Evolutionary genetics of Glossina tsetse flies and Trypanosomes: implications for disease control

Human African Trypanosomiasis (HAT) (a.k.a. African sleeping sickness) kills thousands of people each year in sub-Saharan Africa. The Animal African trypanosomiasis (AAT) or Nagana kills cattle and other livestock, thus impacts African economic in significant ways. Both disease are caused by the African trypanosomes in the Trypanosoma brucei complex and are transmitted by tsetse flies species within the genus Glossina. HAT transmission is complex; it requires mammalian and invertebrate hosts and involves domestic and wild reservoirs. Our general goal is to understand the spatial and temporal patterns of genetic differentiation of the various members of this complex disease transmission which include the Glossina flies and its symbionts and parasites: Trypanosoma, Wolbachia, Sodalis, Spiroplasma, and Wigglesworthia. The interest in the symbionts is fueled by the fact that they impact the fly fitness and/or their capacity to transmit Trypanosomes. The work focuses in East Africa, in particular Uganda, Kenya and Tanzania.

The Glossina tsetse flies:

Through the use of microsatellite and mitochondrial DNA (mtDNA) data together with population genetic and phylogeographic approaches, we try to understand patterns of spatial and temporal distribution of the vector, and its parasite and symbionts, examining their coevolution and evaluating the ecological and environmental processes that impact distribution. This provides baseline data to the agencies that monitor and control both diseases in the endemic countries. More recently we have been using ddRADSeq data and whole genome data to refine our understanding of the historical and environmental forces shaping these vectors distributions. We carry out landscape genetic analyses that integrate genetic and environmental data to produce suitability maps and have predictive power to evaluate the impact of human induced alteration on the distribution of these disease vectors. Using this appraoch we can evaluate the potential risks of increase in disease transmission linked to range expansions. Our work focuses on two speies, Glossina fuscipes fuscipes and Glossina pallidipes and two countries Uganda and Kenya.


Similarly, we have been using Illumina and PacBio data to carry out population genomic analyses of multiple Trypanosoma brucei strains across Africa.  We are using evolutionary principles and approaches to evaluate their evolutionary history and thus provide information to better define their taxonomy, as well as to gain insights on the relation between strain identity and emergence of new disease foci. We also produced the first de novo assembly of Trypanosoma brucei rhodesiense, the parasite responsible for the acute form of HAT, and compared it to the available genomes for the other Trypanosma brucei genomes from the non-human infective strains (T. brucei brucei) and the ones responsible for the chronic form of sleeping sickness (T. brucei gambienese). Using evolutionary approaches we are also working on understanding the dynamics of re-infection in human patients that were treated but then relapsed, to evaluate if the re-emergence of the disease is due to the same strain or to different infections. We have also expanded our analyses Trypanosoma evansi, a strain likely derived from Trypanosoma brucei brucei, whose ability to be transmitted by non-tsetse flies, enabled it to expand outside Africa.

Capacity building:

We are also been involved in building capacity for Trypanosomiasis research in East Africa by training a cadre of young scientists at various stages of their career (graduate students, postdoctoral associates, faculty members) from Uganda, Kenya, and Tanzania that over the past 10 years have received training in our laboratory or participated to in country workshops we helped organized.


Yale postdocs: Jon Beadell, Beckie Symula, Mark Sistrom, Gus Dunn, Joshua Richardson, Andrea Gloria-Soria, Norah Saarman (present)

EEB graduate students: Oliver Balmer

EEB Research Assistants: Chaz Hyseni, Mary Burak, Kirstin Dion and TJ Johnson (present)

Yale Faculty: Serap Aksoy, Alison Galvani, Brain Weiss, John Carlson

Graduate students from Uganda, Kenya and Tanzania: Patrick Abila, Rosemary Bateta, Richard Echodu, Oliver Kijanga, Christine Mujonia, Winnie Okeyo, Robert Opiro

