1
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Aires R, Porto ML, de Assis LM, Pereira PAN, Carvalho GR, Côco LZ, Vasquez EC, Pereira TMC, Campagnaro BP, Meyrelles SS. DNA damage and aging on hematopoietic stem cells: Impact of oxidative stress in ApoE -/ - mice. Exp Gerontol 2021; 156:111607. [PMID: 34715304 DOI: 10.1016/j.exger.2021.111607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022]
Abstract
The effects of aging on ROS production and DNA damage were assessed in hematopoietic stem cells (HSCs) from apolipoprotein E-deficient (ApoE-/-) mice (2-, 12- and 24-month-old), a traditional experimental model of atherogenic dyslipidemia. HSCs from aged ApoE-/- mice were associated with increased ROS levels, leading to loss quiescence, DNA damage, apoptosis and telomere shortening. The concurrence of lack of ApoE and aging result in exhaustion and senescence of HSCs accompanied by increased oxidative stress and inflammation. Therefore, our data open avenues to a better understanding of age-related changes and genetic factors, which may synergistically compromise the efficacy of aged HSC recovery and/or transplantation.
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Affiliation(s)
- R Aires
- Laboratory of Translational Physiology, Health Sciences Center, Federal University of Espirito Santo (UFES), Vitoria, Brazil.
| | - M L Porto
- Federal Institute of Education, Science and Technology (IFES), Vila Velha, ES, Brazil
| | - L M de Assis
- Federal Institute of Education, Science and Technology (IFES), Vila Velha, ES, Brazil
| | - P A N Pereira
- Federal Institute of Education, Science and Technology (IFES), Vila Velha, ES, Brazil
| | - G R Carvalho
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha, ES, Brazil
| | - L Z Côco
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha, ES, Brazil
| | - E C Vasquez
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha, ES, Brazil
| | - T M C Pereira
- Federal Institute of Education, Science and Technology (IFES), Vila Velha, ES, Brazil; Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha, ES, Brazil
| | - B P Campagnaro
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha, ES, Brazil
| | - S S Meyrelles
- Laboratory of Translational Physiology, Health Sciences Center, Federal University of Espirito Santo (UFES), Vitoria, Brazil
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2
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Seymour M, Brown N, Carvalho GR, Wood C, Goertz S, Lo N, de Bruyn M. Ecological community dynamics: 20 years of moth sampling reveals the importance of generalists for community stability. Basic Appl Ecol 2020. [DOI: 10.1016/j.baae.2020.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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3
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Seymour M, Edwards FK, Cosby BJ, Kelly MG, de Bruyn M, Carvalho GR, Creer S. Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks. Sci Total Environ 2020; 729:138801. [PMID: 32498163 DOI: 10.1016/j.scitotenv.2020.138801] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/31/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Current approaches to ecological assessment are limited by the traditional morpho-taxonomic methods presently employed and the inability to meet increasing demands for rapid assessments. Advancements in high throughput sequencing now enable rapid high-resolution ecological assessment using environmental DNA (eDNA). Here we test the ability of using eDNA-based ecological assessment methods against traditional assessment of two key indicator groups (diatoms and macroinvertebrates) and show how eDNA across multiple gene regions (COI, rbcL, 12S and 18S) can be used to infer interactive networks that link to ecological assessment criteria. We compared results between taxonomic and eDNA based assessments and found significant positive associations between macroinvertebrate (p < 0.001 R2 = 0.645) and diatom (p = 0.015, R2 = 0.222) assessment metrics. We further assessed the ability of eDNA based assessment to identify environmentally sensitive genera and found an order of magnitude greater potential for 18S, versus COI or rbcL, to determine environmental filtering of ecologically assessed communities. Lastly, we compared the ability of traditional metrics against co-occurrence network properties of our combined 18S, COI and rbcL indicator genera to infer habitat quality measures currently used by managers. We found that transitivity (network connectivity), linkage density and cohesion were significantly associated with habitat modification scores (HMS), whereas network properties were inconsistent with linking to the habitat quality score (HQS) metric. The incorporation of multi-marker eDNA network assessment opens up a means for finer scale ecological assessment, currently limited using traditional methods. While utilization of eDNA-based assessment is recommended, direct comparisons with traditional approaches are difficult as the methods are intrinsically different and should be treated as such with regards to future research. Overall, our findings show that eDNA can be used for effective ecological assessment while offering a wider range of scope and application compared to traditional assessment methods.
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Affiliation(s)
- Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | | | - Bernard J Cosby
- NERC Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Martyn G Kelly
- Bowburn Consultancy, 11 Monteigne Drive, Bowburn, Durham DH6 5QB, UK
| | - Mark de Bruyn
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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4
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Besnier F, Solberg MF, Harvey AC, Carvalho GR, Bekkevold D, Taylor MI, Creer S, Nielsen EE, Skaala Ø, Ayllon F, Dahle G, Glover KA. Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface. BMC Genet 2020; 21:13. [PMID: 32033538 PMCID: PMC7006396 DOI: 10.1186/s12863-020-0816-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/28/2020] [Indexed: 12/23/2022] Open
Abstract
Background Quantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations. Results After rearing fish in common-garden experiments under aquaculture conditions, we performed a variance component analysis in four mapping populations totaling ~ 7000 individuals from six wild, two domesticated and three F1 wild/domesticated hybrid strains. Across the four independent datasets, genome-wide significant quantitative trait loci (QTLs) associated with weight and length were detected on a total of 18 chromosomes, reflecting the polygenic nature of growth. Significant QTLs correlated with both length and weight were detected on chromosomes 2, 6 and 9 in multiple datasets. Significantly, epistatic QTLs were detected in all datasets. Discussion The observed interactions demonstrated that the phenotypic effect of inheriting an allele deviated between half-sib families. Gene-by-gene interactions were also suggested, where the combined effect of two loci resulted in a genetic effect upon phenotypic variance, while no genetic effect was detected when the two loci were considered separately. To our knowledge, this is the first documentation of epistasis in a quantitative trait in Atlantic salmon. These novel results are of relevance for breeding programs, and for predicting the evolutionary consequences of domestication-introgression in wild populations.
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Affiliation(s)
- Francois Besnier
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - Monica F Solberg
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Alison C Harvey
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Dorte Bekkevold
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Einar E Nielsen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Øystein Skaala
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Fernando Ayllon
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Geir Dahle
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
| | - Kevin A Glover
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
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5
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Mat Jaafar TNA, Taylor MI, Mohd Nor SA, Bruyn MD, Carvalho GR. Comparative genetic stock structure in three species of commercially exploited Indo-Malay Carangidae (Teleosteii, Perciformes). J Fish Biol 2020; 96:337-349. [PMID: 31721192 DOI: 10.1111/jfb.14202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
We examine genetic structuring in three commercially important species of the teleost family Carangidae from Malaysian waters: yellowtail scad Atule mate, bigeye scad Selar crumenophthalmus and yellowstripe scad Selaroides leptolepis, from the Indo-Malay Archipelago. In view of their distribution across contrasting habitats, we tested the hypothesis that pelagic species display less genetic divergence compared with demersal species, due to their potential to undertake long-distance migrations in oceanic waters. To evaluate population genetic structure, we sequenced two mitochondrial (mt)DNA [650 bp of cytochrome oxidase I (coI), 450 bp of control region (CR)] and one nuclear gene (910 bp of rag1) in each species. One hundred and eighty samples from four geographical regions within the Indo-Malay Archipelago including a population of yellowtail from Kuwait were examined. Findings revealed that the extent of genetic structuring among populations in the semi-pelagic and pelagic, yellowtail and bigeye were lower than demersal yellowstripe, consistent with the hypothesis that pelagic species display less genetic divergence compared with demersal species. The yellowtail phylogeny identified three distinct clades with bootstrap values of 86%-99% in mtDNA and 63%-67% in rag1. However, in bigeye, three clades were also observed from mtDNA data while only one clade was identified in rag1 dataset. In yellowstripe, the mtDNA tree was split into three closely related clades and two clades in rag1 tree with bootstraps value of 73%-99% and 56% respectively. However, no geographic structure appears in both mtDNA and rag1 datasets. Hierarchical molecular variance analysis (AMOVA), pair wise FST comparisons and the nearest-neighbour statistic (Snn ) showed significant genetic differences among Kuwait and Indo-Malay yellowtail. Within the Indo-Malay Archipelago itself, two distinct mitochondrial lineages were detected in yellowtail suggesting potential cryptic species. Findings suggests varying degrees of genetic structuring, key information relevant to management of exploited stocks, though more rapidly evolving genetic markers should be used in future to better delimit the nature and dynamics of putative stock boundaries.
