Dr Alexander Zizka


Research interests


I am a biogeographer and botanist, my two major fields of interest are:

The evolution of tropical biodiversity. The unequal distribution of biodiversity has puzzled humanity for centuries.  Generally biodiversity decreases with latitude, but very interestingly there are also large continental and regional difference within the generally species rich tropical regions. For instance, the South American tropics harbor more than three times as many plant species as the African tropics! I am particularly interested describing patterns of tropical biodiversity, to identify co-variants (climatic or geologic) of high and low diversity areas in the American and African tropics and to investigate mechanisms of increases and decreases in diversity through time. In a recent study, we have investigated the distribution of rare plant species in tropical America and compared diversification of angiosperms between Africa and South America.

Big data in biodiversity research. The public availability of species distribution information has increased drastically in the last 10 years. Public aggregators such as GBIF, IUCN, idigbio or BIEN provide more than 1 billion occurrence records across all taxonomic groups. This tremendous development has brought ‘big data’ into biogeography and enables an entire new perspective on macroscopic spatial scales. However the consequent use of this data has been hampered by issues on data quality and a lack of bioinformatics tools to process such large amount of data. One of my major interests is to develop tools to improve data quality in large scale species distribution databases and apply these data to biogeographic questions, in particular in the context of a similar revolution in data availability currently ongoing for genetic data. Recently I have developed tools for automatic geographic data cleaning and preparation of large scale distribution data for analyses in historical biogeography. Furthermore I contribute to tools for bioregionalization based on large scale distribution data and to make biogeographic inferences from fossils.



I like teaching, mostly in two major courses:

“Big data Biogeography – Species occurrences through space and time”. A one week graduate course on the use of geographic occurrences and fossils for (historical) biogeography. Next time [November 4-8 in Berlin] (https://www.physalia-courses.org/courses-workshops/course48/).

“Biodiversity data – from field to yield”. A one-week graduate course on the collection and processing on species geographic occurrences from collection specimens and citizen science (course material at azizka.github.io/Biodiversity_Data_from_Field_to_Yield/).

And several minor workshops from various occasions

“Evolution and biogeography with focus on the Neotropics”

“Biodiversity data in Ecology and Biogeography” (course material at https://github.com/azizka/Using_biodiversity_data_for_biogeography)

“R in biodiversity informatics”

Selected publications


1. Zizka A, Silvestro D, Andermann T, Azevedo J, Duarte Ritter C, Edler D, Farooq H, Herdean A, Ariza M, Scharn R, Svanteson S, Wengström N, Zizka V & Antonelli A. (2019) CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution, 00:1-8

2. Zizka A. & Antonelli A (2018) Mountains of diversity. Nature 555:173-174.

3. Antonelli A*, Zizka A*, Antunes-Carvalho F*, Scharn R, Bacon CD, Silvestro D, Condamine FL (2018) Amazonia is the primary source of Neotropical biodiversity. Proceedings of the National Academy of Sciences of the USA, 115(23):6034-6039.

4. Zizka A, ter Steege H, do Céo R. Pessoa M & Antonelli A (2018) Finding needles in the haystack: where to look for rare species in the American tropics. Ecography, 41(2):321-330

5. Töpel M*, Zizka A*, Calió MF, Scharn R, Silvestro D & Antonelli A (2016) Speciesgeocoder: fast categorization of species occurrences for analyses of biodiversity, biogeography, ecology, and evolution. Systematic biology, 66(2):145-151

iDiv publications


E. Arlé, A. Zizka, P. Keil, M. Winter, F. Essl, T. Knight, P. Weigelt, M. Jiménez-Muñoz, C. Meyer

(2021): bRacatus: A method to estimate the accuracy and biogeographical status of georeferenced biological data. Methods in Ecology and Evolution

M. Freiberg, M. Winter, A. Gentile, A. Zizka, A. N. Muellner-Riehl, A. Weigelt, C. Wirth

(2021): A New and Improved Online Catalogue of all Extant Vascular Plant Names Available. TAXON 70(1) *

Carrillo, J. D., S. Faurby, D. Silvestro, A. Zizka, C. Jaramillo, C. D. Bacon, A. Antonelli

(2020): Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange. Proceedings of the National Academy of Sciences 117(42) *

Freiberg, M., M. Winter, A. Gentile, A. Zizka, A. N. Muellner-Riehl, A. Weigelt, C. Wirth

(2020): LCVP, The Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants. Scientific Data 7(1) *

Helmstetter, A. J., Kamga, S. M., Bethune, K., Lautenschlager, T., Zizka, A., Bacon, C. D., Wieringa, J. J., Stauffer, F., Antonelli, A., Sonke, B., Couvreur, T. L. P.

(2020): Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae). Plants-Basel 9(4) *

Helmstetter, A. J., Kamga, S. M., Bethune, K., Lautenschläger, T., Zizka, A., Bacon, C. D., Wieringa, J. J., Stauffer, F., Antonelli, A., Sonké, B., Couvreur, T. L. P.

(2020): Unravelling the Phylogenomic Relationships of the Most Diverse African Palm Genus <em>Raphia</em> (Calamoideae, Arecaceae). bioRxiv (in press) *

Pimiento, C., Bacon, C. D., Silvestro, D., Hendy, A., Jaramillo, C., Zizka, A., Meyer, X., Antonelli, A.

(2020): Selective extinction against redundant species buffers functional diversity. Proceedings of the Royal Society B-Biological Sciences 287(1931) *

Zizka, A., Carvalho-Sobrinho, J. G., Pennington, R. T., Queiroz, L. P., Alcantara, S., Baum, D. A., Bacon, C. D., Antonelli, A.

(2020): Transitions between biomes are common and directional in Bombacoideae (Malvaceae). Journal of Biogeography *

Zizka, A., F. Antunes Carvalho, A. Calvente, M. Rocio Baez-Lizarazo, A. Cabral, J. F. R. Coelho, M. Colli-Silva, M. R. Fantinati, M. F. Fernandes, T. Ferreira-Araújo, F. Gondim Lambert Moreira, N. M. C. Santos, T. A. B. Santos, R. C. dos Santos-Costa, F. C. Serrano, A. P. Alves da Silva, A. de Souza Soares, P. G. Cavalcante de Souza, E. Calisto Tomaz, V. F. Vale, T. L. Vieira, A. Antonelli

(2020): No one-size-fits-all solution to clean GBIF. PeerJ 8

Zizka, A., Silvestro, D., Vitt, P., Knight, T. M.

(2020): Automated conservation assessment of the orchid family with deep learning. Conservation Biology (in press) *

Ritter, C. D., Faurby, S., Bennett, D. J., Naka, L. N., ter Steege, H., Zizka, A., Haenel, Q., Nilsson, R. H., Antonelli, A.

(2019): The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia. Scientific Reports 9(1) *

Rydén, O., A. Zizka, S. C. Jagers, S. I. Lindberg, A. Antonelli

(2019): Linking democracy and biodiversity conservation: Empirical evidence and research gaps. Ambio 49(2), 419-433 *

Zizka, A., Azevedo, J., Leme, E., Neves, B., da Costa, A. F., Caceres, D., Zizka, G.

(2019): Biogeography and conservation status of the pineapple family (Bromeliaceae). Diversity and Distributions 26(2), 183-195 *

Zizka, A., Silvestro, D., Andermann, T., Azevedo, J., Duarte Ritter, C., Edler, D., Farooq, H., Herdean, A., Ariza, M., Scharn, R., et al.

(2019): CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution 10(5), 744-751
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