Overview
I am an evolutionary biologist with interests in the use of population genomics in understanding how species adapt, particularly in a conservation and management context. I am especially interested in the use of genome-wide signals generated by massive parallel sequencing applications: whole-genome sequencing, RADseq and RNAseq.
I am currently a postdoctoral research associate in the Fraser Lab working on a NERC-NSF funded project investigating the ecological genomics of adaptive polymorphism in the Trinidadian guppy (Poecilia reticulata).
Qualifications
PhD Molecular Ecology and Evolution, University of Exeter
BSc Ecology and Conservation, University of Sussex
Career
POSTDOCTORAL RESEARCHER October 2017-present University of Sussex (1 year), transfer to University of Exeter
Principal Investigator: Dr Bonnie Fraser
Funder: Natural Environment Research Council
Role: Ecological genomics of the Trinidadian guppy (Poecilia reticulata). Populations genomics of balanced polymorphisms
POSTDOCTORAL RESEARCHER March 2017-October 2017 University of Exeter
Principal Investigator: Professor Chris Thornton & Dr Jamie Stevens
Funder: The Leverhulme Trust
LABORATORY VISIT March-May 2016 University of Illinois
Principal Investigator: Dr Julian Catchen
Funder: The Genetics Society, Santander
PHD IN MOLECULAR
ECOLOGY AND EVOLUTION September 2012-March 2017 University of Exeter
PhD Supervisors: Dr Jamie Stevens & Dr Eduarda Santos
Funder: Environment Agency, Westcountry Rivers Trust and University of Exeter
Thesis title: Brown trout and toxic metals: Local adaptation to the legacy of Britain’s mining history
BSC ECOLOGY AND CONSERVATION 2009-2012 University of Sussex
First Class Honours
Links
Research group links
Publications
Key publications | Publications by category | Publications by year
Publications by category
Journal articles
Whiting JR, Paris JR, van der Zee MJ, Parsons PJ, Weigel D, Fraser BA (In Press). Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies.
Abstract:
Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
ABSTRACTStudies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signalling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.
Abstract.
Lange A, Paris JR, Gharbi K, Cézard T, Miyagawa S, Iguchi T, Studholme DJ, Tyler CR (2020). A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (. Rutilus rutilus. ).
Molecular Ecology Resources,
20(4), 1007-1022.
Full text.
Fraser BA, Whiting JR, Paris JR, Weadick CJ, Parsons PJ, Charlesworth D, Bergero R, Bemm F, Hoffmann M, Kottler VA, et al (2020). Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata).
Genome Biology and Evolution,
12(10), 1789-1805.
Abstract:
Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)
Abstract
. Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favor the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male color patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low-predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
Abstract.
Full text.
Sherman KD, Paris J, King RA, Moore KA, Dahlgren CP, Knowles LC, Stump K, Tyler CR, Stevens JR (2020). RAD-Seq Analysis and in situ Monitoring of Nassau Grouper Reveal Fine-Scale Population Structure and Origins of Aggregating Fish.
FRONTIERS IN MARINE SCIENCE,
7 Author URL.
Full text.
Paris JR, Usher J (2019). Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis.
Scientific Reports,
9(1).
Abstract:
Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis
© 2019, the Author(s). Metal pollution has made a significant impact on the earth’s ecosystems and tolerance to metals in a wide variety of species has evolved. Metallothioneins, a group of cysteine-rich metal-ion binding proteins, are known to be a key physiological mechanism in regulating protection against metal toxicity. Many rivers across the southwest of England are detrimentally affected by metal pollution, but brown trout (Salmo trutta L.) populations are known to reside within them. In this body of work, two isoforms of metallothionein (MetA and MetB) isolated from trout occupying a polluted and a control river are examined. Using synthetic genetic array (SGA) analyses in the model yeast, Saccharomyces cerevisiae, functional genomics is used to explore the role of metallothionein isoforms in driving metal tolerance. By harnessing this experimental system, S. cerevisiae is used to (i) determine the genetic interaction maps of MetA and MetB isoforms; (ii) identify differences between the genetic interactions in both isoforms and (iii) demonstrate that pre-exposure to metals in metal-tolerant trout influences these interactions. By using a functional genomics approach leveraged from the model yeast Saccharomyces cerevisiae, we demonstrate how such approaches could be used in understanding the ecology and evolution of a non-model species.
