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Marcionetti A, Bertrand JAM, Cortesi F, Donati GFA, Heim S, Huyghe F, Kochzius M, Pellissier L, Salamin N. Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex. Mol Ecol 2024; 33:e17347. [PMID: 38624248 DOI: 10.1111/mec.17347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole-genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo-Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Joris A M Bertrand
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Laboratoire Génome et Développement Des Plantes (UMR 5096 UPVD/CNRS), University of Perpignan via Domitia, Perpignan, France
| | - Fabio Cortesi
- School of the Environment and Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giulia F A Donati
- EAWAG Swiss Federal Institute of Aquatic Science & Technology, Dübendorf, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Sara Heim
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Filip Huyghe
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Marc Kochzius
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
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Suresh E, Rathipriya A, Shanmugam SA, Hamsavalli R, Kathirvelpandian A. Character-based diagnostic keys, molecular identification and phylogenetic relationships of threadfin breams (family: Nemipteridae) based on mitochondrial genes from the Southern coromandel Coast, India. Anim Biotechnol 2023; 34:1553-1565. [PMID: 35259071 DOI: 10.1080/10495398.2022.2040522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
DNA barcoding, primarily focusing on cytochrome c oxidase subunit I (COI) gene has been appraised as an effective tool for species identification. In this study, we focused on the marine fishes of Family Nemipteridae, one of the commercially important group distributed within the Coromandel Coast. The Partial sequences of COI and 16S rRNA of mitochondrial genes were analyzed for species identification and phylogenetic relationship of Nemipterus species (Nemipterus japonicus, Nemipterus peronii, Nemipterus bipunctatus, Nemipterus bathybius). Character-based identification approaches that categorize specimens to species using classification rules that compactly identify species in terms of key diagnostic nucleotides in selected gene sequences. Using the BLOG 2.0 software, species-specific diagnostic nucleotides were identified for the selected group of species. A data set of 198 mtCOI sequences was obtained from published resources and used to screen character-based molecular diagnostic keys for species in silico. Partial sequences of both the genes provided sufficient phylogenetic information to distinguish the four Nemipterus species indicating the usefulness of mtDNA-based approach in species identification. This study proves the use of mtDNA genes sequence-based approach is a support tool along with traditional taxonomy for identifying fish species at a faster pace.
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Affiliation(s)
- E Suresh
- Institute of Fisheries Postgraduate Studies, TNJFU OMR Campus, Vaniyanchavadi, Chennai, Tamil Nadu, India
| | - A Rathipriya
- Institute of Fisheries Postgraduate Studies, TNJFU OMR Campus, Vaniyanchavadi, Chennai, Tamil Nadu, India
| | - S A Shanmugam
- Institute of Fisheries Postgraduate Studies, TNJFU OMR Campus, Vaniyanchavadi, Chennai, Tamil Nadu, India
| | - R Hamsavalli
- Institute of Fisheries Postgraduate Studies, TNJFU OMR Campus, Vaniyanchavadi, Chennai, Tamil Nadu, India
| | - A Kathirvelpandian
- Institute of Fisheries Postgraduate Studies, TNJFU OMR Campus, Vaniyanchavadi, Chennai, Tamil Nadu, India
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Herrera M, Ravasi T, Laudet V. Anemonefishes: A model system for evolutionary genomics. F1000Res 2023; 12:204. [PMID: 37928172 PMCID: PMC10624958 DOI: 10.12688/f1000research.130752.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the genomic architecture underlying this process has indeed become one of the holy grails of evolutionary research in these fishes. Recently, anemonefishes have also been used as a model system to study the molecular basis of highly complex traits such as color patterning, social sex change, larval dispersal and life span. Extensive genomic resources including several high-quality reference genomes, a linkage map, and various genetic tools have indeed enabled the identification of genomic features controlling some of these fascinating attributes, but also provided insights into the molecular mechanisms underlying adaptive responses to changing environments. Here, we review the latest findings and new avenues of research that have led to this group of fish being regarded as a model for evolutionary genomics.
