Research Associates

Dr Alan Lee

Dr Alan Tristram Kenneth Lee

BSc Hons (Witwatersrand, RSA), Dip Comp (Open, UK), PhD (Manchester Metropolitan, UK)

Tel: +27 (0)44 752 1254
Cell: +27 (0)79 245 4015


Research interests

Alan’s principal research interest is in conservation biology and southern Africa’s endemic birds, specifically the use of the South African Bird Atlas Project (SABAP2) database for informing conservation decisions. Alan’s research has been focused extensively on the fynbos biome of South Africa, with a focus now on the Karoo biome through the Karoo Birds Survey in partnership with BirdLife South Africa and SANBI’s Karoo BioGaps project. Alan is additionally involved in research on parrots and aspects of tropical rainforest ecology. He enjoys R and statistical modelling.

About Alan

Alan did his PhD at the Manchester Metropolitan University, UK, with Stuart Marsden and Donald Brightsmith (Texas A&M University) investigating the use of riverside claylicks by an Amazon rainforest parrot community (2006-10). Prior to this, Alan was involved with Project Fauna Forever (2003-05), run by Dr Chris Kirkby (University of East Anglia), which investigates the human impact across a wide range of biological taxa. Alan has also worked in partnership with award winning conversation organisation Biosphere Expeditions on monitoring both Amazon and South African wildlife.

Alan joined the Fitz in 2012 to begin a postdoctoral research fellowship investigating the impacts of climate change on the Fynbos bird community, supervised by Phil Hockey and Phoebe Barnard. This research developed in partnership with other researchers and students to cover a wide variety of topics focused on fynbos birds and ran for 5 years. He currently lives on, and hosts much of his research from, the Blue Hill Nature Reserve, a CapeNature stewardship nature research on the edge of the Baviaanskloof. He has won awards for photography and research presentations, and blogs at

As of July 2016 Alan serves as Editor-in-Chief of Ostrich: Journal of African Ornithology. 


Amazonian parrots and geophagy

Working in conjunction with tourism lodges like Rainforest Expeditions, Alan spent 5 years working on his MPhil/PhD in the Peruvian Amazon rainforests of Tambopata. The focus was on counting birds in the forests and on the claylicks, resulting in guidelines for tourist and boat traffic management at sites where tourists frequently visit the hundreds of birds consuming soil on riverside claylicks. Alan continues to work through and publish on the dataset accumulated during this time.

Fynbos birds and ecology

Alan is probably most well known locally for his biome wide surveys of the Fynbos, done initially by bicycle. He used distance sampling techniques as well as species distribution modelling approaches to examine distributions and population trends of six endemic passerine birds of the Fynbos. Then, in conjunction with BirdLife South Africa, he resurveyed the biome with multiple teams of people to track down and document density and distribution of the elusive, endemic Hottentot Buttonquail. Undertaking these impossible tasks has resulted him being labelled an ‘extreme biologist’.

Karoo birds

A survey of the massive Karoo biome (an arid environment 5x larger than the fynbos) is Alan’s next research challenge, again in partnership with BirdLife South Africa. The Karoo hosts many specialist bird species which pose unique challenges in determining their ranges and populations. This project is scheduled to run from 2017 to 2018, offering further opportunities for collaboration and student projects. This is fundamentally a conservation biology project aiming to determine estimates of population size, range and trends; and map conservation priority areas. However, another important aim is to link SABAP2 reporting rates to density estimates to facilitate dynamic and real time monitoring of populations through this impressive citizen science program.

Citizen Science

Alan is a big fan of citizen science, as not only does it allow the collection of ‘Big Data’, but it also creates an important bridge between ivory tower academia and the lay person. Many of his publications during his postdoc used, or commented on methods of using, SABAP data. He contributes regularly, both to the atlas project and as a bird ringer.

Current students

Campbell Fleming: Population genetics of Cape Sugarbird (Co-supervisors: Peter Ryan, Jaqui Bishop, Phoebe Barnard)

Krista Oswald: Threats of climate change to a Fynbos-endemic bird: flexibility in physiological and behavioural mechanisms in the Cape Rockjumper (Co-supervisors: Ben Smit, Susan Cunningham)

Graduated students

Jerry Mokgatla Molepo. MSc 2017. Comparative physiology of Cape Sugarbird (Co-supervisors: Ben Smit (NMMU), Susie Cunningham)

Matthew Macray. CB MSc 2017. Impact of fence type on tortoise distribution in the southeastern Karoo (Co-supervisor: Peter Ryan)

Peter Cowen. MSc 2008: Parrot ecology in a modified landscape, Tambopata, Peru (Co-supervisor: Stuart Marsden).

Robyn Milne. CB MSc 2014. Physiological consequences of high temperatures in fynbos birds and implications for climate change. (Co-supervisors: Peter Ryan, Ben Smit, Susan Cunningham)

Recent peer-reviewed publications


Lee, A.T.K., Wright, D.R. and Reeves, B. 2017. Habitat variables associated with encounters of hottentot buttonquail turnix hottentottus during flush surveys across the fynbos biome. Ostrich 89: 13-18.