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Affiliation(s)
- Tun N A Mat Jaafar
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor, UK
| | - Martin I Taylor
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor, UK
| | - Siti A Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor, UK
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6
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Thomas JE, Carvalho GR, Haile J, Rawlence NJ, Martin MD, Ho SYW, Sigfússon AÞ, Jósefsson VA, Frederiksen M, Linnebjerg JF, Samaniego Castruita JA, Niemann J, Sinding MHS, Sandoval-Velasco M, Soares AER, Lacy R, Barilaro C, Best J, Brandis D, Cavallo C, Elorza M, Garrett KL, Groot M, Johansson F, Lifjeld JT, Nilson G, Serjeanston D, Sweet P, Fuller E, Hufthammer AK, Meldgaard M, Fjeldså J, Shapiro B, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLife 2019; 8:e47509. [PMID: 31767056 PMCID: PMC6879203 DOI: 10.7554/elife.47509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/22/2019] [Indexed: 01/23/2023] Open
Abstract
The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
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Affiliation(s)
- Jessica E Thomas
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorUnited Kingdom
| | - James Haile
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Michael D Martin
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Simon YW Ho
- School of Life and Environmental SciencesUniversity of SydneySydneyAustralia
| | | | | | | | | | | | - Jonas Niemann
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Mikkel-Holger S Sinding
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Greenland Institute of Natural ResourcesNuukGreenland
| | | | - André ER Soares
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Robert Lacy
- Department of Conservation ScienceChicago Zoological SocietyBrookfieldUnited States
| | | | - Juila Best
- Department of Archaeology, Anthropology and Forensic Science, Faculty of Science and TechnologyBournemouth UniversityPooleUnited Kingdom
- School of History, Archaeology and ReligionCardiff UniversityCardiffUnited Kingdom
| | | | - Chiara Cavallo
- Amsterdam Centre for Ancient Studies and ArchaeologyUniversity of AmsterdamAmsterdamNetherlands
| | - Mikelo Elorza
- Arqueología PrehistóricaSociedad de Ciencias AranzadiSan SebastiánSpain
| | - Kimball L Garrett
- Natural History Museum of Los Angeles CountyLos AngelesUnited States
| | - Maaike Groot
- Institut für Prähistorische ArchäologieFreie Universität BerlinBerlinGermany
| | | | | | - Göran Nilson
- Gothenburg Museum of Natural HistoryGothenburgSweden
| | - Dale Serjeanston
- Humanities ArchaeologyUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Paul Sweet
- Department of OrnithologyAmerican Museum of Natural HistoryNew YorkUnited States
| | | | | | | | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUnited States
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural SciencesUniversity of PotsdamPotsdamGermany
| | - John R Stewart
- Faculty of Science and TechnologyBournemouth UniversityDorsetUnited Kingdom
| | - M Thomas P Gilbert
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Department of Natural History, University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Michael Knapp
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
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Vieira PE, Desiderato A, Holdich DM, Soares P, Creer S, Carvalho GR, Costa FO, Queiroga H. Deep segregation in the open ocean: Macaronesia as an evolutionary hotspot for low dispersal marine invertebrates. Mol Ecol 2019; 28:1784-1800. [DOI: 10.1111/mec.15052] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/30/2019] [Accepted: 02/01/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Pedro E. Vieira
- Departamento de Biologia and CESAM — Centro de Estudos do Ambiente e do Mar Universidade de Aveiro Aveiro Portugal
- Departamento de Biologia, CBMA — Centro de Biologia Molecular e Ambiental Universidade do Minho Braga Portugal
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences Bangor University Bangor UK
| | - Andrea Desiderato
- Programa de Pós‐graduação em Zoologia (PGZOO) Universidade Federal do Paraná Curitiba Brazil
- Department of Functional Ecology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | | | - Pedro Soares
- Departamento de Biologia, CBMA — Centro de Biologia Molecular e Ambiental Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences Bangor University Bangor UK
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences Bangor University Bangor UK
| | - Filipe O. Costa
- Departamento de Biologia, CBMA — Centro de Biologia Molecular e Ambiental Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Henrique Queiroga
- Departamento de Biologia and CESAM — Centro de Estudos do Ambiente e do Mar Universidade de Aveiro Aveiro Portugal
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8
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Fairweather R, Bradbury IR, Helyar SJ, de Bruyn M, Therkildsen NO, Bentzen P, Hemmer‐Hansen J, Carvalho GR. Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod. Ecol Evol 2018; 8:12140-12152. [PMID: 30598806 PMCID: PMC6303715 DOI: 10.1002/ece3.4672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/11/2022] Open
Abstract
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range-wide examinations suggest significant transatlantic divergence, although the fine-scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data-synthesis approach, integrating multiple genome-wide single-nucleotide polymorphism (SNP) datasets representative of different regions to create a single range-wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post-glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.
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Affiliation(s)
- Robert Fairweather
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- School of Biological SciencesBangor UniversityBangorUK
| | - Ian R. Bradbury
- Science Branch, Department of FisheriesSt John’s, Newfoundland and LabradorCanada
| | - Sarah J. Helyar
- Institute of Global Food SecurityQueen’s University BelfastBelfastUK
| | - Mark de Bruyn
- School of Biological SciencesBangor UniversityBangorUK
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | | | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jakob Hemmer‐Hansen
- Section for Marine Living Resources, National Institute for Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
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9
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Young EF, Tysklind N, Meredith MP, de Bruyn M, Belchier M, Murphy EJ, Carvalho GR. Stepping stones to isolation: Impacts of a changing climate on the connectivity of fragmented fish populations. Evol Appl 2018; 11:978-994. [PMID: 29928304 PMCID: PMC5999207 DOI: 10.1111/eva.12613] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/05/2018] [Indexed: 01/02/2023] Open
Abstract
In the marine environment, understanding the biophysical mechanisms that drive variability in larval dispersal and population connectivity is essential for estimating the potential impacts of climate change on the resilience and genetic structure of populations. Species whose populations are small, isolated and discontinuous in distribution will differ fundamentally in their response and resilience to environmental stress, compared with species that are broadly distributed, abundant and frequently exchange conspecifics. Here, we use an individual-based modelling approach, combined with a population genetics projection model, to consider the impacts of a warming climate on the population connectivity of two contrasting Antarctic fish species, Notothenia rossii and Champsocephalus gunnari. Focussing on the Scotia Sea region, sea surface temperatures are predicted to increase significantly by the end of the 21st century, resulting in reduced planktonic duration and increased egg and larval mortality. With shorter planktonic durations, the results of our study predict reduced dispersal of both species across the Scotia Sea, from Antarctic Peninsula sites to islands in the north and east, and increased dispersal among neighbouring sites, such as around the Antarctic Peninsula. Increased mortality modified the magnitude of population connectivity but had little effect on the overall patterns. Whilst the predicted changes in connectivity had little impact on the projected regional population genetic structure of N. rossii, which remained broadly genetically homogeneous within distances of ~1,500 km, the genetic isolation of C. gunnari populations in the northern Scotia Sea was predicted to increase with rising sea temperatures. Our study highlights the potential for increased isolation of island populations in a warming world, with implications for the resilience of populations and their ability to adapt to ongoing environmental change, a matter of high relevance to fisheries and ecosystem-level management.
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Affiliation(s)
| | - Niklas Tysklind
- School of Biological SciencesBangor UniversityBangorGwyneddUK
- Present address:
INRAUMR8172 EcoFoGAgroParisTechCiradCNRSUniversité des AntillesUniversité de GuyaneKourouFrance
| | | | - Mark de Bruyn
- School of Life and Environmental SciencesThe University of SydneySydneyNSWAustralia
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10
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Bista I, Carvalho GR, Tang M, Walsh K, Zhou X, Hajibabaei M, Shokralla S, Seymour M, Bradley D, Liu S, Christmas M, Creer S. Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples. Mol Ecol Resour 2018; 18:1020-1034. [PMID: 29667329 DOI: 10.1111/1755-0998.12888] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/11/2018] [Accepted: 03/29/2018] [Indexed: 01/10/2023]
Abstract
New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read-biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR-450 bp, FF130R-130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read-biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large-scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment.
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Affiliation(s)
- Iliana Bista
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Gary R Carvalho
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Min Tang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Kerry Walsh
- Environment Agency, Horizon House, Bristol, UK
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Mehrdad Hajibabaei
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Shadi Shokralla
- Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Mathew Seymour
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | | | - Shanlin Liu
- Natural History Museum of Denmark, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
| | | | - Simon Creer
- School of Biological Sciences, Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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11
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Seymour M, Durance I, Cosby BJ, Ransom-Jones E, Deiner K, Ormerod SJ, Colbourne JK, Wilgar G, Carvalho GR, de Bruyn M, Edwards F, Emmett BA, Bik HM, Creer S. Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms. Commun Biol 2018; 1:4. [PMID: 30271891 PMCID: PMC6123786 DOI: 10.1038/s42003-017-0005-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/26/2017] [Indexed: 01/12/2023] Open
Abstract
Accurate quantification of biodiversity is fundamental to understanding ecosystem function and for environmental assessment. Molecular methods using environmental DNA (eDNA) offer a non-invasive, rapid, and cost-effective alternative to traditional biodiversity assessments, which require high levels of expertise. While eDNA analyses are increasingly being utilized, there remains considerable uncertainty regarding the dynamics of multispecies eDNA, especially in variable systems such as rivers. Here, we utilize four sets of upland stream mesocosms, across an acid–base gradient, to assess the temporal and environmental degradation of multispecies eDNA. Sampling included water column and biofilm sampling over time with eDNA quantified using qPCR. Our findings show that the persistence of lotic multispecies eDNA, sampled from water and biofilm, decays to non-detectable levels within 2 days and that acidic environments accelerate the degradation process. Collectively, the results provide the basis for a predictive framework for the relationship between lotic eDNA degradation dynamics in spatio-temporally dynamic river ecosystems. Mathew Seymour et al. investigate the persistence of environmental DNA (eDNA) in river systems in environments of varying pH. Using four sets of upland stream mesocosms, they find that eDNA degrades to non-detectable levels within two days and this degradation is accelerated in acidic environments.
