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Dr Bonnie Fraser

Dr Bonnie Fraser

Senior Lecturer

 3406

 Hatherly C11

 

Hatherly Building, University of Exeter, Prince of Wales Road, Exeter, EX4 4PS, UK

Overview

The main goal of our research group is to investigate how adaptation to the local environment shapes evolution at the genomic level. The connections between genotype, phenotype, and selection are at the centre of evolutionary biology. By studying these connections, our research can begin to address fundamental questions in evolutionary biology. 

Our research focuses on the Trinidadian guppy (Poecilia reticulata), a fish that has long served as a model system for evolutionary and ecological research. We explore local adaptation in this system using an interdisciplinary approach that combines population genomics, quantitative genetics, behavioural ecology, and experimental evolution.

Qualifications

2004 BSc. Marine and Freshwater Biology, University of Guelph

2009 PhD Biology, University of Western Ontario

Career

2018 - present Senior Lecturer University of Exeter

2016 - 2018 Lecturer, University of Sussex

2011 - 2016 Postdoctoral Research Fellow, Max Planck Institute for Developmental Biology

2009 - 2011 Postdoctoral Research Fellow, Florida State University and University of Toronto

Research group links

Research

Research interests

Local adaptation in the Trinidadian guppy

Guppies in the Northern Mountain Range of Trinidad offer a natural laboratory for studying evolutionary change and the genetics of adaptation.  Waterfalls separate the rivers the guppies call home into downstream stretches, which contain many predators, and upstream stretches, where the guppies live relatively free of predation.  In response to this naturally replicated environmental gradient, guppies from low predation sites have evolved to be larger and more colourful, and to display less anti-predator behaviour.  We are exploring how this convergent evolution plays out at the genomic level, using a combination of population genomics, quantitative genetics, and laboratory evolution experiments. 

How do populations adapt to new environments?

The simple ecology of the guppy’s home streams in Trinidad allows for in situ experimental studies of adaptation.  Guppy populations that were moved from high predation to low predation sites have shown consistent and rapid evolutionary responses to reduced predation.  By examining genomic differences between experimental populations and their source populations, and between experimental populations established at different time points, we hope to learn more about which types of molecular changes are important in the process of adaptation. 

What maintains variation in natural populations?

Selection is expected to eliminate genetic diversity within populations.  Surprisingly, guppies exhibit high within-population genetic diversity for male body colour even though it is subject to strong natural and sexual selection.  Previous studies suggest that two different behavioural mechanisms might explain this unusual finding: (1) learned hunting behaviour by one of the guppy’s predators, the killifish Rivulus hartii, and (2) female mate choice for males with unfamiliar colour patterns.  We are using a combination of ecological, behavioural, and genomic data to test alternative hypotheses for the role of behaviour in maintaining variation in guppy colouration, and to identify the genes targeted by behaviour-mediated selection.

