Research Experience
Scientist
Eidg. Forschungsanstalt WSL
PI: Dr Christian Rellstab (SNSF funded)
(March 2022 - ongoing)
Oak genomics
An investigation into local and regional drought adaptation in white oaks. Through a mixture of landscape genetics and a common garden experiment, we aim to identify the genes underpinning drought adaptation and improve planting guidelines for oaks with regards to climate change.
Postdoctoral Fellow
Eidg. Forschungsanstalt WSL
PI: Dr Christian Rellstab (SNSF funded)
(September 2021 - ongoing)
Oak genomics
An investigation into local and regional drought adaptation in white oaks. Through a mixture of landscape genetics and a common garden experiment, we aim to identify the genes underpinning drought adaptation and improve planting guidelines for oaks with regards to climate change.
Postdoctoral Fellow
Eidg. Forschungsanstalt WSL
PI: Dr Daniel Rigling (SNSF funded)
(March 2019 - August 2021)
Fungal viral genomics
An investigation into the CHV-1 hypovirus. An essential component of the chestnut blight system, the CHV1 hypovirus mitigates the effects of the chestnut blight fungus in Europe and increases the survival probability of infected chestnut trees. In this postdoc I studied the natural variation in CHV-1 and the dynamics of variation during infection/across space.
Postdoctoral Fellow
Queen’s University
PI: Prof. Vicki Friesen (NERC funded)
(August 2017-September 2018)
Population and adaptive genomics of Arctic Seabirds
&
An evaluation of the status of genetic variation in wild populations
I used whole genome re-sequencing to investigate potential cryptic speciation in the puffin. I also collaborated on a number of other seabird focused projects and helped to secure funding for sequencing of the Eider genome. The information we obtained through these projects was used to help inform Environment Climate Change Canada’s species management and ultimately support Marine Protected Area design.
During my time at Queen's I also became involved in the IPBES NCP evaluations and contributed to a short evaluation on the status of genetic variation. I expanded on this initial evaluation and conducted a synthesis of temporal studies of wild population's genetic variation. This allowed me to assess the status of genetic variation and estimate how it has declined in the modern world.
Education
PhD Student Evolutionary Biology
University of Zurich
PI: Prof. Andreas Wagner/ Prof. Lukas Keller (URPP funded)
(2013-2017)
Conservation genomics of the Alpine ibex
An investigation into the parameters that influence the adaptive potential and on-going evolutionary processes of reintroduced populations. This study focused on the Alpine ibex (Capra ibex), a successfully reintroduced species that underwent a severe bottleneck of less than 100 individuals, but has a current population size of over 40,000 due to reintroduction efforts. I utilized next generation sequencing (RADseq) to understand how signals of selection and genome-wide diversity vary between these populations. Using a combination of simulations and selection detection methods, I explored if reliable signals of selection can be identified across populations given the history of strong genetic drift. This was with the aim of identifying a reliable method that could be used in other outlier scans on bottlenecked species and to understand the confidence we can place in such results. I also characterised and explored biases that can arise in next generation sequencing data, specifically when data is added incrementally to a study. Finally, I contributed to a book chapter aimed at conservation managers that focused on genetic issues reintroduced populations can face.
MRes Ecology, Evolution and Conservation
Imperial College London
(Distinction)
2011-2012
Summer Thesis: Conservation Genetics of the Corncrake (Crex crex)
An investigation into the genetic health of captive, reintroduced and wild populations of British Corncrakes. This involved both microsatellite and mitochondrial sequencing analysis.
Winter Thesis: Diet quality and morph expression in the male dimorphic bulb mite
An examination of the influence of juvenile diet quality on the expression of alternative reproductive phenotypes Rhizoglyphus robini.
BSc Biological Sciences Hons. Zoology
University of Edinburgh
(First Class)
2008-2011
Dissertation: Do female Nicrophorus vespilloides suppress larval begging through cuticular chemicals?