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Affiliation(s)
- Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
| | - Isabelle Durance
- Water Research Institute and Cardiff School of Biosciences, Cardiff, CF10 3AX, UK
| | - Bernard J Cosby
- NERC Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Emma Ransom-Jones
- School of Biological Sciences and Natural Resources and Geography, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Kristy Deiner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Steve J Ormerod
- Water Research Institute and Cardiff School of Biosciences, Cardiff, CF10 3AX, UK
| | - John K Colbourne
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Gregory Wilgar
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | | | - Bridget A Emmett
- NERC Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Holly M Bik
- Department of Nematology, University of California-Riverside, Riverside, CA, 92521, USA
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
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12
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Beck SV, Carvalho GR, Barlow A, Rüber L, Hui Tan H, Nugroho E, Wowor D, Mohd Nor SA, Herder F, Muchlisin ZA, de Bruyn M. Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax. PLoS One 2017; 12:e0179557. [PMID: 28742862 PMCID: PMC5526567 DOI: 10.1371/journal.pone.0179557] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/30/2017] [Indexed: 11/19/2022] Open
Abstract
The complex climatic and geological history of Southeast Asia has shaped this region’s high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods.
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Affiliation(s)
- Samantha V. Beck
- Hólar University College, Department of Aquaculture and Fish Biology, Háskólinn á Hólum, Sauðárkrókur, Iceland
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- * E-mail: (MdB); (SVB)
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor, United Kingdom
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse, Potsdam (Golm), Germany
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse, Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse, Bern, Switzerland
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Estu Nugroho
- Indonesian Research Institute for Freshwater Aquaculture, Bogor, Java, Indonesia
| | - Daisy Wowor
- Research Center for Biology (Puslit Biologi), Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | | | - Fabian Herder
- Sektion Ichthyologie, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee, Bonn, Germany
| | - Zainal A. Muchlisin
- Department of Aquaculture, Marine & Fishery Sciences, Syiah Kuala University, Banda Aceh, Indonesia
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor, United Kingdom
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- * E-mail: (MdB); (SVB)
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13
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Bista I, Carvalho GR, Walsh K, Seymour M, Hajibabaei M, Lallias D, Christmas M, Creer S. Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat Commun 2017; 8:14087. [PMID: 28098255 PMCID: PMC5253663 DOI: 10.1038/ncomms14087] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 11/22/2016] [Indexed: 01/11/2023] Open
Abstract
The use of environmental DNA (eDNA) in biodiversity assessments offers a step-change in sensitivity, throughput and simultaneous measures of ecosystem diversity and function. There remains, however, a need to examine eDNA persistence in the wild through simultaneous temporal measures of eDNA and biota. Here, we use metabarcoding of two markers of different lengths, derived from an annual time series of aqueous lake eDNA to examine temporal shifts in ecosystem biodiversity and in an ecologically important group of macroinvertebrates (Diptera: Chironomidae). The analyses allow different levels of detection and validation of taxon richness and community composition (β-diversity) through time, with shorter eDNA fragments dominating the eDNA community. Comparisons between eDNA, community DNA, taxonomy and UK species abundance data further show significant relationships between diversity estimates derived across the disparate methodologies. Our results reveal the temporal dynamics of eDNA and validate the utility of eDNA metabarcoding for tracking seasonal diversity at the ecosystem scale.
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Affiliation(s)
- Iliana Bista
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Kerry Walsh
- Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Mehrdad Hajibabaei
- Department of Integrative Biology &Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Delphine Lallias
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Martin Christmas
- Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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14
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Darling JA, Galil BS, Carvalho GR, Rius M, Viard F, Piraino S. Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems. Mar Policy 2017; 85:56-64. [PMID: 29681680 PMCID: PMC5909192 DOI: 10.1016/j.marpol.2017.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The European Union's Marine Strategy Framework Directive (MSFD) aims to adopt integrated ecosystem management approaches to achieve or maintain "Good Environmental Status" for marine waters, habitats and resources, including mitigation of the negative effects of non-indigenous species (NIS). The Directive further seeks to promote broadly standardized monitoring efforts and assessment of temporal trends in marine ecosystem condition, incorporating metrics describing the distribution and impacts of NIS. Accomplishing these goals will require application of advanced tools for NIS surveillance and risk assessment, particularly given known challenges associated with surveying and monitoring with traditional methods. In the past decade, a host of methods based on nucleic acids (DNA and RNA) analysis have been developed or advanced that promise to dramatically enhance capacity in assessing and managing NIS. However, ensuring that these rapidly evolving approaches remain accessible and responsive to the needs of resource managers remains a challenge. This paper provides recommendations for future development of these genetic tools for assessment and management of NIS in marine systems, within the context of the explicit requirements of the MSFD. Issues considered include technological innovation, methodological standardization, data sharing and collaboration, and the critical importance of shared foundational resources, particularly integrated taxonomic expertise. Though the recommendations offered here are not exhaustive, they provide a basis for future intentional (and international) collaborative development of a genetic toolkit for NIS research, capable of fulfilling the immediate and long term goals of marine ecosystem and resource conservation.
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Affiliation(s)
- John A. Darling
- National Exposure Research Laboratory, United States Environmental
Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711,
USA
- Corresponding author.
(J.A. Darling)
| | - Bella S. Galil
- The Steinhardt Museum of Natural History, Israel National Center for
Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Marc Rius
- Ocean and Earth Science, National Oceanography Centre, University of
Southampton, UK
- Centre for Ecological Genomics and Wildlife Conservation, University
of Johannesburg, South Africa
| | - Frédérique Viard
- Sorbonne Université, Université Paris 06, CNRS, UMR
7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff,
France
| | - Stefano Piraino
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali,
Università del Salento, Lecce, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare
(CoNISMa), Roma, Italy
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15
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Carvalho GR, Hauser L, Martinsohn J, Naish K. Fish, genes and genomes: contributions to ecology, evolution and management. J Fish Biol 2016; 89:2471-2478. [PMID: 27921308 DOI: 10.1111/jfb.13228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- G R Carvalho
- Molecular Ecology & Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
| | - L Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, U.S.A
| | - J Martinsohn
- European Commission, Joint Research Centre (JRC), Directorate D - Sustainable Resources, Water and Marine Resources, Via E. Fermi 2749, I-21027, Ispra, VA, Italy
| | - K Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, U.S.A
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16
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Harvey AC, Solberg MF, Glover KA, Taylor MI, Creer S, Carvalho GR. Plasticity in response to feed availability: Does feeding regime influence the relative growth performance of domesticated, wild and hybrid Atlantic salmon Salmo salar parr? J Fish Biol 2016; 89:1754-1768. [PMID: 27460446 DOI: 10.1111/jfb.13076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/09/2016] [Indexed: 06/06/2023]
Abstract
Growth of farmed, wild and F1 hybrid Atlantic salmon parr Salmo salar was investigated under three contrasting feeding regimes in order to understand how varying levels of food availability affects relative growth. Treatments consisted of standard hatchery feeding (ad libitum), access to feed for 4 h every day, and access to feed for 24 h on three alternate days weekly. Mortality was low in all treatments, and food availability had no effect on survival of all groups. The offspring of farmed S. salar significantly outgrew the wild S. salar, while hybrids displayed intermediate growth. Furthermore, the relative growth differences between the farmed and wild S. salar did not change across feeding treatments, indicating a similar plasticity in response to feed availability. Although undertaken in a hatchery setting, these results suggest that food availability may not be the sole driver behind the observed reduced growth differences found between farmed and wild fishes under natural conditions.