Publications

Key publications | Publications by category | Publications by year

Publications by category


Journal articles

Paris JR, Whiting JR, Daniel MJ, Obiol JF, Parsons PJ, van der Zee MJ, Wheat CW, Hughes KA, Fraser BA (In Press). A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy.  Abstract.
Whiting JR, Paris JR, van der Zee MJ, Fraser BA (In Press). AF-vapeR: a multivariate genome scan for detecting parallel evolution using allele frequency change vectors.  Abstract.
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.
Whiting JR, Paris JR, Parsons PJ, Matthews S, Reynoso Y, Hughes KA, Reznick D, Fraser BA (In Press). On the genetic architecture of rapidly adapting and convergent life history traits in guppies.  Abstract.
Paris JR, Whiting JR, Daniel MJ, Ferrer Obiol J, Parsons PJ, van der Zee MJ, Wheat CW, Hughes KA, Fraser BA (2022). A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy. Nature Communications, 13(1). Abstract.
Whiting JR, Paris JR, Parsons PJ, Matthews S, Reynoso Y, Hughes KA, Reznick D, Fraser BA (2022). On the genetic architecture of rapidly adapting and convergent life history traits in guppies. Heredity, 128(4), 250-260. Abstract.
van der Zee MJ, Whiting JR, Paris JR, Bassar RD, Travis J, Weigel D, Reznick DN, Fraser BA (2022). Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata). Evolution Letters, 6(2), 149-161. Abstract.
Whiting JR, Paris JR, van der Zee MJ, Parsons PJ, Weigel D, Fraser BA (2021). Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies. PLOS Genetics, 17(5), e1009566-e1009566. Abstract.
Wannell GJ, Griffiths AM, Spinou A, Batista R, Mendonca MB, Wosiacki WB, Fraser B, Wintner S, Papadopoulos AI, Krey G, et al (2020). A new minibarcode assay to gacilitate species identification from processed, degraded or historic ray (batoidea) samples. CONSERVATION GENETICS RESOURCES, 12(4), 659-668. Author URL.
Whiting JR, Fraser BA (2020). Contingent Convergence: the Ability to Detect Convergent Genomic Evolution is Dependent on Population Size and Migration. G3 Genes|Genomes|Genetics, 10(2), 677-693. Abstract.
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.
Fraser B, Whiting JR (2019). What can be learned by scanning the genome for molecular convergence in wild populations?. Annals of the New York Academy of Sciences
Zhan L, Paterson IG, Fraser BA, Watson B, Bradbury IR, Nadukkalam Ravindran P, Reznick D, Beiko RG, Bentzen P (2017). megasat: automated inference of microsatellite genotypes from sequence data. Molecular Ecology Resources, 17(2), 247-256. Abstract.
K�nstner A, Hoffmann M, Fraser BA, Kottler VA, Sharma E, Weigel D, Dreyer C (2016). The genome of the trinidadian guppy, Poecilia reticulata, and variation in the Guanapo population. PLoS ONE, 11(12). Abstract.
Fraser BA, Künstner A, Reznick DN, Dreyer C, Weigel D (2015). Population genomics of natural and experimental populations of guppies (<i>Poecilia reticulata</i>). Molecular Ecology, 24(2), 389-408.
Fraser BA, Janowitz I, Thairu M, Travis J, Hughes KA (2014). Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies. Proceedings of the Royal Society B: Biological Sciences, 281(1781). Abstract.
Sharma E, Künstner A, Fraser BA, Zipprich G, Kottler VA, Henz SR, Weigel D, Dreyer C (2014). Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata. BMC Genomics, 15(1). Abstract.
Fraser BA, Hughes KA, Tosh DN, Rodd FH (2013). The role of learning by a predator, Rivulus hartii, in the rare-morph survival advantage in guppies. Journal of Evolutionary Biology, 26(12), 2597-2605. Abstract.
Fraser BA, Weadick CJ, Janowitz I, Rodd FH, Hughes KA (2011). Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. BMC Genomics, 12(1).
NEFF BD, FRASER BA (2010). A program to compare genetic differentiation statistics across loci using resampling of individuals and loci. Molecular Ecology Resources, 10(3), 546-550. Abstract.
Fraser BA, Ramnarine IW, Neff BD (2010). Selection at the MHC class IIB locus across guppy (Poecilia reticulata) populations. Heredity, 104(2), 155-167. Abstract.
Fraser BA, Ramnarine IW, Neff BD (2010). TEMPORAL VARIATION AT THE MHC CLASS IIB IN WILD POPULATIONS OF THE GUPPY (<i>POECILIA RETICULATA</i>). Evolution
Fraser BA, Neff BD (2009). MHC class IIB additive and non-additive effects on fitness measures in the guppy Poecilia reticulata. Journal of Fish Biology, 75(9), 2299-2312. Abstract.
Fraser BA, Neff BD (2009). Parasite mediated homogenizing selection at the MHC in guppies. Genetica, 138(2), 273-278.
Fraser BA, Mandrak NE, McLaughlin RL (2005). Lack of morphological differentiation in eastern (<i>Rhinichthys atratulus</i>) and western (<i>Rhinichthys obtusus</i>) blacknose dace in Canada. Canadian Journal of Zoology, 83(11), 1502-1509. Abstract.

Publications by year


In Press

Paris JR, Whiting JR, Daniel MJ, Obiol JF, Parsons PJ, van der Zee MJ, Wheat CW, Hughes KA, Fraser BA (In Press). A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy.  Abstract.
Whiting JR, Paris JR, van der Zee MJ, Fraser BA (In Press). AF-vapeR: a multivariate genome scan for detecting parallel evolution using allele frequency change vectors.  Abstract.
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.
Whiting JR, Paris JR, Parsons PJ, Matthews S, Reynoso Y, Hughes KA, Reznick D, Fraser BA (In Press). On the genetic architecture of rapidly adapting and convergent life history traits in guppies.  Abstract.

2022

Paris JR, Whiting JR, Daniel MJ, Ferrer Obiol J, Parsons PJ, van der Zee MJ, Wheat CW, Hughes KA, Fraser BA (2022). A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy. Nature Communications, 13(1). Abstract.
Whiting JR, Paris JR, Parsons PJ, Matthews S, Reynoso Y, Hughes KA, Reznick D, Fraser BA (2022). On the genetic architecture of rapidly adapting and convergent life history traits in guppies. Heredity, 128(4), 250-260. Abstract.
van der Zee MJ, Whiting JR, Paris JR, Bassar RD, Travis J, Weigel D, Reznick DN, Fraser BA (2022). Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata). Evolution Letters, 6(2), 149-161. Abstract.

