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Ojeda V, Serra B, Lagares C, Rojo-Francàs E, Sellés M, Marco-Herrero E, García E, Farré M, Arenas C, Abelló P, Mestres F. Interannual fluctuations in connectivity among crab populations (Liocarcinus depurator) along the Atlantic-Mediterranean transition. Sci Rep 2022; 12:9797. [PMID: 35697727 PMCID: PMC9192654 DOI: 10.1038/s41598-022-13941-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/30/2022] [Indexed: 11/18/2022] Open
Abstract
An interesting evolutionary question that still remains open is the connectivity between marine populations. Marine currents can favour the dispersal of larvae or adults, but they can also produce eddies and gyres generating oceanographic fronts, thus limiting gene flow. To address this subject, we selected the Atlantic-Mediterranean transition, where several fronts are located: Gibraltar Strait (GS), Almeria-Oran Front (AOF) and Ibiza Channel (IC). Seven populations of the marine crab Liocarcinus depurator (Cadiz, West and East Alboran, Alacant, Valencia, Ebro Delta and North Catalonia) located along this transition were analysed in six consecutive years (2014–2019) using a fragment of the COI (Cytochrome Oxidase subunit I) gene. All sequences (966) belonged to two well defined haplogroups: ATL (most abundant in Atlantic waters) and MED (predominant in Mediterranean waters). Following a geographic variation, the frequency of ATL decreased significantly from Cadiz to North Catalonia. However, this variation presented steps due to the effect of oceanographic restrictions/fronts. Significant effects were recorded for GS (2015, 2017, 2018 and 2019), AOF (all years except 2018) and IC (2016). The intensity and precise location of these fronts changed over time. Multivariate analyses distinguished three main population groups: Cadiz, Alboran Sea and the remaining Mediterranean populations. These findings could be relevant to properly define Marine Protected Areas and for conservation and fisheries policies.
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Affiliation(s)
- Víctor Ojeda
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | - Bruna Serra
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | - Clàudia Lagares
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | - Eva Rojo-Francàs
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | - Maria Sellés
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | | | - Encarnación García
- Instituto Español de Oceanografía - C.O. Murcia (IEO-CSIC), San Pedro del Pinatar, Spain
| | - Marc Farré
- Instituto Español de Oceanografía - C.O. Balears (IEO-CSIC), Palma de Mallorca, Spain.,Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Concepció Arenas
- Dept. Genètica, Microbiologia i Estadística, Secció d'Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Pere Abelló
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Francesc Mestres
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain. .,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain.
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2
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Rossi AR, Petrosino G, Crescenzo S, Milana V, Talarico L, Martinoli M, Rakaj A, Lorenzoni M, Carosi A, Ciuffardi L, Tancioni L. Phylogeography and population structure of Squalius lucumonis: A baseline for conservation of an Italian endangered freshwater fish. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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3
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Francisco SM, Castilho R, Lima CS, Almada F, Rodrigues F, Šanda R, Vukić J, Pappalardo AM, Ferrito V, Robalo JI. Genetic hypervariability of a Northeastern Atlantic venomous rockfish. PeerJ 2021; 9:e11730. [PMID: 34306828 PMCID: PMC8280884 DOI: 10.7717/peerj.11730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Understanding the interplay between climate and current and historical factors shaping genetic diversity is pivotal to infer changes in marine species range and communities' composition. A phylogeographical break between the Atlantic and the Mediterranean has been documented for several marine organisms, translating into limited dispersal between the two basins. METHODS In this study, we screened the intraspecific diversity of 150 individuals of the Madeira rockfish (Scorpaena maderensis) across its distributional range (seven sampling locations in the Atlantic and Mediterranean basins) using the mitochondrial control region and the nuclear S7 first intron. RESULTS The present work is the most comprehensive study done for this species, yielding no genetic structure across sampled locations and no detectable Atlantic-Mediterranean break in connectivity. Our results reveal deep and hyper-diverse bush-like genealogies with large numbers of singletons and very few shared haplotypes. The genetic hyper-diversity found for the Madeira rockfish is relatively uncommon in rocky coastal species, whose dispersal capability is limited by local oceanographic patterns. The effect of climate warming on the distribution of the species is discussed.
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Affiliation(s)
- Sara M. Francisco
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Rita Castilho
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Cristina S. Lima
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Frederico Almada
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Francisca Rodrigues
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Radek Šanda
- Department of Zoology, National Museum, Prague, Czeck Republic
| | - Jasna Vukić
- Faculty of Science, Department of Ecology, Charles University, Prague, Czech Republic
| | - Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology Biology ‘‘Marcello La Greca’’, University of Catania, Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology Biology ‘‘Marcello La Greca’’, University of Catania, Catania, Italy
| | - Joana I. Robalo
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
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4
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Cheng J, Zhang N, Sha Z. Nuclear microsatellites reveal population genetic structuring and fine-scale pattern of hybridization in the Japanese mantis shrimp Oratosquilla oratoria. PeerJ 2020; 8:e10270. [PMID: 33194430 PMCID: PMC7649012 DOI: 10.7717/peerj.10270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/08/2020] [Indexed: 11/27/2022] Open
Abstract
The interplay between historical and contemporary processes can produce complex patterns of genetic differentiation in the marine realm. Recent mitochondrial and nuclear sequence analyses revealed cryptic speciation in the Japanese mantis shrimp Oratosquilla oratoria. Herein, we applied nuclear microsatellite markers to examine patterns and causes of genetic differentiation in this morphotaxon. Population structure analyses revealed two genetically divergent and geographically structured clades in O. oratoria, one dominating the temperate zone of the Northwestern (NW) Pacific and the other occurring in the subtropical and tropical waters where are influenced by the Kuroshio Current. Two sympatric zones, one around the Changjiang Estuary in China coast and the other in the northern Japan Sea, were demonstrated to be hybrid zones where introgressive hybridization occurred asymmetrically. The interaction between historical climate shifts and contemporary factors (e.g., freshwater discharge, temperature gradient and isolation by distance) may contribute to the present-day genetic architecture in the Japanese mantis shrimp. Range shift induced by climate changes and oceanographic factors may promote hybridization and gene flow between the O. oratoria complex. Our results provide insights into the interacting mechanisms that give rise to diversification and speciation of coastal species in the NW Pacific.
