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Rashwan AM, El-Gendy SAA, Alsafy MAM, Haddad SS. Comparative morphological analysis of telson and uropods in Penaeus canaliculatus (Olivier, 1811), Penaeus semisulcatus (De Haan, 1844), and Metapenaeus stebbingi (Nobili, 1904) using scanning electron microscopy and EDX analysis. Micron 2024; 181:103636. [PMID: 38579377 DOI: 10.1016/j.micron.2024.103636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/16/2024] [Accepted: 03/29/2024] [Indexed: 04/07/2024]
Abstract
The telson and uropods collectively form the tail fan, playing crucial roles in locomotion, buoyancy, defense, and respiration. We aimed to compare telson and uropod structures in three shrimp species-Penaeus canaliculatus, Penaeus semisulcatus, and Metapenaeus stebbingi-to identify the species with the most robust telson for its environment. Our analysis involved morphological measurements and scanning electron microscopy (SEM), supplemented by a novel approach-Energy-Dispersive X-ray (EDX) spectroscopy, a technique not previously utilized in studies on these three species. M. stebbingi exhibited the longest telson length, whereas P. semisulcatus had the longest uropod. P. canaliculatus featured a single pair of fixed spines, while P. semisulcatus had evenly spaced small conical spines along the sides of the median elevation and groove. A distinctive feature of M. stebbingi was the telson, which had three pairs of large spines. Diverse setae on telsons included simple, unipennate, and plumose setae. Notably, specialized branched tubular setae on uropods' endopods may aid in grooming or swimming behavior. EDX spectroscopy revealed that the telson cuticle primarily consists of carbon, nitrogen, and oxygen, with significantly high concentrations alongside comparatively lower calcium and phosphorous concentrations. P. semisulcatus exhibited the highest calcium and phosphorus content among the three species. In conclusion, M. stebbingi's telson is structurally robust, emphasizing the importance of morphology, while P. semisulcatus demonstrated a hard telson through EDX analysis. Our study underscores not solely relying on morphology for telson strength assessment but considering telson composition. These variations among species may be attributed to diverse ecological and physiological adaptations.
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Affiliation(s)
- Ahmed M Rashwan
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt; Laboratory of Life science frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Samir A A El-Gendy
- Anatomy and Embryology Department, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21944, Egypt
| | - Mohamed A M Alsafy
- Anatomy and Embryology Department, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21944, Egypt.
| | - Seham S Haddad
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, University of Sadat City Sadat City 32897, Egypt
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Verly T, Pita S, Carbajal-de-la-Fuente AL, Burgueño-Rodríguez G, Piccinali RV, Fiad FG, Ríos N, Panzera F, Lobbia P, Sánchez-Casaccia P, Rojas de Arias A, Cavallo MJ, Gigena GV, Rodríguez CS, Nattero J. Relationship between genetic diversity and morpho-functional characteristics of flight-related traits in Triatoma garciabesi (Hemiptera: Reduviidae). Parasit Vectors 2024; 17:145. [PMID: 38500121 PMCID: PMC10949591 DOI: 10.1186/s13071-024-06211-x] [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: 11/16/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Triatoma garciabesi, a potential vector of the parasitic protozoan Trypanosoma cruzi, which is the causative agent of Chagas disease, is common in peridomestic and wild environments and found throughout northwestern and central Argentina, western Paraguay and the Bolivian Chaco. Genetic differentiation of a species across its range can help to understand dispersal patterns and connectivity between habitats. Dispersal by flight is considered to be the main active dispersal strategy used by triatomines. In particular, the morphological structure of the hemelytra is associated with their function. The aim of this study was to understand how genetic diversity is structured, how morphological variation of dispersal-related traits varies with genetic diversity and how the morphological characteristics of dispersal-related traits may explain the current distribution of genetic lineages in this species. METHODS Males from 24 populations of T. garciabesi across its distribution range were examined. The cytochrome c oxidase I gene (coI) was used for genetic diversity analyses. A geometric morphometric method based on landmarks was used for morpho-functional analysis of the hemelytra. Centroid size (CS) and shape of the forewing, and contour of both parts of the forewing, the head and the pronotum were characterised. Length and area of the forewing were measured to estimate the aspect ratio. RESULTS The morphometric and phylogenetic analysis identified two distinct lineages, namely the Eastern and Western lineages, which coincide with different ecological regions. The Eastern lineage is found exclusively in the eastern region of Argentina (Chaco and Formosa provinces), whereas the Western lineage is prevalent in the rest of the geographical range of the species. CS, shape and aspect ratio of the hemelytra differed between lineages. The stiff portion of the forewing was more developed in the Eastern lineage. The shape of both portions of the hemelytra were significantly different between lineages, and the shape of the head and pronotum differed between lineages. CONCLUSIONS The results provide preliminary insights into the evolution and diversification of T. garciabesi. Variation in the forewing, pronotum and head is congruent with genetic divergence. Consistent with genetic divergence, morphometry variation was clustered according to lineages, with congruent variation in the size and shape of the forewing, pronotum and head.
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Affiliation(s)
- Thaiane Verly
- Centro Nacional de Diagnóstico e Investigación en Endemo-Epidemias (CeNDIE), Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos Malbrán" (ANLIS), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Sebastián Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
| | - Ana Laura Carbajal-de-la-Fuente
- Centro Nacional de Diagnóstico e Investigación en Endemo-Epidemias (CeNDIE), Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos Malbrán" (ANLIS), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Romina V Piccinali
- Departamento de Ecología Genética y Evolución, Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución (IEGEBA), CONICET/Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico G Fiad
- Cátedras de Introducción a la Biología y Morfología Animal, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Facultad de Ciencias Exactas Físicas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)/Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Néstor Ríos
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Francisco Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Patricia Lobbia
- Unidad Operativa de Vectores y Ambiente (UnOVE), Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos Malbrán", Centro Nacional de Diagnostico e Investigación en Endemo-Epidemias (CeNDIE), Córdoba, Argentina
| | - Paz Sánchez-Casaccia
- Centro Nacional de Diagnóstico e Investigación en Endemo-Epidemias (CeNDIE), Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos Malbrán" (ANLIS), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Centro para el Desarrollo de la Investigación Científica (CEDIC), Asunción, Paraguay
| | | | - María José Cavallo
- Centro Regional de Energía y Ambiente Para el Desarrollo Sustentable (CREAS-CONICET), Universidad Nacional de Catamarca (UNCA), San Fernando del Valle de Catamarca, Catamarca, Argentina
| | - Gisel V Gigena
- Cátedras de Introducción a la Biología y Morfología Animal, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Facultad de Ciencias Exactas Físicas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)/Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Claudia S Rodríguez
- Cátedras de Introducción a la Biología y Morfología Animal, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Facultad de Ciencias Exactas Físicas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)/Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Julieta Nattero
- Departamento de Ecología Genética y Evolución, Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Instituto de Ecología, Genética y Evolución (IEGEBA), CONICET/Universidad de Buenos Aires, Buenos Aires, Argentina.
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Layton KKS, Wilson NG. Validating a molecular clock for nudibranchs-No fossils to the rescue. Ecol Evol 2024; 14:e11014. [PMID: 38362166 PMCID: PMC10867498 DOI: 10.1002/ece3.11014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024] Open
Abstract
Time calibrated phylogenies are typically reconstructed with fossil information but for soft-bodied marine invertebrates that lack hard parts, a fossil record is lacking. In these cases, biogeographic calibrations or the rates of divergence for related taxa are often used. Although nudibranch phylogenies have advanced with the input of molecular data, no study has derived a divergence rate for this diverse group of invertebrates. Here, we use an updated closure date for the Isthmus of Panama (2.8 Ma) to derive the first divergence rates for chromodorid nudibranchs using multigene data from a geminate pair with broad phylogeographic sampling. Examining the species Chromolaichma sedna (Marcus & Marcus, 1967), we uncover deep divergences among eastern Pacific and western Atlantic clades and we erect a new species designation for the latter (Chromolaichma hemera sp. nov.). Next, we discover extensive phylogeographic structure within C. hemera sp. nov. sensu lato, thereby refuting the hypothesis of a recent introduction. Lastly, we derive divergence rates for mitochondrial and nuclear loci that exceed known rates for other gastropods and we highlight significant rate heterogeneity both among markers and taxa. Together, these findings improve understanding of nudibranch systematics and provide rates useful to apply to divergence scenarios in this diverse group.
