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Briones C, Nuñez JJ, Pérez M, Garrido O, Campos B, Godoy K, Hartley R, Oyarzún PA, Guiñez R. Linking Acrosome Size and Genetic Divergence in an Inter-Oceanic Mussel from the Pacific and Atlantic Coasts: A Case of Incipient Speciation? Animals (Basel) 2024; 14:674. [PMID: 38473058 DOI: 10.3390/ani14050674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
In recent years, advances in analyses of the sperm morphology and genetics of Perumytilus purpuratus have allowed to two evolutionary scenarios for this mussel to be suggested: (1) the scenario of cryptic species and (2) the scenario of incipient or in progress speciation. For a better understanding of the evolutionary history of P. purpuratus, we performed extensive sampling along a latitudinal gradient of ca. 7180 km of coastline-from the Southern Pacific Ocean to the Atlantic Ocean-and we delved deeper into the sperm morphology of P. purpuratus, exploring its association with the phylogeny and population genetics to determine whether the variability in sperm traits between the northern and southern regions was a signal of cryptic or incipient species. Overall, our results showed that sperm sizes were strongly correlated with the genetic structure in males of P. purpuratus. We identified at 37° S on the Pacific coast a coincident break of both sperm size and genetic disruption that can be explained by historical events and postglacial recolonization as causal phenomena for the observed divergences. Furthermore, evidence of genetic admixture between lineages was found at 38° S, suggesting the presence of an introgressive hybridization zone and incomplete reproductive isolation in an in fraganti or incipient speciation process.
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Affiliation(s)
- Carolina Briones
- Instituto de Ciencias Naturales Alexander von Humbodt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta 1270300, Chile
| | - José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia 5090000, Chile
| | - Montse Pérez
- AquaCOV, Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas (IEO, CSIC), 36390 Vigo, Spain
| | - Orlando Garrido
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia 5090000, Chile
| | | | - Karina Godoy
- Núcleo Científico y Tecnológico de Biorecursos (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
| | - Ricardo Hartley
- Instituto de Investigación y Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Central de Chile, Santiago 8330507, Chile
| | - Pablo A Oyarzún
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay 2340000, Chile
| | - Ricardo Guiñez
- Instituto de Ciencias Naturales Alexander von Humbodt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta 1270300, Chile
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Martínez M, Harms L, Abele D, Held C. Mitochondrial Heteroplasmy and PCR Amplification Bias Lead to Wrong Species Delimitation with High Confidence in the South American and Antarctic Marine Bivalve Aequiyoldia eightsii Species Complex. Genes (Basel) 2023; 14:genes14040935. [PMID: 37107693 PMCID: PMC10138075 DOI: 10.3390/genes14040935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The species delimitation of the marine bivalve species complex Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. In this study, we compare different data sources (mitochondrial cytochrome c oxidase subunit I (COI) sequences; nuclear and mitochondrial SNPs). Whilst all the data suggest that populations on either side of the Drake Passage belong to different species, the picture is less clear within Antarctic populations, which harbor three distinct mitochondrial lineages (p-dist ≈ 6%) that coexist in populations and in a subset of individuals with heteroplasmy. Standard barcoding procedures lead to amplification bias favoring either haplotype unpredictably and thus overestimate the species richness with high confidence. However, nuclear SNPs show no differentiation akin to the trans-Drake comparison, suggesting that the Antarctic populations represent a single species. Their distinct haplotypes likely evolved during periods of temporary allopatry, whereas recombination eroded similar differentiation patterns in the nuclear genome after secondary contact. Our study highlights the importance of using multiple data sources and careful quality control measures to avoid bias and increase the accuracy of molecular species delimitation. We recommend an active search for mitochondrial heteroplasmy and haplotype-specific primers for amplification in DNA-barcoding studies.
