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Vijayan N, McAnulty SJ, Sanchez G, Jolly J, Ikeda Y, Nishiguchi MK, Réveillac E, Gestal C, Spady BL, Li DH, Burford BP, Kerwin AH, Nyholm SV. Evolutionary history influences the microbiomes of a female symbiotic reproductive organ in cephalopods. Appl Environ Microbiol 2024; 90:e0099023. [PMID: 38315021 PMCID: PMC10952459 DOI: 10.1128/aem.00990-23] [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: 06/14/2023] [Accepted: 12/09/2023] [Indexed: 02/07/2024] Open
Abstract
Many female squids and cuttlefishes have a symbiotic reproductive organ called the accessory nidamental gland (ANG) that hosts a bacterial consortium involved with egg defense against pathogens and fouling organisms. While the ANG is found in multiple cephalopod families, little is known about the global microbial diversity of these ANG bacterial symbionts. We used 16S rRNA gene community analysis to characterize the ANG microbiome from different cephalopod species and assess the relationship between host and symbiont phylogenies. The ANG microbiome of 11 species of cephalopods from four families (superorder: Decapodiformes) that span seven geographic locations was characterized. Bacteria of class Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were found in all species, yet analysis of amplicon sequence variants by multiple distance metrics revealed a significant difference between ANG microbiomes of cephalopod families (weighted/unweighted UniFrac, Bray-Curtis, P = 0.001). Despite being collected from widely disparate geographic locations, members of the family Sepiolidae (bobtail squid) shared many bacterial taxa including (~50%) Opitutae (Verrucomicrobia) and Ruegeria (Alphaproteobacteria) species. Furthermore, we tested for phylosymbiosis and found a positive correlation between host phylogenetic distance and bacterial community dissimilarity (Mantel test r = 0.7). These data suggest that closely related sepiolids select for distinct symbionts from similar bacterial taxa. Overall, the ANGs of different cephalopod species harbor distinct microbiomes and thus offer a diverse symbiont community to explore antimicrobial activity and other functional roles in host fitness.IMPORTANCEMany aquatic organisms recruit microbial symbionts from the environment that provide a variety of functions, including defense from pathogens. Some female cephalopods (squids, bobtail squids, and cuttlefish) have a reproductive organ called the accessory nidamental gland (ANG) that contains a bacterial consortium that protects eggs from pathogens. Despite the wide distribution of these cephalopods, whether they share similar microbiomes is unknown. Here, we studied the microbial diversity of the ANG in 11 species of cephalopods distributed over a broad geographic range and representing 15-120 million years of host divergence. The ANG microbiomes shared some bacterial taxa, but each cephalopod species had unique symbiotic members. Additionally, analysis of host-symbiont phylogenies suggests that the evolutionary histories of the partners have been important in shaping the ANG microbiome. This study advances our knowledge of cephalopod-bacteria relationships and provides a foundation to explore defensive symbionts in other systems.
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Affiliation(s)
- Nidhi Vijayan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sarah J. McAnulty
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
- Graduate School of Integrated Science for Life, Hiroshima University, Hiroshima, Japan
| | - Jeffrey Jolly
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Yuzuru Ikeda
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of Ryukyus, Ryukyus, Japan
| | - Michele K. Nishiguchi
- Department of Molecular and Cell Biology, University of California, Merced, California, USA
| | - Elodie Réveillac
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS–La Rochelle Université, La Rochelle, France
| | - Camino Gestal
- Institute of Marine Research (IIM), CSIC, Vigo, Spain
| | - Blake L. Spady
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- U.S. National Oceanic and Atmospheric Administration, National Environmental Satellite Data and Information Service, Center for Satellite Applications and Research, Coral Reef Watch, College Park, Maryland, USA
| | - Diana H. Li
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, USA
| | - Benjamin P. Burford
- Institute of Marine Sciences, University of California, affiliated with the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, California, USA
| | - Allison H. Kerwin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Biology, McDaniel College, Westminster, Maryland, USA
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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2
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Göpel A, Oesterwind D, Barrett C, Cannas R, Caparro LS, Carbonara P, Donnaloia M, Follesa MC, Larivain A, Laptikhovsky V, Lefkaditou E, Robin JP, Santos MB, Sobrino I, Valeiras J, Valls M, Vieira HC, Wieland K, Bastrop R. Phylogeography of the veined squid, Loligo forbesii, in European waters. Sci Rep 2022; 12:7817. [PMID: 35551472 PMCID: PMC9098544 DOI: 10.1038/s41598-022-11530-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/21/2022] [Indexed: 11/10/2022] Open
Abstract
The veined squid, Loligo forbesii Steenstrup, 1856, occurs at the European Shelf areas including the Azores and represents a valuable resource for the European commercial fishery in the North East Atlantic. However, very little is known about its population structure and phylogeography. This lack of knowledge also impedes the development of sustainable fishery management for this species. The present study combined the use of two types of markers that retrieve patterns of gene flow in different time spans; the analysis of 16 nuclear microsatellites and sequencing of the mitochondrial cytochrome oxidase subunit I (COI). Whereas the high mutation rate of microsatellites allows the description of recent patterns of connectivity in species, the lower mutation rate of COI provides phylogeographic patterns on a longer timescale. A total of 347 individuals of L. forbesii were investigated from nearly the entire distribution range of the species, including the North East Atlantic Shelf, the Azores and the Mediterranean. Individuals from the Western and Eastern Mediterranean Sea have never been included in a genetic study before. We were able to analyse COI sequences from all 12 sampling areas and define three clades of L. forbesii. Due to our large sampling area, we are presenting 13 COI-haplotypes that were previously unknown. The microsatellite analysis does not include the Azores but three main clades could be identified at the remaining 11 sampling sites. Low FST values indicate gene flow over large geographical distances. However, the genetically significant differences and an additional slight grouping in the microsatellite structure reveal that geographical barriers seem to influence the population structure and reduce gene flow. Furthermore, both markers provide strong evidence that the observed phylogeographic pattern reflects the geographical history of the Azores and the Mediterranean Sea.
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Affiliation(s)
- Anika Göpel
- Thünen Institute of Baltic Sea Fisheries, Alter Hafen Süd 2, 18069, Rostock, Germany.,Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Daniel Oesterwind
- Thünen Institute of Baltic Sea Fisheries, Alter Hafen Süd 2, 18069, Rostock, Germany.
| | | | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Luis Silva Caparro
- Centro Oceanográfico de Cádiz, Instituto Español de Oceanografía, Puerto Pesquero, Muelle de Levante S/N, 11006, Cádiz, Spain
| | | | | | | | - Angela Larivain
- University of Caen Normandy, CS 14032, 14032, Caen Cedex 05, France
| | | | - Evgenia Lefkaditou
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 576 SideRD Vouliagmenis Ave, 16452, Athens, Greece
| | - Jean-Paul Robin
- University of Caen Normandy, CS 14032, 14032, Caen Cedex 05, France
| | - Maria Begoña Santos
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO), Subida a Radio Faro, 50, 36390, Vigo, Spain
| | - Ignacio Sobrino
- Centro Oceanográfico de Cádiz, Instituto Español de Oceanografía, Puerto Pesquero, Muelle de Levante S/N, 11006, Cádiz, Spain
| | - Julio Valeiras
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO), Subida a Radio Faro, 50, 36390, Vigo, Spain
| | - Maria Valls
- Centre Oceanográfic de les Balears s/n, Instituto Español de Oceanografía (IEO), 07015, Palma, Spain
| | - Hugo C Vieira
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Kai Wieland
- Technical University of Denmark, National Institute of Aquatic Resources, Nordsøen Forskerpark, Willemoesvej 2, 9850, Hirtshals, Denmark
| | - Ralf Bastrop
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
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3
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Çetin C, Furman A, Kalkan E, Bilgin R. Mitonuclear genetic patterns of divergence in the marbled crab, Pachygrapsus marmoratus (Fabricius, 1787) along the Turkish seas. PLoS One 2022; 17:e0266506. [PMID: 35381029 PMCID: PMC8982882 DOI: 10.1371/journal.pone.0266506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 03/22/2022] [Indexed: 12/03/2022] Open
Abstract
Biogeographical transition zones present good opportunities for studying the effect of the past ice ages on genetic structure of species because secondary contact zones of post-glacial lineages can be formed. In this study, we investigated the population genetic structure of the marbled rock crab, Pachygrapsus marmoratus along the coasts of Turkey. We genotyped 334 individuals from the Black Sea, the Turkish Straits System (TSS), the Aegean, and the Eastern Mediterranean basins. In order to reveal its evolutionary history and its population connectivity, we used mitochondrial CO1 region and five microsatellite loci. CO1 analyzes also included 610 additional samples from Genbank, which covered most of its distribution range. Both microsatellites and mtDNA showed decreased diversity in sampling sites of the TSS and the Black Sea as compared to those along the Aegean and the Levantine coasts. There is an especially strong geographical pattern in distributions of haplotypes in mtDNA, most probably as a result of genetic drift in the Black Sea and the Sea of Marmara (SoM). Microsatellite data analyses revealed two genetically distinct clusters of P. marmoratus (clusters C and M). While individuals belonging to cluster C are present in all the sampling locations, those belonging to cluster M are only detected along the Mediterranean coasts including the Aegean and the Levantine basins. These clusters shared similar haplotypes in the Mediterranean. Haplotypes of two sympatric clusters could be similar due to incomplete lineage sorting of ancestral polymorphisms. In order to retrieve the complex demographic history and to investigate evolutionary processes resulting in sympatric clusters in the Aegean Sea and the Levantine basin, mitochondrial markers with faster mutation rates than CO1 and/or SNP data will be useful.