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Affiliation(s)
- Jiao Cheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Nan Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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5
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Brophy D, Rodríguez-Ezpeleta N, Fraile I, Arrizabalaga H. Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus). Sci Rep 2020; 10:14675. [PMID: 32895410 PMCID: PMC7477220 DOI: 10.1038/s41598-020-71355-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/13/2020] [Indexed: 11/09/2022] Open
Abstract
Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning populations in the Mediterranean and Gulf of Mexico occur together in the western, central and eastern Atlantic. Stock composition of catches from mixing areas is uncertain, presenting a major challenge to the sustainable management of the fisheries. This study combines genetic and chemical markers to develop an integrated method of population assignment. Stable isotope signatures (δ13C and δ18O) in the otolith core of adults from the two main spawning populations (adult baselines) showed less overlap than those of yearlings (12-18 months old) from western and eastern nursery areas suggesting that some exchange occurs towards the end of the yearling phase. The integrated model combined δ18O with four genetic markers (SNPs) to distinguish the adult baselines with greater accuracy than chemical or genetic markers alone. When used to assign individuals from the mixing areas to their population of origin, the integrated model resolved some (but not all) discrepancies between the chemistry and genetic methods. Some individuals in the mixing area had otolith δ18O values and genetic profiles which when taken together, were not representative of either population. These fish may originate from another Atlantic spawning area or may represent population contingents that move away from the main spawning areas during the first year of life. This complexity in stock structure is not captured by the current two-stock model.
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Affiliation(s)
- Deirdre Brophy
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin road, Galway, H91 T8NW, Ireland.
| | | | - Igaratza Fraile
- Marine Research Division, AZTI, Txatxarramendi Ugartea Z/G, 48395, Sukarrieta, Bizkaia, Spain
| | - Haritz Arrizabalaga
- Marine Research Division, AZTI, Txatxarramendi Ugartea Z/G, 48395, Sukarrieta, Bizkaia, Spain
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6
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McKeown NJ, Gwilliam MP, Healey AJE, Skujina I, Potts WM, Sauer WHH, Shaw PW. Deep phylogeographic structure may indicate cryptic species within the Sparid genus Spondyliosoma. JOURNAL OF FISH BIOLOGY 2020; 96:1434-1443. [PMID: 32154919 DOI: 10.1111/jfb.14316] [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] [Received: 08/26/2019] [Revised: 12/27/2019] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Two geographically nonoverlapping species are currently described within the sparid genus Spondyliosoma: Spondyliosoma cantharus (Black Seabream) occurring across Mediterranean and eastern Atlantic waters from NW Europe to Angola and S. emarginatum (Steentjie) considered endemic to southern Africa. To address prominent knowledge gaps this study investigated range-wide phylogeographic structure across both species. Mitochondrial DNA sequences revealed deep phylogeographic structuring with four regionally partitioned reciprocally monophyletic clades, a Mediterranean clade and three more closely related Atlantic clades [NE Atlantic, Angola and South Africa (corresponding to S. emarginatum)]. Divergence and distribution of the lineages reflects survival in, and expansion from, disjunct glacial refuge areas. Cytonuclear differentiation of S. emarginatum supports its validity as a distinct species endemic to South African waters. However, the results also indicate that S. cantharus may be a cryptic species complex wherein the various regional lineages represent established/incipient species. A robust multilocus genetic assessment combining morphological data and detailing interactions among lineages is needed to determine the full diversity within Spondyliosoma and the most adequate biological and taxonomic status.
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Affiliation(s)
- Niall J McKeown
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael P Gwilliam
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Amy J E Healey
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ilze Skujina
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Warren M Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Warwick H H Sauer
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Paul W Shaw
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
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7
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Healey AJE, Farthing MW, Nunoo FKE, Potts WM, Sauer WHH, Skujina I, King N, de Becquevort S, Shaw PW, McKeown NJ. Genetic analysis provides insights into species distribution and population structure in East Atlantic horse mackerel (Trachurus trachurus and T. capensis). JOURNAL OF FISH BIOLOGY 2020; 96:795-805. [PMID: 32031244 PMCID: PMC7079130 DOI: 10.1111/jfb.14276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
Two sister species of horse mackerel (Trachurus trachurus and T. capensis) are described that are intensively harvested in East Atlantic waters. To address long-standing uncertainties as to their respective geographical ranges, overlap and intraspecific population structure this study combined genetic (mitochondrial DNA and microsatellite) analysis and targeted sampling of the hitherto understudied West African coast. mtDNA revealed two reciprocally monophyletic clades corresponding to each species with interspecies nuclear differentiation supported by FST values. The T. trachurus clade was found across the north-east Atlantic down to Ghana but was absent from Angolan and South African samples. The T. capensis clade was found only in South Africa, Angola and a single Ghanaian individual. This pattern suggests that both species may overlap in the waters around Ghana. The potential for cryptic hybridization and/or indiscriminate harvesting of both species in the region is discussed. For T. capensis mtDNA supports high gene flow across the Benguela upwelling system, which fits with the species' ecology. The data add to evidence of a lack of significant genetic structure throughout the range of T. trachurus though the assumption of demographic panmixia is cautioned against. For both species, resolution of stock recruitment heterogeneity relevant to fishery management, as well as potential hybridization, will require more powerful genomic analyses.
