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Staff Profile of Prof. Gary Carvalho

Name
Prof. Gary Carvalho
Position
Professor of Molecular Ecology
Email
g.r.carvalho@bangor.ac.uk
Phone
+44(0)1248 382100
Location
School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK

About

Using primarily DNA-based tools, my research is aimed at the elucidation of fundamental aspects of a species’ biology such as patterns of dispersal and gene flow, evolution of life histories and behaviour, response to environmental stress, and mechanisms of speciation, as well as the application of molecular tools to the management and conservation of exploited aquatic species from temperate, tropical and Antarctic marine and freshwater ecosystems.

Research includes the molecular analysis of population and species biodiversity of aquatic animals, with studies aimed at understanding the forces that shape genetic structure in the wild, and how such structure may influence adaptation, population persistence and distribution. Notable areas of activity include: the evolution and ecological significance of population differentiation, phylogeography and phylogenetics of aquatic taxa, the molecular analysis of past populations using PCR-based recovery of DNA (ancient DNA) from resting eggs and preserved material (e.g. fish otoliths and scales), DNA barcoding, traceability of fish and fish products, the evolutionary genetics of clonal animals, the evolution of adaptive traits using molecular, genomic and quantitative genetic analysis, and fisheries and conservation genetics of exploited fish in temperate, tropical and Antarctic waters.

In addition to current research, I contribute to various external bodies, as detailed in my CV, which include current roles as Vice-President of the Fisheries Society of the British Isles, Chair of the Expert ICES (International Council for Exploration of the Sea) Group on the Application of Genetics in Fisheries and Mariculture (WGAGFM), Vice-Chair of European Commission Panels (Marie Curie Actions and ITN), and Member of the Species Survival Commission (IUCN) Specialist Group in Conservation Genetics. I am currently Editor of the Proceedings of the Royal Society B, Fish and Fisheries, and members of the editorial boards of Molecular Ecology and Conservation Genetics.

Recent significant areas of investigation include the use of environmental DNA (eDNA) for exploring the biodiversity of aquatic environments, and application of next generation sequencing for investigating microbiomes, especially in fishes. If you want to find out more, click on the research tab above.

The Bangor-based Molecular Ecology and Fisheries Genetics Laboratory (MEFGL) that I continue to coordinate now represents among the largest European groupings focusing on the molecular ecology and evolution of aquatic taxa. In addition to exploring fundamental issues in molecular ecology and evolution, the MEFGL contributed significantly to the 2014 UK Research Excellence Framework (REF) exercise, through both the inclusion of high impact outputs, and in the provision of an Impact Case Study focusing on wildlife forensics and traceability in marine fisheries. The MEFGL also contributes significantly at an international level, with members on the editorial teams of leading journals in the field, such as Proceedings of the Royal Society Lond. B, Molecular Ecology, Molecular Ecology Resources, Fish and Fisheries, and Conservation Genetics. It hosted an annual meeting of the UK Environmental DNA (eDNA) working group in 2015, preceded by a training workshop in eDNA for Indonesian colleagues. The MEFGL also coordinated a major international symposium on Fish, Genes and Genomes in July 2016 with leading key-note speakers such as Robin Waples, Craig Primmer, Louis Bernatchez, Dorte Bekkevold, Jenny Ovenden and John Casey. A special issue of the Journal of Fish Biology published the key note and selection of oral presentations (http://onlinelibrary.wiley.com/doi/10.1111/jfb.2016.89.issue-6/issuetoc) Carvalho is also contributing to a EuroMarine workshop focusing on the Application of Genomics in Fisheries (https://goo.gl/g1cLun ), to be held in Portugal in May 2017. More broadly, research in the School of Biological Sciences is ranked n the top 20 Universities in the UK (2014 REF). Across the University, three-quarters of Bangor’s research is either world-leading or internationally excellent.

CV

Education and honours

  • Fellowship of the Linnean Society (F.L.S.) (2000)
  • Fellowship of the Society of Biology (F.S.B.) (2011)
  • PhD. (Wales, 1985) – Ecological genetics of Daphnia
  • M.Sc. (Wales, 1980) – Ecology
  • B.Sc. (Class I, London, 1978) – Environmental Biology

Career

  • 2009– Visiting Professor, University of Penang, Malaysia
  • 2005–present Professor of Molecular Ecology, School of Biological Sciences/Environment Centre Wales, Bangor University
  • 2006–2008 Deputy Head of School of Biological Sciences
  • 2007- Chair, Environment Centre Wales, Management Board
  • 1996–2004 Professor of Molecular Ecology, Dept. Biological Sciences, Hull University
  • 1998–2004 Research Director, Department of Biological Sciences, Hull
  • 1995–1996 Senior Lecturer in Marine Biology, University of Wales, Swansea
  • 1990–1995 Lecturer in Marine Biology, Biological Sciences, University of Wales, Swansea
  • 1988–1989 AFRC R.A. (University of Southampton), DNA fingerprinting of aphids
  • 1986–1988 NERC Post-doctoral Fellowship (Univ. Wales, Bangor), population structure of isopods
  • 1986–1987 Max-Planck-Society Research Fellowship (M.P.I. of Limnology, Germany), Clonal Structure of Daphnia

Editorial Work

  • 1995–2000 Asst. Editor (Genetics and Evolution): Journal of Fish Biology
  • 1996–2000 Editorial Board: Reviews in Fish Biology and Fisheries
  • 1998–2003 Editorial Board: Heredity
  • 2000 -present Editorial Board: Molecular Ecology
  • 2000–2007 Associate Editor: Fish and Fisheries
  • 2000 – present Editorial Board: Conservation Genetics
  • 2003–2009 Editorial Board, Proceedings of Royal Society, London, B.
  • 2007- present Editor, Fish and Fisheries
  • 2011- present Editor, Proceedings of Royal Society, London, B.
  • 2012–2013 Editorial Board, Biological Invasions

External Professional Activities

  • 1998-present ICES Working Group on the Application of Genetics in Fisheries and Mariculture
  • 2000–2007 NERC Steering Committee: Environmental Genomics Thematic Prog.
  • 2003- NERC ad hoc Advisory Committee on Post-genomic Science and Proteomics
  • 2003–2007 Management Group of Directors Working Group (CEFAS, DEFRA, DARDNI, FRS) on Cod Population Structure
  • 2004–2008 Scientific Advisory Panel, Environment Agency
  • 2004–2007 NERC Steering Committee, UK Molecular Genetics Facilities
  • 2005–2009 Chair, European Coordinator of FISH-BOL (DNA Barcoding of Marine Fishes) and Steering Committee member
  • 2005–2008 NERC Peer Review College
  • 2005–2006 Vice-President of the Fisheries Society of the British Isles
  • 2005–2006 Member of SEBI2010 Expert Group on Fishes (EEA/ECNC/UNEP). Streamlining European 2010 Biodiversity Indicators.
  • 2006- Expert Evaluator Panel- Norwegian Research Council (Seas and the Oceans)
  • 2007- Member Academy of Finland Biosiences Grant Review Panel- Ecology Panel
  • 2007- Chair of NERC Moderating Panel A (Molecular Ecology & Evolution)
  • 2008-present External Consultant on various programmes for FCT (Portuguese Research Council for Science and Technology)
  • 2008- ERA-Net BiodivERsA Evaluation Committee (EU Commission)
  • 2008–2011 Coordinator of EU FP 7 Consortium, FishPopTrace
  • 2008: Member of Research Quality Review, University College Cork
  • 2009–2011 FAO Expert Group on Fisheries Forensics
  • 2009 Visiting Professor, University of Penang, Malaysia
  • 2009–2010 Expert Group of Marine Biodiversity for IFREMER, French Ministry of the Environment
  • 2010 Organising Committee,SNP III International Conference Seattle, Washington
  • 2010 Organising Committee, ECBOL2:2nd European Conference on DNA Barcoding
  • 2000-present Editorial Board: Molecular Ecology
  • 2000–2007 Associate Editor: Fish and Fisheries
  • 2008-present Editor: Fish and Fisheries
  • 2000-present Editorial Board: Conservation Genetics
  • 2003–2009 Editorial Board, Proceedings of Royal Society, London, B
  • 2011-present Editor, Proceedings of Royal Society, London, B
  • 2011 Guest Editor, Applications of SNP Genotyping in Non-model organisms, Molecular Ecology Resources
  • 2012 Editorial Board, Biological Invasions
  • 2012 – Founder Member – UK Biodiversity Science Committee – to represent the UK in the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystems (IPBES) and other International biodiversity initiatives
  • 2012 – European Expert Group on Fish Stock Assessment (Joint Research Centre- “Assessment for All”- EC)
  • 2012 – DEFRA Stakeholder Advisory Group on Fish Traceability
  • 2012 – Appointment by Centre for Independent Experts, US – scientific advice on petition for two species of river herring (blueback and alewife) to be included under Endangered Species Act
  • 2012–2014 – NERC Peer Review College and Panel Member, Natural Environment Research Council, UK
  • 2013 – FAO Expert Advisor on Establishment of Advisory Group on Aquatic Genetic Resources, Bangkok
  • 2013, 2014 – Chair, Academy of Finland Biosiences Grant Review Panel- Ecology Panel
  • 2013 – Member of the Advisory Board and Task Force for the Natural Environment Research Council (NERC, UK) knowledge exchange program on sustainable fisheries & aquaculture
  • 2013 – Co-Convenor of Congress of the European Society for Evolutionary Biology, special symposium: Genomic Islands: their role in adaptation and speciation (August, Lisbon)
  • 2013 – Member and Chair of Review Panel, Belgian Research Action through Interdisciplinary Networks, Belgian Government, Belgian Science Policy Office, Brussels
  • 2013, 2014 – Member of the European Commission Evaluation Panel for Marie-Curie Actions, Environment. Brussels
  • 2013 – Independent External Advisor, Marine Stewardship Council, DNA testing and certification of sustainable fisheries
  • 2014 – present – NERC Core Panel Member – Panel E and others.
  • 2014–2017 – Chair, ICES Working Group on the Application of Genetics in Fisheries and Mariculture (WGAGFM)
  • 2014 – Founder Member of Species Survival Commission (IUCN) Specialist Group in Conservation Genetics.
  • 2015 - OECD Expert Group Member on the  long-term potential of marine biotechnology
  • 2015-2018 - Vice-President, Fisheries Society of the British Isles (FSBI)
  • 2015-2018- Chair, FSBI Publications Committee
  • 2016 - Co-Convenor Bioeconomics, Sociobiology and Other Mixes.The Advantage of Linking Disparate Data to Gain New Insights into the Exploitation of Marine Fish. Special Theme Session, World Fisheries Congress, South Korea (May, 2016)
  • 2016 – Convener, Fisheries Society of the British Isles (FSBI) Annual International Symposium: Fish, Genes and Genomes: Contributions to Ecology, Evolution and Management. Bangor, UK, July 2016.
  • 2016- 2017 Vice Chair, European Commission Evaluation Panel for Marie-Curie Actions, Environment. Brussels
  • 2017 - Vice-Chair, European Commission Evaluation Panel for Innovative Training Networks, Environment, Brussels

Outreach and Public Communication of Science

a. Communicating genetic principles to environmental managers

For over 2 decades, effort has been focused on communicating the value of molecular tools and genetic diversity as core components of environmental management and conservation of biodiversity, especially among exploited species. Targeted publications such as Special Issues of international fisheries journals (e.g. 1995, 2008) aimed to render genetic concepts and tools more accessible to fisheries managers and conservation biologists. Direct input has been facilitated by engagement in appropriate bodies charged with responsibility for managing natural resources (e.g. ICES Working Group on the Application of Genetics in Fisheries and Mariculture; Management Group of Directors Working Group (CEFAS, DEFRA, DARDNI, FRS) on Cod Population Structure; Member of SEBI2010 Expert Group on Fishes (EEA/ECNC/UNEP). Streamlining European 2010 Biodiversity Indicators; FAO Expert Group on Fisheries Forensics; Expert Group on Marine Biodiversity for IFREMER, French Ministry of the Environment, 2009–2010; Founder Member – UK Biodiversity Science Committee – to represent the UK in the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystems (IPBES) and other International biodiversity initiatives; Expert Food and Agriculture Organization of the United Nations State Of World Consultation on Aquatic Genetic Resources, Bangkok).

