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Glass JR, Harrington RC, Cowman PF, Faircloth BC, Near TJ. Widespread sympatry in a species-rich clade of marine fishes (Carangoidei). Proc Biol Sci 2023; 290:20230657. [PMID: 37909084 PMCID: PMC10618865 DOI: 10.1098/rspb.2023.0657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023] Open
Abstract
A universal paradigm describing patterns of speciation across the tree of life has been debated for decades. In marine organisms, inferring patterns of speciation using contemporary and historical patterns of biogeography is challenging due to the deficiency of species-level phylogenies and information on species' distributions, as well as conflicting relationships between species' dispersal, range size and co-occurrence. Most research on global patterns of marine fish speciation and biogeography has focused on coral reef or pelagic species. Carangoidei is an ecologically important clade of marine fishes that use coral reef and pelagic environments. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a time-calibrated phylogeny of Carangoidei and its parent clade, Carangiformes. Age-range correlation analyses of the geographical distributions and divergence times of sister species pairs reveal widespread sympatry, with 73% of sister species pairs exhibiting sympatric geographical distributions, regardless of node age. Most species pairs coexist across large portions of their ranges. We also observe greater disparity in body length and maximum depth between sympatric relative to allopatric sister species. These and other ecological or behavioural attributes probably facilitate sympatry among the most closely related carangoids.
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Affiliation(s)
- Jessica R. Glass
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- South African Institute for Aquatic Biodiversity, Makhanda 6140, South Africa
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Richard C. Harrington
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Peter F. Cowman
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, Queensland 4810, Australia
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Yale Peabody Museum of Natural History, Division of Vertebrate Zoology. New Haven, CT 06520, USA
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2
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López-Romero FA, Stumpf S, Kamminga P, Böhmer C, Pradel A, Brazeau MD, Kriwet J. Shark mandible evolution reveals patterns of trophic and habitat-mediated diversification. Commun Biol 2023; 6:496. [PMID: 37156994 PMCID: PMC10167336 DOI: 10.1038/s42003-023-04882-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
Environmental controls of species diversity represent a central research focus in evolutionary biology. In the marine realm, sharks are widely distributed, occupying mainly higher trophic levels and varied dietary preferences, mirrored by several morphological traits and behaviours. Recent comparative phylogenetic studies revealed that sharks present a fairly uneven diversification across habitats, from reefs to deep-water. We show preliminary evidence that morphological diversification (disparity) in the feeding system (mandibles) follows these patterns, and we tested hypotheses linking these patterns to morphological specialisation. We conducted a 3D geometric morphometric analysis and phylogenetic comparative methods on 145 specimens representing 90 extant shark species using computed tomography models. We explored how rates of morphological evolution in the jaw correlate with habitat, size, diet, trophic level, and taxonomic order. Our findings show a relationship between disparity and environment, with higher rates of morphological evolution in reef and deep-water habitats. Deep-water species display highly divergent morphologies compared to other sharks. Strikingly, evolutionary rates of jaw disparity are associated with diversification in deep water, but not in reefs. The environmental heterogeneity of the offshore water column exposes the importance of this parameter as a driver of diversification at least in the early part of clade history.
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Affiliation(s)
- Faviel A López-Romero
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Palaeontology, Evolutionary Morphology Research Group, Josef-Holaubek-Platz 2, 1190, Vienna, Austria.
- University of Vienna, Vienna Doctoral School of Ecology and Evolution (VDSEE), Djerassiplatz 1, 1030, Vienna, Austria.
