Dr Jon Ellis

Dr Jon Ellis

Lecturer in Environmental Science

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

  • A417, Portland Square, Drake Circus, Plymouth, Devon, PL4 8AA
  • +44 1752 585946


Lecturer in Environmental Science, Applied Ecology

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


  • 2013-  Lecturer in Environmental Science, Plymouth University
  • 2011 - 2013; Lecturer in Molecular Conservation Biology, MMU
  • 2010 -2011; Postdoctoral Research Fellow, Plymouth University
  • 2008-2010; Associate Research Fellow, Exeter University
  • Autumn 2008; Experiential Learning Development Project, Plymouth University
  • November 2006- December 2007; Post-doctoral Research Fellow, Plymouth University
  • 2002-2005; PhD. Population genetics and ecology of rare bumblebees in the UK
  • 1999-2002; BSc. (Hons) Zoology with Animal Ecology, University of Wales, Bangor

Teaching interests

Teaching interests

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

I teach on the modules:

  • ENVS 104 - The Biosphere
  • ENVS 207- Natural Ecosystems
  • ENVS 304 - Contemporary Issues
  • ENVS 309 - Biodiversity management in tropical ecosystems

I also teach on field courses in the UK (Slapton) and abroad (Malaysia) as well as supervising undergraduate and postgraduate research projects

Research interests

I am interested in the use of molecular tools to understand processes that maintain and erode genetic diversity in natural populations. I am also interested in the application of these tools to solve ecological problems of importance for conservation and management.

My previous research has involved assessing genetic diversity, gene-flow and population structure in declining populations of bumblebee species. I have also developed molecular tools to identify cryptic species of bumblebee and to identify wireworms (which are significant agricultural pests of potato). In addition to work on insects, I have also been involved in a large-scale research project to help understand the marine ecology of Atlantic salmon (the ‘SALSEA-Merge’ project).

More recently, I have become interested in the nature of the relationship between estimates of genetic diversity based on neutral markers and those based on functional regions: it is important to understand how adaptively important genetic variation is affected by the forces known to shape neutral genetic variation and the consequences for conservation. Recent work has focussed on identifying patterns of selection at potential candidate loci involved in immunity and metabolism in bumblebees within this context.

Current projects include: (1) Conservation genetics of the Hazel dormouse with Dr Ed Harris and Fraser Combe (MMU PhD student) (2) Population genetics of the colonization of the UK by Bombus hypnorum with Dr Mairi Knight (Plymouth University) 3. Adaptive conservation genomics of European Grayling with Dr Martin Taylor (UEA), Dr Robin Sen (MMU) and the Grayling Research Trust. (4) Ecological restoration of china clay mining sites with Dr Michael Hanley, Dr Mairi Knight and Dr Paul Lunt and Sibelco

The beauty of molecular tools is that they can be broadly applied across a wide range of taxa. If you have research interests on any group that you feel match my interests I am very happy to discuss potential PhD studentship applications, post-doctoral research or other collaborations


Victoria Buswell & B4 'Bringing back black bees', NERC-CASE studentship:

With Mairi Knight (PI), Vanessa Huml and the B4 organisation, 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.

Vanessa Huml, PhD project:

Vanessa is funded by Manchester Metropolitan University (where I used to work) and the Grayling Research Trust, but is based in Plymouth. She is examining 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 (Ion Torrent). Collaborating on the project are Dr Ed Harris and Dr Robin Sen (MMU), Dr Martin Taylor (UEA), Richard Cove (Natural Resources Wales). Dr Steven Weiss is an external advisor.

Vanessa Huml & Kirsty Lloyd:

With P.I. Dr Mairi Knight (Plymouth University, DoS), Dr Mark Brown (Royal Holloway) and Prof Dave Goulson (Sussex) this project is examining the population genetics of the colonisation and subsequent expansion of Bombus hypnorum in the UK. 

Mary Lane, PhD student:

Mary is working on the ecological restoration of heathland after china clay extraction. Her PhD is part-funded by Sibelco. Her work involves the investigation of the role of mycorrhizal fungi as well as metal nutrients. It involves laboratory work and field-scale trials

Fraser Combe, PhD student:

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

Sarah Rustage:

Sarah recently completed her PhD with Dr Mairi Knight (Plymouth Unversity, DoS), Dr Richard Billington and Dr Mark Brown (Royal Holloway) examining genetic diversity and fitness (parasite load and immunocompetence) in Bombus monticola (in contrast to the closely related but widespread B. pratorum). Research outputs are in prep.

Grants & contracts

Grants and awards


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

£10712 ‘The application of a novel population genomicapproach to provide fresh insights into the causes of rarity among a major UKpollinator group’ PI Mairi Knight.


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

Funds to supportnext-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).