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Affiliation(s)
- A C Harvey
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
| | - M F Solberg
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - K A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
- Department of Biology, Sea Lice Research Centre, University of Bergen, P. O. Box 7803, N-5020, Bergen, Norway
| | - M I Taylor
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich, U.K
| | - S Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
| | - G R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
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17
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Pereira TB, Setotaw TA, Santos DN, Mendes ANG, Salgado SML, Carvalho GR, Rezende RM. Identification of microsatellite markers in coffee associated with resistance to Meloidogyne exigua. Genet Mol Res 2016; 15:gmr8054. [PMID: 27525876 DOI: 10.4238/gmr.15038054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Meloidogyne species are destructive phytonematodes that result in reduced yields of coffee. The classic test for resistance to Meloidogyne exigua in coffee progenies is both expensive and time-consuming. The use of molecular marker techniques can assist the selection process when it is difficult to measure the phenotype, such as in cases of resistance to nematode infestation. The objective of this study was to identify microsatellite markers associated with resistance to M. exigua in F5 progenies of coffee derived from a cross between Híbrido de Timor 440-10 and Catuaí Amarelo IAC 86. Of the 44 simple sequence repeat (SSR) markers evaluated, 11 showed a polymorphic pattern with a mean number of 4.5 alleles per marker. Clustering analysis classified 82 progenies into three groups related to the response to nematodes and parental genotypes allocated to different groups (resistant and susceptible). SSRCafé 40 allele 2, SSRCafé 15 allele 3, SSRCafé 20 allele 3, and SSRCafé 13 allele 1 were negatively correlated with reproduction factor. In addition, SSRCafé 13 allele 2, SSRCafé 19 allele 3, SSRCafé 40 allele 2, SSRCafé 15 allele 3, and SSRCafé 20 allele 3 were correlated with the root gall index of M. exigua. These SSR markers, which have been validated in this population, represent a potential method to select progenies resistant to nematodes in coffee-breeding programs.
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Affiliation(s)
- T B Pereira
- Departamento de Agricultura, Universidade Federal de Lavras, Lavras, MG, Brasil
| | - T A Setotaw
- Departamento de Agricultura, Universidade Federal de Lavras, Lavras, MG, Brasil
| | - D N Santos
- Departamento de Agricultura, Universidade Federal de Lavras, Lavras, MG, Brasil
| | - A N G Mendes
- Departamento de Agricultura, Universidade Federal de Lavras, Lavras, MG, Brasil
| | - S M L Salgado
- Unidade Regional do Sul de Minas, Empresa de Pesquisa Agropecuária de Minas Gerais, Lavras, MG, Brasil
| | - G R Carvalho
- Unidade Regional do Sul de Minas, Empresa de Pesquisa Agropecuária de Minas Gerais, Lavras, MG, Brasil
| | - R M Rezende
- Unidade Regional do Sul de Minas, Empresa de Pesquisa Agropecuária de Minas Gerais, Lavras, MG, Brasil
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18
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Harvey AC, Juleff G, Carvalho GR, Taylor MI, Solberg MF, Creer S, Dyrhovden L, Matre IH, Glover KA. Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions? R Soc Open Sci 2016; 3:160152. [PMID: 27493772 PMCID: PMC4968464 DOI: 10.1098/rsos.160152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/27/2016] [Indexed: 06/06/2023]
Abstract
The conditions encountered by Atlantic salmon, Salmo salar L., in aquaculture are markedly different from the natural environment. Typically, farmed salmon experience much higher densities than wild individuals, and may therefore have adapted to living in high densities. Previous studies have demonstrated that farmed salmon typically outgrow wild salmon by large ratios in the hatchery, but these differences are much less pronounced in the wild. Such divergence in growth may be explained partly by the offspring of wild salmon experiencing higher stress and thus lower growth when compared under high-density farming conditions. Here, growth of farmed, wild and F1 hybrid salmon was studied at contrasting densities within a hatchery and semi-natural environment. Farmed salmon significantly outgrew hybrid and wild salmon in all treatments. Importantly, however, the reaction norms were similar across treatments for all groups. Thus, this study was unable to find evidence that the offspring of farmed salmon have adapted more readily to higher fish densities than wild salmon as a result of domestication. It is suggested that the substantially higher growth rate of farmed salmon observed in the hatchery compared with wild individuals may not solely be caused by differences in their ability to grow in high-density hatchery scenarios.
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Affiliation(s)
- Alison C. Harvey
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Gareth Juleff
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Martin I. Taylor
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
- Biological Sciences, University of East Anglia, Norwich, UK
| | | | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | | | | | - Kevin A. Glover
- Havforskningsinstituttet, Bergen, Norway
- Sea Lice Research Centre, Universitetet i Bergen Institutt for Biologi, Bergen, Norway
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19
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Harvey AC, Glover KA, Taylor MI, Creer S, Carvalho GR. A common garden design reveals population-specific variability in potential impacts of hybridization between populations of farmed and wild Atlantic salmon, Salmo salar L. Evol Appl 2016; 9:435-49. [PMID: 26989435 PMCID: PMC4778114 DOI: 10.1111/eva.12346] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 11/13/2015] [Indexed: 11/30/2022] Open
Abstract
Released individuals can have negative impacts on native populations through various mechanisms, including competition, disease transfer and introduction of maladapted gene complexes. Previous studies indicate that the level of farmed Atlantic salmon introgression in native populations is population specific. However, few studies have explored the potential role of population diversity or river characteristics, such as temperature, on the consequences of hybridization. We compared freshwater growth of multiple families derived from two farmed, five wild and two F1 hybrid salmon populations at three contrasting temperatures (7°C, 12°C and 16°C) in a common garden experiment. As expected, farmed salmon outgrew wild salmon at all temperatures, with hybrids displaying intermediate growth. However, differences in growth were population specific and some wild populations performed better than others relative to the hybrid and farmed populations at certain temperatures. Therefore, the competitive balance between farmed and wild salmon may depend both on the thermal profile of the river and on the genetic characteristics of the respective farmed and wild strains. While limited to F1 hybridization, this study shows the merits in adopting a more complex spatially resolved approach to risk management of local populations.
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Affiliation(s)
- Alison C Harvey
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK
| | | | - Martin I Taylor
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK; School of Biological Sciences University of East Anglia Norwich UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK
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20
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Young EF, Belchier M, Hauser L, Horsburgh GJ, Meredith MP, Murphy EJ, Pascoal S, Rock J, Tysklind N, Carvalho GR. Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species. Evol Appl 2015; 8:486-509. [PMID: 26029262 PMCID: PMC4430772 DOI: 10.1111/eva.12259] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/27/2015] [Indexed: 01/27/2023] Open
Abstract
Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a 'seascape genetics' approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts.
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Affiliation(s)
| | | | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Gavin J Horsburgh
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK
| | | | | | - Sonia Pascoal
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
| | - Jennifer Rock
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK ; School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Department of Zoology, University of Otago Dunedin, 9054, New Zealand
| | - Niklas Tysklind
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Campus Agronomique BP 709-97387, Kourou Cedex, France
| | - Gary R Carvalho
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
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21
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Oliveira RR, Rates DM, Pugliesi G, Ker PG, Arruda RP, Moraes EA, Carvalho GR. Use of cholesterol-loaded cyclodextrin in donkey semen cryopreservation improves sperm viability but results in low fertility in mares. Reprod Domest Anim 2014; 49:845-50. [PMID: 25124746 DOI: 10.1111/rda.12379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/19/2014] [Indexed: 11/27/2022]
Abstract
The use of cholesterol-loaded cyclodextrin (CLC) on semen cryopreservation has been related with better sperm viability in several species; however, the effect on fertility is not known in donkey semen. Ejaculates (n = 25) from five donkeys were diluted in S-MEDIUM with 0, 1, 2 or 3 mg of CLC/120 × 10(6) spermatozoa. Semen was frozen, and thawed samples were evaluated by computer-assisted sperm analyser system (CASA), supravital test, hyposmotic swelling test and fluorescent dyes to assess the integrity of sperm membranes. Mares (n = 60) were inseminated with frozen-thawed semen treated with the doses of 0 or 1 mg CLC. Percentages of sperm with progressive motility and with functional plasma membrane were greater (p < 0.05) in the CLC-treated groups than in the control. Percentages of intact plasma membrane and intact plasma membrane and acrosome detected by fluorescent dyes were also greater (p < 0.05) in CLC-treated groups. Although no difference (p > 0.05) in conception rates was detected between groups (control, 3/30, 10%; CLC-treated, 1/30, 3.3%), fertility was low for artificial insemination programs in mares. Therefore, we firstly demonstrated that frozen semen treated with CLC in S-MEDIA extender before freezing improves the in vitro sperm viability, but semen treated or not with CLC in S-MEDIUM extender results in a very low conception rate in mares inseminated with thawed donkey semen.
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Affiliation(s)
- R R Oliveira
- Department of Animal Science, Federal University of Viçosa, Viçosa, MG, Brazil
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Helyar SJ, Lloyd HAD, de Bruyn M, Leake J, Bennett N, Carvalho GR. Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing. PLoS One 2014; 9:e98691. [PMID: 24921655 PMCID: PMC4055496 DOI: 10.1371/journal.pone.0098691] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 05/07/2014] [Indexed: 11/19/2022] Open
Abstract
Increasing consumer demand for seafood, combined with concern over the health of our oceans, has led to many initiatives aimed at tackling destructive fishing practices and promoting the sustainability of fisheries. An important global threat to sustainable fisheries is Illegal, Unreported and Unregulated (IUU) fishing, and there is now an increased emphasis on the use of trade measures to prevent IUU-sourced fish and fish products from entering the international market. Initiatives encompass new legislation in the European Union requiring the inclusion of species names on catch labels throughout the distribution chain. Such certification measures do not, however, guarantee accuracy of species designation. Using two DNA-based methods to compare species descriptions with molecular ID, we examined 386 samples of white fish, or products labelled as primarily containing white fish, from major UK supermarket chains. Species specific real-time PCR probes were used for cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) to provide a highly sensitive and species-specific test for the major species of white fish sold in the UK. Additionally, fish-specific primers were used to sequence the forensically validated barcoding gene, mitochondrial cytochrome oxidase I (COI). Overall levels of congruence between product label and genetic species identification were high, with 94.34% of samples correctly labelled, though a significant proportion in terms of potential volume, were mislabelled. Substitution was usually for a cheaper alternative and, in one case, extended to a tropical species. To our knowledge, this is the first published study encompassing a large-scale assessment of UK retailers, and if representative, indicates a potentially significant incidence of incorrect product designation.
