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Damadi E, Yazdani Moghaddam F, Ghanbarifardi M. Species delimitation, molecular phylogeny and historical biogeography of the sweetlips fish (Perciformes, Haemulidae). ZOOSYST EVOL 2023. [DOI: 10.3897/zse.99.96386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The subfamily Plectorhinchinae (sweetlips) is composed of poorly-known species with high commercially and ecologically values that exhibit phenotypic plasticity and various morphologies. Few studies have assessed the validity of sweetlips, intergeneric relationships and evolutionary survey in this subfamily, which have not yet been resolved. This study investigated the DNA sequences of (1) the mitochondrial COI gene to delimit species, and (2) two mitochondrial (COI and Cyt b), and one nuclear (RAG1) markers to infer phylogenetic relationships and evolutionary and biogeographic history. The molecular results could differentiate Diagramma punctatum from the other species, but failed to distinguish D. labiosum as a distinct species with considerably lower genetic distances for the COI (0.53%) and Cyt b (0.51%) markers. However, additional taxonomic investigations are required to shed light on this issue. All previously described nominal species of sweetlips in the northwest Indian Ocean were found to be well supported. The monophyly of Plectorhinchus is not supported and Diagramma pictum and D. punctatum should be assigned to the genus Plectorhinchus. The biogeographic history of Plectorhinchinae likely originated in the Indo-Pacific ca. 34 Ma (30–39 Ma; late Eocene/ middle Oligocene) and subsequently colonised the Western Indian Ocean and the Central Indo-Pacific. Maximum diversification within the subfamily occurred from the middle Miocene to Pliocene, coinciding with dispersal and vicariance events. Diversification was probably driven by both biological and geographical factors.
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2
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Fainburg L, Sabadin D, Díaz de Astarloa JM, Fernández Iriarte P. Population structure of mud flounder Paralichthys orbignyanus from the south-western Atlantic Ocean. JOURNAL OF FISH BIOLOGY 2023; 102:455-464. [PMID: 36427018 DOI: 10.1111/jfb.15271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
The mud flounder Paralichthys orbignyanus (Pleuronectiformes, Paralichthyidae) inhabits shallow waters of low salinities and mud bottoms in the temperate marine coastal regions of the Bonaerensean Ecoregion of the Argentinean Biogeographic Province in the south-western Atlantic Ocean. Specimens of P. orbignyanus were collected from Lagoa dos Patos (LDP) (southern Brazil), Mar Chiquita (MCH) and Marisol (MAR) both located in Buenos Aires (Argentina), and San Antonio Oeste (SAO) in the San Matías Gulf, Rio Negro (Argentina). A fragment of the mitochondrial DNA of the Control Region and seven microsatellite loci were characterized. In the Control Region, P. orbignyanus showed high variability, low nucleotide diversity, mild population expansion and a coalescence time of 35,000 years before the present. Flounders provided evidence of a genetic structure between the sampling sites LDP, MCH, MAR vs. SAO. On the other hand, P. orbignyanus displayed a lower to moderate contemporary genetic structure among all samples except between LDP and MCH. With no evidence of isolation by distance, this analysis supports a model of limited gene flow that is likely to be associated with a consistent larvae retention in all sampling sites. In addition, the present connectivity is ascribed to a lower migration process from SAO in the San Matías Gulf congruent with the prevailing littoral drift.
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Affiliation(s)
- Leandro Fainburg
- Departamento de Biología-Instituto de Investigaciones Marinas y Costeras, Laboratorio de Genética, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - David Sabadin
- Instituto de Investigaciones Marinas y Costeras, Laboratorio Biología de Peces, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Juan Martín Díaz de Astarloa
- Departamento de Biología-Instituto de Investigaciones Marinas y Costeras, Laboratorio de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Pedro Fernández Iriarte
- Departamento de Biología-Instituto de Investigaciones Marinas y Costeras, Laboratorio de Genética, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
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3
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Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus). Heredity (Edinb) 2023; 130:30-39. [PMID: 36463371 DOI: 10.1038/s41437-022-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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Huang W, Chen H, Tseng Y, Liao T. Assessing phenovariant species pairs of moray eels: Hybridization, introgression, and morphology. ZOOL SCR 2022. [DOI: 10.1111/zsc.12560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wen‐Chien Huang
- Doctoral Degree Program in Marine Biotechnology National Sun Yat‐sen University Kaohsiung Taiwan
- Doctoral Degree Program in Marine Biotechnology, Academia Sinica Taipei Taiwan
| | - Hong‐Ming Chen
- Department of Aquaculture National Taiwan Ocean University Keelung Taiwan
| | - Yung‐Che Tseng
- Marine Research Station Institute of Cellular and Organismic Biology, Academia Sinica Yilan Taiwan
| | - Te‐Yu Liao
- Department of Oceanography National Sun Yat‐sen University Kaohsiung Taiwan
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Stiller J, Short G, Hamilton H, Saarman N, Longo S, Wainwright P, Rouse GW, Simison WB. Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates. BMC Biol 2022; 20:75. [PMID: 35346180 PMCID: PMC8962102 DOI: 10.1186/s12915-022-01271-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/04/2022] [Indexed: 12/03/2022] Open
Abstract
Background Seahorses, seadragons, pygmy pipehorses, and pipefishes (Syngnathidae, Syngnathiformes) are among the most recognizable groups of fishes because of their derived morphology, unusual life history, and worldwide distribution. Despite previous phylogenetic studies and recent new species descriptions of syngnathids, the evolutionary relationships among several major groups within this family remain unresolved. Results Here, we provide a reconstruction of syngnathid phylogeny based on genome-wide sampling of 1314 ultraconserved elements (UCEs) and expanded taxon sampling to assess the current taxonomy and as a basis for macroevolutionary insights. We sequenced a total of 244 new specimens across 117 species and combined with published UCE data for a total of 183 species of Syngnathidae, about 62% of the described species diversity, to compile the most data-rich phylogeny to date. We estimated divergence times using 14 syngnathiform fossils, including nine fossils with newly proposed phylogenetic affinities, to better characterize current and historical biogeographical patterns, and to reconstruct diversification through time. We present a phylogenetic hypothesis that is well-supported and provides several notable insights into syngnathid evolution. We found nine non-monophyletic genera, evidence for seven cryptic species, five potentially invalid synonyms, and identified a novel sister group to the seahorses, the Indo-Pacific pipefishes Halicampus macrorhynchus and H. punctatus. In addition, the morphologically distinct southwest Pacific seahorse Hippocampus jugumus was recovered as the sister to all other non-pygmy seahorses. As found in many other groups, a high proportion of syngnathid lineages appear to have originated in the Central Indo-Pacific and subsequently dispersed to adjoining regions. Conversely, we also found an unusually high subsequent return of lineages from southern Australasia to the Central Indo-Pacific. Diversification rates rose abruptly during the Middle Miocene Climate Transition and peaked after the closure of the Tethys Sea. Conclusions Our results reveal a previously underappreciated diversity of syngnathid lineages. The observed biogeographic patterns suggest a significant role of the southern Australasian region as a source and sink of lineages. Shifts in diversification rates imply possible links to declining global temperatures, the separation of the Atlantic and Pacific faunas, and the environmental changes associated with these events. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01271-w.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA. .,Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Graham Short
- Ichthyology, Australian Museum, Sydney, Australia.,Ichthyology, California Academy of Sciences, San Francisco, USA.,Ichthyology, Burke Museum of Natural History and Culture, Seattle, USA
| | | | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Sarah Longo
- Department of Biological Science, Towson University, Towson, MD, 21252, USA
| | - Peter Wainwright
- Department of Evolution & Ecology, University of California, Davis, USA
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, USA
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6
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Giachini Tosetto E, Bertrand A, Neumann-Leitão S, Nogueira Júnior M. The Amazon River plume, a barrier to animal dispersal in the Western Tropical Atlantic. Sci Rep 2022; 12:537. [PMID: 35017566 PMCID: PMC8752809 DOI: 10.1038/s41598-021-04165-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/03/2021] [Indexed: 11/09/2022] Open
Abstract
The dispersal of marine organisms can be restricted by a set of isolation mechanisms including hard barriers or hydrological features. In the Western Atlantic Ocean, the Amazon River discharge has been shown to act as a biogeographical barrier responsible for the differences in reef fish communities between Caribbean Sea and Northeast Brazil continental shelves. Here, we compare the diversity of all Animalia phyla from biogeographic ecoregions along the Tropical Western Atlantic continental shelf to test the hypothesis that the Amazon River plume spatially structures species diversity. For that, we used beta diversity estimators and multivariate ecological analysis on a database of species occurrence of the whole animal kingdom including 175,477 occurrences of 8,375 species from six ecoregions along the Western Tropical Atlantic. Results of the whole animal kingdom and the richest phyla showed that the Caribbean Sea and Tropical Brazil ecoregions are isolated by the Amazon River Plume, broadening and confirming the hypothesis that it acts as a soft barrier to animal dispersal in the Western Tropical Atlantic. Species sharing is larger northwestwards, in direction of the Caribbean than the opposite direction. Beyond species isolation due to local characteristics such as low salinity and high turbidity, our results suggest the dominant northwestward currents probably play a major role in animal dispersion: it enhances the flux of larvae and other planktonic organisms with reduced mobility from Brazil to Caribbean and hinders their contrary movement. Thus, the Amazon area is a strong barrier for taxa with reduced dispersal capacity, while species of pelagic taxa with active swimming may transpose it more easily.