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Affiliation(s)
- Cansu Çetin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- * E-mail:
| | - Andrzej Furman
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey
| | - Evrim Kalkan
- Institute of Marine Sciences, Middle East Technical University, Erdemli-Mersin, Turkey
| | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey
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4
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David Wells RJ, Rooker JR, Addis P, Arrizabalaga H, Baptista M, Bearzi G, Fraile I, Lacoue-Labarthe T, Meese EN, Megalofonou P, Rosa R, Sobrino I, Sykes AV, Villanueva R. Regional patterns of δ 13C and δ 15N for European common cuttlefish ( Sepia officinalis) throughout the Northeast Atlantic Ocean and Mediterranean Sea. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210345. [PMID: 34540247 PMCID: PMC8437227 DOI: 10.1098/rsos.210345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Stable isotope compositions of carbon and nitrogen (expressed as δ 13C and δ 15N) from the European common cuttlefish (Sepia officinalis) were measured in order to evaluate the utility of using these natural tracers throughout the Northeast Atlantic Ocean and Mediterranean Sea (NEAO-MS). Mantle tissue was obtained from S. officinalis collected from 11 sampling locations spanning a wide geographical coverage in the NEAO-MS. Significant differences of both δ 13C and δ 15N values were found among S. officinalis samples relative to sampling location. δ 13C values did not show any discernable spatial trends; however, a distinct pattern of lower δ 15N values in the Mediterranean Sea relative to the NEAO existed. Mean δ 15N values of S. officinalis in the Mediterranean Sea averaged 2.5‰ lower than conspecifics collected in the NEAO and showed a decreasing eastward trend within the Mediterranean Sea with the lowest values in the most eastern sampling locations. Results suggest δ 15N may serve as a useful natural tracer for studies on the population structure of S. officinalis as well as other marine organisms throughout the NEAO-MS.
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Affiliation(s)
- R. J. David Wells
- Department of Marine Biology, Texas A&M University, 1001 Texas Clipper Road, Galveston, TX 77553, USA
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| | - Jay R. Rooker
- Department of Marine Biology, Texas A&M University, 1001 Texas Clipper Road, Galveston, TX 77553, USA
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77843, USA
| | - Piero Addis
- Department of Environmental and Life Science, University of Cagliari, Via Fiorelli 1, 09126 Cagliari, Italy
| | - Haritz Arrizabalaga
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia-Portualdea z/g, 20110 Pasaia – Gipuzkoa, Spain
| | - Miguel Baptista
- Marine and Environmental Sciences Centre, Laboratorio Maritimo da Guia, Faculdade de Ciencias, Universidade de Lisboa, Avenida Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
| | - Giovanni Bearzi
- Dolphin Biology and Conservation, Cordenons, Pordenone, Italy
| | - Igaratza Fraile
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia-Portualdea z/g, 20110 Pasaia – Gipuzkoa, Spain
| | - Thomas Lacoue-Labarthe
- LIttoral Environnement et Sociétés (LIENSs) – UMR 7266 Bâtiment ILE, 2, rue Olympe de Gouges, 17000 La Rochelle, France
| | - Emily N. Meese
- Department of Marine Biology, Texas A&M University, 1001 Texas Clipper Road, Galveston, TX 77553, USA
| | - Persefoni Megalofonou
- Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Rui Rosa
- Marine and Environmental Sciences Centre, Laboratorio Maritimo da Guia, Faculdade de Ciencias, Universidade de Lisboa, Avenida Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
| | - Ignacio Sobrino
- Instituto Español de Oceanografía, Puerto Pesquero s/n, 11006, Cádiz, Spain
| | - Antonio V. Sykes
- Center of Marine Sciences, Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
| | - Roger Villanueva
- Institut de Ciències del Mar (CSIC), Passeig Maritim, 37-49, 08003, Barcelona, Spain
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5
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Pavičić M, Žužul I, Matić-Skoko S, Triantafyllidis A, Grati F, Durieux EDH, Celić I, Šegvić-Bubić T. Population Genetic Structure and Connectivity of the European Lobster Homarus gammarus in the Adriatic and Mediterranean Seas. Front Genet 2020; 11:576023. [PMID: 33365046 PMCID: PMC7750201 DOI: 10.3389/fgene.2020.576023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
Highly selective fishing has the potential to permanently change the characteristics within a population and could drive the decline of genetic diversity. European lobster is an intensively fished crustacean species in the Adriatic Sea which reaches high market value. Since knowledge of population structure and dynamics is important for effective fisheries management, in this study, we used 14 neutral microsatellites loci and partial mitochondrial COI region sequencing to explore population connectivity and genetic structure by comparing samples from the Adriatic Sea and the adjacent basins of the Mediterranean Sea. The obtained results suggest that neutral genetic diversity has not been significantly affected by decrease in population size due to overfishing, habitat degradation and other anthropogenic activities. Global genetic differentiation across all populations was low (F ST = 0.0062). Populations from the Adriatic Sea were panmictic, while genetic differentiation was found among populations from different Mediterranean basins. Observed gene flow for European lobster suggest that populations in the north eastern Adriatic act as a source for surrounding areas, emphasizing the need to protect these populations by establishing interconnected MPAs that will be beneficial for both fisheries and conservation management.
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Affiliation(s)
- Mišo Pavičić
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Iva Žužul
- Institute of Oceanography and Fisheries, Split, Croatia
| | | | | | - Fabio Grati
- Institute for Biological Resources and Marine Biotechnologies (IRBIM), National Research Council (CNR), Ancona, Italy
| | - Eric D. H. Durieux
- UMR CNRS 6134 Sciences Pour l’Environnement, Università di Corsica Pasquale Paoli, Corte, France
- UMS CNRS 3514 STELLA MARE, Università di Corsica Pasquale Paoli, Biguglia, France
| | - Igor Celić
- National Institute of Oceanography and Applied Geophysics – OGS, Trieste, Italy
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6
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González-Castellano I, Pons J, González-Ortegón E, Martínez-Lage A. Mitogenome phylogenetics in the genus Palaemon (Crustacea: Decapoda) sheds light on species crypticism in the rockpool shrimp P. elegans. PLoS One 2020; 15:e0237037. [PMID: 32810189 PMCID: PMC7444591 DOI: 10.1371/journal.pone.0237037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
The genus Palaemon comprises worldwide marine and freshwater shrimps and prawns, and some of them are ecologically or commercially important species. Palaemon is not currently a monophyletic group, so phylogenetics and systematics are constantly changing. Species crypticism has been pointed out in several Palaemon species, being the clearest evidence in the European rockpool shrimp P. elegans. Here we sequenced and described seven European Palaemon mitochondrial genomes. The mitochondrial protein-coding genes were used, along with those of three other Palaemon species, to perform mitogenome phylogenetic analyses to clarify the evolutionary relationships within the genus, and particularly to shed light on the cryptic species found within P. elegans. The Messinian Salinity Crisis (5.3-5.9 Ma, late Miocene) was proposed to be the origin of this cryptic species and it was used as aged constraint for calibration analysis. We provide the largest and the first time-calibrated mitogenome phylogeny of the genus Palaemon and mitogenome substitution rate was estimated (1.59% per million years) in Decapoda for the first time. Our results highlighted the need for future systematics changes in Palaemon and crypticism in P. elegans was confirmed. Mitochondrial genome and cox1 (1.41%) substitution rate estimates matched those published elsewhere, arguing that the Messinian Salinity Crisis was a plausible event driving the split between P. elegans and its cryptic species. Molecular dating suggested that Pleistocene glaciations were likely involved in the differentiation between the Atlantic and Mediterranean populations of P. elegans. On the contrary, the divergence between the Atlantic and Mediterranean populations of the common littoral shrimp P. serratus was greater and dated to be much older (4.5-12.3 Ma, Plio-Miocene), so we considered that they could represent two separated species. Therefore, species crypticism in the genus Palaemon seems to be a common phenomenon.
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Affiliation(s)
- Inés González-Castellano
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
| | - Joan Pons
- Instituto Mediterráneo de Estudios Avanzados (IMEDEA), Consejo Superior de Investigaciones Científicas (CSIC) and Universitat de les Illes Balears, Esporles, Spain
| | - Enrique González-Ortegón
- Instituto de Ciencias Marinas de Andalucía (ICMAN), Consejo Superior de Investigaciones Científicas (CSIC), Puerto Real, Spain
| | - Andrés Martínez-Lage
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
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7
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A new framework for growth curve fitting based on the von Bertalanffy Growth Function. Sci Rep 2020; 10:7953. [PMID: 32409646 PMCID: PMC7224396 DOI: 10.1038/s41598-020-64839-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/17/2020] [Indexed: 11/17/2022] Open
Abstract
All organisms grow. Numerous growth functions have been applied to a wide taxonomic range of organisms, yet some of these models have poor fits to empirical data and lack of flexibility in capturing variation in growth rate. We propose a new VBGF framework that broadens the applicability and increases flexibility of fitting growth curves. This framework offers a curve-fitting procedure for five parameterisations of the VBGF: these allow for different body-size scaling exponents for anabolism (biosynthesis potential), besides the commonly assumed 2/3 power scaling, and allow for supra-exponential growth, which is at times observed. This procedure is applied to twelve species of diverse aquatic invertebrates, including both pelagic and benthic organisms. We reveal widespread variation in the body-size scaling of biosynthesis potential and consequently growth rate, ranging from isomorphic to supra-exponential growth. This curve-fitting methodology offers improved growth predictions and applies the VBGF to a wider range of taxa that exhibit variation in the scaling of biosynthesis potential. Applying this framework results in reliable growth predictions that are important for assessing individual growth, population production and ecosystem functioning, including in the assessment of sustainability of fisheries and aquaculture.
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8
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Quinteiro J, Rodríguez-Castro J, Rey-Méndez M, González-Henríquez N. Phylogeography of the insular populations of common octopus, Octopus vulgaris Cuvier, 1797, in the Atlantic Macaronesia. PLoS One 2020; 15:e0230294. [PMID: 32191765 PMCID: PMC7082011 DOI: 10.1371/journal.pone.0230294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/25/2020] [Indexed: 11/20/2022] Open
Abstract
Exploited, understudied populations of the common octopus, Octopus vulgaris Cuvier, 1797, occur in the northeastern Atlantic (NEA) throughout Macaronesia, comprising the Azores, Madeira and Canaries, and also the Cabo Verde archipelago. This octopus species, found from the intertidal to shallow continental-shelf waters, is largely sedentary, and the subject of intense, frequently unregulated fishing effort. We infer connectivity among insular populations of this octopus. Mitochondrial control region and COX1 sequence datasets reveal two highly divergent haplogroups (α and β) at similar frequencies, with opposing clinal distributions along the sampled latitudinal range. Haplogroups have different demographic and phylogeographic patterns, with origins related to the two last glacial maxima. FST values suggest a significant differentiation for most pairwise comparisons, including insular and continental samples, from the Galicia and Morocco coasts, with the exception of pairwise comparisons for samples from Madeira and the Canaries populations. Results indicate the existence of genetically differentiated octopus populations throughout the NEA. This emphasizes the importance of regulations by autonomous regional governments of the Azores, Madeira and the Canaries, for appropriate management of insular octopus stocks.
