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 A. Matteen Rafiqi



2003–2008   PhD, The University of Chicago, Chicago, USA.

Laboratory of Professor Urs Schmidt-Ott.


Official degree was issued by Wageningen University, The Netherlands although the work was entirely done at The University of Chicago and Max Planck Institute.


2002–2003   , Max Planck Institute for Biophysical Chemistry, Gottingen, Germany.

Laboratory of Professor Urs Schmidt-Ott.

2000–2002   MSc, Wageningen University, The Netherlands, with distinction.

Laboratory of Molecular Biology Prof. Ton Bisseling; Dr. Henk Franssen group.

1995–1999   BSc, SK University of Agricultural Sciences and Technology, Kash- mir, India.


 Professional Experience

2017–         Assistant Professor, Bezmialem Vakıf University, İstanbul, Turkey.

                   Beykos Institute of Life Sciences and Biotechnology

2013–2017  Research Associate, McGill University, Montreal, Canada.

Laboratory of Professor Ehab Abouheif

2011–2013   Postdoctoral Fellow, McGill University, Montreal, Canada.

Laboratory of Professor Ehab Abouheif (in collaboration with Prof. Laura Nilson and Prof. David Juncker)

2009–2010   Postdoctoral Fellow, The University of Chicago, Chicago, USA.

Laboratory of Professor Urs Schmidt-Ott


Abouheif E., Rafiqi A. M. (2014) "Sex combs find middle ground in evolution debate." Proceedings of the NationalAcademy of Sciences of the U S A. 111, 14011-14012.

Abouheif E., Fave M. J., Ibarraran-Viniegra A. S., Lesoway M., Rafiqi A. M., Rajakumar R. (2013). "Eco-evo-devo: the time has come." Advances in Experimental Medicine and Biology.


Rafiqi A. M., Park C. H., Kwan C. W., Lemke S., Schmidt-Ott U. (2012) "BMP-dependent serosa and amnion specification in the scuttle fly Megaselia abdita." Development 139, 3373-82.

Rafiqi A. M., Lemke S., Schmidt-Ott U. (2011). "The scuttle fly Megaselia abdita (Phoridae): A link between Drosophila and mosquito development." Cold Spring Harbor Protocols doi:


Rafiqi, A. M., Lemke S.J., Schmidt-Ott, U. (2010) "Postgastrular zen expression is required to develop distinct amniotic and serosal epithelia in the scuttle fly Megaselia." Developmental Biology, 341, 282-90.

Schmidt-Ott U., Rafiqi, A. M., Lemke, S. J. (2010). "hox3/zen and the Evolution of Extraembry- onic Epithelia in Insects". Advances in Experimental Medicine and Biology, 689: 133-144.

Schmidt-Ott U., Rafiqi A. M., Sander K., Johnston J.S. (2009) "Extremely small genomes in two unrelated dipteran insects with shared early developmental traits." Development Genes and Evolution, 219, 207-10.

Rafiqi, A. M., Lemke, S. J., Ferguson, S., Stauber, M., Schmidt-Ott, U. (2008) "Evolutionary origin of the amnioserosa in cyclorrhaphan flies correlates with spatial and temporal expression changes of zenProceedings of the National Academy of Sciences of the U S A 105, 234-239.

Lemke, S. J., Stauber, M., Shaw, P. J., Rafiqi, A. M., Prell, A., Schmidt-Ott, U. (2008)"bicoid occurrence and Bicoid-dependent hunchback regulation in lower cyclorrhaphan flies" Evolution Development, 10, 413-420.


Publications: Novel Methodologies

Rafiqi A. M., Lemke S, Schmidt-Ott U. (2011). Megaselia abdita: Culturing and egg collection.

Cold Spring Harbor Protocols doi: 10.1101/pdb.prot5600.

Rafiqi A. M., Lemke S, Schmidt-Ott U. (2011). Megaselia abdita: Preparing embryos for injection.

Cold Spring Harbor Protocols doi: 10.1101/pdb.prot5601.

Rafiqi A. M., Lemke S, Schmidt-Ott U. (2011). Megaselia abdita: Fixing and devitellinizing embryos. Cold Spring HarborProtocols doi: 10.1101/pdb.prot5602.

Rafiqi A. M., Lemke S, Schmidt-Ott U. (2011). Megaselia abdita: Cuticle preparation from injected embryos. Cold SpringHarbor Protocols doi: 10.1101/pdb.prot5603.


Conference presentations

Rafiqi A. M., Rajakumar A., Abouheif E. (2016) "A novel developmental mechanism underlying the evolutionary transition to obligate mutualism in ants (platform)

Canadian Society of Zoologists Conference London, Ontario.