| | - Sebastian Stumpf
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Palaeontology, Evolutionary Morphology Research Group, Josef-Holaubek-Platz 2, 1190, Vienna, Austria
| | - Pepijn Kamminga
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Christine Böhmer
- MECADEV UMR 7179 CNRS/MNHN, Département Adaptations du Vivant, Muséum National d'Histoire Naturelle, CP 55, 57 rue Cuvier, 75231, Paris, France
- Department für Geo- und Umweltwissenschaften und GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333, München, Germany
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Alan Pradel
- CR2P, Centre de Recherche en Paléontologie - Paris, Muséum National d'Histoire Naturelle-Sorbonne Université-CNRS, CP 38, 57 rue Cuvier, F75231, Paris, Cedex 05, France
| | - Martin D Brazeau
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, London, UK
- The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Jürgen Kriwet
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Palaeontology, Evolutionary Morphology Research Group, Josef-Holaubek-Platz 2, 1190, Vienna, Austria
- University of Vienna, Vienna Doctoral School of Ecology and Evolution (VDSEE), Djerassiplatz 1, 1030, Vienna, Austria
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Pickett BD, Glass JR, Johnson TP, Ridge PG, Kauwe JSK. The genome of a giant (trevally): Caranx ignobilis. GIGABYTE 2022; 2022:gigabyte67. [PMID: 36824527 PMCID: PMC9694125 DOI: 10.46471/gigabyte.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
Caranx ignobilis, commonly known as giant kingfish or giant trevally, is a large, reef-associated apex predator. It is a prized sportfish, targeted throughout its tropical and subtropical range in the Indian and Pacific Oceans. It also gained significant interest in aquaculture due to its unusual freshwater tolerance. Here, we present a draft assembly of the estimated 625.92 Mbp nuclear genome of a C. ignobilis individual from Hawaiian waters, which host a genetically distinct population. Our 97.4% BUSCO-complete assembly has a contig NG50 of 7.3 Mbp and a scaffold NG50 of 46.3 Mbp. Twenty-five of the 203 scaffolds contain 90% of the genome. We also present noisy, long-read DNA, Hi-C, and RNA-seq datasets, the latter containing eight distinct tissues and can help with annotations and studies of freshwater tolerance. Our genome assembly and its supporting data are valuable tools for ecological and comparative genomics studies of kingfishes and other carangoid fishes.
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Affiliation(s)
| | - Jessica R. Glass
- South African Institute for Aquatic Biodiversity, Makhanda, South Africa,College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | | | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, Utah, USA
| | - John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, Utah, USA,Brigham Young University – Hawai‘i, Laie, Hawai‘i, USA, Corresponding author. E-mail:
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4
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Evolutionary trends of the conserved neurocranium shape in angel sharks (Squatiniformes, Elasmobranchii). Sci Rep 2020; 10:12582. [PMID: 32724124 PMCID: PMC7387474 DOI: 10.1038/s41598-020-69525-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/19/2020] [Indexed: 11/24/2022] Open
Abstract
Elasmobranchii (i.e., sharks, skates, and rays) forms one of the most diverse groups of marine predators. With a fossil record extending back into the Devonian, several modifications in their body plan illustrate their body shape diversity through time. The angel sharks, whose fossil record dates back to the Late Jurassic, some 160 Ma, have a dorsoventrally flattened body, similar to skates and rays. Fossil skeletons of this group show that the overall morphology was well established earlier in its history. By examining the skull shape of well-preserved fossil material compared to extant angel sharks using geometric morphometric methods, within a phylogenetic framework, we were able to determine the conservative skull shape among angel sharks with a high degree of integration. The morphospace occupation of extant angel sharks is rather restricted, with extensive overlap. Most of the differences in skull shape are related to their geographic distribution patterns. We found higher levels of disparity in extinct forms, but lower ones in extant species. Since angel sharks display a highly specialized prey capture behaviour, we suggest that the morphological integration and biogeographic processes are the main drivers of their diversity, which might limit their capacity to display higher disparities since their origin.
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Gillet A, Frédérich B, Parmentier E. Divergent evolutionary morphology of the axial skeleton as a potential key innovation in modern cetaceans. Proc Biol Sci 2019; 286:20191771. [PMID: 31771481 DOI: 10.1098/rspb.2019.1771] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cetaceans represent the most diverse clade of extant marine tetrapods. Although the restructuring of oceans could have contributed to their diversity, other factors might also be involved. Similar to ichthyosaurs and sharks, variation of morphological traits could have promoted the colonization of new ecological niches and supported their diversification. By combining morphological data describing the axial skeleton of 73 cetacean species with phylogenetic comparative methods, we demonstrate that the vertebral morphology of cetaceans is associated with their habitat. All riverine and coastal species possess a small body size, lengthened vertebrae and a low vertebral count compared with open ocean species. Extant cetaceans have followed two distinct evolutionary pathways relative to their ecology. Whereas most offshore species such as baleen whales evolved towards an increased body size while retaining a low vertebral count, small oceanic dolphins underwent deep modifications of their axial skeleton with an extremely high number of short vertebrae. Our comparative analyses provide evidence these vertebral modifications have potentially operated as key innovations. These novelties contributed to their explosive radiation, resulting in an efficient swimming style that provides energetic advantages to small-sized species.