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Affiliation(s)
- Javier Quinteiro
- Molecular Systematics Laboratory, Department of Biochemistry and Molecular Biology, University Santiago de Compostela, A Coruña, Galicia, Spain
- * E-mail:
| | - Jorge Rodríguez-Castro
- Molecular Systematics Laboratory, Department of Biochemistry and Molecular Biology, University Santiago de Compostela, A Coruña, Galicia, Spain
| | - Manuel Rey-Méndez
- Molecular Systematics Laboratory, Department of Biochemistry and Molecular Biology, University Santiago de Compostela, A Coruña, Galicia, Spain
| | - Nieves González-Henríquez
- BIOMOL Laboratory, Department of Biology, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
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9
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Xiong G, Wang XQ, Zhou XW, Zeng D, Chen ZN, Wang P, Kang L. Genetic variation in the Chinese soft-shell turtles ( Pelodiscus spp.) revealed by sequences of mitochondrial Cytb gene. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:874-879. [PMID: 31766905 DOI: 10.1080/24701394.2019.1693551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Genetic diversity is an important component of biodiversity and investigating and protecting the wild genetic diversity of species has always been an important research topic in conservation biology. Due to habitat destruction and over catching, wild Chinese soft-shell turtles (Pelodiscus spp.) have been severely damaged, resulting in the species being listed on the IUCN Red List of Threatened Species in 2000. However, only few studies with contradictory results on the genetic diversity of Pelodiscus turtles have been reported. To investigate the genetic diversity and population structure of Pelodiscus turtles, 123 specimens were collected from five localities in East Asia, and their genetic variation was analyzed on the basis of a 922-bp partial sequence of the mitochondrial cytb gene. Forty-nine polymorphic sites were detected, revealing 56 haplotypes. A pattern of high haplotype diversity (Hd = 0.994) and nucleotide diversity (π = 0.01655) was found in the examined range. A maximum likelihood phylogenetic tree and median-joining network analyses indicated that the Pelodiscus turtles divided in four populations throughout East Asia, and the Pelodiscus turtles probably originate from the Yangtze River and was introduced to Yellow River, Taiwan, and Japan through Xijiang River. These results served a helpful resource for conservation of Pelodiscus turtles.
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Affiliation(s)
- Gang Xiong
- Hunan Biological and Electromechanical Polytechnic, Changsha, China
| | - Xiao-Qing Wang
- College of Animal Science and Technology, Hunan Agriculture University, Changsha, China
| | - Xian-Wen Zhou
- Aquatic Science Extension Station, Xiangxi Autonomous State of Tujia and Miao Minorities, Jishou, China
| | - Dan Zeng
- College of Animal Science and Technology, Hunan Agriculture University, Changsha, China
| | - Zhen-Nian Chen
- College of Animal Science and Technology, Hunan Agriculture University, Changsha, China
| | - Pei Wang
- College of Animal Science and Technology, Hunan Agriculture University, Changsha, China
| | - Li Kang
- Hunan Biological and Electromechanical Polytechnic, Changsha, China
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10
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Population co-divergence in common cuttlefish (Sepia officinalis) and its dicyemid parasite in the Mediterranean Sea. Sci Rep 2019; 9:14300. [PMID: 31586090 PMCID: PMC6778094 DOI: 10.1038/s41598-019-50555-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022] Open
Abstract
Population structure and biogeography of marine organisms are formed by different drivers than in terrestrial organisms. Yet, very little information is available even for common marine organisms and even less for their associated parasites. Here we report the first analysis of population structure of both a cephalopod host (Sepia officinalis) and its dicyemid parasite, based on a homologous molecular marker (cytochrome oxidase I). We show that the population of common cuttlefish in the Mediterranean area is fragmented into subpopulations, with some areas featuring restricted level of gene flow. Amongst the studied areas, Sardinia was genetically the most diverse and Cyprus the most isolated. At a larger scale, across the Mediterranean, the population structure of the parasite shows co-diversification pattern with its host, but a slower rate of diversification. Differences between the two counterparts are more obvious at a finer scale, where parasite populations show increased level of fragmentation and lower local diversities. This discrepancy can be caused by local extinctions and replacements taking place more frequently in the dicyemid populations, due to their parasitic lifestyle.
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Deli T, Kiel C, Schubart CD. Phylogeographic and evolutionary history analyses of the warty crab Eriphia verrucosa (Decapoda, Brachyura, Eriphiidae) unveil genetic imprints of a late Pleistocene vicariant event across the Gibraltar Strait, erased by postglacial expansion and admixture among refugial lineages. BMC Evol Biol 2019; 19:105. [PMID: 31101005 PMCID: PMC6525375 DOI: 10.1186/s12862-019-1423-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/16/2019] [Indexed: 11/17/2022] Open
Abstract
Background The Pleistocene cyclic sea-level fluctuations are thought to have markedly affected the distribution and genetic architecture of Atlanto-Mediterranean biota. Despite the acknowledged key role played by these historical events in shaping population genetic structure of marine species, little is still known about the processes involved in shaping the spatial distribution of genetic variation within intertidal species. We intended in this study to reconstruct the phylogeography of a common and widely distributed coastal species across the East Atlantic and Mediterranean Sea (the warty crab Eriphia verrucosa), aiming to unravel potential microevolutionary processes likely involved in shaping its genetic polymorphism. For this purpose, a total of 155 specimens of E. verrucosa from 35 locations across the entire distribution range were analyzed by comparing a 453 basepairs region of the mitochondrial gene cytochrome oxidase subunit 1 (Cox1). Results Our results unveiled the prevalence of high genetic connectivity among East Atlantic and Mediterranean populations, with noticeable genetic distinctiveness of the peripheral population from the Azores. Spatio-temporal patterns of genetic diversification and demographic history allowed retrieving genetic imprints of late Pleistocene vicariant event across the Gibraltar Strait followed by subsequent postglacial expansion events for both the East Atlantic and Mediterranean regions. Integrative evidences from the outcomes of comparison of regional genetic diversification, as well as evolutionary and biogeographic histories reconstructions, support the existence of potential glacial refugia for E. verrucosa in the East Atlantic and western Mediterranean. Our results also revealed low levels of genetic variability along with recent demographic and spatial expansion events for eastern Mediterranean warty crabs, suggesting that the eastern areas within the distribution range of the species might have been recently colonized from putative glacial refugia. Conclusions These findings provide new insights into the phylogeography and evolutionary history of a common but poorly studied Atlanto-Mediterranean decapod species. Specifically, they contribute to the understanding of the impact of historical processes on shaping contemporary population genetic structure and diversity in intertidal marine species. Electronic supplementary material The online version of this article (10.1186/s12862-019-1423-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Temim Deli
- Zoology and Evolutionary Biology, University of Regensburg, D-93040, Regensburg, Germany
| | - Christina Kiel
- Zoology and Evolutionary Biology, University of Regensburg, D-93040, Regensburg, Germany
| | - Christoph D Schubart
- Zoology and Evolutionary Biology, University of Regensburg, D-93040, Regensburg, Germany.
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12
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Riesgo A, Taboada S, Pérez-Portela R, Melis P, Xavier JR, Blasco G, López-Legentil S. Genetic diversity, connectivity and gene flow along the distribution of the emblematic Atlanto-Mediterranean sponge Petrosia ficiformis (Haplosclerida, Demospongiae). BMC Evol Biol 2019; 19:24. [PMID: 30651060 PMCID: PMC6335727 DOI: 10.1186/s12862-018-1343-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/28/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Knowledge about the distribution of the genetic variation of marine species is fundamental to address species conservation and management strategies, especially in scenarios with mass mortalities. In the Mediterranean Sea, Petrosia ficiformis is one of the species most affected by temperature-related diseases. Our study aimed to assess its genetic structure, connectivity, and bottleneck signatures to understand its evolutionary history and to provide information to help design conservation strategies of sessile marine invertebrates. RESULTS We genotyped 280 individuals from 19 locations across the entire distribution range of P. ficiformis in the Atlanto-Mediterranean region at 10 microsatellite loci. High levels of inbreeding were detected in most locations (especially in the Macaronesia and the Western Mediterranean) and bottleneck signatures were only detected in Mediterranean populations, although not coinciding entirely with those with reported die-offs. We detected strong significant population differentiation, with the Atlantic populations being the most genetically isolated, and show that six clusters explained the genetic structure along the distribution range of this sponge. Although we detected a pattern of isolation by distance in P. ficiformis when all locations were analyzed together, stratified Mantel tests revealed that other factors could be playing a more prominent role than isolation by distance. Indeed, we detected a strong effect of oceanographic barriers impeding the gene flow among certain areas, the strongest one being the Almeria-Oran front, hampering gene flow between the Atlantic Ocean and the Mediterranean Sea. Finally, migration and genetic diversity distribution analyses suggest a Mediterranean origin for the species. CONCLUSIONS In our study Petrosia ficiformis showed extreme levels of inbreeding and population differentiation, which could all be linked to the poor swimming abilities of the larva. However, the observed moderate migration patterns are highly difficult to reconcile with such poor larval dispersal, and suggest that, although unlikely, dispersal may also be achieved in the gamete phase. Overall, because of the high genetic diversity in the Eastern Mediterranean and frequent mass mortalities in the Western Mediterranean, we suggest that conservation efforts should be carried out specifically in those areas of the Mediterranean to safeguard the genetic diversity of the species.