In addition to various research projects focusing on fisheries genetics, a notable recent programme, FishPopTrace, provided an opportunity for directly influencing the revision of major policies (Revised EC Common Fisheries Policy). FishPopTrace, an EU FP7 project (2002–11), coordinated by Carvalho, aimed to generate forensic tools (primarily single nucleotide polymorphisms, SNPs), to deliver a breakthrough in the legal enforcement of regulatory policies within the fishing industry. The key quest was to trace fish back to localities or spawning populations: the target and unit of harvesting and spatially resolved policies. For the first time, by applying high differentiation SNP assays, in four commercial marine fish, on a pan-European scale, it was possible to correctly assign unknown individuals back to their source spawning populations with unprecedented accuracy (93–100%). Outputs demonstrated how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide. Recognising the impact of FishPopTrace (e.g. in Annex 1of the Commission Regulation for establishing a control system to secure compliance with the rules of the Common Fisheries Policy (COM (2008)721 final), it was stated “It is interesting to note the innovative contribution of FishPopTrace …for implementation of modern technologies”. Such distinction, combined with the new regulations imposed by the EC (EC Regulation 1224/2009 (Art 13), requiring EU States to undertake pilot studies of novel traceability tools by 2013, the Department of Environment Food and Rural Affairs (DEFRA, UK Govt.), is tailoring FishPopTrace tools for use by the UK fishing industry. FishPopTrace, and direct partnership with the Joint Research Centre (the science wing of the European Commission), also provided opportunities for direct input to consultation exercises on the Revised Common Fisheries Policy, in particular the successful adoption of advanced technologies for use in traceability and legal enforcement of regulations covering importation and capture of fish and fish products. The FishPopTrace SNP tools are also now being extended to new marine fish species around Europe (sea bream, bass, turbot), to generate a DNA reference data base for tests of traceability of escapee fish back to fish farms, as well as monitoring impact on fitness of wild fish species.

In July 2013, Carvalho was appointed by the Marine Stewardship Council as an Independent External Advisor on DNA testing of fish and fish products in the context of certification of sustainable stocks. Recent public and Government concern over traceability of food products, in conjunction with sustainability targets, demands a concerted, transparent and robust application of forensic standard authentic tests.

b. Broader outreach activities

Societal interest in biodiversity and management of natural resources has secured regular opportunities for communicating scientific outputs to the general public directly and through the media. Most notably, since 2010, contributions have been made to the week-long Bangor Science Festival, through evening public lectures on topics such as sustainability and fisheries forensics, as well as engagement with school children to introduce them to the excitement and wonder of the natural world through illustrating the uses of DNA tools to environmental management. The recent award of a Royal Society Partnership Grant, for partnership with a comprehensive school on Anglesey (the first such award in North Wales), has provided an interactive opportunity to discuss our research on “climate change, Antarctica and ice fish” – all topics that generate curiosity and interest, especially how scientific evidence can be gathered to support notions of climate change. In 2013, we coordinated a day-long event (with over 500 public visitors), as part of an event “The Hidden World”, where we provided hands-on and interactive displays illustrating life in the Antarctic, the life history of ice fish, and how climate change will likely impact these fragile marine ecosystems. Pupils aged 13–15 from our local partnered School presented talks to the general public on their own work to date as part of the Partnership Grant.

There has also been much media interest in our work– including interviews on BBC Radio on advances in using genetic fingerprinting to monitor the invasion of pest aphids (BBC Radio Wales; various national newspapers); the use of allozymes to manage and conserve the Falkland Island Fishery (BBC North East, local news); and more recently the generation of DNA-based tools for use in tackling illegal fishing and eco-certification of fish and fish products: (BBC World Service; Science In Action: http://www.bbc.co.uk/programmes/p00s1t04); Radio 4, BBC Farming Today; episode of the BBC Science Programme, in May 2013, Bang Goes the Theory, on the use of DNA forensics in traceability of fish products; NERC podcast on illegal fishing; http://planetearth.nerc.ac.uk/multimedia/story.aspx?id=452), as well an numerous regional and national newspapers.

Research

I arrived in the School of Biological Sciences, University of Wales Bangor, in January 2005, having moved from the Molecular and Evolutionary Ecology Group at Hull University. My initial remit was to expand in particular, studies on the molecular ecology of aquatic animals, including the use of molecular markers in fish and fisheries genetics. Although most research projects incorporate DNA-based tools, my research is aimed at the elucidation of fundamental aspects of a species’ biology such as patterns of dispersal and gene flow, evolution of life histories and behaviour, response to environmental stress, and mechanisms of speciation, as well as the application of molecular tools to the management and conservation of exploited aquatic species from temperate, tropical and Antarctic marine and freshwater ecosystems. In addition to my existing areas of interest, my new position at Bangor provides additional opportunities to develop studies on functional aspects of adaptive variation through genomic analysis, links between dispersal, gene flow and physical oceanography in the sea, and the use of high throughout sequencing in DNA barcoding.

The Bangor-based Molecular Ecology and Fisheries Genetics Laboratory (MEFGL) that I continue to coordinate now represents among the largest European groupings focusing on the molecular ecology and evolution of aquatic taxa, which in 2013 will be extended further with the appointment of two new lecturers. Martin Taylor, who was a founder member of the MEFGL since 2005, on 1 January 2013 took up a new post as Senior Lecturer in Molecular Ecology at the University of East Anglia (martin.taylor@uea.ac.uk). The two new lecturers are: Dr Mark de Bruyn, who has been based in MEFGL since his Marie-Curie Fellowship in 2009, and Dr Michael Knapp, former Research Fellow in the Allan Wilson Centre for Molecular Ecology and Evolution Department of Anatomy University of Otago. The new appointments signal a significant expansion in the strength and scope of research and training activities of the MEFGL, especially in the area of ancient DNA to explore the impacts of long-term environmental change on biodiversity, and to reveal novel insights into the demographic history of extinct species, especially birds and mammals.

The purpose-built suite of molecular ecology laboratories in the Environment Centre Wales (ECW) provides a fully integrated and dedicated platform for the molecular analysis of biodiversity in wild populations. In addition to on-going work on fundamental evolutionary processes more opportunities are available for engagement with environmental agencies through links with the Centre for Ecology and Hydrology (NERC), Environment Agency (UK), Forestry Commission and Countryside Council for Wales, all of which have representation within ECW. Additionally, we have string and productive links with the NERC Molecular Genetic Facility in Liverpool, providing access to training and facilities for analysis of gene expression with microarrays, ultra-sequencing (and digital transcriptomics) and bioinformatics. Such additional facilities dove-tail with recent key developments within the MEFGL.

Below I summarise some current key areas of interest:

Molecular analysis of population structure

Molecular markers can be used to examine the relative roles of various microevolutionary forces on the levels and significance of genetic differentiation among populations. For example, one current project, in conjunction with the British Antarctic Survey and University of Hull, aims to disentangle the relative roles of life history variation and hydrographic processes on dispersal and gene flow in Antarctic fishes. It is becoming increasingly apparent that despite high dispersal capacity, some marine species continue to exhibit significant population structuring, occasionally on fine geographic scales. We are also examining, in collaboration with the University of Aveiro, links between hydrographic variability and larval dispersal and recruitment in the shore crab Carcinus maenas (see Carla Domingues, MEFGL projects). In addition to exploring the role of hydrography in dispersal, we aim to assess methods for population assignment, and in conjunction with fine-scale genotypic monitoring, the role of selective mortality in the early stages of population recruitment.

Use of ancient DNA to study long-term environmental change

The availability of PCR enables recovery of DNA from natural (e.g. resting eggs of zooplankton: e.g. rotifers) and archived (e.g. fish scales and otoliths: e.g. cod) material to examine long-term changes in genetic structure. Using such approaches it is possible to examine the impact of natural and man-made environmental change on population and community structure. In collaboration with CEFAS (see Niklas Tysklind, MEFGL projects) we are currently developing robust and sensitive methods for recovering DNA from archived histological samples of the flatfish, dab, Limanda limanda, as a basis for comparing genetic structuring in contemporary and past populations.

Evolution of adaptive variation

A core approach in molecular ecology has been to utilise neutral molecular markers to generate inferences about adaptive variation. Other approaches include either direct analysis of gene function or the use of quantitative genetic approaches to identify quantitative trait loci or to estimate heritabilities in biological traits. In conjunction with colleagues at the University of Hull we have for example: (1) examined geographic variation and performance under semi-controlled conditions of a key gene (Pantophysin I) associated with growth rate variation, (2) examined adaptive variation in freshwater bullhead using a combination of neutral and quantitative traits to assess heritabilities in relation to habitat variation.

Recently we have enhanced our approaches to exploring adaptive variation in the wild by encompassing transcriptomics to explore the impact of environmental stress on gene expression and associated adaptive phenotypes. Systems include Nucella lapillus and differential gene expression in response to environmental changes (natural and man-made), including the impact of contaminants on sex reversal (“imposex”) (See Sonia Pascoal, MEFGL projects), and impact of environmental stress on gene expression in marine nematodes (see Simon Creer and Vera Fonseca, MEFGL projects). We are the first to generate a transcriptome of a marine gastropod, and in early 2013, one of the major outcomes of the work will be published in Molecular Ecology, alongside a Perspective to explore its wider contribution to the field of genomics in non-model species. The paper: “Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus”, provides novel insights into the control of imposex, and importantly, yields evidence for a common signalling pathway between invertebrate and vertebrate species that has previously been overlooked in the study of endocrine disruption. With funding from the NERC, and in conjunction with the Liverpool Microarray Facility, we are utilizing microarrays to explore genetic changes associated with phenotypic shifts associated with anadromy in brown trout, Salmo trutta (see Martin Taylor, MEFGL).

Fisheries Genetics and Conservation

We utilise molecular genetic markers to examine the stock structure of commercial fishes, as well as examining demographic processes that may affect response to harvesting and environmental change. In particular we have utilised archived scales and otiliths to explore changes in genetic diversity and structure in relation to over-exploitation, and have demonstrated not only rapid short-term genetic change in North Sea cod during periods of population decline, but also a loss of genetic diversity following population collapse in New Zealand snapper. In conjunction with the Environment Agency, UK, our work now extends to examining population structure and biodiversity of salmonid fishes.

Recent funding from the NERC (2008) has been obtained to examine the population structure of cod in UK coastal waters as part of the NERC-DEFRA-FRS-AFBI initiative, Sustainable Marine Bioresources. Many global marine fisheries have collapsed, or are at record low levels of abundance. Continuing exploitation and the uncertain impacts of climate change are adding further pressures on fish resources. New strategies are therefore required to assist in our management and conservation efforts. One such development will be to incorporate the extent and dynamics of spatially-associated biological differences that exist among fish stocks into stock assessment. Such information is important since most exploited fish species comprise assemblages of individuals that differ in their vital rates of growth, reproduction, migratory tendency and mortality. It therefore becomes desirable, for example, to match the level of fishing intensity to the projected rate of replenishment following harvesting, thereby reducing the probability that individual stocks will become extinct. Conserving such biological differences among stocks is also important in the maintenance of genetic diversity in wild fish populations, so endowing them with greater evolutionary potential for adapting to changes in the environment. A critical component of such work involves the testing of hypotheses relating to the relative contributions of such factors as dispersal of eggs and larvae, and behaviour of juveniles and adults in maintaining such biological differences. By integrating research efforts across each of the three major UK fisheries agencies (FRS, CEFAS, AFBI) with partners in UK Universities, a NERC Institute and an international cod expert from Denmark, we will for the first time examine the extent, patterns and stability of cod (Gadus morhua) population structuring throughout UK waters.

