Skip to main content
Contact Us

Joan’s research interests within the Genetic Conservation Project include the following topics; assessment of adaptive traits in provenance trials of native tree species, distribution of intraspecific genetic diversity, gene flow between populations. She also maintains an interest in Molecular Tree Breeding and in the application of molecular marker technology in ecological and pest and disease research.

She has been involved in several large EU funded projects such as PROCOGEN, FORGENIUS and OptFORESTS. She was a partner in the DEFRA funded LWEC projects GRIPP and PROTREE. She is also participating in the TREESCAPES newLEAF project and a Centre for Forest Protection project that aims to understand the genetic basis of silver birch adaptation.

She has been an active research collaborator and has worked with staff in the following British organisations: the James Hutton Institute, Centre for Ecology & Hydrology, University of Edinburgh, Southampton University, York University, Bristol University, RSPB, East Malling Research. She also has a network of European collaborators through her active participation in EUFORGEN and various EU Cost actions. She has supervisory responsibility for several PhD students.

Following several postdoctoral posts in the Botany Dept at Edinburgh University and in the Scottish Agricultural College, Joan joined Forest Research in 1991.


  • 2004 Silvicultural Prize awarded by the Institute of Chartered Foresters for best paper in the journal ‘Forestry’.
  • British representative for EUFORGEN network
  • Member of the UK Plant Genetic Resources Group
  • PhD supervision of students from Edinburgh, York and Aberdeen Universities and external examiner for PhD theses from Bangor and Southampton University.
  • Awarded George Campbell Trophy for co-authorship of best paper in ‘Scottish Forestry’ in 2017.
Science group leader
Forest genetics


Northern Research Station

Bush Estate



Related Research


UK Forest Genetic Resources Strategy

Forest Genetic Resources Strategy

Status current



Forest Research is collaborating with several organisations in order to harness this novel DNA approach for a range of applications in which monitoring of forest biodiversity is required.

Status current
Genetic conservation

This project conducts research on adaptive and neutral genetic variation in our native tree species and woodland dwelling organisms. The results of the work contribute to the development of appropriate policy relating to future resilience of our native woodlands.

Intra and interspecific gene flow in oaks (OAKFLOW)

The page summarises the ‘Intra and interspecific gene flow in oaks’ (OAKFLOW) project, funded by the EU’s Fifth Framework Programme (FP5).

Selection and testing of conifers

Selection and testing of phenotypes. Progeny and clonal testing. Estimating breeding values. Use of Marker Aided Selection to improve operational efficiencies.

Related Publications


Factsheet: Climate change and biodiversity

More biodiverse woodlands are better able to resist or adapt to threats, such as climate change. This enhanced resilience supports the continuity of woodlands and the ecosystem services they provide. Biodiversity is the variation at different levels of biological organisation - the genes within a species; the species within a community; and the diversity between communities and ecosystems.



Species diversification - which species should we use?

This paper stresses that future use of ‘alternative’ species for diversification should be contingent on rigorous biological risk assessment, results from forestry scale trials, and the establishment of sustainable British seed sources.

Genetic considerations for provenance choice of native trees under climate change in England

This Research Report provides a review of published results from provenance tests of relevance to English native trees to identify factors which may influence the risk, suitability and desirability of the use of local versus non-local seed under climate change.

Is the introduction of novel exotic forest tree species a rational response to rapid environmental change? A British perspective.

A suggested way for British woodlands to combat the problems they are facing due to climate change and exotic pests and diseases is to grow a range of novel exotic tree species. Here we examine the arguments for doing this in the context of British forestry where the objectives are either commercial timber production or conservation of biodiversity.

Cryptic genetic variation and adaptation to waterlogging in Caledonian Scots pine, Pinus sylvestris L.

Exposure to a contrasting novel environment such as waterlogging under common garden conditions can trigger release of otherwise unobservable (cryptic) genetic variation. Under a flooding treatment, there was a greater increase in variability in Scots pine populations originating from drier sites in Scotland which likely reflects a relative absence of past selection. Under climate change this cryptic genetic variation may provide considerable potential to adapt.

Conservation of black poplar: insights from a DNA fingerprinting approach

Black poplar is Great Britain’s rarest native hardwood and there is considerable interest in conserving the genetic diversity present in the remaining population. However, multiplication by vegetative propagation has led to issues in identifying and selecting genetically diverse native planting material. The ability to use DNA markers to identify poplars at the level of the […]

Encouraging biodiversity at multiple scales in support of resilient woodlands

Woodland ecosystems are integral to our health, well-being, security and economy, but they face a number of pressures including climate change, land-use intensification, and emerging pests and diseases. This Research Note explores the links between biodiversity, measured at different levels of organisation (genes, species and communities), and the ability of woodland ecosystems to withstand and […]

Do non-native conifer plantations provide benefits for a native forest specialist, the wood ant Formica lugubris?

