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CV

Academic History

I completed my Bachelor’s degree in Ecology & Conservation at the School of Life Sciences, University of Sussex, UK. 

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I did a PhD in Molecular Ecology & Evolution at the University of Exeter, UK,  where I studied the genetic (microsatellites and RAD-seq) and transcriptomic (RNA-seq) signatures of metal tolerance in wild brown trout (Salmo trutta L.). I also undertook a physiology experiment in the laboratory, where I exposed wild brown trout from metal-impacted, and relatively clean control rivers to metal pollutants. During my PhD, I was the Graduate Teaching Assistant for the Marine Biology Course in The Bahamas, which I helped coordinate and teach on for 5 years. 

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I then moved back to the University of Sussex for a NERC postdoc, where I used genomic data to detect signatures of balancing selection (specifically NFDS) in the Trinidadian guppy (Poecilia reticulata). One year into this postdoc, my PI was offered a position at the University of Exeter, so I moved back again to Exeter! This postdoctoral position lasted more than 4 years, where, alongside my main research line, I undertook analyses to detect convergent evolution and rapid adaptation.

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I then moved northern Italy with my partner (also in academia), where I took on a remote BBSRC postdoc (University of Exeter, UK) to assemble the first reference genome of the European lobster (Homarus gammarus).

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After this, I was awarded a postdoctoral position at the University of L'Aquilla (Italy) where I generated several genomic datasets to explore the population genomics of three species: the Italian wall lizard (Podarcis siculus), the endemic Aeolian wall lizard (Podarcis raffonei), and the European leaf-toed gecko (Eulpetes europea). During this time, I also worked on the chromosome-level genome assemblies of the Sardinian/Tyrrhenian tree frog (Hyla sarda) and the European leaf-toed gecko (Euleptes europea).  

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I was then awarded a Marie Skłodowska-Curie Fellowship to investigate the genomic signatures of rapid adaptation in the King penguin (Aptenodytes patagonicus). I generated the chromosome-level reference genome for the species. I'm still working on the genomic analyses (the MSCA finished in May 2025).

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I moved to the US in May 2025, where I'm currently a visiting researcher, working with Kristen Ruegg on constructing the demographic history of rosy finches (Leucosticte sp.). I'll soon be starting a postdoc with Chris Funk on genomics of chronic wasting disease (CWD) transmission in mule deer (Odocoileus hemionus).   

Employment

Research Scientist

Colorado State University,  USA

upcoming ...

PI: Chris Funk

Genomics of Chronic Wasting Disease in mule deer

Visiting Researcher

Colorado State University,  USA

May 2025 - present

PI: Kristen Ruegg

Demographic history of rosy finches

Affiliated Researcher

University of Milan, Italy

Aug 2025 - Oct 2025

PI: Carlo Polidori 

Convergent adaptation to urban environments in the Italian sparrow

Marie Sklodowska-Curie Fellowship

Marche Polytechnic University, Italy

May 2023 - May 2025

PI: Emiliano Trucchi

Genomic adaptation to climate change in King penguins

Postdoc

University of Exeter, UK (remote)

Feb 2023 - May 2023

PI: Jamie Stevens

Population genetics of salmonids

Postdoc

University of L'Aquila, Italy

Feb 2022 - Feb 2023

PI: Daniele Salvi

Population genomics of Mediterranean reptiles

Postdoc

University of Exeter, UK (remote)

Jul 2021 - Jan 2022

PI: Eduarda Santos

Reference genome of the European lobster

Postdoc

University of Exeter, UK

Oct 2017 - Jun 2022

PI: Bonnie Fraser

Genomics of adaptive polymorphism (NFDS) in the Trinidadian guppy

Graduate Research Assistant

University of Exeter, UK

March 2017 - Jun 2017

PI: Chris Thornton

Generation of lateral flow devices (LFDs) to detect Bd

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Professional experience

Director of the Workshop on Genomics, ÄŒeský Krumlov, Czech Republic

 

Two-weeks, annually: 2023, 2024, 2025, 2026

 

I am the Director of the international Workshop on Genomics, which delivers advanced training in bioinformatics analysis of genomic data to ~70 participants from ~15 countries annually. See the 2025 program here.

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Genomics Consultant for The National Oceanic and Atmospheric Administration (NOAA).
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I am sub-contracted to provide consultancy, genomics analyses, and advice and interpretation for several projects involving the generation and use of genomic data for legal and mitigation purposes for damage and injury cases

Education

PhD in Molecular Ecology and Evolution

September 2012 - April 2017

Brown trout and toxic metals: Local adaptation to the legacy of Britain’s mining history

University of Exeter

BSc in Ecology and Conservation

2009 - 2012

University of Sussex

Research
Secondments

​​2022. Two-week research secondment with Prof. Dan MacQueen & Dr. Tim Bean (Roslin Institute, Edinburgh, UK). Secondment to collaborate with members of The Roslin Institute to generate the first reference genome of the European lobster (Homarus gammarus). Output: Paris et al. 2025, bioRxiv)

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2019. Two-week research secondment with Prof. Christopher Wheat (Stockholm University, Sweden). Secondment to analyse pool-seq data to detect signatures of colour polymorphism. Publication (Paris et al. 2022, Nature Communications).

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2016. Three-month research secondment with Dr Julian Catchen (University of Illinois Urbana-Champaign, USA). Secondment to develop methods for accurate locus recovery in RAD-seq. Publication (Paris et al 2017, Methods in Ecology and Evolution).

Grants & Awards

2022

2019

2017

2016

2015

2014

2013

2012

  • Grant: European Union Marie SkÅ‚odowska-Curie Actions (188,542 EUR).

  • Genetics Society Training Grant (£500)

  • ‘Lost in Parameter Space’, 2017, Paris, Stevens, Catchen. Top Downloaded Article 2017-2018 and top 20 most read paper in Methods in Ecology and Evolution

  • Genetics Society Training Grant (£500)

  • FSBI Small Research Grant (£4900)

  • University of Exeter Research Enhancement Fund (£480)

  • Genetics Society Training Grant (£700)

  • Santander Postgraduate Research Award (£500)

  • Award nomination: Linnean Society of London Nomination for The Bicentenary Medal

  • FSBI Small Research Grant (£1000), 

  • GBS Workshop Funding, The Genome Analysis Centre (TGAC) (€800), 

  • University of Exeter Research Enhancement Fund (£500)

  • Genetics Society Junior Scientist Travel Grant (£750)

  • NoWPaS 2013 Conference Committee (£21,000, as a committee of six)

  • John Maynard Smith Award for Ecology and Conservation (2012), University of Sussex

Other Stuff

  • Director of the Workshop on Genomics (2023-present)

  • Co-Director for the Workshop on Genomics (2018-present)​

  • Teaching Assistant for the Workshop on Genomics (2015-2018)

  • Graduate Teaching Assistant, Coral Reef Field Course, The Bahamas, University of Exeter (2013-2018)

Email

parisjosephine<at>gmail.com

Follow Me

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© 2021 By Josephine Paris
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