Dr Jon Ellis

Dr Jon Ellis

Lecturer in Conservation Genetics

School of Biological and Marine Sciences (Faculty of Science and Engineering)

Lecturer in Conservation Genetics

Contact: jonathan.s.ellis@plymouth.ac.uk

  • 2013 - present; Lecturer in Environmental Science then Lecturer in Conservation Genetics, Plymouth University
  • 2011 - 2013; Lecturer in Molecular Conservation Biology, MMU
  • 2010 - 2011; Postdoctoral Research Fellow, Plymouth University
  • 2008-2010; Associate Research Fellow, Exeter University
  • 2008 Experiential Learning Development Project, Plymouth University
  • 2006 - 2007; Post-doctoral Research Fellow, Plymouth University


  • 2002-2005; PhD. Population Genetics and Ecology of Rare Bumblebees in the UK, University of Southampton
  • 1999-2002; BSc. (Hons) Zoology with Animal Ecology, University of Wales, Bangor

Professional membership

Member Genetics Society

Member British Ecological Society

Teaching interests

Teaching interests

  • conservation biology and conservation genetics,
  • molecular ecology,
  • evolution & biodiversity,
  • terrestrial invertebrate ecology, esp. insects and moss invertebrates

I teach on undergraduate and postgraduate courses in biological and environmental sciences. This includes residential field courses in the UK and abroad, practical classes, tutorials and lectures as well as supervising undergraduate and postgraduate research projects.

I am also the Senior Tutor in the School of Biological and Marine Sciences. I believe that science students should leave university with new conceptual knowledge, improved academic and practical skills, enhanced critical thinking and an analytical mindset, but also improved resilience and determination with a good mindset for life's future challenges.

Research interests

I am interested in molecular ecology and the use of genetic tools to study natural populations, as well as the evolution of biodiversity and its conservation. I am especially interested in insects and fungi, but also work on tardigrades and fish. I am also keen to establish red spider mite as an experimental model of evolutionary conservation in the laboratory.


Current projects

1. ‘Wherefore the magic? Investigating the origin of psychedelic compounds in nature’ Leverhulme Trust, PI

This project will begin in 2021. It will combine microbiology, molecular ecology and genetic methods (barcoding, RNA-Seq, gene editing), behavioural trials and fieldwork to investigating evolutionary hypotheses for psilocybin biosynthesis.


2.  'Bringing back black bees', NERC-CASE studentship with Victoria Buswell, Dr Mairi Knight, Dr Vanessa Huml, B4. Co-Investigator.

Victoria is investigating the phenotypic and genotypic basis of local adaptation in UK populations of the dark European honey bee, Apis mellifera mellifera. Collaborative work with Washington State University is planned on cryopreservation of honey bee sperm.


3. Modelling insect dispersal with Dr Rich Billington, Dr Mairi Knight and Joe Eva. Co-Investigator.

Joe has recently started his Ph.D and will be investigating morphometry, wind, weather and climate in relation to insect dispersal and invasions.


4. Population genetics of the colonization of the UK by Bombus hypnorum with Dr Mairi Knight (Plymouth University), Dr Vanessa Huml, Kirsty Lloyd and Dr Mark Brown (Royal Holloway). Co-Investigator.

This project is examining the population genetics of the colonisation and subsequent expansion of Bombus hypnorum in the UK.


5. Extremophiles in a changing world - the mechanistic bases of stress resistance in rotifers and tardigrades, Dr Chiara Boschetti (PI), Prof Simon Rundle. Co-Investigator

This Ph.D project will begin in 2021 and will use bioinformatics approaches to characterise genes and pathways involved in stress tolerance in meiofauna.


Past projects

Ecological restoration of china clay mining sites with Mary Lane, Dr Michael Hanley, Dr Charlotte Braungardt, Dr Mairi Knight and Dr Paul Lunt and Sibelco. P.I.

Mary recently completed her PhD on the ecological restoration of heathland after china clay extraction. This project was part-funded by Sibelco. Her work involved the investigation of the role of mycorrhizal fungi as well as metal nutrients. It involved laboratory work and field-scale trials


Adaptive conservation genomics of European grayling with Vanessa Huml, Dr Ed Harris, Dr Martin Taylor (UEA), Dr Robin Sen (MMU) and the Grayling Research Trust. P.I.