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Affiliation(s)
- Kara K. S. Layton
- School of Biological SciencesUniversity of AberdeenAberdeenUK
- Department of BiologyUniversity of Toronto MississaugaMississaugaOntarioCanada
| | - Nerida G. Wilson
- Scripps Institution of OceanographyUC San DiegoLa JollaCaliforniaUSA
- School of Biological SciencesUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
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Kawato S, Nozaki R, Kondo H, Hirono I. Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans. Microbiol Spectr 2024; 12:e0055923. [PMID: 38063384 PMCID: PMC10871703 DOI: 10.1128/spectrum.00559-23] [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: 02/07/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.
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Affiliation(s)
- Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Assessing penaeid shrimp diversity in the northwest of Peninsular Malaysia: an integrated framework in taxonomy and phylogeny. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01283-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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MANTELATTO FERNANDOL, TAMBURUS ANAF, CARVALHO-BATISTA ABNER, ROSSI NATALIA, BURANELLI RAQUELC, PANTALEÃO JOÃOA, TELES JENIFFERN, ZARA FERNANDOJ, CARVALHO FABRICIOL, BOCHINI GABRIELL, TEROSSI MARIANA, ROBLES RAFAEL, CASTILHO ANTONIOL, COSTA ROGÉRIOC. Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: V. Dendrobranchiata and Pleocyemata [Achelata, Astacidea, Axiidea, Caridea (Alpheoidea and Processoidea excluded), Gebiidea, Stenopodidea]. Zootaxa 2022; 5121:1-74. [DOI: 10.11646/zootaxa.5121.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Indexed: 11/04/2022]
Abstract
This checklist is the fifth and last compilation on the decapod crustaceans reported to São Paulo (Brazil) coastal area, resulting from long-term multidisciplinary projects, which combined morphological analyses and molecular techniques. The current research includes 75 decapod species, herein referred as shrimps/lobsters-like (shrimps, ghost-shrimps, lobsters, and related groups), reported to São Paulo coastal area. These species occur in marine, estuarine, and amphidromous habitats and are classified into 21 families as follow: Aristeidae (2 spp., 2 genera), Atyidae (4 spp., 2 genera), Axianassidae (1 sp., 1 genus), Callianassidae (1 sp., 1 genus), Callichiridae (6 spp., 4 genera), Crangonidae (1 sp., 1 genus), Glyphocrangonidae (1 sp., 1 genus), Luciferidae (2 spp., 2 genera), Nephropidae (4 spp., 2 genera), Palaemonidae (15 spp., 9 genera), Palinuridae (2 spp., 1 genus), Pandalidae (1 sp., 1 genus), Pasiphaeidae (1 sp., 1 genus), Penaeidae (10 spp., 6 genera), Sergestidae (3 spp., 3 genera), Sicyoniidae (4 spp., 1 genus), Scyllaridae (5 spp., 3 genera), Solenoceridae (4 spp., 3 genera), Stenopodidae (2 spp., 1 genus), and Upogebiidae (6 spp., 1 genus). We generated new sequences of cytochrome oxidase subunit I (barcode region) and 16S genes (51 and 54, respectively) of 54 species. Our examination concluded that 75 shrimps/lobsters-like species are reported to the São Paulo coast. We excluded Leander tenuicornis (Palaemonidae), Penaeus setiferus (Penaeidae), Philocheras gorei (Crangonidae), and Rhynchocinetes typus (Rhynchocinetidae) from this list.
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Halim SAAA, Othman AS, Akib NAM, Jamaludin NA, Esa Y, Nor SAM. Mitochondrial Markers Identify a Genetic Boundary of the Green Tiger Prawn ( Penaeus semisulcatus) in the Indo-Pacific Ocean. Zool Stud 2021; 60:e8. [PMID: 34386093 PMCID: PMC8315928 DOI: 10.6620/zs.2021.60-08] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/31/2020] [Indexed: 11/18/2022]
Abstract
A population genetics study of the commercially important Green Tiger Prawn (Penaeus semisulcatus) was conducted in the Indo-Pacific Ocean with a focus on the Indo-Malay Archipelago waters of the South China Sea (SCS), Sulu Sea (SLS), Celebes Sea (CLS) and the Strait of Malacca (SOM), the latter being the main waterway that connects the Indian Ocean with the Pacific Ocean. A 548-base-pair region of mitochondrial COI and 571 base pairs of the control region (CR) were analysed in 284 specimens from 15 locations. Genetic divergences (Tamura 3-parameter) for COI ranged from 0.1% to 7.2% and CR 2.3% to 21.7%, with Bagan Pasir (BGP) in central SOM being the most genetically different from other populations (COI: 3.3-4.2%; CR: 7.1-16.5%). All populations were differentiated into two lineages with a genetic break in the vicinity of BGP; Lineage I comprised populations south of this site (SCS, SLS, CLS and part of SOM) and Lineage II comprised populations north of BGP (part of the SOM). Specifically, most individuals of Bagan Pasir (BGP) and another site just south of it, Batu Pahat (BPT), clustered in Lineage I, while all SOM populations to the north of these sites clustered in Lineage II. The BGP population is believed to be a mixed gene pool between the two lineages. The results could be attributed to the fluctuations of Pleistocene sea levels and a possible influence of the One Fathom Bank in SOM. High genetic diversity was recorded, π (Lineage I: COI: 3.4%; CR: 7.4%) (Lineage II: COI: 3.8%; CR: 12.6%) and, h (Lineage I: COI: 0.81; CR: 1.0) (Lineage II: COI: 0.57; CR: 0.99). Demographic statistics revealed that both lineages underwent a sudden expansion and consequent stabilisation in genetic variability. The findings of this study have wide implications for fisheries in the Indo-Pacific. The increased sampling effort within a narrower geographical scale by the current study permitted a precise locality of the genetic break for this species within the Indo-Pacific Ocean to be identified. The substantial genetic diversity within both lineages should be considered in fishery management and aquaculture development programs of this species in this region.
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Affiliation(s)
- Siti Amalia Aisyah Abdul Halim
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia. E-mail: (Halim); E-mail: (Othman)
| | - Ahmad Sofiman Othman
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia. E-mail: (Halim); E-mail: (Othman)
| | | | - Noorul-Azliana Jamaludin
- Marine Capture Fisheries Division, FRI Kampung Acheh, 32000 Sitiawan, Perak, Malaysia. E-mail: (Jamaludin)
| | - Yuzine Esa
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Universiti Putra Malaysia, Serdang, Selangor, Malaysia. E-mail: (Esa)
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Port Dickson, Negeri Sembilan, Malaysia
| | - Siti Azizah Mohd Nor
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia. E-mail: (Halim); E-mail: (Othman)
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia. E-mail: (Nor)
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Katneni VK, Shekhar MS, Jangam AK, Paran BC, Selvaraj A, Krishnan K, Kaikkolante N, Prabhudas SK, Gopalapillai G, Koyadan VK. Phylogenetic relations and mitogenome-wide similarity metrics reveal monophyly of Penaeus sensu lato. Ecol Evol 2021; 11:2040-2049. [PMID: 33717440 PMCID: PMC7920775 DOI: 10.1002/ece3.7148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 11/24/2022] Open
Abstract
Splitting of the genus Penaeus sensu lato into six new genera based on morphological features alone has been controversial in penaeid shrimp taxonomy. Several studies focused on building phylogenetic relations among the genera of Penaeus sensu lato. However, they lack in utilizing full mitochondrial DNA genome of shrimp representing all the six controversial genera. For the first time, the present study targeted the testing of all the six genera of Penaeus sensu lato for phylogenetic relations utilizing complete mitochondrial genome sequence. In addition, the study reports for the first time about the complete mitochondrial DNA genome sequence of Fenneropenaeus indicus, an important candidate species in aquaculture and fisheries, and utilized it for phylogenomics. The maximum likelihood and Bayesian approaches were deployed to generate and comprehend the phylogenetic relationship among the shrimp in the suborder, Dendrobranchiata. The phylogenetic relations established with limited taxon sampling considered in the study pointed to the monophyly of Penaeus sensu lato and suggested collapsing of the new genera to a single genus. Further, trends in mitogenome-wide estimates of average amino acid identity in the order Decapoda and the genus Penaeus sensu lato supported restoration of the old genus, Penaeus, rather promoting the creation of new genera.