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Affiliation(s)
- Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, 4811, Australia
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Marine Research Station, Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, 23-10, Dah-Uen Rd, Jiau Shi I-Lan 262, Taiwan
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Inter and intra-specific relationship between goat fishes Upeneus vittatus (Forsskal, 1775) and Upeneus tragula based on their mtCOI gene from Palk Bay and Gulf of Mannar Coast (Mandapam, Tamil Nadu) of India. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Species-specific molecular signatures for the commercially important scombrids using mitochondrial gene analysis; a tool for fisheries management. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2022. [DOI: 10.1016/j.japb.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Tang KL, Stiassny MLJ, Mayden RL, DeSalle R. Systematics of Damselfishes. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin L. Tang
- University of Michigan–Flint, Department of Biology, 303 East Kearsley St., Flint, Michigan 48502; . Send reprint requests to this address
| | - Melanie L. J. Stiassny
- American Museum of Natural History, Department of Ichthyology, Central Park West at 79th St., New York, New York 10024;
| | - Richard L. Mayden
- Saint Louis University, Department of Biology, 3507 Laclede Ave., St. Louis, Missouri 63103;
| | - Robert DeSalle
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York, New York 10024;
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Gainsford A, Jones GP, Hobbs JA, Heindler FM, van Herwerden L. Species integrity, introgression, and genetic variation across a coral reef fish hybrid zone. Ecol Evol 2020; 10:11998-12014. [PMID: 33209265 PMCID: PMC7663085 DOI: 10.1002/ece3.6769] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 11/10/2022] Open
Abstract
Hybridization and introgression are evolutionarily significant phenomena breaking down species boundaries. "Hybrid zones" (regions of species overlap and hybridization) enable quantification of hybridization frequency and examination of mechanisms driving and maintaining gene flow. The hybrid anemonefish Amphiprion leucokranos is found where parent species (A. chrysopterus; A. sandaracinos) distributions overlap. Here, we examine geographic variation in hybridization and introgression, and potential impacts on parent species integrity through assessing relative abundance, social group composition, and genetic structure (mtDNA cytochrome b, 21 microsatellite loci) of taxa at three hybrid zone locations: Kimbe Bay (KB) and Kavieng (KA), Papua New Guinea; the Solomon Islands (SO). Relative abundances of and size disparities between parent species apparently drive hybridization frequency, introgression patterns, and genetic composition of taxa. Conspecific groups are most common in KB (65%) where parent species are similarly abundant. Conversely, mixed species groups dominate SO (82%), where A. chrysopterus is more abundant. Hybrids most commonly cohabit with A. sandaracinos in KB (17%), but with A. chrysopterus in KA (22%) and SO (50%). Genetic differentiation (nDNA) analyses indicate that parent species remain distinct, despite ongoing hybridization and hybrids are genetically similar to A. sandaracinos-resulting from persistent backcrossing with this smallest species. This study shows that hybridization outcomes may depend on the social and ecological context in which taxa hybridize, where relative abundance and disparate size of parent species explain the frequency and patterns of hybridization and introgression in the A. leucokranos hybrid zone, reflecting size-based dominance behaviors of anemonefish social groups.
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Affiliation(s)
- Ashton Gainsford
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQLDAustralia
- Faculty of Science and EngineeringJames Cook UniversityTownsvilleAustraliaAustralia
| | - Geoffrey P. Jones
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQLDAustralia
- Faculty of Science and EngineeringJames Cook UniversityTownsvilleAustraliaAustralia
| | - Jean‐Paul A. Hobbs
- School of Biological SciencesThe University of QueenslandBrisbaneQLDAustralia
| | | | - Lynne van Herwerden
- Faculty of Science and EngineeringJames Cook UniversityTownsvilleAustraliaAustralia
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Rathipriya A, Karal Marx K, Jeyashakila R. Molecular identification and phylogenetic relationship of flying fishes of Tamil Nadu coast for fishery management purposes. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:500-510. [PMID: 30691341 DOI: 10.1080/24701394.2018.1558220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The partial sequences of cytochrome c oxidase subunit I (COI) mitochondrial gene were analysed for developing species specific molecular signatures and phylogenetic relationship among the commercially important flying fishes (Cheilopogon cyanopterus, Cheilopogon furcatus and Hirundichthys coromandelensis) distributed in Tamil Nadu coast. Accurate identification of these species is important for fishery management as its morphological characters are very similar. Since the morphological features are very similar, accurate identification using molecular tools is essential for sustainable utilization and management of these species across their distributional range. The estimated transition/transversion bias (R) is 3.45. The average nucleotide sequences calculated were A = 30.00%, T/U = 26.40%, C = 17.00% and G = 26.60%. Using COI data analysis, the intraspecies genetic distance ranged from 0.00 to 0.05, while it varied from 0.06 to 0.08 for interspecies. Partial sequences of the genes provided sufficient phylogenetic information to distinguish the three flying fishes indicating the usefulness of mtDNA-based approach in species identification.
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Affiliation(s)
- A Rathipriya
- a Tamil Nadu Dr. J. Jayalalithaa Fisheries University , Nagapattinam , India
| | - K Karal Marx
- b Institute of Postgraduate Studies, OMR Campus , Chennai , India
| | - R Jeyashakila
- c Fisheries College and Research Institute , Thoothukudi , India
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Thongtam Na Ayudhaya P, Areesirisuk P, Singchat W, Sillapaprayoon S, Muangmai N, Peyachoknagul S, Srikulnath K. Complete mitochondrial genome of 10 anemonefishes belonging to Amphiprion and Premnas. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1546145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Pradipunt Thongtam Na Ayudhaya
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Faculty of Science, Department of Genetics, Kasetsart University, Bangkok, Thailand
- Biology Program, Faculty of Science and Technology, Phetchaburi Rajabahat University, Phetchaburi, Thailand
| | - Prapatsorn Areesirisuk
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Faculty of Science, Department of Genetics, Kasetsart University, Bangkok, Thailand
- Human Genetic Laboratory, Faculty of Medicine, Department of Pathology, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Faculty of Science, Department of Genetics, Kasetsart University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, Thailand
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Faculty of Science, Department of Genetics, Kasetsart University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, Thailand
| | - Narongrit Muangmai
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, Thailand
- Faculty of Fisheries, Department of Fishery Biology, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Faculty of Science, Department of Genetics, Kasetsart University, Bangkok, Thailand
- Faculty of Science, Department of Biology, Naresuan University, Phitsanulok, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Faculty of Science, Department of Genetics, Kasetsart University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Bangkok, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University Kasetsart University, Bangkok, Thailand
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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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Otwoma LM, Diemel V, Reuter H, Kochzius M, Meyer A. Genetic population structure of the convict surgeonfish Acanthurus triostegus: a phylogeographic reassessment across its range. JOURNAL OF FISH BIOLOGY 2018; 93:597-608. [PMID: 29956317 DOI: 10.1111/jfb.13686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
This study investigates the genetic population structure and connectivity of Acanthurus triostegus in five Indo-Pacific biogeographic regions (western and eastern Indian Ocean, western, central and eastern Pacific Ocean), using a mitochondrial DNA marker spanning the ATPase8 and ATPase6 gene regions. In order to assess the phylogeography and genetic population structure of A. triostegus across its range, 35 individuals were sampled from five localities in the western Indian Ocean and complemented with 227 sequences from two previous studies. Results from the overall analysis of molecular variance (AMOVA) without a priori grouping showed evidence of significant differentiation in the Indo-Pacific, with 25 (8.3%) out of 300 pairwise ΦST comparisons being significant. However, the hierarchical AMOVA grouping of Indian and Pacific Ocean populations failed to support the vicariance hypothesis, showing a lack of a genetic break between the two ocean basins. Instead, the correlation between pairwise ΦST values and geographic distance showed that dispersal of A. triostegus in the Indo-Pacific Ocean follows an isolation-by-distance model. Three haplogroups could be deduced from the haplotype network and phylogenetic tree, with haplogroup 1 and 2 dominating the Indian and the Pacific Ocean, respectively, while haplogroup 3 exclusively occurring in the Hawaiian Archipelago of the central Pacific Ocean.