Gilbey J., Coughlan J., Wennevik V., Prodohl P., Stevens J.R., Garcia de Leaniz C., Ensing D., Cauwelier E., Cherbonnel C., Consuegra S., Coulson M.W.,  Cross T.F., Crozier W., Dillane E., Ellis J.S., Garcia-Vazques E., Griffiths M., Gudjonsson S., Hindar K., Karlsson S., Knox D., Machado_Schiaffino, Meldrup D., Nielsen E.E., Olafsson K., Primmer C.R., Pusov S., Stradmeyer L, Vaha j-P., Veselow A. J., Webster L.M.I., McGinnity P., Verspoor E. (2017) A microsatellite baseline for genetic stock identification of European Atlantic Salmon (Salmo salar L.) ICES Journal of Marine Science 10.1093/icesjms/fsx184

Firth, L.B., Grant L.M., Crowe T.P., Ellis J.S., Wiler C., Convery C., O'Connor N.E. (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 http://dx.doi.org/10.1016/j.jembe.2017.01.026

Combe,F.J., Ellis, J.S., Lloyd, K.L., Cain, B., Wheater, C.P., Harris, W. E.(2016) After the ice age: the impact of post-glacial dispersal on thephylogeography of a small mammal, Muscardinus avellanarius. Frontiers inEcology and Evolution 4:72

Ellis, J.S., Turner, L.M, Knight, M.E. Lack of variation at phosphoglucose isomerase (Pgi) in bumblebees: implications for conservation genetics studies. PLoS One  8: e65600

Benefer , C.M., 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: 19-27

Cooper, E.M., Lunt, P.H., Ellis, J.S., & Knight, M.E. (online 2012) Biogeographical patterns of variation in western European populations of the Great Green Bush-cricket (Tettigonia viridissima; Orthoptera Tettigoniidae). Journal of Insect Conservation. DOI 10.1007/s10841-012-9525-9

Ellis, J.S, Turner, L.M., Knight, M.E. (2012) Patterns of selection and polymorphism of innate immunity genes in bumblebees (Hymenoptera: Apidae). Genetica 140: 205-217

Benefer, C., Knight, M.E., Ellis, J.S., Hicks, H., Blackshaw, R. (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

Griffiths, A.M., Ellis, J.S., Clifton-Dey, D., Machado- Schiaffino, G., Bright, D., Garcia-Vazquez, E. & Stevens, J.R. (2011) Restoration versus recolonisation; the origin of Atlantic salmon (Salmo salar L.) currently in the River Thames. Biological Conservation 144: 2733-2738

Ellis J.S. , Gilbey J. , Armstrong A., Balstad T., Cauwelier C., Cherbonnel C., Consuegra S., Coughlan J., Cross T.F., Crozier W., Dillane E., Ensing D., García de Leániz C., García- Vázquez E., Griffiths A.M., Hindar K., Hjorleifsdottir S., Knox D., Machado-Schiaffino G., McGinnity P., Meldrup D., Nielsen E.E., Olafsson K., Primmer C.R., Prodohl P., Stradmeyer L., Vähä J-P., Verspoor E., Wennevik V. and Stevens J. R. (2011) Microsatellite standardization and genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.) Genetica 139: 353-367.

Ellis, J.S., Sumner, K., Bright, D. & Stevens, J.R.(2011) Population genetic structure of Atlantic salmon populations (Salmo salar L.) in the River Tamar catchment, UK. Fisheries Management and Ecology 18: 233-245

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: 269-274

Ellis, J.S., Blackshaw, R.P., Parker, W.E., Hicks, H. & Knight, M.E. (2009) Genetic identification of morphologically cryptic agricultural pests. Agricultural and Forest Entomology 11: 115-121

Ellis, J.S., Knight, M.E., Darvill, B., & Goulson, D. (2006b) Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera: Apidae). Molecular Ecology 15: 4375-4386

Goulson, D., Hanley, M.E., Darvill, B. & Ellis, J.S. (2006) Biotope associations and the decline of bumblebees (Bombus spp.). Journal of Insect Conservation 10: 95-103

Darvill B., Ellis, J.S., Lye, G.C. & Goulson, D. (2006) Population structure and inbreeding in a rare and declining bumblebee, Bombus muscorum, (Hymenoptera: Apidae). Molecular Ecology 15: 601-611

Ellis, J.S., Knight, M.E., Carvell, C. & Goulson, D. (2006) Cryptic species identification: a simple diagnostic tool for discriminating between two problematic bumblebee species. Molecular Ecology Notes 6: 540-542

Ellis, J.S., Knight, M.E. & Goulson, D. (2005) Delineating species for conservation using mitochondrial sequence data: the taxonomic status of two Bombus species (Hymenoptera: Apidae). Journal of Insect Conservation 9: 75-83

Peat, J., Darvill, B., Ellis, J. & Goulson, D. (2005) Effects of climate on intra- and inter-specific size variation in bumblebees. Functional Ecology 19: 145-151

Goulson, D., Hanley, M.E., Darvill, B., Ellis, J.S. & Knight, M.E. (2005) Causes of rarity in bumblebees. Biological Conservation 122: 1-8.

Goulson, D., Darvill, B., Ellis, J.S., Knight, M.E. & Hanley, M.E. (2004) Interspecific differences in response to novel landmarks in bumblebees. Apidologie 35: 619-622

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 also enjoy reading, especially Russian literature. I am attempting to learn Russian and Polish. 


Bumblebee conservation trust

BWARS, the bees, wasps and ants recording society