Recent research by Forest Research scientists and colleagues at the University of York shows that northern hairy wood ants (Formica lugubris) have successfully colonised plantations of largely non-native coniferous species in the North York Moors National Park. The studies show that there has been a remarkable expansion of the population of this ant into new […]

Establishing and managing gene conservation units

Conserving the genetic diversity within our tree species and the processes that determine it are important for sustainable forest management and increasing the resilience of Britain’s forests and woodlands. The genetic diversity within a tree species at any one time is the result of many dynamic processes, and it provides the source for future adapted […]

Peer reviewed journal articles

Gonzales Diaz, Patricia, Cavers, Stephen, Matias, Luis, Ennos, Richard A., Cottrell            Joan E., Jump, Alistair (Submitted) Neighbouring Scots pine populations from contrasting climates show substantial variability but consistent response to warming. Available at:

Munzer Aldarvish, Anas Al Kaddour, Akram Bourgol, Yasser Ramazan, Yousef Hallak, Stephen Cavers, Joan Cottrell (2023) Wild relatives of fruit trees in Syria: Genetic Resources threatened by conflict. Genetic Resources 4: 68-75.

Finžgar, D., Ennos, R., Whittet, R. and Cottrell, J. (2023) Measuring and managing genetic diversity in the British Sitka spruce improvement programme. Scottish Forestry 77: 38-44.

Beaton, Joan; Perry, Annika ; Cottrell, Joan; Iason, Glenn; Stockan, Jenni; Cavers, Stephen (2022) Phenotypic trait variation in a long-term multisite common garden experiment of Scots pine in Scotland. Scientific Data 9: 671.

Kristina K. Gagalova, Rene L. Warren, Lauren Coombe, Johnathan Wong, Ka Ming Nip, Macaire Manaint Yuen, Justin G. A. Whitehill, Jose M. Celedon, Carol Ritland, Greg A. Taylor, Dean Cheng, Patrick Plettner, S. Austin Hammond, Hamid Mohamadi, Yongjun Zhao, Richard A. Moore, Andrew J. Mungall, Brian Boyle, Jerome Laroche, Joan Cottrell, John J. Mackay, Manuel Lamothe, Sebastien Gerardi, Nathalie Isabel, Nathalie Pavy, Steven J. M. Jones, Joerg Bohlmann, Jean Bousquet and Inanc Birol (2022) Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. The Plant Journal 111: 1469–1485.

Schönrogge K, Gibbs M, Oliver A, Cavers S, Gweon HS, Ennos RA, Cottrell J, Iason GR, Taylor J. (2022) Environmental factors and host genetic variation shape the fungal endophyte communities within needles of Scots pine (Pinus sylvestris). Fungal Ecology 57–8: 101162 Annika Perry, Witold Wachowiak, Joan Beaton, Glenn Iason, Joan Cottrell, Stephen Cavers (2022) Identifying and testing marker-trait associations for growth and phenology in three pine species. Evolutionary Applications. 15(2) DOI: 10.1111/eva.13345

Perry, A.; Beaton, J.; Iason, G.; Cottrell, J.; Stockan, J.; Cavers, S. (2021) Long-term multi-site Scots pine single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis.

Barsoum, N., A’Hara, S. W., Cottrell, J.E., Forster, J., Garcia, M.S.J., Schonrogge, K. and Shaw, L. (2021) Root ectomycorrhizal status of oak trees symptomatic and asymptomatic for Acute Oak Decline in southern Britain. Forest Ecology and Management 482, 118800

Martha Rendón-Anaya, Jonathan Wilson, Sæmundur Sveinsson, Aleksey 5 Fedorkov, Joan Cottrell, Mark E.S. Bailey, Dainis Ruņģis, Christian Lexer, Stefan Jansson, Kathryn M. Robinson, Nathaniel R. Street, Pär K. Ingvarsson (2021) Adaptive introgression and standing genetic variation, two facilitators of adaptation to high latitudes in European aspen (Populus tremula L.). Molecular Biology and Evolution 38(4) DOI: 10.1093/molbev/msab229

Stuart A’Hara, Roger Moore and Joan Cottrell (2021) Molecular investigation of the pine-tree lappet moth Dendrolimus pini (L.) population in Scotland –a new arrival or an old acquaintance? Agricultural & Forest Entomology DOI: 10.1111/afe.12467

Hayley R. Tumas, Ziad Soufi, John A. Woolliams, J. Paul McLean, Steve Lee, Joan E. Cottrell, Joanna J. Ilska, Gustavo Lopez, and John MacKay (2021) Stranger in a strange land: Genetic variation of native insect resistance biomarkers in UK Sitka spruce (Picea sitchensis [Bong.] Carr.). Forestry 94(5):734-744.

Melissa Minter, David O’Brien, Joan Cottrell, Richard Ennos, Jane K Hill & Jeanette Hall (2021) Exploring the potential for ‘Gene Conservation Units’ to conserve genetic diversity in wild populations. Ecological Solutions & Evidence.

Rosique-Esplugas, C., Cottrell, J.E., Cavers, S., Whittet, R., and Ennos, R.A. (2021) Clinal genetic variation in leaf phenology, growth and stem form in common ash (Fraxinus excelsior L.). Forestry 1–12, doi:10.1093/forestry/cpab026

Ennos, R., Cottrell, J., O’Brien, D., Hall, J. & Mason, W.  (2020) Species diversification – which species should we use? Quarterly Journal of Forestry 114(1):33-41.