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Affiliation(s)
- Levy M Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Valeska Diemel
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | | | - Achim Meyer
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
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Chowdhury LM, A K, Pr D, Vs B, Shanis R, Chelath M, Pavan-Kumar A, Krishna G. Molecular identification and phylogenetic assessment of species under genus Parapenaeopsis Alcock, 1901, from Indian waters. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:191-200. [PMID: 29989478 DOI: 10.1080/24701394.2018.1472249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Genus Parapenaeopsis constitute an important fishery resource in Indian waters. Parapenaeopsis stylifera, being morphologically very similar to Parapenaeopsis coromandelica, mainly differentiated using telsonic armature and it is subject of controversy regarding the number of armature for the species. The present study was aimed to resolve the taxonomic ambiguity between P. stylifera and P. coromandelica and to study phylogenetic relationship among five species under the genus Parapenaeopsis using partial sequences of mitochondrial 16S ribosomal DNA (rDNA) and cytochrome c oxidase subunit I (COI) genes. Sequence analysis revealed an average genetic divergence value ranging from 7.65 to 20.3% for COI gene and 2.4 to 12.0% for 16S rDNA gene between five species under study. The result shows that P. stylifera and P. coromandelica Alcock, 1906 are genetically a distinct species with average divergence value of 7.6% based on COI sequence and 2.4% based on the 16S rDNA. However, systematic relationship between the P. stylifera and P. coromandelica were closer than other species, thus formed separate clade in phylogenetic tree. The species specific molecular signatures developed in the present study will be helpful in effective fisheries management of the species in Indian waters.
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Affiliation(s)
- L Mog Chowdhury
- a ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
| | - Kathirvelpandian A
- b ICAR-National Bureau of Fish Genetic Resources, PMFGR Centre , Kochi , India
| | - Divya Pr
- b ICAR-National Bureau of Fish Genetic Resources, PMFGR Centre , Kochi , India
| | - Basheer Vs
- b ICAR-National Bureau of Fish Genetic Resources, PMFGR Centre , Kochi , India
| | - Rajool Shanis
- b ICAR-National Bureau of Fish Genetic Resources, PMFGR Centre , Kochi , India
| | - Mohitha Chelath
- b ICAR-National Bureau of Fish Genetic Resources, PMFGR Centre , Kochi , India
| | - A Pavan-Kumar
- c ICAR-Central Institute of Fisheries Education , Mumbai , India
| | - Gopal Krishna
- c ICAR-Central Institute of Fisheries Education , Mumbai , India
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Abstract
Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.
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Otwoma LM, Kochzius M. Genetic Population Structure of the Coral Reef Sea Star Linckia laevigata in the Western Indian Ocean and Indo-West Pacific. PLoS One 2016; 11:e0165552. [PMID: 27798700 PMCID: PMC5087890 DOI: 10.1371/journal.pone.0165552] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/13/2016] [Indexed: 11/18/2022] Open
Abstract
The coral reef sea star Linckia laevigata is common on shallow water coral reefs of the Indo-West Pacific. Its large geographic distribution and comprehensive data from previous studies makes it suitable to examine genetic differentiation and connectivity over large geographical scales. Based on partial sequences of the mitochondrial cytochrome oxidase I (COI) gene this study investigates the genetic population structure and connectivity of L. laevigata in the Western Indian Ocean (WIO) and compares it to previous studies in the Indo-Malay-Philippines Archipelago (IMPA). A total of 138 samples were collected from nine locations in the WIO. AMOVA revealed a low but significant ΦST-value of 0.024 for the WIO populations. In the hierarchical AMOVA, the following grouping rejected the hypothesis of panmixia: (1) Kenya (Watamu, Mombasa, Diani) and Tanzanian Island populations (Misali and Jambiani) and (2) the rest of the WIO sites (mainland Tanzania and Madagascar; ΦCT = 0.03). The genetic population structure was stronger and more significant (ΦST = 0.13) in the comparative analysis of WIO and IMPA populations. Three clades were identified in the haplotype network. The strong genetic differentiation (ΦCT = 0.199, P < 0.001) suggests that Indo-West Pacific populations of L. laevigata can be grouped into four biogeographic regions: (1) WIO (2) Eastern Indian Ocean (3) IMPA and (4) Western Pacific. The findings of this study support the existence of a genetic break in the Indo-West Pacific consistent with the effect of lowered sea level during the Pleistocene, which limited gene flow between the Pacific and Indian Ocean.