Vanessa's Ph.D project examined genetic diversity of MHC loci in European grayling (Thymallus thymallus) in relation to bacterial and environmental parameters as well as in contrast to neutral variation, using next-generation sequencing approaches. Vanessa is now a post-doc in our group and continues to publish her recent work.


Conservation genetics of the hazel dormouse with Fraser Combe and Dr Ed Harris (MMU). Co-Investigator.

Fraser completed his PhD at Manchester Metropolitan under Dr Ed Harris (DoS). Fraser was examining landscape and conservation genetics of the hazel dormouse (Muscardinus avellanarius) in the UK. He worked closely with a number of wildlife trusts, but particularly with Dr Simone Bullion at Suffolk Wildlife Trust.


Genetic diversity, immunity and parasite load in widespread versus declining bumblebee species with Sarah Rustage. Dr Mairi Knight, Dr Richard Billington and Dr Mark Borwn (Royal Holloway). Co-Investigator.

This project examined genetic diversity and fitness (parasite load and immunocompetence) in Bombus monticola (in contrast to the closely related but widespread B. pratorum). The project is currently being followed up by NGS RAD-Seq of Bombus monticola populations (Dr Vanessa Huml). Research outputs are in prep.

Grants & contracts

Grants and awards


£242,910 Leverhulme Trust ‘Wherefore the magic? Investigating evolutionary hypotheses for the evolution of psychedelic compounds in nature’


£5289 Seale-Hayne Trust ‘Adaptation to novel plant hosts in highly polyphagous invertebrate pests’ PI Dr Michael Thom



£5836 Seale-Hayne Educational Trust ‘Ecological restoration of mineral extraction sites: role of mycobiont in ericaceous plant growth on restored mine spoil’. Funds to support PhD research of Mary Lane on ecological restorationof china clay sites.


£10712 ‘The application of a novel population genomic approach to provide fresh insights into the causes of rarity among a major UK pollinator group’ PI Dr Mairi Knight.



£4118 Seale-Hayne Educational Trust ‘Maintaining sustainability of natural resources’

Funds to support next-generation sequencing of hatchery reared grayling


Internal faculty-wide PhD studentship competition MMU, plus £10,000 Grayling Research Trust. ‘Assessing adaptive genetic variation for effective conservation and management of European Grayling’


£4870 Research accelerator grant. ‘Adaptive conservation genomics of an important insect pollinator’. Internal grant competition MMU.


£1080 Society of Biology, Undergraduate Research Bursary. Identifying evolutionary significant units in the hazel dormouse.


NERC quota studentship. ‘Neutral and functional genetic variation, parasite load and immunocompetence in social insects’. Co-applicant with Dr. Mairi Knight on a successful bid for an internal PhD studentship, Plymouth University.


£72990 Leverhulme trust, ‘Neutral versus functional genetic diversity: a new conservation genetic agenda’ (P.I. Dr Mairi Knight, University of Plymouth; named researcher, Jonathan Ellis).


£6340 Seale-Hayne Educational Trust ‘Development of molecular techniques to further understanding of wireworm ecology’ (with Prof. Rod Blackshaw).


£300 Genetics Society travel grant (conference attendance).

