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Jamie Stevens

University of Exeter, School of Biosciences, Faculty Member

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Jamie currently works in the Department of Biosciences in the College of Life and Environmental Sciences, University of Exeter. His team undertake research in evolutionary biology, ecology and population genetics. Current projects include Salmonid Management Around the Channel (SAMARCH), an EU-funded INTERREG project exploring the movements of sea trout in marine and coastal waters, and research into the population genetics and connectivity of soft corals and various lobster species.

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Kristen J Gremillion

Ohio State University

Armando Marques-Guedes

UNL - New University of Lisbon

Gwen Robbins Schug

University of North Carolina at Greensboro

Jesper Hoffmeyer

University of Copenhagen

Universidade Federal de Santa Catarina - UFSC (Federal University of Santa Catarina)

Griffith University

Richard Cloutier

Université du Québec à Rimouski

Juan J. Morrone

Universidad Nacional Autónoma de México

Jeffrey Schwartz

University of Pittsburgh

Arizona State University

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Papers by Jamie Stevens

A low‐density single nucleotide polymorphism panel for brown trout ( <i>Salmo trutta</i> L.) suitable for exploring genetic diversity at a range of spatial scales

Journal of Fish Biology, Nov 25, 2022

The version presented here may differ from the published version. If citing, you are advised to c... more

A tale of two hatcheries: Assessing bias in the hatchery process for Atlantic salmon (Salmo salar L.)

Aquaculture, Oct 1, 2014

Stock enhancement of Atlantic salmon (Salmo salar L.), a fish of considerable 39 economic and soc... more Stock enhancement of Atlantic salmon (Salmo salar L.), a fish of considerable 39 economic and social importance, is commonplace. Supportive-breeding is a well-40 recognised method of enhancement which, when compared with traditional hatchery 41 practices, is thought to reduce the severity of selection pressures on broodstock fish. 42 Critically, in supportive-breeding programmes, the eggs and sperm used in the 43 breeding process are taken from wild adult fish originating from the same catchment 44 that resulting juvenile fish are subsequently stocked into, thereby avoiding problems 45 associated with a lack of local adaptation in the stocked fish. Previous studies have 46 indicated that sex bias during the hatchery process may result in reduced genetic 47 diversity of the offspring. Utilising 16 microsatellite loci and two expressed sequence 48 tag (EST) loci, we examined progeny from two hatcheries located on the rivers Exe and 49 Tamar in southwest England, assessing the genetic diversity and parental contribution 50 at each. Two strains were assessed within each hatchery. Genetic diversity was found 51 to be reduced in offspring compared with that of the parent fish. This is likely the result 52 of utilising a small number of broodstock in combination with parental bias. In the four 53 hatchery strains studied (Bar, LEx, Lyd and TXL), parental contribution ranged between 54 2.1-29.2%, 12.2-51.0%, 2.0-70.0% and 4.0-40.0%, respectively. If this practice is to 55 be continued, efforts should be made to improve adherence to national rearing 56 guidelines by increasing the number of broodstock fish utilised and ensuring a more 57 balanced contribution of all adults during the crossing process. Ultimately, we suggest 58 a need to review the suitability of current national Atlantic salmon hatchery guidelines, 59 particularly with regard to their use and relevance in small European rearing systems. 60

Harnessing genomics to fast-track genetic improvement in aquaculture

Nature Reviews Genetics, Apr 16, 2020

Aquaculture is the fastest growing farmed food sector and will soon become the primary source of ... more Aquaculture is the fastest growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crops and livestock, production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.

An improved genetic sex test for Atlantic salmon (Salmo salar L.)

Conservation Genetics Resources, Apr 30, 2019

Accurate determination of sex ratios is an important metric for the conservation and management o... more Accurate determination of sex ratios is an important metric for the conservation and management of wild Atlantic salmon populations. Previously published primers for a male-specific gene were shown to be unreliable at determining sex due to the presence of deletions in the forward primer-binding site. A new forward primer, used in conjunction with the existing reverse primer, greatly improved reliability of the genetic test, correctly assigning gender in samples of known sex. Using DNA extracted from both contemporary and archive tissues, comparison between the two primer sets screened on collections of unknown sex ratio showed significant discrepancies in the number of males identified. The new primer will help improve the management and conservation of Atlantic salmon by providing accurate sex ratios for the setting of Conservation Limits.