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Affiliation(s)
- Vinaya Kumar Katneni
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Mudagandur S. Shekhar
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Ashok Kumar Jangam
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | | | - Ashok Selvaraj
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Karthic Krishnan
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Nimisha Kaikkolante
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Sudheesh K. Prabhudas
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Gopikrishna Gopalapillai
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
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Vance DJ, Rothlisberg PC. The biology and ecology of the banana prawns: Penaeus merguiensis de Man and P. indicus H. Milne Edwards. ADVANCES IN MARINE BIOLOGY 2020; 86:1-139. [PMID: 32600543 DOI: 10.1016/bs.amb.2020.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The two banana prawns Penaeus merguiensis and P. indicus are arguably the most commercially important species of penaeid prawns in the tropical and sub-tropical Indo-West Pacific region. They are fecund, short-lived, and have a complex life history involving offshore spawning, inshore mangrove-lined nursery grounds, and migrations between the two locations. We have reviewed and assessed published research on: the fisheries and aquaculture; taxonomy and identification; distribution and habitat preferences; growth; mortality; food and feeding; predation, and the importance of the mangrove habitat to banana prawns. We have examined the life history patterns of these two banana prawns and the many environmental and biological factors that affect different life history stages, often resulting in large interannual variations in abundances of adult prawns and commercial catches. We have also reviewed research on the ecosystem relationships involving these prawns, including fishery impacts on the environment and other species caught as bycatch. In reviewing the published information on factors affecting recruitment dynamics and variability, we have sometimes found contrasting and confounding results, suggesting that these factors are not yet fully understood. Therefore, for each aspect of the prawns' biology we have pointed to areas with incomplete or conflicted understanding, which will hopefully guide future research on these extremely valuable prawn species.
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Affiliation(s)
- David J Vance
- CSIRO Oceans & Atmosphere, Queensland BioSciences Precinct, St Lucia, QLD, Australia.
| | - Peter C Rothlisberg
- CSIRO Oceans & Atmosphere, Queensland BioSciences Precinct, St Lucia, QLD, Australia
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Hurzaid A, Chan T, Mohd Nor SA, Muchlisin ZA, Chen W. Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South‐East Asian waters. ZOOL SCR 2020. [DOI: 10.1111/zsc.12428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amirah Hurzaid
- Institute of Oceanography National Taiwan University Taipei Taiwan
- Biological Sciences Department School of Distance Education Universiti Sains Malaysia Penang Malaysia
| | - Tin‐Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans National Taiwan Ocean University Keelung Taiwan
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology Universiti Malaysia Terengganu Kuala Terengganu Malaysia
| | | | - Wei‐Jen Chen
- Institute of Oceanography National Taiwan University Taipei Taiwan
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Kerkhove TRH, Boyen J, De Backer A, Mol JH, Volckaert FAM, Leliaert F, De Troch M. Multilocus data reveal cryptic species in the Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Decapoda). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe recognition of cryptic biodiversity provides valuable insights for the management of exploited species. The Atlantic seabob shrimp (Xiphopenaeus kroyeri) is a commercially important fishery resource in the Guianan ecoregion, South America. Previous research in Brazil suggested the presence of cryptic species within the genus. Here, we confirm this presence and delimit the species by applying a multilocus approach based on two mitochondrial (COI and cytb) and two nuclear (PEPCK and NaK) genes. Species boundaries were tested using BPP, GMYC and bPTP delimitation algorithms. These analyses provided strong support for three clades within the genus Xiphopenaeus, including one undescribed clade, which occurs sympatrically with X. kroyeri in the Western Atlantic. Unexpectedly, this undescribed clade is more closely related to the Pacific Xiphopenaeus riveti than to their Atlantic congener. Our DNA-based species delimitation was further supported by new ecological information on habitat and morphology (colour). We also expand the known distribution range of the cryptic species, currently restricted to Brazil, to include French Guiana, Suriname and Colombia. Our findings have important consequences for the management of the species, in terms of both biodiversity management and fisheries management.
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Affiliation(s)
- Thomas R H Kerkhove
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
| | - Jens Boyen
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
| | - Annelies De Backer
- Institute for Agricultural and Fisheries Research (ILVO), Animal Sciences, Bio-Environmental Research Group, Ankerstraat, Ostend, Belgium
| | - Jan H Mol
- Anton de Kom University of Suriname, Faculty of Mathematics and Natural Sciences, Department of Biology, Leysweg, Postbus, Paramaribo, Suriname
| | - Filip A M Volckaert
- University of Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Ch. Deberiotstraat, Leuven, Belgium
| | - Frederik Leliaert
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
- Meise Botanic Garden, Nieuwelaan, Meise, Belgium
| | - Marleen De Troch
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
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12
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Sajeela KA, Gopalakrishnan A, Basheer VS, Mandal A, Bineesh KK, Grinson G, Gopakumar SD. New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean. Mol Phylogenet Evol 2019; 136:53-64. [PMID: 30954588 DOI: 10.1016/j.ympev.2019.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 03/09/2019] [Accepted: 04/03/2019] [Indexed: 01/03/2023]
Abstract
Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.
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Affiliation(s)
- K A Sajeela
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India.
| | - A Gopalakrishnan
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India
| | - V S Basheer
- Peninsular and Marine Fish Genetic Resources (PMFGR) Centre-NBFGR, CMFRI, Kochi 682 018, Kerala, India
| | - A Mandal
- Rajiv Gandhi Centre for Aquaculture (RGCA), Sirkali 609 113, Nagapattinam, Tamil Nadu, India
| | - K K Bineesh
- Zoological Survey of India, Andaman and Nicobar Regional Centre, Haddo, Port Blair 744 102, India
| | - G Grinson
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India
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13
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Loeza-Quintana T, Carr CM, Khan T, Bhatt YA, Lyon SP, Hebert PD, Adamowicz SJ. Recalibrating the molecular clock for Arctic marine invertebrates based on DNA barcodes. Genome 2019; 62:200-216. [DOI: 10.1139/gen-2018-0107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Divergence times for species assemblages of Arctic marine invertebrates have often been estimated using a standard rate (1.4%/MY) of molecular evolution calibrated using a single sister pair of tropical crustaceans. Because rates of molecular evolution vary among taxa and environments, it is essential to obtain clock calibrations from northern lineages. The recurrent opening and closure of the Bering Strait provide an exceptional opportunity for clock calibration. Here, we apply the iterative calibration approach to investigate patterns of molecular divergence among lineages of northern marine molluscs and arthropods using publicly available sequences of the cytochrome c oxidase subunit I (COI) gene and compare these results with previous estimates of trans-Bering divergences for echinoderms and polychaetes. The wide range of Kimura two-parameter (K2P) divergences among 73 trans-Bering sister pairs (0.12%–16.89%) supports multiple pulses of migration through the Strait. Overall, the results indicate a rate of K2P divergence of 3.2%/MY in molluscs, 5%–5.2%/MY in arthropods, and 3.5%–4.7%/MY in polychaetes. While these rates are considerably higher than the often-adopted 1.4%/MY rate, they are similar to calibrations (3%–5%/MY) in several other studies of marine invertebrates. This upward revision in rates means there is a need both to reevaluate the evolutionary history of marine lineages and to reexamine the impact of prior climatic changes upon the diversification of marine life.