Key publications

Key publications are highlighted


Huml JV, Harris WE, Taylor MI, Sen R, Prudhomme C & Ellis JS 2020 'Pollution control can help mitigate future climate change impact on European grayling in the UK' Diversity and Distributions , DOI PEARL
Murphy TR, Hanley ME, Ellis JS & Lunt PH 2019 'Taking the higher ground: deviation between projected and observed precipitation trends varies with altitude' Climate Research , DOI PEARL
Lane M, Hanley ME, Lunt P, Knight ME, Braungardt CB & Ellis JS 2019 'Chronosequence of former kaolinite open cast mines suggests active intervention is required for the restoration of Atlantic heathland' Restoration Ecology , DOI PEARL
Huml JV, Taylor MI, Harris WE, Sen R & Ellis JS 2018 'Neutral variation does not predict immunogenetic variation in the European grayling (Thymallus thymallus) - implications for management' Molecular Ecology 27, (21) , DOI PEARL
Ellis JS, Soland-Reckeweg G, Buswell VG, Huml JV, Brown A & Knight ME 2018 'Introgression in native populations of Apis mellifera mellifera L: implications for conservation' Journal of Insect Conservation , DOI PEARL
Gilbey J, Coughlan J, Wennevik V, Prodohl P, Stevens JR, Garcia de Leaniz C, Ensing D, Cauwelier E, Cherbonnel C & Consuegra S 2017 'A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)' ICES Journal of Marine Science , DOI PEARL
Firth LB, Grant LM, Crowe TP, Ellis JS, Wiler C, Convery C & O'Connor NE 2017 'Factors affecting the prevalence of the trematode parasite Echinostephilla patellae (Lebour, 1911) in the limpet Patella vulgata (L.)' Journal of Experimental Marine Biology and Ecology , DOI PEARL
Combe FJ, Ellis JS, Lloyd KL, Cain B, Wheater CP & Harris WE 2016 'After the Ice Age: The Impact of Post-Glacial Dispersal on the Phylogeography of a Small Mammal, Muscardinus avellanarius' Frontiers in Ecology and Evolution 4, , DOI PEARL
Ellis JS, Turner LM & Knight ME 2013 'Lack of Variation at Phosphoglucose Isomerase (Pgi) in Bumblebees: Implications for Conservation Genetics Studies' PLOS One 8, (6) 1-11 , DOI PEARL
Cooper EM, Lunt PH, Ellis JS & Knight ME 2013 'Biogeographical patterns of variation in European populations of the Great Green Bush-cricket (Tettigonia viridissima; Orthoptera Tettigoniidae)' Insect Conservation 17, (3) 431-440 , DOI
Benefer C, van Herk WG, Ellis JS, Blackshaw RP, Vernon RS & Knight ME 2013 'The molecular identification and genetic diversity of economically important wireworm species (Coleoptera: Elateridae) in Canada' Journal of Pest Science 86, (1) 19-27 , DOI
Ellis JS, Turner LM & Knight ME 2012 'Patterns of selection and polymorphism of innate immunity genes in bumblebees (Hymenoptera: Apidae)' GENETICA 140, (4-6) 205-217 Author Site , DOI
Benefer CM, Knight ME, Ellis JS, Hicks H & Blackshaw RP 2012 'Understanding the relationship between adult and larval Agriotes distributions: The effect of sampling method, species identification and abiotic variables' Applied Soil Ecology 53, 39-48 , DOI
Griffiths AM, Ellis JS, Clifton-Dey D, Machado-Schiaffino G, Bright D, Garcia-Vazquez E & Stevens JR 2011 'Restoration versus recolonisation: The origin of Atlantic salmon (Salmo solar L.) currently in the River Thames' BIOLOGICAL CONSERVATION 144, (11) 2733-2738 Author Site , DOI
Ellis JS, Sumner KJ, Griffiths AM, Bright DI & Stevens JR 2011 'Population genetic structure of Atlantic salmon, Salmo salar L., in the River Tamar, southwest England' Fisheries Management and Ecology 18, (3) 233-245 , DOI PEARL
Ellis JS, Gilbey J, Armstrong A, Balstad T, Cauwelier E, Cherbonnel C, Consuegra S, Coughlan J, Cross TF & Crozier W 2011 'Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.)' GENETICA 139, (3) 353-367 Author Site , DOI
Benefer C, Andrew P, Blackshaw R, Ellis J & Knight M 2010 'The spatial distribution of phytophagous insect larvae in grassland soils' APPLIED SOIL ECOLOGY 45, (3) 269-274 Author Site , DOI
Ellis JS, Blackshaw R, Parker W, Hicks H & Knight ME 2009 'Genetic identification of morphologically cryptic agricultural pests' AGRICULTURAL AND FOREST ENTOMOLOGY 11, (1) 115-121 Author Site , DOI