Evans, P. M., Newton, A.C., Cantarello, E., Sanderson, N., Jones, D.L., Barsoum, N., Cottrell, J. E., A’Hara, S. W. and Fuller, L. (2019) Testing the relative sensitivity of 102 ecological variables as indicators of woodland condition in the New Forest, UK.  Ecological Indicators, 107: 105575

Cottrell J., A’Hara S. and Adams K. (2018) Conservation of black poplar: insights from a DNA fingerprinting approach. Forestry Commission Research Note 34. Forestry Commission, Edinburgh.

Donnelly K., Cavers S., Cottrell J. E., Ennos R. A. (2018) Cryptic genetic variation and adaptation to waterlogging in Caledonian Scots pine, Pinus sylvestris L. Ecology and Evolution, DOI: 10.1002/ece3.4389

Barsoum, N., A’Hara, S., Cottrell, J. and Green, S. (2018) Using DNA barcoding and metabarcoding to detect species and improve forest biodiversity monitoring. Forestry Commission Research Note 32. Forestry Commission, Edinburgh.

Bellamy, C., Barsoum, N., Cottrell, J.  and Watts, K. (2018) Encouraging biodiversity at all scales in support of resilient woodlands. Forestry Commission Research Note 33. Forestry Commission, Edinburgh.

Woodcock, P., Cottrell, J.E., Buggs, R. J.A. and Quine, C. P. (2018) Mitigating pest and pathogen impacts using resistant trees: a framework and overview to inform development and deployment in Europe and North America. Forestry, 91(1), 1-16.

Kubasiewicz, L M, Quine, C P, Summers, R W, Coope, R, Cottrell, J E, A’Hara, S W and Park, K J. (2017) Non-invasive genotyping and spatial mark-recapture methods to estimate European pine marten density in forested landscapes. HYSTRIX – The Italian Journal of Mammalogy, 28(2), 265-271.

Roger Moore, Joan Cottrell, Stuart A’Hara, Duncan Ray (2017) Pine-tree lappet moth(Dendrolimus pini) in Scotland:Discovery, timber movement controls and assessment of risk. Scottish Forestry 71 (2), 34-43.

Richard Whittet, Stephen Cavers, Joan Cottrell, Cristina Rosique-Esplugas, Richard Ennos (2017) Substantial variation in the timing of pollen production reduces reproductive synchrony between distant populations of Pinus sylvestris L. in Scotland. Ecology & Evolution, DOI: 10.1002/ece3.3154

P. M. Evans, A. C. Newton, E. Cantarello, P. Martin, N. Sanderson, D. L. Jones, N. Barsoum, J. E. Cottrell, S. W. A’Hara, L. Fuller (2017) Thresholds of biodiversity and ecosystem function in a forest ecosystem undergoing dieback. Scientific Reports 7(1) DOI: 10.1038/s41598-017-06082-6

Kevin Donnelly, Joan Cottrell, Richard A. Ennos, Stephen Cavers (2016) Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus. Molecular Ecology Resources DOI: 10.1111/1755-0998.12646.

P. Fuentes-Utrilla, C. Goswami, J. E. Cottrell, R. Pong-Wong, A. Law, S. W. A’Hara, S. J. Lee & J. A. Woolliams (2017) QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data. Tree Genetics & Genomes 13: 33.

Richard Whittet, Stephen Cavers, Joan Cottrell and Richard Ennos (2017) Seed sourcing for woodland creation in an era of uncertainty: an analysis of the options for Great Britain. Forestry doi:10.1093/forestry/cpw037

Duncan S. Procter, Joan E. Cottrell, Kevin Watts, Stuart W. A’Hara, Michael Hofreiter and Elva J. H. Robinson Does cooperation mean kinship between spatially discrete ant nests? Ecology & Evolution DOI: 10.1002/ece3.2590

Richard Whittet, Joan Cottrell, Stephen Cavers, Mireia Pecurulc, Richard Ennos 2016. Supplying trees in an era of environmental uncertainty: Identifying challenges faced by the forest nursery sector in Great Britain. Land Use Policy,58:415-426.

R. Axel W. Wiberg, Andrew R. Scobie, Stuart W. A’Hara, Richard A. Ennos, Joan E. Cottrell 2016 The genetic consequences of long term habitat fragmentation on a self-incompatible clonal plant, Linnaea borealis L. Biological Conservation 201:405-413

de Vries, S.M.G., Alan, M., Bozzano, M., Burianek, V., Collin, E., Cottrell, J., Ivankovic, M., Kelleher, C.T., Koskela, J., Rotach, P., Vietto, L. and Yrjänä, L. 2015 Pan-European strategy for genetic conservation of forest trees and establishment of a core network of dynamic conservation units. Publ. European Forest Genetic Resources Programme (EUFORGEN), Bioversity International, Rome, Italy. ISBN 10: 978-92-9255-029-5.