An exploration of the role that parent-offspring chemical communication plays during the offspring transition to nutritional independence.
Research Assistant Experience
Field research assistant on IOZ’s Hihi Project, Zoological Society of London, New Zealand (2012-2013)
Soay Sheep Project summer catch and survey assistant, University of Edinburgh, St Kilda (2011)
Burying beetle lab assistant, University of Edinburgh (2010)
Hoverfly Behaviour and Conservation researcher, Scottish Natural Heritage/Stirling University (2010)
Approved research projects
6) SNSF Project (2022) (2 year postdoc funds) Urban Birds. Role of birds in biosecurity of urban trees and forests. Project Partner. (PI: Eckehard G. Brockerhoff)5) WSL Internal project (2021) CHF 63,176. GenDiB. Feasibility study for a new national database on geo-referenced genetic diversity in populations of wild species. Co-PI (PI: Felix Gugerli)
4) USGS Powell Center FY21 (2021) $299,000 Operationalizing conservation genetic data for biodiversity management. Named Partner and named USGS fellow (declined fellowship due to prior commitments). (PI: Margret E Hunter).
3) CanSeq 150 Genome Sequencing Initiative (2018) €4,000 Eider duck genome sequence. PI.
2) Systematics Research Fund (2018) €1,700 Cryptic speciation in High Arctic Puffins. Main applicant.
1) European Science Foundation. Short Visit Grant for knowledge exchange (2015). €945 To visit Uppsala
University. Main applicant
Additional Funds secured to work with me:
DAAD Rise Intern (2022). €2800 88 days. Funding for Clarincia Gowenia to study adaptation in white oaks. PI.
Mary Kathleen-Hickox NSERC Undergraduate Student Research Award €3,000
Prizes
Gulbenkian Prize for Humanity 2022*. Awarded to IPBES and IPCC. *As a contributing author to IPBES.Wiley “Top Downloaded Paper 2019-2020"
Wiley “Top Downloaded Paper 2018-2019"
Queen's SSE Postdoc Travel Award $1000
Evolution2018 SSE’s W. D. Hamilton Award finalist (2018)
Funded place to attend Polygenic Adaptation Summer School, Zurich (2017)
ESF ConGenomics Travel Grant (2016): Travel grant awarded to attend ConGenomics2016
ESF Short Visit Grant (2015): Awarded to visit Uppsala University for knowledge exchange 945 €
ESF Workshop Place (2015): One of twenty fully funded places for the ESF B@G winter school.
Imperial College London Bursary for Masters studies (2011): £ 1000
Ashworth Prize (2011): For highest achieving Zoology Graduate at the University of Edinburgh £ 200
William Turner Prize (2010): For outstanding academic achievement. £ 200
Official supervision of junior researchers/students
Muhammad Murtaza Shah. DAAD Rise Intern. BSc Student.Supervisor.
Clarincia Goweina. DAAD Rise Intern. BSc Student. Host/official supervisor.
Karla Peranić. PhD Student. Visit support and bioinformatic supervisor.
Dr Lucija Nuskern. Postdoctoral Fellow. Daily supervisor and bioinformatic trainer.
Mary Kathleen-Hickox. NSERC summer student award. Queen’s University, Canada.
Co-supervisor (with Dr F Guillaume) two undergraduate students. University of Zurich. Switzerland.
Teaching Experience
Lecturer, Genomics of Environmental Adaptation. ETH Zurich, Switzerland. (Graduate level)
Guest lecturer on “adaptation” for second year undergraduates. Queen’s University (200 students, 2018)
Guest lecturer on “genetic rescue” to MSc and honours students. Queen’s University (30 students, 2017)
Co-lecturer NGS Course, a lecture introducing RAD sequencing library prep and data analysis to
PhD students. University of Zurich (2015 and 2016)
Co-supervisor for two undergraduate students on a ‘Block course.’ A multi-week course that a involved
data generation and writing a report. University of Zurich (2015)
Teaching assistant on a 3-week long course focusing on helping students develop a scientific question, then designing an experiment to test this. Kalahari Research Station. University of Zurich (2015)
Lab teaching assistant on a weeklong course focusing introducing students to population genetic theory. University of Zurich (2015)
Workshop Organisation
4) ConGen22. European Conservation Genetics meeting. (30/08/2022-2/09/2022) Scientific Committee
3) NSERC Strategic Meeting 2017 (October 19th – 21st, 2017)
Co-organiser of the coordination meeting for the Seabird project that involved multiple
Universities and conservation practitioners.