Investigating patterns of straying and mixed stock exploitation of sea trout,<i>Salmo trutta,</i>in rivers sharing an estuary in south-west England

Fisheries Management and Ecology, Jul 1, 2016

The version presented here may differ from the published version. If citing, you are advised to c... more

Development of SNP markers derived from RAD sequencing for Atlantic salmon (Salmo salar L.) inhabiting the rivers of southern England

Conservation Genetics Resources, May 20, 2021

The rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlanti... more The rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlantic salmon that have suffered dramatic declines in numbers over the last 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 94 single nucleotide polymorphism (SNP) loci for salmon from this region and investigate their applicability and variability in both target (i.e. southern English) and non-target populations. The SNP loci will be useful for population genetic and assignment studies on Atlantic salmon within the UK and beyond.

The trypanosomatid evolution workshop London School of Hygiene and Tropical Medicine

Memorias Do Instituto Oswaldo Cruz, Aug 1, 2000

The trypanosome evolution workshop, a joint meeting of the University of Exeter and the London Sc... more The trypanosome evolution workshop, a joint meeting of the University of Exeter and the London School of Hygiene and Tropical Medicine, focused on topics relating to trypanosomatid and vector evolution. The meeting, sponsored by The Wellcome Trust, The Special Programme for Research and Training in Tropical Disease of World Health Organization and the British Section of the Society of Protozoologists, brought together an international group of experts who presented papers on a wide range of topics including parasite and vector phylogenies, molecular methodology and relevant biogeographical data.

Atlantic salmon<i>Salmo salar</i>in the chalk streams of England are genetically unique

Journal of Fish Biology, Jan 31, 2018

Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.

The Evolution of Salivarian Trypanosomes

Memorias Do Instituto Oswaldo Cruz, Mar 1, 1999

The Trypanosomes of Mammals, Blackwell, Oxford, 749 pp.) divided mammalian trypanosomes into two ... more The Trypanosomes of Mammals, Blackwell, Oxford, 749 pp.) divided mammalian trypanosomes into two sections, the Salivaria and the Stercoraria. The Salivaria comprises all the African tsetse-transmitted trypanosomes of mammals, while the Stercoraria includes mammalian trypanosomes transmitted by the posterior route. However, the status of other tsetsetransmitted species, e.g. Trypanosoma grayi from crocodiles, and of other trypanosomes transmitted by the anterior route, e.g. T. rangeli from South America and leech transmitted trypanosomes, remain under debate. To some extent such unknowns are linked to the limitations of the morphological and transmission characters used in early investigations of trypanosome taxonomy and evolution. With the wealth of molecular sequence data now available, particularly for the phylogenetically versatile 18S rRNA gene (ML Sogin et al. 1986 Proc Natl Acad Sci USA 83: 1383-1387) some of these questions may now be fruitfully re-addressed. Accordingly, we undertook phylogenetic analysis of published ribosomal RNA 18S sequences, supplemented with data from our own studies, our aim being to re-examine the evolutionary relationships of Salivarian trypanosomes of mammals and other vertebrates.

Atlantic Salmon at Risk: Apparent Rapid Declines in Effective Population Size in Southern European Populations

Transactions of The American Fisheries Society, May 21, 2011

Populations of southern European Atlantic salmon Salmo salar are subjected to exploitation by spo... more Populations of southern European Atlantic salmon Salmo salar are subjected to exploitation by sportfishing and exhibit evidence of dramatic catch reduction for the same fishing effort over recent history. We employed nine microsatellite loci as markers to estimate effective population sizes of Atlantic salmon in five rivers of northern Spain for comparison with 1990s data describing the same populations; marked declines in effective population sizes over the last decade were detected, and a reduced census size is proposed to be one of the probable causes. These estimates highlight the endangered status of the Atlantic salmon populations in northern Spain. A reduction in fishing effort and an increase in protective measures are recommended for the conservation of these fragile populations at the southernmost edge of the species’ natural distribution.