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Affiliation(s)
- Everton Giachini Tosetto
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, PE, 50670-901, Brazil. .,Institut de Recherche pour le Développement, MARBEC, Université Montpellier, CNRS, IFREMER, IRD, 34200, Sète, France.
| | - Arnaud Bertrand
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, PE, 50670-901, Brazil.,Institut de Recherche pour le Développement, MARBEC, Université Montpellier, CNRS, IFREMER, IRD, 34200, Sète, France.,Departamento de Pesca e Aquicultura, Universidade Federal Rural de Pernambuco, Recife, PE, 52171-900, Brazil
| | - Sigrid Neumann-Leitão
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife, PE, 50670-901, Brazil
| | - Miodeli Nogueira Júnior
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, 58051-900, Brazil
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7
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Zhang Y, Mao F, Mu H, Huang M, Bao Y, Wang L, Wong NK, Xiao S, Dai H, Xiang Z, Ma M, Xiong Y, Zhang Z, Zhang L, Song X, Wang F, Mu X, Li J, Ma H, Zhang Y, Zheng H, Simakov O, Yu Z. The genome of Nautilus pompilius illuminates eye evolution and biomineralization. Nat Ecol Evol 2021; 5:927-938. [PMID: 33972735 PMCID: PMC8257504 DOI: 10.1038/s41559-021-01448-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Nautilus is the sole surviving externally shelled cephalopod from the Palaeozoic. It is unique within cephalopod genealogy and critical to understanding the evolutionary novelties of cephalopods. Here, we present a complete Nautilus pompilius genome as a fundamental genomic reference on cephalopod innovations, such as the pinhole eye and biomineralization. Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. The nautilus genome constitutes a valuable resource for reconstructing the evolutionary scenarios and genomic innovations that shape the extant cephalopods.
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Affiliation(s)
- Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Fan Mao
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Huawei Mu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Minwei Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Lili Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Nai-Kei Wong
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Shu Xiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | - Zhiming Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Mingli Ma
- Biomarker Technologies Corporation, Beijing, China
| | - Yuanyan Xiong
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziwei Zhang
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lvping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Xiaoyuan Song
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fan Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Xiyu Mu
- Biomarker Technologies Corporation, Beijing, China
| | - Jun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Haitao Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yuehuan Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | | | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Ziniu Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
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8
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Evolutionary origin of the Atlantic Cabo Verde nibbler (Girella stuebeli), a member of a primarily Pacific Ocean family of antitropical herbivorous reef fishes. Mol Phylogenet Evol 2020; 156:107021. [PMID: 33248204 DOI: 10.1016/j.ympev.2020.107021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/21/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022]
Abstract
Nibblers (family Girellidae) are reef fishes that are mostly distributed in the Indo-Pacific, with one exception: Girella stuebeli, which is found in the Cabo Verde Archipelago, in the Atlantic Ocean. We capitalized on this unusual distribution to study the evolutionary history of the girellids, and determine the relationship between G. stuebeli and the remaining nibbler taxa. Based on thousands of genomic markers (RAD sequences), we identified the closest relatives of G. stuebeli as being a clade of three species endemic to the northwestern Pacific, restricted to the Sea of Japan and vicinity. This clade diverged from G. stuebeli approximately 2.2 Mya. Two alternative potential routes of migration may explain this affinity: a western route, from the Tropical Eastern Pacific and the Tropical Western Atlantic, and an eastern route via the Indian Ocean and Southern Africa. The geological history and oceanography of the regions combined with molecular data presented here, suggest that the eastern route of invasion (via the Indian Ocean and Southern Africa) is a more likely scenario.
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Delrieu-Trottin E, Hubert N, Giles EC, Chifflet-Belle P, Suwalski A, Neglia V, Rapu-Edmunds C, Mona S, Saenz-Agudelo P. Coping with Pleistocene climatic fluctuations: Demographic responses in remote endemic reef fishes. Mol Ecol 2020; 29:2218-2233. [PMID: 32428327 DOI: 10.1111/mec.15478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Elucidating demographic history during the settlement of ecological communities is crucial for properly inferring the mechanisms that shape patterns of species diversity and their persistence through time. Here, we used genomic data and coalescent-based approaches to elucidate for the first time the demographic dynamics associated with the settlement by endemic reef fish fauna of one of the most remote peripheral islands of the Pacific Ocean, Rapa Nui (Easter Island). We compared the demographic history of nine endemic species in order to explore their demographic responses to Pleistocene climatic fluctuations. We found that species endemic to Rapa Nui share a common demographic history, as signatures of population expansions were retrieved for almost all of the species studied here, and synchronous demographic expansions initiated during the last glacial period were recovered for more than half of the studied species. These results suggest that eustatic fluctuations associated with Milankovitch cycles have played a central role in species demographic histories and in the final stage of the community assembly of many Rapa Nui reef fishes. Specifically, sea level lowstands resulted in the maximum reef habitat extension for Rapa Nui endemic species; we discuss the potential role of seamounts in allowing endemic species to cope with Pleistocene climatic fluctuations, and we highlight the importance of local historical processes over regional ones. Overall, our results shed light on the mechanisms by which endemism arises and is maintained in peripheral reef fish fauna.
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Affiliation(s)
- Erwan Delrieu-Trottin
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France
| | - Emily C Giles
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pascaline Chifflet-Belle
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Arnaud Suwalski
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Valentina Neglia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
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10
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Baraf LM, Pratchett MS, Cowman PF. Ancestral biogeography and ecology of marine angelfishes (F: Pomacanthidae). Mol Phylogenet Evol 2019; 140:106596. [DOI: 10.1016/j.ympev.2019.106596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 12/27/2022]
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11
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Reid BN, Naro-Maciel E, Hahn AT, FitzSimmons NN, Gehara M. Geography best explains global patterns of genetic diversity and postglacial co-expansion in marine turtles. Mol Ecol 2019; 28:3358-3370. [PMID: 31264298 DOI: 10.1111/mec.15165] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 01/07/2023]
Abstract
For many species, climate oscillations drove cycles of population contraction during cool glacial periods followed by expansion during interglacials. Some groups, however, show evidence of uniform and synchronous expansion, while others display differences in the timing and extent of demographic change. We compared demographic histories inferred from genetic data across marine turtle species to identify responses to postglacial warming shared across taxa and to examine drivers of past demographic change at the global scale. Using coalescent simulations and approximate Bayesian computation (ABC), we estimated demographic parameters, including the likelihood of past population expansion, from a mitochondrial data set encompassing 23 previously identified lineages from all seven marine turtle species. For lineages with a high posterior probability of expansion, we conducted a hierarchical ABC analysis to estimate the proportion of lineages expanding synchronously and the timing of synchronous expansion. We used Bayesian model averaging to identify variables associated with expansion and genetic diversity. Approximately 60% of extant marine turtle lineages showed evidence of expansion, with the rest mainly exhibiting patterns of genetic diversity most consistent with population stability. For lineages showing expansion, there was a strong signal of synchronous expansion after the Last Glacial Maximum. Expansion and genetic diversity were best explained by ocean basin and the degree of endemism for a given lineage. Geographic differences in sensitivity to climate change have implications for prioritizing conservation actions in marine turtles as well as for identifying areas of past demographic stability and potential resilience to future climate change for broadly distributed taxa.
