Exploring Evolutionary Relationships Across the Genome Using Topology Weighting.
We introduce the concept of topology weighting, a method for quantifying relationships between taxa that are not necessarily monophyletic, and visualizing how these relationships change across the genome. A given set of taxa can be related in a limited number of ways, but if each taxon is represented by multiple sequences, the number of possible topologies becomes very large. Topology weighting reduces this complexity by quantifying the contribution of each taxon topology to the full tree. We describe our method for topology weighting by iterative sampling of subtrees (Twisst), and test it on both simulated and real genomic data. Overall, we show that this is an informative and versatile approach, suitable for exploring relationships in almost any genomic dataset. Scripts to implement the method described are available at http://github.com/simonhmartin/twisst.
Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom shm45@cam.ac.uk.
Simon H
0000-0002-0747-7456
SH
Martin
Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom.|Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, Puerto Rico.|Smithsonian Tropical Research Institute, Panamá City 0843-03092, Panama.
Steven M
0000-0002-5083-8114
SM
Van Belleghem
D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics; D008957:Models, Genetic; D010802:Phylogeny
incomplete lineage sorting; introgression; phylogenomics; population genomics