Prof Gary Carvalho | Molecular Ecology and Fisheries Genetics Laboratory | Bangor University

Professor Gary Carvalho

Prof. Gary Carvalho
Prof. Gary Carvalho
Research Professor of Molecular Ecology
+44(0)1248 382100
School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK


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. Gary Carvalho was awarded the Fisheries Society of the British Isles (FSBI) Beverton Medal in 2018, in recognition of ground-breaking research and life-long contribution to fish and fisheries science.

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 ( C

arvalho is also contributing to a EuroMarine workshop focusing on the Application of Genomics in Fisheries ( ), to be held in Portugal in May 2017. Currently, Gary Carvalho, while Chair of the ICES Expert Group on the Application of Genetics in Fisheries and Aquaculture, with other colleagues from the group, submitted a successful proposal to the ICES to host a new training course on “Genomics in Support of Fisheries and Aquaculture”, to take place in June 2018, at the Joint Research Centre, European Commission, Italy. For the first time, the ICES training portfolio offers a course on the design and application of genomics in management and conservation of fisheries and aquaculture. Our new course aims to narrow the science – policy divide by focusing on the need to render genomics more responsive and relevant to management needs, as supported by recent conceptual and technical advances. These will be placed within the context of salient policy frameworks. Further details can be found at:

More broadly, research in the School of Natural Sciences is ranked in 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.


Education and honours

  • FSBI Beverton Medal 2018, for ground-breaking research and life-long contribution to fish and fisheries science
  • 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


  • 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– present External assistant working with the Research Executive Agency– European Commission, Brussels
  • 2018 Member of Peer Review Panel for Genome Canada, Genomics Solutions for Agriculture, Agri-Food, Fisheries and Aquaculture.

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:; 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;, as well an numerous regional and national newspapers.


I arrived at Bangor University 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 ( 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: 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. 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. 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. 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. 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. 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).





















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.