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Burzyński A, Śmietanka B, Fernández-Pérez J, Lubośny M. The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species. Sci Rep 2024; 14:14465. [PMID: 38914611 PMCID: PMC11196677 DOI: 10.1038/s41598-024-63764-8] [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: 08/03/2023] [Accepted: 05/31/2024] [Indexed: 06/26/2024] Open
Abstract
Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.
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Affiliation(s)
- Artur Burzyński
- 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
| | - Jenyfer Fernández-Pérez
- Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
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2
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Cozzolino L, Nicastro KR, Hubbard PC, Seuront L, McQuaid CD, Zardi GI. Intraspecific genetic lineages of a marine mussel show behavioural divergence when exposed to microplastic leachates. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122779. [PMID: 37863252 DOI: 10.1016/j.envpol.2023.122779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Worldwide, microplastic pollution has numerous negative implications for marine biota, exacerbating the effects of other forms of global anthropogenic disturbance. Mounting evidence shows that microplastics (MPs) not only cause physical damage through their ingestion, but also act as vectors for hazardous compounds by leaching absorbed and adsorbed chemicals. Research on the effects of plastic pollution has, however, largely assumed that species respond uniformly, while ignoring intraspecific diversity (i.e., variation within a single species). We investigated the effects of plastic leachates derived from factory-fresh (virgin) and beached microplastics on the behavioural responses of two genetic lineages of the Mediterranean mussel Mytilus galloprovincialis. Through laboratory behavioural experiments, we found that during exposure to leachates from beached microplastics (beached MPLs), Atlantic specimens moved significantly less than Mediterranean individuals in terms of both (i) proportion of individuals responding through movement and (ii) net and gross distances crawled. In contrast, no significant intraspecific differences were observed in the behaviour of either adults or recruits when exposed to MPLs from virgin microplastics (virgin MPLs). Additionally, the reception of cues from three amino acids (L-cysteine, proline and L-leucine) at increasing concentrations (10-5 M to 10-3 M in charcoal-filtered seawater) was tested by electrophysiological analysis using mussels exposed to beached MPLs or control seawater. We found significant intraspecific differences in response to 10-3 M L-cysteine (regardless of treatment) and 10-4 M L-cysteine (in mussels exposed to beached MPLs) and to 10-3 M proline (in mussels exposed to beached MPLs) and 10-5 M L-leucine. Our study suggests that intraspecific variation in a marine mussel may prompt different responses to plastic pollution, potentially triggered by local adaptation and physiological variability between lineages. Our work highlights the importance of assessing the effects of intraspecific variation, especially in environmental sentinel species as this level of diversity could modulate responses to plastic pollution.
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Affiliation(s)
- Lorenzo Cozzolino
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal.
| | - Katy R Nicastro
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal; Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, IRD, UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, F-59000, Lille, France; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Peter C Hubbard
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Laurent Seuront
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, IRD, UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, F-59000, Lille, France; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa; Department of Marine Resources and Energy, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108- 8477, Japan
| | - Christopher D McQuaid
- Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Gerardo I Zardi
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa; Normandie Université, UNICAEN, Laboratoire Biologie des Organismes et Ecosystèmes Aquatiques, UMR 8067 BOREA (CNRS, MNHN, UPMC, UCBN, IRD-207), CS 14032, 14000, Caen, France
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3
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Vendrami DLJ, Hoffman JI, Wilding CS. Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species. Genes (Basel) 2022; 14:14. [PMID: 36672754 PMCID: PMC9858869 DOI: 10.3390/genes14010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria-Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of differentiation along the Pecten genome is unknown. Here, we mapped RADseq data from 235 P. maximus and 27 P. jacobaeus to a chromosome-level reference genome, finding a heterogeneous landscape of genomic differentiation. Highly divergent genomic regions were identified across 14 chromosomes, while the remaining five showed little differentiation. Demographic and comparative genomics analyses suggest that this pattern resulted from an initial extended period of isolation, which promoted divergence, followed by differential gene flow across the genome during secondary contact. Single nucleotide polymorphisms present within highly divergent genomic regions were located in areas of low recombination and contrasting patterns of LD decay were found between the two species, hinting at the presence of chromosomal inversions in P. jacobaeus. Functional annotations revealed that highly differentiated regions were enriched for immune-related processes and mRNA modification. While future work is necessary to characterize structural differences, this study provides new insights into the speciation genomics of P. maximus and P. jacobaeus.