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Affiliation(s)
- Brendan N Reid
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
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12
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Ma KY, van Herwerden L, Newman SJ, Berumen ML, Choat JH, Chu KH, Sadovy de Mitcheson Y. Contrasting population genetic structure in three aggregating groupers (Percoidei: Epinephelidae) in the Indo-West Pacific: the importance of reproductive mode. BMC Evol Biol 2018; 18:180. [PMID: 30514203 PMCID: PMC6278153 DOI: 10.1186/s12862-018-1284-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/30/2018] [Indexed: 11/10/2022] Open
Abstract
Background Understanding the factors shaping population genetic structure is important for evolutionary considerations as well as for management and conservation. While studies have revealed the importance of palaeogeographic changes in shaping phylogeographic patterns in multiple marine fauna, the role of reproductive behaviour is rarely considered in reef fishes. We investigated the population genetics of three commercially important aggregating grouper species in the Indo-West Pacific, namely the camouflage grouper Epinephelus polyphekadion, the squaretail coral grouper Plectropomus areolatus, and the common coral trout P. leopardus, with similar life histories but distinct spatio-temporal characteristics in their patterns of forming spawning aggregations. Results By examining their mitochondrial control region and 9–11 microsatellite markers, we found an overarching influence of palaeogeographic events in the population structure of all species, with genetic breaks largely coinciding with major biogeographic barriers. The divergence time of major lineages in these species coincide with the Pleistocene glaciations. Higher connectivity is evident in E. polyphekadion and P. areolatus that assemble in larger numbers at fewer spawning aggregations and in distinctive offshore locations than in P. leopardus which has multiple small, shelf platform aggregations. Conclusions While palaeogeographic events played an important role in shaping the population structure of the target species, the disparity in population connectivity detected may be partly attributable to differences in their reproductive behaviour, highlighting the need for more investigations on this characteristic and the need to consider reproductive mode in studies of connectivity and population genetics. Electronic supplementary material The online version of this article (10.1186/s12862-018-1284-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ka Yan Ma
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Lynne van Herwerden
- College of Science and Engineering, James Cook University, Douglas, Townsville, QLD, 4811, Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, PO Box 20, North Beach, WA, 6920, Australia
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - John Howard Choat
- College of Science and Engineering, James Cook University, Douglas, Townsville, QLD, 4811, Australia
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yvonne Sadovy de Mitcheson
- Swire Institute of Marine Science, School of Biological Sciences, University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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13
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Argolo LA, Ramos RT, Barreto SB, Bitencourt JA, Sampaio I, Schneider H, Affonso PR. The flounder next door: Closer evolutionary relationship between allopatric than sympatric Bothus (Rafinesque, 1810) species (Pleuronectiformes, Bothidae). ZOOL ANZ 2018. [DOI: 10.1016/j.jcz.2018.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Bakar AA, Adamson EAS, Juliana LH, Nor Mohd SA, Wei-Jen C, Man A, Md DN. DNA barcoding of Malaysian commercial snapper reveals an unrecognized species of the yellow-lined Lutjanus (Pisces:Lutjanidae). PLoS One 2018; 13:e0202945. [PMID: 30183729 PMCID: PMC6124743 DOI: 10.1371/journal.pone.0202945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/13/2018] [Indexed: 11/24/2022] Open
Abstract
Management of wild fisheries resources requires accurate knowledge on which species are being routinely exploited, but it can be hard to identify fishes to species level, especially in speciose fish groups where colour patterns vary with age. Snappers of the genus Lutjanus represent one such group, where fishes can be hard to identify and as a result fisheries statistics fail to capture species-level taxonomic information. This study employs traditional morphological and DNA barcoding approaches to identify adult and juvenile Lutjanus species harvested in Malaysian waters. Our results reveal a suite of species that differs markedly from those that have previously been considered important in the Malaysian wild-capture fishery and show that official fisheries statistics do not relate to exploitation at the species level. Furthermore, DNA barcoding uncovered two divergent groups of bigeye snapper ('Lutjanus lutjanus') distributed on either side of the Malay Peninsula, displaying a biogeographical pattern similar to distributions observed for many co-occurring reef-distributed fish groups. One of these bigeye snapper groups almost certainly represents an unrecognized species in need of taxonomic description. The study demonstrates the utility of DNA barcoding in uncovering overlooked diversity and for assessing species catch composition in a complicated but economically important taxonomic group.
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Affiliation(s)
- Adibah Abu Bakar
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
- Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris (UPSI), Tanjong Malim, Perak, Malaysia
| | | | - Lia Halim Juliana
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Siti Azizah Nor Mohd
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
- Institut Bioteknologi Marin, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Chen Wei-Jen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Alias Man
- Fisheries Research Institute (FRI), Batu Maung, Pulau Pinang, Malaysia
| | - Darlina Naim Md
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
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15
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Dudoit 'A, Iacchei M, Coleman RR, Gaither MR, Browne WE, Bowen BW, Toonen RJ. The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages. PeerJ 2018. [PMID: 29527409 PMCID: PMC5844259 DOI: 10.7717/peerj.4409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120-253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000-400,000 yr) than the Western Atlantic population (95% HPD = 300,000-760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000-1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.
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Affiliation(s)
- 'Ale'alani Dudoit
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Zoology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Matthew Iacchei
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America.,Department of Natural Science, Hawai'i Pacific University, Kāne'ohe, HI, United States of America
| | - Richard R Coleman
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Zoology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Michelle R Gaither
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Current affiliation: Department of Biology, University of Central Florida, Orlando, FL, United States of America
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, United States of America
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
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16
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Pinheiro HT, Rocha LA, Macieira RM, Carvalho-Filho A, Anderson AB, Bender MG, Di Dario F, Ferreira CEL, Figueiredo-Filho J, Francini-Filho R, Gasparini JL, Joyeux JC, Luiz OJ, Mincarone MM, Moura RL, Nunes JDACC, Quimbayo JP, Rosa RS, Sampaio CLS, Sazima I, Simon T, Vila-Nova DA, Floeter SR. South-western Atlantic reef fishes: Zoogeographical patterns and ecological drivers reveal a secondary biodiversity centre in the Atlantic Ocean. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12729] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Hudson T. Pinheiro
- California Academy of Sciences; San Francisco CA USA
- Ecology and Evolutionary Biology Department; University of California Santa Cruz; Santa Cruz CA USA
- Associação Ambiental Voz da Natureza; Vitória ES Brazil
| | - Luiz A. Rocha
- California Academy of Sciences; San Francisco CA USA
- Ecology and Evolutionary Biology Department; University of California Santa Cruz; Santa Cruz CA USA
| | - Raphael M. Macieira
- Laboratório de Ecologia Marinha; Universidade Vila Velha; Vila Velha ES Brazil
| | | | - Antônio B. Anderson
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Mariana G. Bender
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Fabio Di Dario
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé; Universidade Federal do Rio de Janeiro; Macaé RJ Brazil
| | | | - Jessé Figueiredo-Filho
- Centro de Ciências Exatas e da Natureza; Universidade Federal da Paraíba; João Pessoa PB Brazil
| | - Ronaldo Francini-Filho
- Departamento de Engenharia e Meio Ambiente; Universidade Federal da Paraíba; Rio Tinto PB Brazil
| | - João L. Gasparini
- Departamento de Oceanografia e Ecologia; Universidade Federal do Espírito Santo; Vitória ES Brazil
| | - Jean-Christophe Joyeux
- Departamento de Oceanografia e Ecologia; Universidade Federal do Espírito Santo; Vitória ES Brazil
| | - Osmar J. Luiz
- Department of Biological Sciences; Macquarie University; Sydney NSW Australia
- Research Institute for the Environment and Livelihoods; Charles Darwin University; Darwin NT Australia
| | - Michael M. Mincarone
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé; Universidade Federal do Rio de Janeiro; Macaé RJ Brazil
| | - Rodrigo L. Moura
- Instituto de Biologia and SAGE/COPPE; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
| | | | - Juan P. Quimbayo
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Ricardo S. Rosa
- Centro de Ciências Exatas e da Natureza; Universidade Federal da Paraíba; João Pessoa PB Brazil
| | - Cláudio L. S. Sampaio
- Laboratório de Ictiologia e Conservação; Universidade Federal de Alagoas; Penedo AL Brazil
| | - Ivan Sazima
- Museu de Zoologia; Universidade Estadual de Campinas; Campinas SP Brazil
| | - Thiony Simon
- Associação Ambiental Voz da Natureza; Vitória ES Brazil
- Departamento de Oceanografia e Ecologia; Universidade Federal do Espírito Santo; Vitória ES Brazil
| | - Daniele A. Vila-Nova
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Sergio R. Floeter
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
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17
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Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea. PLoS One 2018; 13:e0193220. [PMID: 29466431 PMCID: PMC5821360 DOI: 10.1371/journal.pone.0193220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/07/2018] [Indexed: 11/19/2022] Open
Abstract
The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.