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Affiliation(s)
- Levy Michael Otwoma
- Kenya Marine and Fisheries Research Institute, P.O. BOX 81651, Mombasa, Kenya
- Marine Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Marc Kochzius
- Marine Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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Cooke GM, Schlub TE, Sherwin WB, Ord TJ. Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis. PLoS One 2016; 11:e0150991. [PMID: 27195493 PMCID: PMC4873183 DOI: 10.1371/journal.pone.0150991] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/21/2016] [Indexed: 11/19/2022] Open
Abstract
Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810-11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.
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Affiliation(s)
- Georgina M. Cooke
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
- The Australian Museum, Australian Museum Research Institute, Ichthyology, 6 College Street, Sydney NSW 2010, Australia
| | - Timothy E. Schlub
- Sydney School of Public Health, Sydney Medical School, University of Sydney, 2006 NSW, Australia
| | - William B. Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
| | - Terry J. Ord
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
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16
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Cryptic genetic divergence within threatened species of Acropora coral from the Indian and Pacific Oceans. CONSERV GENET 2016. [DOI: 10.1007/s10592-015-0807-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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17
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K K B, A G, J K J, V S B, C M, N V, M J, Pillai NGK. Molecular identification of Bigeyes (Perciformes, Priacanthidae) from Indian waters. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4638-4642. [PMID: 26681644 DOI: 10.3109/19401736.2015.1101593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Thirty-five individuals of six priacanthid fish species were sampled from different localities along the coast of India covering the Arabian Sea and Bay of Bengal. The partial sequence of 16S rRNA and cytochrome oxidase subunit I (COI) genes were analyzed for species identification and phylogenetic relationship among the Indian priacanthids (Priacanthus hamrur, P. prolixus, P. blochii, P. sagittarius, Cookeolus japonicus, and Pristigenys refulgens). The intraspecies genetic distance ranged from 0.000 to 0.002, while distances varied from 0.008 to 0.157 interspecies based on 16S sequences. Using COI data analysis, the intraspecies genetic distance ranged from 0.000 to 0.005, while interspecies distances varied from 0.009 to 0.108. Several sequences labeled Priacanthus hamrur in GenBank are shown to be P. prolixus. We also observed cryptic speciation in Heteropriacanthus cruentatus. Partial sequences of 16S rRNA and COI genes provided phylogenetic information to distinguish thirteen species of priacanthids, indicating the usefulness of molecular markers in species identification.
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Affiliation(s)
- Bineesh K K
- a National Bureau of Fish Genetic Resources, Central Marine Fisheries Research Institute Campus , Kochi , Kerala , India
| | - Gopalakrishnan A
- b Central Marine Fisheries Research Institute , Kochi , Kerala , India
| | - Jena J K
- c National Bureau of Fish Genetic Resources , Dilkusha , Lucknow , India , and
| | - Basheer V S
- a National Bureau of Fish Genetic Resources, Central Marine Fisheries Research Institute Campus , Kochi , Kerala , India
| | - Mohitha C
- a National Bureau of Fish Genetic Resources, Central Marine Fisheries Research Institute Campus , Kochi , Kerala , India
| | - Vineesh N
- a National Bureau of Fish Genetic Resources, Central Marine Fisheries Research Institute Campus , Kochi , Kerala , India
| | - Joselet M
- d Nirmalagiri College , Kannur , Kerala , India
| | - N G K Pillai
- b Central Marine Fisheries Research Institute , Kochi , Kerala , India
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Devassy A, Kumar R, Shajitha PP, John R, Padmakumar KG, Basheer VS, Gopalakrishnan A, Mathew L. Genetic identification and phylogenetic relationships of Indian clariids based on mitochondrial COI sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3777-80. [PMID: 26358817 DOI: 10.3109/19401736.2015.1079901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondrial cytochrome C Oxidase I (COI) sequence variation among the clariid fishes of India (Clarias magur, C. dussumieri and C. gariepinus) and their relationship with other representative clariids was studied in this work. Three species were sampled and together with 23 COI sequences from GenBank were used to reconstruct phylogenetic relationships in the family Clariidae. The study revealed two clades: one consisting of the African species with C. dussumieri, and the other of Asian species suggesting the prevalence of intra-continental diversification of catfishes. This study further revealed that the genus Clarias is monophyletic. For the COI gene, the interspecies genetic divergence ranged from 0.056 to 0.182. The mean genetic difference between C. dussumieri and other selected African species in this study is 12.1%. It was also observed that the morphological similarity of C. dussumieri and C. magur was not replicated in the genetic level. Clarias dussumieri was more close to African catfish C. gariepinus thus indicating the utility of COI phylogeny to identify the well-known African-Asian relationships within catfishes. The results also showed that C. magur and C. batrachus are genetically distinct from each other.