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Affiliation(s)
- David L. J. Vendrami
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33615 Bielefeld, Germany
| | - Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33615 Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Craig S. Wilding
- School of Biological and Environmental Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
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4
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Ojeda V, Serra B, Lagares C, Rojo-Francàs E, Sellés M, Marco-Herrero E, García E, Farré M, Arenas C, Abelló P, Mestres F. Interannual fluctuations in connectivity among crab populations (Liocarcinus depurator) along the Atlantic-Mediterranean transition. Sci Rep 2022; 12:9797. [PMID: 35697727 PMCID: PMC9192654 DOI: 10.1038/s41598-022-13941-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/30/2022] [Indexed: 11/18/2022] Open
Abstract
An interesting evolutionary question that still remains open is the connectivity between marine populations. Marine currents can favour the dispersal of larvae or adults, but they can also produce eddies and gyres generating oceanographic fronts, thus limiting gene flow. To address this subject, we selected the Atlantic-Mediterranean transition, where several fronts are located: Gibraltar Strait (GS), Almeria-Oran Front (AOF) and Ibiza Channel (IC). Seven populations of the marine crab Liocarcinus depurator (Cadiz, West and East Alboran, Alacant, Valencia, Ebro Delta and North Catalonia) located along this transition were analysed in six consecutive years (2014–2019) using a fragment of the COI (Cytochrome Oxidase subunit I) gene. All sequences (966) belonged to two well defined haplogroups: ATL (most abundant in Atlantic waters) and MED (predominant in Mediterranean waters). Following a geographic variation, the frequency of ATL decreased significantly from Cadiz to North Catalonia. However, this variation presented steps due to the effect of oceanographic restrictions/fronts. Significant effects were recorded for GS (2015, 2017, 2018 and 2019), AOF (all years except 2018) and IC (2016). The intensity and precise location of these fronts changed over time. Multivariate analyses distinguished three main population groups: Cadiz, Alboran Sea and the remaining Mediterranean populations. These findings could be relevant to properly define Marine Protected Areas and for conservation and fisheries policies.
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Affiliation(s)
- Víctor Ojeda
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | - Bruna Serra
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | - Clàudia Lagares
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | - Eva Rojo-Francàs
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | - Maria Sellés
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
| | | | - Encarnación García
- Instituto Español de Oceanografía - C.O. Murcia (IEO-CSIC), San Pedro del Pinatar, Spain
| | - Marc Farré
- Instituto Español de Oceanografía - C.O. Balears (IEO-CSIC), Palma de Mallorca, Spain.,Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Concepció Arenas
- Dept. Genètica, Microbiologia i Estadística, Secció d'Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Pere Abelló
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Francesc Mestres
- Dept. Genètica, Microbiologia i Estadística. Secció de Genètica Biomèdica, Evolució i Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain. .,IRBio (Institut de Recerca Per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain.
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5
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López-Márquez V, Cushman SA, Templado J, Wan HY, Bothwell HM, Machordom A. Genetic connectivity of two marine gastropods in the Mediterranean Sea: seascape genetics reveals species-specific oceanographic drivers of gene flow. Mol Ecol 2021; 30:4608-4629. [PMID: 34260775 DOI: 10.1111/mec.16080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/28/2022]
Abstract
Oceanographic features such as currents, waves, temperature and salinity, together with life history traits, control patterns and rates of gene flow and contribute to shaping the population genetic structure of marine organisms. Seascape genetics is an emerging discipline that adopts a spatially explicit approach to examine biotic and abiotic factors that drive gene flow in marine environments. In this study, we examined factors that contribute to genetic differentiation in two coastal Mediterranean gastropods whose geographical ranges overlap but which inhabit different environments. The two species differ in several life history traits and in their dispersal capabilities. Genetic differentiation was relatively low for the trochid species Gibbula divaricata (FST =0.059), and high for the vermetid species Dendropoma lebeche (FST =0.410). Salinity emerged as the most important variable explaining the genetic structure of both species; sea surface temperature was also important for G. divaricata. For the more sessile D. lebeche, the coastline was predicted to provide important pathways for stepping-stone connectivity and gene flow. Our results provide a greater understanding of the factors influencing marine population connectivity, which may be useful to guide marine conservation and management in the Mediterranean.
