All seminars during the Spring semester 2021 will be online.
Click here for direct access to the Zoom seminar.
NEXT SPEAKER
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.
SEMINAR SCHEDULE
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 |
ABSTRACTS
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.