We will employ existing (microsatellites) and new (single nucleotide polymorphisms) genetic markers to assess the extent to which individuals from different spawning groups interbreed, and will compare these indirect methods of dispersal with direct measures of fish movement taken from chemical analysis of ear-bones (”otoliths”) and individuals that have been electronically “tagged”. We will then input these data to tailored cod population models that will test the likely effects of young-stage and adult dispersal on observed patterns of stock separation, as well as simulating the likely consequences of spatially-based differences in stocks on such things as fishing effort, stock recovery and the design of marine protected areas. The proposal represents the first opportunity for UK Universities and all three UK Fisheries agencies to work together on a problem that has to take account of the interdependence of fish stocks across large regions of UK and adjoining waters. The proposal will generate new genetic estimates of stock separation, especially in areas of uncertainty such as the Celtic and Irish Seas and the Southern North Sea and English Channel, as well as the provision of new theoretical tools (population models) than can be used to forecast the impact of continued fishing pressure and environmental change on cod populations. Moreover, the tools will provide information on the appropriate spatial scale and distribution of marine protected areas and the probable rates of stock recovery in a species that is now formally endangered and listed in the IUCN Red List.

Carvalho (PI), Creer (Bangor co-I) and Taylor (recently moved to University of East Anglia (UEA)-co-I) were recently (2012) awarded a new EU FP7 project, AquaTrace, in partnership with a large consortium of European workers who aim to develop novel tools to explore the impact of aquaculture on native marine fish populations. The Bangor-UEA component of the work will focus on the phenotypic and genetic basis of fitness shifts associated with introgression between wild and captive-bred Atlantic salmon. The latter work will be carried out in conjunction with colleagues at the Bergen Marine Labaoratory, and will utilise state-of-the-art common garden facilities to explore fitness consequences and to map quantitative trait loci. Bangor will receive a PhD studentship that will be advertised early in 2013.

A PhD project completed in 2011 (see Serinde Van Wijk, MEFGL projects) examined the genetic basis of fisheries-induced evolution, using the Trinidadian guppy, Poecilia reticulata, as a model system. Size-selective harvesting can induce rapid phenotypic changes, such as age and size of maturation, in exploited fish populations. Despite the increasing incidence of such shifts, the relative contributions of genetic and environmental factors remain uncertain and are much-debated. Outputs from the study will appear early in 2013 in the journal, Frontiers in Ecology and the Environment, and demonstrate a significant genetic component to fisheries-induced evolution in an experimental system, with major implications for the sustainability of exploited populations, as well as impacts on size-structured communities and ecosystem processes, prompting a reconsideration of adaptation to, and recovery from, harvesting and predation. The work is now being extended by a PhD studentship awarded to Hazel Perry who will examine in more detail the genomic shifts associated with fisheries induced evolution in the model guppy system.

Traceability of fish and fisheries forensics

MEFGL was awarded (2008–2011) a major EU grant (FishPopTrace) to examine the traceability of fish and fish products in European waters, with focus on herring, cod, hake and sole. The 15 partner consortium is coordinated by Gary Carvalho and the MEFGL, and aims to develop a forensic framework for legal enforcement of policies aimed at reducing the amount of Illegal, Unreported and unregulated fishing (IUU). There is an increasing requirement for traceability of fish and fish products, both for consumer protection and for regulatory enforcement. For example, in the UK, the Marine Stewardship Council encourages consumers to eat particular landings of cod that are taken from ‘stocks maintained within safe limits’. A traceability system based on regional stocks is necessary to preclude fraudulent allocations. The underlying rationale of FishPopTrace is to assess and address challenges arising from the development of traceability tools within a forensic framework for four judiciously chosen target species: cod (Gadus morhua), hake (Merluccius merluccius), herring (Clupea harengus) and sole (Solea solea). While current information on levels of population structuring in traits such as life histories, morphometrics, genetics and physiology will be used to inform sample choice, new data will be restricted to markers at two levels: (1) Routine screening: selection of markers that exhibit maximal discriminatory power to identify populations, though with discrete and controlled variance enabling validation (single nucleotide polymorphisms (SNPs) and otolith microchemistry and morphometrics). Data from DNA-based methods provide a mechanism for traceability throughout the food supply chain (“fish to fork”) and indicate discrete spawning populations, whereas otoliths provide an independent on-board traceability system of fish provenance. (2) Testing of novel tools: additional tools will be tested on a selection of populations to assess validity and potential for traceability and validation, including fatty acid analysis, proteomics, gene expression analysis and the generation of high-throughput microarray platforms for SNP genotyping. Thus, FishPopTrace will provide information that relates to geography (“population tag”), as well as providing regional signatures that indicate biological differentiation in relation to spawning identity. Specifically, the consortium brings together recent and current expertise in fish traceability projects (Fish and Chips (GOCE-CT-2003–505491), FishTrace (QLRI-CT-2002–02755, FISH-BOL, Consortium for the Barcode of Life) to address several inter-related objectives:

1.1.2.1 To integrate recent and on-going data from European fish species traceability projects, and to generate a single compatible data base and tissue archive managed by the Joint Research Centre of the European Commission. The outputs will comprise a new data base and associated web links with access to recently generated data on fish species and population identity, together with an archive of associated tissue samples from external and consortium outputs.
1.1.2.2 To examine single nucleotide polymorphisms (SNPs) and otolith microchemistry and morphometrics in widely distributed populations of cod, hake, sole and herring, as tools for discriminating biologically differentiated populations and as a basis for traceability. Outputs will comprise population-level signatures associated with fish origins in early life and representative spawning groups.
1.1.2.3 To undertake validation of traceability tools in relation to end-user technology. Outputs will produce Standard Operating Procedures (SOPs) to allow transfer of technologies to other laboratories throughout EU member states.
1.1.2.4 To develop a population monitoring system based on otolith and genetic data that will assess population stability in a temporal and spatial framework. For each species, alternative parameters will be identified as indicators of population stability, and parameters will be validated using a combination of archived data and tissue samples.
1.1.2.5 To test the utility of additional novel traceability systems (fatty acid profiles, proteomics, gene expression, microarray platform for SNP genotyping). Outputs will comprise an assessment of the utility of additional novel approaches to traceability and population monitoring through estimating the within and among-population components of biological differentiation and population signatures. Additionally, a chip-based platform will be generated to undertake high-throughput SNP genotyping.
1.1.2.6 To facilitate technology transfer in relation to enforcement and conservation policies of the CFP and associated socio-economic consequences. Central elements of the output will be the development and evaluation of end-user tools, a Cost Benefit Analysis and a final report setting FishPopTrace in the context of the CFP.

A major output from the project was published in 2102 in Nature Communications. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93–100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.

Molecular Identification, DNA Barcoding and Phylochips

The use of short, standardised short DNA sequences – a “DNA barcode” has become a valuable addition to the taxonomic toolbox to validate species identity, as well as to identify unknown species, cryptic life history stages, etc. The Consortium for the Barcode of Life (CBOL) launched a new initiative in 2005 to DNA barcode all fishes- “FISH-BOL”, which will generate a global database for biologists and interested naturalists. In the MEFGL, I had the pleasure of acting as founder Chair of the European Regional working group for FishBol between 2005–2011. A past Marie-Curie Fellow, Dr Filipe Costa, is now the European Regional Chair, and continues to coordinate sample collection and data acquisition. Our DNA barcoding of marine fish was recently expanded to include novel data on a hot-spot of biodiversity – the Indo-Malay Archipelago. Some of the findings from a recent PhD programme with a local Malaysian student based in the MEFGL, Tun Nurul Aimi Mat Jaafar, was published in 2012 in PLoS ONE, and represents the first comprehensive analysis of cryptic species in a large ocmmercially important group, the Carangidae. Other DNA barcoding outputs have included the Crustacea, esp. Decapoda, from the completed 2012 PhD thesis of a MEFGL-Portuguese FCT student, Joana Matzen, generating several papers detailed in the Carvalho publication list.

Phylochips are also being developed with funding from the NERC and in conjunction with the Liverpool Microarray Facility, to examine biodiversity of marine nematode communities (see Simon Creer, MEFGL projects).

Selection of current research projects underway include:

  1. DNA barcoding of marine fishes (various sources);
  2. Population structure and traceability of marine fishes- development of novel tools (single nucleotide polymorphisms) to explore population diversity and traceability of fish and fish products in the food supply chain to tackle illegal fishing and promote consumer protection (various sources);
  3. Fisheries-induced evolution (Bangor University) – to assess the genetic and genomic basis of phenotypic shifts in size and age at maturation in exploited fish populations;
  4. The effects of Southern Ocean Warming on the development and population connectivity of Antarctic Ice fish (NERC);
  5. Use of metabarcoding and environmental DNA (eDNA) for biomonitoring of UK freshwaters (Knowledge Economy Skills Scholarships with Environment Agency, UK);
  6. The evolution of polyploidy and significance of gene duplication in tropical catfish (NERC);
  7. Development of tools for assessing the genetic impact of farmed fish on native fish populations (European Commission);
  8. Assessing the fitness consequences of introgression between captive and wild Atlantic salmon (European Commission);
  9. Conservation genetics and adaptive diversity of endangered manta rays (NERC)
  10. Meta-analysis of SNP diversity in globally distributed Atlantic cod (Gadus morhua) populations (Bangor University);
  11. Long-term changes in the biodiversity of moth comunities (Bangor University);
  12. Use of eDNA for monitoring biodiversity of freshwater communities in Malaysia (NERC).
  13. Reconstructing past demographic histories in relation to environmental change using ancient DNA (aDNA).

Publications

2017

  • Bista, I., Carvalho, G.R., Walsh, K., Seymour, M., Hajibabaei, M., Lallias, D., Christmas, M. and Creer, S. (2017). Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nature Communications. 8: 14087. DOI: http://dx.doi.org/10.1038/ncomms14087
  • Llewellyn, M, S, Leadbeater, S, Garcia, C, SylvainF.-E, Custodio, M, Ang, K.P, Powell, F,  Carvalho, GR, Creer, S, Elliot, S., & Derome, N (2017) Parasitism perturbs the mucosal microbiome of Atlantic Salmon. Scientific Reports, 7:43465, DOI: 10.1038/srep43465.