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Affiliation(s)
- Mariano Martínez
- Functional Ecology, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Oceanografía y Ecología Marina, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Lars Harms
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Herrstrasse 231, 26129 Oldenburg, Germany
| | - Doris Abele
- Functional Ecology, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Christoph Held
- Functional Ecology, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, Germany
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3
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Lubośny M, Śmietanka B, Arculeo M, Burzyński A. No evidence of DUI in the Mediterranean alien species Brachidontes pharaonis (P. Fisher, 1870) despite mitochondrial heteroplasmy. Sci Rep 2022; 12:8569. [PMID: 35595866 PMCID: PMC9122905 DOI: 10.1038/s41598-022-12606-6] [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: 12/09/2021] [Accepted: 05/13/2022] [Indexed: 01/05/2023] Open
Abstract
Two genetically different mitochondrial haplogroups of Brachidontes pharaonis (p-distance 6.8%) have been identified in the Mediterranean Sea. This hinted at a possible presence of doubly uniparental inheritance in this species. To ascertain this possibility, we sequenced two complete mitogenomes of Brachidontes pharaonis mussels and performed a qPCR analysis to measure the relative mitogenome copy numbers of both mtDNAs. Despite the presence of two very similar regions composed entirely of repetitive sequences in the two haplogroups, no recombination between mitogenomes was detected. In heteroplasmic individuals, both mitogenomes were present in the generative tissues of both sexes, which argues against the presence of doubly uniparental inheritance in this species.
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Marco Arculeo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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4
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Mohammed-Geba K, Sheir SK, El-Aziz Hamed EA, Galal-Khallaf A. Molecular and morphological signatures for extreme environmental adaptability of the invasive mussel Brachidontes pharaonis (Fischer, 1870). Mol Cell Probes 2020; 53:101594. [PMID: 32437883 DOI: 10.1016/j.mcp.2020.101594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/16/2020] [Accepted: 05/05/2020] [Indexed: 11/29/2022]
Abstract
Brachidontes pharaonis (Bivalvia:Mytilidae) is one of the most successful Lessepsian migrants. Its extensive populations' expansion and phenotypic plasticity might reshape the Mediterranean biodiversity. Individuals of B. pharaonis were collected from various sites in the Mediterranean Sea and the Red Sea in Egypt. Species-specific primers for Cytochrome Oxidase Subunit 1 gene were designed. They were applied for analysis of mussel's population genetics and assessment of its aquatic environmental DNA (eDNA) abundance. Morphological, allometric and morphometric characteristics were also described. The newly designed primers could efficiently detect the species presence, abundance, and genetic diversity. The Northern Red Sea and north-westward populations exhibited higher nucleotide diversities than southwards. Phylogeny and principal coordinates' analysis (PCoA) detected three geographical categories for B. pharaonis: one of the Indian Ocean, other of the Middle Red Sea and southwards, and the other extends from the Northern Red Sea to the westernmost part of the Mediterranean. Intraspecific differences in the shell shape, colour, and biometrics were noted. The shells were significantly smaller and lighter in rocky habitats than in sandy ones. The morphometric indices and allometry were significantly different between rocky and sandy environments. In general, B. pharaonis genetic and morphological features appeared to contribute much to the species success in versatile habitats.
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Affiliation(s)
- Khaled Mohammed-Geba
- Molecular Biology and Biotechnology Laboratory, Department of Zoology, Faculty of Sciences, Menoufia University, Shebin El-Kom, Menoufia, Egypt.
| | - Sherin K Sheir
- Invertebrates Division, Department of Zoology, Faculty of Sciences, Menoufia University, Shebin El-Kom, Menoufia, Egypt
| | | | - Asmaa Galal-Khallaf
- Molecular Biology and Biotechnology Laboratory, Department of Zoology, Faculty of Sciences, Menoufia University, Shebin El-Kom, Menoufia, Egypt
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5
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Maas DL, Prost S, Bi K, Smith LL, Armstrong EE, Aji LP, Toha AHA, Gillespie RG, Becking LE. Rapid divergence of mussel populations despite incomplete barriers to dispersal. Mol Ecol 2018; 27:1556-1571. [DOI: 10.1111/mec.14556] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Diede L. Maas
- Department of Marine Animal Ecology; Wageningen University & Research; Wageningen The Netherlands
| | - Stefan Prost
- Department of Biology; Stanford University; Stanford CA USA
- Department of Integrative Biology; Center for Theoretical Evolutionary Genomics; University of California; Berkeley CA USA
| | - Ke Bi
- Museum of Vertebrate Zoology; University of California; Berkeley CA USA
- Computational Genomics Resource Laboratory; California Institute for Quantitative Biosciences; University of California; Berkley CA USA
| | - Lydia L. Smith
- Museum of Vertebrate Zoology; University of California; Berkeley CA USA
| | | | - Ludi P. Aji
- Research Centre for Oceanography; Indonesian Institute of Sciences; Jakarta Indonesia
| | | | - Rosemary G. Gillespie
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
| | - Leontine E. Becking
- Department of Marine Animal Ecology; Wageningen University & Research; Wageningen The Netherlands