Atlantic Salmon at Risk: Apparent Rapid Declines in Effective Population Size in Southern European Populations

Transactions of The American Fisheries Society, May 21, 2011

Populations of southern European Atlantic salmon Salmo salar are subjected to exploitation by spo... more Populations of southern European Atlantic salmon Salmo salar are subjected to exploitation by sportfishing and exhibit evidence of dramatic catch reduction for the same fishing effort over recent history. We employed nine microsatellite loci as markers to estimate effective population sizes of Atlantic salmon in five rivers of northern Spain for comparison with 1990s data describing the same populations; marked declines in effective population sizes over the last decade were detected, and a reduced census size is proposed to be one of the probable causes. These estimates highlight the endangered status of the Atlantic salmon populations in northern Spain. A reduction in fishing effort and an increase in protective measures are recommended for the conservation of these fragile populations at the southernmost edge of the species’ natural distribution.

Reserve design for uncertain responses of coral reefs to

ABSTRACT Rising sea temperatures cause mass coral bleaching and threaten reefs worldwide. We show... more ABSTRACT Rising sea temperatures cause mass coral bleaching and threaten reefs worldwide. We show how maps of variations in thermal stress can be used to help manage reefs for climate change. We map proxies of chronic and acute thermal stress and develop evidence-based hypotheses for the future response of corals to each stress regime. We then incorporate spatially realistic predictions of larval connectivity among reefs of the Bahamas and apply novel reserve design algorithms to create reserve networks for a changing climate. We show that scales of larval dispersal are large enough to connect reefs from desirable thermal stress regimes into a reserve network. Critically, we find that reserve designs differ according to the anticipated scope for phenotypic and genetic adaptation in corals, which remains uncertain. Attempts to provide a complete reserve design that hedged against different evolutionary outcomes achieved limited success, which emphasises the importance of considering the scope for adaptation explicitly. Nonetheless, 15% of reserve locations were selected under all evolutionary scenarios, making them a high priority for early designation. Our approach allows new insights into coral holobiont adaptation to be integrated directly into an adaptive approach to management.

Research article

Genetic stock identification of sea trout (Salmo trutta L.) along the British North Sea Coast shows prevalent long-distance migration

ICES Journal of Marine Science, 2021

Knowledge of migration behaviour and spatio-temporal habitat use is important for management and ... more Knowledge of migration behaviour and spatio-temporal habitat use is important for management and conservation, not least for diadromous species where population dynamics are affected by processes occurring in both freshwater and marine habitats. Sampling from a commercial capture fishery for the ecologically and economically important salmonid Salmo trutta L. we genotyped 189 single nucleotide polymorphisms and carried out genetic assignment of origin for 916 migratory sea trout sampled along ∼500 km of Britain’s North Sea coast. Population contributions to stocks showed strong geographical differences. Trout from rivers in the northern part of this coast (Tweed, Aln, Coquet, and Tyne) contributed the majority of migrants, irrespective of location, but fish from local rivers contributed to catches in most locations. Almost all (99%) trout assigned to native British populations and a large proportion (34%) of the sampled catches originated in rivers more than 100 km from capture site...

Harnessing genomics to fast-track genetic improvement in aquaculture

Nature Reviews Genetics, 2020

Aquaculture is the fastest growing farmed food sector and will soon become the primary source of ... more Aquaculture is the fastest growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crops and livestock, production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.

