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 bluehillescape.blogspot.com

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, Jacqui Bishop, Phoebe Barnard)

Sanjo Rose:  Breeding ecology, habitat use and threats to the Agulhas Long-billed Lark Certilauda brevirostris in the Overberg Region of South Africa (Co-supervisors: Robert Thomson and Peter Ryan)

Graduated students

Krista Oswald. PhD (Rhodes). 2019. Threats of climate change to a Fynbos-endemic bird: flexibility in physiological and behavioural mechanisms in the Cape Rockjumper (Co-supervisors: Ben Smit and Susan Cunningham)

Jerry Mokgatla Molepo. MSc (NMMU) 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)

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)

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

Recent peer-reviewed publications


Lee, A.T., Herrmann, E., Retief, E.F., van der Westhuizen-Coetzer, E. and Seymour, C.L. 2023. The impact of a massive wildfire event on avian species richness and abundance in an arid African savanna ecosystem. Journal of Arid Environments 217.  https://doi.org/10.1016/j.jaridenv.2023.105039

Lee, A.T.K., Whitecross, M.A., Smit-Robinson, H.A., Allan, D.G., van den Heever, L., Jenkins, A., Retief, E.F., Colyn, R.B., Tarboton, W., Chetty, K. and Brink, C.W. 2023. A review of the conservation status of Black Stork Ciconia nigra in South Africa, Lesotho, and Eswatini. Bird Conservation International 33.  https://doi.org/10.1017/S0959270923000059


Lee, A.T.K. 2022. How do we feel, African Ornithology? A sentiment analysis search for symptoms of eco-anxiety. Ostrich, 93: 141-146.  https://doi.org/10.2989/00306525.2022.2114640

Lee, A.T., Brooks, M., & Underhill, L. G. 2022. The SABAP2 legacy: A review of the history and use of data generated by a long-running citizen science project. South African Journal of Science 118. https://doi.org/10.17159/sajs.2022/12030

Theuerkauf, J., Villavicencio, C.P., Adreani, N.M., Attisano, A., Craig, A., D’Amelio, P.B., Gula, R., Lee, A.T.K., Mentesana, L., Quillfeldt, P. and Quirici, V. 2022. Austral birds offer insightful complementary models in ecology and evolution. Trends in Ecology & Evolution 37: 759-767. https://doi.org/10.1016/j.tree.2022.05.003


Alexander, G.J., Tolley, K.A., Maritz, B., McKechnie, A., Manger, P., Thomson, R.L., Schradin, C., Fuller, A., Meyer, L., Hetem, R.S., Cherry, M., Conradie, W., Bauer, A.M., Maphisa, D., O’Riain, J., Parker, D.M., Mlambo, M.C., Bronner, G., Madikiza, K., Engelbrecht, A., Lee, A.T.K., Jansen van Vuuren, B., Mandiwana-Neudani, T.G., Pietersen, D., Venter, J.A., Somers, M.J., Slotow, E., Strauss, J.M., Humphries, M.S., Ryan, P.G., Kerley, G.I.H. 2021. Excessive red tape is strangling biodiversity research in South Africa. South African Journal of Science 117.  https://doi.org/10.17159/sajs.2021/10787

Lee, A.T.K. 2021. Best student article published in Ostrich during 2020: we hope to see vultures circling again one day. Ostrich 92: iii-iv. https://doi.org/10.2989/00306525.2021.1901339 

Lee, A.T.K. 2021. Effects of climate change on birds (2nd Edn). Ostrich 92: 168-171. https://doi.org/10.2989/00306525.2021.1891763 

Lee, A.T.KMacray, M.B.Ryan, P.G. and Alexander, G.J. 2021. Tortoise mortality along fence lines in the Karoo region of South Africa. Journal for Nature Conservation 59. https://doi.org/10.1016/j.jnc.2020.125945 

Lee, A.T.K., Ottosson, U., Jackson, C., Shema, S. and Reynolds, C. 2021. Urban areas have lower species richness, but maintain functional diversity: insights from the African Bird Atlas Project. Ostrich 92: 1-15. https://doi.org/10.2989/00306525.2021.1902876 IF: 1.364

Lee, A.T., Macray, M.B., Ryan, P.G. and Alexander, G.J. 2021. Tortoise mortality along fence lines in the Karoo region of South Africa. Journal for Nature Conservation 59. https://doi.org/10.1016/j.jnc.2020.125945

Oswald, K.N. and Lee, A.T.K. 2021. Population Viability Analysis for a vulnerable ground-nesting species, the Cape Rockjumper Chaetops frenatus: assessing juvenile mortality as a potential area for conservation management. Ostrich 92: 234-238. https://doi.org/10.2989/00306525.2021.1984337 

Oswald, K.N., Smit, B., Lee, A.T., Peng, C.L., Brock, C. and Cunningham, S.J. 2021. Higher temperatures are associated with reduced nestling body condition in a range‐restricted mountain bird. Journal of Avian Biologyhttps://doi.org/10.1111/jav.02756



Henry, D.A., Lee, A.T. and Altwegg, R. 2020. Can time‐to‐detection models with fewer survey replicates provide a robust alternative to traditional site‐occupancy models? Methods in Ecology and Evolution 11: 643-355. https://doi.org/10.1111/2041-210X.13379 

Lee, A.T.K. 2020. A celebration of 90 years of Ostrich: a review of past, present, and future directions. Ostrich 91(3): iii-xx. https://doi.org/10.2989/00306525.2020.1818045 

Lee, A.T.K. 2020. Best student article published in Ostrich in 2019: hold onto your saddle, Bill, for the story behind a close race. Ostrich 91:1: iii-v. https://doi.org/10.2989/00306525.2020.1739810 