2016

  • Harvey, A.C., Solberg, M.F., Troianou, E., Carvalho, G.R., Taylor, M.I. Creer, S., Dyrhovden, L., Matre, I.H. and Glover, K.A. 2016. Plasticity in growth of farmed and wild Atlantic salmon: is the increased growth rate of farmed salmon caused by evolutionary adaptations to the commercial diet? BMC Evolutionary Biology. 16:264 DOI: 10.1186/s12862-016-0841-7
  • Harvey, A.C., Solberg, M. F., Glover, K. A., Taylor, M. I., Creer, S., and Carvalho, G.R. Plasticity in response to feed availability - does feeding regime influence the relative growth performance of domesticated, wild and hybrid Atlantic salmon Salmo salar parr? Journal of Fish Biology. DOI: 10.1111/jfb.13076
  • Harvey, A.C., Juleff, G., Carvalho, G.R., Taylor, M.I., Solberg, M.F., Creer, S.,"Dyrhovden, L., Matre, I.-H., Glover, K.A. 2016. Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions? Royal Society Open Science. DOI: 10.1098/rsos.160152
  • Harvey, A. C., Glover, K. A., Taylor, M. I., Creer, S. and Carvalho, G. R. (2016) A common garden design reveals population-specific variability in potential impacts of hybridization between populations of farmed and wild Atlantic salmon, Salmo salar L. Evolutionary Applications. doi: 10.1111/eva.12346
  • Bylemans, J, Maes, G, Diopere, E, Cariani, A, Senn, H, Taylor, MI, Helyar, S, Bargelloni, L, Bonaldo, A, Carvalho, GR, Guarniero, I, Hans Komen, Martinsohn, J, Nielsen, E, Tinti, F, Volckaert1, F, & Ogden. R (2016) Evaluating genetic traceability methods for captive bred marine fish and their applications in fisheries management and wildlife forensics. Aquaculture Environment Interactions. 8: 131–145, doi: 10.3354/aei00164.
  • Carvalho, GR, Hauser, L and Naish, K (2016) Fish, Genes and Genomes: Contributions to Ecology, Evolution and Management. Special Issue of Journal of Fish Biology, 89, 2471-2767 (http://onlinelibrary.wiley.com/doi/10.1111/jfb.2016.89.issue-6/issuetoc).
  • Carvalho, GR, Hauser, L and Naish, K (2016) Editorial. Fish, Genes and Genomes: Contributions to Ecology, Evolution and Management. Special Issue of Journal of Fish Biology, 89, 2471-2478.
  • Montes, I, Iriondo, M, Manzano, I, Santos, M, Conklin, D,. Carvalho, GR, Irigoien, X, Estonba, A (2016) No loss of genetic diversity in the exploited and recently collapsed population of Bay of Biscay anchovy (Engraulis encrasicolus, L.). Marine Biology, 163, 98. doi:10.1007/s00227-016-2866-2.
  • Sinniger, F, Pawlowski, J, Harii1, S, G­ooday, AJ, Yamamoto, H, Chevaldonné, P, Cedhagen, T, Carvalho, GR, & Creer, S (2016) Worldwide analysis of sedimentary DNA reveals major gaps in taxonomic knowledge of deep-sea benthos. Frontiers in Marine Science, http://dx.doi.org/10.3389/fmars.2016.00092
  • Llewellyn, M, McGinnity, P, Dionne, M, Letourneau, J, Thonier, F, Carvalho, GR, Creer, S and Derôme, N (2016) The biogeography of the Atlantic Salmon Gut microbiome. The ISME Journal (Nature), 10(5):1280-4. doi: 10.1038/ismej.2015.189.

2015

  • Llewellyn, M.S., McGinnity, P., Dionne, M., Letourneau, J., Thonier, F., Carvalho, G.R., Creer, S. and Derome, N. 2015. The biogeography of the atlantic salmon (Salmo salar) gut microbiome. The ISME Journal. doi:10.1038/ismej.2015.189 http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2015189a.html
  • Piraino, S, Carvalho, GR & Darling, JA (2015) Molecular tools for monitoring marine invasive species. Special issue of Biological Invasions, 17, Issue 3, 809-971.
  • Bekkevold, D, Helyar, S, Limborg, M, Nielsen, E, Hemmer-Hansen1, J, Clausen, L, FishPopTrace Consortium and Carvalho, GR, (2015) Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring. ICES Journal of Marine Science, doi:10.1093/icesjms/fsu247.
  • Young, EF, Belchier, B, Hauser, L, Horsburgh, G.J., Meredith, M.P., Murphy, E.J, Pascoal, S, Rock, J, Tysklind, N, and Carvalho, GR (2015) Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species. Evolutionary Applications, In Press (DOI: 10.1111/eva.12259).
  • Hamilton, PB, Cowx , IG, Oleksiak, MF, Griffiths, AM, Grahn, M, Stevens, JR, Carvalho, GR, Nicol, E and Tyler, CR (2015) Understanding Population Level Consequences for Wild Fish Exposed to Sub-lethal Concentrations of Chemicals. Fish and Fisheries, In Press.

2014

  • Knebelsberger, T., Landl, M., Neumann, H., Kloppmann, M., Sell, A, Campbell, P., Laakmann, S., Raupach, M., Carvalho, GR & Costa, RO (2014) A reliable DNA barcode reference library for theidentification of the North European shelf fish fauna. Molecular Ecology Resources, doi: 10.1111/1755–0998.12238.
  • Bohmann K*, Evans A*, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Yu DW, de Bruyn M (2014) Environmental DNA for wildlife biology and biomonitoring. Trends in Ecology and Evolution. 29: 358–367. (* joint first authors) http://www.sciencedirect.com/science/article/pii/S016953471400086X
  • de Bruyn M*, Stelbrink B*, Morley RJ, Hall R, Carvalho GR, Cannon CH, van den Bergh G, Meijaard E, Metcalfe I, Boitani L, Maiorano L, Shoup R, von Rintelen T (2014) Borneo and Indochina are major evolutionary hotspots for Southeast Asian biodiversity. Systematic Biology, 63(6), 879–901 (* joint first authors) http://sysbio.oxfordjournals.org/content/63/6/879.full
  • Fonseca, V.G., Carvalho, G.R., Nichols, B., Quince, C., Johnson, H., Neill, S., Lambshead, P.J.D., Thomas, W.K., Power, D. and Creer, S. (2014). Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Global Ecology and Biogeography, 23, 1293–1302.
  • Helyar SJ, Lloyd HD, de Bruyn M, Leake J, Bennett N, Carvalho GR (2014) Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing. PLoS One, 9(6), e98691.
  • Milano, I., Babbucci, M, Cariani, A., Miroslova, A., Bekkevold, D., Carvalho, GR, Espi-Neira, M., Florentino, F, Garofalo, G, Geffen, A, Hansen, J, Helyar, S, Nielsen, E, Ogden, R, Patarnello, T, Stagioin, M, FISHPOPTRACE CONSORTIUM, Tinti, F & Bargelloni, L. (2014) Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius). Molecular Ecology, 23, 118–135
  • Landi M, Dimech M, Arculeo M, Biondo G, Martins R, Miguel Carneiro, Carvalho, GR, Lo Brutto, S, Costa, FO (2014) DNA Barcoding for Species Assignment: The Case of Mediterranean Marine Fishes. PLoS ONE 9(9): e106135. doi:10.1371/journal.pone.0106135.

2013

  • van Wijk, SJ, Taylor, MI, Creer, S, Dreyer, C, Rodrigues, FM, Ramnarine, IW, van Oosterhout, C and Carvalho, GR (2013) Experimental harvesting of fish populations drives genetically-based shifts in body size and maturation. Frontiers in Ecology and the Environment 11: 181–187; doi:10.1890/120229; available from: http://wwwesajournals.org/toc/fron/0/0
  • de Bruyn; M, Ruber; L, Nylinder; S, Stelbrink; S, Lovejoy, NR; Lavoue, S;Tan, HH; Nugroho, E; Wowor, D;Ng, PKL; Azizah, MNS; von Rintelen, T; Hall, R; & Carvalho, GR (2013) Paleo-drainage Basin Connectivity Predicts Evolutionary Relationships across Three Southeast Asian Biodiversity Hotspots. Systematic Biology: 62 (3):398–410.
  • Pascoal, S, Carvalho, GR, Vasieva, O, Hughes, R, Cossins, A, Fang, Y, Ashelford, K, Olohan, L, Barroso, C, Mendo, S, Creer, S (2013) Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus. Molecular Ecology, 22, 1589–1608. (News and Views- Perspective in Molecular Ecology: Chapman RW & Guillette, LJ –Contaminants and impoSEX: transcriptomics of contaminated-induced sex change. Molecular Ecology, 22, 1485–1487).
  • Hemmer-Hansen, J, Eg Nielsen, E, Therkildsen, NO, Taylor, MI, Ogden, R, Geffen, R, Bekkevold, D, Helyar, S, Pampoulie, S, Johansen, T, FishPopTrace Consortium, & Gary R. Carvalho (2013) A genomic island linked to ecotype divergence in Atlantic cod. Molecular Ecology, 22, 2653–2667.
  • Tysklind, N, Taylor, MI, Lyons, BT, Goodsir, F, McCarthy, ID & Carvalho, GR (2013) Population genetics provides new insights into biomarker prevalence in dab (Limanda limanda L.): a key marine biomonitoring species. Evolutionary Applications, DOI: 10.1111/eva.12074.
  • Heath, M. R., Culling, M. A., Crozier,W.W., Fox, C. J., Gurney,W. S. C., Hutchinson,W. F., Nielsen, E. E., O’Sullivan, M., Preedy, K. F., Righton, D. A., Speirs, D. C., Taylor, M. I., Wright, P. J., and Carvalho, G. R. Combination of genetics and spatial modelling highlights the sensitivity of cod (Gadus morhua) population diversity in the North Sea to distributions of fishing. – ICES Journal of Marine Science, doi:10.1093/icesjms/fst185.
  • Montes I, Conklin D, Albaina A, Creer S, Carvalho GR, et al. (2013) SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing. PLoS ONE 8(8): e70051. doi:10.1371/journal.pone.0070051.

2012

  • Pascoal S, Carvalho G, Creer S, Mendo S, Hughes R (2012) Plastic and Heritable Variation in Shell Thickness of the Intertidal Gastropod Nucella lapillus Associated with Risks of Crab Predation and Wave Action, and Sexual Maturation. PLoS ONE 7(12): e52134. doi:10.1371/journal.pone.0052134
  • Costa, FO, Landi, M, Martins, R, . Costa, MH, Costa, ME, Carneiro, M, Alves, MJ, Steinke, D, Carvalho, GR (2012) A Ranking System for Reference Libraries of DNA Barcodes: Application to Marine Fish Species from Portugal. PLoS ONE 7(4): e35858. doi:10.1371/journal.pone.0035858
  • Limborg, M, Helyar, SJ, De Bruyn, M, mTaylor, M, Nielsen, E, Ogden, R, Carvalho, GR, FPT Consortium & Bekkevold, D (2012) Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus). Molecular Ecology, 21, 3686–3703
  • Mat Jaafar, TM, Taylor, MI, , Nor, SAM, , Bruyn, M & Carvalho, GR (2012) DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes).PLoS ONE 7(11): e49623. doi:10.1371/journal.pone.0049623
  • Pascoal, S, Carvalho, GR, Vasieva, O, Hughes, R, Cossins, A, Fang, Y, Ashelford, K, Olohan, L, Barroso, C, Mendo, S, Creer, S (2012) Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus. Molecular Ecology, In Press
  • Helyar, S, Limborg, NT, Bekkevold, D, Babbucci, M, van Houdt, J, Maes, G, Bargelloni, L, Nielsen, RO, Taylor, MI, Cariani, A, Carvalho, GR, FishPopTrace Consortium, Panitz, F.(2012) SNP discovery using next generation transcriptomic sequencing in Atlantic herring (Clupea harengus). PLoS ONE 7 (8) e42089. doi:101371/journal.pone.0042089.
  • Nielsen, EE, Cariani, A, Mac Aoidh, E, Maes, GE, Milano, I, Ogden, R, Taylor, MI, 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, J, Volckaert, FAM, Waples, RS, FishPopTrace consortium & GR Carvalho (2012). Gene-associated markers provide tools for tackling illegal fishing and false eco-certification. Nature Communications 3, Article number: 851 doi:10.1038/ncomms1845
  • Fonseca, VG, Nichols, B, Lallias, D, Quince, C, Carvalho, GR, Power, DM & Creer, S (2012) Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Research, 2012, 1–9 doi:10.1093/nar/gks002
  • Pascoal S, Carvalho G, Creer S, Rock J, Kawaii K, et al. (2012) Plastic and Heritable Components of Phenotypic Variation in Nucella lapillus: An Assessment Using Reciprocal Transplant and Common Garden Experiments. PLoS ONE 7(1): e30289. doi:10.1371/journal.pone.0030289
  • Moore, ABM, McCarthy, ID, Carvalho, GR & Pierce, R (2012) Species, sex and male maturity composition of previously unreported elasmobranch landings in Kuwait, Qatar and Abu Dhabi Emirate. J Fish Biol. doi:10.1111/j.1095–8649.2011.03210.x
  • de Bruyn M, von Rintelen K, von Rintelen T, Mather PB, Carvalho GR. (2012) Molecular biogeography and phylogeography of the freshwater fauna of the Indo-Australian Archipelago. In: Biotic Evolution and Environmental Change in South East Asia, Systematics Association Volume- Cambridge University Press, UK. Published August 2012 (Chapter 13), 316–347.
  • Young, EF, Rock, J, Meredith, MP, Belchier, M, Murphy, EJ & Carvalho, GR (2012) Physical and behavioural influences on larval fish retention: constrasting patterns in two Antarctic fishes. Marine Ecology Progress Series, 465: 201–215.