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Affiliation(s)
- Amy J. E. Healey
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Matthew W. Farthing
- Department of Ichthyology & Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
| | | | - Warren M. Potts
- Department of Ichthyology & Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
| | - Warwick H. H. Sauer
- Department of Ichthyology & Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
| | - Ilze Skujina
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Nathan King
- School of Ocean SciencesBangor UniversityMenai Bridge, AngleseyUK
| | - Sophie de Becquevort
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Paul W. Shaw
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Niall J. McKeown
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
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8
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Navarro‐Barranco C, Tierno de Figueroa JM, Ros M, Guerra García JM. Influence of Marine Protected Areas on parasitic prevalence: the case of the isopod
Anilocra physodes
as a parasite of the fish
Lithognathus mormyrus. J Zool (1987) 2019. [DOI: 10.1111/jzo.12674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. Navarro‐Barranco
- Departamento de Biología (Unidad de Zoología) Universidad Autónoma de Madrid Madrid Spain
- Laboratorio de Biología Marina Departamento de Zoología Universidad de Sevilla Sevilla Spain
| | | | - M. Ros
- Departamento de Biología, Área de Zoología Facultad de Ciencias del Mar y Ambientales Universidad de Cádiz Puerto Real (Cádiz) Spain
| | - J. M. Guerra García
- Laboratorio de Biología Marina Departamento de Zoología Universidad de Sevilla Sevilla Spain
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9
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Contemporary and historical river connectivity influence population structure in western brook lamprey in the Columbia River Basin. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1137-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers. PLoS One 2018; 13:e0203866. [PMID: 30208106 PMCID: PMC6135516 DOI: 10.1371/journal.pone.0203866] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 08/29/2018] [Indexed: 11/29/2022] Open
Abstract
The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well.
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11
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Clonorchis sinensis and Clonorchiasis: The Relevance of Exploring Genetic Variation. ADVANCES IN PARASITOLOGY 2018; 100:155-208. [PMID: 29753338 DOI: 10.1016/bs.apar.2018.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Parasitic trematodes (flukes) cause substantial mortality and morbidity in humans. The Chinese liver fluke, Clonorchis sinensis, is one of the most destructive parasitic worms in humans in China, Vietnam, Korea and the Russian Far East. Although C. sinensis infection can be controlled relatively well using anthelmintics, the worm is carcinogenic, inducing cholangiocarcinoma and causing major suffering in ~15 million people in Asia. This chapter provides an account of C. sinensis and clonorchiasis research-covering aspects of biology, epidemiology, pathogenesis and immunity, diagnosis, treatment and control, genetics and genomics. It also describes progress in the area of molecular biology (genetics, genomics, transcriptomics and proteomics) and highlights challenges associated with comparative genomics and population genetics. It then reviews recent advances in the sequencing and characterisation of the mitochondrial and nuclear genomes for a Korean isolate of C. sinensis and summarises salient comparative genomic work and the implications thereof. The chapter concludes by considering how advances in genomic and informatics will enable research on the genetics of C. sinensis and related parasites, as well as the discovery of new fluke-specific intervention targets.
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12
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Ecological and evolutionary consequences of alternative sex-change pathways in fish. Sci Rep 2017; 7:9084. [PMID: 28831108 PMCID: PMC5567342 DOI: 10.1038/s41598-017-09298-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/25/2017] [Indexed: 11/09/2022] Open
Abstract
Sequentially hermaphroditic fish change sex from male to female (protandry) or vice versa (protogyny), increasing their fitness by becoming highly fecund females or large dominant males, respectively. These life-history strategies present different social organizations and reproductive modes, from near-random mating in protandry, to aggregate- and harem-spawning in protogyny. Using a combination of theoretical and molecular approaches, we compared variance in reproductive success (Vk*) and effective population sizes (Ne) in several species of sex-changing fish. We observed that, regardless of the direction of sex change, individuals conform to the same overall strategy, producing more offspring and exhibiting greater Vk* in the second sex. However, protogynous species show greater Vk*, especially pronounced in haremic species, resulting in an overall reduction of Ne compared to protandrous species. Collectively and independently, our results demonstrate that the direction of sex change is a pivotal variable in predicting demographic changes and resilience in sex-changing fish, many of which sustain highly valued and vulnerable fisheries worldwide.
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13
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Catarino D, Stefanni S, Jorde PE, Menezes GM, Company JB, Neat F, Knutsen H. The role of the Strait of Gibraltar in shaping the genetic structure of the Mediterranean Grenadier, Coryphaenoides mediterraneus, between the Atlantic and Mediterranean Sea. PLoS One 2017; 12:e0174988. [PMID: 28459855 PMCID: PMC5411037 DOI: 10.1371/journal.pone.0174988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 03/17/2017] [Indexed: 11/18/2022] Open
Abstract
Population genetic studies of species inhabiting the deepest parts of the oceans are still scarce and only until recently we started to understand how oceanographic processes and topography affect dispersal and gene flow patterns. The aim of this study was to investigate the spatial population genetic structure of the bathyal bony fish Coryphaenoides mediterraneus, with a focus on the Atlantic-Mediterranean transition. We used nine nuclear microsatellites and the mitochondrial cytochrome c oxidase I gene from 6 different sampling areas. No population genetic structure was found within Mediterranean with both marker types (mean ΦST = 0.0960, FST = -0.0003, for both P > 0.05). However, within the Atlantic a contrasting pattern of genetic structure was found for the mtDNA and nuclear markers (mean ΦST = 0.2479, P < 0.001; FST = -0.0001, P > 0.05). When comparing samples from Atlantic and Mediterranean they exhibited high and significant levels of genetic divergence (mean ΦST = 0.7171, FST = 0.0245, for both P < 0.001) regardless the genetic marker used. Furthermore, no shared haplotypes were found between Atlantic and Mediterranean populations. These results suggest very limited genetic exchange between Atlantic and Mediterranean populations of C. mediterraneus, likely due to the shallow bathymetry of the Strait of Gibraltar acting as a barrier to gene flow. This physical barrier not only prevents the direct interactions between the deep-living adults, but also must prevent interchange of pelagic early life stages between the two basins. According to Bayesian simulations it is likely that Atlantic and Mediterranean populations of C. mediterraneus were separated during the late Pleistocene, which is congruent with results for other deep-sea fish from the same region.
