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Responsibilities include Project Leader for Forest Reproductive Material and managing the Molecular Biology Laboratory.

In addition to carrying out conservation and tree breeding based research, the laboratory offers a commercial molecular service for clonal identification and species identification e.g. DNA fingerprinting black poplar clones and species identification from droppings (bat species/pine marten/grouse).

Stuart joined Forest Research in 2003, where he specialises in applying DNA based techniques to tree breeding and ecological issues. He studied Zoology at Aberdeen University (1989-93), Biotechnology at the University of Abertay (1993-94) and received his PhD from Edinburgh University (1994-1998) for his thesis on the Population Structure of Linyphiid Spiders. Prior to joining FR, Stuart worked as a postdoctoral scientist at the Roslin Institute and at the Scottish Agricultural College.


Forest Research representative in EUFORGEN Forest Reproductive Material working group
Memorandum of Understanding with Genome Canada consortium for partnership in Molecular Breeding

Research Scientist
Forest genetics

Forest Research

Northern Research Station


Midlothian EH25 9SY


Related Research



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.

Status current

Related Publications


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 […]



Using DNA barcoding and metabarcoding to detect species and improve forest biodiversity monitoring

Growing threats to biodiversity from pressure of land use, climate change, and invasive pests and diseases highlight the importance of obtaining accurate baseline measurements of current forest biodiversity, as well as improved monitoring to detect early signals of change. Developments in molecular techniques have advanced to the stage that there are now practical methods available […]

The genetic consequences of long term habitat fragmentation on a self-incompatible clonal plant, Linnaea borealis L.

Study finds twinflower in Scotland exhibits genetic effects of chronic population fragmentation Habitat fragmentation is widely thought to contribute to the decline of plant species. In part, this is due to the restriction it places on the flow of genes (which occurs through pollen and seed dispersal) within a plant population, creating sub-populations within which localised […]

Other Research



Genetic Conservation

Monitoring presence of bird and mammal species using molecular markers designed for use with faecal samples.
Development and application of microsatellite DNA markers in Twinflower (Linnae borealis) and squirrel.
Supporting Forest Reproductive Material (FRM) regulations for black poplar and aspen by identification of clones used in propagation.
Genetic investigation of Pine-tree Lappet moth using mitochondrial sequence data and microsatellite markers.
Selection and testing of conifers
Responsible for development of Marker Assisted Selection program in Sitka spruce, including the generation of a Sitka genetic linkage map and QTL discovery for commercial traits of interest.

Involved with NovelTree EU project (2008-2012) which aimed to mobilise and integrate European scientific research and resources on forest tree genetics to (i) develop genomic tools for plant breeding, efficient gene isolation, and optimised exploitation of genetic resources and (ii) demonstrate novel/improved methods to breed trees with improved quality and quantity parameters. This work continued in the EU funded PROCOGEN project (2012-2015). Currently, involved with the BBRSC funded Sitka Spruced project and the PuRpOsE oak health WP2.

Peer reviewed journal articles

A’Hara, S., Moore, R. and Cottrell, J. (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

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

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

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.

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.

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

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. Accepted for publication.

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

Fuentes-Utrilla, P., Goswami, C., Cottrell, J. E, Pong-Wong, R., Law, A., A’Hara, S. W., Lee S. J., Woolliams, J. A. (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. DOI 10.1007/s11295-017-1118-z

Donnelly K, Cottrell J, Ennos RA, Vendramin GG, A’Hara S, King S, Perry A, Wachowiak W and Cavers S. (2016). Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus. Molecular Ecology Resources, doi: 10.1111/1755-0998.12646

M. Coleman, S.W. A’Hara, P.R. Tomlinson, and P.J. Davey Elm clone identification and the conundrum of the slow spread of Dutch Elm Disease on the Isle of Man. New Journal of Botany Vol. 6, Iss. 2-3, 2016

Procter, D.S., Cottrell, J.E., Watts, K., A’Hara, S.W., Hofreiter, M., Robinson, E.J.H. (2016). Does cooperation mean kinship between spatially discrete ant nests? Ecology & Evolution DOI: 10.1002/ece3.2590

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

Konnert, M., Fady, B., Gömöry, D., A’Hara, S., Wolter, F., Ducci, F., Koskela, J., Bozzano, M., Maaten, T. and Kowalczyk, J. 2015 Use and transfer of forest reproductive material in Europe in the context of climate change. Publ. European Forest Genetic Resources Programme (EUFORGEN), Bioversity International, Rome, Italy. ISBN 10: 978-92-9255-031-8

Pankhurst M., A’Hara S. and Cottrell J. (2015). The Fraternal Four. British Wildlife Vol 26 No.3

A’Hara S., Samuel S. and Cottrell J. (2009) The role of DNA-fingerprinting in the conservation of the native Black Poplar. British Wildlife Vol 21 No.2

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.

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

A’Hara, S.W., Scobie, A.R., Broome, A., Long, D. & Cottrell, J.E. (2011). Development of microsatellite markers in twinflower (Linnaea borealis L.), a rare Scottish pinewood plant. Molecular Ecology Resources 12(1):185-9.

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

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

Green, S., Laue, B., Gunnar-Fossdal, C., A’Hara, and S., Cottrell, J. (2008). Quantitative real-time PCR detection of Pseudomonas syringae pv. aesculi in Horse Chestnut (Aesculus hippocastanum). Plant Pathology (2009) 58, 731–744.

A’Hara, S.W. and Cottrell, J.E. (2007). Characterization of a suite of 40 EST-derived microsatellite markers for use in Sitka Spruce (Picea sitchensis (Bong.) Carr). Silvae Genetica.56 (3-4) p. 138-141

Lee, S.J. and A’Hara, S. (2006). Marker Aided Selection in Sitka. Forestry and British Timber: 35(1), January 2006, 14-16.

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

A’Hara, S. and Cottrell, J.E. (2004). A set of microsatellite markers for use in Sitka Spruce (Picea sitchensis) developed from Picea glauca EST sequences. Molecular Ecology Notes 4(4), 659-663.

Schmid, M., Nandra, I., Guttenbach, M., Steinlein, C., Hoehn, H., Schartl, M., Haaf, T., Weigend, S., Fries, R., Buerstedde, J.M., Wimmers, K., Burt, D.W., Smith, J., A’Hara, S. et al. (2000). First report on chicken genes and chromosomes 2000. Cytogenetics and Cell Genetics 90 (3-4) 169-218.

A’Hara, S., Harling, R. and McKinlay, R. (2000). Application of molecular marker technology in practise: population structure in the spiders Lepthyphantes tenuis and Enoplognatha ovata. Proceedings of the Workshop on Molecular Marker Techniques, CIPM, Institut Pertanian Bogor, Indonesia.

A’Hara, S. and Burt, D. (1999). SNPs in Poultry. Proceedings of the Second International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis.

A’Hara, S., Harling, R. and McKinlay, R. (1998). RAPD profiling of spider (Aranea) DNA. Journal of Arachnology, 26, 397-400.

Fenton, B., Malloch, G., Jones, A.T., Armine, J.W., Gordon, S.C., A’Hara, S., McGavin, W.J. and Birch, A.N.E. (1995). Species identification of Cecidophyopsis Mites (Acari, Eriophyidae) from different Ribes species and countries using molecular genetics. Molecular Ecology 4(3), 383-387.