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18
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Braga Goncalves I, Cornetti L, Couperus AS, van Damme CJG, Mobley KB. Phylogeography of the snake pipefish, Entelurus aequoreus (Family: Syngnathidae) in the northeastern Atlantic Ocean. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Tethyan changes shaped aquatic diversification. Biol Rev Camb Philos Soc 2017; 93:874-896. [DOI: 10.1111/brv.12376] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 01/19/2023]
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20
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Silva G, Cunha RL, Ramos A, Castilho R. Wandering behaviour prevents inter and intra oceanic speciation in a coastal pelagic fish. Sci Rep 2017; 7:2893. [PMID: 28588244 PMCID: PMC5460251 DOI: 10.1038/s41598-017-02945-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/26/2017] [Indexed: 11/25/2022] Open
Abstract
Small pelagic fishes have the ability to disperse over long distances and may present complex evolutionary histories. Here, Old World Anchovies (OWA) were used as a model system to understand genetic patterns and connectivity of fish between the Atlantic and Pacific basins. We surveyed 16 locations worldwide using mtDNA and 8 microsatellite loci for genetic parameters, and mtDNA (cyt b; 16S) and nuclear (RAG1; RAG2) regions for dating major lineage-splitting events within Engraulidae family. The OWA genetic divergences (0-0.4%) are compatible with intra-specific divergence, showing evidence of both ancient and contemporary admixture between the Pacific and Atlantic populations, enhanced by high asymmetrical migration from the Pacific to the Atlantic. The estimated divergence between Atlantic and Pacific anchovies (0.67 [0.53-0.80] Ma) matches a severe drop of sea temperature during the Günz glacial stage of the Pleistocene. Our results support an alternative evolutionary scenario for the OWA, suggesting a coastal migration along south Asia, Middle East and eastern Africa continental platforms, followed by the colonization of the Atlantic via the Cape of the Good Hope.
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Affiliation(s)
- Gonçalo Silva
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal.
- MARE - Marine and Environmental Sciences Centre; ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041, Lisboa, Portugal.
| | - Regina L Cunha
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal
| | - Ana Ramos
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal
| | - Rita Castilho
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal
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21
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Delrieu-Trottin E, Shen KN, Chang CW, Borsa P. One Species Hypothesis to Rule Them All: Consistency Is Essential to Delimitate Species. J Hered 2017; 108:334-336. [PMID: 28391307 DOI: 10.1093/jhered/esx008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Erwan Delrieu-Trottin
- Instituto de Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Wei Chang
- National Museum of Marine Biology & Aquarium and Graduate Institute of Marine Biology, National Dong Hwa University, Checheng, Pingtung, Taiwan
| | - Philippe Borsa
- Institut de recherche pour le développement (IRD), UMR 250 "Ecologie marine tropicale des océans Pacifique et Indien"/LabEx "Corail", Nouméa, New Caledonia
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22
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Cowman PF, Parravicini V, Kulbicki M, Floeter SR. The biogeography of tropical reef fishes: endemism and provinciality through time. Biol Rev Camb Philos Soc 2017; 92:2112-2130. [DOI: 10.1111/brv.12323] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/23/2017] [Accepted: 01/26/2017] [Indexed: 12/25/2022]
Affiliation(s)
- 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
| | - Valeriano Parravicini
- Ecole Pratique des Hautes Etudes, USR 3278 EPHE-CNRS-UPVD, Labex Corail, CRIOBE; 66860 Perpignan France
| | - Michel Kulbicki
- Institut de Recherche pour le développement (IRD), UMR Entropie-Labex CORAIL; Université de Perpignan; 66000 Perpignan France
| | - Sergio R. Floeter
- Depto. de Ecologia e Zoologia, Marine Macroecology and Biogeography Laboratory, CCB; Universidade Federal de Santa Catarina; Florianópolis 88040-900 Brazil
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23
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Almada F, Francisco SM, Lima CS, FitzGerald R, Mirimin L, Villegas-Ríos D, Saborido-Rey F, Afonso P, Morato T, Bexiga S, Robalo JI. Historical gene flow constraints in a northeastern Atlantic fish: phylogeography of the ballan wrasse Labrus bergylta across its distribution range. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160773. [PMID: 28386433 PMCID: PMC5367310 DOI: 10.1098/rsos.160773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/16/2017] [Indexed: 05/17/2023]
Abstract
The distribution and demographic patterns of marine organisms in the north Atlantic were largely shaped by climatic changes during the Pleistocene, when recurrent glacial maxima forced them to move south or to survive in northern peri-glacial refugia. These patterns were also influenced by biological and ecological factors intrinsic to each species, namely their dispersion ability. The ballan wrasse (Labrus bergylta), the largest labrid fish along Europe's continental margins, is a target for fisheries and aquaculture industry. The phylogeographic pattern, population structure, potential glacial refugia and recolonization routes for this species were assessed across its full distribution range, using mitochondrial and nuclear markers. The existence of a marked population structure can reflect both recolonization from three distinct glacial refugia and current and past oceanographic circulation patterns. Although isolated in present times, shared haplotypes between continental and Azores populations and historical exchange of migrants in both directions point to a common origin of L. bergylta. This situation is likely to be maintained and/or accentuated by current circulation patterns in the north Atlantic, and may lead to incipient speciation in the already distinct Azorean population. Future monitoring of this species is crucial to evaluate how this species is coping with current environmental changes.
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Affiliation(s)
- Frederico Almada
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Sara M. Francisco
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Cristina S. Lima
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Richard FitzGerald
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Republic of Ireland
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Republic of Ireland
| | - David Villegas-Ríos
- Institute of Marine Research (IMR), Flødevigen Marine Research Station, 4817 His, Norway
| | | | - Pedro Afonso
- MARE—Marine and Environmental Sciences Centre, Universidade dos Açores, 9901-862 Horta, Portugal
- Departamento de Oceanografia e Pescas da Universidade dos Açores, IMAR—Institute of Marine Research, 9901-862 Horta, Portugal
| | - Telmo Morato
- MARE—Marine and Environmental Sciences Centre, Universidade dos Açores, 9901-862 Horta, Portugal
| | - Sérgio Bexiga
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Joana I. Robalo
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
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24
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Henriques R, von der Heyden S, Lipinski MR, du Toit N, Kainge P, Bloomer P, Matthee CA. Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes. Mol Ecol 2016; 25:5843-5861. [PMID: 27862532 DOI: 10.1111/mec.13890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 09/12/2016] [Accepted: 10/07/2016] [Indexed: 11/30/2022]
Abstract
Environmental gradients have been shown to disrupt gene flow in marine species, yet their influence in structuring populations at depth remains poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis) are demersal species co-occurring in the Benguela Current system, where decades of intense fishing resulted in severely depleted stocks in the past. Previous studies identified conflicting mtDNA genetic substructuring patterns and thus contrasting evolutionary trajectories for both species. Using 10 microsatellite loci, the control region of mtDNA and employing a seascape genetics approach, we investigated genetic connectivity and the impact of prolonged exploitation in the two species, which are characterized by different patterns of fishing pressure. Three consecutive years were sampled covering the entire distribution (N = 2100 fishes). Despite large estimated population sizes, both species exhibited low levels of contemporary genetic diversity (0.581 < HE < 0.692), implying that fishing has had a significant impact on their genetic composition and evolutionary trajectories. Further, for M. paradoxus, significant temporal, but not spatial, divergence points to the presence of genetic chaotic patchiness. In contrast, M. capensis exhibited a clear latitudinal cline in genetic differentiation between Namibia and South Africa (FST = 0.063, P < 0.05), with low (0.2% per generation) estimates of contemporary gene flow. Seascape analyses reveal an association with bathymetry and upwelling events, suggesting that adaptation to local environmental conditions may drive genetic differentiation in M. capensis. Importantly, our results highlight the need for temporal sampling in disentangling the complex factors that impact population divergence in marine fishes.