Kevin Watts, Tytti Vanhala, Thomas Connolly, Joan Cottrell 2016. Striking the right balance between site and landscape-scale conservation actions for a woodland insect within a highly fragmented landscape: A landscape genetics perspective. Biological Conservation 195: 146-155.

Kevin Donnelly, Stephen Cavers, Joan E. Cottrell, Richard A. Ennos 2016 Genetic variation for needle traits in Scots pine (Pinus sylvestris L.). Tree Genetics & Genomes 12(3) DOI: 10.1007/s11295-016-1000-4

A. Perry, A. Brown, S. Cavers, J. E. Cottrell and R. A. Ennos 2016 Has Scots pine (Pinus sylvestris) co-evolved with Dothistroma septosporum in Scotland? Evidence for spatial heterogeneity in the susceptibility of native provenances. Evolutionary Applications DOI: 10.1111/eva.12395

Fady, B., Cottrell, J., Ackzell, L., Alía, R., Muys, B., Prada, A., González-Martínez, S. C., 2015. Forests and global change: what can genetics contribute to the major forest management and policy challenges of the twenty-first century? Regional Environmental Change 16: 927-939

Procter, D.S., Cottrell, J., Watts, K., Robinson E.J.H (2015) Do non-native conifer plantations provide benefits for a native forest specialist, the wood ant Formica lugubris? Forest Ecology and Management 357, 22-32

S. Cavers and J. E. Cottrell(2015) The basis of resilience in forest tree species and its use in adaptive forest management in Britain. 88 (1). 13-26

Gerber, S. Chadoeuf, J. Gugerli, F. Lascoux, M. Buiteveld, J. Cottrell J. et al.(2014)High rates of gene flow by pollen and seed in oak populations across Europe. PLOS ONE. January 2014 | Volume 9 | Issue 1 | e85130 DOI: 10.1371/journal.pone.0085130

Tytti Vanhala, Kevin Watts, Stuart A’Hara & Joan Cottrell (2014) Population genetics of Formica aquilonia wood ants in Scotland: the effects of long-term forest fragmentation and recent reforestation. Conservation Genetics DOI 10.1007/s10592-014-0584-1

Telford, A., Cavers, S., Ennos, R. A. & Cottrell, J.E. 2014. Protecting our forests: variation in resistance to pests and pathogens. Forestry. DOI 10.1093/forestry/cpu012

Jason Hubert & Joan Cottrell 2014. Establishing and Managing a Gene Conservation Unit. FC Practice Note FCPN021

Charlotte Bickler, Stuart A’Hara, Joan Cottrell, Lucy Rogers & Jon Bridle 2013. Characterisation of thirteen polymorphic microsatellite markers for cowslip (Primula veris L.) developed using a 454 sequencing approach. Conservation Genet Resources 5:1135-1137.

S A’Hara & J Cottrell 2013. Development and characterisation of ten polymorphic microsatellite markers for the pine-tree lappet moth Dendrolimus pini (Lepidoptera: Lasiocampidae). Conservation Genetics Resources 5: 1135-1137.

Matti J. Salmela, Stephen Cavers, Joan E. Cottrell, Glenn R. Iason, Richard A. Ennos 2013. Spring phenology shows genetic variation among and within populations in seedlings of Scots pine (Pinus sylvestris L.) in the Scottish Highlands. Plant Ecology & Diversity DOI: 10.1080/17550874.2013.795627.

A’Hara, S.W., Scobie, A.R., Broome, A., Long, D. & Cottrell, J.E. (In press). Development of microsatellite markers in twinflower (Linnaea borealis L.), a rare Scottish pinewood plant. Molecular Ecology Resources

Salmela, M.J., Cavers, S., Cottrell, J.E., Iason, G.R.& Ennos, R.A. (2011). Seasonal patterns of photochemical capacity and spring phenology reveal genetic differentiation among native Scots pine (Pinus sylvestris L.) populations in Scotland. Forest Ecology and Management, 262, 1020-1029.

Stephenson, P., Harris, N., Cottrell, J., Ralph, S., Bohlmann, J. & Taylor, G. (2011). A transcriptomic approach to identify genes associated with wood density in Picea sitchensis. Scandinavian Journal of Forest Research, 26, Supplement 11, 82-96.

Salmela, M.J., Cavers, S., Wachowiak, W., Cottrell, J.E., Iason, G.R.& Ennos, R.A. (2010). Understanding the evolution of native pinewoods in Scotland will benefit their future management and conservation. Forestry, 83, 535-545.

Green, S., Studholme, D.J., Laue, B.E., Dorati, F., Lovell, H., Arnold, D., Cottrell, J., Bridgett, S., Blaxter, M., Huitema E., Thwaites, R., Sharp, P.M., Jackson, R.W. & Kamoun, S. (2010). Comparative Genome Analysis Provides Insights into the Evolution and Adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum. PLOS ONE, Vol. 5 (4) e10224.

de Carvalho, D., Ingvarsson, P.K., Joseph, J., Suter, L., Sedivy, C., Macaya-Sanz, D., Cottrell, J., Heinze, B., Schanzer, S. & Lexer, C. (2010). Admixture facilitates adaptation from standing variation in the European aspen (Populus tremula L.), a widespread forest tree. Molecular Ecology 19, 1638–1650.