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
- Wageningen Marine Research; Den Helder The Netherlands
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6
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García-Souto D, Sumner-Hempel A, Fervenza S, Pérez-García C, Torreiro A, González-Romero R, Eirín-López JM, Morán P, Pasantes JJ. Detection of invasive and cryptic species in marine mussels (Bivalvia, Mytilidae): A chromosomal perspective. J Nat Conserv 2017. [DOI: 10.1016/j.jnc.2017.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Tomašových A, Kennedy JD, Betzner TJ, Kuehnle NB, Edie S, Kim S, Supriya K, White AE, Rahbek C, Huang S, Price TD, Jablonski D. Unifying latitudinal gradients in range size and richness across marine and terrestrial systems. Proc Biol Sci 2017; 283:rspb.2015.3027. [PMID: 27147094 DOI: 10.1098/rspb.2015.3027] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/08/2016] [Indexed: 11/12/2022] Open
Abstract
Many marine and terrestrial clades show similar latitudinal gradients in species richness, but opposite gradients in range size-on land, ranges are the smallest in the tropics, whereas in the sea, ranges are the largest in the tropics. Therefore, richness gradients in marine and terrestrial systems do not arise from a shared latitudinal arrangement of species range sizes. Comparing terrestrial birds and marine bivalves, we find that gradients in range size are concordant at the level of genera. Here, both groups show a nested pattern in which narrow-ranging genera are confined to the tropics and broad-ranging genera extend across much of the gradient. We find that (i) genus range size and its variation with latitude is closely associated with per-genus species richness and (ii) broad-ranging genera contain more species both within and outside of the tropics when compared with tropical- or temperate-only genera. Within-genus species diversification thus promotes genus expansion to novel latitudes. Despite underlying differences in the species range-size gradients, species-rich genera are more likely to produce a descendant that extends its range relative to the ancestor's range. These results unify species richness gradients with those of genera, implying that birds and bivalves share similar latitudinal dynamics in net species diversification.
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Affiliation(s)
- Adam Tomašových
- Earth Science Institute, Slovak Academy of Sciences, 84005 Bratislava, Slovakia
| | - Jonathan D Kennedy
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Tristan J Betzner
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | | | - Stewart Edie
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Sora Kim
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - K Supriya
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
| | - Alexander E White
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen, Denmark Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, West Berkshire SL5 7PY, UK
| | - Shan Huang
- Senckenberg Biodiversity and Climate Research Center (BiK-F), 60325 Frankfurt am Main, Germany
| | - Trevor D Price
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - David Jablonski
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
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8
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Gusman A, Lecomte S, Stewart DT, Passamonti M, Breton S. Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA. PeerJ 2016; 4:e2760. [PMID: 27994972 PMCID: PMC5157197 DOI: 10.7717/peerj.2760] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 11/05/2016] [Indexed: 11/20/2022] Open
Abstract
There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA) in the animal kingdom: a system named doubly uniparental inheritance (DUI), which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI) in two bivalve species, i.e., the nuculanoid Yoldia hyperborea(Gould, 1841)and the veneroid Scrobicularia plana(Da Costa,1778), increasing the number of families in which DUI has been found by two. An update on the taxonomic distribution of DUI in the Bivalvia is also presented.
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Affiliation(s)
- Arthur Gusman
- Department of Biological Sciences, Université de Montréal , Montréal , Québec , Canada
| | - Sophia Lecomte
- Department of Biological Sciences, Université de Strasbourg , Strasbourg , France
| | - Donald T Stewart
- Department of Biology, Acadia University , Wolfville , Nova Scotia , Canada
| | - Marco Passamonti
- Department of Biological Geological and Environmental Sciences, University of Bologna , Bologna , Italy
| | - Sophie Breton
- Department of Biological Sciences, Université de Montréal , Montréal , Québec , Canada
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9
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Becking LE, de Leeuw CA, Knegt B, Maas DL, de Voogd NJ, Abdunnur, Suyatna I, Peijnenburg KTCA. Highly divergent mussel lineages in isolated Indonesian marine lakes. PeerJ 2016; 4:e2496. [PMID: 27761314 PMCID: PMC5068364 DOI: 10.7717/peerj.2496] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/27/2016] [Indexed: 11/20/2022] Open
Abstract
Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the mussel Brachidontes from marine lakes in Berau, East Kalimantan (Indonesia) are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI)), and two nuclear markers (18S and 28S). In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations of Brachidontes spp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence), two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%), we suggest that this may have resulted from in situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present). Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago.