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Affiliation(s)
- Sarah J. Helyar
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Wales, United Kingdom
- * E-mail:
| | - Hywel ap D. Lloyd
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Wales, United Kingdom
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Wales, United Kingdom
| | | | | | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Wales, United Kingdom
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Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Yu DW, de Bruyn M. Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 2014; 29:358-67. [DOI: 10.1016/j.tree.2014.04.003] [Citation(s) in RCA: 515] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 01/07/2023]
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Knebelsberger T, Landi M, Neumann H, Kloppmann M, Sell AF, Campbell PD, Laakmann S, Raupach MJ, Carvalho GR, Costa FO. A reliable DNA barcode reference library for the identification of the North European shelf fish fauna. Mol Ecol Resour 2014; 14:1060-71. [PMID: 24618145 DOI: 10.1111/1755-0998.12238] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/29/2014] [Accepted: 01/29/2014] [Indexed: 12/27/2022]
Abstract
Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour-joining analysis based on K2P genetic distances formed nonoverlapping clusters for all species with a ≥99% bootstrap support each. Identification was successful for 100% of the species as the minimum genetic distance to the nearest neighbour always exceeded the maximum intraspecific distance. A barcoding gap was apparent for the whole data set. Within-species distances ranged from 0 to 2.35%, while interspecific distances varied between 3.15 and 28.09%. Distances between congeners were on average 51-fold higher than those within species. The validation of the sequence library by applying BOLDs barcode index number (BIN) analysis tool and a ranking system demonstrated high taxonomic reliability of the DNA barcodes for 85% of the investigated fish species. Thus, the sequence library presented here can be confidently used as a benchmark for identification of at least two-thirds of the typical fish species recorded for the North Sea.
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Affiliation(s)
- Thomas Knebelsberger
- Senckenberg am Meer, German Center for Marine Biodiversity Research (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany
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Milano I, Babbucci M, Cariani A, Atanassova M, Bekkevold D, Carvalho GR, Espiñeira M, Fiorentino F, Garofalo G, Geffen AJ, Hansen JH, Helyar SJ, Nielsen EE, Ogden R, Patarnello T, Stagioni M, Tinti F, Bargelloni L. Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius). Mol Ecol 2013; 23:118-35. [DOI: 10.1111/mec.12568] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 01/27/2023]
Affiliation(s)
- Ilaria Milano
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science-Agripolis-Viale dell'Università 16; I-35020 Legnaro Padova Italy
| | - Alessia Cariani
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Miroslava Atanassova
- Living Resources, Aquaculture and Management of their Traceability Division of ANFACO-CECOPESCA; Ctra. Colegio Universitario 16; 36.310 Vigo Spain
| | - Dorte Bekkevold
- National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 DK-8600 Silkeborg Denmark
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory; School of Biological Sciences; Bangor University; Environment Centre Wales; Bangor UK
| | - Montserrat Espiñeira
- Living Resources, Aquaculture and Management of their Traceability Division of ANFACO-CECOPESCA; Ctra. Colegio Universitario 16; 36.310 Vigo Spain
| | - Fabio Fiorentino
- National Research Council (CNR)-Institute for Coastal Marine Environment (IAMC); Via L. Vaccara 61 91026 Mazara del Vallo Trapani Italy
| | - Germana Garofalo
- National Research Council (CNR)-Institute for Coastal Marine Environment (IAMC); Via L. Vaccara 61 91026 Mazara del Vallo Trapani Italy
| | - Audrey J. Geffen
- Department of Biology; University of Bergen; P.O. Box 7803, N-5020 Bergen Norway
| | - Jakob. H. Hansen
- Living Resources, Aquaculture and Management of their Traceability Division of ANFACO-CECOPESCA; Ctra. Colegio Universitario 16; 36.310 Vigo Spain
| | - Sarah J. Helyar
- Food Safety, Environment & Genetics; Matís ohf, Vínlandsleið 12; 113 Reykjavík Iceland
| | - Einar E. Nielsen
- National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 DK-8600 Silkeborg Denmark
| | - Rob Ogden
- TRACE Wildlife Forensics Network; Royal Zoological Society of Scotland; Edinburgh EH12 6TS UK
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science-Agripolis-Viale dell'Università 16; I-35020 Legnaro Padova Italy
| | - Marco Stagioni
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Fausto Tinti
- Department of Biological; Geological and Environmental Sciences; University of Bologna; via Selmi 3 40126 Bologna Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science-Agripolis-Viale dell'Università 16; I-35020 Legnaro Padova Italy
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Nielsen EE, Cariani A, Mac Aoidh E, Maes GE, Milano I, Ogden R, Taylor M, Hemmer-Hansen J, Babbucci M, Bargelloni L, Bekkevold D, Diopere E, Grenfell L, Helyar S, Limborg MT, Martinsohn JT, McEwing R, Panitz F, Patarnello T, Tinti F, Van Houdt JKJ, Volckaert FAM, Waples RS, Carvalho GR. Erratum: Corrigendum: Gene-associated markers provide tools for tackling illegal fishing and false eco-certification. Nat Commun 2013. [DOI: 10.1038/ncomms2975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Tysklind N, Taylor MI, Lyons BP, Goodsir F, McCarthy ID, Carvalho GR. Population genetics provides new insights into biomarker prevalence in dab (Limanda limanda L.): a key marine biomonitoring species. Evol Appl 2013; 6:891-909. [PMID: 24062799 PMCID: PMC3779091 DOI: 10.1111/eva.12074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 04/03/2013] [Indexed: 12/19/2022] Open
Abstract
Bioindicators are species for which some quantifiable aspect of its biology, a biomarker, is assumed to be sensitive to ecosystem health. However, there is frequently a lack of information on the underlying genetic and environmental drivers shaping the spatiotemporal variance in prevalence of the biomarkers employed. Here, we explore the relative role of potential variables influencing the spatiotemporal prevalence of biomarkers in dab, Limanda limanda, a species used as a bioindicator of marine contaminants. Firstly, the spatiotemporal genetic structure of dab around UK waters (39 samples across 15 sites for four years: 2005–2008) is evaluated with 16 microsatellites. Two temporally stable groups are identified corresponding to the North and Irish Seas (average between basin = 0.007; = 0.022). Secondly, we examine the association between biomarker prevalence and several variables, including genetic structuring, age and contaminant exposure. Genetic structure had significant interactive effects, together with age and some contaminants, in the prevalence of some of the biomarkers considered, namely hyperpigmentation and liver lesions. The integration of these data sets enhanced our understanding of the relationship between biomarker prevalence, exposure to contaminants and population-specific response, thereby yielding more informative predictive models of response and prospects for environmental remediation.
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Affiliation(s)
- Niklas Tysklind
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, School of Biological Sciences, Bangor University Gwynedd, UK
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Hemmer-Hansen J, Nielsen EE, Therkildsen NO, Taylor MI, Ogden R, Geffen AJ, Bekkevold D, Helyar S, Pampoulie C, Johansen T, Carvalho GR. A genomic island linked to ecotype divergence in Atlantic cod. Mol Ecol 2013; 22:2653-67. [DOI: 10.1111/mec.12284] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 01/20/2013] [Accepted: 01/31/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Jakob Hemmer-Hansen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | - Einar E. Nielsen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | - Nina O. Therkildsen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | - Martin I. Taylor
- School of Biological Sciences; University of East Anglia; Norwich NR4 7TJ UK
| | - Rob Ogden
- TRACE Wildlife Forensics Network; Royal Zoological Society of Scotland; Edinburgh EH12 6TS UK
| | - Audrey J. Geffen
- Department of Biology; University of Bergen; PB 7803 Bergen N-5020 Norway
| | - Dorte Bekkevold
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | | | | | - Torild Johansen
- Institute of Marine Research Tromsø; PO Box 6404 Tromsø N-9294 Norway
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory; School of Biological Sciences; Environment Centre Wales; Bangor University; Bangor Gwynedd LL57 2UW UK
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de Bruyn M, Rüber L, Nylinder S, Stelbrink B, Lovejoy NR, Lavoué S, Tan HH, Nugroho E, Wowor D, Ng PKL, Siti Azizah MN, Von Rintelen T, Hall R, Carvalho GR. Paleo-Drainage Basin Connectivity Predicts Evolutionary Relationships across Three Southeast Asian Biodiversity Hotspots. Syst Biol 2013; 62:398-410. [DOI: 10.1093/sysbio/syt007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Helyar SJ, Limborg MT, Bekkevold D, Babbucci M, van Houdt J, Maes GE, Bargelloni L, Nielsen RO, Taylor MI, Ogden R, Cariani A, Carvalho GR, Panitz F. SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus). PLoS One 2012; 7:e42089. [PMID: 22879907 PMCID: PMC3413699 DOI: 10.1371/journal.pone.0042089] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/02/2012] [Indexed: 11/29/2022] Open
Abstract
The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.
