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Popovic I, Bergeron LA, Bozec YM, Waldvogel AM, Howitt SM, Damjanovic K, Patel F, Cabrera MG, Wörheide G, Uthicke S, Riginos C. High germline mutation rates, but not extreme population outbreaks, influence genetic diversity in a keystone coral predator. PLoS Genet 2024; 20:e1011129. [PMID: 38346089 PMCID: PMC10861045 DOI: 10.1371/journal.pgen.1011129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Lewontin's paradox, the observation that levels of genetic diversity (π) do not scale linearly with census population size (Nc) variation, is an evolutionary conundrum. The most extreme mismatches between π and Nc are found for highly abundant marine invertebrates. Yet, the influences of new mutations on π relative to extrinsic processes such as Nc fluctuations are unknown. Here, we provide the first germline mutation rate (μ) estimate for a marine invertebrate in corallivorous crown-of-thorns sea stars (Acanthaster cf. solaris). We use high-coverage whole-genome sequencing of 14 parent-offspring trios alongside empirical estimates of Nc in Australia's Great Barrier Reef to jointly examine the determinants of π in populations undergoing extreme Nc fluctuations. The A. cf. solaris mean μ was 9.13 x 10-09 mutations per-site per-generation (95% CI: 6.51 x 10-09 to 1.18 x 10-08), exceeding estimates for other invertebrates and showing greater concordance with vertebrate mutation rates. Lower-than-expected Ne (~70,000-180,000) and low Ne/Nc values (0.0047-0.048) indicated weak influences of population outbreaks on long-term π. Our findings are consistent with elevated μ evolving in response to reduced Ne and generation time length, with important implications for explaining high mutational loads and the determinants of genetic diversity in marine invertebrate taxa.
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Affiliation(s)
- Iva Popovic
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Lucie A. Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yves-Marie Bozec
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Samantha M. Howitt
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Frances Patel
- Australian Institute of Marine Science, Townsville, Australia
| | | | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Sven Uthicke
- Australian Institute of Marine Science, Townsville, Australia
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
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2
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Sutherland BJG, Itoh N, Gilchrist K, Boyle B, Roth M, Green TJ. Genomic diversity of wild and cultured Yesso scallop Mizuhopecten yessoensis from Japan and Canada. G3 (BETHESDA, MD.) 2023; 13:jkad242. [PMID: 37857308 PMCID: PMC10700054 DOI: 10.1093/g3journal/jkad242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/06/2023] [Accepted: 10/08/2023] [Indexed: 10/21/2023]
Abstract
The Yesso scallop Mizuhopecten yessoensis is an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic differences among hatchery stocks. In this study, we compare cultured Canadian and wild Japanese populations of Yesso scallop using double-digest restriction site-associated DNA (ddRAD) sequencing to genotype 21,048 variants in 71 wild-caught scallops from Japan, 65 scallops from the Vancouver Island University breeding population, and 37 scallops obtained from a commercial farm off Vancouver Island, British Columbia. The wild scallops are largely comprised of equally unrelated individuals, whereas cultured scallops are comprised of multiple families of related individuals. The polymorphism rate estimated in wild scallops was 1.7%, whereas in the cultured strains, it ranged between 1.35 and 1.07%. Interestingly, heterozygosity rates were highest in the cultured populations, which is likely due to shellfish hatchery practices of crossing divergent strains to gain benefits of heterosis and to avoid inbreeding. Evidence of founder effects and drift was observed in the cultured strains, including high genetic differentiation between cultured populations and between cultured populations and the wild population. Cultured populations had effective population sizes ranging from 9 to 26 individuals whereas the wild population was estimated at 25,048-56,291 individuals. Further, a depletion of low-frequency variants was observed in the cultured populations. These results indicate significant genetic diversity losses in cultured scallops in Canadian breeding programs.