Small coastal streams—Critical reservoirs of genetic diversity for trout (Salmo truttaL.) in the face of increasing anthropogenic stressors

Ecology and Evolution, 2020

Identifying patterns of intraspecific genetic diversity and investigating the processes that gene... more Identifying patterns of intraspecific genetic diversity and investigating the processes that generate such patterns is a central tenet of molecular ecology and conservation genetics. It is clear that both historical events, such as the Quaternary glaciations and more recent anthropogenic impacts , have had an influence on levels and patterns of variation. Such factors affect the interplay between the key processes of gene flow, drift, and selection in determining the patterns and levels of variation seen in present day populations. Moreover, in small populations-whether wild , managed, for example, zoo populations , or domesticated -the effects of these factors are typically amplified, leading to increasingly rapid losses of genetic diversity

RAD-Seq Analysis and in situ Monitoring of Nassau Grouper Reveal Fine-Scale Population Structure and Origins of Aggregating Fish

Frontiers in Marine Science, 2020

Numerical taxonomy of Trypanozoon based on polymorphisms in a reduced range of enzymes

Parasitology, 1992

SUMMARYNumerical analyses of Trypanozoon taxonomy are presented, based on the isoenzyme data of S... more SUMMARYNumerical analyses of Trypanozoon taxonomy are presented, based on the isoenzyme data of Stevens et al. (1992). The previous study used a reduced range of enzymes compared with earlier work; the analyses indicate the value of this rationalized system. Both recently isolated trypanosome stocks and previously studied populations were included, allowing detailed comparison with earlier studies. Relationships between zymodemes were calculated with an improved similarity coefficient program, using Jaccard's coefficient (1908), and by Nei's method (1972). Dendrograms were constructed from the matrices produced with the group-average method. The groupings produced by both numerical methods were in close agreement, and the clusters of related principal zymodemes largely matched the species, subspecies and strain groups proposed by previous workers. Trypanozoon biochemical taxonomy is reviewed and the groupings reinforced by this study are: the mainly East African strain group...

Riverine fish diversity varies according to geographical isolation and land use modification

Ecology and Evolution, 2017

The version presented here may differ from the published version. If citing, you are advised to c... more

Lost in parameter space: a road map for stacks

Methods in Ecology and Evolution, 2017

Summary Restriction site‐Associated DNA sequencing (RAD‐seq) has become a widely adopted method f... more Summary Restriction site‐Associated DNA sequencing (RAD‐seq) has become a widely adopted method for genotyping populations of model and non‐model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program stacks. Using three empirical RAD‐seq datasets, we demonstrate a method for optimising a de novo assembly of loci using stacks. By iterating values of the program's main parameters and plotting resultant core metrics for visualisation, researchers can gain a much better understanding of their dataset and select an optimal set of parameters; we present the 80% rule as a generally effective method to select the core parameters for stacks. Visualisation of the metrics plotted for the three RAD‐seq datasets shows that they differ in the optimal parameters that should be used to maximise the amount of available biological information. We also demonstrate that building loci de novo and then integrating...

A low‐density single nucleotide polymorphism panel for brown trout ( <i>Salmo trutta</i> L.) suitable for exploring genetic diversity at a range of spatial scales

Journal of Fish Biology, Nov 25, 2022

The version presented here may differ from the published version. If citing, you are advised to c... more

A tale of two hatcheries: Assessing bias in the hatchery process for Atlantic salmon (Salmo salar L.)

Aquaculture, Oct 1, 2014

Stock enhancement of Atlantic salmon (Salmo salar L.), a fish of considerable 39 economic and soc... more Stock enhancement of Atlantic salmon (Salmo salar L.), a fish of considerable 39 economic and social importance, is commonplace. Supportive-breeding is a well-40 recognised method of enhancement which, when compared with traditional hatchery 41 practices, is thought to reduce the severity of selection pressures on broodstock fish. 42 Critically, in supportive-breeding programmes, the eggs and sperm used in the 43 breeding process are taken from wild adult fish originating from the same catchment 44 that resulting juvenile fish are subsequently stocked into, thereby avoiding problems 45 associated with a lack of local adaptation in the stocked fish. Previous studies have 46 indicated that sex bias during the hatchery process may result in reduced genetic 47 diversity of the offspring. Utilising 16 microsatellite loci and two expressed sequence 48 tag (EST) loci, we examined progeny from two hatcheries located on the rivers Exe and 49 Tamar in southwest England, assessing the genetic diversity and parental contribution 50 at each. Two strains were assessed within each hatchery. Genetic diversity was found 51 to be reduced in offspring compared with that of the parent fish. This is likely the result 52 of utilising a small number of broodstock in combination with parental bias. In the four 53 hatchery strains studied (Bar, LEx, Lyd and TXL), parental contribution ranged between 54 2.1-29.2%, 12.2-51.0%, 2.0-70.0% and 4.0-40.0%, respectively. If this practice is to 55 be continued, efforts should be made to improve adherence to national rearing 56 guidelines by increasing the number of broodstock fish utilised and ensuring a more 57 balanced contribution of all adults during the crossing process. Ultimately, we suggest 58 a need to review the suitability of current national Atlantic salmon hatchery guidelines, 59 particularly with regard to their use and relevance in small European rearing systems. 60