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Affiliation(s)
- Sarah J Helyar
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom.
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Nielsen EE, Cariani A, Aoidh EM, Maes GE, Milano I, Ogden R, Taylor M, Hemmer-Hansen J, Babbucci M, Bargelloni L, Bekkevold D, Diopere E, Grenfell L, Helyar S, Limborg MT, Martinsohn JT, McEwing R, Panitz F, Patarnello T, Tinti F, Van Houdt JKJ, Volckaert FAM, Waples RS, Carvalho GR. Gene-associated markers provide tools for tackling illegal fishing and false eco-certification. Nat Commun 2012; 3:851. [DOI: 10.1038/ncomms1845] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 04/12/2012] [Indexed: 11/09/2022] Open
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Pugliesi G, Khan FA, Hannan MA, Beg MA, Carvalho GR, Ginther OJ. Inhibition of prostaglandin biosynthesis during postluteolysis and effects on CL regression, prolactin, and ovulation in heifers. Theriogenology 2012; 78:443-54. [PMID: 22578618 DOI: 10.1016/j.theriogenology.2012.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/16/2012] [Accepted: 02/17/2012] [Indexed: 11/18/2022]
Abstract
The beginning of postluteolysis (progesterone, <1 ng mL(-1)) in heifers was targeted by using 8 h after ultrasonic detection of a 25% decrease in CL area (cm2) and was designated Hour 0. Flunixin meglumine (FM; n=10) to inhibit PGF2α secretion or vehicle (n=9) were given intramuscularly at Hours 0, 4, 8, 16, 24, 32, and 40. The dose of FM was 2.5 mg/kg at each treatment. Blood sampling and measurement of the CL and dominant follicle were done every 8 h beginning 14 days postovulation in each group. Blood samples for detection of pulses of PRL and pulses of a metabolite of PGF2α (PGFM) were obtained every hour for 24 h beginning at Hour 0. Pulse concentrations of both PGFM and PRL were lower in the FM group than in the vehicle group. Concentration of PRL was greatest at the peak of a PGFM pulse. Neither CL area (cm2) nor progesterone concentration differed between groups during Hours 0 to 48 (postluteolysis). Ovulation occurred in nine of nine heifers in the vehicle group and in three of 10 heifers in the FM group. The anovulatory follicles in the FM group grew to 36.2±2.9 mm, and the wall became thickened from apparent luteinization. The hypothesis that PGF2α was involved in the continued P4 decrease and structural CL regression during postluteolysis was not supported. However, the hypotheses that pulses of PGFM and PRL were temporally related and that systemic FM treatment induced an anovulatory follicle were supported.
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Affiliation(s)
- G Pugliesi
- Eutheria Foundation, Cross Plains, Wisconsin 53528, USA
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Costa FO, Landi M, Martins R, Costa MH, Costa ME, Carneiro M, Alves MJ, Steinke D, Carvalho GR. A ranking system for reference libraries of DNA barcodes: application to marine fish species from Portugal. PLoS One 2012; 7:e35858. [PMID: 22558244 PMCID: PMC3338485 DOI: 10.1371/journal.pone.0035858] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 03/27/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal. METHODOLOGY/PRINCIPAL FINDINGS Specimens (n = 659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A-E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E). CONCLUSION/SIGNIFICANCE We highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the continuous revision and annotation required in taxonomic work.
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Affiliation(s)
- Filipe O Costa
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal.
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Moore ABM, McCarthy ID, Carvalho GR, Peirce R. Species, sex, size and male maturity composition of previously unreported elasmobranch landings in Kuwait, Qatar and Abu Dhabi Emirate. J Fish Biol 2012; 80:1619-1642. [PMID: 22497401 DOI: 10.1111/j.1095-8649.2011.03210.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This paper presents data from the first major survey of the diversity, biology and fisheries of elasmobranchs in the Persian (Arabian) Gulf. Substantial landings of elasmobranchs, usually as gillnet by-catch, were recorded in Kuwait, Qatar and the Emirate of Abu Dhabi (part of the United Arab Emirates), although larger elasmobranchs from targeted line fisheries were landed in Abu Dhabi. The elasmobranch fauna recorded was distinctive and included species that are undescribed, rare and have a highly restricted known distribution. Numerical abundance was dominated by sharks (c. 80%), of which carcharhinids were by far the most important. The milk shark Rhizoprionodon acutus and whitecheek shark Carcharhinus dussumieri together comprised just under half of all recorded individuals. Around 90% of recorded sharks were small (50-90 cm total length, L(T) ) individuals, most of which were mature individuals of species with a small maximum size (<100 cm L(T) ), although immature individuals of larger species (e.g. Carcharhinus sorrah and other Carcharhinus spp.) were also important. The most frequently recorded batoid taxa were cownose rays Rhinoptera spp., an undescribed whipray, and the granulated guitarfish Rhinobatos granulatus. The first size, sex and maturity data for a wide range of Gulf elasmobranch species are presented (including L(T) at 50% maturity for males of four shark species) and include some notable differences from other locations in the Indo-West Pacific Ocean. A number of concerns regarding the sustainability of the fishery were highlighted by this study, notably that most of the batoid species recorded are classed by the IUCN Red List as vulnerable, endangered, data deficient or not evaluated. Despite their considerable elasmobranch landings, none of the three countries sampled have developed a 'Shark Plan' as encouraged to do so under the FAO International Plan of Action: Sharks. Furthermore, Kuwait and Qatar currently report zero or no elasmobranch landings to the FAO.
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Affiliation(s)
- A B M Moore
- School of Ocean Sciences, Bangor University, Askew Street, Menai Bridge, Anglesey, LL59 5AB, UK.
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Fonseca VG, Nichols B, Lallias D, Quince C, Carvalho GR, Power DM, Creer S. Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Res 2012; 40:e66. [PMID: 22278883 PMCID: PMC3351157 DOI: 10.1093/nar/gks002] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Eukaryotic diversity in environmental samples is often assessed via PCR-based amplification of nSSU genes. However, estimates of diversity derived from pyrosequencing environmental data sets are often inflated, mainly because of the formation of chimeric sequences during PCR amplification. Chimeras are hybrid products composed of distinct parental sequences that can lead to the misinterpretation of diversity estimates. We have analyzed the effect of sample richness, evenness and phylogenetic diversity on the formation of chimeras using a nSSU data set derived from 454 Roche pyrosequencing of replicated, large control pools of closely and distantly related nematode mock communities, of known intragenomic identity and richness. To further investigate how chimeric molecules are formed, the nSSU gene secondary structure was analyzed in several individuals. For the first time in eukaryotes, chimera formation proved to be higher in both richer and more genetically diverse samples, thus providing a novel perspective of chimera formation in pyrosequenced environmental data sets. Findings contribute to a better understanding of the nature and mechanisms involved in chimera formation during PCR amplification of environmentally derived DNA. Moreover, given the similarities between biodiversity analyses using amplicon sequencing and those used to assess genomic variation, our findings have potential broad application for identifying genetic variation in homologous loci or multigene families in general.
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Affiliation(s)
- V G Fonseca
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Deiniol Road, Gwynedd LL57 2UW, UK
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Matzen da Silva J, dos Santos A, Cunha MR, Costa FO, Creer S, Carvalho GR. Multigene molecular systematics confirm species status of morphologically convergent Pagurus hermit crabs. PLoS One 2011; 6:e28233. [PMID: 22174780 PMCID: PMC3235110 DOI: 10.1371/journal.pone.0028233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 11/04/2011] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION In spite of contemporary morphological taxonomy appraisals, apparent high morphological similarity raises uncertainty about the species status of certain Pagurus hermit crabs. This is exemplified between two European species, Pagurus excavatus (Herbst, 1791) and Pagurus alatus (Fabricius 1775), whose species status is still difficult to resolve using morphological criteria alone. METHODOLOGY/PRINCIPAL FINDINGS To address such ambiguities, we used combinations of Maximum Likelihood (ML) and Bayesian Inference (BI) methods to delineate species boundaries of P. alatus and P. excavatus and formulate an intermediate Pagurus phylogenetic hypothesis, based upon single and concatenated mitochondrial (cytochrome oxidase I [COI]) and nuclear (16S and 28s ribosomal RNA) gene partitions. The molecular data supported the species status of P. excavatus and P. alatus and also clearly resolved two divergent clades within hermit crabs from the Northeast Atlantic Ocean and the Mediterranean Sea. CONCLUSIONS/SIGNIFICANCE Despite the abundance and prominent ecological role of hermit crabs, Pagurus, in North East Atlantic Ocean and Mediterranean Sea ecosystems, many important aspects of their taxonomy, biology, systematics and evolution remain poorly explored. The topologies presented here should be regarded as hypotheses that can be incorporated into the robust and integrated understanding of the systematic relationships within and between species of the genus Pagurus inhabiting the Northeast Atlantic Ocean and the Mediterranean Sea.