Sutherland, B.G., Belaj, A., Nier, S., Cottrell, J.E., Vaughan, S.P., Hubert, J. & Russell, K. (2010). Molecular biodiversity and population structure in common ash (Fraxinus excelsior L.) in Britain; implications for conservation. Molecular Ecology. 19, 2196-2211.

A’Hara, S., Samuel, S. & Cottrell, J. (2009). The role of DNA fingerprinting in the conservation of the native black poplar. British Wildlife, December 2009 110-115.

Cottrell, J.E., Vaughan, S.P., Connolly, T., Sing L., Moodley, D.J.& Russell, K. (2009). Contemporary pollen flow, characterization of the maternal ecological neighbourhood and mating patterns in wild cherry (Prunus avium L.). Heredity 103 (2) 118-128.

A’Hara, S.W., Hancock, M. Piertney, S.B.& Cottrell, J.E. (2009). The development of a molecular assay to distinguish droppings of black grouse (Tetrao tetrix) from those of capercaillie (Tetrao urogallus) and red grouse (Lagopus lagopus scoticus). Wildlife Biology. 15 (3) 328-337.

Jensen, J. Larsen, A., Nielsen, L.& Cottrell, J. (2009). Hybridization between Quercus robur and Q. petraea in a mixed oak stand in Denmark. Annals of Forest Science 66 706-717.

Green, S., Laue, B., Fossdal,C.G., A’Hara, S.W.& Cottrell, J. E. (2009). Infection of horse chestnut (Aesculus hippocastanum) by Pseudomonas syringae pv. aesculi and its detection by quantitative real-time PCR. Plant Pathology 58 731-744.

A’Hara, S.W. & Cottrell, J.E. (2009). Development of a set of highly polymorphic genomic microsatellites (gSSRs) in Sitka spruce (Picea sitchensis (Bong.) Carr.). Molecular Breeding, 23, 349-355.

Vanhala, T.& Cottrell, J. E. (2008). Development of microsatellite markers for the wood cricket, Nemobius sylvestris (Orthoptera: Gryllidae). Molecular Ecology Resources, 8, 1340-1343.

Smulders, M.J.M., Cottrell, J. E., Lefèvre, F., van der Schoot, J., Arens, P., Vosman, B., Tabbener, H. E., Grassi, F., Fossati, T., Castiglione, S., Krystufek, V., Fluch, S., Burg, K., Vornam, B., Pohl, A., Gebhardt, K., Alba, N., Agúndez, D., Maestro, C., Novitol, E., Volosyanchuk, R. T., Pospíšková, M., Bordács, S., Bovenschen, J., van Dam, B. C., Koelewijn, H. P., Halfmaerten, D., Ivens, B., van Slycken, J., Vanden Broeck, A., Storme, V.& Boerjan, W. (2008). Structure of the genetic diversity in Black poplar (Populus nigra L.) populations across European river systems: consequences for conservation and restoration. Forest Ecology and Management, 255, 1388-1399.

Vaughan, S.P., Cottrell, J. E., Moodley, D.J., Connolly, T.& Russell, K. (2007). Clonal structure and recruitment in British wild cherry (Prunus avium L). Forest Ecology and Management, 242, 419-430.

Vaughan, S.P., Cottrell, J.E., Moodley, D.J., Connolly, T. & Russell, K. (2007). Distribution of fine scale genetic structure in British wild cherry (Prunus avium L.) Heredity, 98, 274-283.

A’Hara, S.W. & Cottrell, J.E. (2007). Characterization of a suite of 40 EST-derived microsatellite markers for use in a Sitka spruce (Picea sitchensis (Bong.) Carr.) marker aided selection program. Silvae Genetica, 56: 138-141.

Lowe, A., Unsworth, C., Gerber, S., Davies, S. White, A., Munro, R., Kelleher, C., King, A., Brewer, S. & Cottrell, J. (2006). Route, speed and mode of oak postglacial colonisation across the British Isles : integrating molecular ecology, palaeoecology and modelling approaches. Botanical Journal of Scotland, Special Issue ‘Atlantic Oakwoods’, pp59-82.

Vanden Broeck, A.N., Cottrell, J.E., Quataert, P., Breyne, P., Storme, V., Boerjan, W.& Van Slycken, J. (2006). Paternity analysis of Populus nigra L. offspring in a Belgian plantation of native and exotic poplars Annals of Forest Science 63: 783-790.

Keary, K., A’Hara, S., Whitaker, H. & Cottrell, J. (2005). Assessment of genetic variation in black poplar in Ireland using microsatellites. Irish Forestry 62, 6-18.

A’Hara, S. W. & Cottrell, J.E. (2004). A set of microsatellite markers for use in Sitka spruce (Picea sitchensis) developed from Picea glauca EST sequences. Mol. Ecol. Notes, 4, 659-663.