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Affiliation(s)
- Tzitziki Loeza-Quintana
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Christina M. Carr
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- University of Northern Iowa, 187 McCollum Science Hall, Cedar Falls, IA 50614, USA
| | - Tooba Khan
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Yash A. Bhatt
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Faculty of Science, University of Western Ontario, 1151 Richmond St, London, ON N6A 3K7, Canada
| | - Samantha P. Lyon
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Sarah J. Adamowicz
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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Timm L, Browder JA, Simon S, Jackson TL, Zink IC, Bracken-Grissom HD. A tree money grows on: the first inclusive molecular phylogeny of the economically important pink shrimp (Decapoda : Farfantepenaeus) reveals cryptic diversity. INVERTEBR SYST 2019. [DOI: 10.1071/is18044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Species of Farfantepenaeus support economically important shrimp fisheries throughout the Western Hemisphere, necessitating proper fisheries management. To be effective, species management should be informed of the potential presence of cryptic species and of the evolutionary forces driving biodiversity. This is best accomplished through a robust phylogenetic framework and evidence-based species delimitation. This study represents the first comprehensive molecular phylogeny and species delimitation analyses of shrimps belonging to the genus Farfantepenaeus. Targeting three mitochondrial genes (12S, 16S, and COI), gene trees and a phylogeny for the genus were inferred using maximum likelihood and Bayesian approaches. In general, the phylogenetic relationships inferred here largely agree with those recovered from morphological data, including the most recent designation of F. isabelae as sister to F. subtilis. Molecular divergence was found between northern and southern populations of F. brasiliensis, suggesting the existence of unrecognised subspecies. However, previous recognition of F. duorarum and F. notialis as two distinct species was not supported by this study. The phylogeny inferred here also uncovers a phylogeographic signal of latitudinal speciation in the genus. The study presented here provides valuable insight into the evolutionary history of Farfantepenaeus, improving our ability to effectively manage these economically important species.
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Morphometrics and Mitochondrial DNA Genes Analysis Suggest a New Species of Penaeus (Crustacea: Penaeidae) from the Persian Gulf. Biochem Genet 2018; 57:193-213. [DOI: 10.1007/s10528-018-9884-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
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16
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Cui F, Yu Y, Bao F, Wang S, Xiao MS. Genetic diversity analysis of the oriental river prawn (Macrobrachium nipponense) in Huaihe River. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:737-744. [PMID: 29671653 DOI: 10.1080/24701394.2017.1350953] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The oriental river prawn (Macrobrachium nipponense) is an economically and nutritionally important species of decapod crustaceans in China. Genetic structure and demographic history of Macrobrachium nipponense were examined using sequence data from portions of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene. Samples of 191 individuals were collected from 10 localities in the upper to middle reaches of the Huaihe River. Variability was detected at a total of 42 nucleotide sites along 684 bp length of homologous sequence (6.14%), and base substitutions occurred mostly at the second codon position. Haplotype diversity (h) and nucleotide diversity (π) of all populations were 0.9136 ± 0.0116 and 0.0078 ± 0.0042, respectively. Phylogenetic tree constructed using the maximum-likelihood (ML) method showed that the 44 haplotypes were assigned to two obvious clades associated with geographic regions. Moreover, the median-joining network was similar to the topology of the phylogenetic tree with 44 haplotypes. The pairwise FST values between the populations varied from -0.0298 to 0.2994. Generally, moderate genetic differentiation (FST = 0.1598, p = .0000) among different geographic populations was detected, with the significant differentiation between the Huaibin (HB) and other Macrobrachium nipponense populations. Both mismatch distribution analyses and neutrality tests suggested the early stage of Late Pleistocene population expansion 85,500 years before present for the species, which was consistent with the palaeoclimatic condition of the Huaihe River Basin.
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Affiliation(s)
- Feng Cui
- a College of Life Science , Anhui Science and Technology University , Fengyang , China
| | - Yanyan Yu
- b College of Science and Technology , Xinyang University , Xinyang , China
| | - Fangyin Bao
- a College of Life Science , Anhui Science and Technology University , Fengyang , China
| | - Song Wang
- a College of Life Science , Anhui Science and Technology University , Fengyang , China
| | - Ming Song Xiao
- a College of Life Science , Anhui Science and Technology University , Fengyang , China
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Wilwet L, Jeyasekaran G, Shakila RJ, Sivaraman B, Padmavathy P. A single enzyme PCR-RFLP protocol targeting 16S rRNA/tRNA val region to authenticate four commercially important shrimp species in India. Food Chem 2017; 239:369-376. [PMID: 28873581 DOI: 10.1016/j.foodchem.2017.06.132] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/12/2017] [Accepted: 06/22/2017] [Indexed: 11/30/2022]
Abstract
Food authenticity is an issue of major concern for food authorities, as mislabeling represents one of the major commercial frauds. In this study, a novel PCR-RFLP protocol was developed as a tool to authenticate four shrimp products of commercial importance belonging to the family, Penaeidae, viz. Litopenaeus vannamei, Penaeus monodon, P. semisulcatus and Fenneropenaeus indicus. PCR amplification was performed targeting 16S rRNA/tRNAval region having an amplicon size of 530bp using the specific primers for shrimps, 16S-Cru4/16S-Cru3. Subsequent restriction analysis with a single restriction enzyme, Tsp5091, yielded distinct RFLP pattern for each species of shrimps having fragment sizes below 150bp. The unique RFLP patterns were also obtained in processed shrimp products without any degradation or alteration in the major fragments. The method was also validated with commercial shrimp products. Thus, the developed protocol can be performed within 8h using a single enzyme to authenticate four shrimp products of commercial significance.
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Affiliation(s)
- Lidiya Wilwet
- Department of Fish Quality Assurance and Management, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India
| | - Geevaretnam Jeyasekaran
- Department of Fish Quality Assurance and Management, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India.
| | - Robinson Jeya Shakila
- Department of Fish Quality Assurance and Management, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India
| | - Balasubramanian Sivaraman
- Department of Fish Quality Assurance and Management, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India
| | - Pandurengan Padmavathy
- Department of Fisheries Environment, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India
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18
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Briggs JC. COINCIDENT BIOGEOGRAPHIC PATTERNS: INDO-WEST PACIFIC OCEAN. Evolution 2017; 53:326-335. [PMID: 28565426 DOI: 10.1111/j.1558-5646.1999.tb03769.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/1998] [Accepted: 12/07/1998] [Indexed: 11/29/2022]
Abstract
The majority of tropical marine families demonstrate their greatest concentration of species within the relatively small East Indies Triangle. In every direction, the species diversity decreases with distance from the East Indies. Other patterns suggest that the East Indies is where the average generic age is youngest, where some historical routes of dispersal originate, where the most apomorphic species occur, where genetic diversity is the greatest, and where extinctions are likely to originate. These coincident patterns provide support for the hypothesis that the East Indies has been operating as a center of evolutionary radiation. The driving force for this dynamic system is apparently the predominance of successful speciation involving relatively large populations with higher genetic diversity. This mechanism fits the centrifugal speciation model that was proposed more than 50 years ago.