Non Yale faculty main collaborators: Anna Malacrida (University of Pavia), Loyce Okedi, Elizabeth Opyo, Richard Echodu (Uganda); Grace Murilla (Kenya), Johnson Ouma (Tanzania), Paul Mireji (Kenya), Imna Malele (Tanzania), Martin Donnelly (Liverpool, England), Wendy Gibson (England), Oliver Balmer and Pascal Maeser (Switzerland), Philippe Buscher (Belgium), Achim Sbhnaufer (Un. of Edimburgh, UK)


Glossina papers: Abila, P.A., M. A. Slotman, A. Parmakelis, K. B. Dion, A. S. Robinson, V. B. Muwanika, J. CK Enyaru, L.M. Okedi, S. Aksoy and A. CACCONE.  2008. High levels of genetic differentiation between Ugandan Glossina fuscipes fuscipes populations separated by Lake Kyoga. PLOS Neglected Tropical Diseases 2(5): e242.

Brown, J.E., K.J. Komatsu1, P.P. Abila, A.S. Robinson, L.M. Okedi, Naomi Dyer, M.J. Donnelly, M.A. Slotman and A. CACCONE. 2008. Polymorphic microsatellite markers for the tsetse fly Glossina fuscipes fuscipes (Diptera: glossinidae), a vector of human African trypanosomiasis. Molecular Ecology Resources 8 (6): 1506-1508.

Beadell, J.S, C. Hyseni, P. Abila, J. C. K. Enyaru, J. Ouma, Y. O. Mohammed, L. M. Okedi, S. Aksoy, A. CACCONE. 2010.  Gene flow among populations of Glossina fuscipes at multiple scales: implications for control of tsetse in Uganda. PLoS Neglected Tropical Diseases 2010;4(3): e636.

Echodu, R., J. S. Beadell, L. M. Okedi, C.Hyseni, S. Aksoy, A.CACCONE. 2011. Temporal stability of Glossina fuscipes fuscipes populations in Uganda. Parasites & Vectors 2011, 4:19.

Hyseni, C., J. Beadell, Z. Ocampo Gomez, J. Ouma, L. Okedi, M. Gaunt, A. CACCONE. The G.m. morsitans (Diptera: Glossinidae) genome as a source of microsatellite markers for other tsetse fly (Glossina) species. 2011. Molecular Ecology Resources (2011) 11, 586–589 doi: 10.1111/j.1755-0998.2011.03004.x.

Bonomi A, Bassetti F, Gabrieli P, Beadell J, Falchetto M, et al. 2011, Polyandry Is a Common Event in Wild Populations of the Tsetse Fly Glossina fuscipes fuscipes and May Impact Population Reduction Measures. PLoS Negl Trop Dis 5(6): e1190. doi:10.1371/journal.pntd.0001190.

Ouma JO, Beadell JS, Hyseni C, Okedi LM, Krafsur ES, Aksoy S, CACCONE A. 2011. Genetic diversity and population structure of Glossina pallidipes in Uganda and western Kenya. Parasit Vectors. 2011 Jun 28;4:122. PMID: 21711519.

Alam, U., C. Hyseni, R/ E. Symula, C. Brelsfoard, Y. Wu,O. Kruglov, R.  Echodu, V. Alioni, L. M. Okedi, A. CACCONE and S. Aksoy. 2012. Implications of microfauna-host interactions for trypanosome transmission dynamics in Glossina fuscipes fuscipes in Uganda. Appl. Environ. Microbiol. 78 (13): 4627-37. PMID: 22544247.

Hyseni, C., Kato, A., L.M. Okedi, C. Masembe, J.O. Ouma, S. Aksoy, A. CACCONE. 2012. Genetic diversity and structure of Glossina fuscipes fuscipes Uganda populations from the lake Victoria basin, insights for vector control and monitoring. Parasites and Vectors 4;5(1): 222. [Epub ahead of print].PMID:23036153.

Symula, R.E, U. Alam, C. Brelsfoard, Y. Wu, S. Aksoy, A. CACCONE.  2013. Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics. BMC Evolutionary Biology 2013, 13:31 doi:10.1186/1471-2148-13-31. PMID: 23384159.

Aksoy, S. A. CACCONE, A.P. Galvani and L. M. Okedi. 2013.  Glossina fuscipes populations provide insights for Human African Trypanosomiasis transmission in Uganda. Trends in Parasitology August 2013, 29 (8): 394-406. PMID: 23845311.