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Affiliation(s)
- Ana Riesgo
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Sergi Taboada
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Department of Biology (Zoology), Autonomous University of Madrid, Faculty of Sciences, Cantoblanco, 28049 Madrid, Spain
| | - Rocío Pérez-Portela
- Department of Geology and Biology, Physics and Inorganic Chemistry, King Juan Carlos I University, C/ Tulipán s.n, 28933 Móstoles, Madrid Spain
| | - Paolo Melis
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Joana R. Xavier
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, 4450-208 Matosinhos, Portugal
- Department of Biology, KG Jebsen Centre for Deep-Sea Research, University of Bergen, Thormøhlensgate 53A, 5006 Bergen, Norway
| | - Gema Blasco
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409 USA
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Ferrari A, Tinti F, Bertucci Maresca V, Velonà A, Cannas R, Thasitis I, Costa FO, Follesa MC, Golani D, Hemida F, Helyar SJ, Mancusi C, Mulas A, Serena F, Sion L, Stagioni M, Cariani A. Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses. PeerJ 2018; 6:e5560. [PMID: 30245927 PMCID: PMC6149499 DOI: 10.7717/peerj.5560] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/09/2018] [Indexed: 11/22/2022] Open
Abstract
Background The unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs. Methods The phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses. Results No spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. However, such structuring of skate lineages was not consistent with the separation between Western and Eastern Mediterranean. Sudden demographic expansions occurred synchronously during the upper Pleistocene (40,000–60,000 years ago) in both skates and G. melastomus, likely related to optimal environmental conditions. In contrast, S. canicula experienced a slow and constant increase in population size over the last 350,000 years. Discussion The comparative analysis of phylogeographic and historical demographic patterns for the Mediterranean populations of these elasmobranchs reveals that historical phylogeographic breaks have not had a large impact on their microevolution. We hypothesize that interactions between environmental and ecological/physiological traits may have been the driving force in the microevolution of these demersal elasmobranch species in the Mediterranean rather than oceanographic barriers.
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Affiliation(s)
- Alice Ferrari
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Fausto Tinti
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Victoria Bertucci Maresca
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy.,Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alessandro Velonà
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Rita Cannas
- Department of Life Sciences and Environment, University of Cagliari, Cagliari, Italy
| | - Ioannis Thasitis
- Department of Fisheries and Marine Research, Ministry of Agriculture, Natural Resources and Environment, Nicosia, Cyprus
| | - Filipe Oliveira Costa
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | | | - Daniel Golani
- Department of Evolution, Systematics and Ecology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Farid Hemida
- Ecole Nationale Supérieure des Sciences de la Mer et de Aménagement du Littoral (ENSSMAL), Algiers, Algeria
| | - Sarah J Helyar
- School of Biological Sciences, Institute for Global Food Security, The Queen's University Belfast, Belfast, United Kingdom
| | - Cecilia Mancusi
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | - Antonello Mulas
- Department of Life Sciences and Environment, University of Cagliari, Cagliari, Italy
| | - Fabrizio Serena
- Institute Coastal Marine Environment, Italian National Research Council (CNR-IAMC), Mazara del Vallo, Italy
| | - Letizia Sion
- Department of Biology, University of Bari, Bari, Italy
| | - Marco Stagioni
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Alessia Cariani
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
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14
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Deli T, Kalkan E, Karhan SÜ, Uzunova S, Keikhosravi A, Bilgin R, Schubart CD. Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean. BMC Evol Biol 2018; 18:53. [PMID: 29642852 PMCID: PMC5896055 DOI: 10.1186/s12862-018-1167-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 03/27/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Recently, population genetic studies of Mediterranean marine species highlighted patterns of genetic divergence and phylogeographic breaks, due to the interplay between impacts of Pleistocene climate shifts and contemporary hydrographical barriers. These factors markedly shaped the distribution of marine organisms and their genetic makeup. The present study is part of an ongoing effort to understand the phylogeography and evolutionary history of the highly dispersive Mediterranean green crab, Carcinus aestuarii (Nardo, 1847), across the Mediterranean Sea. Recently, marked divergence between two highly separated haplogroups (genetic types I and II) of C. aestuarii was discerned across the Siculo-Tunisian Strait, suggesting an Early Pleistocene vicariant event. In order to better identify phylogeographic patterns in this species, a total of 263 individuals from 22 Mediterranean locations were analysed by comparing a 587 basepair region of the mitochondrial gene Cox1 (cytochrome oxidase subunit 1). The examined dataset is composed of both newly generated sequences (76) and previously investigated ones (187). RESULTS Our results unveiled the occurrence of a highly divergent haplogroup (genetic type III) in the most north-eastern part of the Mediterranean Sea. Divergence between the most distinct type III and the common ancestor of both types I and II corresponds to the Early Pleistocene and coincides with the historical episode of separation between types I and II. Our results also revealed strong genetic divergence among adjacent regions (separating the Aegean and Marmara seas from the remaining distribution zone) and confirmed a sharp phylogeographic break across the Eastern Mediterranean. The recorded parapatric genetic divergence, with the potential existence of a contact zone between both groups in the Ionian Sea and notable differences in the demographic history, suggest the likely impact of paleoclimatic events, as well as past and contemporary oceanographic processes, in shaping genetic variability of this species. CONCLUSIONS Our findings not only provide further evidence for the complex evolutionary history of the green crab in the Mediterranean Sea, but also stress the importance of investigating peripheral areas in the species' distribution zone in order to fully understand the distribution of genetic diversity and unravel hidden genetic units and local patterns of endemism.
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Affiliation(s)
- Temim Deli
- Laboratory of Genetics, Biodiversity and Enhancement of Bioresources (LR11ES41), University of Monastir, Higher Institute of Biotechnology of Monastir, Av. Tahar Hadded, B.P. 74, 5000, Monastir, Tunisia
| | - Evrim Kalkan
- Middle East Technical University, Institute of Marine Sciences, P.O.Box 28, 33731, Erdemli-Mersin, Turkey
| | | | - Sonya Uzunova
- Institute of Fish Resources - Varna, Agricultural Academy, Primorski, 4 blvd, 9000, Varna, Bulgaria
| | | | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
| | - Christoph D Schubart
- Zoology & Evolutionary Biology, Universität Regensburg, D-93040, Regensburg, Germany.
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15
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Gong J, Zhao R, Deng J, Zhao Y, Zuo J, Huang L, Jing M. Genetic diversity and population structure of penis fish (Urechis unicinctus) based on mitochondrial and nuclear gene markers. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1261-1268. [PMID: 29482423 DOI: 10.1080/24701394.2018.1444039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Urechis unicinctus is distributed only in Bohai Gulf of China and Korean and Japanese coast. The wild populations of this species have sharply declined in China and Japan. We collected 105 samples from six localities of Bohai Gulf and Korea coast, and investigated genetic diversity and population structure with mitochondrial COI, 16S-rRNA and nuclear 28S-rRNA gene fragments. Genetic diversity of U. unicinctus based on COI sequences was still high (Hd: 0.9595, π: 0.0101), however, 28S-rRNA gene sequences showed low level of genetic diversity (Hd: 0.4084, π: 0.0007). Based on COI sequences, FST values between populations ranged from -0.00204 to 0.05210, and 99.12% genetic diversity was contributed by different individuals within population. Both phylogenetic trees and median-joining network did not show clear geographic cluster, haplotypes from different populations were mixed. Our results indicated low level of genetic divergence among different localities of U. unicinctus, and this species should be treated as a whole population among China, Japan and Korea coast during species conservation.
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Affiliation(s)
- Jie Gong
- a School of Life Sciences , Ludong University , Yantai , Shandong , P. R. China
| | - Ruoping Zhao
- b State Key Laboratory of Genetic Resources and Evolution , Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , Yunnan , P. R. China
| | - Jiaheng Deng
- a School of Life Sciences , Ludong University , Yantai , Shandong , P. R. China
| | - Yancui Zhao
- a School of Life Sciences , Ludong University , Yantai , Shandong , P. R. China
| | - Jincheng Zuo
- a School of Life Sciences , Ludong University , Yantai , Shandong , P. R. China
| | - Ling Huang
- a School of Life Sciences , Ludong University , Yantai , Shandong , P. R. China
| | - Meidong Jing
- a School of Life Sciences , Ludong University , Yantai , Shandong , P. R. China
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16
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Marzouk Z, Aurelle D, Said K, Chenuil A. Cryptic lineages and high population genetic structure in the exploited marine snail Hexaplex trunculus (Gastropoda: Muricidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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17
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Pannacciulli FG, Maltagliati F, de Guttry C, Achituv Y. Phylogeography on the rocks: The contribution of current and historical factors in shaping the genetic structure of Chthamalus montagui (Crustacea, Cirripedia). PLoS One 2017; 12:e0178287. [PMID: 28594840 PMCID: PMC5464549 DOI: 10.1371/journal.pone.0178287] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/10/2017] [Indexed: 11/19/2022] Open
Abstract
The model marine broadcast-spawner barnacle Chthamalus montagui was investigated to understand its genetic structure and quantify levels of population divergence, and to make inference on historical demography in terms of time of divergence and changes in population size. We collected specimens from rocky shores of the north-east Atlantic Ocean (4 locations), Mediterranean Sea (8) and Black Sea (1). The 312 sequences 537 bp) of the mitochondrial cytochrome c oxidase I allowed to detect 130 haplotypes. High within-location genetic variability was recorded, with haplotype diversity ranging between h = 0.750 and 0.967. Parameters of genetic divergence, haplotype network and Bayesian assignment analysis were consistent in rejecting the hypothesis of panmixia. C. montagui is genetically structured in three geographically discrete populations, which corresponded to north-eastern Atlantic Ocean, western-central Mediterranean Sea, and Aegean Sea-Black Sea. These populations are separated by two main effective barriers to gene flow located at the Almeria-Oran Front and in correspondence of the Cyclades Islands. According to the 'isolation with migration' model, adjacent population pairs diverged during the early to middle Pleistocene transition, a period in which geological events provoked significant changes in the structure and composition of palaeocommunities. Mismatch distributions, neutrality tests and Bayesian skyline plots showed past population expansions, which started approximately in the Mindel-Riss interglacial, in which ecological conditions were favourable for temperate species and calcium-uptaking marine organisms.
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Affiliation(s)
| | | | - Christian de Guttry
- ENEA—Marine Environment Research Centre, La Spezia, Italy
- Department of Biology, University of Pisa, Pisa, Italy
| | - Yair Achituv
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
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18
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Rico C, Cuesta JA, Drake P, Macpherson E, Bernatchez L, Marie AD. Null alleles are ubiquitous at microsatellite loci in the Wedge Clam ( Donax trunculus). PeerJ 2017; 5:e3188. [PMID: 28439464 PMCID: PMC5398275 DOI: 10.7717/peerj.3188] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/15/2017] [Indexed: 12/17/2022] Open
Abstract
Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.