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Affiliation(s)
| | - Samuel A Cushman
- USDA Forest Service Rocky Mountain Research Station, Flagstaff, AZ, USA
| | - José Templado
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Ho Yi Wan
- Department of Wildlife, Humboldt State University, Arcata, CA, USA
| | - Helen M Bothwell
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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6
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Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array. Animals (Basel) 2021; 11:ani11061803. [PMID: 34204230 PMCID: PMC8233821 DOI: 10.3390/ani11061803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022] Open
Abstract
Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations' abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted FST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.
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7
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Conroy GC, Lamont RW, Bridges L, Stephens D, Wardell-Johnson A, Ogbourne SM. Conservation concerns associated with low genetic diversity for K'gari-Fraser Island dingoes. Sci Rep 2021; 11:9503. [PMID: 33947920 PMCID: PMC8097078 DOI: 10.1038/s41598-021-89056-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
The dingo population on world heritage-listed K'gari-Fraser Island (K'gari) is amongst the most well-known in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K'gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K'gari population has significantly lower genetic diversity than mainland dingoes (AR, HE, PAR; p < 0.05) with a fourfold reduction in effective population size (Ne = 25.7 vs 103.8). There is also strong evidence of genetic differentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder effects such as bottlenecks leading to decreased diversity and drift. As the first study to incorporate a large sample set of K'gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population.
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Affiliation(s)
- G C Conroy
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia. .,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
| | - R W Lamont
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - L Bridges
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - D Stephens
- Zoological Genetics, Inglewood, Adelaide, SA, 5133, Australia
| | - A Wardell-Johnson
- Senior Professional Fellow, Curtin University, Bentley, WA, Australia
| | - S M Ogbourne
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
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8
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Carducci F, Biscotti MA, Trucchi E, Giuliani ME, Gorbi S, Coluccelli A, Barucca M, Canapa A. Omics approaches for conservation biology research on the bivalve Chamelea gallina. Sci Rep 2020; 10:19177. [PMID: 33154500 PMCID: PMC7645701 DOI: 10.1038/s41598-020-75984-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/30/2020] [Indexed: 12/27/2022] Open
Abstract
The striped venus (Chamelea gallina) is an important economic resource in the Mediterranean Basin; this species has exhibited a strong quantitative decline in the Adriatic Sea. The aim of this work was to provide a comprehensive view of the biological status of C. gallina to elucidate the bioecological characteristics and genetic diversity of wild populations. To the best of our knowledge, this investigation is the first to perform a multidisciplinary study on C. gallina based on two omics approaches integrated with histological, ecotoxicological, and chemical analyses and with the assessment of environmental parameters. The results obtained through RNA sequencing indicated that the striped venus has a notable ability to adapt to different environmental conditions. Moreover, the stock reduction exhibited by this species in the last 2 decades seems not to have negatively affected its genetic diversity. Indeed, the high level of genetic diversity that emerged from our ddRAD dataset analyses is ascribable to the high larval dispersal rate, which might have played a “compensatory role” on local fluctuations, conferring to this species a good adaptive potential to face the environmental perturbations. These findings may facilitate the efforts of conservation biologists to adopt ad hoc management plans for this fishery resource.
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Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Emiliano Trucchi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Maria Elisa Giuliani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Stefania Gorbi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Alessandro Coluccelli
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy.