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Affiliation(s)
- Joana Matzen da Silva
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre for Wales, Bangor University, Bangor, Wales, United Kingdom
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
- * E-mail: (JMdS); (GRC)
| | | | - Marina R. Cunha
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - Filipe O. Costa
- Departamento de Biologia, Centro de Biologia Molecular e Ambiental (CBMA), Universidade do Minho, Braga, Portugal
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre for Wales, Bangor University, Bangor, Wales, United Kingdom
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre for Wales, Bangor University, Bangor, Wales, United Kingdom
- * E-mail: (JMdS); (GRC)
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Lohman DJ, de Bruyn M, Page T, von Rintelen K, Hall R, Ng PK, Shih HT, Carvalho GR, von Rintelen T. Biogeography of the Indo-Australian Archipelago. Annu Rev Ecol Evol Syst 2011. [DOI: 10.1146/annurev-ecolsys-102710-145001] [Citation(s) in RCA: 331] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David J. Lohman
- Department of Biology, The City College of New York, The City University of New York, New York, NY 10031;
| | - Mark de Bruyn
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW United Kingdom; ,
| | - Timothy Page
- Australian Rivers Institute, Griffith University, Nathan, Queensland 4111, Australia;
| | - Kristina von Rintelen
- Museum für Naturkunde—Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, 10115 Berlin, Germany; ,
| | - Robert Hall
- Southeast Asia Research Group, Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom;
| | - Peter K.L. Ng
- Department of Biological Sciences and Raffles Museum of Biodiversity Research, National University of Singapore, Singapore 117546;
| | - Hsi-Te Shih
- Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan;
| | - Gary R. Carvalho
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW United Kingdom; ,
| | - Thomas von Rintelen
- Museum für Naturkunde—Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, 10115 Berlin, Germany; ,
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Zelenina DA, Martinson IT, Ogden R, Volkov AA, Zelenina IA, Carvalho GR. [Advanced approaches to studying the population diversity of marine fishes: new opportunities for fisheries control and management]. Genetika 2011; 47:1629-1641. [PMID: 22384692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent conceptual and technological advances now enable fisheries geneticists to detect and monitor the dynamics and distribution of marine fish populations more effectively than ever before. Information on the extent of genetically-based divergence among populations, so-called "population diversity", is crucial in the quest to manage exploited living resources sustainably since it endows evolutionary potential in the face of environmental change. The generally limited dialogue between scientists, fisheries managers and policy makers, however, continues to constrain integration of population genetic data into tangible policy applications. Largely drawing on the approach and outputs from a European research project, FishPopTrace, we provide an example how the uncovering of marine fish population diversity enables players from genetics, forensics, management and the policy realm to generate a framework tackling key policy-led questions relating to illegal fishing and traceability. We focus on the use of single-nucleotide polymorphisms (SNPs) in European populations of cod, herring, hake and common sole, and explore how forensics together with a range of analytical approaches, and combined with improved communication of research results to stakeholders, can be used to secure sufficiently robust, tractable and targeted data for effective engagement between science and policy. The essentially binary nature of SNPs, together with generally elevated signals of population discrimination by SNPs under selection, allowed assignment of fish to populations from more areas and with higher certainty than previously possible, reaching standards suitable for use in a court of law. We argue that the use of such tools in enforcement and deterrence, together with the greater integration of population genetic principles and methods into fisheries management, provide tractable elements in the arsenal of tools to achieve sustainable exploitation and conservation of depleted marine fish stocks.
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Pugliesi G, Beg MA, Carvalho GR, Ginther OJ. Induction of PGFM pulses and luteolysis by sequential estradiol-17β treatments in heifers. Theriogenology 2011; 77:492-506. [PMID: 22119513 DOI: 10.1016/j.theriogenology.2011.08.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/09/2011] [Accepted: 08/10/2011] [Indexed: 10/15/2022]
Abstract
The effects of sequential induction of PGFM pulses by estradiol-17β (E2) on prominence of PGFM pulses and progesterone (P4) concentration were studied in heifers. Three treatments of vehicle (n = 12) or E2 (n = 12) at doses of 0.05 or 0.1 mg were given at 12-h intervals beginning on Day 15 postovulation. Blood samples were collected every 12 h from Days 13-24 and hourly for 12 h after the first and third treatments. On Day 15, all heifers were in preluteolysis and on Day 16 were in preluteolysis in the vehicle-treated heifers (n = 11) and either preluteolysis (n = 4) or luteolysis (n = 8) in the E2-treated heifers. Peak concentration of induced PGFM pulses during preluteolysis on Day 15 was greater (P < 0.04) than for pulses during preluteolysis on Day 16. The interval from ovulation to the beginning of luteolysis was shorter (P < 0.04) in the E2-treated heifers than in the vehicle-treated heifers. An E2-induced PGFM pulse was less prominent (P < 0.008) in heifers in temporal association with a transient resurgence in P4 than in heifers with a progressive P4 decrease. The hypothesis that repeated E2 exposure stimulates increasing prominence of PGFM pulses was not supported. Instead, repeated exposure reduced the prominence of PGFM pulses, in contrast to the stimulation from the first E2 treatment. Reduced prominence of a PGF(2α) pulse during luteolysis can lead to a transient resurgence in P4 concentration.
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Affiliation(s)
- G Pugliesi
- Eutheria Foundation, Cross Plains, Wisconsin, USA
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41
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Pugliesi G, Beg MA, Carvalho GR, Ginther OJ. Effect of dose of estradiol-17β on prominence of an induced 13,14-dihydro-15-keto-PGF(2α) (PGFM) pulse and relationship of prominence to progesterone, LH, and luteal blood flow in heifers. Domest Anim Endocrinol 2011; 41:98-109. [PMID: 21741578 DOI: 10.1016/j.domaniend.2011.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/20/2011] [Accepted: 05/22/2011] [Indexed: 02/02/2023]
Abstract
Various doses of estradiol-17β (E(2)) were used in heifers to induce a pulse of 13,14-dihydro-15-keto-prostaglandin F(2α) (PGFM). The effect of E(2) concentration on the prominence of PGFM pulses and the relationship between prominence and intrapulse concentration of progesterone (P(4)), LH, and luteal blood flow were studied. A single dose of 0 (vehicle), 0.01, 0.05, or 0.1 mg of E(2) was given (n = six/group) 14 d after ovulation. Blood samples were collected, and luteal blood flow was evaluated hourly for 10 h after the treatment. The 0.05-mg dose increased and the 0.1-mg dose further increased the prominence of the induced PGFM pulse, compared with the 0.0-mg dose and the 0.01-mg dose. The PGFM pulses were subdivided into three different prominence categories (<50, 50 to 150, and >150 pg/mL at the peak). In the 50 to 150 category, P(4) concentration increased (P < 0.05) between -2 h and 0 h (0 h = peak of PGFM pulse). In the >150 category, P(4) decreased (P < 0.05) between -1 h and 0 h, LH increased (P < 0.05) at 1 h, and luteal blood flow apparently decreased (P < 0.05) at 2 h of the PGFM pulse. The novel results supported the following hypotheses: (1) an increase in E(2) concentration increases the prominence of a PGFM pulse, and (2) greater prominence of a PGFM pulse is associated with a greater transient intrapulse depression of P(4) at the peak of the PGFM pulse. In addition, the extent of the effect of prostaglandin F(2α) on the increase in LH and changes in blood flow within the hours of a PGFM pulse was related positively to the prominence of the PGFM pulse.
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Affiliation(s)
- G Pugliesi
- Eutheria Foundation, Cross Plains, WI 53528, USA
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de Bruyn M, Hoelzel AR, Carvalho GR, Hofreiter M. Faunal histories from Holocene ancient DNA. Trends Ecol Evol 2011; 26:405-13. [PMID: 21529992 DOI: 10.1016/j.tree.2011.03.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/24/2011] [Accepted: 03/28/2011] [Indexed: 02/05/2023]
Abstract
Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.
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Affiliation(s)
- Mark de Bruyn
- Molecular Ecology & Fisheries Genetics Laboratory, Environment Centre for Wales, School of Biological Sciences, Bangor University, Bangor, UK, LL57 2UW.