Berkunsky, I., Quillfeldt, P., Brightsmith, D.J., Abbud, M.C., Aguilar, J.M.R.E., Alemán-Zelaya, U., Aramburú, R.M., Arias, A.A., McNab, R.B., Blasby, T.J.S., Barberena, J.M.B., Beissinger, S.R., Rosales, M., Berg, K.S., Bianchi, C.A., Blanco, E., Bodrati, A., Bonilla-Ruz, C., Botero-Delgadillo, E., Canavelli, S.B., Caparroz, R., Cepeda, R.E., Chassot, O., Cinta-Magallón, C., Cockle, K.L., Daniele, D., de Araujo, C.B., de Barbosa, A.E., de Moura, L.N., Castillo, H.D., Díaz, S., Díaz-Luque, J.A., Douglas, L., Rodríguez, A.F., García-Anleu, R.A., Gilardi, J.D., Grilli, P.G., Guix, J.C., Hernández-Muñoz, A., Hiraldo, F., Horstman, E., Portillo, R.I., Isacch, J.P., Jiménez, J.E., Jayner, L., Juarez, M., Kacoliris, F.P., Kanaan, V.T., Klemann-Júnior, L., Latta, S.C., Lee, A.T.K., Lesterhuis, A., Lezama-López, M., Lugarini, C., Marateo, G., Marinelli, C.B., Martínez, J., McReynolds, M.S., Urbina, C.R.M., Monge-Arias, G., Monterrubio-Rico, T.C., Nunes, A.P., Nunes, FdP., Olaciregui, C., Ortega-Arguelles, J., Pacifico, E., Pagano, L., Politi, N., Ponce-Santizo, G., Reyes, H.O.P., Prestes, N.P., Presti, F., Renton, K., Reyes-Macedo, G., Ringler, E., Rivera, L., Rodríguez-Ferraro, A., Rojas-Valverde, A.M., Rojas-Llanos, R.E., Rubio-Rocha, Y.G., Saidenberg, A.B.S., Salinas-Melgoza, A., Sanz, V., Schaefer, H.M., Scherer-Neto, P., Seixas, G.H.F., Serafini, P., Silveira, L.F., Sipinski, E.A.B., Somenzari, M., Susanibar, D., Tella, J.L., Torres-Sovero, C., Trofino-Falasco, C., Vargas-Rodríguez, R., Vázquez-Reyes, L.D., White, T.H. Jr., Williams, S., Zarza, R. and Masello, J.F. 2017. Current threats faced by Neotropical parrot populations. Biological Conservation 214: 278-287.

Lee, A.T.K. 2017. Sentinel behavior or vigilance at a macaw claylick. Ornitología Neotropical 28: 253-260.

Lee, A.T.K. and Barnard, P. 2017. How well do bird atlas reporting rates reflect bird densities? Correlates of detection from the fynbos biome, South Africa, with applications for population estimation. Ostrich 88: 9-17.

Lee, A.T.K., Altwegg, R. and Barnard, P. 2017. Estimating conservation metrics from atlas data: the case of southern African endemic birds. Bird Conservation International 27: 323-336.

Lee, A.T.K., Marsden, S.J., Tatum-Hume, E. and Brightsmith, D.J. 2017. The effects of tourist and boat traffic on parrot geophagy in lowland Peru. Biotropica 49: 716-725.

Lee, A.T.K., Wright, D. and Barnard, P. 2017. Hot bird drinking patterns: drivers of water visitation in a fynbos bird community. African Journal of Ecology 55: 541-553.

Mackay, B., Lee, A.T.K., Barnard, P., Møller, A.P. and Brown, M. 2017. Urbanization, climate and ecological stress indicators in an endemic nectarivore, the Cape Sugarbird. Journal of Ornithology 158: 1013-1024.


Lee, A.T.K. and Barnard, P. 2016. How well do bird atlas reporting rates reflect bird densities? Correlates of detection from the fynbos biome, South Africa, with applications for population estimation. Ostrich.


Lee, A.T.K. and Barnard, P. 2015.  Endemic birds of the Fynbos biome: a conservation assessment and impacts of climate change. Bird International Conservation 26:52-68.

Lee, A.T.K. and Barnard P. 2015. Spatial and temporal patterns of insect-order activity in the fynbos, South Africa. Journal of Entomology and Zoology Studies 3:95-102.

Lee, A.T.K., Barnard, P. and Hockey, P.A.R. 2015. Population metrics for Fynbos birds, South Africa: densities, detection- and capture rates from a Mediterranean type ecosystem. Ostrich 86:179-187.

Milne, R., Cunningham, S.J., Lee, A.T.K. & Smit, B. 2015. The role of thermal physiology in recent declines of birds in a biodiversity hotspot. Conservation Physiology 3:1-17.