Harnessing genomics to fast-track genetic improvement in aquaculture

Nature Reviews Genetics, Apr 16, 2020

Aquaculture is the fastest growing farmed food sector and will soon become the primary source of ... more Aquaculture is the fastest growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crops and livestock, production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.

An improved genetic sex test for Atlantic salmon (Salmo salar L.)

Conservation Genetics Resources, Apr 30, 2019

Accurate determination of sex ratios is an important metric for the conservation and management o... more Accurate determination of sex ratios is an important metric for the conservation and management of wild Atlantic salmon populations. Previously published primers for a male-specific gene were shown to be unreliable at determining sex due to the presence of deletions in the forward primer-binding site. A new forward primer, used in conjunction with the existing reverse primer, greatly improved reliability of the genetic test, correctly assigning gender in samples of known sex. Using DNA extracted from both contemporary and archive tissues, comparison between the two primer sets screened on collections of unknown sex ratio showed significant discrepancies in the number of males identified. The new primer will help improve the management and conservation of Atlantic salmon by providing accurate sex ratios for the setting of Conservation Limits.

Investigating patterns of straying and mixed stock exploitation of sea trout,<i>Salmo trutta,</i>in rivers sharing an estuary in south-west England

Fisheries Management and Ecology, Jul 1, 2016

The version presented here may differ from the published version. If citing, you are advised to c... more

Development of SNP markers derived from RAD sequencing for Atlantic salmon (Salmo salar L.) inhabiting the rivers of southern England

Conservation Genetics Resources, May 20, 2021

The rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlanti... more The rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlantic salmon that have suffered dramatic declines in numbers over the last 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 94 single nucleotide polymorphism (SNP) loci for salmon from this region and investigate their applicability and variability in both target (i.e. southern English) and non-target populations. The SNP loci will be useful for population genetic and assignment studies on Atlantic salmon within the UK and beyond.

The trypanosomatid evolution workshop London School of Hygiene and Tropical Medicine

Memorias Do Instituto Oswaldo Cruz, Aug 1, 2000

The trypanosome evolution workshop, a joint meeting of the University of Exeter and the London Sc... more The trypanosome evolution workshop, a joint meeting of the University of Exeter and the London School of Hygiene and Tropical Medicine, focused on topics relating to trypanosomatid and vector evolution. The meeting, sponsored by The Wellcome Trust, The Special Programme for Research and Training in Tropical Disease of World Health Organization and the British Section of the Society of Protozoologists, brought together an international group of experts who presented papers on a wide range of topics including parasite and vector phylogenies, molecular methodology and relevant biogeographical data.

Atlantic salmon<i>Salmo salar</i>in the chalk streams of England are genetically unique

Journal of Fish Biology, Jan 31, 2018

Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.