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Affiliation(s)
- Amandine Gillet
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium
| | - Bruno Frédérich
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium
| | - Eric Parmentier
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium
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Ecomorphology, trophic niche, and distribution divergences of two common damselfishes in the Gulf of California. C R Biol 2019; 342:309-321. [PMID: 31784218 DOI: 10.1016/j.crvi.2019.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 11/22/2022]
Abstract
Damselfishes of the genus Stegastes are among the most conspicuous benthic reef-associated fish in the Gulf of California, and the two most commonly found species are the Beaubrummel Gregory Stegastes flavilatus and the Cortez damselfish Stegastes rectifraenum. Both species are described as ecologically and morphologically very similar. However, the niche theory predicts that coexisting species will tend to minimize competition through niche partitioning. We, therefore, investigated the degree of their ecological similarity through their morphology, trophic ecology, and spatial distribution, as well as, the effects of environmental variables on their abundance. We showed that S. rectifraenum is highly abundant in the entire Gulf of California while S. flavilatus is only found in the central and southern part. The abundance of S. rectifraenum was higher in shallow water and decreased when the cover of macroalgae and sand increased. No environmental variable was related to the abundance of S. flavilatus. Both species had distinct isotopic niches: S. flavilatus fed almost exclusively on plankton and zoobenthos, while S. rectifraenum had an omnivorous diet mixing turf, zoobenthos and plankton. The diet divergence was reflected in the morphology of the two species. Stegastes flavilatus had a more rounded body shape, with a higher supraoccipital crest and more gill rakers than S. rectifraenum, which may increase its ability to feed on vagile invertebrates and zooplankton. Our results support the hypothesis that a niche partition has occurred between the two species. Furthermore, the importance of planktonic food sources to both species, considered as benthic territorial feeders, challenges the traditional ecological description of the Stegastes species.
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Friedman ST, Martinez CM, Price SA, Wainwright PC. The influence of size on body shape diversification across Indo‐Pacific shore fishes*. Evolution 2019; 73:1873-1884. [DOI: 10.1111/evo.13755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/14/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Sarah T. Friedman
- Department of Evolution and Ecology University of California Davis California 95616
| | | | - Samantha A. Price
- Department of Biological Sciences Clemson University Clemson South Carolina 29634
| | - Peter C. Wainwright
- Department of Evolution and Ecology University of California Davis California 95616
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Marramà G, Klug S, de Vos J, Kriwet J. Anatomy, relationships and palaeobiogeographic implications of the first Neogene holomorphic stingray (Myliobatiformes: Dasyatidae) from the early Miocene of Sulawesi, Indonesia, SE Asia. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Giuseppe Marramà
- University of Vienna, Department of Palaeontology, Althanstrasse, Vienna, Austria
| | - Stefanie Klug
- University of Manchester, School of Earth, Atmospheric and Environmental Sciences, Manchester, UK
| | - John de Vos
- Naturalis Biodiversity Center, Darwinweg, CR Leiden, The Netherlands
| | - Jürgen Kriwet
- University of Vienna, Department of Palaeontology, Althanstrasse, Vienna, Austria
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9
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Liu SYV, Frédérich B, Lavoué S, Chang J, Erdmann MV, Mahardika GN, Barber PH. Buccal venom gland associates with increased of diversification rate in the fang blenny fish Meiacanthus (Blenniidae; Teleostei). Mol Phylogenet Evol 2018; 125:138-146. [PMID: 29597008 DOI: 10.1016/j.ympev.2018.03.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 11/18/2022]
Abstract
At the macroevolutionary level, many mechanisms have been proposed to explain explosive species diversification. Among them morphological and/or physiological novelty is considered to have a great impact on the tempo and the mode of diversification. Meiacanthus is a genus of Blenniidae possessing a unique buccal venom gland at the base of an elongated canine tooth. This unusual trait has been hypothesized to aid escape from predation and thus potentially play an important role in their pattern of diversification. Here, we produce the first time-calibrated phylogeny of Blenniidae and we test the impact of two morphological novelties on their diversification, i.e. the presence of swim bladder and buccal venom gland, using various comparative methods. We found an increase in the tempo of lineage diversification at the root of the Meiacanthus clade, associated with the evolution of the buccal venom gland, but not the swim bladder. Neither morphological novelty was associated with the pattern of size disparification in blennies. Our results support the hypothesis that the buccal venom gland has contributed to the explosive diversification of Meiacanthus, but further analyses are needed to fully understand the factors sustaining this burst of speciation.