2011

  • Matzen da Silva J, Creer S, dos Santos A, Costa AC, Cunha MR, et al. (2011) Systematic and Evolutionary Insights Derived from mtDNA COI Barcode Diversity in the Decapoda (Crustacea: Malacostraca). PLoS ONE 6(5): e19449. doi:10.1371/journal.pone.0019449
  • Young, E, Meredith, M, Murphy, EJ & Carvalho, GR (2011) High-resolution modelling of the shelf and open ocean adjacent to South Georgia, Southern Ocean. Deep Sea Research, 58, 1540–1552
  • Lohman, DJ, de Bruyn, M, Page, T, von Rintelen, K, Hall, R, Ng, PKL, Shih, H-T, Carvalho, GR & von Rintelen, T (2011) Beyond Wallace’s Line: genes and geology inform biogeographic insights in the Indo-Australian archipelago. Annual Reviews in Ecology, Evolution and Systematics, 42, 205–226
  • de Bruyn M, Parenti LR & Carvalho GR. (2011)Successful extraction of DNA from archived ‘white-eye’ alcohol-fixed fish specimens using an ancient DNA protocol. Journal of Fish Biology, 78, 2074–2079.
  • Seeb, JE, Carvalho, GR, Hauser, L, Naish, K, Roberts, S & Seeb, LW (Eds) (2011) Single-nucleotide polymorphisms (SNP) discovery and applications of SNP genotyping in non-model organisms. Special Issue of Molecular Ecology Resources, 11, s1, 1–298.
  • Seeb, JE, Carvalho, GR, Hauser, L, Naish, K, Roberts, S & Seeb, LW (2011) Single nucleotide (SNP) discovery and applications of SNP genotyping in non-model organisms. Molecular Ecology Resources, 11, s1, 1–8.
  • Helyar, S.J., Hemmer- Hansen, J., Bekkevold, D.,Taylor, M.I., Ogden, R., Limborg, M.T., Cariani, A., Maes, G.E., Diopere, E.,Carvalho, G.R. and Nielsen, E.E. (2011) Application of SNPs for population genetics of non-model organisms: new opportunities and challenges. Molecular Ecology Resources 11 (Suppl. 1), 1–14
  • de Bruyn, M, Hoelzel, AR, Carvalho, GR & Hofreiter, M (2011) Faunal histories from Holocene ancient DNA. Trends in Ecology & Evolution, 26, 405–413.
  • Martinsohn, JT, Geffen, AJ, Maes, GE, Nielsen, EE, Waples, RS & Carvalho, GR (2011) Tracing Fish and fish products from ocean to fork using advanced molecular technologies. In: In: Food Chain Integrity: A holistic approach to food traceability, safety, quality and authenticity (Ed. Hoorfar, J, Jordan, K & Prugga, R), pp. 259–282. Woodhead Publishing.
  • Poulsen, NA, Hemmer-Hansen, J, Loeschcke, V, Moen, T, Carvalho, GR, Nielsen, EE (2011) Microgeographical population structure and adaptation in Atlantic cod (Gadus morhua): spatio-temporal insights from gene-associated DNA markers. Marine Ecology Progress Series, 436, 231–243.
  • Milano, I; Babbucci, M; Panitz, F; Ogden, R; Nielsens, RO; Taylor, MI; Helyar, SJ’ Carvalho, GR; Espiñeira, M; Atanassova, M; Tinti, F; Maes, GE; Patarnello, T; Bargelloni, L (2011) Novel Tools for Conservation Genomics: Comparing Two High-Throughput Approaches for SNP Discovery in the Transcriptome of the European Hake. PLoS ONE 6(11): e28008. doi:10.1371/journal.pone.0028008.
  • Zelenina, DA, MNartinsohn, J, Ogden, R, Volkov, AA, Zelenina, IA & Carvalho, GR (2011) Advanced approaches to studying the population diversity of marine fishes: new opportunities for fisheries control and management. Russian J Genetics, 47, 1444–1455.
  • Bekkevold, D, Clausen, LAW, Mariani, S, Andre, C, Hatfield, EMC, Tostensen, E, Ryman, N, Carvalho, GR & Ruzzante, DE (2011) Genetic mixed-stock analysis of Atlantic herring populations in a mixed feeding area. Marine Ecology Progress Series, 442, 187–199.
  • Joana Matzen da Silva; Antonina dos Santos; Marina R Cunha; Filipe O Costa; Simon Creer; Gary R Carvalho (2011) Multigene molecular systematics confirm species status of morphologically convergent Pagurus hermit crabs, PLoS ONE 6 (12): e28233. doi:10.1371/journal.pone.0028233

2010

  • Costa, FO & Carvalho, GR (2010) New insights into molecular evolution: prospects from the Barcode of Life Initiative (BOLI). Theory in Biosciences, DOI 10.1007/s12064–010–0091-y.
  • Genner, MJ, Nichols, P, Shaw, PW, Carvalho, GR, Robinson, RL, Turner, GF (2010) Population structure on breeding grounds of Lake Malawi’s ‘twilight zone’cichlid fishes. Journal of Biogeography, 37, 258–269
  • André C., Larsson, LC, Laikre, L., Bekkevold D, Brigham,J., Carvalho, GR, Dahlgren,TG., Hutchinson, WF, Mariani, S, K Mudde, K, Ruzzante, DE and Ryman N.(2010) Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci. Heredity 106, 270–280.
  • Domingues, CP, Creer, S, Taylor, M, Queiroga, H, Carvalho,GR. (2010). Genetic structure of Carcinus maenas within its native range: larval dispersal and oceanographic variability. Marine Ecology Progress Series 410, 111–123.
  • De Bruyn, M., Grail, W., Barlow, A. (2010). Anonymous nuclear markers for SouthEast Asian halfbeak fishes (Dermogenys). Conservation Genetics Resources 2: 325–327.
  • Domingues CP, Creer S, Taylor MI, Queiroga H and Carvalho GR. (2010).Temporal genetic homogeneity among shore crab (Carcinus maenas) larval events supplied to an estuarine system on the Portuguese northwest coast. Heredity, Heredity, 106, 832–840.
  • Carvalho, GR, Creer, S, Allen, M, Costa, FO, Tsigenopoulos, CS, Le Goff-Vitry, M, Magoulas, AM, Medlin, L & Metfies, K (2010) Genomics in the discovery and monitoring of marine biodiversity. In: An Introduction to Marine Genomics, (ed.) Boyen C & Cock, M, pp. 1–32. Springer-Verlag.
  • Fonseca, V.G., Carvalho, GR, Sung, W, Johnson, HF, Power, DM, Neill, SP, Packer, M, Blaxter, ML, Lambshead, PJD, Thomas, WK, & Creer, S (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications, DOI:http://dx.doi.org/10.038/ncomms1095
  • de Bruyn, M, Grail, W, Barlow A & Carvalho, GR (2010) Anonymous nuclear markers for SouthEast Asian halfbeak fishes (Dermogenys). Conservation Genet Resour. 2, 325–327.
  • de Bruyn M, Grail W, Carvalho GR (2010) Anonymous nuclear markers for the Blue Panchax killifish (Aplocheilus panchax). Conservation Genetics Resources, 3, 53–55.

2009

  • Gaggiotti, OE, Bekkevold D, Jørgensen HBJ, Foll M, Carvalho GR, Andre C, Ruzzante DE (2009) Disentangling the effects of evolutionary, demographic and environmental factors influencing genetic structure of natural populations: Atlantic Herring as a case study. Evolution, 63, 2939–2951.
  • Hughes, RN, Wright, PJ, Carvalho, GR & Hutchinson, WF (2009) Patterns of self-compatibility, inbreeding depression, outcrossing and sex allocation in a marine bryozoan suggest the predominating influence of sperm competition. Biol. J. Linn. Soc, 98, 519–531.
  • Peppin, L, McEwing, R, Ogden, R, Hermes, R, Harper, C, Guthrie, A & Carvalho, GR (2009) Molecular sexing of African rhinoceros. Conservation Genetics, 10, 1–4
  • Nielsen, E, Hammer-Hansen, J, Poulsen, NA, Loeschcke, V, Moen, T, Joahansen, T, Mittelholzer, C, Taranger, G, Ogden, R & Carvalho GR (2009) Genomic signatures of local directional selection in a high gene flow marine organism: the Atlantic cod (Gadus morhua). BMC Evolutionary Biol. 9, 276–287
  • Pascoal, S, Creer, S, Taylor, M, Queiroga H, Carvalho, GR & Mendo, S (2009) Development and application of microsatellites in Carcinus maenas: genetic differentiation between northern and central Portuguese populations. PLoS ONE, 4 (9) e7268
  • Tysklind, N, Taylor, MI, Lyons, BP, McCarthy, ID and Carvalho, GR (2009) Development of 30 microsatellite markers for dab (Limanda limanda L.): a key UK marine biomonitoring species. Molecular Ecology Resources, 9, 951–955
  • Tysklind, N, Neuparth,T, Ashcroft,GR, Taylor, MI, Lyons, BP, McCarthy, IMD, and Carvalho, GR (2009) Isolation and characterization of 28 new microsatellite markers for European flounder (Platichthys flesus L.). Molecular Ecology Resources, 9, 1065–1068.
  • Paulsen; H, Kjesbu, OS; Bühler, V; Case, RA; Clemmesen, C; Carvalho, GR; Hutchinson, WR; Moksness, E; Otterå, H; Thorsen, A; Svåsand, T(2009) Effects of egg size, parental origin and feeding conditions on growth of larval and juvenile cod (Gadus morhua L.). J Fish Biol. 75 (3), 516–537.

2008

  • Rock J, Costa FO, Walker DI, North AW, Hutchinson WF & Carvalho GR (2008) DNA barcodes fo fish of the Antarctic Scotia Sea indicate priority groups for taxonomic and systematic focus. Antarctic Science, 20, 253–262
  • Hauser, L , Waples, RS & Carvalho, GR (2008) Advances in Marine Fish and Fisheries Genetics. Special Issue of Fish and Fisheries, 9 (4), 331–486.
  • Hauser, L & Carvalho, GR (2008) Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts. Fish and Fisheries, 9 (4), 333–362.
  • Peppin L, McEwing R, Carvalho GR & Ogden R (2008) A DNA-based approach for the forensic identification of Asiatic Black Bear (Ursus tibetanus) in a traditional Asian medicine. Journal of Forensic Sciences, 53, 1358–1362.
  • Genner MJ, Nichols P, Shaw PW, Carvalho GR, Robinson RL & Turner GF (2008) Genetic homogeneity among breeding grounds and nursery areas of an exploited Male Malawi cichlid fish. Freshwater Biology, 53, 1823–1831

