Seminar series

The CIGENE seminar series is over for this semester. We thank all presentors for excellent and interesting talks, and look forward to start up the seminars in the Autumn.

Are you interested in presenting your work? Or maybe you have a great suggestion for topics or a speaker for the next semester? Please contact us at


Each seminar will have the following structure (Central European Time):

12:00-12:05 – Setup and ensure everyone’s logged in
12:05-12:35 – Presentation (30 minutes)
12:35-12:50 – Q and A’s

Current seminar schedule is listed below, minor changes may occure. More updated information on each seminar will be published 1-2 weeks before the presentation is due.

Presenter Topic Affiliation Date
Rishi De-Kayne Swiss whitefish  EAWAG Swiss 10/2/2021
Eivind Valen Long read sequencing to study  genome regulation  University of Bergen Postponed
Danang Crysnanto Cattle pan-genomics ETH Zurich 3/3/2021
Annaliese Mason Plants and polyploidization University of Bonn 17/3/2021
Kentaro Shimizu Genome duplication and evolution in plants University of Zurich         24/03/2021
Kara Layton Ecology and evolution of mimicry systems University of Aberdeen 14/4/2021
Fernando Racimo Human evolutionary genetics University of Copenhagen 21/04/2021
Daniel Machado Computational biotechnology NTNU 5/5/2021
Mark Ravinet Evolutionary biology UiO, Nottingham 19/05/2021
Michael Matschiner Ciclid genome evolution Natural history museum 2/6/2021
Cristobal Uauy Wheat genomics John Innes Centre 16/06/2021




Date: 10th February 2021

Presenter: Rishi De-Kayne

Title: Genomic insights into the evolution of the Alpine whitefish radiation

Abstract: Within the Alpine whitefish (Coregonus spp.) species complex, the independent diversification into six or more sympatric whitefish species in multiple lakes across Switzerland are thought to have been facilitated by ecological and reproductive strategy differentiation with sympatric species varying in diet, body length, gill-raker  number, and spawning depth and time. Using a large whole-genome re-sequencing dataset including 97 whitefish individuals, spanning 22 species from five independent lake systems, we investigated the evolutionary mechanisms that have driven Alpine whitefish diversification within Switzerland. Our results indicate that, despite strong lake-specific differentiation between whitefish ecomorphs, the repeated diversification of ecologically distinct species within lake systems is underpinned to some degree by parallel genetic changes distributed along the genome. Additionally, rare ecomorphs show evidence of contemporary introgression between lake systems, likely as a result of the anthropogenic movement of fish between lake systems. This suggests that the postglacial whitefish diversification was facilitated by both wide-spread standing genetic variation enabling the rapid built up of somewhat parallel genome-wide differentiation, and admixture-derived variation.

Presenter: Danang Crysnanto

Date: 3rd March 2021

Title:  Assessing the complete genetic repertoire of a species using a pangenome graph

Abstract: Reference genome is generated from a single or few individuals and thus, it is a poor representation of the full species diversity. This pitfall has led to the development of the pangenome; the use of multiple genomes for genomic analysis. In this study, we integrated six cattle reference-quality genome assemblies into a pangenome graph, and we found 70 Mb sequences are not included in the existing cattle reference genome. We further demonstrated that these non-reference sequences contain functionally active bases and thousands of polymorphic sites that remain undetected with a single linear genome. Our findings call the need for a more representative reference genome that captures the entire diversity of a species.

Date: 17th March 2021

Presenter: Annaliese Mason

Title: Making new crop species

Abstract: By investigating how hybrid species form, we hope to work out how to utilise these natural evolutionary processes for human agricultural benefit, making new Brassica crop types for food, oil and biofuel. Hybridisation and genome doubling are processes which often result in increased vigour and ability to exploit different environmental niches in nature. Hence, if we can harness these processes to produce new hybrid species, such species may have a wider tolerance of environmental conditions such as heat, drought and disease, which would be beneficial to human agriculture.

Date: 24th March 2021

Presenter: Kentaro Shimizu

Title: Genome duplication affected patterns of selection in polyploid Arabidopsis and wheat species

Abstract: In 1970, Susumu Ohno proposed that genome duplication is an important source of novelty in vertebrates. Recent advances in polyploid genomics enabled population genomic studies of initial stages of genome duplication. Our data supported that parental adaptive traits were combined thanks to allopolyploidization in natural Arabidopsis and crop wheat allopolyploid species.



Date: 14th April 2021

Presenter: Kara Layton

Title: Using genomics to untangle marine mimicry systems

Abstract: Mimicry has evolved multiple times across the tree of life, it is maintained by both evolutionary and ecological mechanisms and it contributes to speciation through the generation of adaptive phenotypic diversity. While these processes have been extensively studied in terrestrial taxa, less is known about mimicry in marine systems. Here, I present a novel mimicry system in a group of aposematic and toxic nudibranchs (sea slugs) where multiple polychromatic species have recently been discovered. I use exon capture data to provide evidence for multiple scenarios of mimicry evolution in this group and discuss how future work will look to identify the genomic basis of mimicry.