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Affiliation(s)
- John C Briggs
- Zoological Collections, Museum of Natural History, The University of Georgia, Athens, Georgia, 30602
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Sarower MG, Shahriar SIM, Nakamura H, Rouf MA, Okada S. Taxonomic confirmation of mud crab species (genus Scylla) in Bangladesh by nuclear and mitochondrial DNA markers. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:935-940. [DOI: 10.1080/24701394.2016.1214726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Mohammed Golam Sarower
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo, Tokyo, Japan
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna, Bangladesh
| | | | - Hiromasa Nakamura
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo, Tokyo, Japan
| | - Muhammad Abdur Rouf
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna, Bangladesh
| | - Shigeru Okada
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo, Tokyo, Japan
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20
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O’Dea A, Lessios HA, Coates AG, Eytan RI, Restrepo-Moreno SA, Cione AL, Collins LS, de Queiroz A, Farris DW, Norris RD, Stallard RF, Woodburne MO, Aguilera O, Aubry MP, Berggren WA, Budd AF, Cozzuol MA, Coppard SE, Duque-Caro H, Finnegan S, Gasparini GM, Grossman EL, Johnson KG, Keigwin LD, Knowlton N, Leigh EG, Leonard-Pingel JS, Marko PB, Pyenson ND, Rachello-Dolmen PG, Soibelzon E, Soibelzon L, Todd JA, Vermeij GJ, Jackson JBC. Formation of the Isthmus of Panama. SCIENCE ADVANCES 2016; 2:e1600883. [PMID: 27540590 PMCID: PMC4988774 DOI: 10.1126/sciadv.1600883] [Citation(s) in RCA: 279] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 07/18/2016] [Indexed: 05/22/2023]
Abstract
The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas. To bring clarity to the question of when the Isthmus of Panama formed, we provide an exhaustive review and reanalysis of geological, paleontological, and molecular records. These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.
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Affiliation(s)
- Aaron O’Dea
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
| | - Harilaos A. Lessios
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
| | - Anthony G. Coates
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
| | - Ron I. Eytan
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX 77553, USA
| | - Sergio A. Restrepo-Moreno
- Departamento de Geociencias y Medio Ambiente Universidad Nacional de Colombia, Bogotá, Colombia
- Department of Geological Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Alberto L. Cione
- División Paleontología Vertebrados, Museo de La Plata, B1900FWA La Plata, Buenos Aires, Argentina
| | - Laurel S. Collins
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
- Department of Earth and Environment, and Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Alan de Queiroz
- Department of Biology, University of Nevada, Reno, NV 89557–0314, USA
| | - David W. Farris
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL 32306, USA
| | | | - Robert F. Stallard
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
- U.S. Geological Survey, 3215 Marine Street (Suite E127), Boulder, CO 80303, USA
| | - Michael O. Woodburne
- Department of Geological Sciences, University of California, Riverside, Riverside, CA 92507, USA
| | - Orangel Aguilera
- Universidade Federal Fluminense, Instituto de Biologia, Campus do Valonguinho, Outeiro São João Batista, s/n°, cep. 24020-141, Niterói, Rio de Janeiro, Brazil
| | - Marie-Pierre Aubry
- Department of Earth and Planetary Sciences, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854–8066, USA
| | - William A. Berggren
- Department of Earth and Planetary Sciences, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854–8066, USA
| | - Ann F. Budd
- Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Mario A. Cozzuol
- Laboratório de Paleozoologia, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, cep. 31270 010, Belo Horizonte, MG, Brazil
| | - Simon E. Coppard
- Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323, USA
| | - Herman Duque-Caro
- Academia Colombiana de Ciencias Exactas, Físicas y Naturales, Bogotá, Colombia
| | - Seth Finnegan
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Science Building #3140, Berkeley, CA 94720–3140, USA
| | - Germán M. Gasparini
- División Paleontología Vertebrados, Museo de La Plata, B1900FWA La Plata, Buenos Aires, Argentina
| | - Ethan L. Grossman
- Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA
| | - Kenneth G. Johnson
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | | | - Nancy Knowlton
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Egbert G. Leigh
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
| | - Jill S. Leonard-Pingel
- Department of Geology, Washington and Lee University, 204 West Washington Street, Lexington, VA 24450, USA
| | - Peter B. Marko
- Department of Biology, University of Hawai’i at Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Nicholas D. Pyenson
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Paola G. Rachello-Dolmen
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
- Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA
| | - Esteban Soibelzon
- División Paleontología Vertebrados, Museo de La Plata, B1900FWA La Plata, Buenos Aires, Argentina
| | - Leopoldo Soibelzon
- División Paleontología Vertebrados, Museo de La Plata, B1900FWA La Plata, Buenos Aires, Argentina
| | - Jonathan A. Todd
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Geerat J. Vermeij
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jeremy B. C. Jackson
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
- Scripps Institution of Oceanography, La Jolla, CA 92093–0244, USA
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
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Rajakumaran P, Vaseeharan B, Jayakumar R, Chidambara R. Conformation of phylogenetic relationship of Penaeidae shrimp based on morphometric and molecular investigations. CYTOL GENET+ 2014. [DOI: 10.3103/s0095452714060103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Piergiorge R, Pontes M, Duarte A, Gusmão J. Haplotype-specific single-locus multiplex PCR assay for molecular identification of sea-bob shrimp, Xiphopenaeus kroyeri (Heller, 1862), cryptic species from the Southwest Atlantic using a DNA pooling strategy for simultaneous identification of multiple samples. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.03.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Justi SA, Russo CAM, Mallet JRDS, Obara MT, Galvão C. Molecular phylogeny of Triatomini (Hemiptera: Reduviidae: Triatominae). Parasit Vectors 2014; 7:149. [PMID: 24685273 PMCID: PMC4021723 DOI: 10.1186/1756-3305-7-149] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/15/2014] [Indexed: 11/29/2022] Open
Abstract
Background The Triatomini and Rhodniini (Hemiptera: Reduviidae) tribes include the most diverse Chagas disease vectors; however, the phylogenetic relationships within the tribes remain obscure. This study provides the most comprehensive phylogeny of Triatomini reported to date. Methods The relationships between all of the Triatomini genera and representatives of the three Rhodniini species groups were examined in a novel molecular phylogenetic analysis based on the following six molecular markers: the mitochondrial 16S; Cytochrome Oxidase I and II (COI and COII) and Cytochrome B (Cyt B); and the nuclear 18S and 28S. Results Our results show that the Rhodnius prolixus and R. pictipes groups are more closely related to each other than to the R. pallescens group. For Triatomini, we demonstrate that the large complexes within the paraphyletic Triatoma genus are closely associated with their geographical distribution. Additionally, we observe that the divergence within the spinolai and flavida complex clades are higher than in the other Triatoma complexes. Conclusions We propose that the spinolai and flavida complexes should be ranked under the genera Mepraia and Nesotriatoma. Finally, we conclude that a thorough morphological investigation of the paraphyletic genera Triatoma and Panstrongylus is required to accurately assign queries to natural genera.
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Affiliation(s)
| | | | | | | | - Cleber Galvão
- Laboratório Nacional e Internacional de Referência em Taxonomia de Triatomíneos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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24
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High levels of genetic diversity in Penaeus monodon populations from the east coast of India. SPRINGERPLUS 2013; 2:671. [PMID: 24363984 PMCID: PMC3868705 DOI: 10.1186/2193-1801-2-671] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/26/2013] [Indexed: 11/10/2022]
Abstract
Quality production of the shrimp Penaeus monodon in hatchery operations depends heavily on the evaluation of genetic diversity and population structure of brood stocks. Mitochondrial DNA (mtDNA) sequences have been widely used to study genetic variability and relationships in many crustacean groups, and these same markers may be incorporated into evaluation studies of shrimp broods and populations. For this purpose we looked at variation in mitochondrial D-loop sequences as an indicator of genetic diversity in shrimp populations from a region of India that represents the main sources of new material for brood stocks. In our study of these populations the overall mean genetic diversity was 0.191. The highest level of genetic diversity (0.357) was observed in the Kakinada population, whereas the lowest diversity (0.0171) was observed in the Nellore population. The results also indicate that overall, the populations along the Andhra Pradesh coast are genetically diverse despite the fact that there is considerable gene flow between them. From the results, it is evident that east cost of India shows high genetic diversity among P. monodon broods and no evidence of loss of diversity due to excessive inbreeding. The fact that the genetic variability of these populations has been maintained, despite ten years of dependence on these broods, shows that at the present time there is no indication of over exploitation.
