Going nuclear: gene family evolution and vertebrate phylogeny reconciled


Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenetic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny.

In Proceedings of the Royal Society B:Biological Sciences 269:1555–1561
James Cotton
James Cotton
Senior Staff Scientist

My research interests are in the genomics, and particularly population genomics of parasites, particularly those that cause neglected tropical diseases