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Affiliation(s)
- Diana Catarino
- MARE – Marine and Environmental Sciences Centre, University of the Azores, Department of Oceanography and Fisheries, Horta, Azores, Portugal
- Department of Oceanography and Fisheries, University of the Azores, Horta, Azores, Portugal
| | | | - Per Erik Jorde
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Gui M. Menezes
- MARE – Marine and Environmental Sciences Centre, University of the Azores, Department of Oceanography and Fisheries, Horta, Azores, Portugal
- Department of Oceanography and Fisheries, University of the Azores, Horta, Azores, Portugal
| | | | - Francis Neat
- Marine Scotland-Science, Marine Laboratory, Aberdeen, United Kingdom
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
- Institute of Marine Research, Flødevigen, Norway
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
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14
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Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries. Sci Rep 2016; 6:39152. [PMID: 27991535 PMCID: PMC5171699 DOI: 10.1038/srep39152] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/18/2016] [Indexed: 01/25/2023] Open
Abstract
In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics.
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Sahyoun R, Guidetti P, Di Franco A, Planes S. Patterns of Fish Connectivity between a Marine Protected Area and Surrounding Fished Areas. PLoS One 2016; 11:e0167441. [PMID: 27907100 PMCID: PMC5131959 DOI: 10.1371/journal.pone.0167441] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/14/2016] [Indexed: 11/23/2022] Open
Abstract
Patterns of connectivity and self-recruitment are recognized as key factors shaping the dynamics of marine populations. Connectivity is also essential for maintaining and restoring natural ecological processes with genetic diversity contributing to the adaptation and persistence of any species in the face of global disturbances. Estimates of connectivity are crucial to inform the design of both marine protected areas (MPAs) and MPA networks. Among several approaches, genetic structure is frequently used as a proxy for patterns of connectivity. Using 8 microsatellite loci, we investigated genetic structure of the two-banded sea bream Diplodus vulgaris, a coastal fish that is both commercially and ecologically important. Adults were sampled in 7 locations (stretches of coastline approximately 8 km long) and juveniles in 14 sites (~100 to 200 m of coastline) along 200 km of the Apulian Adriatic coast (SW Adriatic Sea), within and outside an MPA (Torre Guaceto MPA, Italy). Our study found similar genetic diversity indices for both the MPA and the surrounding fished areas. An overall lack of genetic structure among samples suggests high gene flow (i.e. connectivity) across a scale of at least 200 km. However, some local genetic divergences found in two locations demonstrate some heterogeneity in processes renewing the population along the Apulian Adriatic coast. Furthermore, two sites appeared genetically divergent, reinforcing our observations within the genetic makeup of adults and confirming heterogeneity in early stage genetics that can come from either different supply populations or from chaotic genetic patchiness occurring under temporal variation in recruitment and in the reproductive success. While the specific role of the MPA is not entirely known in this case, these results confirm the presence of regional processes and the key role of connectivity in maintaining the local population supply.
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Affiliation(s)
- Rita Sahyoun
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, France
| | - Paolo Guidetti
- Université Côte d'Azur, UCA, CNRS, ECOMERS, Parc Valrose, Avenue Valrose, Nice, France.,CoNISMa-Consorzio Nazionale Interuniversitario per le Scienze del Mare, Piazzale Flaminio, Rome, Italy
| | - Antonio Di Franco
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, France.,Université Côte d'Azur, UCA, CNRS, ECOMERS, Parc Valrose, Avenue Valrose, Nice, France.,CoNISMa-Consorzio Nazionale Interuniversitario per le Scienze del Mare, Piazzale Flaminio, Rome, Italy
| | - Serge Planes
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, France
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16
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Coscia I, Chopelet J, Waples RS, Mann BQ, Mariani S. Sex change and effective population size: implications for population genetic studies in marine fish. Heredity (Edinb) 2016; 117:251-8. [PMID: 27507184 PMCID: PMC5026757 DOI: 10.1038/hdy.2016.50] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 05/18/2016] [Accepted: 05/23/2016] [Indexed: 11/09/2022] Open
Abstract
Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected from two ecologically similar species living along the eastern coast of South Africa: one gonochoristic, the 'santer' sea bream Cheimerius nufar, and one protogynous (female-first) sex changer, the 'slinger' sea bream Chrysoblephus puniceus. For both species, no evidence of genetic structuring, nor significant variation in genetic diversity, was found in the study area. Estimates of contemporary Ne were significantly lower in the protogynous species, but the same pattern was not apparent over historical timescales. Overall, our results show that sequential hermaphroditism may affect Ne differently over varying time frames, and that demographic signatures inferred from genetic markers with different inheritance modes also need to be interpreted cautiously, in relation to sex-changing life histories.