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Affiliation(s)
- Ciro Rico
- School of Marine Studies, Molecular Analytics Laboratory (MOANA), Faculty of Science Technology and Environment, The University of the South Pacific, Suva, Fiji.,Estación Biológica de Doñana, (EBD, CSIC), Sevilla, Spain
| | - Jose Antonio Cuesta
- Instituto de Ciencias Marinas de Andalucía (ICMAN, CSIC), Puerto Real (Cádiz), Spain
| | - Pilar Drake
- Instituto de Ciencias Marinas de Andalucía (ICMAN, CSIC), Puerto Real (Cádiz), Spain
| | | | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Pavillon Charles-Eugène-Marchand, Laval University, Quebec, Canada
| | - Amandine D Marie
- School of Marine Studies, Molecular Analytics Laboratory (MOANA), Faculty of Science Technology and Environment, The University of the South Pacific, Suva, Fiji
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Sales JBDL, Rodrigues-Filho LFDS, Ferreira YDS, Carneiro J, Asp NE, Shaw PW, Haimovici M, Markaida U, Ready J, Schneider H, Sampaio I. Divergence of cryptic species of Doryteuthis plei Blainville, 1823 (Loliginidae, Cephalopoda) in the Western Atlantic Ocean is associated with the formation of the Caribbean Sea. Mol Phylogenet Evol 2017; 106:44-54. [DOI: 10.1016/j.ympev.2016.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/30/2016] [Accepted: 09/14/2016] [Indexed: 10/21/2022]
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20
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Thanou E, Sponza S, Nelson EJ, Perry A, Wanless S, Daunt F, Cavers S. Genetic structure in the European endemic seabird, Phalacrocorax aristotelis, shaped by a complex interaction of historical and contemporary, physical and nonphysical drivers. Mol Ecol 2016; 26:2796-2811. [PMID: 28028864 DOI: 10.1111/mec.13996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 11/30/2022]
Abstract
Geographically separated populations tend to be less connected by gene flow, as a result of physical or nonphysical barriers preventing dispersal, and this can lead to genetic structure. In this context, highly mobile organisms such as seabirds are interesting because the small effect of physical barriers means nonphysical ones may be relatively more important. Here, we use microsatellite and mitochondrial data to explore the genetic structure and phylogeography of Atlantic and Mediterranean populations of a European endemic seabird, the European shag, Phalacrocorax aristotelis, and identify the primary drivers of their diversification. Analyses of mitochondrial markers revealed three phylogenetic lineages grouping the North Atlantic, Spanish/Corsican and eastern Mediterranean populations, apparently arising from fragmentation during the Pleistocene followed by range expansion. These traces of historical fragmentation were also evident in the genetic structure estimated by microsatellite markers, despite significant contemporary gene flow among adjacent populations. Stronger genetic structure, probably promoted by landscape, philopatry and local adaptation, was found among distant populations and those separated by physical and ecological barriers. This study highlights the enduring effect of Pleistocene climatic changes on shag populations, especially within the Mediterranean Basin, and suggests a role for cryptic northern refugia, as well as known southern refugia, on the genetic structure of European seabirds. Finally, it outlines how contemporary ecological barriers and behavioural traits may maintain population divergence, despite long-distance dispersal triggered by extreme environmental conditions (e.g. population crashes).
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Affiliation(s)
- Evanthia Thanou
- Section of Animal Biology, Department of Biology, University of Patras, Patras, GR-26504, Greece.,Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK
| | - Stefano Sponza
- Department of Mathematics and Geosciences, University of Trieste, I-34127, Trieste, Italy
| | - Emily J Nelson
- Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK.,Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Annika Perry
- Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK
| | - Sarah Wanless
- Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK
| | - Francis Daunt
- Centre for Ecology & Hydrology, Penicuik, EH26 0QB, UK
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21
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Taboada S, Pérez-Portela R. Contrasted phylogeographic patterns on mitochondrial DNA of shallow and deep brittle stars across the Atlantic-Mediterranean area. Sci Rep 2016; 6:32425. [PMID: 27585743 PMCID: PMC5009426 DOI: 10.1038/srep32425] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/05/2016] [Indexed: 12/20/2022] Open
Abstract
Previous studies on Ophiothrix in European waters demonstrated the existence of two distinct species, Ophiothrix fragilis and Ophiothrix sp. II. Using phylogenetic and species delimitation techniques based on two mitochondrial genes (cytochrome c oxidase I and 16S rRNA) we prove the existence of a new congeneric species (Ophiothrix sp. III), occurring in the deep Atlantic coast of the Iberian Peninsula and the Alboran Sea. We compared phylogeographic patterns of these three Ophiothrix species to test whether closely related species are differentially affected by past demographic events and current oceanographic barriers. We used 432 sequences (137 of O. fragilis, 215 of Ophiothrix sp. II, and 80 of Ophiothrix sp. III) of the 16S rRNA from 23 Atlantic-Mediterranean locations for the analyses. We observed different geographic and bathymetric distributions, and contrasted phylogeography among species. Ophiothrix fragilis appeared genetically isolated between the Atlantic and Mediterranean basins, attributed to past vicariance during Pleistocene glaciations and a secondary contact associated to demographic expansion. This contrasts with the panmixia observed in Ophiothrix sp. II across the Atlantic-Mediterranean area. Results were not conclusive for Ophiothrix sp. III due to the lack of a more complete sampling within the Mediterranean Sea.
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Affiliation(s)
- Sergi Taboada
- Department of Life Sciences, The Natural History Museum of London, Cromwell Road, SW7 5BD, UK
| | - Rocío Pérez-Portela
- Centro de Estudios Avanzados de Blanes, CSIC, Accés a la cala St. Francesc, 14, 17300, Blanes, 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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23
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Comparison of bovine serum albumin adsorption capacities of α-chitin isolated from an insect and β-chitin from cuttlebone. J IND ENG CHEM 2016. [DOI: 10.1016/j.jiec.2016.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Leasi F, Andrade SCDS, Norenburg J. At least some meiofaunal species are not everywhere. Indication of geographic, ecological and geological barriers affecting the dispersion of species of Ototyphlonemertes
(Nemertea, Hoplonemertea). Mol Ecol 2016; 25:1381-97. [DOI: 10.1111/mec.13568] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/08/2015] [Accepted: 01/25/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Francesca Leasi
- Department of Invertebrate Zoology; Smithsonian National Museum of Natural History; PO Box 37012, NMNH Washington DC 20013-7012 USA
| | | | - Jon Norenburg
- Department of Invertebrate Zoology; Smithsonian National Museum of Natural History; PO Box 37012, NMNH Washington DC 20013-7012 USA
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25
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Drivers of Population Structure of the Bottlenose Dolphin (Tursiops truncatus) in the Eastern Mediterranean Sea. Evol Biol 2015. [DOI: 10.1007/s11692-015-9309-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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26
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Strong population genetic structure and contrasting demographic histories for the small-spotted catshark (Scyliorhinus canicula) in the Mediterranean Sea. Heredity (Edinb) 2014; 114:333-43. [PMID: 25469687 DOI: 10.1038/hdy.2014.107] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 11/08/2022] Open
Abstract
Coastal and demersal chondrichthyans, such as the small-spotted catshark, are expected to exhibit genetic differentiation in areas of complex geomorphology like the Mediterranean Basin because of their limited dispersal ability. To test this hypothesis, we used a fragment of the mitochondrial cytochrome c oxidase subunit I gene and 12 nuclear microsatellite loci in order to investigate the genetic structure and historical demography of this species, and to identify potential barriers to gene flow. Samples were collected from the Balearic Islands, the Algerian Basin, the Ionian Sea, the Corinthian Gulf and various locations across the Aegean Sea. Additional sequences from the Atlantic and the Levantine Basin retrieved from GenBank were included in the mitochondrial DNA analysis. Both mitochondrial and nuclear microsatellite DNA data revealed a strong genetic subdivision, mainly between the western and eastern Mediterranean, whereas the Levantine Basin shared haplotypes with both areas. The geographic isolation of the Mediterranean basins seems to enforce the population genetic differentiation of the species, with the deep sea acting as a strong barrier to its dispersal. Contrasting historical demographic patterns were also observed in different parts of the species' distribution, most notably a population growth trend in the western Mediterranean/Atlantic area and a slight decreasing one in the Aegean Sea. The different effects of the Pleistocene glacial periods on the habitat availability may explain the contrasting demographic patterns observed. The current findings suggest that the small-spotted catshark exhibits several genetic stocks in the Mediterranean, although further study is needed.
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27
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Genetic diversity and population structure of Sepia officinalis from the Tunisian cost revealed by mitochondrial COI sequences. Mol Biol Rep 2014; 42:77-86. [DOI: 10.1007/s11033-014-3743-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 05/24/2014] [Indexed: 10/24/2022]
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28
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Microsatellite loci for studies of the common cuttlefish, Sepia officinalis. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0191-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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29
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Villamor A, Costantini F, Abbiati M. Genetic structuring across marine biogeographic boundaries in rocky shore invertebrates. PLoS One 2014; 9:e101135. [PMID: 24983738 PMCID: PMC4077735 DOI: 10.1371/journal.pone.0101135] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 06/04/2014] [Indexed: 11/23/2022] Open
Abstract
Biogeography investigates spatial patterns of species distribution. Discontinuities in species distribution are identified as boundaries between biogeographic areas. Do these boundaries affect genetic connectivity? To address this question, a multifactorial hierarchical sampling design, across three of the major marine biogeographic boundaries in the central Mediterranean Sea (Ligurian-Tyrrhenian, Tyrrhenian-Ionian and Ionian-Adriatic) was carried out. Mitochondrial COI sequence polymorphism of seven species of Mediterranean benthic invertebrates was analysed. Two species showed significant genetic structure across the Tyrrhenian-Ionian boundary, as well as two other species across the Ionian Sea, a previously unknown phylogeographic barrier. The hypothesized barrier in the Ligurian-Tyrrhenian cannot be detected in the genetic structure of the investigated species. Connectivity patterns across species at distances up to 800 km apart confirmed that estimates of pelagic larval dispersal were poor predictors of the genetic structure. The detected genetic discontinuities seem more related to the effect of past historical events, though maintained by present day oceanographic processes. Multivariate statistical tools were used to test the consistency of the patterns across species, providing a conceptual framework for across-species barrier locations and strengths. Additional sequences retrieved from public databases supported our findings. Heterogeneity of phylogeographic patterns shown by the 7 investigated species is relevant to the understanding of the genetic diversity, and carry implications for conservation biology.