2) UZH Evolutionary Biology PhD Retreat (June 1st-3rd, 2015)
Co-organiser of a 3 day long conference for over 50 PhD students from the UZH Evolutionary Biology program.
1)URPP Conservation Genomics Mini Symposium (March 14th, 2014)
Organiser of a daylong event based around conservation genomics, with external talks from experts and an afternoon workshop session with the speakers and interested attendees.
Representative positions
PhD representative to the UZH Institute of Evolutionary Biology and Environmental Studies (2015-17)
Mittelbau representative (PhD and Postdocs) for the hiring committee for the “Succession of Prof. Bernhard Schmidt.” (2015-17)
Skills
Highly experienced in creating bioinformatics pipelines and scripts.
Comfortable navigating and working in Unix and bash scripting.
Familiar using genomic tools such as: Bowtie2, Stacks, VCFtools and GATK.
Knowledge of Python and R.
Experienced in NGS library prep (RADseq, PacBio).
Comfortable writing forward simulations in Nemo.
Experienced working in remote and difficult field conditions.
Experienced biopsy darting with a pressure rifle.
Project management
Scientific writing
Workshops, Conferences and Seminars
GenDiv Conference. Zurich. Oral presentation. Invited Speaker. Switzerland. (2023 - upcoming)
British Ecological Society. Invited Oral presentation. United Kingdom.(2022 - upcoming)
Gottingen PhD Retreat. Germany. United Kingdom.(2022 - upcoming)
ConGen22. Edinburgh. Oral presentation. United Kingdom. (2022)
Biology22. Basel. Poster. (2022)
AGA2021 President’s Symposium. Invited Speaker. (2021)
WABIO seminar. Zurich. Invited Guest Speaker (2021)
2nd Genetic Diversity Monitoring Workshop. Zurich. Oral presentation. (2021)
Temporal Genomics Working group. USA. Invited Guest Speaker (2021)
Hendry/Barret lab internal talk. Canada. Invited Guest Speaker (2020)
Host-Microbe Meeting. Zurich. Oral presentation. (2020)
CPH:DOX Science Film Factory, Copenhagen. Invited Guest Speaker. (2020).
European Viral Bioinfromatics Meeting. Bern. Poster. (2020).
Biodiversity seminar, WSL Switzerland. Talk. (2020)
Mycovirus minisymposium, Agroscope Switzerland. Talk. (2020).
NSERC strategic meeting. Queen’s University. Invited Speaker. (2020)
Evolution2018. Oral presentation. Hamilton Award Finalist (2018)
University of Toronto Biology Department's seminar series. Invited speaker (2018).
Arctic Change (2018). Poster presentation.
Queen’s University Biology Department's seminar series. Invited speaker (2017).
Conservation of adaptive potential and functional diversity (2017). Oral presentation.
Integrated methods to detect polygenic adaptation from genomics data (2017). Poster and funded place
GDC conference, ETH Zurich (2016). Invited speaker.
Congenomics (2016). Best Talk Award. Travel award.
ESEB (2015). Poster presentation.
Bioinformatics for Adaptation Genomics (March 2015). ESF funded place.
Guarda Course in Evolutionary Biology (June 2014).
Evomics (January, 2014).
SIB (January, 2014).
Hobbies and Outside Interests
I enjoy bouldering, travelling, experiencing new cultures and hiking. On rainy days I like to cook and bake.
