Genomic insights from two emerging model systems: Polygenic adaptation to simian immunodeficiency virus (SIV) infection in vervet monkeys, and the role of gene flow in rapid speciation in Lake Malawi cichlids
Hannes Svardal (Sanger Institute, UK)
Friday 1st July, 2016
ESJ King Theatre, Medical Building, The University of Melbourne
Vervet monkeys (Chlorocebus sp.) are amongst the most widely distributed non-human primates and are natural hosts of simian immunodeficiency virus (SIV) with a high viral prevalence observed in all sampled African populations. We use whole-genome sequencing data from 163 individuals covering six subspecies across the continent to infer relationships and demonstrate cross-taxon gene flow. A scan for diversifying selection across subtaxa yields strong enrichment for viral response genes and genes whose human orthologs interact with human immunodeficiency virus (HIV). Selection scores are also highly elevated in genes that show a response to experimental SIV infection in vervet monkeys but not in rhesus macaques. Because the latter species is not a natural SIV host, and develops immunodeficiency disease upon SIV infection, this interaction likely reflects adaptation to SIV.
I will also discuss results from whole genome sequencing data from 156 individuals from 71 species of the Lake Malawi cichlid radiation. We find that Lake Malawi cichlid species are much more closely related than previously thought and D-statistics (ABBA-BABA test) reveals massive signatures of ancient genetic exchange both with riverine out-groups and across the major clades within the radiation. Both paleogeological records of low lake level and a striking excess of haplotypes that are approximately 10 times more diverged than the genomic average are consistent with an ancestral hybrid swarm giving rise to the current radiation.
Hannes strives to understand natural evolution trough mathematical models and genome sequencing data analysis. In particular, the role of natural selection in creating and maintaining species diversity, and the discovery and interpretation of its genomic traces, have been a focus of his research. After undergraduate and master’s education in physics and engineering, he did his PhD in theoretical population genetics on evolutionary diversification under varying selection pressures and in high-dimensional trait-spaces. For his first postdoc, he went on to analyse population structure and historical selection events from whole genome sequence data in vervet monkeys and Arabidopsis thaliana. Last year, he joined Richard Durbin’s group at the Wellcome Trust Sanger Institute to study the genomics of the Lake Malawi cichlid adaptive radiation, where he is particularly interested in tracing cross-species gene flow and understanding the genomic basis for convergent morphological evolution.
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