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Affiliation(s)
- Adriana Villamor
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Emilia-Romagna, Italy
- * E-mail:
| | - Federica Costantini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Emilia-Romagna, Italy
| | - Marco Abbiati
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Emilia-Romagna, Italy
- Institute of Marine Sciences, National Research Council, Bologna, Emilia-Romagna, Italy
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30
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Lim HC, Ahmad AT, Nuruddin AA, Mohd Nor SA. Cytochrome b gene reveals panmixia among Japanese Threadfin Bream, Nemipterus japonicus (Bloch, 1791) populations along the coasts of Peninsular Malaysia and provides evidence of a cryptic species. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:575-84. [PMID: 24724977 DOI: 10.3109/19401736.2014.908354] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We evaluated genetic differentiation among ten presumed Japanese threadfin bream, Nemipterus japonicus populations along the coast of Peninsular Malaysia based on the partial sequence of the mitochondrial cytochrome b gene (982 bp). Genetic divergences (Kimura-2 parameter) ranged from 0.5% to 0.8% among nine of the ten populations while these nine populations were 4.4% to 4.6% diverged from the Kuala Besar population located at the Northeast coast. The constructed Neighbour Joining (NJ) phylogenetic trees based on haplotypes showed the Kuala Besar population forming an isolated cluster. The Analysis of Molecular Variance (AMOVA) of the ten populations a priori assigned into four regions, revealed that most of the variation occurred within population with a fairly low but significant level of regional differentiation (FST = 0.07, p < 0.05, FSC = 0.00, p > 0.05 and FCT = 0.07, p < 0.05) attributed to the Kuala Besar population. p Value after Bonferroni correction revealed that only pairwise FST values involving the Kuala Besar population with the other nine populations were significant. Thus, this study revealed that the N. japonicus populations off Peninsular Malaysia were panmictic. However, the Kuala Besar population, although morphologically identical was composed of a genetically discrete taxon from the rest. These findings are important contributions in formulating sustainable fishery management policies for this important fishery in Peninsular Malaysia.
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Affiliation(s)
- Hong-Chiun Lim
- a School of Biological Sciences, Universiti Sains Malaysia , 11800, Penang , Malaysia
| | - Abu Talib Ahmad
- b Fisheries Research Institute , 11900 Batu Maung , Penang , Malaysia , and
| | | | - Siti Azizah Mohd Nor
- a School of Biological Sciences, Universiti Sains Malaysia , 11800, Penang , Malaysia .,c Centre for Marine and Coastal Studies, Universiti Sains Malaysia , 11800, Penang , Malaysia
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31
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Allcock AL, Lindgren A, Strugnell J. The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review. J NAT HIST 2014. [DOI: 10.1080/00222933.2013.825342] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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32
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Rodhouse PGK, Pierce GJ, Nichols OC, Sauer WHH, Arkhipkin AI, Laptikhovsky VV, Lipiński MR, Ramos JE, Gras M, Kidokoro H, Sadayasu K, Pereira J, Lefkaditou E, Pita C, Gasalla M, Haimovici M, Sakai M, Downey N. Environmental effects on cephalopod population dynamics: implications for management of fisheries. ADVANCES IN MARINE BIOLOGY 2014; 67:99-233. [PMID: 24880795 DOI: 10.1016/b978-0-12-800287-2.00002-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Cephalopods are a relatively small class of molluscs (~800 species), but they support some large industrial scale fisheries and numerous small-scale, local, artisanal fisheries. For several decades, landings of cephalopods globally have grown against a background of total finfish landings levelling off and then declining. There is now evidence that in recent years, growth in cephalopod landings has declined. The commercially exploited cephalopod species are fast-growing, short-lived ecological opportunists. Annual variability in abundance is strongly influenced by environmental variability, but the underlying causes of the links between environment and population dynamics are poorly understood. Stock assessment models have recently been developed that incorporate environmental processes that drive variability in recruitment, distribution and migration patterns. These models can be expected to improve as more, and better, data are obtained on environmental effects and as techniques for stock identification improve. A key element of future progress will be improved understanding of trophic dynamics at all phases in the cephalopod life cycle. In the meantime, there is no routine stock assessment in many targeted fisheries or in the numerous by-catch fisheries for cephalopods. There is a particular need for a precautionary approach in these cases. Assessment in many fisheries is complicated because cephalopods are ecological opportunists and stocks appear to have benefited from the reduction of key predator by overexploitation. Because of the complexities involved, ecosystem-based fisheries management integrating social, economic and ecological considerations is desirable for cephalopod fisheries. An ecological approach to management is routine in many fisheries, but to be effective, good scientific understanding of the relationships between the environment, trophic dynamics and population dynamics is essential. Fisheries and the ecosystems they depend on can only be managed by regulating the activities of the fishing industry, and this requires understanding the dynamics of the stocks they exploit.
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Affiliation(s)
| | - Graham J Pierce
- Oceanlab, University of Aberdeen, Newburgh, Aberdeenshire, United Kingdom; CESAM & Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Owen C Nichols
- School for Marine Science and Technology, University of Massachusetts - Dartmouth, Fairhaven, Massachusetts, USA; Center for Coastal Studies, Provincetown, Massachusetts, USA
| | - Warwick H H Sauer
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | | | | | - Marek R Lipiński
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Jorge E Ramos
- Institute for Marine and Antarctic Studies, Marine Research Laboratories Taroona, Nubeena Crescent, Taroona, Tasmania, Australia
| | - Michaël Gras
- Université de Caen Basse-Normandie, Institut de Biologie Fondamentale et Appliquée Department, UMR BOREA: Biologie des ORganismes et des Ecosystèmes Aquatiques, Esplanade de la paix, CS 14032, Caen, France; BOREA, UMR CNRS7208, IRD207, UPMC, MNHN, UCBN, Caen, France
| | - Hideaki Kidokoro
- Japan Sea National Fisheries Research, Institute, Fisheries Research Agency, Suido-cho, Niigata, Japan
| | - Kazuhiro Sadayasu
- Marine Fisheries Research and Development Center, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - João Pereira
- Instituto de Investigação das Pescas e do Mar (IPIMAR), Lisboa, Portugal
| | - Evgenia Lefkaditou
- Helenic Centre for Marine Research, Aghios Kosmas, Hellinikon, Athens, Greece
| | - Cristina Pita
- Oceanlab, University of Aberdeen, Newburgh, Aberdeenshire, United Kingdom; CESAM & Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Maria Gasalla
- Fisheries Ecosystems Laboratory, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Manuel Haimovici
- Institute of Oceanography, Federal University of Rio Grande, CEP, Rio Grande, Brazil
| | - Mitsuo Sakai
- National Research Institute of Far Seas Fisheries, Shizuoka, Japan
| | - Nicola Downey
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
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Cordero D, Peña JB, Saavedra C. Phylogeographic analysis of introns and mitochondrial DNA in the clam Ruditapes decussatus uncovers the effects of Pleistocene glaciations and endogenous barriers to gene flow. Mol Phylogenet Evol 2013; 71:274-87. [PMID: 24269315 DOI: 10.1016/j.ympev.2013.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 10/30/2013] [Accepted: 11/06/2013] [Indexed: 12/22/2022]
Abstract
Studies on the phylogeography of species inhabiting the Mediterranean and the nearby coasts of the NE Atlantic Ocean (MEDAT) have found subdivision and/or phylogeographic structure in one or more of the Atlantic, western Mediterranean and eastern Mediterranean basins. This structure has been explained as the result of past population fragmentation caused by Pleistocene sea level changes and current patterns of marine circulation. However, the increasing use of nuclear markers has revealed that these two factors alone are not enough to explain the phylogeographic patterns, and an additional role has been suggested for endogenous barriers to gene flow or natural selection. In this article we examined the role of these factors in Ruditapes decussatus, a commercial clam species native to MEDAT. A genetic analysis of 11 populations was carried out by examining 6 introns with a PCR-RFLP technique. We found subdivision in three regions: Atlantic (ATL), western Mediterranean plus Tunisia (WMED), and Aegean and Adriatic seas (AEGAD). Two introns (Ech and Tbp) showed alleles that were restricted to AEGAD. Sequencing a subsample of individuals for these introns indicated that AEGAD-specific alleles were separate clades, thus revealing a phylogeographic brake at the WMED-AEGAD boundary. Sequencing of the mitochondrial COI locus confirmed this phylogeographic break. Dating of the AEGAD mitochondrial haplotypes and nuclear alleles with a Bayesian MCMC method revealed that they shared common ancestors in the Pleistocene. These results can be explained in the framework of Pleistocene sea level drops and patterns of gene flow in MEDAT. An additional observation was a lack of differentiation at COI between the ATL and WMED, in sharp contrast with 4 introns that showed clear genetic subdivision. Neutrality tests did not support the hypothesis of a selective sweep acting on mtDNA to explain the contrasting levels of differentiation between mitochondrial and nuclear markers across the ATL-WMED transition, and we argue that the difference between markers is best explained by the existence of an endogenous genetic barrier, rather than by a physical barrier to larval migration alone.
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Affiliation(s)
- David Cordero
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, 12595 Ribera de Cabanes (Castellón), Spain
| | - Juan B Peña
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, 12595 Ribera de Cabanes (Castellón), Spain
| | - Carlos Saavedra
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, 12595 Ribera de Cabanes (Castellón), Spain.
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Han Z, Zheng W, Chen G, Shui B, Liu S, Zhuang Z. Population genetic structure and larval dispersal strategy of portunid crab Charybdis bimaculata in Yellow sea and East China sea. MITOCHONDRIAL DNA 2013; 26:402-8. [PMID: 24117187 DOI: 10.3109/19401736.2013.840592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Larval dispersal may have an important effect on genetic structure of benthic species. However, different species may choose different larval dispersal strategy. To examine the population genetic structure and larval dispersal strategy of portunid crab Charybdis bimaculata, a 658 base pair (bp) fragment of mtDNA COI gene was sequenced in this species. In total, 67 individuals were collected from 5 locations in Yellow Sea and East China, and 24 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the five populations ranged from 0.2000 ± 0.1541 (Zhoushan) to 0.8333 ± 0.1265 (Nanji island), and from 0.0003 ± 0.0005 (Zhoushan) to 0.0026 ± 0.0019 (Nanji island). Analysis of molecular variance and pairwise FST revealed no significant differentiation between the Yellow Sea and the East China Sea in C. bimaculata, supporting high larval dispersal ability in this species, rejecting larval retention. Mismatch distribution revealed that C. bimaculata had undergone population expansion. Larval drift in the ocean currents, and recent range expansion could be the reasons for little genetic structure in the studied area.