Scientist
Eidg. Forschungsanstalt WSL
PI: Dr Christian Rellstab (SNSF funded)
(March 2022 - ongoing)
Oak genomics
An investigation into local and regional drought adaptation in white oaks. Through a mixture of landscape genetics and a common garden experiment, we aim to identify the genes underpinning drought adaptation and improve planting guidelines for oaks with regards to climate change.
Postdoctoral Fellow
Eidg. Forschungsanstalt WSL
PI: Dr Christian Rellstab (SNSF funded)
(September 2021 - ongoing)
Oak genomics
An investigation into local and regional drought adaptation in white oaks. Through a mixture of landscape genetics and a common garden experiment, we aim to identify the genes underpinning drought adaptation and improve planting guidelines for oaks with regards to climate change.
Postdoctoral Fellow
Eidg. Forschungsanstalt WSL
PI: Dr Daniel Rigling (SNSF funded)
(March 2019 - August 2021)
Fungal viral genomics
An investigation into the CHV-1 hypovirus. An essential component of the chestnut blight system, the CHV1 hypovirus mitigates the effects of the chestnut blight fungus in Europe and increases the survival probability of infected chestnut trees. In this postdoc I studied the natural variation in CHV-1 and the dynamics of variation during infection/across space.
Postdoctoral Fellow
Queen’s University
PI: Prof. Vicki Friesen (NERC funded)
(August 2017-September 2018)
Population and adaptive genomics of Arctic Seabirds
&
An evaluation of the status of genetic variation in wild populations
I used whole genome re-sequencing to investigate potential cryptic speciation in the puffin. I also collaborated on a number of other seabird focused projects and helped to secure funding for sequencing of the Eider genome. The information we obtained through these projects was used to help inform Environment Climate Change Canada’s species management and ultimately support Marine Protected Area design.
During my time at Queen's I also became involved in the IPBES NCP evaluations and contributed to a short evaluation on the status of genetic variation. I expanded on this initial evaluation and conducted a synthesis of temporal studies of wild population's genetic variation. This allowed me to assess the status of genetic variation and estimate how it has declined in the modern world.
Education
PhD Student Evolutionary Biology
University of Zurich
PI: Prof. Andreas Wagner/ Prof. Lukas Keller (URPP funded)
(2013-2017)
Conservation genomics of the Alpine ibex
An investigation into the parameters that influence the adaptive potential and on-going evolutionary processes of reintroduced populations. This study focused on the Alpine ibex (Capra ibex), a successfully reintroduced species that underwent a severe bottleneck of less than 100 individuals, but has a current population size of over 40,000 due to reintroduction efforts. I utilized next generation sequencing (RADseq) to understand how signals of selection and genome-wide diversity vary between these populations. Using a combination of simulations and selection detection methods, I explored if reliable signals of selection can be identified across populations given the history of strong genetic drift. This was with the aim of identifying a reliable method that could be used in other outlier scans on bottlenecked species and to understand the confidence we can place in such results. I also characterised and explored biases that can arise in next generation sequencing data, specifically when data is added incrementally to a study. Finally, I contributed to a book chapter aimed at conservation managers that focused on genetic issues reintroduced populations can face.
MRes Ecology, Evolution and Conservation
Imperial College London
(Distinction)
2011-2012
Summer Thesis: Conservation Genetics of the Corncrake (Crex crex)
An investigation into the genetic health of captive, reintroduced and wild populations of British Corncrakes. This involved both microsatellite and mitochondrial sequencing analysis.
Winter Thesis: Diet quality and morph expression in the male dimorphic bulb mite
An examination of the influence of juvenile diet quality on the expression of alternative reproductive phenotypes Rhizoglyphus robini.
BSc Biological Sciences Hons. Zoology
University of Edinburgh
(First Class)
2008-2011
Dissertation: Do female Nicrophorus vespilloides suppress larval begging through cuticular chemicals?