Darvill B, Ellis JS, Lye GC & Goulson D 2006 'Population structure and inbreeding in a rare and declining bumblebee, Bombus muscorum (Hymenoptera: Apidae)' Mol Ecol 15, (3) 601-611 Author Site , DOI
Goulson D, Hanley ME, Darvill B & Ellis JS 2006 'Biotope associations and the decline of bumblebees (Bombus spp.)' Journal of Insect Conservation 10, (2) 95-103
Goulson D, Hanley ME, Darvill B & Ellis J 2006 'Biotope associations and the decline of bumblebees (Bombus spp.)' Journal of Insect Conservation 10, 95-103
Ellis JS, Knight ME, Carvell C & Goulson D 2006 'Cryptic species identification: a simple diagnostic tool for discriminating between two problematic bumblebee species' Molecular Ecology Notes 6, (2) 540-542
Ellis JS, Knight ME, Darvill B & Goulson D 2006 'Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera : Apidae)' Molecular Ecology 15, (14) 4375-4386
Ellis JS, Knight ME & Goulson D 2005 'Delineating species for conservation using mitochondrial sequence data: the taxonomic status of two problematic Bombus species (Hymenoptera: Apidae)' Journal of Insect Conservation 9, (2) 75-83 , DOI
Peat J, Darvill B, Ellis J & Goulson D 2005 'Effects of climate on intra- and interspecific size variation in bumble-bees' FUNCTIONAL ECOLOGY 19, (1) 145-151 Author Site , DOI
Goulson D, Hanley ME, Darvill B, Ellis JS & Knight ME 2005 'Causes of rarity in bumblebees' Biological Conservation 122, (1) 1-8
Ellis JS, Knight ME & Goulson D 2005 'Delimiting species for conservation using molecular markers: the taxonomic status of Bombus ruderatus (Fabricus) and Bombus hortorum (Linnaeus) (Hymenoptera: Apidae)' Journal of Insect Conservation 9, 75-83
Goulson D, Darvill B, Ellis J, Knight ME & Hanley ME 2004 'Interspecific differences in response to novel landmarks in bumblebees (Bombus sp.)' APIDOLOGIE 35, (6) 619-622 Author Site , DOI
Conference Papers
Benefer C, Blackshaw R, Knight M & Ellis J 2011 'Development of amplified fragment length polymorphism (AFLP) markers for assessing Agriotes click beetle dispersal in agricultural land' in Ehlers R; Crickmore N; Enkerli J; Glazer I; Kirchmair M; Lopez-Ferber M; Neuhauser S; Strasser H; Tkaczuk C; Traugott M Insect Pathogens and Entomopathogenic Nematodes Biological Control in IPM Systems Innsbruck, Austria 6-/-0/20116-/-0/2011Darmstadt, Germany International Organization for Biological and Integrated Control of Noxious Animals and Plants, West Palearctic Regional Section (IOBC/WPRS) 541-541 Publisher Site
Benefer C, Blackshaw RP, Knight ME & Ellis JS 2011 'Male Agriotes click beetle walking behaviour and response to sex pheromones' in Ehlers RU; Crickmore N; Enkerli J; Glazer I; Kirchmair M; Lopez-Ferber M; Neuhauser S; Strasser H; Tkaczuk C; Traugott M Insect Pathogens and Entomopathogenic Nematodes Biological Control in IPM Systems Innsbruck, Austria 6-/-0/20116-/-0/2011Darmstadt, Germany International Organisation for Biological and INtegrated Control of Noxious Animals and Plants, West Palearctic Regional Section (IOBC/WPRS) 504-504 Publisher Site
Benefer C, Blackshaw RP, Knight ME & Ellis JS 2009 'The relationship between Agriotes click beetle (Coleoptera: Elateridae) wireworms and environmental factors' in Ehlers RU; Crickmore N; Enkerli J; Glazer I; Lopez-Ferber M; Tkaczuk C Insect Pathogens and Insect Parasitic Nematodes Pamplona, Spain 6-/-0/20096-/-0/2009International Organisation for Biological and Integrated Control of Noxious Animals and Plants, West Palearctic Regional Section (IOBC/WPRS) Publisher Site

Additional information

In my spare time I am a keen cyclist (roadie) and used to compete at an amateur level on the local scene as part of Team Certini. I now ride and race for Plymouth Corinthian CC. I am learning Russian (reading comprehension ~ lower intermediate, speaking - beginner) and Polish (beginner). 


Bumblebee conservation trust

BWARS, the bees, wasps and ants recording society