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Affiliation(s)
- I Coscia
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), Leuven, Belgium
| | - J Chopelet
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - R S Waples
- NOAA Fisheries, Northwest Fisheries Science Center, Seattle, WA, USA
| | - B Q Mann
- Oceanographic Research Institute, Durban, South Africa
| | - S Mariani
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, The University of Salford, Greater Manchester, UK
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Reid K, Hoareau TB, Graves JE, Potts WM, Dos Santos SMR, Klopper AW, Bloomer P. Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone. Heredity (Edinb) 2016; 117:307-315. [PMID: 27436525 DOI: 10.1038/hdy.2016.51] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 12/16/2022] Open
Abstract
The combination of oceanographic barriers and habitat heterogeneity are known to reduce connectivity and leave specific genetic signatures in the demographic history of marine species. However, barriers to gene flow in the marine environment are almost never impermeable which inevitably allows secondary contact to occur. In this study, eight sampling sites (five along the South African coastline, one each in Angola, Senegal and Portugal) were chosen to examine the population genetic structure and phylogeographic history of the cosmopolitan bluefish (Pomatomus saltatrix), distributed across a large South-east Atlantic upwelling zone. Molecular analyses were applied to mtDNA cytochrome b, intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically high genetic differentiation (FST 0.15-0.20; P<0.001) between the fish sampled from South Africa and the other sites, strongly influenced by five outlier microsatellite loci located in conserved intergenic regions. In addition, differentiation among the remaining East Atlantic sites was detected, although mtDNA indicated past isolation with subsequent secondary contact between these East Atlantic populations. We further identified secondary contact, with unidirectional gene flow from South Africa to Angola. The directional contact is likely explained by a combination of the northward flowing offshore current and endogenous incompatibilities restricting integration of certain regions of the genome and limiting gene flow to the south. The results confirm that the dynamic system associated with the Benguela current upwelling zone influences species distributions and population processes in the South-east Atlantic.
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Affiliation(s)
- K Reid
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - T B Hoareau
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - J E Graves
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William & Mary, Williamsburg, VA, USA
| | - W M Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - S M R Dos Santos
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - A W Klopper
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - P Bloomer
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
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Pascual M, Palero F, García-Merchán VH, Macpherson E, Robainas-Barcia A, Mestres F, Roda T, Abelló P. Temporal and spatial genetic differentiation in the crab Liocarcinus depurator across the Atlantic-Mediterranean transition. Sci Rep 2016; 6:29892. [PMID: 27431989 PMCID: PMC4949458 DOI: 10.1038/srep29892] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/23/2016] [Indexed: 11/09/2022] Open
Abstract
Spatial genetic studies often require sampling broadly separated areas, difficult to access simultaneously. Although comparing localities surveyed at different time periods might result in spurious genetic differentiation, there is a general believe on the stability of genetic structure through time, particularly if sampled localities are isolated or very distant. By analysing spatial and temporal genetic differentiation of the portunid crab Liocarcinus depurator we assessed the contribution of historical and contemporary processes on population connectivity patterns across three main oceanographic discontinuities along the Atlantic-Mediterranean transition: Gibraltar Strait, Almeria-Oran Front and Ibiza Channel. A partial fragment of the cytochrome oxidase I gene was sequenced in 366 individuals collected from localities at both sides of each discontinuity during three time periods. Although localities showed genetic fluctuations through time, a significant gradient was detected along the coast for all sampling periods. Significant inter-annual differences identified within the Alicante area, north of the Almeria-Oran Front, were associated with shifts in the relative contribution of Atlantic and Mediterranean water masses. The persistence of a clinal pattern in the Atlantic-Mediterranean transition area together with local fluctuations suggests a complex balance of dispersal and selection.
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Affiliation(s)
- Marta Pascual
- Dept. Genètica, Microbiologia i Estadística and IRBio, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Ferran Palero
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Carrer d'Accés a la Cala Sant Francesc 14, 17300 Blanes, Spain
| | | | - Enrique Macpherson
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Carrer d'Accés a la Cala Sant Francesc 14, 17300 Blanes, Spain
| | - Aymée Robainas-Barcia
- Dept. Genètica, Microbiologia i Estadística and IRBio, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Francesc Mestres
- Dept. Genètica, Microbiologia i Estadística and IRBio, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Tania Roda
- Dept. Genètica, Microbiologia i Estadística and IRBio, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Pere Abelló
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
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Lattig P, Muñoz I, Martin D, Abelló P, Machordom A. Comparative phylogeography of two symbiotic dorvilleid polychaetes ( Iphitime cuenotiand Ophryotrocha mediterranea) with contrasting host and bathymetric patterns. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patricia Lattig
- Museo Nacional de Ciencias Naturales (MNCN-CSIC); C. José Gutiérrez Abascal 2 Madrid 28006 Spain
| | - Isabel Muñoz
- Instituto Español de Oceanografía; Centro Oceanográfico de Santander (IEO); Promontorio San Martín s/n Santander Cantabria 39004 Spain
| | - Daniel Martin
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC); Carrer d'accès a la Cala Sant Francesc 14 Blanes (Girona) Catalunya 17300 Spain
| | - Pere Abelló
- Institut de Ciències del Mar (ICM-CSIC); Passeig Marítim de la Barceloneta 37-49 Barcelona Catalunya E-08003 Spain
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN-CSIC); C. José Gutiérrez Abascal 2 Madrid 28006 Spain
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20
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Population genetics of a widely distributed small freshwater fish with varying conservation concerns: the southern purple-spotted gudgeon, Mogurnda adspersa. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0829-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Shum P, Pampoulie C, Kristinsson K, Mariani S. Three-dimensional post-glacial expansion and diversification of an exploited oceanic fish. Mol Ecol 2015; 24:3652-67. [PMID: 26073046 PMCID: PMC4744735 DOI: 10.1111/mec.13262] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/22/2015] [Accepted: 05/29/2015] [Indexed: 01/27/2023]
Abstract
Vertical divergence in marine organisms is being increasingly documented, yet much remains to be carried out to understand the role of depth in the context of phylogeographic reconstruction and the identification of management units. An ideal study system to address this issue is the beaked redfish, Sebastes mentella – one of four species of ‘redfish’ occurring in the North Atlantic – which is known for a widely distributed ‘shallow‐pelagic’ oceanic type inhabiting waters between 250 and 550 m, and a more localized ‘deep‐pelagic’ population dwelling between 550 and 800 m, in the oceanic habitat of the Irminger Sea. Here, we investigate the extent of population structure in relation to both depth and geographic spread of oceanic beaked redfish throughout most of its distribution range. By sequencing the mitochondrial control region of 261 redfish collected over a decadal interval, and combining 160 rhodopsin coding nuclear sequences and previously genotyped microsatellite data, we map the existence of two strongly divergent evolutionary lineages with significantly different distribution patterns and historical demography, and whose genetic variance is mostly explained by depth. Combined genetic data, analysed via independent approaches, are consistent with a Late Pleistocene lineage split, where segregation by depth probably resulted from the interplay of climatic and oceanographic processes with life history and behavioural traits. The ongoing process of diversification in North Atlantic S. mentella may serve as an ‘hourglass’ to understand speciation and adaptive radiation in Sebastes and in other marine taxa distributed across a depth gradient.