An exploration of the role that parent-offspring chemical communication plays during the offspring transition to nutritional independence.
Research Assistant Experience
Field research assistant on IOZ’s Hihi Project, Zoological Society of London, New Zealand (2012-2013)
Soay Sheep Project summer catch and survey assistant, University of Edinburgh, St Kilda (2011)
Burying beetle lab assistant, University of Edinburgh (2010)
Hoverfly Behaviour and Conservation researcher, Scottish Natural Heritage/Stirling University (2010)
Approved research projects
6) SNSF Project (2022) (2 year postdoc funds) Urban Birds. Role of birds in biosecurity of urban trees and forests. Project Partner. (PI: Eckehard G. Brockerhoff)5) WSL Internal project (2021) CHF 63,176. GenDiB. Feasibility study for a new national database on geo-referenced genetic diversity in populations of wild species. Co-PI (PI: Felix Gugerli)
4) USGS Powell Center FY21 (2021) $299,000 Operationalizing conservation genetic data for biodiversity management. Named Partner and named USGS fellow (declined fellowship due to prior commitments). (PI: Margret E Hunter).
3) CanSeq 150 Genome Sequencing Initiative (2018) €4,000 Eider duck genome sequence. PI.
2) Systematics Research Fund (2018) €1,700 Cryptic speciation in High Arctic Puffins. Main applicant.
1) European Science Foundation. Short Visit Grant for knowledge exchange (2015). €945 To visit Uppsala
University. Main applicant
Additional Funds secured to work with me:
DAAD Rise Intern (2022). €2800 88 days. Funding for Clarincia Gowenia to study adaptation in white oaks. PI.
Mary Kathleen-Hickox NSERC Undergraduate Student Research Award €3,000
Prizes
Gulbenkian Prize for Humanity 2022*. Awarded to IPBES and IPCC. *As a contributing author to IPBES.Wiley “Top Downloaded Paper 2019-2020"
Wiley “Top Downloaded Paper 2018-2019"
Queen's SSE Postdoc Travel Award $1000
Evolution2018 SSE’s W. D. Hamilton Award finalist (2018)
Funded place to attend Polygenic Adaptation Summer School, Zurich (2017)
ESF ConGenomics Travel Grant (2016): Travel grant awarded to attend ConGenomics2016
ESF Short Visit Grant (2015): Awarded to visit Uppsala University for knowledge exchange 945 €
ESF Workshop Place (2015): One of twenty fully funded places for the ESF B@G winter school.
Imperial College London Bursary for Masters studies (2011): £ 1000
Ashworth Prize (2011): For highest achieving Zoology Graduate at the University of Edinburgh £ 200
William Turner Prize (2010): For outstanding academic achievement. £ 200
Official supervision of junior researchers/students
Muhammad Murtaza Shah. DAAD Rise Intern. BSc Student.Supervisor.
Clarincia Goweina. DAAD Rise Intern. BSc Student. Host/official supervisor.
Karla Peranić. PhD Student. Visit support and bioinformatic supervisor.
Dr Lucija Nuskern. Postdoctoral Fellow. Daily supervisor and bioinformatic trainer.
Mary Kathleen-Hickox. NSERC summer student award. Queen’s University, Canada.
Co-supervisor (with Dr F Guillaume) two undergraduate students. University of Zurich. Switzerland.
Teaching Experience
Lecturer, Genomics of Environmental Adaptation. ETH Zurich, Switzerland. (Graduate level)
Guest lecturer on “adaptation” for second year undergraduates. Queen’s University (200 students, 2018)
Guest lecturer on “genetic rescue” to MSc and honours students. Queen’s University (30 students, 2017)
Co-lecturer NGS Course, a lecture introducing RAD sequencing library prep and data analysis to
PhD students. University of Zurich (2015 and 2016)
Co-supervisor for two undergraduate students on a ‘Block course.’ A multi-week course that a involved
data generation and writing a report. University of Zurich (2015)
Teaching assistant on a 3-week long course focusing on helping students develop a scientific question, then designing an experiment to test this. Kalahari Research Station. University of Zurich (2015)
Lab teaching assistant on a weeklong course focusing introducing students to population genetic theory. University of Zurich (2015)
Workshop Organisation
4) ConGen22. European Conservation Genetics meeting. (30/08/2022-2/09/2022) Scientific Committee
3) NSERC Strategic Meeting 2017 (October 19th – 21st, 2017)
Co-organiser of the coordination meeting for the Seabird project that involved multiple
Universities and conservation practitioners.