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Affiliation(s)
- Aneesha Devassy
- a School of Biosciences, Mahatma Gandhi University , Kottayam , Kerala , India
| | - Raj Kumar
- b Peninsular and Marine Fish Genetic Resources Centre, NBFGR, CMFRI Campus , Cochin , Kerala , India
| | - P P Shajitha
- a School of Biosciences, Mahatma Gandhi University , Kottayam , Kerala , India
| | - Reshma John
- a School of Biosciences, Mahatma Gandhi University , Kottayam , Kerala , India
| | - K G Padmakumar
- c Regional Agricultural Research Station (RARS), Kerala Agricultural University , Kumarakom , Kottayam , Kerala , India , and
| | - V S Basheer
- b Peninsular and Marine Fish Genetic Resources Centre, NBFGR, CMFRI Campus , Cochin , Kerala , India
| | - A Gopalakrishnan
- d Central Marine Fisheries Research Institute , Cochin , Kerala , India
| | - Linu Mathew
- a School of Biosciences, Mahatma Gandhi University , Kottayam , Kerala , India
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Dohna TA, Timm J, Hamid L, Kochzius M. Limited connectivity and a phylogeographic break characterize populations of the pink anemonefish, Amphiprion perideraion, in the Indo-Malay Archipelago: inferences from a mitochondrial and microsatellite loci. Ecol Evol 2015; 5:1717-33. [PMID: 25937914 PMCID: PMC4409419 DOI: 10.1002/ece3.1455] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 11/25/2022] Open
Abstract
To enhance the understanding of larval dispersal in marine organisms, species with a sedentary adult stage and a pelagic larval phase of known duration constitute ideal candidates, because inferences can be made about the role of larval dispersal in population connectivity. Members of the immensely diverse marine fauna of the Indo-Malay Archipelago are of particular importance in this respect, as biodiversity conservation is becoming a large concern in this region. In this study, the genetic population structure of the pink anemonefish, Amphiprion perideraion, is analyzed by applying 10 microsatellite loci as well as sequences of the mitochondrial control region to also allow for a direct comparison of marker-derived results. Both marker systems detected a strong overall genetic structure (ΦST = 0.096, P < 0.0001; mean D est = 0.17; F ST = 0.015, P < 0.0001) and best supported regional groupings (ΦCT = 0.199 P < 0.0001; F CT = 0.018, P < 0.001) that suggested a differentiation of the Java Sea population from the rest of the archipelago. Differentiation of a New Guinea group was confirmed by both markers, but disagreed over the affinity of populations from west New Guinea. Mitochondrial data suggest higher connectivity among populations with fewer signals of regional substructure than microsatellite data. Considering the homogenizing effect of only a few migrants per generation on genetic differentiation between populations, marker-specific results have important implications for conservation efforts concerning this and similar species.
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Affiliation(s)
- Tina A Dohna
- Biotechnology and Molecular Genetics, UFT, University of BremenBremen, 28359, Germany
| | - Janne Timm
- Biotechnology and Molecular Genetics, UFT, University of BremenBremen, 28359, Germany
| | - Lemia Hamid
- Biotechnology and Molecular Genetics, UFT, University of BremenBremen, 28359, Germany
| | - Marc Kochzius
- Marine Biology, Vrije Universiteit BrusselBrussel, Belgium
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Litsios G, Salamin N. Hybridisation and diversification in the adaptive radiation of clownfishes. BMC Evol Biol 2014; 14:245. [PMID: 25433367 PMCID: PMC4264551 DOI: 10.1186/s12862-014-0245-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The importance of hybridisation during species diversification has long been debated among evolutionary biologists. It is increasingly recognised that hybridisation events occurred during the evolutionary history of numerous species, especially during the early stages of adaptive radiation. We study the effect of hybridisation on diversification in the clownfishes, a clade of coral reef fish that diversified through an adaptive radiation process. While two species of clownfish are likely to have been described from hybrid specimens, the occurrence and effect of hybridisation on the clade diversification is yet unknown. RESULTS We generate sequences of three mitochondrial genes to complete an existing dataset of nuclear sequences and document cytonuclear discordance at a node, which shows a drastic increase of diversification rate. Then, using a tree-based jack-knife method, we identify clownfish species likely stemming from hybridisation events. Finally, we use molecular cloning and identify the putative parental species of four clownfish specimens that display the morphological characteristics of hybrids. CONCLUSIONS Our results show that consistently with the syngameon hypothesis, hybridisation events are linked with a burst of diversification in the clownfishes. Moreover, several recently diverged clownfish lineages likely originated through hybridisation, which indicates that diversification, catalysed by hybridisation events, may still be happening.
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Affiliation(s)
- Glenn Litsios
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Génopode, Quartier Sorge, 1015, Lausanne, Switzerland.
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Génopode, Quartier Sorge, 1015, Lausanne, Switzerland.