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25
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Zhang D, Ding G, Ge B, Zhang H, Tang B. Population genetic structure and historical demography of Oratosquilla oratoria revealed by mitochondrial DNA sequences. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412110142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Ortea I, Pascoal A, Cañas B, Gallardo JM, Barros-Velázquez J, Calo-Mata P. Food authentication of commercially-relevant shrimp and prawn species: From classical methods to Foodomics. Electrophoresis 2012; 33:2201-11. [DOI: 10.1002/elps.201100576] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ignacio Ortea
- Department of Food Technology; Institute for Marine Research; Spanish National Research Council (CSIC); Vigo; Spain
| | - Ananías Pascoal
- Department of Analytical Chemistry; Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology; University of Santiago de Compostela; Lugo; Spain
| | - Benito Cañas
- Department of Analytical Chemistry; University Complutense of Madrid; Madrid; Spain
| | - José M. Gallardo
- Department of Food Technology; Institute for Marine Research; Spanish National Research Council (CSIC); Vigo; Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry; Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology; University of Santiago de Compostela; Lugo; Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry; Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology; University of Santiago de Compostela; Lugo; Spain
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Czerniejewski P, Skuza L, Drotz MK, Berggren M. Molecular connectedness between self and none self-sustainable populations of Chinese mitten crab (Eriocheir sinensis, H. Milne Edwards, 1853) with focus to the Swedish Lake Vänern and the Oder and Vistula River in Poland. Hereditas 2012; 149:55-61. [PMID: 22568700 DOI: 10.1111/j.1601-5223.2012.02246.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The highly invasive Chinese mitten crabs (Eriocheir sinensis) was studied to reveal the genetic relationship between three none self-sustainable population within the Polish Oder and Vistula River and Lake Vänern in Sweden. Crabs from self-sustainable populations were collected from the Elbe River (Germany), San Francisco Bay (USA) and five Asian river estuaries. Both parsimony and maximum likelihood analysis of the nuclear ITS 1 and ITS 2 regions reveal a similar topological pattern. The mitochondrial cytochrome c oxidase subunit I (COI) sequence had too low resolution to be informative. The Oder River haplotypes showed high sequence similarities to both the Elbe population and/or the native spawning areas in China. The Vistula River showed haplotypic similarity to specimens from the Oder River in Poland or the Elbe River. Also high sequence similarities were observed to the specimens from the Swedish Lake Vänern indicating to an origin from the River Elbe. Minor changes in evolutionary interpretation exist depending on how gaps are treated and the analytic method. There is a complex movement involving back and forth transoceanic colonization of the Chinese mitten crab haplotypes. Invasion routes are discussed in relation to ship transfer routes and canal waterways.
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Affiliation(s)
- Przemysław Czerniejewski
- Department of Fish Management in Open Waters, Westpomeranian University of Technology, Szczecin, Poland
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28
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Mandal A, Rao D, Karuppaiah D, Gopalakrishnan A, Pozhoth J, Thampi Samraj YC, Doyle RW. Population genetic structure of Penaeus monodon, in relation to monsoon current patterns in Southwest, East and Andaman coastal waters of India. Gene 2012; 491:149-57. [DOI: 10.1016/j.gene.2011.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/05/2011] [Accepted: 10/01/2011] [Indexed: 11/26/2022]
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29
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Chow S, Jeffs A, Miyake Y, Konishi K, Okazaki M, Suzuki N, Abdullah MF, Imai H, Wakabayasi T, Sakai M. Genetic isolation between the Western and Eastern Pacific populations of pronghorn spiny lobster Panulirus penicillatus. PLoS One 2011; 6:e29280. [PMID: 22195038 PMCID: PMC3240654 DOI: 10.1371/journal.pone.0029280] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 11/23/2011] [Indexed: 11/18/2022] Open
Abstract
The pronghorn spiny lobster, Panulirus penicillatus, is a circumtropical species which has the widest global distribution among all the species of spiny lobster, ranging throughout the entire Indo-Pacific region. Partial nucleotide sequences of mitochondrial DNA COI (1,142–1,207 bp) and 16S rDNA (535–546 bp) regions were determined for adult and phyllosoma larval samples collected from the Eastern Pacific (EP)(Galápagos Islands and its adjacent water), Central Pacific (CP)(Hawaii and Tuamotu) and the Western Pacific (WP)(Japan, Indonesia, Fiji, New Caledonia and Australia). Phylogenetic analyses revealed two distinct large clades corresponding to the geographic origin of samples (EP and CP+WP). No haplotype was shared between the two regional samples, and average nucleotide sequence divergence (Kimura's two parameter distance) between EP and CP+WP samples was 3.8±0.5% for COI and 1.0±0.4% for 16S rDNA, both of which were much larger than those within samples. The present results indicate that the Pacific population of the pronghorn spiny lobster is subdivided into two distinct populations (Eastern Pacific and Central to Western Pacific), with no gene flow between them. Although the pronghorn spiny lobster have long-lived teleplanic larvae, the vast expanse of Pacific Ocean with no islands and no shallow substrate which is known as the East Pacific Barrier appears to have isolated these two populations for a long time (c.a. 1MY).
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Affiliation(s)
- Seinen Chow
- Stock Enhancement and Aquaculture Division, National Research Institute of Aquaculture, Yokosuka, Kanagawa, Japan.
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30
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Pascoal A, Ortea I, Gallardo JM, Cañas B, Barros-Velázquez J, Calo-Mata P. Species identification of the Northern shrimp (Pandalus borealis) by polymerase chain reaction-restriction fragment length polymorphism and proteomic analysis. Anal Biochem 2011; 421:56-67. [PMID: 22080038 DOI: 10.1016/j.ab.2011.10.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 10/15/2011] [Accepted: 10/17/2011] [Indexed: 10/16/2022]
Abstract
Genomic and proteomic techniques for species identification of meat and seafood products are being widely used. In this study, a genomic approach was used to differentiate Pandalus borealis (the Northern shrimp), which belongs to the superfamily Pandaloidea, from 30 crustaceans consisting of 19 commercially relevant prawns/shrimps species that belong to the superfamily Penaeoidea, which include the families Penaeidae and Solenoceridae, and 11 other crustacean species, including prawns, shrimps, lobsters, and crabs. For this purpose, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was designed based on the amplification of the 16S rRNA/tRNA(Val)/12S rRNA mitochondrial regions using the primers 16S-CruF and 16S-CruR. The 966-bp PCR products were produced and cleaved with the restriction enzymes AluI, TaqI, and HinfI, which provided species-specific restriction patterns. In addition, a proteomic approach, based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization-ion trap (ESI-IT) mass spectrometry, was used to identify and characterize new P. borealis-specific peptides that could be useful as potential markers of this species in protein-based detection methods. To our knowledge, this is the first time a molecular method has been successfully applied to identify a wide range of prawn and shrimp species, including P. borealis, for either whole individuals or processed products. However, validation of the methods proposed here is required by applying them to a larger sample of individuals from different populations and geographic origins in order to avoid mainly false-negative results.