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Affiliation(s)
- Leontine E Becking
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA; Department of Marine Animal Ecology, Wageningen University & Research, Wageningen, The Netherlands; Department of Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Christiaan A de Leeuw
- Department of Marine Animal Ecology, Wageningen University & Research, Wageningen, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Bram Knegt
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam , The Netherlands
| | - Diede L Maas
- Department of Marine Animal Ecology, Wageningen University & Research , Wageningen , The Netherlands
| | - Nicole J de Voogd
- Department of Marine Biodiversity, Naturalis Biodiversity Center , Leiden , The Netherlands
| | - Abdunnur
- Faculty of Fisheries and Marine Sciences, Mulawarman University , Samarinda , East Kalimantan , Indonesia
| | - Iwan Suyatna
- Faculty of Fisheries and Marine Sciences, Mulawarman University , Samarinda , East Kalimantan , Indonesia
| | - Katja T C A Peijnenburg
- Department of Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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10
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Fourdrilis S, Mardulyn P, Hardy OJ, Jordaens K, de Frias Martins AM, Backeljau T. Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda). PeerJ 2016; 4:e2549. [PMID: 27761337 PMCID: PMC5068447 DOI: 10.7717/peerj.2549] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022] Open
Abstract
We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M. neritoides is characterized by extremely high haplotype diversity (Hd = 0.999 ± 0.001), high nucleotide diversity (π = 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn = 0.0677). Haplotype richness is very high even at spatial scales as small as 100m2. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identify M. neritoides. The mtDNA hyperdiversity in M. neritoides is best explained by the remarkably high mutation rate at the COI locus (μ = 5.82 × 10−5 per site per year or μ = 1.99 × 10−4 mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne = 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to high μ values and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.
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Affiliation(s)
- Séverine Fourdrilis
- Directorate Taxonomy and Phylogeny & JEMU, Royal Belgian Institute of Natural Sciences , Brussels , Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles , Brussels , Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology, Université Libre de Bruxelles , Brussels , Belgium
| | - Kurt Jordaens
- Department of Biology, Invertebrate Section, Royal Museum for Central Africa , Tervuren , Belgium
| | - António Manuel de Frias Martins
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Departamento de Biologia da Universidade dos Açores, University of the Azores , Ponta Delgada , Portugal
| | - Thierry Backeljau
- Directorate Taxonomy and Phylogeny & JEMU, Royal Belgian Institute of Natural Sciences, Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
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11
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Devloo-Delva F, Miralles L, Ardura A, Borrell YJ, Pejovic I, Tsartsianidou V, Garcia-Vazquez E. Detection and characterisation of the biopollutant Xenostrobus securis (Lamarck 1819) Asturian population from DNA Barcoding and eBarcoding. MARINE POLLUTION BULLETIN 2016; 105:23-29. [PMID: 26971231 DOI: 10.1016/j.marpolbul.2016.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/01/2016] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
DNA efficiently contributes to detect and understand marine invasions. In 2014 the potential biological pollutant pygmy mussel (Xenostrobus securis) was observed for the first time in the Avilés estuary (Asturias, Bay of Biscay). The goal of this study was to assess the stage of invasion, based on demographic and genetic (DNA Barcoding) characteristics, and to develop a molecular tool for surveying the species in environmental DNA. A total of 130 individuals were analysed for the DNA Barcode cytochrome oxidase I gene in order to determine genetic diversity, population structure, expansion trends, and to inferring introduction hits. Reproduction was evidenced by bimodal size distributions of 1597 mussels. High population genetic variation and genetically distinct clades might suggest multiple introductions from several source populations. Finally, species-specific primers were developed within the DNA barcode for PCR amplification from water samples in order to enabling rapid detection of the species in initial expansion stages.
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Affiliation(s)
- Floriaan Devloo-Delva
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Laura Miralles
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Alba Ardura
- USR3278-CRIOBE-CNRS-EPHE. Laboratoire d'excellence "CORAIL". Université de Perpignan-CBETM. 58 Rue Paul Alduy. 66860-Perpignan, CEDEX. France
| | - Yaisel J Borrell
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Ivana Pejovic
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Valentina Tsartsianidou
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/ Julián Clavería s/n, 33006 Oviedo, Spain.