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Affiliation(s)
- Peter Shum
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
| | | | | | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
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22
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A review of molecular approaches for investigating patterns of coevolution in marine host-parasite relationships. ADVANCES IN PARASITOLOGY 2014; 84:209-52. [PMID: 24480315 DOI: 10.1016/b978-0-12-800099-1.00004-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Parasites and their relationships with hosts play a crucial role in the evolutionary pathways of every living organism. One method of investigating host-parasite systems is using a molecular approach. This is particularly important as analyses based solely on morphology or laboratory studies of parasites and their hosts do not take into account historical evolutionary interactions that can shape the distribution, abundance and population structure of parasites and their hosts. However, the predominant host-parasite coevolution literature has focused on terrestrial hosts and their parasites, and there still is a lack of studies in marine environments. Given that marine systems are generally more open than terrestrial ones, they provide fascinating opportunities for large-scale (as well as small-scale) geographic studies. Further, patterns and processes of genetic structuring and systematics are becoming more available across many different taxa (but especially fishes) in many marine systems, providing an excellent basis for examining whether parasites follow host population/species structure. In this chapter, we first highlight the factors and processes that challenge our ability to interpret evolutionary patterns of coevolution of hosts and their parasites in marine systems at different spatial, temporal and taxonomic scales. We then review the use of the most commonly utilized genetic markers in studying marine host-parasite systems. We give an overview and discuss which molecular methodologies resolve evolutionary relationships best and also discuss the applicability of new approaches, such as next-generation sequencing and studies utilizing functional markers to gain insights into more contemporary processes shaping host-parasite relationships.
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Catalano SR, Whittington ID, Donnellan SC, Gillanders BM. Parasites as biological tags to assess host population structure: Guidelines, recent genetic advances and comments on a holistic approach. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2013; 3:220-6. [PMID: 25197624 PMCID: PMC4152261 DOI: 10.1016/j.ijppaw.2013.11.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/21/2013] [Accepted: 11/21/2013] [Indexed: 11/30/2022]
Abstract
Parasites as biological tags to assess host population structure. Recent molecular advances support incorporation of parasite genetic data. Guidelines for selection of a parasite species as a tag candidate updated. Holistic approach allows for robustness and support of observed result.
We review the use of parasites as biological tags of marine fishes and cephalopods in host population structure studies. The majority of the work published has focused on marine fish and either single parasite species or more recently, whole parasite assemblages, as biological tags. There is representation of host organisms and parasites from a diverse range of taxonomic groups, although focus has primarily been on host species of commercial importance. In contrast, few studies have used parasites as tags to assess cephalopod population structure, even though records of parasites infecting cephalopods are well-documented. Squid species are the only cephalopod hosts for which parasites as biological tags have been applied, with anisakid nematode larvae and metacestodes being the parasite taxa most frequently used. Following a brief insight into the importance of accurate parasite identification, the population studies that have used parasites as biological tags for marine fishes and cephalopods are reviewed, including comments on the dicyemid mesozoans. The advancement of molecular genetic techniques is discussed in regards to the new ways parasite genetic data can be incorporated into population structure studies, alongside host population genetic analyses, followed by an update on the guidelines for selecting a parasite species as a reliable tag candidate. As multiple techniques and methods can be used to assess the population structure of marine organisms (e.g. artificial tags, phenotypic characters, biometrics, life history, genetics, otolith microchemistry and parasitological data), we conclude by commenting on a holistic approach to allow for a deeper insight into population structuring.
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Affiliation(s)
- Sarah R Catalano
- Marine Parasitology Laboratory, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia ; Southern Seas Ecology Laboratories, University of Adelaide, Adelaide, SA 5005, Australia ; Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ian D Whittington
- Marine Parasitology Laboratory, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia ; Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, SA 5005, Australia ; Parasitology Section, South Australian Museum, Adelaide, SA 5000, Australia
| | - Stephen C Donnellan
- Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, SA 5005, Australia ; Evolutionary Biology Unit, South Australian Museum, Adelaide, SA 5000, Australia
| | - Bronwyn M Gillanders
- Southern Seas Ecology Laboratories, University of Adelaide, Adelaide, SA 5005, Australia ; Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
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Underwood JN, Wilson SK, Ludgerus L, Evans RD. Integrating connectivity science and spatial conservation management of coral reefs in north-west Australia. J Nat Conserv 2013. [DOI: 10.1016/j.jnc.2012.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pavesi L, Tiedemann R, De Matthaeis E, Ketmaier V. Genetic connectivity between land and sea: the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea. Front Zool 2013; 10:21. [PMID: 23618554 PMCID: PMC3640956 DOI: 10.1186/1742-9994-10-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/03/2013] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces. RESULTS Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set. CONCLUSIONS We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.
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Affiliation(s)
- Laura Pavesi
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, D-14476, Germany.