2021

Whiting JR, Paris JR, van der Zee MJ, Parsons PJ, Weigel D, Fraser BA (2021). Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies. PLOS Genetics, 17(5), e1009566-e1009566. Abstract.

2020

Wannell GJ, Griffiths AM, Spinou A, Batista R, Mendonca MB, Wosiacki WB, Fraser B, Wintner S, Papadopoulos AI, Krey G, et al (2020). A new minibarcode assay to gacilitate species identification from processed, degraded or historic ray (batoidea) samples. CONSERVATION GENETICS RESOURCES, 12(4), 659-668. Author URL.
Whiting JR, Fraser BA (2020). Contingent Convergence: the Ability to Detect Convergent Genomic Evolution is Dependent on Population Size and Migration. G3 Genes|Genomes|Genetics, 10(2), 677-693. Abstract.
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.

2019

Fraser B, Whiting JR (2019). What can be learned by scanning the genome for molecular convergence in wild populations?. Annals of the New York Academy of Sciences

2017

Zhan L, Paterson IG, Fraser BA, Watson B, Bradbury IR, Nadukkalam Ravindran P, Reznick D, Beiko RG, Bentzen P (2017). megasat: automated inference of microsatellite genotypes from sequence data. Molecular Ecology Resources, 17(2), 247-256. Abstract.

2016

K�nstner A, Hoffmann M, Fraser BA, Kottler VA, Sharma E, Weigel D, Dreyer C (2016). The genome of the trinidadian guppy, Poecilia reticulata, and variation in the Guanapo population. PLoS ONE, 11(12). Abstract.

2015

Fraser BA, Künstner A, Reznick DN, Dreyer C, Weigel D (2015). Population genomics of natural and experimental populations of guppies (<i>Poecilia reticulata</i>). Molecular Ecology, 24(2), 389-408.

2014

Fraser BA, Janowitz I, Thairu M, Travis J, Hughes KA (2014). Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies. Proceedings of the Royal Society B: Biological Sciences, 281(1781). Abstract.
Sharma E, Künstner A, Fraser BA, Zipprich G, Kottler VA, Henz SR, Weigel D, Dreyer C (2014). Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata. BMC Genomics, 15(1). Abstract.

2013

Fraser BA, Hughes KA, Tosh DN, Rodd FH (2013). The role of learning by a predator, Rivulus hartii, in the rare-morph survival advantage in guppies. Journal of Evolutionary Biology, 26(12), 2597-2605. Abstract.

2011

Fraser BA, Weadick CJ, Janowitz I, Rodd FH, Hughes KA (2011). Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. BMC Genomics, 12(1).

2010

NEFF BD, FRASER BA (2010). A program to compare genetic differentiation statistics across loci using resampling of individuals and loci. Molecular Ecology Resources, 10(3), 546-550. Abstract.
Fraser BA, Ramnarine IW, Neff BD (2010). Selection at the MHC class IIB locus across guppy (Poecilia reticulata) populations. Heredity, 104(2), 155-167. Abstract.
Fraser BA, Ramnarine IW, Neff BD (2010). TEMPORAL VARIATION AT THE MHC CLASS IIB IN WILD POPULATIONS OF THE GUPPY (<i>POECILIA RETICULATA</i>). Evolution

2009

Fraser BA, Neff BD (2009). MHC class IIB additive and non-additive effects on fitness measures in the guppy Poecilia reticulata. Journal of Fish Biology, 75(9), 2299-2312. Abstract.
Fraser BA, Neff BD (2009). Parasite mediated homogenizing selection at the MHC in guppies. Genetica, 138(2), 273-278.

2005

Fraser BA, Mandrak NE, McLaughlin RL (2005). Lack of morphological differentiation in eastern (<i>Rhinichthys atratulus</i>) and western (<i>Rhinichthys obtusus</i>) blacknose dace in Canada. Canadian Journal of Zoology, 83(11), 1502-1509. Abstract.

Bonnie_Fraser Details from cache as at 2023-09-27 07:53:41

Refresh publications

Teaching

Modules

2023/24

Information not currently available


Supervision / Group

Postgraduate researchers

  • Ali Hudson

Research Technicians

  • Jenna Corcoran

Alumni

  • Mijke Van Der zee

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