Abstract.
Full text.
Paris JR, Usher J (2019). Publisher Correction: Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis.
Sci Rep,
9(1).
Abstract:
Publisher Correction: Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis.
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Abstract.
Author URL.
Full text.
Ikediashi C, Paris JR, King RA, Beaumont WRC, Ibbotson A, Stevens JR (2018). Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.
J Fish Biol,
92(3), 621-641.
Abstract:
Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.
Recent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar.
Abstract.
Author URL.
Full text.
Paris JR, Sherman KD, Bell E, Boulenger C, Delord C, El-Mahdi MBM, Fairfield EA, Griffiths AM, Gutmann Roberts C, Hedger RD, et al (2018). Understanding and managing fish populations: keeping the toolbox fit for purpose.
J Fish Biol,
92(3), 727-751.
Abstract:
Understanding and managing fish populations: keeping the toolbox fit for purpose.
Wild fish populations are currently experiencing unprecedented pressures, which are projected to intensify in the coming decades. Developing a thorough understanding of the influences of both biotic and abiotic factors on fish populations is a salient issue in contemporary fish conservation and management. During the 50th Anniversary Symposium of the Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017, scientists from diverse research backgrounds gathered to discuss key topics under the broad umbrella of 'Understanding Fish Populations'. Below, the output of one such discussion group is detailed, focusing on tools used to investigate natural fish populations. Five main groups of approaches were identified: tagging and telemetry; molecular tools; survey tools; statistical and modelling tools; tissue analyses. The appraisal covered current challenges and potential solutions for each of these topics. In addition, three key themes were identified as applicable across all tool-based applications. These included data management, public engagement, and fisheries policy and governance. The continued innovation of tools and capacity to integrate interdisciplinary approaches into the future assessment and management of fish populations is highlighted as an important focus for the next 50 years of fisheries research.
Abstract.
Author URL.
Full text.
Paris JR, Stevens JR, Catchen JM (2017). Lost in parameter space: a road map for. stacks.
Methods in Ecology and Evolution,
8(10), 1360-1373.
Full text.
Paris JR, King RA, Stevens JR (2015). Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations.
Evolutionary ApplicationsAbstract:
Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations
Humans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well-defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal-impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal-impacted trout populations have low genetic diversity and have experienced severe population declines. Metal-river trout populations are genetically distinct from clean-river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal-impacted populations from clean-river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human-altered landscapes can change the genetic makeup of a species.
Abstract.
Full text.
Publications by year
In Press
Whiting JR, Paris JR, van der Zee MJ, Parsons PJ, Weigel D, Fraser BA (In Press). Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies.
Abstract:
Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
ABSTRACTStudies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signalling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.
Abstract.
2020
Lange A, Paris JR, Gharbi K, Cézard T, Miyagawa S, Iguchi T, Studholme DJ, Tyler CR (2020). A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (. Rutilus rutilus. ).
Molecular Ecology Resources,
20(4), 1007-1022.
Full text.
Fraser BA, Whiting JR, Paris JR, Weadick CJ, Parsons PJ, Charlesworth D, Bergero R, Bemm F, Hoffmann M, Kottler VA, et al (2020). Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata).
Genome Biology and Evolution,
12(10), 1789-1805.
Abstract:
Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)
Abstract
. Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favor the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male color patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low-predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
Abstract.
Full text.
Sherman KD, Paris J, King RA, Moore KA, Dahlgren CP, Knowles LC, Stump K, Tyler CR, Stevens JR (2020). RAD-Seq Analysis and in situ Monitoring of Nassau Grouper Reveal Fine-Scale Population Structure and Origins of Aggregating Fish.
FRONTIERS IN MARINE SCIENCE,
7 Author URL.
Full text.
2019
Paris JR, Usher J (2019). Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis.
Scientific Reports,
9(1).