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Coscia I, Robins PE, Porter JS, Malham SK, Ironside JE. Modelled larval dispersal and measured gene flow: seascape genetics of the common cockle Cerastoderma edule in the southern Irish Sea. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0404-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nuclear and mitochondrial markers reveal evidence for genetically segregated cryptic speciation in giant Pacific octopuses from Prince William Sound, Alaska. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0392-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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DiBattista JD, Rocha LA, Craig MT, Feldheim KA, Bowen BW. Phylogeography of two closely related Indo-Pacific butterflyfishes reveals divergent evolutionary histories and discordant results from mtDNA and microsatellites. ACTA ACUST UNITED AC 2012; 103:617-29. [PMID: 22888133 DOI: 10.1093/jhered/ess056] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Marine biogeographic barriers can have unpredictable consequences, even among closely related species. To resolve phylogeographic patterns for Indo-Pacific reef fauna, we conducted range-wide surveys of sister species, the scrawled butterflyfish (Chaetodon meyeri; N = 134) and the ornate butterflyfish (Chaetodon ornatissimus; N = 296), using mitochondrial DNA cytochrome b sequences and 10 microsatellite loci. The former is distributed primarily in the Indian Ocean but also extends to the Line Islands in the Central Pacific, whereas the latter is distributed primarily in the Central-West Pacific (including Hawaii and French Polynesia) but extends to the eastern margin of the Indian Ocean. Analyses of molecular variance and Bayesian STRUCTURE results revealed 1 range-wide group for C. meyeri and 3 groups for C. ornatissimus: 1) eastern Indian Ocean and western Pacific, 2) Central Pacific, and 3) Hawaii. Estimates of the last population expansion were much more recent for C. meyeri (61 500 to 95 000 years) versus C. ornatissimus (184 700 to 286 300 years). Despite similarities in ecology, morphology, life history, and a broadly overlapping distribution, these sister species have divergent patterns of dispersal and corresponding evolutionary history. The mtDNA and microsatellite markers did not provide concordant results within 1 of our study species (C. meyeri), or in 7 out of 12 other cases of marine fishes in the published literature. This discordance renews caution in relying on one or a few markers for reconstructing historical demography.
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Coscia I, Vogiatzi E, Kotoulas G, Tsigenopoulos CS, Mariani S. Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic. Heredity (Edinb) 2012; 108:537-46. [PMID: 22126850 PMCID: PMC3331784 DOI: 10.1038/hdy.2011.120] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 10/17/2011] [Accepted: 10/27/2011] [Indexed: 11/08/2022] Open
Abstract
Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here, we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 expressed sequence tag-linked markers, as well as a portion of the mitochondrial DNA (mtDNA) control region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, although the potential 'surfing effect' of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.
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Affiliation(s)
- I Coscia
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
| | - E Vogiatzi
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Genetics (IMBG), Crete, Greece
- Department of Molecular Biology and Genetics, Democritian University of Thrace, Alexandroupolis, Greece
| | - G Kotoulas
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Genetics (IMBG), Crete, Greece
| | - C S Tsigenopoulos
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Genetics (IMBG), Crete, Greece
| | - S Mariani
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
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SALA-BOZANO MARIA, VAN OOSTERHOUT COCK, MARIANI STEFANO. Impact of a mouth parasite in a marine fish differs between geographical areas. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01838.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Phylogeographic patterns of decapod crustaceans at the Atlantic-Mediterranean transition. Mol Phylogenet Evol 2011; 62:664-72. [PMID: 22138160 DOI: 10.1016/j.ympev.2011.11.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 09/23/2011] [Accepted: 11/14/2011] [Indexed: 11/21/2022]
Abstract
Comparative multispecies studies allow contrasting the effect of past and present oceanographic processes on phylogeographic patterns. In the present study, a fragment of the COI gene was analyzed in seven decapod crustacean species from five families and with different bathymetric distributions. A total of 769 individuals were sampled along the Atlantic-Mediterranean transition area in order to test the effect of three putative barriers to gene flow: Strait of Gibraltar, Almeria-Oran Front and Ibiza Channel. A significant effect of the Strait of Gibraltar was found in the crabs Liocarcinus depurator and Macropipus tuberculatus. The Ibiza Channel had a significant effect for L. depurator. However, the Almeria-Oran front was not found to have a significant effect on any of the studied species. Higher levels of population structure were found in shallow-water species, although the number of species sampled should be increased to obtain a conclusive pattern. The haplotypes within the different species coalesced at times that could be related with past climatic events occurring before, during and after the last glacial maximum. Given the large diversity of phylogeographic patterns obtained within decapods, it is concluded that both historical and contemporary processes (marine current patterns, bathymetry and life-history traits) shape the phylogeographic patterns of these crustaceans.
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Schunter C, Carreras-Carbonell J, Macpherson E, Tintoré J, Vidal-Vijande E, Pascual A, Guidetti P, Pascual M. Matching genetics with oceanography: directional gene flow in a Mediterranean fish species. Mol Ecol 2011; 20:5167-81. [PMID: 22097887 DOI: 10.1111/j.1365-294x.2011.05355.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of marine organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional gene flow on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts.
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Affiliation(s)
- C Schunter
- Centre d'Estudis Avançats de Blanes-CSIC, Car Acc Cala St Francesc 14, Blanes, 17300 Girona, Spain
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COSCIA ILARIA, MARIANI STEFANO. Phylogeography and population structure of European sea bass in the north-east Atlantic. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01712.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Baldwin RE, Rew MB, Johansson ML, Banks MA, Jacobson KC. Population Structure of Three Species of Anisakis Nematodes Recovered From Pacific Sardines (Sardinops sagax) Distributed Throughout the California Current System. J Parasitol 2011; 97:545-54. [DOI: 10.1645/ge-2690.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mokhtar-Jamaï K, Pascual M, Ledoux JB, Coma R, Féral JP, Garrabou J, Aurelle D. From global to local genetic structuring in the red gorgonian Paramuricea clavata: the interplay between oceanographic conditions and limited larval dispersal. Mol Ecol 2011; 20:3291-305. [PMID: 21762434 DOI: 10.1111/j.1365-294x.2011.05176.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Defining the scale of connectivity among marine populations and identifying the barriers to gene flow are tasks of fundamental importance for understanding the genetic structure of populations and for the design of marine reserves. Here, we investigated the population genetic structure at three spatial scales of the red gorgonian Paramuricea clavata (Cnidaria, Octocorallia), a key species dwelling in the coralligenous assemblages of the Mediterranean Sea. Colonies of P. clavata were collected from 39 locations across the Mediterranean Sea from Morocco to Turkey and analysed using microsatellite loci. Within three regions (Medes, Marseille and North Corsica), sampling was obtained from multiple locations and at different depths. Three different approaches (measures of genetic differentiation, Bayesian clustering and spatially explicit maximum-difference algorithm) were used to determine the pattern of genetic structure. We identified genetic breaks in the spatial distribution of genetic diversity, which were concordant with oceanographic conditions in the Mediterranean Sea. We revealed a high level of genetic differentiation among populations and a pattern of isolation by distance across the studied area and within the three regions, underlining short effective larval dispersal in this species. We observed genetic differentiation among populations in the same locality dwelling at different depths, which may be explained by local oceanographic conditions and which may allow a process of local adaptation of the populations to their environment. We discuss the implications of our results for the conservation of the species, which is exposed to various threats.