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Affiliation(s)
- Zhiqiang Han
- Fishery College, Zhejiang Ocean University , Zhoushan , China
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35
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Lo Brutto S, Maggio T, Arculeo M. Isolation By Distance (IBD) signals in the deep-water rose shrimp Parapenaeus longirostris (Lucas, 1846) (Decapoda, Panaeidae) in the Mediterranean Sea. MARINE ENVIRONMENTAL RESEARCH 2013; 90:1-8. [PMID: 23769335 DOI: 10.1016/j.marenvres.2013.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/06/2013] [Accepted: 05/11/2013] [Indexed: 06/02/2023]
Abstract
The identification of boundaries of genetic demes is one of the major goals for fishery management, and few Mediterranean commercial species have not been studied from a genetic point of view yet. The deep-water rose shrimp Parapenaeus longirostris (Lucas, 1846) is one of the most important components of commercial landings in Mediterranean, its fishery aspects have received much attention, regrettably without any concern for the genetic architecture of its populations. The population structure in the central and eastern Mediterranean Sea (captures from six Italian and two Greek landings) has been analysed on the basis of surveys carried out with mitochondrial and AFLP markers. Data revealed the presence of a gradual discrepancy along a west-east axis. This species, occurring mainly at a depth of between 100 and 400 m, is not strongly confined in isolated demes, but it demonstrates an 'Isolation By Distance' model, within the Mediterranean Sea, which includes geographical areas with a some degree of isolation. The role of hydrodynamic forces, such as currents, water fronts, is discussed; and a further evidence of the 'Levantine isolation' within Mediterranean basin is shown.
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Affiliation(s)
- S Lo Brutto
- Dept. STEBICEF, University of Palermo, Via Archirafi 18, 90123 Palermo, Italy.
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Sanna D, Cossu P, Dedola GL, Scarpa F, Maltagliati F, Castelli A, Franzoi P, Lai T, Cristo B, Curini-Galletti M, Francalacci P, Casu M. Mitochondrial DNA reveals genetic structuring of Pinna nobilis across the Mediterranean Sea. PLoS One 2013; 8:e67372. [PMID: 23840684 PMCID: PMC3696058 DOI: 10.1371/journal.pone.0067372] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 05/18/2013] [Indexed: 11/18/2022] Open
Abstract
Pinna nobilis is the largest endemic Mediterranean marine bivalve. During past centuries, various human activities have promoted the regression of its populations. As a consequence of stringent standards of protection, demographic expansions are currently reported in many sites. The aim of this study was to provide the first large broad-scale insight into the genetic variability of P. nobilis in the area that encompasses the western Mediterranean, Ionian Sea, and Adriatic Sea marine ecoregions. To accomplish this objective twenty-five populations from this area were surveyed using two mitochondrial DNA markers (COI and 16S). Our dataset was then merged with those obtained in other studies for the Aegean and Tunisian populations (eastern Mediterranean), and statistical analyses (Bayesian model-based clustering, median-joining network, AMOVA, mismatch distribution, Tajima's and Fu's neutrality tests and Bayesian skyline plots) were performed. The results revealed genetic divergence among three distinguishable areas: (1) western Mediterranean and Ionian Sea; (2) Adriatic Sea; and (3) Aegean Sea and Tunisian coastal areas. From a conservational point of view, populations from the three genetically divergent groups found may be considered as different management units.
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Affiliation(s)
- Daria Sanna
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Piero Cossu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Gian Luca Dedola
- Dipartimento di Medicina Veterinaria - Sezione di Anatomia, Università di Sassari, Sassari, Italy
| | - Fabio Scarpa
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | | | | | - Piero Franzoi
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Cà Foscari, Venezia, Italy
| | - Tiziana Lai
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Benedetto Cristo
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Marco Curini-Galletti
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Paolo Francalacci
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
| | - Marco Casu
- Dipartimento di Scienze della Natura e del Territorio - Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari, Sassari, Italy
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Sá-Pinto A, Branco MS, Alexandrino PB, Fontaine MC, Baird SJE. Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean. PLoS One 2012; 7:e50330. [PMID: 23239977 PMCID: PMC3519802 DOI: 10.1371/journal.pone.0050330] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 10/17/2012] [Indexed: 11/25/2022] Open
Abstract
Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.
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Affiliation(s)
- Alexandra Sá-Pinto
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/UP), Campus Agrário de Vairão, Vairão, Portugal
- * E-mail: (ASP); (MCF)
| | - Madalena S. Branco
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/UP), Campus Agrário de Vairão, Vairão, Portugal
| | - Paulo B. Alexandrino
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/UP), Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Zoologia-Antropologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- * E-mail: (ASP); (MCF)
| | - Michaël C. Fontaine
- Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France
- CNRS, Orsay, France
- Ecoanthropology and Ethnobiology UMR 5145 CNRS-MNHN-Université Paris 7 Musée de l'Homme, Paris, France
| | - Stuart J. E. Baird
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/UP), Campus Agrário de Vairão, Vairão, Portugal
- Centre de Biologie et de Gestion des Populations (CBGP), Campus International de Baillarguet, CS 30 016, Montpelier/Lez, France
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A legacy of contrasting spatial genetic structure on either side of the Atlantic-Mediterranean transition zone in a marine protist. Proc Natl Acad Sci U S A 2012; 109:20998-1003. [PMID: 23213247 DOI: 10.1073/pnas.1214398110] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The mechanisms that underpin the varied spatial genetic structures exhibited by free-living marine microorganisms remain controversial, with most studies emphasizing a high dispersal capability that should redistribute genetic diversity in contrast to most macroorganisms whose populations often retain a genetic signature of demographic response to historic climate fluctuations. We quantified the European phylogeographic structure of the marine flagellate Oxyrrhis marina and found a marked difference in spatial genetic structure, population demography, and genetic diversity between the northwest Atlantic and Mediterranean Sea that reflects the persistent separation of these regions as well as context-dependent population responses to contrasting environments. We found similar geographic variation in the level of genetic diversity in the sister species Oxyrrhis maritima. Because the capacity for wide dispersal is not always realized, historic genetic footprints of range expansion and contraction persist in contemporary populations of marine microbes, as they do in larger species. Indeed, the well-described genetic effects of climatic variation on macroorganisms provide clear, testable hypotheses about the processes that drive genetic divergence in marine microbes and thus about the response to future environmental change.
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39
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Pérez-Portela R, Almada V, Turon X. Cryptic speciation and genetic structure of widely distributed brittle stars (Ophiuroidea) in Europe. ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00573.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species). Mol Phylogenet Evol 2012; 65:203-12. [DOI: 10.1016/j.ympev.2012.06.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 06/08/2012] [Accepted: 06/12/2012] [Indexed: 11/20/2022]
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41
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Liu H, Liu M, Ge S, Wang Q, Yu D, Guan S. Population structuring and historical demography of a common clam worm Perinereris aibuhitensis near the coasts of Shandong Peninsula. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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42
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Karl SA, Toonen RJ, Grant WS, Bowen BW. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol Ecol 2012; 21:4171-89. [PMID: 22574714 DOI: 10.1111/j.1365-294x.2012.05576.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.
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Affiliation(s)
- Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Kāne'ohe, HI 96744, USA.
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Oellermann M, Pörtner HO, Mark FC. Mitochondrial dynamics underlying thermal plasticity of cuttlefish (Sepia officinalis) hearts. J Exp Biol 2012; 215:2992-3000. [DOI: 10.1242/jeb.068163] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Summary
In the eurythermal cuttlefish Sepia officinalis, performance greatly depends on hearts that ensure systemic oxygen supply over a broad range of temperatures. We therefore aimed to identify adjustments in energetic cardiac capacity and underlying mitochondrial function supporting thermal acclimation that could be critical for the cuttlefish's competitive success in variable environments. Two genetically distinct cuttlefish populations were acclimated to 11°C, 16°C and 21°C, respectively. Subsequently, skinned and permeabilised heart fibres were used to assess mitochondrial functioning by means of high-resolution respirometry and a substrate-inhibitor protocol, followed by measurements of cardiac citrate synthase activity. In cuttlefish hearts, thermal sensitivity of mitochondrial substrate oxidation was high for proline and pyruvate but low for succinate. Oxygen efficiency of catabolism rose from 11°C to 21°C via shifts to oxygen-conserving oxidation of proline and pyruvate as well as via reduced proton leak. Acclimation to 21°C decreased mitochondrial complex I activity in Adriatic cuttlefish and increased complex IV activity in English Channel cuttlefish. However, compensation of mitochondrial capacities did not occur during cold acclimation to 11°C. Moreover, cold adapted English Channel cuttlefish had larger hearts with lower mitochondrial capacities than warm adapted Adriatic cuttlefish. The changes observed for substrate oxidation, mitochondrial complexes, proton leak or heart weights improve energetic efficiency and essentially seem to extend tolerance to high temperatures and reduce associated tissue hypoxia. We conclude that cuttlefish sustain cardiac performance and thus, systemic oxygen delivery over short and long-term changes of temperature and environmental conditions by multiple adjustments in cellular and mitochondrial energetics.