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Affiliation(s)
- Ananias Pascoal
- Department of Analytical Chemistry, Nutrition, and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, E-27002 Lugo, Spain
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31
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Flight PA, O'Brien MA, Schmidt PS, Rand DM. Genetic structure and the North American postglacial expansion of the barnacle, Semibalanus balanoides. ACTA ACUST UNITED AC 2011; 103:153-65. [PMID: 21885571 DOI: 10.1093/jhered/esr083] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Population genetic characteristics are shaped by the life-history traits of organisms and the geologic history of their habitat. This study provides a neutral framework for understanding the population dynamics and opportunities for selection in Semibalanus balanoides, a species that figures prominently in ecological and evolutionary studies in the Atlantic intertidal. We used mitochondrial DNA (mtDNA) control region (N = 131) and microsatellite markers (∼40 individuals/site/locus) to survey populations of the broadly dispersing acorn barnacle from 8 sites spanning 800 km of North American coast and 1 site in Europe. Patterns of mtDNA sequence evolution were consistent with larger population sizes in Europe and population expansion at the conclusion of the last ice age, approximately 20 000 years ago, in North America. A significant portion of mitochondrial diversity was partitioned between the continents (ϕ(ST) = 0.281), but there was only weak structure observed from mtDNA within North America. Microsatellites showed significant structuring between the continents (F(ST) = 0.021) as well as within North America (F(ST) = 0.013). Isolation by distance in North America was largely driven by a split between populations south of Cape Cod and all others (P < 10(-4)). The glacial events responsible for generating allelic diversity at mtDNA and microsatellites may also be responsible for generating selectable variation at metabolic enzymes in S. balanoides.
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Affiliation(s)
- Patrick A Flight
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.
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32
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Ma KY, Chan TY, Chu KH. Refuting the six-genus classification of Penaeus s.l. (Dendrobranchiata, Penaeidae): a combined analysis of mitochondrial and nuclear genes. ZOOL SCR 2011. [DOI: 10.1111/j.1463-6409.2011.00483.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Alvarado Bremer JR, Ditty JG, Turner JS, Saxton BL. Molecular species identification of commercially important penaeid shrimp from the Gulf of Mexico using a multiplex haplotype-specific PCR assay. BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2010.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Identification of commercial prawn and shrimp species of food interest by native isoelectric focusing. Food Chem 2010. [DOI: 10.1016/j.foodchem.2009.12.049] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Calleros L, Panzera F, Bargues M, Monteiro F, Klisiowicz D, Zuriaga M, Mas-Coma S, Pérez R. Systematics of Mepraia (Hemiptera-Reduviidae): Cytogenetic and molecular variation. INFECTION GENETICS AND EVOLUTION 2010; 10:221-8. [DOI: 10.1016/j.meegid.2009.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 12/02/2009] [Accepted: 12/05/2009] [Indexed: 11/25/2022]
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36
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Ortea I, Cañas B, Gallardo JM. Mass spectrometry characterization of species-specific peptides from arginine kinase for the identification of commercially relevant shrimp species. J Proteome Res 2010; 8:5356-62. [PMID: 19891510 DOI: 10.1021/pr900663d] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyses, is proposed for the identification of shrimp species with commercial interest. MALDI-TOF peptide mass fingerprint from arginine kinase tryptic digests were used for the identification of seven commercial, closely related species of Decapoda shrimps. Further identification and characterization of these peptides was performed by CID on an ESI-IT instrument, database search and de novo sequence interpretation, paying special attention to differential, species-specific peptides. Fisheries and manufacturers may take advantage of this methodology as a tool for a rapid and effective seafood product identification and authentication, providing and guaranteeing the quality and safety of the foodstuffs to consumers.
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Affiliation(s)
- Ignacio Ortea
- Marine Research Institute, Spanish National Research Council (CSIC), Eduardo Cabello 6, E-36208 Vigo, Spain.
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37
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Calo-Mata P, Pascoal A, Fernández-No I, Böhme K, Gallardo JM, Barros-Velázquez J. Evaluation of a novel 16S rRNA/tRNAVal mitochondrial marker for the identification and phylogenetic analysis of shrimp species belonging to the superfamily Penaeoidea. Anal Biochem 2009; 391:127-34. [DOI: 10.1016/j.ab.2009.05.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2009] [Revised: 05/10/2009] [Accepted: 05/11/2009] [Indexed: 10/20/2022]
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38
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Ortea I, Cañas B, Calo-Mata P, Barros-Velázquez J, Gallardo JM. Arginine kinase peptide mass fingerprinting as a proteomic approach for species identification and taxonomic analysis of commercially relevant shrimp species. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:5665-5672. [PMID: 19489608 DOI: 10.1021/jf900520h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A proteomic approach aimed at species identification and taxonomic analysis of shrimp species of commercial interest is presented. Six different species belonging to the order Decapoda were considered. Preliminary, two-dimensional gel electrophoresis (2-DE) analysis of the sarcoplasmic proteome revealed interspecific variability in the isoelectric point (pI) of arginine kinase. For this reason, arginine kinase spot was selected as a potential molecular marker and subjected to tryptic digestion followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) peptide mass fingerprinting (PMF) analysis. Arginine kinase PMF allowed the differentiation of the six species studied. Four samples of commercial origin obtained in local markets were analyzed to validate the methodology. The PMF cluster analysis also provided information about the phylogenetic relationships in these species. The application of this methodology may be of interest for the differentiation and taxonomic analysis of shrimp species complementing DNA-based phylogenetic studies.
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Affiliation(s)
- Ignacio Ortea
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas, Vigo, Spain.
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39
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Ortea I, Barros L, Gallardo JM. Closely Related Shrimp Species Identification by MALDI-ToF Mass Spectrometry. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2009. [DOI: 10.1080/10498850802584280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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40
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Mitochondrial DNA variation in the caramote prawn Penaeus (Melicertus) kerathurus across a transition zone in the Mediterranean Sea. Genetica 2008; 136:439-47. [PMID: 19109695 DOI: 10.1007/s10709-008-9344-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 12/06/2008] [Indexed: 10/21/2022]
Abstract
In this study we analysed mitochondrial DNA variation in Penaeus kerathurus prawns collected from seven locations along a transect across the Siculo-Tunisian region in order to verify if any population structuring exists over a limited geographical scale and to delineate the putative transition zone with sufficient accuracy. Partial DNA sequences of COI and 16S genes were analysed. In contrast to the highly conservative 16S gene, the COI sequences exhibited sufficient diversity for population analysis. The COI gene revealed low levels of haplotype and nucleotide diversities. The size of the annual landings of this commercial species suggests large population sizes. Hence, the low genetic diversity detected in this study could indicate a possible reduction in effective population sizes in the past. We detected significant genetic differentiation between eastern and western populations likely due to restricted gene flow across the Siculo-Tunisian boundary. We discuss the different evolutionary forces that may have shaped the genetic variation and suggest that the genetic divide is probably maintained by present-day dispersal limitation.