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Affiliation(s)
- K Mokhtar-Jamaï
- Aix-Marseille Université, CNRS UMR 6540 DIMAR, Centre d'Océanologie de Marseille, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007 Marseille, France.
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Shen KN, Jamandre BW, Hsu CC, Tzeng WN, Durand JD. Plio-Pleistocene sea level and temperature fluctuations in the northwestern Pacific promoted speciation in the globally-distributed flathead mullet Mugil cephalus. BMC Evol Biol 2011; 11:83. [PMID: 21450111 PMCID: PMC3079632 DOI: 10.1186/1471-2148-11-83] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 03/31/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The study of speciation in the marine realm is challenging because of the apparent absence of physical barriers to dispersal, which are one of the main drivers of genetic diversity. Although phylogeographic studies using mitochondrial DNA (mtDNA) information often reveal significant genetic heterogeneity within marine species, the evolutionary significance of such diversity is difficult to interpret with these markers. In the northwestern (NW) Pacific, several studies have emphasised the potential importance of sea-level regression during the most recent glaciations as a driver of genetic diversity in marine species. These studies have failed, however, to determine whether the period of isolation was long enough for divergence to attain speciation. Among these marine species, the cosmopolitan estuarine-dependent fish Mugil cephalus represents an interesting case study. Several divergent allopatric mtDNA lineages have been described in this species worldwide, and three occur in sympatry in the NW Pacific. RESULTS Ten nuclear microsatellites were surveyed to estimate the level of genetic isolation of these lineages and determine the role of sea-level fluctuation in the evolution of NW Pacific M. cephalus. Three cryptic species of M. cephalus were identified within this region (NWP1, 2 and 3) using an assignment test on the microsatellite data. Each species corresponds with one of the three mtDNA lineages in the COI phylogenetic tree. NWP3 is the most divergent species, with a distribution range that suggests tropical affinities, while NWP1, with a northward distribution from Taiwan to Russia, is a temperate species. NWP2 is distributed along the warm Kuroshio Current. The divergence of NWP1 from NWP2 dates back to the Pleistocene epoch and probably corresponds to the separation of the Japan and China Seas when sea levels dropped. Despite their subsequent range expansion since this period of glaciation, no gene flow was observed among these three lineages, indicating that speciation has been achieved. CONCLUSIONS This study successfully identified three cryptic species in M. cephalus inhabiting the NW Pacific, using a combination of microsatellites and mitochondrial genetic markers. The current genetic architecture of the M. cephalus species complex in the NW Pacific is the result of a complex interaction of contemporary processes and historical events. Sea level and temperature fluctuations during Plio-Pleistocene epochs probably played a major role in creating the marine species diversity of the NW Pacific that is found today.
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Affiliation(s)
- Kang-Ning Shen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan, China.
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Humphries EM, Winker K. Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds. Mol Ecol 2010; 20:573-83. [PMID: 21199027 DOI: 10.1111/j.1365-294x.2010.04965.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically stratified phenotypic levels of differentiation (populations, subspecies and species) among nine avian lineages using paired, trans-Beringian samples from three lineages each in three orders (Anseriformes, Charadriiformes, and Passeriformes) to test this assumption. Using mitochondrial DNA sequence data and nuclear genomic data (amplified fragment length polymorphisms), we found a lack of concordance between these two genomes in their respective estimates of divergence and little or no relationship between phenotype (taxonomic relatedness) and genetic differentiation between taxon pairs. There are several possible reasons for the discord observed (e.g. selection on one of the genomes or perhaps lineage sorting), but the implications are that genetic estimates of lineage divergence may not be correlated with estimates from other parts of the genome, are not well correlated with the speciation process and are thus not reliable indicators of species limits.
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Affiliation(s)
- Elizabeth M Humphries
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK 99775, USA
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Yudkovski Y, Ramšak A, Ausland M, Tom M. Potential of the hepatic transcriptome expression profile of the striped seabream (Lithognathus mormyrus) as an environmental biomarker. Biomarkers 2010; 15:625-38. [PMID: 20846022 DOI: 10.3109/1354750x.2010.510579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The potential of the hepatic transcriptome expression profile evaluated in a sentinel feral fish to serve as an environmental biomarker was examined. Expression profiles of Lithognathus mormyrus individuals were exhibited using cDNA microarray and were related to the set of exposure conditions at their sites and dates of collection. Expression profiles of individual fish were reasonably clustered according to the fish samples. In addition, several sample-specific gene clusters were determined, designated sample gene signatures. The selection procedure for future optimal reference RNA is discussed. The relationship between transcriptome expression and fish samples indicated a potential for using the former as an environmental biomarker.
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Affiliation(s)
- Yana Yudkovski
- Israel Oceanographic and Limnological Research, Haifa, Israel
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