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9
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Haye PA, Segovia NI, Varela AI, Rojas R, Rivadeneira MM, Thiel M. Genetic and morphological divergence at a biogeographic break in the beach-dwelling brooder Excirolana hirsuticauda Menzies (Crustacea, Peracarida). BMC Evol Biol 2019; 19:118. [PMID: 31185884 PMCID: PMC6560899 DOI: 10.1186/s12862-019-1442-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND There is a biogeographic break located at 30°S in the southeast Pacific, in a coastal area of strong environmental discontinuities. Several marine benthic taxa with restricted dispersal have a coincident phylogeographic break at 30°S, indicating that genetic structure is moulded by life history traits that limit gene flow and thereby promote divergence and speciation. In order to evaluate intraspecific divergence at this biogeographic break, we investigated the genetic and morphological variation of the directly developing beach isopod Excirolana hirsuticauda along 1900 km of the southeast Pacific coast, across 30°S. RESULTS The COI sequences and microsatellite data both identified a strong discontinuity between populations of E. hirsuticauda to the north and south of 30°S, and a second weaker phylogeographic break at approximately 35°S. The three genetic groups were evidenced by different past demographic and genetic diversity signatures, and were also clearly distinguished with microsatellite data clustering. The COI sequences established that the genetic divergence of E. hirsuticauda at 30°S started earlier than divergence at 35°. Additionally, the three groups have different past demographic signatures, with probable demographic expansion occurring earlier in the southern group (south of 35°S), associated with Pleistocene interglacial periods. Interestingly, body length, multivariate morphometric analyses, and the morphology of a fertilization-related morphological character in males, the appendix masculina, reinforced the three genetic groups detected with genetic data. CONCLUSIONS The degree of divergence of COI sequences, microsatellite data, and morphology was concordant and showed two geographic areas in which divergence was promoted at differing historical periods. Variation in the appendix masculina of males has probably promoted reproductive isolation. This variation together with gene flow restrictions promoted by life history traits, small body size, oceanographic discontinuities and sandy-beach habitat continuity, likely influenced species divergence at 30°S in the southeast Pacific coast. The degree of genetic and morphological differentiation of populations to the north and south of 30°S suggests that E. hirsuticauda harbours intraspecific divergence consistent with reproductive isolation and an advanced stage of speciation. The speciation process within E. hirsuticauda has been shaped by both restrictions to gene flow and a prezygotic reproductive barrier.
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Affiliation(s)
- Pilar A. Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
| | - Nicolás I. Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
| | - Andrea I. Varela
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
- Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Universidad Católica del Norte, Coquimbo, Chile
| | - Rodrigo Rojas
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
| | - Marcelo M. Rivadeneira
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
| | - Martin Thiel
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
- Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Universidad Católica del Norte, Coquimbo, Chile
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
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10
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Carella F, Carrasco N, De Vico G. Baseline pathological data of the wedge clam Donax trunculus from the Tyrrhenian Sea (Mediterranean Basin). DISEASES OF AQUATIC ORGANISMS 2019; 133:107-118. [PMID: 31019135 DOI: 10.3354/dao03336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In recent years, a collapse in Donax trunculus fishing yields has occurred in the Tyrrhenian Sea (Mediterranean Basin). There is little information available on the impact disease may have had on D. trunculus populations. For the first time, a pathological survey was performed on the natural beds of the bivalve on the Campania and Lazio coasts, western Italy. Detected pathogens and related diseases were analysed, and their prevalence and mean intensity values were calculated. Viral particles, Chlamydia-like organisms, ciliates, coccidians, microcells and trematodes were observed. An unknown ciliate was linked to severe inflammatory and necrotic lesions in the digestive gland. Metacercariae of the trematode Postmonorchis sp. were also strongly represented in almost all samples, reaching high levels of infection; however, none of the pathogens described required the World Organisation for Animal Health to be notified. Initial results indicated that further surveys related to environmental data are necessary in order to assess the relevance of these early observations in managing the declining D. trunculus population in the Tyrrhenian Sea.
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Affiliation(s)
- F Carella
- Department of Biology, University of Naples Federico II, MSA, 80126 Naples, Italy
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Fernández-Pérez J, Nantón A, Méndez J. Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae). BMC Genet 2018; 19:97. [PMID: 30367592 PMCID: PMC6204057 DOI: 10.1186/s12863-018-0684-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/11/2018] [Indexed: 01/04/2023] Open
Abstract
Background The whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and their variation were described. The phylogenetic usefulness of 5S and ITS sequences in the inference of evolutionary relationships among these wedge clams was also investigated. Results The length of the 5S repeat presented little variation among species, except D. trunculus that differed from the rest of the Donax species in 170–210 bp. The deduced coding region covered 120 bp, and showed recognizable internal control regions (ICRs) involved in the transcription. The length of non-transcribed spacer region (NTS) ranged from 157 bp to 165 bp in Donax trunculus and from 335 bp to 367 bp in the other three species. The conservation degree of transcriptional regulatory regions was analysed revealing a conserved TATA-like box in the upstream region. Regarding ITS sequences, the four Donax species showed slight size differences among clones due to the variation occurring in the ITS1 and ITS2, except Donax variegatus did not display size differences in the ITS2. The total length of the ITS sequence ranged between 814 and 1014 bp. Resulting phylogenetic trees display that the two ribosomal DNA regions provide well-resolved phylogenies where the four European Donax species form a single clade receiving high support in nodes. The topology obtained with 5S sequences was in agreement with Donax evolutionary relationships inferred from several sequences of different nature in previous studies. Conclusions This is not only a basic research work, where new data and new knowledge is provided about Donax species, but also have allowed the authentication of these wedge clams and offers future applications to provide other genetic resources. Electronic supplementary material The online version of this article (10.1186/s12863-018-0684-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain.
