Phylogenetic profiling on large scale bird genomic data

Phylogenetic profiling is a computational method used to infer functional relationships between genes based on their patterns of presence or absence across different species. In recent years, the availability of extensive genomic data has enabled its reliable use to detect eukaryotic protein interaction networks. Here we present preliminary results using this type of analysis on a large-scale publicly available bird genome dataset (Feng, Shaohong, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve, Duo Xie, et al. 2020. "Dense Sampling of Bird Diversity Increases Power of Comparative Genomics.” Nature 587 (7833): 252–57.). Birds, as a diverse group, provide a unique opportunity to investigate the evolution of traits and gene functions by associated phenotypic shifts with phylogenetic patterns. Using profiling we searched for genes and modifications in pathways associated with changes in key avian characteristics, such as flight, trophic level and beak morphology. Additionally, this approach can provide evidence for lineage-specific gene losses and expansions, indicating the unique adaptations of different bird species to their ecological niches.

David Moi is currently a postdoc at the Dessimoz Lab at the University of Lausanne in Switzerland, and is considering applying for an ERC grant with CIBIO as the host institution.

[Host: James Harris, Applied Phylogenetics - AP]