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12
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Trovant B, Basso NG, Orensanz JM, Lessa EP, Dincao F, Ruzzante DE. Scorched mussels (Brachidontes spp., Bivalvia: Mytilidae) from the tropical and warm-temperate southwestern Atlantic: the role of the Amazon River in their speciation. Ecol Evol 2016; 6:1778-98. [PMID: 26929816 PMCID: PMC4758806 DOI: 10.1002/ece3.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 11/16/2022] Open
Abstract
Antitropicality is a distribution pattern where closely related taxa are separated by an intertropical latitudinal gap. Two potential examples include Brachidontes darwinianus (south eastern Brazil to Uruguay), considered by some authors as a synonym of B. exustus (Gulf of Mexico and the Caribbean), and B. solisianus, distributed along the Brazilian coast with dubious records north of the intertropical zone. Using two nuclear (18S and 28S rDNA) and one mitochondrial gene (mtDNA COI), we aimed to elucidate the phylogeographic and phylogenetic relationships among the scorched mussels present in the warm-temperate region of the southwest Atlantic. We evaluated a divergence process mediated by the tropical zone over alternative phylogeographic hypotheses. Brachidontes solisianus was closely related to B. exustus I, a species with which it exhibits an antitropical distribution. Their divergence time was approximately 2.6 Ma, consistent with the intensification of Amazon River flow. Brachidontes darwinianus, an estuarine species is shown here not to be related to this B. exustus complex. We suspect ancestral forms may have dispersed from the Caribbean to the Atlantic coast via the Trans-Amazonian seaway (Miocene). The third species, B rodriguezii is presumed to have a long history in the region with related fossil forms going back to the Miocene. Although scorched mussels are very similar in appearance, their evolutionary histories are very different, involving major historical contingencies as the formation of the Amazon River, the Panama Isthmus, and the last marine transgression.
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Affiliation(s)
- Berenice Trovant
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Néstor G. Basso
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - José María Orensanz
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Enrique P. Lessa
- Departamento de Ecología y EvoluciónFacultad de CienciasUniversidad de la RepúblicaIguá 4225C.P. 11400MontevideoUruguay
| | - Fernando Dincao
- Universidade Federal do Rio Grande – FURGAv. Itália km 8 Bairro Carreiros96203‐900Rio GrandeBrazil
| | - Daniel E. Ruzzante
- Department of BiologyDalhousie University1355 Oxford St.HalifaxNova ScotiaB3H 4R2Canada
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Vargas J, Pérez M, Toro J, Astorga MP. Presence of two mitochondrial genomes in the mytilid Perumytilus purpuratus: Phylogenetic evidence for doubly uniparental inheritance. Genet Mol Biol 2015; 38:173-81. [PMID: 26273220 PMCID: PMC4530645 DOI: 10.1590/s1415-47573822201420140262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 01/22/2015] [Indexed: 11/24/2022] Open
Abstract
This study presents evidence, using sequences of ribosomal 16S and COI mtDNA, for the presence of two mitochondrial genomes in Perumytilus purpuratus. This may be considered evidence of doubly uniparental mtDNA inheritance. The presence of the two types of mitochondrial genomes differentiates females from males. The F genome was found in the somatic and gonadal tissues of females and in the somatic tissues of males; the M genome was found in the gonads and mantle of males only. For the mitochondrial 16S region, ten haplotypes were found for the F genome (nucleotide diversity 0.004), and 7 haplotypes for the M genome (nucleotide diversity 0.001), with a distance Dxy of 0.125 and divergence Kxy of 60.33%. For the COI gene 17 haplotypes were found for the F genome (nucleotide diversity 0.009), and 10 haplotypes for the M genome (nucleotide diversity 0.010), with a genetic distance Dxy of 0.184 and divergence Kxy of 99.97%. Our results report the presence of two well-differentiated, sex-specific types of mitochondrial genome (one present in the male gonad, the other in the female gonad), implying the presence of DUI in P. purpuratus. These results indicate that care must be taken in phylogenetic comparisons using mtDNA sequences of P. purpuratus without considering the sex of the individuals.
