Chapter

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

Jeffrey L. Boore and Susan I. Fuerstenberg

in Animal Evolution

Published in print August 2009 | ISBN: 9780199549429
Published online September 2009 | e-ISBN: 9780191721601 | DOI: http://dx.doi.org/10.1093/acprof:oso/9780199549429.003.0013
 Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction

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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

Chapter.  3649 words.  Illustrated.

Subjects: Evolutionary Biology

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