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Affiliation(s)
| | | | - Felix C. Mark
- Alfred Wegener Institute for Polar and Marine Research
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44
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Borrero-Pérez GH, González-Wangüemert M, Marcos C, Pérez-Ruzafa A. Phylogeography of the Atlanto-Mediterranean sea cucumber Holothuria (Holothuria) mammata: the combined effects of historical processes and current oceanographical pattern. Mol Ecol 2011; 20:1964-75. [PMID: 21463375 DOI: 10.1111/j.1365-294x.2011.05068.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We assessed the genetic structure of populations of the widely distributed sea cucumber Holothuria (Holothuria) mammata Grube, 1840, and investigated the effects of marine barriers to gene flow and historical processes. Several potential genetic breaks were considered, which would separate the Atlantic and Mediterranean basins, the isolated Macaronesian Islands from the other locations analysed, and the Western Mediterranean and Aegean Sea (Eastern Mediterranean). We analysed mitochondrial 16S and COI gene sequences from 177 individuals from four Atlantic locations and four Mediterranean locations. Haplotype diversity was high (H=0.9307 for 16S and 0.9203 for COI), and the haplotypes were closely related (π=0.0058 for 16S and 0.0071 for COI). The lowest genetic diversities were found in the Aegean Sea population. Our results showed that the COI gene was more variable and more useful for the detection of population structure than the 16S gene. The distribution of mtDNA haplotypes, the pairwise F(ST) values and the results of exact tests and amova revealed: (i) a significant genetic break between the population in the Aegean Sea and those in the other locations, as supported by both mitochondrial genes, and (ii) weak differentiation of the Canary and Azores Islands from the other populations; however, the populations from the Macaronesian Islands, Algarve and West Mediterranean could be considered to be a panmictic metapopulation. Isolation by distance was not identified in H. (H.) mammata. Historical events behind the observed findings, together with the current oceanographic patterns, were proposed and discussed as the main factors that determine the population structure and genetic signature of H. (H.) mammata.
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Affiliation(s)
- G H Borrero-Pérez
- Departamento de Ecología e Hidrología, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain.
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Panova M, Blakeslee AMH, Miller AW, Mäkinen T, Ruiz GM, Johannesson K, André C. Glacial history of the North Atlantic marine snail, Littorina saxatilis, inferred from distribution of mitochondrial DNA lineages. PLoS One 2011; 6:e17511. [PMID: 21412417 PMCID: PMC3055875 DOI: 10.1371/journal.pone.0017511] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 02/07/2011] [Indexed: 11/29/2022] Open
Abstract
The North Atlantic intertidal gastropod, Littorina saxatilis (Olivi, 1792), exhibits extreme morphological variation between and within geographic regions and has become a model for studies of local adaptation; yet a comprehensive analysis of the species' phylogeography is lacking. Here, we examine phylogeographic patterns of the species' populations in the North Atlantic and one remote Mediterranean population using sequence variation in a fragment of the mitochondrial cytochrome b gene (607 bp). We found that, as opposed to many other rocky intertidal species, L. saxatilis has likely had a long and continuous history in the Northwest Atlantic, including survival during the last glacial maximum (LGM), possibly in two refugia. In the Northeast Atlantic, several areas likely harboured refugial populations that recolonized different parts of this region after glacial retreat, resulting in strong population structure. However, the outlying monomorphic Venetian population is likely a recent anthropogenic introduction from northern Europe and not a remnant of an earlier wider distribution in the Mediterranean Sea. Overall, our detailed phylogeography of L. saxatilis adds an important piece to the understanding of Pleistocene history in North Atlantic marine biota as well as being the first study to describe the species' evolutionary history in its natural range. The latter contribution is noteworthy because the snail has recently become an important model species for understanding evolutionary processes of speciation; thus our work provides integral information for such endeavours.
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Affiliation(s)
- Marina Panova
- Department of Marine Ecology-Tjärnö, University of Gothenburg, Strömstad, Sweden.
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Zamborsky DJ, Nishiguchi MK. Phylogeographical patterns among Mediterranean sepiolid squids and their Vibrio symbionts: environment drives specificity among sympatric species. Appl Environ Microbiol 2011; 77:642-9. [PMID: 21075896 PMCID: PMC3020525 DOI: 10.1128/aem.02105-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 11/02/2010] [Indexed: 11/20/2022] Open
Abstract
Bobtail squid from the genera Sepiola and Rondeletiola (Cephalopoda: Sepiolidae) form mutualistic associations with luminous Gram-negative bacteria (Gammaproteobacteria: Vibrionaceae) from the genera Vibrio and Photobacterium. Symbiotic bacteria proliferate inside a bilobed light organ until they are actively expelled by the host into the surrounding environment on a diel basis. This event results in a dynamic symbiont population with the potential to establish the symbiosis with newly hatched sterile (axenic) juvenile sepiolids. In this study, we examined the genetic diversity found in populations of sympatric sepiolid squid species and their symbionts by the use of nested clade analysis with multiple gene analyses. Variation found in the distribution of different species of symbiotic bacteria suggests a strong influence of abiotic factors in the local environment, affecting bacterial distribution among sympatric populations of hosts. These abiotic factors include temperature differences incurred by a shallow thermocline, as well as a lack of strong coastal water movement accompanied by seasonal temperature changes in overlapping niches. Host populations are stable and do not appear to have a significant role in the formation of symbiont populations relative to their distribution across the Mediterranean Sea. Additionally, all squid species examined (Sepiola affinis, S. robusta, S. ligulata, S. intermedia, and Rondeletiola minor) are genetically distinct from one another regardless of location and demonstrate very little intraspecific variation within species. These findings suggest that physical boundaries and distance in relation to population size, and not host specificity, are important factors in limiting or defining gene flow within sympatric marine squids and their associated bacterial symbionts in the Mediterranean Sea.
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Affiliation(s)
- D. J. Zamborsky
- Department of Biology, MSC 3AF, New Mexico State University, P.O. Box 30001, Las Cruces, New Mexico 88003-8001
| | - M. K. Nishiguchi
- Department of Biology, MSC 3AF, New Mexico State University, P.O. Box 30001, Las Cruces, New Mexico 88003-8001
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Mejri R, Arculeo M, Hassine OKB, Brutto SL. Genetic architecture of the marbled goby Pomatoschistus marmoratus (Perciformes, Gobiidae) in the Mediterranean Sea. Mol Phylogenet Evol 2010; 58:395-403. [PMID: 21167289 DOI: 10.1016/j.ympev.2010.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 11/26/2010] [Accepted: 12/03/2010] [Indexed: 11/19/2022]
Abstract
The marbled goby Pomatoschistus marmoratus, a species inhabiting coastal Mediterranean lagoons, has been studied by measuring its mitochondrial DNA variation. This analysis revealed a Mediterranean west vs east split and, subsequently, an eastern differentiation among the Libyan-Tunisian Gulf, the Adriatic Sea and the Aegean Sea. The high cohesion between the samples collected in the vast area of western Mediterranean contrasts with the genetic mosaic of the more sub-structured eastern Mediterranean. This western homogeneity can not yet be fully explained even if a human-mediated migratory flow, due to a maritime traffic, has been posited. The pattern in the eastern basin revealed a genetic architecture possibly due to the non-migratory habit of the gobid. Within this perspective, the role of the Mediterranean lagoon habitat should be related to how much it amplifies the effects of historical (e.g. past sea-level changes) and environmental (e.g. present-day hydrographic regime) processes as regards the genetic structure of the inhabiting species.
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Affiliation(s)
- Randa Mejri
- Unité de Recherche de Biologie, Ecologie et Parasitologie des Organismes Aquatiques, Département de Biologie, Tunis El Manar 2092, Tunisia
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Robles-Sikisaka R, Bohonak AJ, McClenaghan LR, Dhar AK. Genetic signature of rapid IHHNV (infectious hypodermal and hematopoietic necrosis virus) expansion in wild Penaeus shrimp populations. PLoS One 2010; 5:e11799. [PMID: 20668694 PMCID: PMC2909959 DOI: 10.1371/journal.pone.0011799] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 06/15/2010] [Indexed: 11/18/2022] Open
Abstract
Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is a widely distributed single-stranded DNA parvovirus that has been responsible for major losses in wild and farmed penaeid shrimp populations on the northwestern Pacific coast of Mexico since the early 1990's. IHHNV has been considered a slow-evolving, stable virus because shrimp populations in this region have recovered to pre-epizootic levels, and limited nucleotide variation has been found in a small number of IHHNV isolates studied from this region. To gain insight into IHHNV evolutionary and population dynamics, we analyzed IHHNV capsid protein gene sequences from 89 Penaeus shrimp, along with 14 previously published sequences. Using Bayesian coalescent approaches, we calculated a mean rate of nucleotide substitution for IHHNV that was unexpectedly high (1.39×10−4 substitutions/site/year) and comparable to that reported for RNA viruses. We found more genetic diversity than previously reported for IHHNV isolates and highly significant subdivision among the viral populations in Mexican waters. Past changes in effective number of infections that we infer from Bayesian skyline plots closely correspond to IHHNV epizootiological historical records. Given the high evolutionary rate and the observed regional isolation of IHHNV in shrimp populations in the Gulf of California, we suggest regular monitoring of wild and farmed shrimp and restriction of shrimp movement as preventative measures for future viral outbreaks.
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Affiliation(s)
- Refugio Robles-Sikisaka
- Department of Biology, San Diego State University, San Diego, California, United States of America.
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49
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SÁ-PINTO ALEXANDRA, BAIRD STUARTJE, PINHO CATARINA, ALEXANDRINO PAULO, BRANCO MADALENA. A three-way contact zone between forms of Patella rustica (Mollusca: Patellidae) in the central Mediterranean Sea. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01405.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Marine biogeographic boundaries and human introduction along the European coast revealed by phylogeography of the prawn Palaemon elegans. Mol Phylogenet Evol 2010; 55:765-75. [PMID: 20307676 DOI: 10.1016/j.ympev.2010.03.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 03/10/2010] [Accepted: 03/12/2010] [Indexed: 11/24/2022]
Abstract
A phylogeographic analysis is carried out for the widely distributed European littoral prawn Palaemon elegans in order to test for potential genetic differentiation and geographic structure. Mitochondrial sequences were obtained from 283 specimens from the northeastern Atlantic, the Baltic, Mediterranean, Black and Caspian Seas. Our study revealed a surprisingly complex population structure. Three main haplogroups can be separated: one from the Atlantic (Type I) and two from the Mediterranean (Types II and III). While the Mediterranean types occur in sympatry, a clear phylogeographic break was observed along the Almería-Oran Front separating Type I and giving evidence for a genetic isolation of Atlantic and Mediterranean populations. Type III represents the most distinct haplogroup with high levels of nucleotide divergence, indicating the occurrence of a cryptic species with a Messinian origin. The colonization of the southeastern Baltic Sea is most likely due to human introduction.
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