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Affiliation(s)
- Shang-Yin Vanson Liu
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan.
| | - Bruno Frédérich
- Laboratoire d'Océanologie, UR FOCUS, Université de Liège, 4000 Liège, Belgium
| | - Sébastien Lavoué
- Institute of Oceanography, National Taiwan University, Roosevelt Road, Taipei 10617, Taiwan
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-7239, USA
| | - Mark V Erdmann
- Conservation International Indonesia Marine Program, 80235 Bali, Indonesia
| | - Gusti Ngurah Mahardika
- The Indonesian Biodiversity Research Centre, The Animal Biomedical and Molecular Biology Laboratory of Udayana University, Jl Sesetan-Markisa 6, Denpasar, Bali, Indonesia
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-7239, USA
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10
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Marramà G, Kriwet J. Principal component and discriminant analyses as powerful tools to support taxonomic identification and their use for functional and phylogenetic signal detection of isolated fossil shark teeth. PLoS One 2017; 12:e0188806. [PMID: 29182683 PMCID: PMC5705141 DOI: 10.1371/journal.pone.0188806] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 11/13/2017] [Indexed: 11/21/2022] Open
Abstract
Identifying isolated teeth of fossil selachians only based on qualitative characters is sometimes hindered by similarity in their morphology, resulting often in heated taxonomic debates. On the other hand, the use of quantitative characters (i.e. measurements) has been often neglected or underestimated in characterization and identification of fossil teeth of selachians. Here we show that, employing a robust methodological protocol based on principal component and discriminant analyses on a sample of 175 isolated fossil teeth of lamniform sharks, the traditional morphometrics can be useful to support and complement the classic taxonomic identification made on qualitative features. Furthermore, we show that discriminant analysis can be successfully useful to assign indeterminate isolated shark teeth to a certain taxon. Finally, the degree of separation of the clusters might be used to predict functional and probably also phylogenetic signals in lamniform shark teeth. However, this needs to be tested in the future employing teeth of more extant and extinct lamniform sharks and it must be pointed out that this approach does not replace in any way the qualitative analysis, but it is intended to complement and support it.
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Affiliation(s)
- Giuseppe Marramà
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Jürgen Kriwet
- Department of Palaeontology, University of Vienna, Vienna, Austria
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11
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Floeter SR, Bender MG, Siqueira AC, Cowman PF. Phylogenetic perspectives on reef fish functional traits. Biol Rev Camb Philos Soc 2017; 93:131-151. [PMID: 28464469 DOI: 10.1111/brv.12336] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/24/2017] [Accepted: 03/29/2017] [Indexed: 01/13/2023]
Abstract
Functional traits have been fundamental to the evolution and diversification of entire fish lineages on coral reefs. Yet their relationship with the processes promoting speciation, extinction and the filtering of local species pools remains unclear. We review the current literature exploring the evolution of diet, body size, water column use and geographic range size in reef-associated fishes. Using published and new data, we mapped functional traits on to published phylogenetic trees to uncover evolutionary patterns that have led to the current functional diversity of fishes on coral reefs. When examining reconstructed patterns for diet and feeding mode, we found examples of independent transitions to planktivory across different reef fish families. Such transitions and associated morphological alterations may represent cases in which ecological opportunity for the exploitation of different resources drives speciation and adaptation. In terms of body size, reconstructions showed that both large and small sizes appear multiple times within clades of mid-sized fishes and that extreme body sizes have arisen mostly in the last 10 million years (Myr). The reconstruction of range size revealed many cases of disparate range sizes among sister species. Such range size disparity highlights potential vicariant processes through isolation in peripheral locations. When accounting for peripheral speciation processes in sister pairs, we found a significant relationship between labrid range size and lineage age. The diversity and evolution of traits within lineages is influenced by trait-environment interactions as well as by species and trait-trait interactions, where the presence of a given trait may trigger the development of related traits or behaviours. Our effort to assess the evolution of functional diversity across reef fish clades adds to the burgeoning research focusing on the evolutionary and ecological roles of functional traits. We argue that the combination of a phylogenetic and a functional approach will improve the understanding of the mechanisms of species assembly in extraordinarily rich coral reef communities.
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Affiliation(s)
- Sergio R Floeter
- Depto. de Ecologia e Zoologia, Marine Macroecology and Biogeography Laboratory, CCB, Universidade Federal de Santa Catarina, Florianopolis, 88040-900, Brazil
| | - Mariana G Bender
- Depto. de Ecologia e Zoologia, Marine Macroecology and Biogeography Laboratory, CCB, Universidade Federal de Santa Catarina, Florianopolis, 88040-900, Brazil
| | - Alexandre C Siqueira
- Depto. de Ecologia e Zoologia, Marine Macroecology and Biogeography Laboratory, CCB, Universidade Federal de Santa Catarina, Florianopolis, 88040-900, Brazil
| | - Peter F Cowman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, U.S.A.,Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, Australia
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