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Affiliation(s)
- Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Marek R Lipinski
- Department of Ichthyology and Fisheries Sciences, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa
| | - Nina du Toit
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Paulus Kainge
- National Marine Information and Research Centre, Private Bag 912, Swakopmund, Namibia
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Conrad A Matthee
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
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25
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Bernard AM, Feldheim KA, Heithaus MR, Wintner SP, Wetherbee BM, Shivji MS. Global population genetic dynamics of a highly migratory, apex predator shark. Mol Ecol 2016; 25:5312-5329. [DOI: 10.1111/mec.13845] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Andrea M. Bernard
- Save Our Seas Shark Research Center Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
| | - Kevin A. Feldheim
- The Field Museum of Natural History Pritzker Laboratory for Molecular Systematics and Evolution 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - Michael R. Heithaus
- School of Environment and Society Florida International University Miami FL USA
| | - Sabine P. Wintner
- KwaZulu‐Natal Sharks Board Private Bag 2 Umhlanga Rocks 4320 South Africa
- Biomedical Resource Unit University of KwaZulu‐Natal Durban 4000 South Africa
| | - Bradley M. Wetherbee
- Department of Biological Sciences University of Rhode Island Kingston RI USA
- Guy Harvey Research Institute Dania Beach, FL 33004 USA
| | - Mahmood S. Shivji
- Save Our Seas Shark Research Center and Guy Harvey Research Institute Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
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26
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DiBattista JD, Gaither MR, Hobbs JPA, Rocha LA, Bowen BW. Angelfishes, Paper Tigers, and the Devilish Taxonomy of theCentropyge flavissimaComplex. J Hered 2016; 107:647-653. [DOI: 10.1093/jhered/esw062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 09/11/2016] [Indexed: 11/13/2022] Open
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27
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Shen KN, Chang CW, Lin ZH, Chan YF, Tsai SY, Chen CH, Hsiao CD. Complete mitogenomes of Whitetail angelfish ( Centropyge flavicauda) and Orangeback angelfish ( Centropyge acanthops) (Teleostei: Pomacanthidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:2951-2. [DOI: 10.3109/19401736.2015.1060456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan,
| | - Chih-Wei Chang
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan,
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan,
| | - Zi-Han Lin
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Yen-Fan Chan
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Shiou-Yi Tsai
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | | | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
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28
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Phylogeny of deepwater snappers (Genus Etelis) reveals a cryptic species pair in the Indo-Pacific and Pleistocene invasion of the Atlantic. Mol Phylogenet Evol 2016; 100:361-371. [DOI: 10.1016/j.ympev.2016.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 11/19/2022]
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The historical biogeography of groupers: Clade diversification patterns and processes. Mol Phylogenet Evol 2016; 100:21-30. [PMID: 26908372 DOI: 10.1016/j.ympev.2016.02.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 02/12/2016] [Accepted: 02/16/2016] [Indexed: 11/20/2022]
Abstract
Groupers (family Epinephelidae) are a clade of species-rich, biologically diverse reef fishes. Given their ecological variability and widespread distribution across ocean basins, it is important to scrutinize their evolutionary history that underlies present day distributions. This study investigated the patterns and processes by which grouper biodiversity has been generated and what factors have influenced their present day distributions. We reconstructed a robust, time-calibrated molecular phylogeny of Epinephelidae with comprehensive (∼87%) species sampling, whereby diversification rates were estimated and ancestral ranges were reconstructed. Our results indicate that groupers originated in what is now the East Atlantic during the mid-Eocene and diverged successively to form six strongly supported main clades. These clades differ in age (late Oligocene to mid-Miocene), geographic origin (West Atlantic to West Indo-Pacific) and temporal-spatial diversification pattern, ranging from constant rates of diversification to episodes of rapid radiation. Overall, divergence within certain biogeographic regions was most prevalent in groupers, while vicariant divergences were more common in Tropical Atlantic and East Pacific groupers. Our findings reveal that both biological and geographical factors have driven grouper diversification. They also underscore the importance of scrutinizing group-specific patterns to better understand reef fish evolution.
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30
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Koblmüller S, Steinwender B, Weiß S, Sefc KM. Gene flow, population growth and a novel substitution rate estimate in a subtidal rock specialist, the black-faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the Adriatic Sea. J ZOOL SYST EVOL RES 2015; 53:291-299. [PMID: 26617435 PMCID: PMC4658704 DOI: 10.1111/jzs.12110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2015] [Indexed: 11/27/2022]
Abstract
Population histories depend on the interplay between exogeneous and endogeneous factors. In marine species, phylogeographic and demographic patterns are often shaped by sea level fluctuations, water currents and dispersal ability. Using mitochondrial control region sequences (n = 120), we infer phylogeographic structure and historic population size changes of a common littoral fish species, the black-faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the north-eastern Adriatic Sea. We find that Adriatic T. delaisi are differentiated from conspecific populations in the remaining Mediterranean, but display little phylogeographic structure within the Adriatic basin. The pattern is consistent with passive dispersal of planktonic larvae along cyclonic currents within the Adriatic Sea, but limited active dispersal of adults. Demographic reconstructions are consistent with recent population expansion, probably triggered by rising sea levels after the last glacial maximum (LGM). Placing the onset of population growth between the LGM and the warming of surface waters (18 000-13 000 years BP) and employing a novel expansion dating approach, we inferred a substitution rate of 2.61-3.61% per site per MY. Our study is one of only few existing investigations of the genetic structure of animals within the Adriatic basin and is the first to provide an estimate for mitochondrial control region substitution rates in blennioid fishes.
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Affiliation(s)
| | | | - Sara Weiß
- Institute of ZoologyUniversity of GrazGrazAustria
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31
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Gaither MR, Bernal MA, Fernandez-Silva I, Mwale M, Jones SA, Rocha C, Rocha LA. Two deep evolutionary lineages in the circumtropical glasseye Heteropriacanthus cruentatus (Teleostei, Priacanthidae) with admixture in the south-western Indian Ocean. JOURNAL OF FISH BIOLOGY 2015; 87:715-727. [PMID: 26333139 DOI: 10.1111/jfb.12754] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 06/19/2015] [Indexed: 06/05/2023]
Abstract
A phylogeographic study of the circumtropical glasseye Heteropriacanthus cruentatus was conducted. Molecular analyses indicate two mitochondrial cytochrome c oxidase subunit I (coI) lineages that are 10·4% divergent: one in the western Atlantic (Caribbean) and another that was detected across the Indo-Pacific. A fixed single nucleotide polymorphism (SNP) was detected at a nuclear locus (S7 ribosomal protein) and is consistent with this finding. There is evidence of recent dispersal from the Atlantic to the Indian Ocean with individuals of mixed lineages detected in South Africa and the Mozambique Channel. Using coalescent analyses of the mitochondrial dataset, time of divergence between lineages was estimated to be c. 15·3 million years. The deep divergence between these two lineages indicates distinct evolutionary units, however, due to the lack of morphological differences and evidence of hybridization between lineages, taxonomic revision is not suggested at this time.