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Affiliation(s)
- Ben J G Sutherland
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, British Columbia V9R 5S5, Canada
- Sutherland Bioinformatics, Lantzville, British Columbia V0R 2H0, Canada
| | - Naoki Itoh
- Laboratory of Fish Diseases, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Korrina Gilchrist
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, British Columbia V9R 5S5, Canada
| | - Brian Boyle
- Plateforme d’Analyses Génomiques, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Quebec G1V 0A6, Canada
| | - Myron Roth
- BC Ministry of Agriculture and Food, Victoria, British Columbia V8W 9B4, Canada
| | - Timothy J Green
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, British Columbia V9R 5S5, Canada
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3
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Cryptic diversity and population genetic structure of the mantis shrimp Oratosquilla oratoria in South Korea. Genes Genomics 2022; 44:1343-1352. [DOI: 10.1007/s13258-022-01303-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/07/2022] [Indexed: 11/04/2022]
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4
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Varney RM, Speiser DI, McDougall C, Degnan BM, Kocot KM. The Iron-Responsive Genome of the Chiton Acanthopleura granulata. Genome Biol Evol 2021; 13:evaa263. [PMID: 33320175 PMCID: PMC7850002 DOI: 10.1093/gbe/evaa263] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 12/27/2022] Open
Abstract
Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many genes associated with biomineralization in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc may have had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization.
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Affiliation(s)
- Rebecca M Varney
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama
| | - Daniel I Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | - Carmel McDougall
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Kevin M Kocot
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama
- Alabama Museum of Natural History, Tuscaloosa, Alabama
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5
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Kenny NJ, McCarthy SA, Dudchenko O, James K, Betteridge E, Corton C, Dolucan J, Mead D, Oliver K, Omer AD, Pelan S, Ryan Y, Sims Y, Skelton J, Smith M, Torrance J, Weisz D, Wipat A, Aiden EL, Howe K, Williams ST. The gene-rich genome of the scallop Pecten maximus. Gigascience 2020; 9:giaa037. [PMID: 32352532 PMCID: PMC7191990 DOI: 10.1093/gigascience/giaa037] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/26/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. FINDINGS Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. CONCLUSIONS The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
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Affiliation(s)
- Nathan J Kenny
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | - Shane A McCarthy
- University of Cambridge, Department of Genetics,Cambridge CB2 3EH, UK
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
| | - Katherine James
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | | | - Craig Corton
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Jale Dolucan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Dan Mead
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Pelan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Yan Ryan
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Institute of Infection and Global Health, Liverpool University, iC2, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | | | | | | | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Erez L Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China
- School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Kerstin Howe
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Suzanne T Williams
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
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6
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Hierarchical biogeographical processes largely explain the genomic divergence pattern in a species complex of sea anemones (Metridioidea: Sagartiidae: Anthothoe). Mol Phylogenet Evol 2018; 127:217-228. [DOI: 10.1016/j.ympev.2018.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 11/20/2022]
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7
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Teske PR, Golla TR, Sandoval-Castillo J, Emami-Khoyi A, van der Lingen CD, von der Heyden S, Chiazzari B, Jansen van Vuuren B, Beheregaray LB. Mitochondrial DNA is unsuitable to test for isolation by distance. Sci Rep 2018; 8:8448. [PMID: 29855482 PMCID: PMC5981212 DOI: 10.1038/s41598-018-25138-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/16/2018] [Indexed: 12/04/2022] Open
Abstract
Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species' true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.
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Affiliation(s)
- Peter R Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa.
| | - Tirupathi Rao Golla
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Carl D van der Lingen
- Branch: Fisheries Management, Department of Agriculture, Forestry and Fisheries, Private Bag X2, Vlaeberg, 8012, South Africa
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Private Bag X3, Rondebosch, 7700, South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, 7602, Matieland, South Africa
| | - Brent Chiazzari
- School of Life Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Luciano B Beheregaray
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
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8
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Mallien C, Porro B, Zamoum T, Olivier C, Wiedenmann J, Furla P, Forcioli D. Conspicuous morphological differentiation without speciation in Anemonia viridis (Cnidaria, Actiniaria). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1383948] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Cédric Mallien
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Barbara Porro
