EBU3B, Room CSE 1202
However, to realize the full potential in genomic and evolutionary studies, we require accurate, efficient, and scalable methods that are widely applicable. In this talk, I address this need by developing novel computational approaches for reconstructing gene evolutionary histories. In particular, I consider models for gene family evolution that take into account (1) duplication, (2) loss, (3) horizontal gene transfer, (4) genetic drift (leading to deep coalescence), and (5) nucleotide or amino acid substitution, and I present new phylogenetic algorithms for (1) eukaryotic gene tree reconstruction, (2) prokaryotic gene tree reconstruction, and (3) gene tree-species tree reconciliation. Through extensive benchmarking, I show that these methods dramatically improve reconstructions compared to state-of-the-art programs; in addition, they are efficient and require few modeling assumptions or parameters, making them applicable to a broad range of species and large datasets. As evidence, I apply these methods to clades of 12 Drosophila, 16 fungi, 15 primates, and 11 cyanobacteria, as well as to simulated phylogenies with up to 200 taxa, and demonstrate the large impact of accurate phylogenetic inference on downstream evolutionary analyses.
These results demonstrate the power of computational phylogenetics, and I believe that with the continued development and adoption of such methods, we can address fundamental biological questions with many important implications for future investigations of gene and genome evolution.
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