Reconstructing phylogenies from gene-content and gene-order data

Gene-order data have been used successfully to reconstruct organellar phylogenies; they offer low error rates, the potential to reach farther back in time than through DNA sequences (because genome-level events are rarer than DNA point mutations), and immunity from the so-called gene-tree vs. species-tree problem (caused by the fact that the evolutionary history of specific genes is not isomorphic to that of the organism as a whole). They have also provided deep mathematical and algorithmic results dealing with permutations and shortest sequences of operations on these permutations. Recent developments include generalizations to handle insertions, duplications, and deletions, scaling to large numbers of organisms, and, to a lesser extent, to larger genomes; and the first Bayesian approach to the reconstruction problem. We survey the state-of-the-art in using such data for phylogenetic reconstruction, focusing on recent work by our group that has enabled us to handle arbitrary insertions, duplications, and deletions of genes, as well as inversions of gene subsequences. We conclude with a list of research questions (mathematical, algorithmic, and biological) that will need to be addressed in order to realize the full potential of this type of data. 12.

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