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Tornabene L, Valdez S, Erdmann M, Pezold F. Support for a 'Center of Origin' in the Coral Triangle: cryptic diversity, recent speciation, and local endemism in a diverse lineage of reef fishes (Gobiidae: Eviota). Mol Phylogenet Evol 2014; 82 Pt A:200-10. [PMID: 25300452 DOI: 10.1016/j.ympev.2014.09.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/10/2014] [Accepted: 09/13/2014] [Indexed: 11/17/2022]
Abstract
The Coral Triangle is widely regarded as the richest marine biodiversity hot-spot in the world. One factor that has been proposed to explain elevated species-richness within the Coral Triangle is a high rate of in situ speciation within the region itself. Dwarfgobies (Gobiidae: Eviota) are a diverse genus of diminutive cryptobenthic reef fishes with limited dispersal ability, and life histories and ecologies that increase potential for speciation. We use molecular phylogenetic and biogeographic data from two clades of Eviota species to examine patterns, processes and timing associated with species origination within the Coral Triangle. Sequence data from mitochondrial and nuclear DNA were used to generate molecular phylogenies and median-joining haplotype networks for the genus Eviota, with emphasis on the E. nigriventris and E. bifasciata complexes - two species groups with distributions centered in the Coral Triangle. The E. nigriventris and E. bifasciata complexes both contain multiple genetically distinct, geographically restricted color morphs indicative of recently-diverged species originating within the Coral Triangle. Relaxed molecular-clock dating estimates indicate that most speciation events occurred within the Pleistocene, and the geographic pattern of genetic breaks between species corresponds well with similar breaks in other marine fishes and sessile invertebrates. Regional isolation due to sea-level fluctuations may explain some speciation events in these species groups, yet other species formed with no evidence of physical isolation. The timing of diversification events and present day distributions of Eviota species within the Coral Triangle suggest that both allopatric speciation (driven by ephemeral and/or 'soft' physical barriers to gene flow) and sympatric speciation (driven by niche partitioning and assortative mating) may be driving diversification at local scales within the Coral Triangle. The presence of multiple young, highly-endemic cryptic species of Eviota within the Coral Triangle suggests that (i) the Coral Triangle is indeed a "cradle" of reef fish biodiversity and that (ii) our current approximations of reef fish diversity in the region may be significantly underestimated.
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Affiliation(s)
- Luke Tornabene
- College of Science and Engineering, Texas A & M University - Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.
| | - Samantha Valdez
- College of Science and Engineering, Texas A & M University - Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Mark Erdmann
- Conservation International Indonesia Marine Program, Jl. Muwardi No. 17 Renon Denpasar, Bali 80235, Indonesia; California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118, USA
| | - Frank Pezold
- College of Science and Engineering, Texas A & M University - Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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Van Der Meij SE, Reijnen BT. The curious case ofNeotroglocarcinus dawydoffi(Decapoda, Cryptochiridae): unforeseen biogeographic patterns resulting from isolation. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.946979] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Basheer VS, Mohitha C, Vineesh N, Divya PR, Gopalakrishnan A, Jena JK. Molecular phylogenetics of three species of the genus Rastrelliger using mitochondrial DNA markers. Mol Biol Rep 2014; 42:873-9. [DOI: 10.1007/s11033-014-3710-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/26/2014] [Indexed: 10/24/2022]
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24
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Richards ZT, Miller DJ, Wallace CC. Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation. Mol Phylogenet Evol 2013; 69:837-51. [PMID: 23850500 DOI: 10.1016/j.ympev.2013.06.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 06/18/2013] [Accepted: 06/27/2013] [Indexed: 10/26/2022]
Abstract
To better understand the underlying causes of rarity and extinction risk in Acropora (staghorn coral), we contrast the minimum divergence ages and nucleotide diversity of an array of species with different range sizes and levels of threat. Time-calibrated Bayesian analyses based upon concatenated nuclear and mitochondrial sequence data implied contemporary range size and vulnerability are linked to species age. However, contrary to previous hypotheses that suggest geographically restricted Acropora species evolved in the Plio-Pleistocene, the molecular phylogeny depicts some Indo-Australian species have greater antiquity, diverging in the Miocene. Species age is not related to range size as a simple positive linear function and interpreting the precise tempo of evolution in this genus is greatly complicated by morphological homoplasy and a sparse fossil record. Our phylogenetic reconstructions provide new examples of how morphology conceals cryptic evolutionary relationships in this keystone genus, and offers limited support for the species groupings currently used in Acropora systematics. We hypothesize that in addition to age, other mechanisms (such as a reticulate ancestry) delimit the contemporary range of some Acropora species, as evidenced by the complex patterns of allele sharing and paraphyly we uncover. Overall, both new and ancient evolutionary information may be lost if geographically restricted and threatened Acropora species are forced to extinction. In order to protect coral biodiversity and resolve the evolutionary history of staghorn coral, further analyses based on comprehensive and heterogeneous morphological and molecular data utilizing reticulate models of evolution are needed.
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Affiliation(s)
- Z T Richards
- Aquatic Zoology, Western Australian Museum, 49 Kew Street, Welshpool, WA 6106, Australia.