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Thamilla Zamoum
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Caroline Olivier
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Jörg Wiedenmann
- Coral Reef Laboratory, Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Paola Furla
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
| | - Didier Forcioli
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine – Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France
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9
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David P, Perdieu MA, Pernot AF, Jarne P. FINE-GRAINED SPATIAL AND TEMPORAL POPULATION GENETIC STRUCTURE IN THE MARINE BIVALVE SPISULA OVALIS. Evolution 2017; 51:1318-1322. [PMID: 28565480 DOI: 10.1111/j.1558-5646.1997.tb03979.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/1996] [Accepted: 03/06/1997] [Indexed: 11/27/2022]
Affiliation(s)
- Patrice David
- Génétique et Environnement, CC 065, Université Montpellier II, F34095, Montpellier Cedex 05, France
| | - Mireille-Ange Perdieu
- Génétique et Environnement, CC 065, Université Montpellier II, F34095, Montpellier Cedex 05, France
| | - Anne-Françoise Pernot
- Génétique et Environnement, CC 065, Université Montpellier II, F34095, Montpellier Cedex 05, France
| | - Philippe Jarne
- Génétique et Environnement, CC 065, Université Montpellier II, F34095, Montpellier Cedex 05, France
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Klautau M, Russo CAM, Lazoski C, Boury-Esnault N, Thorpe JP, Solé-Cava AM. DOES COSMOPOLITANISM RESULT FROM OVERCONSERVATIVE SYSTEMATICS? A CASE STUDY USING THE MARINE SPONGE CHONDRILLA NUCULA. Evolution 2017; 53:1414-1422. [PMID: 28565563 DOI: 10.1111/j.1558-5646.1999.tb05406.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/1998] [Accepted: 04/20/1999] [Indexed: 11/30/2022]
Abstract
The sponge species Chondrilla nucula has a simple morphology and a very wide geographical distribution. To verify whether the latter might be an artifact of the former, samples of this species were collected across 10,000 km of its range, in the Mediterranean, the Caribbean, and the southwestern atlantic. The classical (spicule morphology) and molecular (allozymes) systematic approaches were compared, to try to define the geographic limits between populations and detect possible cryptic species. We found five distinct genetic forms within C. nucula that sometimes showed morphological homogeneity and other times plasticity. The difference in size of spicules could not be related to the clear-cut genetic differences, suggesting that the use of spicule sizes for sponge systematics should be reappraised. The population of one of the genetic forms along 3000 km of the Brazilian coast was highly structured (FST = 0.21; Ne m = 0.96). Our results reject the null hypothesis of cosmopolitanism of C. nucula and indicate that the putative worldwide distribution of some marine sponges, and possibly many other benthic invertebrates, may be the result of overly conservative systematics. Cryptic species appear to be particularly prevalent when genera are well defined but species are characterized by only a few morphological characters.
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Affiliation(s)
- Michelle Klautau
- Departamento de Genética, Instituto de Biologia, Bloco A, CCS, Universidade Federal do Rio de Janeiro, Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brazil
| | - Claudia A M Russo
- Departamento de Genética, Instituto de Biologia, Bloco A, CCS, Universidade Federal do Rio de Janeiro, Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brazil
| | - Cristiano Lazoski
- Departamento de Genética, Instituto de Biologia, Bloco A, CCS, Universidade Federal do Rio de Janeiro, Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brazil
| | - Nicole Boury-Esnault
- Centre d'Océanologie de Marseille, Station Marine d'Endoume, Université de la Méditerranée, UMR-CNRS 6540, Marseille, France
| | - John P Thorpe
- Port Erin Marine Laboratory, University of Liverpool, Isle of Man, IM9 6JA, United Kingdom
| | - Antonio M Solé-Cava
- Departamento de Genética, Instituto de Biologia, Bloco A, CCS, Universidade Federal do Rio de Janeiro, Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brazil.,Port Erin Marine Laboratory, University of Liverpool, Isle of Man, IM9 6JA, United Kingdom
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11
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Coelho-Bortolo T, Mangolin CA, Lapenta AS. Genetic variability in the natural populations of Lasioderma serricorne (F.) (Coleoptera: Anobiidae), detected by RAPD markers and by esterase isozymes. BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:47-53. [PMID: 26459013 DOI: 10.1017/s0007485315000723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Lasioderma serricorne (F.) is a small cosmopolitan beetle regarded as a destructive pest of several stored products such as grains, flour, spices, dried fruit and tobacco. Chemical insecticides are one of the measures used against the pest. However, intensive insecticide use has resulted in the appearance of resistant insect populations. Therefore, for the elaboration of more effective control programs, it is necessary to know the biological aspects of L. serricorne. Among these aspects, the genetic variability knowledge is very important and may help in the development of new control methods. The objective of this study was to evaluate the genetic variability of 11 natural populations of L. serricorne collected respectively in three and four towns in the states of Paraná and São Paulo, Brazil, using 20 primers random amplified polymorphic DNA (RAPD) and polymorphisms of esterases. These primers produced 352 polymorphic bands. Electrophoretic analysis of esterases allowed the identification of four polymorphic loci (Est-2, Est-4, Est-5 and Est-6) and 18 alleles. Results show that populations are genetically differentiated and there is a high level of genetic variability within populations. The high degree of genetic differentiation is not directly correlated to geographical distance. Thus, our data indicate that movement of infested commodities may contribute to the dissemination of L. serricorne, facilitating gene flow.