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
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Fernández-Pérez J, Nantón A, Ruiz-Ruano FJ, Camacho JPM, Méndez J. First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order. PLoS One 2017; 12:e0184464. [PMID: 28886105 PMCID: PMC5590976 DOI: 10.1371/journal.pone.0184464] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Four species of the genus Donax (D. semistriatus, D. trunculus, D. variegatus and D. vittatus) are common on Iberian Peninsula coasts. Nevertheless, despite their economic importance and overexploitation, scarce genetic resources are available. In this work, we newly determined the complete mitochondrial genomes of these four representatives of the family Donacidae, with the aim of contributing to unveil phylogenetic relationships within the Veneroida order, and of developing genetic markers being useful in wedge clam identification and authentication, and aquaculture stock management. PRINCIPAL FINDINGS The complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand. A long non-coding region was identified in each of the four Donax species between cob and cox2 genes, presumably corresponding to the Control Region. The Bayesian and Maximum Likelihood phylogenetic analysis of the Veneroida order indicate that all four species of Donax form a single clade as a sister group of other bivalves within the Tellinoidea superfamily. However, although Tellinoidea is actually monophyletic, none of its families are monophyletic. CONCLUSIONS Sequencing of complete mitochondrial genomes provides highly valuable information to establish the phylogenetic relationships within the Veneroida order. Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource.
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Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | | | - Juan Pedro M. Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
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Pascual M, Rives B, Schunter C, Macpherson E. Impact of life history traits on gene flow: A multispecies systematic review across oceanographic barriers in the Mediterranean Sea. PLoS One 2017; 12:e0176419. [PMID: 28489878 PMCID: PMC5425013 DOI: 10.1371/journal.pone.0176419] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/10/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Marine species can demonstrate strong genetic differentiation and population structure despite the hypothesis of open seas and high connectivity. Some suggested drivers causing the genetic breaks are oceanographic barriers and the species' biology. We assessed the relevance of seven major oceanographic fronts on species connectivity while considering their dispersal capacity and life strategy. METHODS We systematically reviewed the scientific articles reporting population genetic differentiation along the Mediterranean Sea and across the Atlantic-Mediterranean transition. We retained those considering at least one sampling locality at each side of an oceanographic front, and at least two localities with no-front between them to correctly assess the effect of the front. To estimate the impact of life history characteristics affecting connectivity we considered the planktonic larval duration (PLD) and adult life strategy. RESULTS Oceanographic barriers in the Mediterranean Sea seem to reduce gene flow globally; however, this effect is not homogeneous considering the life history traits of the species. The effect of the oceanographic fronts reduces gene flow in highly mobile species with PLD larger than 2-4 weeks. Benthic sessile species and/or with short PLD (< 2 weeks) have more significant genetic breaks between localities than species with higher motility; however, genetic differentiation occurs independently of the presence of a front. CONCLUSION Genetic connectivity is important for populations to recover from anthropogenic or natural impacts. We show that species with low mobility, mostly habitat-formers, have high genetic differentiation but low gene flow reduction mediated by the front, therefore, considering the importance of these species, we emphasize the vulnerability of the Mediterranean ecosystems and the necessity of protection strategies based on the whole ecosystem.
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Affiliation(s)
- Marta Pascual
- Dept Genetics, Microbiology and Statistics/IrBio, Universitat de Barcelona, Diagonal 643, Barcelona, Spain
- * E-mail:
| | - Borja Rives
- Dept Genetics, Microbiology and Statistics/IrBio, Universitat de Barcelona, Diagonal 643, Barcelona, Spain
| | - Celia Schunter
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Enrique Macpherson
- Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Car. Acc. Cala St. Francesc 14, Blanes, Girona, Spain
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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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