Echodu, R., M. Sistrom, C. Hyseni, J. Enjaru, L. M. Okedi, S. Aksoy, and A. CACCONE. 2013. Genetically distinct Glossina fuscipes fuscipes populations in the Lake Kyoga region of Uganda and its relevance for Human Africa trypanosomiasis. Biomed Res Int. 2013;2013:614721. doi: 10.1155/2013/614721. PMID:24199195.

Aksoy, E., E. Telleria, R. Echodu, Y. Wu, L. Okedi, B. Weiss, S. Aksoy and A. CACCONE. 2014. Analysis of multiple tsetse fly populations in Uganda reveals restricted and species-specific gut microbiomes. Applied and Environmental Microbiology, 80:18 5844-5853. PMID:24814785.

Gloria-Soria, A, WA Dunn WA, EL Telleria, BR Evans, L. Okedi L, R. Echodu, WC Warren, S.  Aksoy S, A. CACCONE.  2016. Patterns of genome-wide variation in Glossina fuscipes fuscipes tsetse flies from Uganda.  G3: Genes|Genomes|Genetics Early Online, published on April 13, 2016 as doi:10.1534/g3.116.027235.

Opiro, R., N.P. Saarman, R. Echodu, E. A. Opiyo, K. Dion, A. Haylard, S. Aksoy and A.CACCONE. 2016. Evidence of temporal stability in allelic and mitochondrial haplotype diversity in populations of Glossina fuscipes fuscipes (Diptera: Glossinidae) in northern Uganda. Parasites and Vectors. 9:258.

Manangwa O, N. Gamba, J.O. Ouma, F. Mramba, I. Malele, K. Dion, M. Sistrom, F. Khan, S. Aksoy S and A. CACCONE. Genetic diversity of Glossina fuscipes fuscipes along the shores of Lake Victoria in Tanzania and Kenya: implication for management. Parasites & Vectors 2017, 10:268. DOI: 10.1186/s13071-017-2201-X. PMID :28558831.

Opiro, R, N. P. Saarman, R. Echodu, E. A. Opiyo, K. Dion, A. Halyard, A. W. Dunn, S. Aksoy and A. CACCONE. 2017. Genetic Diversity and Population Structure of the Tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: Implications for Vector Control. Plos Neglected Diseases Apr 28;11(4):e0005485. doi: 10.1371/journal.pntd.0005485. [Epub ahead of print]. PMID: 28453513.

Okeyo, W.O., N. P. Saarman, M. Mengual, K. Dion, R. Bateta, P. O. Mireji, S. Okoth, J. O. Ouma, C. Ouma, J. Ochieng, G. Murilla, S. Aksoy and A. CACCONE. 2017, Temporal genetic differentiation in Glossina pallidipes tsetse fly populations in Kenya. Parasites & Vectors, 10: 471.

Saarman, N. P., Burak, M., N., R. Opiro, C. Hyseni, G. Amatulli, R. Echodu, E. Opiyo, K. Dion, A. Dunn, S. Aksoy and A. CACCONE. 2018. A spatial genetics approach to inform vector control of tsetse flies (Glossina fuscipes fuscipes) in Northern Uganda. Ecology & Evolution (https://doi.org/10.1002/ece3.4050).

Gloria-Soria, A, W.A. Dunn, WA, X Yu, A. Vigneron A, K-Y Lee, BL Weiss, H. Zhao , S. Aksoy, S., and A. CACCONE. 2018. Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes. G3: Genes, Genomes, Genetics March 1, 2018 vol. 8 no. 3 887-897; https://doi.org/10.1534/g3.117.300493.

Okeyo, W.A., R. Bateta, N. P. Saarman, K. Dion, M. Mengual, P. O. Mireji, C. Ouma, G. Murilla2, S. Aksoy, A. CACCONE. 2018. Genetic differentiation of Glossina pallidipes tsetse flies in Kenya. AJTMH 99: 945-953.