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Affiliation(s)
- T Coelho-Bortolo
- Department of Cell Biology and Genetics,State University of Maringá,87020-900 Maringá,Paraná,Brazil
| | - C A Mangolin
- Department of Cell Biology and Genetics,State University of Maringá,87020-900 Maringá,Paraná,Brazil
| | - A S Lapenta
- Department of Cell Biology and Genetics,State University of Maringá,87020-900 Maringá,Paraná,Brazil
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12
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Genetic variation and species identification among selected leeches (Hirudinea) revealed by RAPD markers. Biologia (Bratisl) 2012. [DOI: 10.2478/s11756-012-0063-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Abstract
Recent advances in deep-sea exploration technology coupled with an increase in worldwide biotic surveys, biological research, and underwater photography in shallow water marine regions such as coral reefs, has allowed for a relatively rapid expansion of our knowledge in the global diversity of many groups of marine organisms. This paper is part of the PLoS ONE review collection of WoRMS (the Worldwide Register of Marine Species), on the global diversity of marine species, and treats the pennatulacean octocorals, a group of cnidarians commonly referred to as sea pens or sea feathers. This also includes sea pansies, some sea whips, and various vermiform taxa. Pennatulaceans are a morphologically diverse group with an estimated 200 or more valid species, displaying worldwide geographic and bathymetric distributions from polar seas to the equatorial tropics and from intertidal flats to over 6100 m in depth. The paper treats new discoveries and taxa new to science, and provides greater resolution in geographic and bathymetric distributions data than was previously known, as well as descriptions of life appearances in life and in situ observations at diverse depth.
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Affiliation(s)
- Gary C Williams
- California Academy of Sciences, San Francisco, California, United States of America.
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14
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Abstract
SummaryThree tests of neutral theory were carried out using a large dataset of vertebrate allozyme studies. The first test considered the relationship between the mean and variance of single locus heterozygosity across a sample of enzymes and non-enzymatic proteins. The second test compared the distributions of heterozygosity between paired proteins in balanced datasets in which each protein is scored for the same sample of species. The third test compared the observed distribution of single locus heterozygosity with theoretical distributions predicted by neutral theory. The results show an excellent quantitative fit with the predictions of neutral theory, though some small deviations from neutrality were observed which are consistent with the action of natural selection.
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Abstract
Worldwide degradation of coral reef communities has prompted a surge in restoration efforts. They proceed largely without considering genetic factors because traditionally, coral populations have been regarded as open over large areas with little potential for local adaptation. Since, biophysical and molecular studies indicated that most populations are closed over shorter time and smaller spatial scales. Thus, it is justified to re-examine the potential for site adaptation in corals. There is ample evidence for differentiated populations, inbreeding, asexual reproduction and the occurrence of ecotypes, factors that may facilitate local adaptation. Discovery of widespread local adaptation would influence coral restoration projects mainly with regard to the physical and evolutionary distance from the source wild and/or captive bred propagules may be moved without causing a loss of fitness in the restored population. Proposed causes for loss of fitness as a result of (plant) restoration efforts include founder effects, genetic swamping, inbreeding and/or outbreeding depression. Direct evidence for any of these processes is scarce in reef corals due to a lack of model species that allow for testing over multiple generations and the separation of the relative contributions of algal symbionts and their coral hosts to the overall performance of the coral colony. This gap in our knowledge may be closed by employing novel population genetic and genomics approaches. The use of molecular tools may aid managers in the selection of appropriate propagule sources, guide spatial arrangement of transplants, and help in assessing the success of coral restoration projects by tracking the performance of transplants, thereby generating important data for future coral reef conservation and restoration projects.
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Affiliation(s)
- Iliana B Baums
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, USA.