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Affiliation(s)
- M R Gaither
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, U.K
| | - M A Bernal
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
- University of Texas Marine Science Institute, 750 Channel View Drive, Port Aransas, TX, 78373, U.S.A
| | - I Fernandez-Silva
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - M Mwale
- South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown, 6140, South Africa
- National Zoological Gardens of South Africa, P. O. Box 754, Pretoria, 001, South Africa
| | - S A Jones
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
| | - C Rocha
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
| | - L A Rocha
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
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32
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Gaither MR, Bernal MA, Coleman RR, Bowen BW, Jones SA, Simison WB, Rocha LA. Genomic signatures of geographic isolation and natural selection in coral reef fishes. Mol Ecol 2015; 24:1543-57. [PMID: 25753379 DOI: 10.1111/mec.13129] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 01/17/2023]
Abstract
The drivers of speciation remain among the most controversial topics in evolutionary biology. Initially, Darwin emphasized natural selection as a primary mechanism of speciation, but the architects of the modern synthesis largely abandoned that view in favour of divergence by geographic isolation. The balance between selection and isolation is still at the forefront of the evolutionary debate, especially for the world's tropical oceans where biodiversity is high, but isolating barriers are few. Here, we identify the drivers of speciation in Pacific reef fishes of the genus Acanthurus by comparative genome scans of two peripheral populations that split from a large Central-West Pacific lineage at roughly the same time. Mitochondrial sequences indicate that populations in the Hawaiian Archipelago and the Marquesas Islands became isolated approximately 0.5 Ma. The Hawaiian lineage is morphologically indistinguishable from the widespread Pacific form, but the Marquesan form is recognized as a distinct species that occupies an unusual tropical ecosystem characterized by upwelling, turbidity, temperature fluctuations, algal blooms and little coral cover. An analysis of 3737 SNPs reveals a strong signal of selection at the Marquesas, with 59 loci under disruptive selection including an opsin Rh2 locus. While both the Hawaiian and Marquesan populations indicate signals of drift, the former shows a weak signal of selection that is comparable with populations in the Central-West Pacific. This contrast between closely related lineages reveals one population diverging due primarily to geographic isolation and genetic drift, and the other achieving taxonomic species status under the influence of selection.
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Affiliation(s)
- Michelle R Gaither
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK; Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
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Dornburg A, Moore J, Beaulieu JM, Eytan RI, Near TJ. The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes). Evolution 2014; 69:146-61. [DOI: 10.1111/evo.12562] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/27/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Alex Dornburg
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History; Yale University; New Haven Connecticut
| | - Jon Moore
- Wilkes Honors College; Florida Atlantic University; Jupiter Florida
- Harbor Branch Oceanographic Institution; Florida Atlantic University; Fort Pierce Florida
| | - Jeremy M. Beaulieu
- National Institute of Mathematical and Biological Synthesis; University of Tennessee; Knoxville Tennessee
| | - Ron I. Eytan
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History; Yale University; New Haven Connecticut
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History; Yale University; New Haven Connecticut
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Bernard AM, Shivji MS, Prince ED, Hazin FHV, Arocha F, Domingo A, Feldheim KA. Comparative population genetics and evolutionary history of two commonly misidentified billfishes of management and conservation concern. BMC Genet 2014; 15:141. [PMID: 25494814 PMCID: PMC4278234 DOI: 10.1186/s12863-014-0141-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/01/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Misidentifications between exploited species may lead to inaccuracies in population assessments, with potentially irreversible conservation ramifications if overexploitation of either species is occurring. A notable showcase is provided by the realization that the roundscale spearfish (Tetrapturus georgii), a recently validated species, has been historically misidentified as the morphologically very similar and severely overfished white marlin (Kajikia albida) (IUCN listing: Vulnerable). In effect, no information exists on the population status and evolutionary history of the enigmatic roundscale spearfish, a large, highly vagile and broadly distributed pelagic species. We provide the first population genetic evaluation of the roundscale spearfish, utilizing nuclear microsatellite and mitochondrial DNA sequence markers. Furthermore, we re-evaluated existing white marlin mitochondrial genetic data and present our findings in a comparative context to the roundscale spearfish. RESULTS Microsatellite and mitochondrial (control region) DNA markers provided mixed evidence for roundscale spearfish population differentiation between the western north and south Atlantic regions, depending on marker-statistical analysis combination used. Mitochondrial DNA analyses provided strong signals of historical population growth for both white marlin and roundscale spearfish, but higher genetic diversity and effective female population size (1.5-1.9X) for white marlin. CONCLUSIONS The equivocal indications of roundscale spearfish population structure, combined with a smaller effective female population size compared to the white marlin, already a species of concern, suggests that a species-specific and precautionary management strategy recognizing two management units is prudent for this newly validated billfish.
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Affiliation(s)
- Andrea M Bernard
- The Guy Harvey Research Institute, Oceanographic Center, Nova Southeastern University, 8000 N. Ocean Drive, Dania Beach, FL, 33004, USA.
| | - Mahmood S Shivji
- The Guy Harvey Research Institute, Oceanographic Center, Nova Southeastern University, 8000 N. Ocean Drive, Dania Beach, FL, 33004, USA.
| | - Eric D Prince
- National Marine Fisheries Service, Southeast Fisheries Science Center, 75 Virginia Beach Drive, Miami, FL, 33149, USA.
| | - Fabio H V Hazin
- Departamento de Pesca e Aquicultura, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-032, Brazil.
| | - Freddy Arocha
- Instituto Oceanográfico de Venezuela, Universidad de Oriente, Apartado de Correos, 204, Cumaná, 6101, Venezuela.
| | - Andres Domingo
- Laboratorio de Recursos Pelágicos, Dirección Nacional de Recursos Acuáticos, Constituyente 1497, Montevideo, CP, 11200, Uruguay.
| | - Kevin A Feldheim
- The Field Museum of Natural History, Pritzker Laboratory for Molecular Systematics and Evolution, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA.
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35
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Jean CT, Wu CY, Tsai KC, Wang WK, Hsu YY, Chang YM, Lin HD. Population genetic structure in the endemic cyprinid fish Microphysogobio alticorpus in Taiwan: Evidence for a new phylogeographical area. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Cowman PF. Historical factors that have shaped the evolution of tropical reef fishes: a review of phylogenies, biogeography, and remaining questions. Front Genet 2014; 5:394. [PMID: 25431581 PMCID: PMC4230204 DOI: 10.3389/fgene.2014.00394] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/27/2014] [Indexed: 12/21/2022] Open
Abstract
Biodiversity patterns across the marine tropics have intrigued evolutionary biologists and ecologists alike. Tropical coral reefs host 1/3 of all marine species of fish on 0.1% of the ocean's surface. Yet our understanding of how mechanistic processes have underpinned the generation of this diversity is limited. However, it has become clear that the biogeographic history of the marine tropics has played an important role in shaping the diversity of tropical reef fishes we see today. In the last decade, molecular phylogenies and age estimation techniques have provided a temporal framework in which the ancestral biogeographic origins of reef fish lineages have been inferred, but few have included fully sampled phylogenies or made inferences at a global scale. We are currently at a point where new sequencing technologies are accelerating the reconstruction and the resolution of the Fish Tree of Life. How will a complete phylogeny of fishes benefit the study of biodiversity in the tropics? Here, I review the literature concerning the evolutionary history of reef-associated fishes from a biogeographic perspective. I summarize the major biogeographic and climatic events over the last 65 million years that have regionalized the tropical marine belt and what effect they have had on the molecular record of fishes and global biodiversity patterns. By examining recent phylogenetic trees of major reef associated groups, I identify gaps to be filled in order to obtain a clearer picture of the origins of coral reef fish assemblages. Finally, I discuss questions that remain to be answered and new approaches to uncover the mechanistic processes that underpin the evolution of biodiversity on coral reefs.
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Affiliation(s)
- Peter F Cowman
- Department of Ecology and Evolutionary Biology, Yale University New Haven, CT, USA
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37
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He L, Zhang A, Weese D, Li S, Li J, Zhang J. Demographic response of cutlassfish (Trichiurus japonicus and T. nanhaiensis) to fluctuating palaeo-climate and regional oceanographic conditions in the China seas. Sci Rep 2014; 4:6380. [PMID: 25223336 PMCID: PMC4165270 DOI: 10.1038/srep06380] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 08/26/2014] [Indexed: 11/09/2022] Open
Abstract
Glacial cycles of the Quaternary have heavily influenced the demographic history of various species. To test the evolutionary impact of palaeo-geologic and climatic events on the demographic history of marine taxa from the coastal Western Pacific, we investigated the population structure and demographic history of two economically important fish (Trichiurus japonicus and T. nanhaiensis) that inhabit the continental shelves of the East China and northern South China Seas using the mitochondrial cytochrome b sequences and Bayesian Skyline Plot analyses. A molecular rate of 2.03% per million years, calibrated to the earliest flooding of the East China Sea shelf (70-140 kya), revealed a strong correlation between population sizes and primary production. Furthermore, comparison of the demographic history of T. japonicus populations from the East China and South China Seas provided evidence of the postglacial development of the Changjiang (Yangtze River) Delta. In the South China Sea, interspecific comparisons between T. japonicus and T. nanhaiensis indicated possible evolutionary responses to changes in palaeo-productivity that were influenced by East Asian winter monsoons. This study not only provides insight into the demographic history of cutlassfish but also reveals potential clues regarding the historic productivity and regional oceanographic conditions of the Western Pacific marginal seas.
