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

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

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

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

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

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

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

Recent peer-reviewed publications


Lee, Barnard & Wright (in press) Hot birds drink more: patterns and drivers of water visitation in a fynbos bird community. African Journal of Ecology.

Lee, Altwegg & Barnard (in press) Estimating conservation metrics from atlas data: the case of southern African endemic birds. Bird Conservation International.

Lee, Marsden, Tatum-Hume & Brightsmith (in press) Tourist and boat traffic impacts on parrot geophagy in lowland Peru. Biotropica.


Lee & Barnard. 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. & Barnard, P 2016. Endemic birds of the Fynbos biome: a conservation assessment and impacts of climate change. Bird Conservation International 26(1): 52-68.


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: doi:10.1093/conphys/cov048.

Lee, A.T.K. & Barnard, P 2015. Spatial and temporal patterns of insect-order activity in the fynbos, South Africa. Journal of Entomology and Zoology Studies. 3(6): 95-102.

Lee, A.T.K. & Barnard, P; Hockey, P. 2015. Population metrics for fynbos birds, South Africa: densities, and detection and capture rates from a Mediterranean-type ecosystem. Ostrich 86(1-2): 179-186. Ostrich.


Lee, A.T.K. & Barnard, P 2014. Aspects of the ecology and morphology of the protea seedeater, Crithagra leucopterus, a little-known Fynbos endemic. African Zoology 49(2): 295–300

Lee, A.T.K., Donald J. Brightsmith, Mario P. Vargas, Karina Q. Leon, Aldo J. Mejia and Stuart J. Marsden 2014. Diet and Geophagy Across a Western Amazonian Parrot Assemblage Biotropica 46(3): 322–330.


Lee, A.T.K and Marsden, S.J. 2012 The Influence of Habitat, Season, and Detectability on Abundance Estimates across an Amazonian Parrot Assemblage. Biotropica. 44(4): 537-544.


Lee, Kumar, Brightsmith and Marsden 2010 Claylick distribution in South America - do patterns of where help answer the question why? Ecography 33(3): 503-513.