Cottrell, J.E., Krystufek, V., Tabbener, H.E., Milner, A., Connelly, T. Sing, L., Fluch, S., Burg, K., Lefèvre, F. Achard, P. Bordács, S., Gebhardt, K., Vornam, B., Smulders R., Vanden Broeck, A.H., Van Slycken, J., Storme, V., Boerjan, W., Castiglione, S. Fossati, T., Alba, N., Agúndez, D., Maestro, C., Novitol, E., Bovenschen, J. & van Dam, B. (2005). Post glacial migration of Populus nigra L: lessons learnt from chloroplast DNA. For. Ecol. Manag., 206, 71-90.

Vanden Broeck, A.H., Storme, V., Cottrell, J.E., Boejeran, W., Van Bockstaele, E., Quatert, P. & Van Slycken, J. (2004). Gene flow between cultivated poplars and native black poplar (Populus nigra L.): a case study along the Meuse on the Dutch-Belgian border. For. Ecol. Manag., 107, 285-294.

Storme, V., Boejeran, W., Vanden Broeck, A.H., Ivens, B., Halfmaerten, D., Van Slycken, J, Castiglione, S., Grassi, F., Fossati, T., Cottrell, J.E., Tabbener, HE Lefevre, F., Imbert, E., Fluch, S., Krustufek, V., Burg, K., Bordacs, S., Gebhardt, K., Vornam, B., Pohl, A., Alba, N., Bovenschen, J., van Dam, B., van der Schoot, J., Vosman, B. & Smulders, M.J.M. (2004). Ex situ conservation of black poplar in Europe: duplications and diversity in nine genebank collections and their use for conservation and nature development. Theoretical & Applied Genetics, 108, 969-981

Lowe A.J., Munro, R., Samuel, S. & Cottrell, J.E.(2004). The utility and limitations of chloroplast DNA analysis for identifying native British oak stands and for guiding replanting strategy. Forestry, 77, 335-347.

Cottrell, J.E. Samuel C. J. & Sykes, R. (2004). The species and chloroplast DNA haplotype composition of oakwoods in the Forest of Dean planted between 1720 and 1993. Forestry, 77(2), 100-106.

Tabbener, H.E. & Cottrell, J.E. (2003). The use of PCR based DNA markers to study paternity of poplar seedlings. For. Ecol. Manag. 179, 363-376.

Cottrell, J.E., Munro, R.C., Tabbener, H.E., Milner, A.D., Forrest, G.I. & Lowe, A. (2002). Comparisons of fine scale genetic structure within two British oakwoods using microsatellites; impacts of recolonisation dynamics and past management. For. Ecol & Manag. 176, 287-303.

Forrest, I., Tabbener, H., Cottrell, J. & Connolly, T. (2001). The genetic structures of a range of Douglas-fir provenance collections after planting in different European countries, assessed with two biochemical marker systems. Biochemical Systematics and Ecology. 29, 769-792.

Kremer, A., Dupouey, J. L., Deans, J. D, Cottrell, J., Csaikl, U., Finkeldey, R., Espinel, S., Jensen, J., Kleinschmit, J., Van Dam, B.,Ducousso, A., Forrest, I., Lopez de Heredia, U., Lowe, A. J., Tutkova, M., Munro, R. C., Steinhoff, S. & Badeau, V. (2002). Leaf morphological differentiation between Quercus robur and Quercus petraea is stable across western European mixed oak stands. Annals of Forest Science, 59, 777-787.

Petit, R.J., Brewer, S.,Bordacs, S.,Burg, K.,Cheddadi, R., Coart, E., Cottrell, J., Csaikl, U., Deans, D., Fineschi, S., Finkeldey, R., Goicoechea, P., Jensen, J., Konig, A., Lowe, A., Madsen, S.F., Matyas, G., Munro, R.C., Oledska, I., Slade, F.P.D., Tabbener, H., Van Dam, B., Ziegenhagen, B., de Beaulieu, J.& Kremer, A.(2002). Postglacial colonisation routes of European white oaks inferred from the variation of chloroplast DNA and from the analysis of fossil pollen. For Ecol Manag 156, 49-74.

Petit, R.J., Csaikl, U., Bordacs, S., Burg, K., Coart, E., Cottrell, J., Deans, D., Dumolin-Lapegue, S., Fineschi, S., Finkeldey, R., Gillies, A., Goicoechea, P., Jensen, J., Konig, A., Lowe, A., Madsen, S.F., Matyas, G., Oledska, I., Pemonge, M., Slade, F.P.D., Tabbener, H., Taurchini, D., Van Dam, B., Ziegenhagen, B.& Kremer, A.(2002). Chloroplast DNA variation in European white oaks: synthesis based on data from over 2500 populations. For Ecol Manag 156, 5-26.

Mariette, S., Cottrell, J.E., Csaikl, U., Goikoetxea, P., Konig, A., Lowe, AJ., Van Dam, B.C., Barreneche, T., Bodenes, C., Streiff, R. & Kremer, A. (2002). Comparison of levels of genetic diversity detected with AFLP and microsatellite markers within and among mixed Q. petraea (Matt) Leibl. and Q. robur stands. Silvae Genetica, 51, 72-79.