Lee, A.T.K. and Nel, H. 2020. BirdLasser: The influence of a mobile app on a citizen science project. African Zoologyhttps://doi.org/10.1080/15627020.2020.1717376 

Lee, A.T.K. and Wright, D.R. 2020. Patterns of bird species richness at two sampling scales in the Karoo biome of South Africa. Journal of Arid Environments 174. https://doi.org/10.1016/j.jaridenv.2019.104077 

Lee, A.T.K., Barnard, P., Fraser, M., Lennard, C., Smit, B. and Oschadleus, H.D. 2020. Body mass and condition of a fynbos bird community: investigating impacts of time, weather and raptor abundance from long-term citizen- science datasets. Ostrich 91(2): 142-157. https://doi.org/10.2989/00306525.2019.1683093 

Lee, A.T.K., Macray, M.B., Ryan, P.G. and Alexander, G.J. 2020. Tortoise mortality along fence lines in the Karoo region of South Africa. Journal for Nature Conservation 59. https://doi.org/10.1016/j.jnc.2020.125945 

Oswald, K.N., Diener, E.F., Diener, J.P., Cunningham, S.J., Smit, B. and Lee, A.T.K. 2020. Increasing temperatures increase the risk of reproductive failure in a near threatened alpine ground‐nesting bird, the Cape Rockjumper Chaetops frenatusIbishttps://doi.org/10.1111/ibi.12846 

Oswald, K.N., Lee, A.T. and Smit, B. 2020. Seasonal metabolic adjustments in an avian evolutionary relict restricted to mountain habitat. Journal of Thermal Biology 95. https://doi.org/10.1016/j.jtherbio.2020.102815 


de Kock, C. and Lee, A.T.K. 2019. Agulhas long-billed lark (Certhilauda brevirostris) densities, population estimates and habitat association in a transformed landscape. African Zoology 54(3): 161-168. https://doi.org/10.1080/15627020.2019.1629339 

de Swardt, D.H., Lee, A., Butler, H.J.B. and Oschadleus, H.D. 2019. Biometrics and diet of two closely related birds: Karoo Prinia (Prinia maculosa) and Drakensberg Prinia (Prinia hypoxantha). Indago 34(2): 125-133. 

Lee, A.T.K. 2019. Best student research paper published in Ostrich 2018. Ostrich 90(1): iii-v. https://doi.org/10.2989/00306525.2019.1581550 


Lee, A.T.K., Geary, C., Wright, D.R. and Dean, W.R.J. 2019. Vulnerability of birds to contaminated water sources in the Karoo region of South Africa. Ostrich 90:4. https://doi.org/10.2989/00306525.2019.1638846 

Lee, A.T., Reeves, B. and Wright, D.R. 2019. Hottentot Buttonquail Turnix hottentottus: Endangered or just overlooked?. Bird Conservation International 29(1): 136-143. https://doi.org/10.1017/S0959270918000059

Oswald, K.N., Smit, B., Lee, A.T. and Cunningham, S.J., 2019. Behaviour of an alpine range-restricted species is described by interactions between microsite use and temperature. Animal Behaviour 157: 177-187. https://doi.org/10.1016/j.anbehav.2019.09.006 


Abdu, S., Lee, A.T.K. and Cunningham, S.J. 2018. The presence of artificial water points structures an arid-zone avian community over small spatial scales. Ostrich http://dx.doi.org/10.2989/00306525.2018.1509904 

Abdu, S., McKechnie, A.E., Lee, A.T.K. and Cunningham, S.J. 2018. Can providing shade at water points help Kalahari birds beat the heat? Journal of Arid Environments. 152:21-27. http://dx.doi.org/10.1016/j.jaridenv.2018.01.018 

de Swardt, D.H., Lee, A., Butler, H.J.B. and Oschadleus, H.D. 2018. Biometrics and diet of two closely related birds: Karoo Prinia (Prinia maculosa) and Drakensberg Prinia (Prinia hypoxantha). Indago  34(2): 125–133.

Lee, A.T.K. 2018. Book review: why birds matter: avian ecological function and ecosystem services. Ostrich 89: 203-204. http://dx.doi.org/10.2989/00306525.2018.1465788 

Oswald, K.N., Lee, A.T.K. and Smit, B. 2018. Seasonal physiological responses to heat in an alpine range-restricted bird: the Cape Rockjumper (Chaetops frenatus). Journal of Ornithology 159:1063-1072. http://dx.doi.org/10.1007/s10336-018-1582-8

Oswald, K.N., Lee, A.T.K. and Smit, B. 2018.  Comparison of physiological responses to high temperatures in juvenile and adult Cape Rockjumpers Chaetops frenatus. Ostrich 89: 377-382. http://dx.doi/0.2989/00306525.2018.1509905


Berkunsky, I., Quillfeldt, P., Brightsmith, D.J., ... Lee, A.T.K. et al.  2017. Current threats faced by Neotropical parrot populations. Biological Conservation 214: 278-287. http://dx.doi.org/10.1016/j.biocon.2017.08.016

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. http://dx.doi.org/10.2989/00306525.2016.1219413

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. http://dx.doi.org/10.1017/S0959270916000307

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. http://dx.doi.org/10.1111/aje.12384

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: 13-18http://dx.doi.org/10.2989/00306525.2017.1343209 

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. http://dx.doi.org/10.1111/btp.12426


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. http://dx.doi.org/10.1007/s10336-017-1460-9


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. http://dx.doi.org/10.2989/00306525.2016.1219413


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. http://dx.doi.org/10.1017/S0959270914000537

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. http://dx.doi.org/10.2989/00306525.2015.1021287

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. http://dx.doi.org/10.1093/conphys/cov048