Rafiqi A. M., Lemke S.J., Schmidt-Ott U. (2005) "Episyrphus balteatus has four zen genes and a serosa" Drosophila research conference, San Diego, CA (May 2016)

Rafiqi A. M., Turner K., Nilson L., Juncker, D., Abouheif, E. (2014) "To Study The Evolutionary Developmental Basis Of Ant Mimicry In Body Plans Of Insects - Artificial Selection On Embryonic Gene Expression Patterns In Insects." Genomes toBiomes, Montreal, Canada. (poster)


Publications in preparation

Rafiqi A. M., Rajakumar, A., Abouheif E. "Obligate endosymbiosis in ants reveals developmental steps to major evolutionary transitions."

Chen T. W. L., Rafiqi A. M., Fung B. A., Lamouret T., Rajakumar R., and Abouheif E. "Embryonic, Larval and Pupal Development in the Carpenter Ant Camponotus floridanus."

Rafiqi A. M., Turner K., Nilson L., Juncker, D., Abouheif, E. "High throughput imaging reveals differences between endogenous gene expression and transgenic gene expression in Drosophila."


Fellowships / Awards

2017   Ramalingaswamy Fellowship – Department of Biotechnology, Govt. of India.

2015   Quebec Center For Biodiversity Research - Excellence Award.

2014   Quebec Center For Biodiversity Research - Excellence Award.

2000–2002   University Fellowships Program of NUFFICThe Netherlands Organization For

International Cooperation In Higher Education.



- Member of Pan-American Society for Evolutionary Developmental Biology

- Member of Canadian Society for Ecology and Evolution

- Member of Society for the Study of Evolution​

Research in our lab studies Ecological Evolutionary Developmental Biology (Eco-Evo-Devo), a field of research that integrates concepts such as developmental plasticity, robustness, and endosymbiosis into evolutionary theory. We focus on molecular mechanisms of endosymbiosis by studying bacterial endosymbiosis during early development in ants and true bugs. Endosymbiosis is a rule rather than an exception among multicellular organisms and both micro- and macro-evolutionary events have been shaped by endosymbiotic association, such as hybrid incompatibility and speciation in flies and evolution of eukaryotic cell by symbiogenesis of mitochondria. Molecular mechanisms of endosymbiosis have been treated at the inter-organismal level, our lab explores this phenomenon at the intracellular level during early development in case of endocytic symbionts.


Ants of the genus Camponotus, commonly known as carpenter ants, are a hyperdiverse genus of ants with over 1500 species, which harbor the endosymbiotic bacteria Candidatus Blochmania. This bacteria colonizes specialized cells in the host that persist throughout development and adult life and are maternally transmitted to the next generation. Camponotus have acquired endocytic bacteria through a horizontal evolutionary transfer from true bugs by feeding on their honey dew, a nutrient rich substance they excrete. This has led to the evolution of a three-way symbiotic relationship: (1) between true bugs and bacterial endosymbionts, (2) between true bugs and ants, and (3) between ants and bacterial endosymbionts. We exploit this three-way symbiotic relationship to study the ontogeny of the cells and organs that harbour these endosymbionts, the genes that regulate the specification of these cells and the developmental program that mediates these associations in the ant and bug hosts and in the bacterial endosymbionts. By these studies we hope to address questions of developmental integration of endosymbiont within the host, questions of evolutionary origins of endosymbiotic associations, relevance of endosymbiotic associations to organismal biology in general and to ultimately reveal the steps towards the evolution of complexity in higher life forms.

Current Projects

Developmental basis of endosymbiosis: comparative developmental studies

This project involves comparative studies between true bugs and ants and between various ant genera. Bacterial endosymbiosis has independently evolved at least three times within ants in the genera CamponotusFormica and Polyrhachis. One the one hand the bacterial species associated with Camponotus and true bugs have a common origin but on the other hand the ones associated with Formica and Polyrhachis are independently evolved associations. At the same time the endosymbionts have diverged within each lineage together with their hosts. We exploit this phenomenon to study host-symbiont co-evolution and evolutionary divergence and evolutionary convergence of endosymbiosis. In this project we aim to sample carpenter ants and associated true bugs from Turkey and to survey the presence of endosymbionts in these organisms. Based on developmental gene expression and gene function studies, we wish to establish the genetic basis of the establishment of these associations to understand whether conserved, converged or parallel mechanisms exist in these separate lineages. Data from true bugs and our own data in ants suggest that the genes for patterning of the endosymbionts are similar providing a starting point for developmental genetic studies in these diverged lineages.

Human gut microbiome in Turkish populations

There is growing data about association between endosymbionts in the human body that appear to vary between individuals based on their geographical location, their lifestyle, prescription regimes, and most importantly their state of health. We are developing a comprehensive record of microbiome of human gut in Turkey. This database will be used to develop an association map of endosymbionts with disease and healthy state, geographical location, gender, age, and other biometric characteristics. The database aims to be used as a tool to develop microbes unique to Turkish populations for diagnostic and therapeutic purposes.

Lab members

Abdul Matteen Rafiqi (Principal Investigator)

Hilal Şentürk (PhD student)

Priscila Gomez Polo (Postdoc)

TBA (Technician)​