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Bowen BW, Rocha LA, Toonen RJ, Karl SA. The origins of tropical marine biodiversity. Trends Ecol Evol 2013; 28:359-66. [DOI: 10.1016/j.tree.2013.01.018] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 01/30/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
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Drew JA, Barber PH. Comparative phylogeography in Fijian coral reef fishes: a multi-taxa approach towards marine reserve design. PLoS One 2012; 7:e47710. [PMID: 23118892 PMCID: PMC3484158 DOI: 10.1371/journal.pone.0047710] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/13/2012] [Indexed: 11/18/2022] Open
Abstract
Delineating barriers to connectivity is important in marine reserve design as they describe the strength and number of connections among a reserve's constituent parts, and ultimately help characterize the resilience of the system to perturbations at each node. Here we demonstrate the utility of multi-taxa phylogeography in the design of a system of marine protected areas within Fiji. Gathering mtDNA control region data from five species of coral reef fish in five genera and two families, we find a range of population structure patterns, from those experiencing little (Chrysiptera talboti, Halichoeres hortulanus, and Pomacentrus maafu), to moderate (Amphiprion barberi, Φ(st) = 0.14 and Amblyglyphidodon orbicularis Φ(st) = 0.05) barriers to dispersal. Furthermore estimates of gene flow over ecological time scales suggest species-specific, asymmetric migration among the regions within Fiji. The diversity among species-specific results underscores the limitations of generalizing from single-taxon studies, including the inability to differentiate between a species-specific result and a replication of concordant phylogeographic patterns, and suggests that greater taxonomic coverage results in greater resolution of community dynamics within Fiji. Our results indicate that the Fijian reefs should not be managed as a single unit, and that closely related species can express dramatically different levels of population connectivity.
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Affiliation(s)
- Joshua A Drew
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, United States of America.
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van der Meer MH, Jones GP, Hobbs JPA, van Herwerden L. Historic hybridization and introgression between two iconic Australian anemonefish and contemporary patterns of population connectivity. Ecol Evol 2012; 2:1592-604. [PMID: 22957165 PMCID: PMC3434915 DOI: 10.1002/ece3.251] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Accepted: 03/01/2012] [Indexed: 11/15/2022] Open
Abstract
Endemic species on islands are considered at risk of extinction for several reasons, including limited dispersal abilities, small population sizes, and low genetic diversity. We used mitochondrial DNA (D-Loop) and 17 microsatellite loci to explore the evolutionary relationship between an endemic anemonefish, Amphiprion mccullochi (restricted to isolated locations in subtropical eastern Australia) and its more widespread sister species, A. akindynos. A mitochondrial DNA (mtDNA) phylogram showed reciprocal monophyly was lacking for the two species, with two supported groups, each containing representatives of both species, but no shared haplotypes and up to 12 species, but not location-specific management units (MUs). Population genetic analyses suggested evolutionary connectivity among samples of each species (mtDNA), while ecological connectivity was only evident among populations of the endemic, A. mccullochi. This suggests higher dispersal between endemic anemonefish populations at both evolutionary and ecological timeframes, despite separation by hundreds of kilometers. The complex mtDNA structure results from historical hybridization and introgression in the evolutionary past of these species, validated by msat analyses (NEWHYBRIDS, STRUCTURE, and DAPC). Both species had high genetic diversities (mtDNA h > 0.90, π = 4.0%; msat genetic diversity, gd > 0.670). While high gd and connectivity reduce extinction risk, identifying and protecting populations implicated in generating reticulate structure among these species should be a conservation priority.
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High similarity of genetic population structure in the false clown anemonefish (Amphiprion ocellaris) found in microsatellite and mitochondrial control region analysis. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0318-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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FAUVELOT CÉCILE, BORSA PHILIPPE. Patterns of genetic isolation in a widely distributed pelagic fish, the narrow-barred Spanish mackerel (Scomberomorus commerson). Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01754.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Eble JA, Rocha LA, Craig MT, Bowen BW. Not All Larvae Stay Close to Home: Insights into Marine Population Connectivity with a Focus on the Brown Surgeonfish ( Acanthurus nigrofuscus). JOURNAL OF MARINE BIOLOGY 2011; 2011:518516. [PMID: 25505914 PMCID: PMC4260469 DOI: 10.1155/2011/518516] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Recent reports of localized larval recruitment in predominately small-range fishes are countered by studies that show high genetic connectivity across large oceanic distances. This discrepancy may result from the different timescales over which genetic and demographic processes operate or rather may indicate regular long-distance dispersal in some species. Here, we contribute an analysis of mtDNA cytochrome b diversity in the widely distributed Brown Surgeonfish (Acanthurus nigrofuscus; N = 560), which revealed significant genetic structure only at the extremes of the range (ΦCT = 0.452; P < .001). Collections from Hawaii to the Eastern Indian Ocean comprise one large, undifferentiated population. This pattern of limited genetic subdivision across reefs of the central Indo-Pacific has been observed in a number of large-range reef fishes. Conversely, small-range fishes are often deeply structured over the same area. These findings demonstrate population connectivity differences among species at biogeographic and evolutionary timescales, which likely translates into differences in dispersal ability at ecological and demographic timescales. While interspecific differences in population connectivity complicate the design of management strategies, the integration of multiscale connectivity patterns into marine resource planning will help ensure long-term ecosystem stability by preserving functionally diverse communities.
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Affiliation(s)
- Jeff A. Eble
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, P.O. Box 1346, Kaneohe, HI 96744, USA
| | - Luiz A. Rocha
- Marine Science Institute, University of Texas at Austin, Port Aransas, TX 78373, USA
| | - Matthew T. Craig
- Department of Marine Sciences, University of Puerto Rico Mayagüez, P.O. Box 9000, Mayagüez, PR 00681, USA
| | - Brian W. Bowen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, P.O. Box 1346, Kaneohe, HI 96744, USA
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Kochzius M, Seidel C, Antoniou A, Botla SK, Campo D, Cariani A, Vazquez EG, Hauschild J, Hervet C, Hjörleifsdottir S, Hreggvidsson G, Kappel K, Landi M, Magoulas A, Marteinsson V, Nölte M, Planes S, Tinti F, Turan C, Venugopal MN, Weber H, Blohm D. Identifying Fishes through DNA Barcodes and Microarrays. PLoS One 2010; 5:e12620. [PMID: 20838643 PMCID: PMC2935389 DOI: 10.1371/journal.pone.0012620] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Accepted: 07/08/2010] [Indexed: 11/20/2022] Open
Abstract
Background International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.