Kremer, A., Kleinschmit, J., Cottrell, J., Cundall, N., Deans, J.D., Ducousso, A., Koenig, A., Lowe, A.J.,Munro, R.C., Petit, R.J. & Ziegenhagen, B. (2002). Is there a correlation between chloroplastic and nuclear divergence, or what are the roles of history and selection on genetic diversity in European oaks? For. Ecol. Manag. 156, 75-88.

Cottrell, J.E., Munro, R.C., Tabbener, H.E., Gillies, A.C.M., Forrest, G.I., Deans, J.D. & Lowe, A.J. (2002). Distribution of chloroplast DNA variation in British oaks (Quercus robur and Q. petraea):the influence of postglacial colonisation and human management. For. Ecol. Manag. 156,181-196

Provan, J., Soranzo, N., Wilson, N.J., McNicol, J.W., Forrest, G.I., Cottrell, J. & Powell W. (1998). Gene pool variation in Caledonian and European Scots pine (Pinus sylvestris L.) revealed by chloroplast simple sequence repeats Proceedings of the Royal Society of London B, 265: 1697-1705.

Cottrell, J.E., Forrest, G. I. & White, I.M.S. (1997). The use of RAPD analysis to study diversity in British black poplar (Populus nigra L. (Pursch) W. Wettst. (Salicaceae) in Great Britain. Watsonia, 21, 305-312.

Cottrell, J.E., Forrest, G. I. & White, I.M.S. (1997). The use of Random Amplified Polymorphic DNA markers to identify and estimate the relatedness of clones belonging to the genus Populus. Bot J. Scotl. 49, 89-102.

Cottrell, J.E. & White, I.M.S. (1995). The use of isozyme genetic markers to estimate the rate of outcrossing in a Sitka spruce (Picea sitchensis (Bong. Carr.) seed orchard. New Forests, 10, 111-122.

Cottrell J.E., Duffus, C. M., Paterson, L. & Mackay, G.R. (1995). Properties of potato starch: effects of genotype and growing conditions. Phytochemistry, 40, 1057-1064.

Cottrell, J.E., Duffus, C.M., Mackay, G.R. & Allison, M.J. (1993). The effects of storage on the surface morphology of starch granules of the cultivated potato, Solanum tuberosum L. Potato Research, 36, 107-117.

Cottrell, J.E., Duffus, C.M., Mackay, G.R., Allison, M.J. & Bain, H. (1993). The effect of storage temperature on reducing sugar concentration and the activities of three amylolytic enzymes in tubers of the cultivated potato, Solanum tuberosum L. Potato Research, 36, 119-125.

Duffus, C.M., Cottrell, J.E., Mackay, G.R. & Allison M.J. (1991). Low temperature sweetening in potatoes. Plant Physiology, 96, 58-60.

Cottrell, J.E. & Dale, J.E. (1986). The effects of photoperiod and gibberellic acid on the concentration of soluble carbohydrate in the shoot apex of spring barley. New Phytologist, 102, 365-373.

Cottrell, J.E., Dale, J.E. & Jeffcoat, B. (1985). Early growth of the developing ear in barley. Annals of Botany, 55, 827-833.

Cottrell, J.E., Easton, R.H., Dale, J.E., Wadsworth, A.C., Adam, J.S., Child, R.D. & Hoad, G.V. (1985). A comparison of spike and spikelet survival in mainstem and tillers of barley. Annals of Applied Biology, 106, 365-77.

Cottrell, J.E. & Dale, J.E. (1984). Variation in size and development of spikelets within the ear of barley. New Phytologist, 97, 565-573.

Cottrell, J.E., Dale, J.E. & Jeffcoat, B. (1983). The effect of application of gibberellic acid on vegetative and apical development of nutans and erectum barleys. Zeitschrift fur Pflanzenphysiologie, 112, 123-130.

Cottrell, J.E., Dale, J.E. & Jeffcoat, B. (1981). The effects of daylength and treatment with gibberellic acid on spikelet initiation and development in Clipper barley. Annals of Botany, 50, 57-68.

Cottrell, J.E., Dale, J.E. & Jeffcoat, B. (1981). Development of the apical dome in response to treatment with gibberellic acid. Plant Science Letters, 22, 161-168.

Popular/technical papers

Whittet, R., Ennos, R., Cavers, S., Cottrell, J. (2019) Genetic considerations for provenance choice of native trees under climate change in England. Forestry Commission Research Report. Forestry Commission, Edinburgh.

Joan Cottrell, Stuart A’Hara and Ken Adams (2018) Conservation of black poplar: insights from a DNA fingerprinting approach. FCRN034: 1-16.

Barsoum, N., A’Hara, S., Cottrell, J. and Green, S. (2018) Using DNA barcoding and metabarcoding to detect species and improve forest biodiversity monitoring. Forestry Commission Research Note 32. Forestry Commission, Edinburgh.