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16
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Sauvage C, Bierne N, Lapègue S, Boudry P. Single Nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene 2007; 406:13-22. [PMID: 17616269 DOI: 10.1016/j.gene.2007.05.011] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 05/14/2007] [Accepted: 05/18/2007] [Indexed: 10/23/2022]
Abstract
DNA sequence polymorphism and codon usage bias were investigated in a set of 41 nuclear loci in the Pacific oyster Crassostrea gigas. Our results revealed a very high level of DNA polymorphism in oysters, in the order of magnitude of the highest levels reported in animals to date. A total of 290 single nucleotide polymorphisms (SNPs) were detected, 76 of which being localised in exons and 214 in non-coding regions. Average density of SNPs was estimated to be one SNP every 60 bp in coding regions and one every 40 bp in non-coding regions. Non-synonymous substitutions contributed substantially to the polymorphism observed in coding regions. The non-synonymous to silent diversity ratio was 0.16 on average, which is fairly higher to the ratio reported in other invertebrate species recognised to display large population sizes. Therefore, purifying selection does not appear to be as strong as it could have been expected for a species with a large effective population size. The level of non-synonymous diversity varied greatly from one gene to another, in accordance with varying selective constraints. We examined codon usage bias and its relationship with DNA polymorphism. The table of optimal codons was deduced from the analysis of an EST dataset, using EST counts as a rough assessment of gene expression. As recently observed in some other taxa, we found a strong and significant negative relationship between codon bias and non-synonymous diversity suggesting correlated selective constraints on synonymous and non-synonymous substitutions. Codon bias as measured by the frequency of optimal codons for expression might therefore provide a useful indicator of the level of constraint upon proteins in the oyster genome.
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Affiliation(s)
- C Sauvage
- Laboratoire de Génétique et Pathologie - IFREMER - La Tremblade, France
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17
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José J, Solferini VN. Population genetics of Collisella subrugosa (Patellogastropoda: Acmaeidae): evidence of two scales of population structure. Genetica 2006; 130:73-82. [PMID: 16897456 DOI: 10.1007/s10709-006-0024-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Accepted: 05/31/2006] [Indexed: 11/30/2022]
Abstract
Marine invertebrate populations usually show high levels of genetic variability that has frequently been associated with spatial and temporal environmental heterogeneity. One of the most heterogeneous marine environments is the intertidal zone, the habitat of Collisella subrugosa, the most widespread and abundant Brazilian limpet. C. subrugosa has planktonic larvae that can disperse over long distances, what can promote gene flow among shores, working against interpopulational differentiation. In this study we investigated the genetic variability and populational substructure of C. subrugosa through analysis of 24 allozyme loci in 14 samples (590 individuals) collected along 2,700 km of the Brazilian coast. The genetic variability was high ([Formula: see text] and [Formula: see text]), as expected for intertidal species. Genetic differentiation among samples was low (F (ST) = 0.03) what may reflect intensive gene flow associated with larval dispersal. However, we detected an isolation-by-distance pattern of population substructure in one sampled region. High levels of heterozygote deficiency were also observed for many loci in each sample. Alternative hypothesis are discussed, and the "breeding groups" is suggested to explain these pattern, indicating the main cause as environmental heterogeneity.
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Affiliation(s)
- Juliana José
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), CP6109, Campinas, São Paulo, Brazil.
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18
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Andrade SCS, Magalhaes CA, Solferini VN. Patterns of genetic variability in Brazilian Littorinids (Mollusca): a macrogeographic approach. J ZOOL SYST EVOL RES 2003. [DOI: 10.1046/j.1439-0469.2003.00227.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Manchenko GP, Dautova TN, Latypov YY. High level of genetic divergence between sympatric color morphs of the littoral sea anemone Anthopleura orientalis (Anthozoa: Actiniaria). BIOCHEM SYST ECOL 2000; 28:737-750. [PMID: 10856633 DOI: 10.1016/s0305-1978(99)00120-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using enzyme electrophoresis and nematocyst analysis, the sympatrically occurring "light" and "dark" color morphs of the sea anemone Anthopleura orientalis from the Sea of Japan were shown to be two valid species. The "light" morph was identified as A. orientalis (Averintsev, 1967 Issledovaniya fauny morei: Vyp. 5 (13). Nanka, Leningrad, pp. 62-77), while the "dark" morph was designated as Anthopleura sp. The analysis of 21 isozyme loci revealed high value of Nei's genetic distance (D=1.284) between the two species, which are indistinguishable in their external morphology. The mean values of observed and expected heterozygosities for A. orientalis and Anthopleura sp. are high (H(o)=0.252+/-0.061, H(e)=0.250+/-0.061 and H(o)=0.327+/-0.052, H(e)=0.351+/-0.054, respectively). The species differ significantly in the size of spirocysts and nematocysts, among which the atrichs from acrorhagi and the basitrichs from actinopharynx contribute most to the observed difference. Strong qualitative difference is revealed between distributions of nematocysts in mesenteric filaments of the two sea anemone species studied. The possible conspecificity of Anthopleura sp. with Anthopleura artemisia (Dana, 1848) is discussed and the conclusion made that these are two separate species.
