Dr Jon Ellis

Dr Jon Ellis

Associate Professor in Molecular Ecology

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



2023 - present  Associate Professor in Molecular Ecology

2013 - 2023    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

Member, Royal Entomological Society

Roles on external bodies

Scientific Board Member SICAMM (Societas Internationalis pro Conservatione Apis melliferae melliferae)



Teaching interests

Teaching interests

  • conservation biology and conservation genetics
  • molecular ecology
  • evolution & biodiversity
  • entomology

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 Academic Wellbeing Lead 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, evolution, genetics of natural populations and the conservation of biodiversity. I am especially interested in insects and fungi, but work on a range of biological systems.


Current projects

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

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


2.  Hard-wired for success? Unravelling genomic signatures in pollinators

Saam Hassan's PhD is investigating the genomics of Pyrobombus bumblebees. This sub-genus stands in contrast to other sub-genera of bumblebees due to the number of successful species in terms of abundance and range expansion


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

Joe Eva's PhD is investigating morphometry, wind, weather and climate in relation to insect dispersal and invasions, especially with regard to the colonisation of the UK by Bombus hypnorum


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

Ellis Moloney is investigating stress tolerance in meiofauna using experimental biology methods and bioinformatics approaches


Past projects

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

Victoria's Ph.D investigated introgression and the phenotypic and genotypic basis of local adaptation in UK populations of the dark European honey bee, Apis mellifera mellifera. 

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 examined the population genetics of the colonisation and subsequent expansion of Bombus hypnorum in the UK


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 PhD 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.

Research groups

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 restoration of 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

Buswell V, Ellis J, Huml J, Wragg D, Barnett M, Brown A & Knight M (2023) 'When One’s Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera' Insects 14, (5) , DOI Open access
Huml JV, Ellis JS, Rustage S, Brown MJF, Billington R & Knight ME (2023) 'The tragedy of the common? A comparative population genomic study of two bumblebee species' Insect Conservation and Diversity , DOI Open access
Combe FJ, Juškaitis R, Trout RC, Bird S, Ellis JS, Norrey J, Al-Fulaij N, White I & Harris WE (2022) 'Density and climate effects on age‐specific survival and population growth: consequences for hibernating mammals' Animal Conservation , DOI Open access
Murphy TR, Hanley ME, Ellis JS & Lunt PH (2022) 'Optimizing opportunities for oak woodland expansion into upland pastures' Ecological Solutions and Evidence 3, (1) , DOI Open access
Lane M, Hanley M, Lunt P, Braungardt C, Knight M & Ellis J (2021) 'Addition of composted green waste and ericoid mycorrhizal fungi fails to facilitate establishment of Atlantic heathland species' Restoration Ecology , DOI Open access
Huml JV, Ellis JS, Lloyd K, Benefer C, Kiernan M, Brown MJF & Knight M (2021) 'Bucking the trend of pollinator decline: the population genetics of a range expanding bumblebee' Evolutionary Ecology , DOI Open access
Murphy TR, Hanley ME, Ellis JS & Lunt PH (2020) 'Native woodland establishment improves soil hydrological functioning in UK upland pastoral catchments' Land Degradation & Development 32, (2) 1034-1045 , DOI Open access
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 26, (4) 517-532 , DOI Open access
Murphy TR, Hanley ME, Ellis JS & Lunt PH (2019) 'Deviation between projected and observed precipitation trends greater with altitude' Climate Research , DOI Open access
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 Open access
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 Open access
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 Open access
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 Open access
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 Open access
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 Open access
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 Open access
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
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
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 , 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 Open access
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 (<i>Salmo solar</i> L.) currently in the River Thames' BIOLOGICAL CONSERVATION 144, (11) 2733-2738 , DOI
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 (<i>Salmo salar</i> L.)' GENETICA 139, (3) 353-367 , 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 , 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 , 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
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
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 & 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
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
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 , DOI
Goulson D, Darvill B, Ellis J, Knight ME & Hanley ME (2004) 'Interspecific differences in response to novel landmarks in bumblebees (<i>Bombus</i> sp.)' APIDOLOGIE 35, (6) 619-622 , 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