The Evolution of Salivarian Trypanosomes

Memorias Do Instituto Oswaldo Cruz, Mar 1, 1999

The Trypanosomes of Mammals, Blackwell, Oxford, 749 pp.) divided mammalian trypanosomes into two ... more The Trypanosomes of Mammals, Blackwell, Oxford, 749 pp.) divided mammalian trypanosomes into two sections, the Salivaria and the Stercoraria. The Salivaria comprises all the African tsetse-transmitted trypanosomes of mammals, while the Stercoraria includes mammalian trypanosomes transmitted by the posterior route. However, the status of other tsetsetransmitted species, e.g. Trypanosoma grayi from crocodiles, and of other trypanosomes transmitted by the anterior route, e.g. T. rangeli from South America and leech transmitted trypanosomes, remain under debate. To some extent such unknowns are linked to the limitations of the morphological and transmission characters used in early investigations of trypanosome taxonomy and evolution. With the wealth of molecular sequence data now available, particularly for the phylogenetically versatile 18S rRNA gene (ML Sogin et al. 1986 Proc Natl Acad Sci USA 83: 1383-1387) some of these questions may now be fruitfully re-addressed. Accordingly, we undertook phylogenetic analysis of published ribosomal RNA 18S sequences, supplemented with data from our own studies, our aim being to re-examine the evolutionary relationships of Salivarian trypanosomes of mammals and other vertebrates.

Atlantic Salmon at Risk: Apparent Rapid Declines in Effective Population Size in Southern European Populations

Transactions of The American Fisheries Society, May 21, 2011

Populations of southern European Atlantic salmon Salmo salar are subjected to exploitation by spo... more Populations of southern European Atlantic salmon Salmo salar are subjected to exploitation by sportfishing and exhibit evidence of dramatic catch reduction for the same fishing effort over recent history. We employed nine microsatellite loci as markers to estimate effective population sizes of Atlantic salmon in five rivers of northern Spain for comparison with 1990s data describing the same populations; marked declines in effective population sizes over the last decade were detected, and a reduced census size is proposed to be one of the probable causes. These estimates highlight the endangered status of the Atlantic salmon populations in northern Spain. A reduction in fishing effort and an increase in protective measures are recommended for the conservation of these fragile populations at the southernmost edge of the species’ natural distribution.

Atlantic Salmon at Risk: Apparent Rapid Declines in Effective Population Size in Southern European Populations

Transactions of The American Fisheries Society, May 21, 2011

Populations of southern European Atlantic salmon Salmo salar are subjected to exploitation by spo... more Populations of southern European Atlantic salmon Salmo salar are subjected to exploitation by sportfishing and exhibit evidence of dramatic catch reduction for the same fishing effort over recent history. We employed nine microsatellite loci as markers to estimate effective population sizes of Atlantic salmon in five rivers of northern Spain for comparison with 1990s data describing the same populations; marked declines in effective population sizes over the last decade were detected, and a reduced census size is proposed to be one of the probable causes. These estimates highlight the endangered status of the Atlantic salmon populations in northern Spain. A reduction in fishing effort and an increase in protective measures are recommended for the conservation of these fragile populations at the southernmost edge of the species’ natural distribution.

Reserve design for uncertain responses of coral reefs to

ABSTRACT Rising sea temperatures cause mass coral bleaching and threaten reefs worldwide. We show... more ABSTRACT Rising sea temperatures cause mass coral bleaching and threaten reefs worldwide. We show how maps of variations in thermal stress can be used to help manage reefs for climate change. We map proxies of chronic and acute thermal stress and develop evidence-based hypotheses for the future response of corals to each stress regime. We then incorporate spatially realistic predictions of larval connectivity among reefs of the Bahamas and apply novel reserve design algorithms to create reserve networks for a changing climate. We show that scales of larval dispersal are large enough to connect reefs from desirable thermal stress regimes into a reserve network. Critically, we find that reserve designs differ according to the anticipated scope for phenotypic and genetic adaptation in corals, which remains uncertain. Attempts to provide a complete reserve design that hedged against different evolutionary outcomes achieved limited success, which emphasises the importance of considering the scope for adaptation explicitly. Nonetheless, 15% of reserve locations were selected under all evolutionary scenarios, making them a high priority for early designation. Our approach allows new insights into coral holobiont adaptation to be integrated directly into an adaptive approach to management.