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Affiliation(s)
- GP Manchenko
- Institute of Marine Biology, 690041, Vladivostok, Russia
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20
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Warwick RM, Robinson J. Sibling species in the marine pollution indicator genusPontonemaLeidy (Nematoda: Oncholaimidae), with a description ofP. mediterraneasp. nov. J NAT HIST 2000. [DOI: 10.1080/002229300299327] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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21
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22
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Pancer Z, Skorokhod A, Blumbach B, Müller WE. Multiple Ig-like featuring genes divergent within and among individuals of the marine sponge Geodia cydonium. Gene 1998; 207:227-33. [PMID: 9511765 DOI: 10.1016/s0378-1119(97)00631-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The receptor tyrosine kinase of the marine sponge Geodia cydonium features two extracellular Ig-like domains in which we recently documented RT-PCR polymorphism among individuals. Genomic-PCR analysis presented here revealed 14 unique sequences from four sponges, differing predominantly in the sequence of an intron which splits the Ig-like domains. Nevertheless, analysis of putative coding regions in 19 distinct clones (156-159 aa) from seven sponges revealed 69 positions of nucleotide substitutions, 67.6% of them non-synonymous, translating into 43 positions of divergent residues. Excluding aa deletions, these 19 sequences share pairwise aa identities of 89-99%. In three sponges, four or five unique Ig-like coding regions were scored. PCR amplification across this intron revealed multiple bands, polymorphic among five of six sponges. Further substantiated by Southern and Northern blots, it is evident that the genome of G. cydonium harbors multicopies of moderately divergent Ig-like domains. Presently, this only appears paralleled by the human KIR multigene family of NK cells MHC class I-specific receptors, which consist of two or three moderately divergent extracellular Ig-like domains.
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Affiliation(s)
- Z Pancer
- Institut für Physiologische Chemie, Abteilung Angewandte Molekularbiologie, Universität, Mainz, Germany
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Fernàndez-Busquets X, Burger MM. The main protein of the aggregation factor responsible for species-specific cell adhesion in the marine sponge Microciona prolifera is highly polymorphic. J Biol Chem 1997; 272:27839-47. [PMID: 9346930 DOI: 10.1074/jbc.272.44.27839] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Species-specific cell recognition in sponges, the oldest living metazoans, is based on a proteoglycan-like aggregation factor. We have screened individual sponge cDNA libraries, identifying multiple related forms for the aggregation factor core protein (MAFp3). Northern blots show the presence in several human tissues of transcripts strongly binding a MAFp3-specific probe. The open reading frame for MAFp3 is not interrupted in the 5' direction, revealing variable protein sequences that contain numerous introns equally spaced. We have studied tissue histocompatibility within a sponge population, finding 100% correlation between rejection behavior and the individual-specific restriction fragment length polymorphism pattern using aggregation factor-related probes. PCR amplifications with specific primers showed that at least some of the MAFp3 forms are allelic and distribute in the population used. A pronounced polymorphism is also observed when analyzing purified aggregation factor in polyacrylamide gels. Protease digestion of the polymorphic glycosaminoglycan-containing bands indicates that glycans are also responsible for the variability. The data presented reveal a high polymorphism of aggregation factor components, which matches the elevated sponge alloincompatibility, suggesting an involvement of the cell adhesion system in sponge allogeneic reactions.
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Klautau M, Solé-Cava AM, Borojevic R. Biochemical systematics of sibling sympatric species of Clathrina (Porifera: Calcarea). BIOCHEM SYST ECOL 1994. [DOI: 10.1016/0305-1978(94)90027-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Boury-Esnault N, Sole-Cava A, Thorpe J. Genetic and cytological divergence between colour morphs of the Mediterranean spongeOscarella lobularisSchmidt (Porifera, Demospongiae, Oscarellidae). J NAT HIST 1992. [DOI: 10.1080/00222939200770131] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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