Dr. Niloofar Alaei Kakhki

Hybrid zones are defined as areas where genetically differentiated groups of individuals meet, mate, and produce offspring of mixed ancestry. For decades’ hybrid zones have been considered as natural laboratories that can provide direct insights into the traits and genes underlying barriers to gene flow between incipient species. Yet, we still have a poor understanding of which genomic regions underlie such initial stages of reproductive isolation and whether the strength of selection associated with those mechanisms can effectively reduce gene flow over time and hence facilitate species formation. Addressing these longstanding questions requires studying hybrid zones where traits associated to reproductive isolation can be measured, and where temporal sampling over several generations is available. Here, we address these questions using the hybrid zonebetween two songbirds – black-headed bunting Emberiza melanocephala and red-headed bunting E. bruniceps – where species are hypothesized to be behaviourally isolated due to association between male signalling (such as plumage) and female preference. By integrating whole genome sequencing methods with genotypic and phenotypic studies of museum collections of the hybrid zone spanning the last ~25 generations, we will assess:

1. How heterogeneous is the genomic landscape of differentiation?
2. Which genomic regions are associated with the plumage traits?
3. How does selection in those regions maintain local genetic differentiationover time in the face of gene flow?

Addressing these questions in the bunting hybrid zone will provide general insights into how coloration traits involved in reproductive isolation evolve, and how they contribute to maintaining species boundaries at early stages of species formation. Additionally, this research program will provide a transferable framework to demonstrate how museum collections provide unique windows for understanding the role of hybridization over time, insights that often cannot be achieved from extant populations alone.

In coorporation with Dr. Ricardo Pereira internally and Dr. Reto burri from Schweizerische Vogelwarte Sempach and Prof. Dr. Holger Schielzeth from Friedrich-Schiller-Universität Jena

Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives).

In coorporation with Dr. Reto burri from Schweizerische Vogelwarte Sempach 

Theoretical work predicts that during a species invasion, genes from a native species often move into the genome of the invasive species, potentially facilitating its adaptation to local environmental conditions. Such asymmetric introgression has been confirmed in diverse taxa such as plants, fish, and even humans. It is yet unclear if introgression is selectively adaptive, facilitating invasiveness, or if it is neutral, reflecting demographic history. We provide insights into this question by studying the divergence and gene flow of Arion slugs. Within the last 100 years, likely facilitated by changes in climate and land use, the slug species Arion vulgaris expanded from southwestern France to all of Europe, and more recently to North America, becoming an important plague in agriculture. In this process, this invasive species hybridized with several native slug species, leading to their destruction across most of their range. We use genomic methods to understand: 1) how species diverged in the past, 2) if the demographic history of invasion led to introgression, and 3) if there is a signature of adaptive introgression in locally adaptive genes.

In coorporation with Dr. Niloofar Alaei Kakhki & Dr. Ira Richling internally and Dr. Heike Reise und John M. C. Hutchinson from the Senckenberg Museum für Naturkunde Görlitz