Abstract:
Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis
© 2019, the Author(s). Metal pollution has made a significant impact on the earth’s ecosystems and tolerance to metals in a wide variety of species has evolved. Metallothioneins, a group of cysteine-rich metal-ion binding proteins, are known to be a key physiological mechanism in regulating protection against metal toxicity. Many rivers across the southwest of England are detrimentally affected by metal pollution, but brown trout (Salmo trutta L.) populations are known to reside within them. In this body of work, two isoforms of metallothionein (MetA and MetB) isolated from trout occupying a polluted and a control river are examined. Using synthetic genetic array (SGA) analyses in the model yeast, Saccharomyces cerevisiae, functional genomics is used to explore the role of metallothionein isoforms in driving metal tolerance. By harnessing this experimental system, S. cerevisiae is used to (i) determine the genetic interaction maps of MetA and MetB isoforms; (ii) identify differences between the genetic interactions in both isoforms and (iii) demonstrate that pre-exposure to metals in metal-tolerant trout influences these interactions. By using a functional genomics approach leveraged from the model yeast Saccharomyces cerevisiae, we demonstrate how such approaches could be used in understanding the ecology and evolution of a non-model species.
Abstract.
Full text.
Paris JR, Usher J (2019). Publisher Correction: Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis.
Sci Rep,
9(1).
Abstract:
Publisher Correction: Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis.
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Abstract.
Author URL.
Full text.
2018
Ikediashi C, Paris JR, King RA, Beaumont WRC, Ibbotson A, Stevens JR (2018). Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.
J Fish Biol,
92(3), 621-641.
Abstract:
Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.
Recent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar.
Abstract.
Author URL.
Full text.
Paris JR, Sherman KD, Bell E, Boulenger C, Delord C, El-Mahdi MBM, Fairfield EA, Griffiths AM, Gutmann Roberts C, Hedger RD, et al (2018). Understanding and managing fish populations: keeping the toolbox fit for purpose.
J Fish Biol,
92(3), 727-751.
Abstract:
Understanding and managing fish populations: keeping the toolbox fit for purpose.
Wild fish populations are currently experiencing unprecedented pressures, which are projected to intensify in the coming decades. Developing a thorough understanding of the influences of both biotic and abiotic factors on fish populations is a salient issue in contemporary fish conservation and management. During the 50th Anniversary Symposium of the Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017, scientists from diverse research backgrounds gathered to discuss key topics under the broad umbrella of 'Understanding Fish Populations'. Below, the output of one such discussion group is detailed, focusing on tools used to investigate natural fish populations. Five main groups of approaches were identified: tagging and telemetry; molecular tools; survey tools; statistical and modelling tools; tissue analyses. The appraisal covered current challenges and potential solutions for each of these topics. In addition, three key themes were identified as applicable across all tool-based applications. These included data management, public engagement, and fisheries policy and governance. The continued innovation of tools and capacity to integrate interdisciplinary approaches into the future assessment and management of fish populations is highlighted as an important focus for the next 50 years of fisheries research.
Abstract.
Author URL.
Full text.
2017
Paris JR, Stevens JR, Catchen JM (2017). Lost in parameter space: a road map for. stacks.
Methods in Ecology and Evolution,
8(10), 1360-1373.
Full text.
2015
Paris JR, King RA, Stevens JR (2015). Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations.
Evolutionary ApplicationsAbstract:
Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations
Humans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well-defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal-impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal-impacted trout populations have low genetic diversity and have experienced severe population declines. Metal-river trout populations are genetically distinct from clean-river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal-impacted populations from clean-river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human-altered landscapes can change the genetic makeup of a species.
Abstract.
Full text.
Josephine_Paris Details from cache as at 2021-03-02 15:13:02
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Teaching
2020 Co-director, Workshop on Genomics, evomics
2019 Co-director, Workshop on Genomics, evomics
2013 – 2017 Graduate Teaching Assistant, University of Exeter BIO2081: Bahamas Coral Reef Field Trip
2013 – 2017 Co-organiser, Population Variation Genetics, Earlham Institute (formerly The Genome Analysis Centre), Norwich, UK
2014 – 2018 Teaching Assistant, Workshop on Genomics, evomics, Czech Republic
2017 Co-organiser, RADseq Data Analysis, Physalia, Berlin, Germany
2016 Co-organiser, RAD-Sequencing analysis workshop, NTNU University Museum, Trondheim, Norway
2015 Co-organiser, Advanced course in RADSeq analyses and data interpretation, Lund University, GENECO, Sweden
2015 Teaching Assistant, Wellcome Trust Short Read Genomics Workshop, Exeter, Devon, UK
2014 Teaching Assistant, NERC Population Genomics and Metagenomics Workshop, Devon, UK