Research article

Genetic stock identification of sea trout (Salmo trutta L.) along the British North Sea Coast shows prevalent long-distance migration

ICES Journal of Marine Science, 2021

Knowledge of migration behaviour and spatio-temporal habitat use is important for management and ... more Knowledge of migration behaviour and spatio-temporal habitat use is important for management and conservation, not least for diadromous species where population dynamics are affected by processes occurring in both freshwater and marine habitats. Sampling from a commercial capture fishery for the ecologically and economically important salmonid Salmo trutta L. we genotyped 189 single nucleotide polymorphisms and carried out genetic assignment of origin for 916 migratory sea trout sampled along ∼500 km of Britain’s North Sea coast. Population contributions to stocks showed strong geographical differences. Trout from rivers in the northern part of this coast (Tweed, Aln, Coquet, and Tyne) contributed the majority of migrants, irrespective of location, but fish from local rivers contributed to catches in most locations. Almost all (99%) trout assigned to native British populations and a large proportion (34%) of the sampled catches originated in rivers more than 100 km from capture site...

Harnessing genomics to fast-track genetic improvement in aquaculture

Nature Reviews Genetics, 2020

Aquaculture is the fastest growing farmed food sector and will soon become the primary source of ... more Aquaculture is the fastest growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crops and livestock, production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.

Small coastal streams—Critical reservoirs of genetic diversity for trout (Salmo truttaL.) in the face of increasing anthropogenic stressors

Ecology and Evolution, 2020

Identifying patterns of intraspecific genetic diversity and investigating the processes that gene... more Identifying patterns of intraspecific genetic diversity and investigating the processes that generate such patterns is a central tenet of molecular ecology and conservation genetics. It is clear that both historical events, such as the Quaternary glaciations and more recent anthropogenic impacts , have had an influence on levels and patterns of variation. Such factors affect the interplay between the key processes of gene flow, drift, and selection in determining the patterns and levels of variation seen in present day populations. Moreover, in small populations-whether wild , managed, for example, zoo populations , or domesticated -the effects of these factors are typically amplified, leading to increasingly rapid losses of genetic diversity

RAD-Seq Analysis and in situ Monitoring of Nassau Grouper Reveal Fine-Scale Population Structure and Origins of Aggregating Fish

Frontiers in Marine Science, 2020

Numerical taxonomy of Trypanozoon based on polymorphisms in a reduced range of enzymes

Parasitology, 1992

SUMMARYNumerical analyses of Trypanozoon taxonomy are presented, based on the isoenzyme data of S... more SUMMARYNumerical analyses of Trypanozoon taxonomy are presented, based on the isoenzyme data of Stevens et al. (1992). The previous study used a reduced range of enzymes compared with earlier work; the analyses indicate the value of this rationalized system. Both recently isolated trypanosome stocks and previously studied populations were included, allowing detailed comparison with earlier studies. Relationships between zymodemes were calculated with an improved similarity coefficient program, using Jaccard's coefficient (1908), and by Nei's method (1972). Dendrograms were constructed from the matrices produced with the group-average method. The groupings produced by both numerical methods were in close agreement, and the clusters of related principal zymodemes largely matched the species, subspecies and strain groups proposed by previous workers. Trypanozoon biochemical taxonomy is reviewed and the groupings reinforced by this study are: the mainly East African strain group...

Riverine fish diversity varies according to geographical isolation and land use modification

Ecology and Evolution, 2017

The version presented here may differ from the published version. If citing, you are advised to c... more

Lost in parameter space: a road map for stacks

Methods in Ecology and Evolution, 2017

Summary Restriction site‐Associated DNA sequencing (RAD‐seq) has become a widely adopted method f... more Summary Restriction site‐Associated DNA sequencing (RAD‐seq) has become a widely adopted method for genotyping populations of model and non‐model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program stacks. Using three empirical RAD‐seq datasets, we demonstrate a method for optimising a de novo assembly of loci using stacks. By iterating values of the program's main parameters and plotting resultant core metrics for visualisation, researchers can gain a much better understanding of their dataset and select an optimal set of parameters; we present the 80% rule as a generally effective method to select the core parameters for stacks. Visualisation of the metrics plotted for the three RAD‐seq datasets shows that they differ in the optimal parameters that should be used to maximise the amount of available biological information. We also demonstrate that building loci de novo and then integrating...