2007

  • Dawney, N, Ogden, R, McEwing, R, Carvalho, GR & Thorpe, RS (2007) Validation of the barcoding gene CO1 for use in forensice genetic species identification. Forensic Science International. 173, 1–6. PDF
  • Genner MJ, Seehausen O, Lunt DH, Joyce DA, Shaw, PW, Carvalho GR and Turner GF (2007) Age of cichlids: New dates for ancient lake fish radiations. Molecular Biology and Evolution. 24: 1269–1282. PDF
  • Genner, MJ, Nichols, P, Carvalho, GR, Robinson, RL, Shaw, PW, Smith, A & Turner, GF (2007) Evolution of a cichlid fish in a Lake Malawi satellite lake. Proceedings of the Royal Society of London, B. 274, 2249–2252.
  • Genner MJ, Nichols P, Carvalho GR, Robinson RL, Shaw, PW and Turner GF (2007) Reproductive isolation among deep-water cichlid fishes of Lake Malawi differing in monochromatic male breeding dress. Molecular Ecology. 16: 651–662. PDF
  • Gomez A, Wright PJ, Lunt DH, Cancino JM, Carvalho GR and Hughes RN (2007) Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proceedings of the Royal Society of London, B. 24: 199–207. PDF
  • Gomez A, Hughes RN, Wright PJ, Carvalho GR and Lunt DH (2007) Mitochondrial DNA phylogeography and mating compatability reveal marked genetic structuring and speciation in the NE Atlantic bryozoan Celleporella hyalina. Molecular Ecology, 16, 2173–2188. PDF
  • Hughes RN, Gómez A, Wright PJ, Moyano HI, Cancino JM, Carvalho GR, Lunt DH (2008) Molecular phylogeny supports division of the “cosmopolitan” taxon, Celleporella (Bryozoa: Cheilostomata) into four major clades. Molecular Phylogenetics and Evolution, 46, 369–374
  • Larsson L, Laikre L, Palm S, Andre C, Carvalho GR & Ryman N (2007) Concordance of allozymes and microsatellite differentiation in a marine fish, but evidence of selection as a microsatellite locus. Molecular Ecology, 16, 1135–1147. PDF
  • Le Vay L, Carvalho GR, Quinitio ET, Lebata JH, Ut VN & Fiushimi H (2007) Quality of hatchery-reared juveniles for marine fisheries stock enhancement. Aquaculture, 268, 169–180.
  • Costa, FO & Carvalho, GR (2007) The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish. Genomics, Society and Policy 3, 29–40 (available on line at www.gspjournal.com./)

2006

Refereed Papers

  • Ruzzante, D, Mariani, S, Bekkevold, D, Andre, C, Mosegaard, H, Clausen, L, Dahlgren, T, Hutchinson, WF, Hatfield, E, Torstensen, E, Brigham, J, Simmonds, J, Laikre, L, Larsson, L, Stet, R, Ryman, N and Carvalho, GR (2006) Biocomplexity in a highly migratory pelagic marine fish, Atlantic herring. Proceedings of the Royal Society of London, B. 273: 1459–1464. PDF
  • Case, RAJ, Hutchinson, WF, Hauser, L, Buchler, V, Clemmesen, C, Dahle, G, Kjesbu, OS, Moksness, E, Otterå, H, Paulsen, H, Svåsand, T, Thorsen, A, Carvalho, GR (2006) Association between growth and PanI* genotype within Atlantic cod full sibling families. Transactions of the American Fisheries Societies. 135: 241–250. PDF
  • Dorte Bekkevold, Carl Andre, Thomas Dahlgreen, Lotte AW Clausen, Else Torstensen, Henrik Mosegaard, Gary R Carvalho, Tina B Christensen and Daniel E Ruzzante. (2006) Environmental correlates of population differentiation in Atlantic herring. Evolution, 59, 2656–2668.
  • Ryman, N, Palm, S, Andre, C, Carvalho, GR, Dahlgren, TG, Jorde, PE, Laikre, L., Larsson, LC, Palme, A & Ruzzante, DE (2006) Power for detecting genetic divergence: differences between statistical methods and marker loci. Molecular Ecology, 15, 2031–2045.
  • Weetman, D, Hauser, L & Carvalho, GR (2006) Heterogeneous evolution of miicrosatellites revealed by reconstruction of recent mutation history in an invasive apomictic snail, Potamopyrgus antipodarum. Genetica, 127, 285–293.

2005

Refereed Papers

  • Hänfling, B, Bolton, P, Harley, M and Carvalho, GR (2005) A molecular approach to detect hybridisation between crucian carp (Carassius carassius) and non-indigenous carp species (Carassius spp. and Cyprinus carpio). Freshwater Biology. 50: 403–417.
  • Mahmoud, HA, Goulder, R and Carvalho, GR (2005) The response of epilithic bacteria to different metals regime in two upland streams assessed by conventional microbiological methods and PCR-DGGE. Archiv fur Hydrobiol. 163: 405–427.
  • Mesquita, M, Hänfling, B. Carvalho, GR and Coelho, MM (2005) Phylogeography of the cyprinid Squalius aradensis and implications for conservation of the endemic freshwater fauna of Southern Portugal. Molecular Ecology, 14: 1939–1954. PDF
  • D’Amato, MED and Carvalho, GR (2005) Population genetic structure and history of the long-tailed hake, Macruronus magellanicus, in the SW Atlantic as revealed by mtDNA RFLP analysis. ICES Journal of Marine Science, 62: 247–255.
  • Mariani, S, Hutchinson, WH, Hatfield, EMC, Ruzzante, DE, Simmonds, EJ, Dahlgren, TG, Andre, C, Brigham, J, Torestenses, E and Carvalho, GR (2005) North Sea herring population structure revealed by microsatellite analysis. Marine Ecology Progress Series, 303: 245–257.
  • Case, RAJ, Hutchinson, WF, Hauser, L, Van Oosterhout, C and Carvalho, GR (2005) Macro- and micro-geographic variation in Pantophysin (Pan I) allele frequencies in NE Atlantic cod (Gadus morhua L.). Marine Ecology Progress Series, 301: 267–278.
  • Hughes, RN, D’Amato, ME, Bishop, JDD, Carvalho, GR, Craig, SF, Hansson, LJ, Harley, MA and Pemberton, AJ (2005). Paradoxical polyembryony? Embryonic cloning in an ancient order of marine bryozoans. Biology Letters. 1: 178–180 PDF
  • Bekkevold D, Andre C, Dahlgreen TG, Clausen LAW, Torstensen E, Mosegaard H., Carvalho GR, Christensen TB and Ruzzante DE. (2005) Environmental correlates of population differentiation in Atlantic herring. Evolution, 59: 2656–2668. PDF

2004

Refereed Papers

  • Shaw, PW, Arkhipkin, AI, Adcock, GJ, Burnett, WJ, Carvalho, GR, Scherbich, JN and Villegas, PA (2004) DNA markers indicate that distinct spawning cohorts and aggregations of Patagonian squid, Loligo gahi, do not represent genetically discrete subpopulations. Marine Biology: 144, 961–970 PDF

Invited reviews

  • Turner, G.F., Robinson, R.L., Shaw, P.W. and Carvalho, GR (2004). Identification and biology of Diplotaxodon, Rhamphochromis and Pallidochromis. In: The cichlid diversity of Lake Malawi/Niassa: identification, distribution and taxonomy (J. Snoeks, ed.). Cichlid Press, El Paso, pp. 198–251.

2003

Invited reviews

  • Cajaraville, MP, Hauser, L, Carvalho, GR, Hylland, K, Olabarrieta, I., Lawrence, ASJ, Lowe, D and Gokoyr (2003) Genetic damage and the Molecular/Cellular Response to Pollution. In: Effects of Pollution on Fish (AJ Lawrence and KL Hemingway, eds.). Blackwell Publishing, pp. 14–82.

Refereed Papers

  • Bernal-Ramirez, JH, Adcock, GJ, Hauser, L, Carvalho, GR and Smith, PJ (2003) Temporal stability of genetic structure in the New Zealand snapper, Pagrus auratus, and relationship to coastal currents. Marine Biology, 142: 567–574
  • Clemmesen, C, Buhler, V, Carvalho, GR, Case, R, Evans, G, Hauser, L, Hutchinson, WF, Kjesbu, OS, Mempel, H, Moksness, E, Otterae, H, Paulsen, T, Svaasand, T and Thorsen, A (2003) Measurements of condition and growth of cod larvae reared in mesocosms: individual variability as a function of environmental conditions- maternal effects or genetic inheritance? J. Fish Biology, 62: 706–723. PDF
  • Hutchinson, WF, van Oosterhout, C, Rogers SI and Carvalho, GR (2003) Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod. Proceedings of the Royal Society, Lond., B, 270: 2125–2132.
  • Mesquita, N, Cunha, C, Hänfling, B, Carvalho, GR, Zé Zé, L, Tenreiro, R and Coelho, MM (2003) Isolation and characterization of polymorphic microsatellite loci in the endangered Portuguese freshwater fish Squalius ardensis (Cyprinidae). Molecular Ecology Notes, 3: 572–574. PDF
  • Salgueiro, P, Carvalho, GR, Collares-Pereira, MJ and Coelho, MM (2003) Microsatellite analysis of genetic population structure of the endangered cycprinid, Anaecypris hisanica, in Portugal: implications for conservation. Biological Conservation, 109: 47–56. PDF

2002

Invited reviews

  • Turner, GF, Robinson, RL, Ngatunga, BP, Shaw, PW and Carvalho, GR (2002) Pelagic cichlid fishes of Lake Malawi/Nyasa: biology, management and conservation. In: Management and ecology of lake and reservoir fisheries (IG Cowx, ed.). Blackwell, pp. 353–366.
  • Carvalho, GR, van Oosterhout, C., Hauser, L and Magurran, AE (2002) Measuring genetic variation in wild populations: from molecular markers to adaptive traits. In: Genes in the Environment (J Behringer, RS Hails and C Godfrey, eds.). Blackwell Science, pp. 91–111.

Refereed Papers

  • Gomez, A, Adcock, GJ, Lunt, DH and Carvalho, GR (2002) The interplay between colonization and gene flow in passively dispersing zooplankton: microsatellite analysis of rotifer resting egg banks. Journal of Evolutionary Biology, 15: 158–171. PDF
  • Mitchell, SE and Carvalho, GR (2002) Comparative demographic impacts of “info-chemicals” and exploitative competition: an empirical test using Daphnia magna. Freshwater Biology, 47: 459–471.
  • Gomez, A, Adcock, GJ, Lunt, DH and Carvalho, GR (2002) Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera). Evolution, 56: 1431–1444. PDF
  • Porter J.S., Ryland J.S. and Carvalho GR 2002. Micro- and macrogeographic genetic structure in bryozoans with different larval strategies. Journal of Experimental Marine Biology and Ecology 272: 119–130.
  • Hänfling, B, Hellemans, B, Volckaert, FAM and Carvalho, GR (2002) Late glacial history of the cold-adapted freshwater fish Cottus gobio, revealed by microsatellites. Molecular Ecology, 11: 1717–1729. PDF
  • Weetman, D, Hauser, L and Carvalho, GR (2002) Reconstruction of microsatellite mutation history reveals a strong and consistent deletion bias in invasive clonal snails, Potamopyrgus antipodarum. Genetics, 162: 813–822.
  • Hänfling, B, Carvalho, GR and Brandl, R (2002) An invasion history of the Chinese mitten crab revealed by mt-DNA sequences. Marine Ecology Progress Series, 238: 307–310. PDF
  • Hauser, L, Adcock, GJ, Smith, PJ, Bernal Ramirez, J and Carvalho, GR (2002) Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper. Proceedings of the National Academy of Sciences, USA, 99: 11742–11747. PDF
  • Reid, VA, Carvalho, GR, George, DG and Griffiths, HI (2002) A technique for the molecular genetic analyses of Daphnia resting eggs from sub-recent lake sediments. J. Paleolimnology, 27: 481–486. PDF
  • Volckaert, FAM, Haenfling, B, Hellemans, B and Carvalho, GR (2002) Timing of the population dynamics of bullhead Cottus gobio during the Pleistocene. Journal of Evolutionary Biology, 15: 930–944. PDF
  • Perez-Losada, M, Guerra, A, Carvalho, GR, Sanjuan, A and Shaw, PW (2002) Extensive population subdivision of the cuttlefish Sepia officinalis around the Iberian Peninsula indicated by microsatellite DNA variation. Heredity, 89: 417–424. PDF
  • Oosterhout, C van, Trigg, RE, Carvalho, GR, Magurran, AE, Hauser, L and Shaw, PW (2002) Inbreeding depression and genetic load of sexually selected traits: how the guppy lost its spots. Journal of Evolutionary Biology, 16: 273–281.

2001

Invited reviews

  • Turner, GF, Robinson, RL, Ngatunga, BB, Shaw, PW and Carvalho, GR (2001) Pelagic cichlid fishes of Lake Malawi/Nyasa. In: Cichlid Research State of the Art. J. Aquariology and Aquatic Sciences 9 (RM Coleman, ed.), pp. 287–302.