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Canisso IF, Carvalho GR, Morel MD, Ker PG, Rodrigues AL, Silva EC, Coutinho Da Silva MA. Seminal parameters and field fertility of cryopreserved donkey jack semen after insemination of horse mares. Equine Vet J 2011; 43:179-83. [PMID: 21592212 DOI: 10.1111/j.2042-3306.2010.00130.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
REASONS FOR PERFORMING STUDY As mule production is often concentrated in remote areas of the world, a simplified semen cryopreservation protocol is required. AIM To compare the seminal parameters of cryopreserved donkey semen in lactose-EDTA and lactose-yolk extenders and the fertility rates on horse mares. METHODS TRIAL 1: Sperm total and progressive motility, vigour (scale 0-5), morphology (major and minor defects) and plasma membrane integrity (HOST) were evaluated in 25 ejaculates from 5 donkey jacks immediately after collection (raw), after chilling to 5°C (chilled) and after freezing/thawing. The semen was mixed with skimmed-milk extender, centrifuged, and then re-suspended in lactose-EDTA or lactose-yolk extender. Semen was loaded into 0.5 ml straws and chilled to 5°C for 1 h, after which samples were either evaluated (chilled semen) or placed above liquid nitrogen for 20 min prior to immersion. Seminal parameters were evaluated by ANOVA and Tukey's test. TRIAL 2: Cryopreserved semen from 3 males was used to inseminate 53 mares at 60 oestrous cycles randomly assigned to lactose-yolk (n = 30 cycles) or lactose-EDTA (n = 30 cycles) extenders. Pregnancy diagnosis was performed 15 and 25 days post ovulation. The pregnancy rates were compared using Chi-squared tests. RESULTS TRIAL 1: No significant differences were evident in any seminal parameters between extenders after either chilling or cryopreservation. Total and progressive motility were significantly (P<0.05) lower in cryopreserved semen than raw and chilled semen for both extenders. TRIAL 2: Pregnancy rates did not significantly differ between extenders (lactose-EDTA extender 53.33 and 43.33%; lactose-yolk 50.0 and 46.66% for Days 15 and 25 post ovulation, respectively). CONCLUSIONS Cryopreservation of donkey semen using the simplified lactose-yolk extender resulted in similar seminal parameters and fertility rates when compared to lactose-EDTA extender. POTENTIAL RELEVANCE Lactose-yolk extender may be advocated as a simple, easy to prepare extender, for use in geographically isolated enterprises producing mules throughout the world.
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Affiliation(s)
- I F Canisso
- Equid Breeding Centre, Animal Science Department, Federal University of Viçosa, Minas Gerais Brazil.
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de Bruyn M, Parenti LR, Carvalho GR. Successful extraction of DNA from archived alcohol-fixed white-eye fish specimens using an ancient DNA protocol. J Fish Biol 2011; 78:2074-2079. [PMID: 21651551 DOI: 10.1111/j.1095-8649.2011.02975.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A protocol used routinely for rapid ancient DNA extraction was applied to fish tissue archived over 80 years ago. The method proved successful, whereas other extraction protocols failed. Researchers working on DNA from older archived fish samples are encouraged to continue to concentrate their efforts on 'white-eye' specimens, which indicate an alcohol-based fixative and are thus likely to yield viable DNA.
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Affiliation(s)
- M de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre for Wales, Biological Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, UK.
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Matzen da Silva J, Creer S, dos Santos A, Costa AC, Cunha MR, Costa FO, Carvalho GR. Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS One 2011; 6:e19449. [PMID: 21589909 PMCID: PMC3093375 DOI: 10.1371/journal.pone.0019449] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 04/06/2011] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world. METHODOLOGY/PRINCIPAL FINDINGS We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content. CONCLUSIONS/SIGNIFICANCE Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.
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Affiliation(s)
- Joana Matzen da Silva
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre for Wales, Bangor University, Bangor, Wales, United Kingdom.
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Domingues CP, Creer S, Taylor MI, Queiroga H, Carvalho GR. Temporal genetic homogeneity among shore crab (Carcinus maenas) larval events supplied to an estuarine system on the Portuguese northwest coast. Heredity (Edinb) 2011; 106:832-40. [PMID: 20959862 PMCID: PMC3186222 DOI: 10.1038/hdy.2010.126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 07/30/2010] [Accepted: 09/02/2010] [Indexed: 11/09/2022] Open
Abstract
Despite the importance of larval biology in the life histories of many marine animals, relatively little information exists on the dynamics and genetic composition of larval cohorts. The supply of megalopae larvae of the shore crab, Carcinus maenas, was measured on a daily basis during 8 months spread along two larval periods (2006 and 2007) at the Ria de Aveiro estuary, on the Portuguese northwest coast. A total of 10 microsatellite DNA loci were employed to explore the genetic structure, variability and relatedness of temporally distinct megalopal events, selected from the major pulses of supply. Larval variation was also compared genetically with that of a previously studied adult crabs sample, at the same loci, collected in 2006 and 2007 along the Iberian Peninsula. Results revealed a lack of genetic differentiation and identical diversity levels among larval events over time. No evidence of reduced genetic diversity between megalopae relative to the diversity assessed from the pooled sample of adults was found. Moreover, there was no evidence of any family relatedness among larvae from temporal events. The results obtained for C. maenas contradict predictions made by the sweepstakes reproduction hypothesis, in which large variance in reproductive success is expected, which is presumably detectable as sharp genetic discontinuities among separate larval events. Data here indicate conversely a high degree of temporal genetic stability among larval supply to a given estuary under variable oceanographic conditions, consistent with the hypothesis that sampled larvae were drawn from a large number of adults that do not differ in reproductive success.
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Affiliation(s)
- C P Domingues
- CESAM & Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
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André C, Larsson LC, Laikre L, Bekkevold D, Brigham J, Carvalho GR, Dahlgren TG, Hutchinson WF, Mariani S, Mudde K, Ruzzante DE, Ryman N. Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci. Heredity (Edinb) 2011; 106:270-80. [PMID: 20551979 PMCID: PMC3183876 DOI: 10.1038/hdy.2010.71] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 04/14/2010] [Accepted: 05/05/2010] [Indexed: 11/09/2022] Open
Abstract
In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.
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Affiliation(s)
- C André
- Department of Marine Ecology-Tjärnö, University of Gothenburg, Strömstad, Sweden.
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Fonseca VG, Carvalho GR, Sung W, Johnson HF, Power DM, Neill SP, Packer M, Blaxter ML, Lambshead PJD, Thomas WK, Creer S. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Commun 2010; 1:98. [PMID: 20981026 PMCID: PMC2963828 DOI: 10.1038/ncomms1095] [Citation(s) in RCA: 258] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 09/22/2010] [Indexed: 11/22/2022] Open
Abstract
Biodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude and organization of marine diversity at a range of spatial and taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Richness estimates from the current benchmarked Operational Clustering of Taxonomic Units from Parallel UltraSequencing analyses are broadly aligned with those derived from morphological assessments. However, the slope of taxon rarefaction curves for many phyla remains incomplete, suggesting that the true alpha diversity is likely to exceed current perceptions. The approaches provide a rapid, objective and cost-effective taxonomic framework for exploring links between ecosystem structure and function of all hitherto intractable, but ecologically important, communities. Recent developments in sequencing technologies have provided the opportunity to investigate the biodiversity of ecosystems. Such a metagenomic approach, combined with taxon clustering, is used here to demonstrate that the species richness of a marine community in Scotland is much greater than anticipated.
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Affiliation(s)
- Vera G Fonseca
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Deiniol Road, Gwynedd LL57 2UW, UK
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Nielsen EE, Hemmer-Hansen J, Poulsen NA, Loeschcke V, Moen T, Johansen T, Mittelholzer C, Taranger GL, Ogden R, Carvalho GR. Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua). BMC Evol Biol 2009; 9:276. [PMID: 19948077 PMCID: PMC2790465 DOI: 10.1186/1471-2148-9-276] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 12/01/2009] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution. RESULTS Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread and complex, i.e. outlier loci were generally not only associated with one of a few divergent local populations. Even on a limited geographical scale between the proximate North Sea and Baltic Sea populations four loci displayed evidence of adaptive evolution. Temporal genome scan analysis applied to DNA from archived otoliths from a Faeroese population demonstrated stability of the intra-population variation over 24 years. An exploratory landscape genetic analysis was used to elucidate potential effects of the most likely environmental factors responsible for the signatures of local adaptation. We found that genetic variation at several of the outlier loci was better correlated with temperature and/or salinity conditions at spawning grounds at spawning time than with geographic distance per se. CONCLUSION These findings illustrate that adaptive population divergence may indeed be prevalent despite seemingly high levels of gene flow, as found in most marine fishes. Thus, results have important implications for our understanding of the interplay of evolutionary forces in general, and for the conservation of marine biodiversity under rapidly increasing evolutionary pressure from climate and fisheries induced changes in local environments.
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Affiliation(s)
- Einar E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
| | - Jakob Hemmer-Hansen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
| | - Nina A Poulsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
- Department of Biological Sciences, Genetics and Ecology, University of Aarhus, Building 1540, Ny Munkegade, DK-8000 Aarhus C, Denmark
| | - Volker Loeschcke
- Department of Biological Sciences, Genetics and Ecology, University of Aarhus, Building 1540, Ny Munkegade, DK-8000 Aarhus C, Denmark
| | | | - Torild Johansen
- Institute of Marine Research Tromsø, PO Box 6404, N-9294 Tromsø, Norway
| | - Christian Mittelholzer
- Institute of Marine Research, PO Box 1870, Nordnes N-5817 Bergen, Norway
- Current address: University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | | | - Rob Ogden
- Tepnel Research Products and Services, Appleton Place, Livingston, EH54 7EZ, UK
| | - Gary R Carvalho
- Molecular Ecology & Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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