2) UZH Evolutionary Biology PhD Retreat (June 1st-3rd, 2015)
Co-organiser of a 3 day long conference for over 50 PhD students from the UZH Evolutionary Biology program.
1)URPP Conservation Genomics Mini Symposium (March 14th, 2014)
Organiser of a daylong event based around conservation genomics, with external talks from experts and an afternoon workshop session with the speakers and interested attendees.
Representative positions
PhD representative to the UZH Institute of Evolutionary Biology and Environmental Studies (2015-17)
Mittelbau representative (PhD and Postdocs) for the hiring committee for the “Succession of Prof. Bernhard Schmidt.” (2015-17)
Skills
Highly experienced in creating bioinformatics pipelines and scripts.
Comfortable navigating and working in Unix and bash scripting.
Familiar using genomic tools such as: Bowtie2, Stacks, VCFtools and GATK.
Knowledge of Python and R.
Experienced in NGS library prep (RADseq, PacBio).
Comfortable writing forward simulations in Nemo.
Experienced working in remote and difficult field conditions.
Experienced biopsy darting with a pressure rifle.
Project management
Scientific writing
Workshops, Conferences and Seminars
GenDiv Conference. Zurich. Oral presentation. Invited Speaker. Switzerland. (2023 - upcoming)
British Ecological Society. Invited Oral presentation. United Kingdom.(2022 - upcoming)
Gottingen PhD Retreat. Germany. United Kingdom.(2022 - upcoming)
ConGen22. Edinburgh. Oral presentation. United Kingdom. (2022)
Biology22. Basel. Poster. (2022)
AGA2021 President’s Symposium. Invited Speaker. (2021)
WABIO seminar. Zurich. Invited Guest Speaker (2021)
2nd Genetic Diversity Monitoring Workshop. Zurich. Oral presentation. (2021)
Temporal Genomics Working group. USA. Invited Guest Speaker (2021)
Hendry/Barret lab internal talk. Canada. Invited Guest Speaker (2020)
Host-Microbe Meeting. Zurich. Oral presentation. (2020)
CPH:DOX Science Film Factory, Copenhagen. Invited Guest Speaker. (2020).
European Viral Bioinfromatics Meeting. Bern. Poster. (2020).
Biodiversity seminar, WSL Switzerland. Talk. (2020)
Mycovirus minisymposium, Agroscope Switzerland. Talk. (2020).
NSERC strategic meeting. Queen’s University. Invited Speaker. (2020)
Evolution2018. Oral presentation. Hamilton Award Finalist (2018)
University of Toronto Biology Department's seminar series. Invited speaker (2018).
Arctic Change (2018). Poster presentation.
Queen’s University Biology Department's seminar series. Invited speaker (2017).
Conservation of adaptive potential and functional diversity (2017). Oral presentation.
Integrated methods to detect polygenic adaptation from genomics data (2017). Poster and funded place
GDC conference, ETH Zurich (2016). Invited speaker.
Congenomics (2016). Best Talk Award. Travel award.
ESEB (2015). Poster presentation.
Bioinformatics for Adaptation Genomics (March 2015). ESF funded place.
Guarda Course in Evolutionary Biology (June 2014).
Evomics (January, 2014).
SIB (January, 2014).
Hobbies and Outside Interests
I enjoy bouldering, travelling, experiencing new cultures and hiking. On rainy days I like to cook and bake.