Refereed Papers

  • Weetman, D, Hauser, L and Carvalho, GR (2001) Isolation and characterization of di- and trinucleotide microsatellites in the freshwater snail, Potamopyrgus antipodarum. Molecular Ecology Notes, 1: 185–187. PDF
  • Turner, GF, Robinson, RL, Ngatunga BP, Shaw, PW and Carvalho, GR (2001) Pelagic cichlid fishes of Lake Malawi/Nyasa: Biology, Management and Conservation. In: Management and Ecology of Lake Reservoir Fisheries (ed. IG Cowx), pp. 353–366. Blackwell Science.
  • Hauser, L, Turan, C and Carvalho, GR (2001) Haplotype frequency discriminatory power of 2 mtDNA fragments in a marine pelagic teleost (Atlantic herring, Clupea harengus). Heredity, 87: 621–630. PDF
  • Mesquita, N, Carvalho, GR, Shaw, PW, Crespo, E and Coelho, MM (2001) River basin-related genetic structuring in an endangered fish species, Chondrostoma lusitanicum, based on mtDNA sequencing and RFLP analysis. Heredity, 86: 253–264. PDF
  • Craig, SF, D’Amato, ME, Harley, M, Bishop J, Hughes, R and Carvalho, GR (2001) Isolation and characterization of microsatellites in the bryozoan, Crisia denticulata. Molecular Ecology Notes, 1: 281–282. PDF
  • Hutchinson, W, Carvalho, GR and Rogers, SI (2001) Marked genetic structuring in localised populations of cod (Gadus morhua) within the North Sea and adjoining waters, as revealed by microsatellites. Marine Ecology Progress Series, 223: 251–260. PDFPorter, JS, Dyrynda PEJ, Ryland, JS and Carvalho, GR (2001) Morphological and genetic adaptation to a lagoon environment: a case study in the bryozoan genus, Alcyonidium. Marine Biology, 139: 575–585. PDF

2000

Refereed Papers

  • Carvalho, GR and Hauser, L (2000) Molecular markers and the species concept: New techniques to resolve old disputes? Rev. Fish Biol. Fish. 9: 379–382. PDF
  • Gomez, A and Carvalho, GR (2000) Sex, parthenogenesis and genetic structure of rotifers: microsatellite analysis of contemporary and resting egg bank populations. Molecular Ecology, 9: 203–214. PDF
  • Reid, VA, Carvalho, GR and George, DG (2000) Molecular genetic analysis of Daphnia in the English Lake District: Species identity, hybridization and resting eggs. Freshwater Biology, 44: 247–253
  • Adcock, GJ, Ramirez JHB, Hauser, L., Smith, P and Carvalho, GR (2000) Screening of polymorphisms in samples of archived scales from New Zealand snapper. J Fish Biol. 56: 1283–1287. PDF
  • Gomez, A, Carvalho, GR and Lunt, DH (2000) Phylogeography and regional endemism of a passively dispersing zooplankter: mtDNA variation in rotifer resting eggs. Proc. Roy. Soc. Lond. B, 267: 2189–2197. PDFShaw, PW, Turner, GF, Idid, MR, Robinson, RL and Carvalho, GR (2000) Genetic population structure indicates sympatric speciation of Lake Malawi pelagic cichlids. Proc. Roy. Soc. Lond. B, 267: 2273–2280. PDF

1999

Refereed Papers

  • Adcock, GJ, Carvalho, GR, Rodhouse, PG and Shaw, PW (1999) Highly polymorphic microsatellite loci of the heavily fished squid genus Illex (Ommastrephidae). Molecular Ecology, 8: 165–167.
  • Hutchinson, WF, Carvalho, GR and Rogers, SI (1999) A non-destructive technique for the recovery of DNA from dried fish otoliths for subsequent molecular genetic analysis. Molecular Ecology, 8: 893–894.
  • D’Amato, ME, Lunt, DH and Carvalho, GR (1999) Microsatellite markers for the hake Macruronus magellanicus amplify other gadoids. Molecular Ecology, 8: 1086–1088.
  • Lunt, DH, Hutchinson, WF and Carvalho, GR (1999) An efficient method for PCR-based isolation of microsatellite arrays (PIMA). Molecular Ecology, 8: 891–894. PDF
  • Adcock, GJ, Shaw, PW, Rodhouse, PG and Carvalho, GR (1999) Microsatellite analysis of genetic diversity in the squid Illex argentinus during a period of heavy fishing. Mar. Ecol. Prog. Ser. 187: 171–178.Shaw, PW, Turan, C, Wright, JM, O’Connell, M and Carvalho, GR (1999) Microsatellite DNA analysis of population structure in Atlantic herring (Clupea harengus), with direct comparison to allozyme and mtDNA RFLP analyses. Heredity, 83: 490–499. PDF

1998

Edited books

  • Carvalho, GR (1998) Advances in Molecular Ecology. NATO ASI Series, IOS Press, Amsterdam.

Invited reviews

  • Carvalho, GR and Nigmatullin, C.H. (1998) Stock structure analysis and species identity in the genus, Illex. In Illex Recruitment Dynamics (PG Rodhouse and R O’Dor, eds.). FAO, Rome, pp. 199–231.
  • Carvalho, GR and Cross, TF (1998) Enhancing fish production through introductions and stocking: genetic perspectives. In: Stocking and Introduction of Fish (IG Cowx, ed.). Blackwell, Oxford, pp. 329–337.
  • Carvalho, GR (1998) Molecular ecology: origins and approaches. In: Advances in Molecular Ecology (ed. GR Carvalho). IOS Press, Amsterdam, pp. 1–24.Carvalho, GR and Hauser, L (1998) Advances in the molecular analysis of fish population structure. Italian Journal of Zoology, 65, Suppl., 21–33.
  • Turan, C, Carvalho, GR and Mork, J (1998) Molecular genetic of Atlanto-Scandian herring, Clupea harengus, using allozyme and mtDNA markers. J. Mar. Biol. Assoc. U.K., 78: 269–283.
  • Hauser, L., Carvalho, G.R., Pitcher, T.J. and Ogutu-Ohwayo, R. (1998) Genetic affinities of an introduced predator: Nile perch in Lake Victoria, East Africa. Molecular Ecology, 7: 849–857. PDF
  • Hauser, L, Carvalho, GR and Pitcher, TJ (1998) Genetic population structure in the Lake Tanganyika sardine, Limnothrissa miodon. Journal of Fish Biology, 53: (Supplement A), 413–429. PDF
  • Gomez, A, Clabby C. and Carvalho, GR (1998) Isolation and characterization of microsatellite loci in a cyclically parthenogenetic rotifer, Brachionus plicatilis. Molecular Ecology , 7: 1613–1621.Mitchell, SE, Carvalho, GR and Weider, LJ (1998) Stability of genotype frequencies in an intermittent Daphnia magna population. Arch. Hydrobiol. Spec. Issues Advan. Limnol. 52: 185–194.

1997

Refereed Papers

  • Carvalho, GR and Piertney, SB (1997) Interspecific comparisons of genetic population structure in members of the Jaera albifrons species complex. J. Mar. Biol. Assoc. U.K, 77: 77–93.
  • Hauser, L, Carvalho, GR and Pitcher, TJ (1997) Genetic similarity of a phenotypically divergent population of the clupeid, Limnothrissa miodon, following introduction into a man-made lake. In: Impacts of stocking and fish introductions ( I. Cowyx ed.). Fishing News Books, Oxford, pp. 338–354.Carvalho, GR and Cross, TF (1997) Enhancing fish production through introductions and stocking: genetic perspectives. In: Impacts of stocking and fish introductions (ed. I. Cowyx), 329–337. Fishing News Books, Oxford.

1996

Refereed Papers

  • Magurran, AE, Paxton, CGM, Seghers, BH, Shaw, PW and Carvalho, GR (1996) Genetic divergence, female choice and mating success in Trinidadian guppies. Behaviour, 133: 505–517
  • Carvalho, GR, Shaw, PW, Hauser, L, Seghers, B and Magurran, AE (1996) Artificial introductions, evolutionary rates and population differentiation in Trinidadian guppies (Poecilia reticulata). Biol. J. Linn. Soc. 57: 219–234. PDF
  • Piertney, SB and Carvalho, GR (1996) Sex ratio variation in the intertidal isopod, Jaera albifrons. Marine Biology, 76: 825–828
  • Bembo, DG, Pitcher, TJ and Carvalho, GR (1996) Stock discrimination of Northern Mediterranean anchovies (Engraulis encrasicolus L.) using PCR-RFLP analysis of mitochondrial DNA. Fisheries Bulletin. 94: 31–40.Bembo, DG, Carvalho, GR, Cingolani, N, Arneri, E, Giannetti, G and Pitcher, TJ (1996) Allozymic and morphometric evidence for two stocks of the European anchovy, Eugraulis encrasicolus, within Adriatic waters. Marine Biology, 126: 529–538.

    Bembo, DG, Carvalho, GR, Cingolani, N and Pitcher, TJ (1996) Electrophoretic analysis of stock structure in Northern Mediterranean anchovies, Engraulis encrasicolus L. ICES Journal of Marine Science. 53: 115–128. PDF

  • 1995

    Edited books

    • Carvalho, GR and Pitcher, TJ (ed.) (1995) Molecular Genetics in Fisheries. London and New York. Chapman and Hall. pp. 141. (Also published as a Special issue of Reviews in Fish Biology and Fisheries 4, (3) 269–399; edited by GR Carvalho and TJ Pitcher).

    Invited reviews

    • Carvalho, GR and Hauser, L (1995) Genetic impacts of fish introductions: an African perspective, In Species Changes in African Lakes (TJ Pitcher and P Hart, eds.). Chapman and Hall: London, pp. 457–494.Magurran, AE, Seghers, BH, Shaw, PW and Carvalho, GR (1995) Behavioural and genetic diversity of guppy, Poecilia reticulata, populations in Trinidad. Advances in the Study of Behaviour, 24, 155–202.
    • Naish, KA, Warren, M, Bardicka, F, Skibinski, DOF, Carvalho, GR and Mair, G (1995) Multilocus DNA fingerprinting and RAPD reveals similar genetic relationships between strains of Oreochromis niloticus. Molecular Ecology 4: 265–269.
    • Piertney, SB and Carvalho, GR (1995) Microgeographic differentiation in the intertidal isopod, Jaera albifrons Leach. II. Temporal variation in allele frequencies. J. Exp. Mar. Biol. Ecol. 188: 277–288. PDF
    • Piertney, SB and Carvalho, GR (1995) Multi-locus DNA fingerprinting detects high levels of genetic relatedness within rock-populations of the intertidal isopod, Jaera albifrons. J. Mar. Biol. Assoc. U.K. 75: 967–976.
    • De Barro, PJ, Sherratt, TN, Carvalho, GR, Nicol, D, Iyengar, A and Maclean, N (1995) Geographic and microgeographic genetic differentiation in two aphid species over southern England using the multilocus (GATA)4 probe. Molecular Ecology, 4: 375–382.
    • Mitchell, S, De Meester, L, Weider, L and Carvalho, GR (1995) No evidence for kin-preferential swarming in a Daphnia magna population coexisting with fish. J. Animal Ecology. 64: 777–779.Hauser, L, Pitcher, TJ and Carvalho, GR (1995) Phenotypic and genetic differentiation of Limnothrissa miodon (Pisces: Clupeiidae) introduced to Lake Kivu, East Africa, 34 years after introduction. J. Fish Biology. 47: 127–144.

    1994

    Invited reviews

    • Carvalho, GR (1994) Evolutionary genetics of aquatic clonal invertebrates: concepts, problems and prospects, In Genetics and Evolution of Aquatic Organisms (AR Beaumont, ed.). Chapman and Hall: London, pp. 291–323.
    • Carvalho, GR and Hauser, L (1994) Molecular genetics and the stock concept in fisheries. Special Issue of Reviews in Fish and Fisheries Biology (GR Carvalho and TJ Pitcher, eds.), 4, 351–373.