Date: 21st April 2021

Presenter: Fernando Racimo

Title: Dynamic and descriptive models for spatiotemporal population genomics

Abstract: Ancient genome sequencing provides the opportunity to study population genomic processes as they unfolded in time and space. We can now directly observe how and when alleles moved across a landscape over succeeding generations with unprecedented detail. Here, I will describe several methods developed in our group to relate these spatiotemporal observations to informative parameters about migration, admixture and species ranges. First, I will present new way to model the spread of ancestry in ancient genomes through time and space. We have recently applied this method to a dataset containing thousands of ancient human genomes and inferred the geographic spread of major population movements in the past 13 millennia of Western Eurasian history. Our group has also developed a new dynamic framework for inferring the diffusion of a positively selected allele in a landscape, and a new wrapper to a forwards simulation framework, which makes it easy for users to readily generate spatiotemporal genetic processes programmatically. Finally, I will present a model to jointly infer changes in species distributions, using a combination of fossil records, sedimentary DNA data and paleo-climate records. We have applied this model to an arctic Pleistocene mega-fauna dataset and demonstrate that incorporating different types of data allows us to evince patterns that would not be visible if these were studied in isolation.


Date: 5th May 2021

Presenter: Daniel Machado

Title: Genome-scale models of microbial communities and their application to biotechnology

Abstract: From controlling our gut-brain axis to regulating the planetary geochemical cycles, the role of microbes in our lives seems endless. Microbes are everywhere, and they are usually not alone, but rather operating as part of complex microbial ecosystems. It thus becomes fundamental to understand how microbes interact with each other and with their environment. Next-generation sequencing technologies are shedding a light on the vast taxonomic and functional diversity of microbial communities. In this talk, I will discuss how we are using these data to build genome-scale models of single species and communities, and how we use such models to simulate the metabolic phenotype of microbial communities and their response to different kinds of perturbations. These are some of our preliminary steps towards the design and control of synthetic communities for application in industrial biotechnology.


Date: 19.05.2021

Presenter: Mark Ravinet

Title: The evolution of human commensalism in Passer sparrows. 

Abstract: From early civilization to the development of modern cities, human activity has shaped the evolution of other species. Some taxa are able to survive, adapt and even thrive in an anthropogenic niche. Human commensal species are a special case, having evolved a dependency on human resources without our direct influence. Intriguingly, human commensal relationships have arisen multiple times across many different species and even in parallel within the same genus. What factors drive the evolution of human commensalism? Is it a case of being in the right place at the right time? Or are there particular (pre)adaptations, traits and genes that mean some species are better able to exploit human resources than others? To explore these questions, I will focus on the repeated evolution of human commensalism in a single genus – Passer sparrows. I will show that we are able to use genomic data to reconstruct when and where human commensalism arose in each species. In particular, I will demonstrate that major human cultural transitions, i.e. the development of agriculture, have led to range expansions in these widespread and well-known birds. Finally, I will show that by combining phenotypic and genomic data, we are able to investigate the genetic basis for key traits involved in adapting to a human commensal life history.


Date: 02.06.2021

Presenter: Michael Matschiner,

Title: The adaptive radiation of cichlid fishes in Lake Tanganyika

Abstract: Adaptive radiation – the explosive diversification of a group adapting to various niches within the same environment – may have generated a large part of Earth’s biodiversity. A prime example of this process are cichlid fishes of Lake Tanganyika, which diversified into over 250 species of great morphological and ecological variation. In this talk I will present insights into this radiation that were gained from whole-genome sequencing and phenotypic characterization of all species in the lake. These extensive datasets allowed us to reconstruct the unfolding of the radiation in unprecedented detail, revealing how several discrete stages of morphological evolution produced the spectacular current cichlid diversity of Lake Tanganyika.


Date: 16th June 2021

Presenter: Cristobal Uauy

Title: Unlocking the Polyploid Potential of Wheat Through Genomics

Abstract: Developments over the past few years have radically changed the way we work with polyploid wheat. These developments have dramatically lowered the barriers to undertake biological research in polyploid wheat. For many purposes, wheat can now be treated (almost) like a model crop species. The next phase will be to start understanding the biological mechanisms underlying the most important traits in polyploid wheat and to design strategies to ensure this knowledge is quickly transferred to the field.  I will argue that given polyploidy, breeders have exploited only a fraction of the potential genetic variation in the wheat genome. The recent breakthroughs in wheat genomics now allow us to make a decisive effort towards exploiting this under-utilised variation, thereby unleashing the full potential of the polyploid wheat genome.


Previous CIGENE seminars can be found here