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Affiliation(s)
- Lijun He
- 1] State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, P. R. China [2] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, P. R. China
| | - Aibing Zhang
- 1] College of Life Sciences, Capital Normal University, Beijing, 100048, P. R. China [2]
| | - David Weese
- 1] Department of Biological and Environmental Sciences, Georgia College &State University, Milledgeville, GA 31061, USA [2]
| | - Shengfa Li
- 1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, P. R. China [2]
| | - Jiansheng Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, P. R. China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, P. R. China
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38
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Li H, Lin H, Li J, Ding S. Phylogeography of the Chinese beard eel, Cirrhimuraena chinensis Kaup, inferred from mitochondrial DNA: a range expansion after the last glacial maximum. Int J Mol Sci 2014; 15:13564-77. [PMID: 25100169 PMCID: PMC4159811 DOI: 10.3390/ijms150813564] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 06/10/2014] [Accepted: 07/10/2014] [Indexed: 12/01/2022] Open
Abstract
The Chinese beard eel (Cirrhimuraena chinensis Kaup) is an intertidal fish and a model organism for the study of impacts caused by topological fluctuations during the Pleistocene and current intricate hydrological conditions on fauna living in the coastal areas of China. In this study, we examined the phylogeographical pattern, population genetic profile and demographical history of C. chinensis using mitochondrial DNA (cytochrome b (cyt b) and control region (CR)) from 266 individuals sampled in seven localities across the coastal area of southeastern China. The combined data indicated high levels of haplotype diversity and low levels of nucleotide diversity. Analyses of molecular variance (AMOVA) and FST statistics suggested the absence of a significant population structure across the Chinese coast. Neutrality tests, mismatch distributions and Bayesian skyline plots uniformly indicated a recent population expansion. The phylogeographic structure of C. chinensis may be attributed to past population expansion and long-distance pelagic larval dispersal facilitated by present-day ocean currents.
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Affiliation(s)
- Hai Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
| | - Hungdu Lin
- Department of Physical Therapy, Shu Zen College of Medicine and Management, Kaohsiung 821, Taiwan.
| | - Jianlong Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
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Vignaud TM, Maynard JA, Leblois R, Meekan MG, Vázquez-Juárez R, Ramírez-Macías D, Pierce SJ, Rowat D, Berumen ML, Beeravolu C, Baksay S, Planes S. Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline. Mol Ecol 2014; 23:2590-601. [DOI: 10.1111/mec.12754] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/08/2014] [Accepted: 04/13/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas M. Vignaud
- Laboratoire d'Excellence «CORAIL» USR 3278 CNRS - EPHE; CRIOBE; Papetoai Moorea French Polynesia
| | - Jeffrey A. Maynard
- Laboratoire d'Excellence «CORAIL» USR 3278 CNRS - EPHE; CRIOBE; Papetoai Moorea French Polynesia
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14568 USA
| | | | - Mark G. Meekan
- Australian Institute of Marine Science; UWA Oceans Institute (MO96); 35 Stirling Hwy Crawley WA 6009 Australia
| | - Ricardo Vázquez-Juárez
- Centro de Investigaciones Biologicas del Noroeste; Mar Bermejo 195, Col. Playa Palo de Santa Rita La Paz B.C.S. 23096 Mexico
| | - Dení Ramírez-Macías
- Centro de Investigaciones Biologicas del Noroeste; Mar Bermejo 195, Col. Playa Palo de Santa Rita La Paz B.C.S. 23096 Mexico
- Tiburón Ballena México proyecto de Conciencia Mexico; Manatí 4802, Col. Esperanza III La Paz B.C.S. 23090 Mexico
| | - Simon J. Pierce
- Marine Megafauna Foundation; 3024 Frandoras Circle Oakley CA 94561 USA
- Wild Me; Praia do Tofo; Inhambane Mozambique
| | - David Rowat
- Marine Conservation Society Seychelles; PO Box 1299 Victoria Mahe Seychelles
| | - Michael L. Berumen
- Red Sea Research Center; King Abdullah University of Science and Technology; 23955-6900 Thuwal Kingdom of Saudi Arabia
| | | | - Sandra Baksay
- Laboratoire d'Excellence «CORAIL» USR 3278 CNRS - EPHE; CRIOBE; Papetoai Moorea French Polynesia
| | - Serge Planes
- Laboratoire d'Excellence «CORAIL» USR 3278 CNRS - EPHE; CRIOBE; Papetoai Moorea French Polynesia
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Evolution of pygmy angelfishes: Recent divergences, introgression, and the usefulness of color in taxonomy. Mol Phylogenet Evol 2014; 74:38-47. [DOI: 10.1016/j.ympev.2014.01.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 01/18/2014] [Accepted: 01/20/2014] [Indexed: 11/19/2022]
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41
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First molecular phylogeny of the circumtropical bivalve family Pinnidae (Mollusca, Bivalvia): evidence for high levels of cryptic species diversity. Mol Phylogenet Evol 2014; 75:11-23. [PMID: 24569016 DOI: 10.1016/j.ympev.2014.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/05/2014] [Accepted: 02/13/2014] [Indexed: 11/22/2022]
Abstract
The family Pinnidae Leach, 1819, includes approximately 50 species of large subtidal and coastal marine bivalves. These commercially important species occur in tropical and temperate waters around the world and are most frequently found in seagrass meadows. The taxonomy of the family has been revised a number of times since the early 20th Century, the most recent revision recognizing 55 species distributed in three genera: Pinna, Atrina and Streptopinna, the latter being monotypic. However, to date no phylogenetic analysis of the family has been conducted using morphological or molecular data. The present study analyzed 306 pinnid specimens from around the world, comprising the three described genera and ca. 25 morphospecies. We sequenced the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I, and the nuclear ribosomal genes 18S rRNA and 28S rRNA. Phylogenetic analysis of the data revealed monophyly of the genus Atrina but also that the genus Streptopinna is nested within Pinna. Based on the strong support for this relationship we propose a new status for Streptopinna Martens, 1880 and treat it as a subgenus (status nov.) of Pinna Linnaeus, 1758. The phylogeny and the species delimitation analyses suggest the presence of cryptic species in many morphospecies displaying a wide Indo-Pacific distribution, including Pinna muricata, Atrina assimilis, A. exusta and P. (Streptopinna) saccata but also in the Atlantic species A. rigida. Altogether our results highlight the challenges associated with morphological identifications in Pinnidae due to the presence of both phenotypic plasticity and morphological stasis and reveal that many pinnid species are not as widely distributed as previously thought.
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Cowman PF, Bellwood DR. Vicariance across major marine biogeographic barriers: temporal concordance and the relative intensity of hard versus soft barriers. Proc Biol Sci 2013; 280:20131541. [PMID: 23945690 PMCID: PMC3757981 DOI: 10.1098/rspb.2013.1541] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/15/2013] [Indexed: 11/12/2022] Open
Abstract
The marine tropics contain five major biogeographic regions (East Pacific, Atlantic, Indian Ocean, Indo-Australian Archipelago (IAA) and Central Pacific). These regions are separated by both hard and soft barriers. Reconstructing ancestral vicariance, we evaluate the extent of temporal concordance in vicariance events across three major barriers (Terminal Tethyan Event (TTE), Isthmus of Panama (IOP), East Pacific Barrier, EPB) and two incomplete barriers (either side of the IAA) for the Labridae, Pomacentridae and Chaetodontidae. We found a marked lack of temporal congruence within and among the three fish families in vicariance events associated with the EPB, TTE and IOP. Vicariance across hard barriers separating the Atlantic and Indo-Pacific (TTE, IOP) is temporally diffuse, with many vicariance events preceding barrier formation. In marked contrast, soft barriers either side of the IAA hotspot support tightly concordant vicariance events (2.5 Myr on Indian Ocean side; 6 Myr on Central Pacific side). Temporal concordance in vicariance points to large-scale temporally restricted gene flow during the Late Miocene and Pliocene. Despite different and often complex histories, both hard and soft barriers have comparably strong effects on the evolution of coral reef taxa.
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Affiliation(s)
- Peter F Cowman
- School of Marine and Tropical Biology, and Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia.
