Dr. Ricardo J. Pereira

Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics can contribute to resolving those conflicts by identifying management units and understanding how past climatic cycles resulted in current patterns of genetic diversity. We addressed these issues on an undescribed but already overexploited species of sardine of the genus Harengula. We find that the species distribution is determined by salinity and depth, with a continuous distribution along the Brazilian mainland and two disconnected oceanic archipelagos. Genomic data indicates that such biogeographic barriers are associated with two divergent intraspecific lineages. Changes in habitat availability during the last glacial cycle led to different demographic histories among stocks. One coastal population experienced a 3.6-fold expansion, whereas an island-associated population contracted 3-fold, relative to the size of the ancestral population. Our results indicate that the island population should be managed separately from the coastal population, and that a Marine Protected Area covering part of the island population distribution can support the viability of this lineage.

In coorporation with Dr. Julia Tovar Verba from LMU München and Dr. Sergio MQ Lima from UFRN

The ‘omics’ era reveals an increasing number of species that are practically indistinguishable in morphology, ecology or even in genetics, despite being reproductively isolated from one another in sympatry. While such species complexes present an example of a taxonomic conundrum for systematists, they are prized as valuable study systems for evolutionary biologists because the behavioral traits that maintain species boundaries can directly be observed. Here, we propose to study one of such systems, sympatric grasshopper species of the genus Chorthippus that have radiated under pervasive gene flow. This offers opportunities for identifying the genes underlying behavioral isolation and speciation. Using a comparative phylogeographic approach we will test if species have diverged in allopatric glacial refugia, facilitating the evolution of behavioural isolation. Using experimental crosses, we will test for a genetic association between cues and preference of behavioral isolation, which facilitates the maintenance of species boundaries in the face of gene flow. Lastly, using population genomics and behavioral assays, we will test if gene flow has played a role in generating hybrid species that are reproductively isolated from their parentals. This research program will not only offer new insights on how gene flow interacts with sexual selection during species formation, but it will provide a transferable multi-disciplinary approach for evolutionary studies in organisms characterized by large genomes that remain challenging to study.

In coorporation with Prof. Dr. Holger Schielzeth from Friedrich-Schiller-Universität Jena

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

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 zone between 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. Niloofar Alaei Kakhki internally and Dr. Reto burri from Schweizerische Vogelwarte Sempach and Prof. Dr. Holger Schielzeth from Friedrich-Schiller-Universität Jena