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41
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Survey of the authenticity of prawn and shrimp species in commercial food products by PCR-RFLP analysis of a 16S rRNA/tRNAVal mitochondrial region. Food Chem 2008. [DOI: 10.1016/j.foodchem.2007.12.079] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Pascoal A, Barros-Velázquez J, Cepeda A, Gallardo JM, Calo-Mata P. Identification of shrimp species in raw and processed food products by means of a polymerase chain reaction-restriction fragment length polymorphism method targeted to cytochrome b mitochondrial sequences. Electrophoresis 2008; 29:3220-8. [DOI: 10.1002/elps.200800132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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43
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Azuma N, Kunihiro Y, Sasaki J, Mihara E, Mihara Y, Yasunaga T, Jin DH, Abe S. Genetic variation and population structure of hair crab (Erimacrus isenbeckii ) in Japan inferred from mitochondrial DNA sequence analysis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2008; 10:39-48. [PMID: 17955293 DOI: 10.1007/s10126-007-9033-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Revised: 05/29/2007] [Accepted: 06/10/2007] [Indexed: 05/25/2023]
Abstract
Genetic variation and population structure of hair crab (Erimacrus isenbeckii) were examined using nucleotide sequence analysis of 580 base pairs (bp) in the 3' portion of the mitochondrial cytochrome c oxidase subunit I gene (COI) of 20 samples collected from 16 locales in Japan (the Hokkaido and Honshu Islands) and one in Korea. A total of 27 haplotypes was defined by 23 variable nucleotide sites in the examined COI region. Pairwise population F (ST) estimates and neighbor-joining tree inferred distinct genetic differentiation between the representative samples from the Pacific Ocean off the Eastern Hokkaido Island and the Sea of Japan, while others were intermediate between these two groups. AMOVA also showed a weak but significant differentiation among these three groups. The present results suggest a moderate population structure of hair crab, probably influenced by high gene flow between regional populations due to sea current dependent larval dispersal of this species.
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Affiliation(s)
- Noriko Azuma
- Division of Marine Bioscience, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
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44
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Pascoal A, Barros-Velázquez J, Cepeda A, Gallardo JM, Calo-Mata P. A polymerase chain reaction-restriction fragment length polymorphism method based on the analysis of a 16S rRNA/tRNAVal mitochondrial region for species identification of commercial penaeid shrimps (Crustacea: Decapoda: Penaeoidea) of food interest. Electrophoresis 2008; 29:499-509. [DOI: 10.1002/elps.200700406] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Miura T, Kawane M, Wada K. A New Species of Deiratonotus (Crustacea: Brachyura: Camptandriidae) Found in the Kumanoe River Estuary, Kyushu, Japan. Zoolog Sci 2007; 24:1045-50. [DOI: 10.2108/zsj.24.1045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 07/06/2007] [Indexed: 11/17/2022]
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46
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Shen X, Ren J, Cui Z, Sha Z, Wang B, Xiang J, Liu B. The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations. Gene 2007; 403:98-109. [PMID: 17890021 DOI: 10.1016/j.gene.2007.06.021] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Revised: 06/18/2007] [Accepted: 06/29/2007] [Indexed: 01/28/2023]
Abstract
Complete mitochondrial genomes have proven extremely valuable in helping to understand the evolutionary relationships among metazoans. However, uneven taxon sampling may lead to unclear or even erroneous phylogenetic topologies. The decapod crustaceans are relatively well-sampled, but sampling is still uneven within this group. We have sequenced the mitochondrial genomes of two shrimps Litopenaeus vannamei and Fenneropenaeus chinensis. As seen in other metazoans, the genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and an AT-rich non-coding region. The gene arrangements are consistent with the pancrustacean ground pattern. Both the pattern of gene rearrangements and phylogenomic analyses using concatenated nucleic acid and amino acid sequences of the 13 mitochondrial protein-coding genes strengthened the support that Caridea and Palinura are primitive members of Pleocyemata. These sequences, in combination with two previously published penaeid mitochondrial genomes, suggest that genera within the family Penaeidae have the following relationship: (((Penaeus+Fenneropenaeus)+Litopenaeus)+Marsupenaeus). The analyses of nucleic acid and amino acid sequences of the mitochondrial genomes also strongly support the monophyly of Penaeidae, Brachyura and Pleocyemata. In addition, the analyses of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group.
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Affiliation(s)
- Xin Shen
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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47
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Padhi A, Verghese B, Vaid A, Otta SK. Pattern of nucleotide substitution and divergence of prophenoloxidase in decapods. FISH & SHELLFISH IMMUNOLOGY 2007; 22:628-40. [PMID: 17046283 DOI: 10.1016/j.fsi.2006.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 08/08/2006] [Accepted: 08/08/2006] [Indexed: 05/12/2023]
Abstract
Despite the unprecedented development in identification and characterization of prophenoloxidase (proPO) in commercially important decapods, little is known about the evolutionary relationship, rate of amino acid replacement and differential selection pressures operating on proPO of different species of decapods. Here we report the evolutionary relationship among these nine decapod species based on proPO gene and types of selective pressures operating on proPO codon sites. Our analyses revealed that all the nine decapod species shared a common ancestor. The mean percentage sequence divergence at proPO gene was 34.4+/-0.6%. Pairwise estimates of nonsynonymous to synonymous ratio (omega) for Homarus americanus-H. gammarus is greater than one, therefore indicating adaptive evolution (functional diversification) of proPO in these two species. In contrast, strong purifying selection (omega<1) was observed in all other species pairs. However, phylogenetically closely related decapods revealed relatively higher omega value (omega=0.15+/-0.3) than the distantly related species pairs (omega=0.0075+/-0.005). These discrepancies could be due to higher fixation probability of beneficial mutation in closely related species. Maximum likelihood-based codon substitution analyses revealed a strong purifying selection operating on most of the codon sites, therefore suggesting proPO is functionally constrained (purifying selection). Codon substitution analyses have also revealed the evidence of strong purifying selection in haemocyanin subunits of decapods.
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Affiliation(s)
- Abinash Padhi
- Department of Biological Science, University of Tulsa, 600 South College Avenue, Tulsa, OK 74104, USA.
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48
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Bowen BW, Bass AL, Rocha LA, Grant WS, Robertson DR. PHYLOGEOGRAPHY OF THE TRUMPETFISHES (AULOSTOMUS): RING SPECIES COMPLEX ON A GLOBAL SCALE. Evolution 2007. [DOI: 10.1111/j.0014-3820.2001.tb00619.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Lessios HA, Kessing BD, Pearse JS. POPULATION STRUCTURE AND SPECIATION IN TROPICAL SEAS: GLOBAL PHYLOGEOGRAPHY OF THE SEA URCHIN DIADEMA. Evolution 2007. [DOI: 10.1111/j.0014-3820.2001.tb00613.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Bowen BW, Muss A, Rocha LA, Grant WS. Shallow mtDNA Coalescence in Atlantic Pygmy Angelfishes (Genus Centropyge) Indicates a Recent Invasion from the Indian Ocean. J Hered 2006; 97:1-12. [PMID: 16394255 DOI: 10.1093/jhered/esj006] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pygmy angelfishes (genus Centropyge) are widespread and species-rich in the Indo-Pacific, but only three species are recognized in the Atlantic: Centropyge resplendens on the Mid-Atlantic Ridge, Centropyge argi in the Caribbean, and Centropyge aurantonotus in Brazil and the southern Caribbean. Atlantic species are distinguished only by color patterns and are very similar to Centropyge acanthops (Cac) in the western Indian Ocean, raising the possibility that pygmy angelfish recently invaded the Atlantic Ocean via southern Africa. To test this zoogeographic hypothesis, we compared a 454-bp segment of the mitochondrial DNA (mtDNA) control region among pygmy angelfishes of the subgenus Xiphypops, which includes the three Atlantic species, the Indian Ocean species, and an Indo-Pacific species [Centropyge fisheri (Cfi)]. The Indian Ocean species Cac is closest to the Atlantic species (d = 0.059) relative to Cfi (d = 0.077). The mtDNA genealogy indicates a colonization pathway from the Indian Ocean directly to the West Atlantic, followed by at least two waves of dispersal to the Mid-Atlantic Ridge. The gene tree for the three Atlantic species is polyphyletic, raising questions about taxonomic assignments based on color pattern. Mismatch distributions place Atlantic founder events and population expansions at about 250,000-500,000 years ago. Estimates of effective female population sizes from mismatch and coalescence analyses are consistent with founder events by tens of individuals in the western Atlantic, followed by expansions to several million individuals.
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Affiliation(s)
- B W Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, PO Box 1346, Kaneohe, HI 96744, USA.
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