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Affiliation(s)
- Jaime Vargas
- Instituto de Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile
| | - Montse Pérez
- > Instituto Español de Oceanografía. Centro Oceanográfico de Vigo, Vigo, Spain
| | - Jorge Toro
- Instituto de Ciencias Marinas y Limnológicas. Universidad Austral de Chile, Valdivia, Chile
| | - Marcela P Astorga
- Instituto de Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile
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Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes. Antonie van Leeuwenhoek 2015; 107:821-34. [PMID: 25563637 DOI: 10.1007/s10482-014-0375-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/30/2014] [Indexed: 10/24/2022]
Abstract
In the present study, we sampled bacterial communities associated with mussels inhabiting two distinct coastal marine ecosystems in Kalimantan, Indonesia, namely, marine lakes and coastal mangroves. We used 16S rRNA gene pyrosequencing and predicted metagenomic analysis to compare microbial composition and function. Marine lakes are small landlocked bodies of seawater isolated to varying degrees from the open sea environment. They contain numerous endemic taxa and represent natural laboratories of speciation. Our primary goals were to (1) use BLAST search to identify closely related organisms to dominant bacterial OTUs in our mussel dataset and (2) to compare bacterial communities and enrichment in the predicted bacterial metagenome among lakes. Our sequencing effort yielded 3553 OTUs belonging to 44 phyla, 99 classes and 121 orders. Mussels in the largest marine lake (Kakaban) and the coastal mangrove habitat were dominated by bacteria belonging to the phylum Proteobacteria whereas smaller lakes, located on the island of Maratua, were dominated by bacteria belonging to the phyla Firmicutes and Tenericutes. The single most abundant OTU overall was assigned to the genus Mycoplasma. There were several significant differences among locations with respect to metabolic pathways. These included enrichment of xenobiotic biodegradation pathways in the largest marine lake and coastal mangrove. These locations were also the most enriched with respect to nitrogen metabolism. The presence of genes related to isoquinoline alkaloids, polyketides, hydrolases, mono and dioxygenases in the predicted analysis of functional pathways is an indication that the bacterial communities of Brachidontes mussels may be potentially important sources of new marine medicines and enzymes of industrial interest. Future work should focus on measuring how mussel microbial communities influence nutrient dynamics within the marine lake environment and isolating microbes with potential biotechnological applications.
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First molecular phylogeny of the circumtropical bivalve family Pinnidae (Mollusca, Bivalvia): evidence for high levels of cryptic species diversity. Mol Phylogenet Evol 2014; 75:11-23. [PMID: 24569016 DOI: 10.1016/j.ympev.2014.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/05/2014] [Accepted: 02/13/2014] [Indexed: 11/22/2022]
Abstract
The family Pinnidae Leach, 1819, includes approximately 50 species of large subtidal and coastal marine bivalves. These commercially important species occur in tropical and temperate waters around the world and are most frequently found in seagrass meadows. The taxonomy of the family has been revised a number of times since the early 20th Century, the most recent revision recognizing 55 species distributed in three genera: Pinna, Atrina and Streptopinna, the latter being monotypic. However, to date no phylogenetic analysis of the family has been conducted using morphological or molecular data. The present study analyzed 306 pinnid specimens from around the world, comprising the three described genera and ca. 25 morphospecies. We sequenced the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I, and the nuclear ribosomal genes 18S rRNA and 28S rRNA. Phylogenetic analysis of the data revealed monophyly of the genus Atrina but also that the genus Streptopinna is nested within Pinna. Based on the strong support for this relationship we propose a new status for Streptopinna Martens, 1880 and treat it as a subgenus (status nov.) of Pinna Linnaeus, 1758. The phylogeny and the species delimitation analyses suggest the presence of cryptic species in many morphospecies displaying a wide Indo-Pacific distribution, including Pinna muricata, Atrina assimilis, A. exusta and P. (Streptopinna) saccata but also in the Atlantic species A. rigida. Altogether our results highlight the challenges associated with morphological identifications in Pinnidae due to the presence of both phenotypic plasticity and morphological stasis and reveal that many pinnid species are not as widely distributed as previously thought.
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Goto TV, Tamate HB, Hanzawa N. Phylogenetic Characterization of Three Morphs of Mussels (Bivalvia, Mytilidae) Inhabiting Isolated Marine Environments in Palau Islands. Zoolog Sci 2011; 28:568-79. [DOI: 10.2108/zsj.28.568] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Stroscio S, Baviera C, Frati F, Lo Paro G, Nardi F. Deep genetic divergence in the darkling beetle Pimelia rugulosa (Coleoptera, Tenebrionidae) reflects Plio-Pleistocenic paleogeographic history of Sicily. J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2011.00617.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Four years of DNA barcoding: Current advances and prospects. INFECTION GENETICS AND EVOLUTION 2008; 8:727-36. [DOI: 10.1016/j.meegid.2008.05.005] [Citation(s) in RCA: 240] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 05/23/2008] [Accepted: 05/27/2008] [Indexed: 11/21/2022]
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