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High Genetic Diversity in Geographically Remote Populations of Endemic and Widespread Coral Reef Angelfishes (genus: Centropyge). DIVERSITY-BASEL 2013. [DOI: 10.3390/d5010039] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Horne JB, van Herwerden L. Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species. J Evol Biol 2013; 26:783-99. [DOI: 10.1111/jeb.12092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 11/23/2012] [Indexed: 11/26/2022]
Affiliation(s)
- J. B. Horne
- Molecular Ecology and Evolution Laboratory; School of Tropical and Marine Biology; James Cook University; Townsville Qld Australia
- Centre of Marine Sciences; University of Algarve; Faro Portugal
| | - L. van Herwerden
- Molecular Ecology and Evolution Laboratory; School of Tropical and Marine Biology; James Cook University; Townsville Qld Australia
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Phylogeny of Parablennius Miranda Ribeiro, 1915 reveals a paraphyletic genus and recent Indo-Pacific diversification from an Atlantic ancestor. Mol Phylogenet Evol 2012; 67:1-8. [PMID: 23277159 DOI: 10.1016/j.ympev.2012.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 11/12/2012] [Accepted: 12/15/2012] [Indexed: 11/22/2022]
Abstract
A molecular phylogeny of 15 (out of 26 recognized) species of Parablennius Miranda Ribeiro, 1915 was constructed based on two mitochondrial and two nuclear gene fragments, and using maximum parsimony, maximum likelihood and Bayesian approaches. The closely related genera Hypleurochilus, Salaria and Scartella were also studied to ascertain their relationship with Parablennius. Phylogenetic analyses were compared with morphology-based taxonomical studies. Hypleurochilus, Salaria and Scartella appear well supported within a clade including all Parablennius, indicating that this genus is paraphyletic. The species pairs P. parvicornis-P. sanguinolentus and P. gattorugine-P. ruber are well-supported and relatively distant from remaining Parablennius. Remaining Parablennius form two distinct well-supported groups: (1) a clade of Atlantic-Mediterranean Parablennius (P. pilicornis, P. marmoreus, P. rouxi, P. salensis and P. tentacularis); (2) a clade including Hypleurochilus, the Indo-Western Pacific Parablennius (P. cornutus, P. intermedius, P. tasmanianus and P. yatabei) and the Atlantic-Mediterranean P. incognitus and P. zvonimiri. Use of a relaxed molecular clock suggests that Indo-Pacific Parablennius originated recently from an Atlantic Parablennius that may have dispersed via southern Africa, rather than via the Tethys seaway.
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Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species). Mol Phylogenet Evol 2012; 65:203-12. [DOI: 10.1016/j.ympev.2012.06.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 06/08/2012] [Accepted: 06/12/2012] [Indexed: 11/20/2022]
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Robalo JI, Castilho R, Francisco SM, Almada F, Knutsen H, Jorde PE, Pereira AM, Almada VC. Northern refugia and recent expansion in the North Sea: the case of the wrasse Symphodus melops (Linnaeus, 1758). Ecol Evol 2012; 2:153-64. [PMID: 22408733 PMCID: PMC3297185 DOI: 10.1002/ece3.77] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 10/21/2011] [Indexed: 11/10/2022] Open
Abstract
Pleistocene climate changes have imposed extreme conditions to intertidal rocky marine communities, forcing many species to significant range shifts in their geographical distributions. Phylogeographic analyses based on both mitochondrial and nuclear genetic markers provide a useful approach to unravel phylogeographic patterns and processes of species after this time period, to gain general knowledge of how climatic changes affect shifts in species distributions. We analyzed these patterns on the corkwing wrasse (Symphodus melops, Labridae), a rocky shore species inhabiting North Sea waters and temperate northeastern Atlantic Ocean from Norway to Morocco including the Azores, using a fragment of the mitochondrial control region and the first intron of the nuclear S7 ribosomal protein gene. We found that S. melops shows a clear differentiation between the Atlantic and the Scandinavian populations and a sharp contrast in the genetic diversity, high in the south and low in the north. Within each of these main geographic areas there is little or no genetic differentiation. The species may have persisted throughout the last glacial maximum in the southern areas as paleotemperatures were not lower than they are today in North Scandinavia. The North Sea recolonization most likely took place during the current interglacial and is dominated by a haplotype absent from the south of the study area, but present in Plymouth and Belfast. The possibility of a glacial refugium in or near the English Channel is discussed.
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Almada VC, Almada F, Francisco SM, Castilho R, Robalo JI. Unexpected high genetic diversity at the extreme northern geographic limit of Taurulus bubalis (Euphrasen, 1786). PLoS One 2012; 7:e44404. [PMID: 22952971 PMCID: PMC3431372 DOI: 10.1371/journal.pone.0044404] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/02/2012] [Indexed: 11/19/2022] Open
Abstract
The longspined bullhead (Taurulus bubalis, Euphrasen 1786) belongs to the family Cottidae and is a rocky shore species that inhabits the intertidal zones of the Eastern Atlantic since Iceland, southward to Portugal and also the North Sea and Baltic, northward to the Gulf of Finland, with some occurrences in the northern Mediterranean coasts eastward to the Gulf of Genoa. We analysed the phylogeographic patterns of this species using mitochondrial and nuclear markers in populations throughout most of its distributional range in west Europe. We found that T. bubalis has a relatively shallow genealogy with some differentiation between Atlantic and North Sea. Genetic diversity was homogeneous across all populations studied. The possibility of a glacial refugium near the North Sea is discussed. In many, but not all, marine temperate organisms, patterns of diversity are similar across the species range. If this phenomenon proves to be most common in cold adapted species, it may reflect the availability of glacial refugia not far from their present-day northern limits.
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Affiliation(s)
- Vítor C. Almada
- Eco-Ethology Research Unit, ISPA University Institute, Lisboa, Portugal
| | - Frederico Almada
- Eco-Ethology Research Unit, ISPA University Institute, Lisboa, Portugal
| | - Sara M. Francisco
- Eco-Ethology Research Unit, ISPA University Institute, Lisboa, Portugal
- * E-mail:
| | - Rita Castilho
- Centro de Ciências do Mar (CCMAR, CIMAR- Associate Laboratory), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Joana I. Robalo
- Eco-Ethology Research Unit, ISPA University Institute, Lisboa, Portugal
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Sun P, Shi Z, Yin F, Peng S. Population genetic structure and demographic history of Pampus argenteus in the Indo-West Pacific inferred from mitochondrial cytochrome b sequences. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.02.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ludt WB, Bernal MA, Bowen BW, Rocha LA. Living in the past: phylogeography and population histories of Indo-Pacific wrasses (genus Halichoeres) in shallow lagoons versus outer reef slopes. PLoS One 2012; 7:e38042. [PMID: 22701597 PMCID: PMC3368945 DOI: 10.1371/journal.pone.0038042] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 05/01/2012] [Indexed: 11/19/2022] Open
Abstract
Sea level fluctuations during glacial cycles affect the distribution of shallow marine biota, exposing the continental shelf on a global scale, and displacing coral reef habitat to steep slopes on oceanic islands. In these circumstances we expect that species inhabiting lagoons should show shallow genetic architecture relative to species inhabiting more stable outer reefs. Here we test this expectation on an ocean-basin scale with four wrasses (genus Halichoeres): H. claudia (N = 194, with ocean-wide distribution) and H. ornatissimus (N = 346, a Hawaiian endemic) inhabit seaward reef slopes, whereas H. trimaculatus (N = 239) and H. margaritaceus (N = 118) inhabit lagoons and shallow habitats throughout the Pacific. Two mitochondrial markers (cytochrome oxidase I and control region) were sequenced to resolve population structure and history of each species. Haplotype and nucleotide diversity were similar among all four species. The outer reef species showed significantly less population structure, consistent with longer pelagic larval durations. Mismatch distributions and significant negative Fu's F values indicate Pleistocene population expansion for all species, and (contrary to expectations) shallower histories in the outer slope species. We conclude that lagoonal wrasses may persist through glacial habitat disruptions, but are restricted to refugia during lower sea level stands. In contrast, outer reef slope species have homogeneous and well-connected populations through their entire ranges regardless of sea level fluctuations. These findings contradict the hypothesis that shallow species are less genetically diverse as a consequence of glacial cycles.
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Affiliation(s)
- William B Ludt
- Department of Marine Science, University of Texas, Austin, Texas, United States of America.
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