    Refereed Papers

    • Magurran, AE, Seghers, BH, Shaw, PW and Carvalho, GR (1994) Schooling preferences for familiar fish in the guppy, Poecilia reticulata. J. Fish Biol. 45: 401–406.
    • Shaw, PW, Carvalho, GR, Magurran, AE and Seghers, BH (1994) Factors affecting the distribution of genetic variability in the guppy, Poecilia reticulata. J. Fish Biol. 45: 875–888.
    • Piertney, SB and Carvalho, GR (1994). Microgeographic differentiation in the intertidal isopod, Jaera albifrons Leach. I. Spatial distribution of allozyme variation. Proc. Roy. Soc. Lond. 256: 195–201.De Barro, PJ, Sherratt, TN, Carvalho, GR, Nicol, D, Iyengar, A and Maclean, N (1994) An analysis of secondary spread by putative clones of Sitobion avenae within a Hampshire wheat field using the multilocus (GATA)4 probe. J. Insect Molecular Biology 3: 253–260.

    1993

    Invited reviews

    • Carvalho, GR (1993) Evolutionary aspects of fish distributions: genetic variability and adaptation. J. Fish Biol. 43, (Suppl. A), 53–73.

    Refereed Papers

    • Naish, K-A, Carvalho, GR and Pitcher, TJ (1993) The genetic structure and microdistribution of shoals of Phoxinus phoxinus, the European minnow. J. Fish. Biol. 43, (Suppl. A), 75–89.

    1992

    Invited reviews

    • Magurran, AE, Seghers, BH, Carvalho, GR and Shaw, PW (1992) Evolution of adaptive variation in antipredator behaviour. In: Behavioural Ecology of Fish (F Huntingford and A Porricelli, eds.). Mar. Behav. Physiol. 22: 29–44.

    Refereed Papers

    • Shaw, PW, Carvalho, GR, Seghers, BH and Magurran, AE (1992) Genetic consequences of an artificial introduction of guppies (Poecilia reticulata) in N. Trinidad. Proc. Roy. Soc. B 247: 111–116.
    • Magurran, AE, Seghers, BH, Carvalho, GR and Shaw, PW (1992) Behavioural consequences of an artificial introduction of guppies, Poecilia reticulata in N. Trinidad: evidence for the evolution of anti-predator behaviour in the wild. Proc. Roy. Soc. B 247: 117–122.
    • Carvalho, GR, Thompson, A and Stoner, AL (1992) Genetic diversity and population differentiation of the shortfin squid (Illex argentinus) in the South-West Atlantic. J. Exp. Mar. Biol. Ecol. 158: 105–121.Hauser, L, Carvalho, GR, Hughes, RN and Carter, RE (1992) Clonal structure of the introduced freshwater snail, Potamopyrgus antipodarum (Prosobranchia: Hydrobiidae), as revealed by DNA fingerprinting. Proc. Roy. Soc. B. 249: 19–25.

    1991

    Refereed Papers

    • Carvalho, GR, Shaw, PW, Magurran, AE and Seghers, B (1991) Marked genetic divergence revealed by isozymes among populations of the guppy, Poecilia reticulata (Poeciliidae), in Trinidad. Biological Journal of the Linnean Society, 42: 389–405.
    • Carvalho, GR, Maclean, N, Wratten, SD, Carter, RE and Thurston, JP (1991) Differentiation of aphid clones using DNA fingerprints from individual aphids. Proceedings of the Royal Society, B, 243: 109–114.
    • Wratten, SD, Carvalho, GR and Maclean, N (1991) Separation of individual clonal aphids using DNA fingerprinting. In: Aphid-Plant Interactions (Ed. by D.C. Peters and J.A. Webster). Oklahoma University Press, Stillwater, Oklahoma, p.287–288.Shaw, PW, Carvalho GR, Magurran, AE and Seghers, BH (1991) Population differentiation in Trinidadian guppies (Poecilia reticulata): patterns and problems. Journal of Fish Biology. 39: 203–209. PDF

    1990

    Invited reviews

    • Carvalho, GR (1990) Molecular population genetics of marine animals: some future lines of research. In: The Genetics of Marine and Estuarine Organisms (H Hummel, ed.). Delta Institute, Yerseke, pp. 27–31.

    1989

    Refereed Papers

    • Carvalho, GR and Loney, KH (1989) Biochemical genetic studies on the Patagonian squid, Loligo gahi. I. Electrophoretic survey of genetic variability. Journal of Experimental Marine Biology and Ecology, 126: 231–241.
    • Carvalho, GR and Pitcher, TJ (1989) Biochemical genetic studies on the Patagonian squid, Loligo gahi. II. Population structure in Falkland waters using isozymes, morphometrics and life history data. Journal of Experimental Marine Biology and Ecology, 126: 243–258.
    • Carvalho, GR (1989) Microgeographic genetic differentiation and dispersal capacity in the intertidal isopod, Jaera albifrons. In: Reproduction, Genetics and Distribution of Marine Organisms (Ed. by J.S. Ryland and P.A. Tyler), pp.265–271. Proceedings of the 23rd European Marine Biology Symposium. Olsen and Olsen, Denmark.
    • Carvalho, GR and Wolf, HG (1989) Resting eggs of lake-Daphnia. I. Distribution, abundance and hatching of eggs collected from various depths in lake sediments. Freshwater Biology, 22: 459–470.Wolf, HG and Carvalho, GR (1989) Resting eggs of lake-Daphnia. II. In situ observations on the hatching of eggs and their contribution to population and community structure. Freshwater Biology, 22: 471–478.

    1988

    Refereed Papers

    • Carvalho, GR (1988) Differences in the frequency and fecundity of PGI-marked genotypes in a natural population of Daphnia magna (Crustacea:Cladocera). Functional Ecology, 2: 453–462.

    1987

    Refereed Papers

    • Carvalho, GR and Crisp, DJ (1987) The clonal ecology of Daphnia magna (Crustacea:Cladocera). I. Temporal changes in the clonal structure of a natural population. Journal of Animal Ecology, 56: 453–468.
    • Carvalho, GR (1987) The clonal ecology of Daphnia magna (Crustacea:Cladocera). II. Thermal differentiation among seasonal clones. Journal of Animal Ecology, 56: 469–478.Carvalho, GR and Hughes, RN (1983) The effect of food availability, female culture-density and photoperiod on ephippia production in Daphnia magna Straus (Crustacea:Cladocera). Freshwater Biology, 13: 37–46

    1984

    Refereed Papers

    • Carvalho, GR (1984) Haemoglobin synthesis in Daphnia magna Straus (Crustacea:Cladocera): ecological differentiation between neighbouring populations. Freshwater Biology, 14: 501–506.

Past Students and Postdocs/Fellows

Since first appointment to academia in 1990, I have invested considerable effort in the promotion and support of early-career postgraduates and postdoctoral staff, a significant proportion of who are now leaders in Molecular Ecology and Evolution. An early opportunity for such training on a global scale was provided by the award of a NATO Advanced Study Institute ASI) held in Erice, Sicily, together with the resulting textbook: Advances in Molecular Ecology (1998), (Ed. GR Carvalho). The ASI provided the first international opportunity for consideration of advances in concepts, analysis and use of PCR-based tools and in ecology and evolution, with 74 NATO students and 15 lecturers for 10 days of seminars, student poster sessions, debate and hands-on use of new software). Lecturers incl. P Beerli, A Estoup, PDN Hebert, DM Hillis, JB Mitton, LH Riesberg, F Rollo, RC Vrijenhoek, RD Ward, JP Young- individuals that represent pioneers in the field of evolutionary/molecular ecology. ASI students included early career scientists who are now major contributors in molecular ecology, incl. J-C Simon, C Primmer, JC Vogel, B Angers, C Biermann L Bargelloni, A Gómez, K Naish, L Hauser, S Piertney.

Large, interactive research groups were established at Swansea, Hull and Bangor by Carvalho (e.g. Hull (e.g. 1996- Carvalho established a new molecular ecology group, which by 2002 had membership of 35, inc. O. Seehausen, Univ. Berne, T Kocher (Visiting Fellow, now Univ. Maryland), GF Turner (Past Head of Biological Sciences, Bangor University; C. van Oosterhout (now, Reader Univ. East Anglia); A Gómez, (now NERC Advanced Fellow); S. Mariani, (now Professor of Conservation Genetics, Salford Univ.) and Bangor Universities, currently with 4 postdoctoral staff (incl. NERC Fellow), 11 PhD students and 3 Masters students ). Collectively, Carvalho has supervised and collaborated with numerous early-stage scientists (to date: 16 Masters; 36 PhD (24 as lead supervisor); 17 postdoctoral, including 3 Marie-Curie, 1 NATO, 1 United Nations, 3 NERC Fellows, 2 Visiting Professorial Fellowships (TD Kocher, USA; P Bloomer, S Africa), and 9 Erasmus Scholars.

To support early career scientists, the first author of most primary papers is the respective PhD student or postdoctoral scientist. Additionally, where other junior colleagues have made significant input, they are given prominence.

He has acted as external examiner of 35 PhD students, including candidates from James Cook University of N Queensland, Rhodes University, SA, Griffith University, Australia, Guelph University, Canada, Open University (Naples), Stockholm University, University of Cork, University of Dublin, University of Essex, Nottingham University, Bristol University, York University, Bangor University, Plymouth University, University of Leeds, Liverpool John Moores University, University of Stirling, University of Hull, University of Southampton.

A selection of past Carvalho PhD students and postdoctoral Associates/Research Fellows include: KA Naish (PhD student) – Tenured Professor in Molecular Ecology, School of Aquatic Sciences & Fisheries, University of Washington, Seattle; SB Piertney (PhD student) – Professor of Molecular Ecology and Evolution, Aberdeen University, UK; L Hauser (PhD student, PDR) – Tenured Professor in Molecular Ecology, School of Aquatic Sciences & Fisheries, University of Washington, Seattle; R. Idid (PhD student) – Senior Lecturer in Evolutionary Biology, University of Malaya, Kuala Lumpur, Malaysia; C Turan (PhD student) – Professor of Fisheries, Head of Department of Basic Sciences, and past Dean of Faculty of Fisheries, Mustafa Kemal University, Turkey; J Porter (PhD student) – Senior Lecturer in Marine Biology, Heriot Watt University, Edinburgh, UK; H Abdullah (PhD student) – Senior Lecturer in Ecology, Kuwait University; PW Shaw (PDR) –Professor of Population Genetics & Genomics, Leader of Aquatic, Behavioural and Evolutionary Biology (ABEB), Aberystwyth University, UK; A Gómez (PDR) – NERC Advanced Fellow, Hull University, UK; E D’Amato (PDR) – Research Manager, Forensic DNA laboratory, University of the Western Cape, SA; S. Helyar (PDR) – Head of Genetics, MATIS Icelandic Food and & Biotech. Lab R&D, Iceland; C van Ooosterhout (PDR) – Professor of Evolutionary Biology, Univ. East Anglia, UK; J Rock (PDR) – Lecturer, Univ. Otago, New Zealand; MI Taylor (UK-RUC-Fellow) – Senior Lecturer, Univ. East Anglia, UK; S Creer (Fellow) – Senior Lecturer, Bangor University, UK; S Mariani (PDR) –Professor of Conservation Genetics, University Salford, UK; F Costa (Marie-Curie Fellow) – Asst. Professor & Chair, CBOL European FishBol, Univ. Braga, Portugal; M de Bruyn (Fellow/PDR) – Senior Lecturer in Molecular Ecology, Bangor University; 2012 winner of 14th R.J.H. Hintelmann Scientific Award for Zoological Systematics; V. Fonseca (PhD student) - Head of Env. Genomics Section, Zoological Research Museum Alexander Koenig (ZFMK), Germany; N Tysklind (PhD student/PDR) – INRA, Team Leader – Population Genetics and Genomics, French Guyana.

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