Bellamy, C., Barsoum, N., Cottrell, J.  and Watts, K. (2018) Encouraging biodiversity at all scales in support of resilient woodlands. Forestry Commission Research Note FCRN033. Forestry Commission, Edinburgh.

Jason Hubert & Joan Cottrell (2014) Establishing and managing gene conservation units. FCPN 2: 1-7.

Hubert, J. & Cottrell, J. (2007). The role of forest genetic resources in helping British forests respond to the effects of climate change (PDF-960K). Research Information Note 86.

Lee, S.J., A’Hara, S., & Cottrell, J. (2006). The use of DNA technology to advance the Sitka spruce breeding programme (PDF-1635K). In:Forest Research Annual Report, pp 30-35.

Cottrell, J., Trout, R., Quine, C. & O’Reilly, C. (2006). Molecular method to differentiate pine marten and fox scats (PDF-2295). In:Forest Research Annual Report, pp 17.

Cottrell, J.E. (2004). Conservation of Black Poplar (Populus nigra L.)(PDF-184K). Forestry Commission Information Note 57.

Lee, S.J., Cottrell, J. & John, A. (2004). Advances in Biotechnology-powerful tools for tree breeding and genetic conservation. Research Information Note

Van Dam, B., Vanden Broeck, A., Cottrell, J. & Heinze, B. (2002). Genetic diversity in Black poplar and the implication for riparian ecosystem management, summary of the panel discussion. In ‘Genetic diversity in river populations of European Black Poplar-implications for riparian eco-system management.’ Eds. B. van Dam & S. Bordacs, pp 229-231.

Lefevre, F., Bordacs, S., Cottrell, J., Gebhardt, K., Smulders, M.J.M., Vanden Broeck, A., Vornam, B. & van Dam, B.C. (2002). Recommendations for riparian ecosystem management based on the general frame defined in EUFORGEN and results from Europop. In ‘Genetic diversity in river populations of European Black Poplar-implications for riparian eco-system management.’ Eds. B. van Dam & S. Bordacs, pp 157-162.

Cottrell, J.E., Tabbener, H.E. & Forrest, G.I. (2002). Distribution of variation in British black poplar: the role of human management. In ‘Genetic diversity in river populations of European Black Poplar-implications for riparian eco-system management. Eds. B. van Dam & S. Bordacs. Pp 73-84.

Kremer, A., Petit, R. J., Csaikl, U., Beaulieu, J. L., Bordacs, S., Brewer, S., Burg, K., Cheddadi, R., Coart, E., Cottrell, J., Cundall, N., Deans, D., Fineschi, S., Finkeldey, R., Gillies, A., Goicoechea, P., Grossini, P., Halle, C. L., Jensen, J. S. Kleinschmit, J., Konig, A., Lowe, A., Madsen, S. F., Matyas, G., Munro, R., Olalde, M., Oledska, I., Pemonge, M. H., Popescu F., Reille, M., Slade, D., Steinhoff, S., Tabbener, H.E., Van Dam, B., De Vries, S. & Ziegenhagen, B. (2001). Range wide distribution of the chloroplast DNA and pollen deposits in European white oaks: Inferences about colonisation routes, impact of chloroplastic divergence on phenotypic differentiation. IUFRO Conference, Zagreb.

Cottrell, J. E., Tabbener, H. E. Munro, R.C. Gillies, A.C.M., Forrest, G.I., Deans, D. & Lowe, A.J. (2001). Chloroplast DNA variation in British oak populations. Forest Research Annual Report, 39-41.

Cottrell, J., Tabbener, H., Munro, R., Gillies, A., Forrest, I., Deans, D. & Lowe, A. (2000). Chloroplast DNA variation in British oak populations. Forest Research Annual Report and Accounts 199-2000, pp 38-41.

Forrest, I. & Cottrell, J. (1996). Genetic diversity of native black poplar. Report on Forest Research 1996, pp 48-50.

Cottrell, J.E., Cochrane, M.P., Duffus, C.M., Allison, M.J. & Mackay, G.R. (1990). The effect of low temperature storage on the amylolytic activity of potato tubers. In ‘Abstracts of conference papers and posters of the 11th Triennial conference of the EAPR. 151 pages.

Cottrell, J.E., Dale, J.E. & Jeffcoat, B. (1981). Endogenous control of spikelet initiation and development in barley. British Plant Growth Regulator Group, Monograph 7, 130-139.

Book chapters

‘Spruce’. Jean Bousquet, Nathalie Isabel, Betty Pelgas, Joan Cottrell, Dainis Rungis, Kermit Ritland. In: Genome Mapping and Molecular Breeding in Plants, Vol. 7 Forest Trees, Chitta R. Kole (Ed). Springer, Heidelberg, Berlin, New York, Tokyo (in press).

Edited proceedings

‘Atlantic Oakwoods – A Botanical Society of Scotland Symposium’ 2005. Edited by Douglas Malcolm, Patricia Cochrane, Joan Cottrell & David Chamberlain. Edinburgh University Press.