Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
J L Boore, Susan I Fuerstenberg

Abstract

The first whole genomes to be compared for phylogenetic inference were those of mitochondria, which provided the first sets of genome-level characters for phylogenetic reconstruction. Most powerful among these characters has been the comparisons of the relative arrangements of genes, which has convincingly resolved numerous branch points, including those that had remained recalcitrant even to very large molecular sequence comparisons. Now the world faces a tsunami of complete nuclear genome sequences. In addition to the tremendous amount of DNA sequence that is becoming available for comparison, there is also a potential for many more genome-level characters to be developed, including the relative positions of introns, the domain structures of proteins, gene family membership, the presence of particular biochemical pathways, aspects of DNA replication or transcription, and many others. These characters can be especially convincing owing to their low likelihood of reverting to a primitive condition or occurring independently in separate lineages, thereby reducing the occurrence of homoplasy. The comparisons of organelle genomes pioneered the way for using such features for phylogenetic reconstructions, and it is almost certainly...Continue Reading

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Citations

Jan 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Maximilian J Telford, D Timothy J Littlewood
Jan 11, 2013·BMC Evolutionary Biology·Ehsan KayalDennis V Lavrov
Sep 10, 2013·PloS One·Arun N Prasanna, Sarika Mehra
Jul 30, 2014·Proceedings of the National Academy of Sciences of the United States of America·Robert C ThomsonBrian R Moore
Jan 31, 2013·International Journal for Parasitology·Bonnie L Webster, D Timothy J Littlewood
Jan 21, 2015·Molecular Phylogenetics and Evolution·Tzu-Hsuan TuMing-Shiou Jeng
Dec 19, 2016·Molecular Phylogenetics and Evolution·Healy HamiltonW Brian Simison

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