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Affiliation(s)
- Marc Kochzius
- Centre for Applied Gene Sensor Technology, FB2-UFT, University of Bremen, Bremen, Germany.
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Species delineation in Pampus (Perciformes) and the phylogenetic status of the Stromateoidei based on mitogenomics. Mol Biol Rep 2010; 38:1103-14. [DOI: 10.1007/s11033-010-0207-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 06/11/2010] [Indexed: 11/26/2022]
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Steinke D, Zemlak TS, Hebert PDN. Barcoding nemo: DNA-based identifications for the ornamental fish trade. PLoS One 2009; 4:e6300. [PMID: 19621079 PMCID: PMC2708913 DOI: 10.1371/journal.pone.0006300] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 06/23/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Trade in ornamental fishes represents, by far, the largest route for the importation of exotic vertebrates. There is growing pressure to regulate this trade with the goal of ensuring that species are sustainably harvested and that their point of origin is accurately reported. One important element of such regulation involves easy access to specimen identifications, a task that is currently difficult for all but specialists because of the large number of species involved. The present study represents an important first step in making identifications more accessible by assembling a DNA barcode reference sequence library for nearly half of the ornamental fish species imported into North America. METHODOLOGY/PRINCIPAL FINDINGS Analysis of the cytochrome c oxidase subunit I (COI) gene from 391 species from 8 coral reef locations revealed that 98% of these species exhibit distinct barcode clusters, allowing their unambiguous identification. Most species showed little intra-specific variation (adjusted mean = 0.21%), but nine species included two or three lineages showing much more divergence (2.19-6.52%) and likely represent overlooked species complexes. By contrast, three genera contained a species pair or triad that lacked barcode divergence, cases that may reflect hybridization, young taxa or taxonomic over-splitting. CONCLUSIONS/SIGNIFICANCE Although incomplete, this barcode library already provides a new species identification tool for the ornamental fish industry, opening a realm of applications linked to collection practices, regulatory control and conservation.
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Affiliation(s)
- Dirk Steinke
- Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.
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Timm J, Kochzius M. Geological history and oceanography of the Indo-Malay Archipelago shape the genetic population structure in the false clown anemonefish (Amphiprion ocellaris). Mol Ecol 2009; 17:3999-4014. [PMID: 19238702 DOI: 10.1111/j.1365-294x.2008.03881.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Like many fishes on coral reefs, the false clown anemonefish, Amphiprion ocellaris, has a life history with two different phases: adults are strongly site attached, whereas larvae are planktonic. Therefore, the larvae have the potential to disperse, but the degree of dispersal potential depends primarily on the period of the larval stage, which is only 8-12 days in A. ocellaris. In this study, we investigated the genetic population structure and gene flow in A. ocellaris across the Indo-Malay Archipelago by analysing a fragment of the mitochondrial control region. Population genetic analysis, using AMOVA, revealed a significant and high overall phi(ST)-value of 0.241 (P < 0.001), clearly showing limited gene flow. Haplotype network analysis detected eight distinct clades corresponding mainly to different geographical areas, which were most probably separated during sea level low stands in the Pleistocene. The distribution of the clades among the different populations indicated slow partial re-mixing mainly in the central region of the archipelago. Major surface currents seem to facilitate larval dispersal, indicated by higher connectivity along major surface currents in the region (e.g. Indonesian Throughflow). Four main groups were found by the hierarchical AMOVA within the archipelago. These different genetic lineages should be managed and protected as separate ornamental fishery stocks and resource contributing to the genetic diversity of the area. Regarding the high diversity and the differentiation among areas within the Indo-Malay Archipelago of A. ocellaris populations, the centre-of-origin theory is supported to be the main mechanism by which the high biodiversity evolved in this area.
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Affiliation(s)
- Janne Timm
- Biotechnology and Molecular Genetics, FB2-UFT, University of Bremen, 28359 Bremen, Germany.
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Chiba SN, Iwatsuki Y, Yoshino T, Hanzawa N. Comprehensive phylogeny of the family Sparidae (Perciformes: Teleostei) inferred from mitochondrial gene analyses. Genes Genet Syst 2009; 84:153-70. [DOI: 10.1266/ggs.84.153] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Satoru N. Chiba
- Graduate school of Science and Engineering, Yamagata University
| | - Yukio Iwatsuki
- Division of Fisheries Science, Faculty of Agriculture, University of Miyazaki
| | - Tetsuo Yoshino
- Department of Marine Sciences, Faculty of Science, University of the Ryukyus
| | - Naoto Hanzawa
- Graduate school of Science and Engineering, Yamagata University
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KOCHZIUS MARC, NURYANTO AGUS. Strong genetic population structure in the boring giant clam,Tridacna crocea,across the Indo-Malay Archipelago: implications related to evolutionary processes and connectivity. Mol Ecol 2008; 17:3775-87. [DOI: 10.1111/j.1365-294x.2008.03803.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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