Competition (biology) ,media_common ,Spatial heterogeneity - Abstract
Understanding biodiversity maintenance when species compete for shared limiting resources remains an outstanding ecological problem. For a half century, the competition–colonization trade-off has been invoked to explain species coexistence. More recently, asymmetric dispersal has been shown to alter the conditions for species coexistence under pure scramble competition for space, even in the absence of spatial heterogeneity. Therefore, in this study, we investigated why and how asymmetric dispersal may alter the effect of competition–colonization trade-off on species coexistence. Our main findings are that: (1) self-recruitment of a superior competitor facilitates persistence of an inferior competitor; (2) the degree to which a community is recruitment-limited influences the threshold dispersal asymmetry required for persistence of a species with a birth or survival disadvantage; (3) an inferior competitor with a high recruitment strategy is better able to benefit from spatial asymmetries in dispersal than one with a high survival strategy, and (4) an inferior competitor may persist, and even exclude the superior competitor, when dispersal is highly asymmetric (i.e., the competition–colonization trade-off can be violated). These results underscore the importance of dispersal patterns promoting species coexistence and their synergies with species' colonization and competition abilities, and highlight the need to assess dispersal-mediated coexistence within a framework that incorporates the interactive effects of dispersal patterns, demographic and competitive strategies.
- Published
- 2012
- Full Text
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