Saarman, N.P., R. Opiro, C. Hyseni, Chaz, R. Echodu, E. Opiyo, K. Dion, T. Johnson, S. Aksoy, A. CACCONE. 2018. The population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) hybrid zones in Uganda meet expectations of the coupling hypothesis on the genetic basis of speciation. Mol. Ecol., 8 (11): 5336-5354.

Trypanosoma papers: Balmer, O., C. Palma, A. MacLeod, A. CACCONE. 2006. Characterization of di-, tri-, and tetranucleotide microsatellite markers with perfect repeats for Trypanosoma brucei and related species. Molecular Ecology Notes 6:508-510.

Balmer O. and A. CACCONE. Frequency of multiple-strain infections in Trypanosoma brucei. 2008.  Acta Tropica,107(3): 275-279.

Balmer , O., Beadell, J.S. Gibson W., A. CACCONE. 2011. Phylogeography and Taxonomy of Trypanosoma brucei. PLoS Negl Trop Dis 5(2): e961. doi:10.1371/journal.pntd.0000961.

Alam, U., C. Hyseni, R/ E. Symula, C. Brelsfoard, Y. Wu,O. Kruglov, R.  Echodu, V. Alioni, L. M. Okedi, A. CACCONE and S. Aksoy. 2012. Implications of microfauna-host interactions for trypanosome transmission dynamics in Glossina fuscipes fuscipes in Uganda. Appl. Environ. Microbiol. 78 (13): 4627-37. PMID: 22544247.

Symula, R.E., J. S. Beadell, M. Sistrom1, K. Agbebakun1 , O.Balmer, W. Gibson, S. Aksoyand A. CACCONE. 2012. Trypanosoma brucei gambiense group 1 is distinguished by a unique amino acid substitution in the HpHb receptor implicated in human serum resistance. PLoS Negl Trop Dis., 6(7):e1728. Epub 2012 Jul 10.160. PMID:22802982.

Sistrom, M. B. Evans, R. Bjornson, W. Gibson, O. Balmer, P. Mäser, S. Aksoy and  A. CACCONE. 2014. Comparative genomics reveals multiple genetic backgrounds of human pathogenicity in the Trypanosoma brucei complex. 
Genome Biol. Evol.6(10):2811–2819. PMID:25287146.

Echodu, R., M.Sistrom, R. Bateta, G. Murilla, L. Okedi, S. Aksoy, C. Enyioha, J. Enyaru, E. Opiyo, W. Gibson, and A. CACCONE. 2015. Genetic diversity and population structure of Trypanosoma brucei in Uganda: implications for the epidemiology of sleeping sickness and Nagana. PLOS Neglected Tropical Diseases 10.1371/journal.pntd.0003353. PMID:25695634.

Sistrom, M.J., B. Evans, J. Benoit, O. Balmer, S. Aksoy and A. CACCONE. 2015. De novo genome assembly shows genome wide similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense. Plos One, Published: February 24, 2016. http://dx.doi.org/10.1371/journal.pone.0147660.

Graf, F.E., P. Ludin, J. C. Munday, J. Krezdorn, N. Schaub, C. Kunz-Renggli,  O. Balmer, A. CACCONE, H. P. de Koning, and P. Mäser. 2016.  Comparative genomics of drug resistance of the sleeping sickness parasite Trypanosoma brucei rhodesiense. Cell. Mol. Life Sci. DOI 10.1007/s00018-016-2173-6.

Kamidi, C.M, N.P. Saarman, K. Dion, P.O. Mireji, C. Ouma, G. Murilla, S. Aksoy, A. Schnaufer, A. CACCONE. 2017. Multiple evolutionary origins of Trypanosoma evansi in Kenya. PLoS Negl Trop Dis. 2017 Sep 7;11(9):e0005895. doi: 10.1371/journal.pntd.0005895. eCollection 2017 Sep. PMID:28880965.

Richardson, J., K.-Y. Lee, P. Mireji, J. Enyaru, M. Sistrom, S. Aksoy, H. Zhao, A. Caccone. 2017. Genomic analyses of African Trypanosoma strains to assess evolutionary relationships and identify markers for strain identification PLoS Negl Trop Dis. 2017 Sep 29;11(9):e0005949. doi: 10.1371/journal.pntd.0005949. eCollection 2017 Sep.