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Animal EvolutionGenomes, Fossils, and Trees$
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Maximilian J. Telford and D.T.J. Littlewood

Print publication date: 2009

Print ISBN-13: 9780199549429

Published to Oxford Scholarship Online: September 2009

DOI: 10.1093/acprof:oso/9780199549429.001.0001

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

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

Chapter:
(p.139) CHAPTER 13 Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction
Source:
Animal Evolution
Author(s):

Jeffrey L. Boore

Susan I. Fuerstenberg

Publisher:
Oxford University Press
DOI:10.1093/acprof:oso/9780199549429.003.0013

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 comparisons of the relative arrangements of genes, which have convincingly resolved numerous branching points, including some 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 the potential for many more genome-level characters to be developed, including the relative positions of introns, the domain structures of proteins, gene family membership, presence of particular biochemical pathways, aspects of DNA replication or transcription, and many others. These characters can be especially convincing because of their low likelihood of reverting to a primitive condition or occurring independently in separate lineages, so 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 true, as ever more genomic sequence becomes available, that further use of genome-level characters will play a big role in outlining the relationships among major animal groups.

Keywords:   genome, evolution, phylogeny, PhIGs, genome level characters, gene family

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