Linked Life Data

19686857

Source:http://linkedlifedata.com/resource/pubmed/id/19686857

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2010-2-22
pubmed:abstractText
A phylogenomic approach was used to generate an amino acid phylogeny for 12 whole genomes representing 10 species in the family Pasteurellaceae. Orthology of genes was determined using an approach similar to OrthologID (http://nypg.bio.nyu.edu/orthologid/about.html) and resulted in the generation of a matrix with 3130 genes with 1,194,615 aligned amino acid characters of which 239,504 characters are phylogenetically informative. Phylogenetic analysis of the concatenated matrix using all standard approaches (maximum parsimony, maximum likelihood, and Bayesian analysis) results in a single extremely robust phylogenetic hypothesis for the species examined in this study. Remarkably, no single gene partition gives the same tree as the concatenated analysis. By analyzing partitioned support in the data matrix, we show that there is very little negative support emanating from individual gene partitions to suggest that the concatenated hypothesis is not tenable. The large number of characters in the matrix allows us to test hypotheses concerning missing data and character number in phylogenomic studies, and we conclude that matrices constructed using genome level information are very robust to missing data. We show that a very large number of concatenated gene sequences (>160) are needed to reliably obtain the same topology as the overall analysis.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
1095-9513
pubmed:author
pubmed:copyrightInfo
Copyright 2009 Elsevier Inc. All rights reserved.
pubmed:issnType
Electronic
pubmed:volume
54
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
950-6
pubmed:meshHeading
pubmed:year
2010
pubmed:articleTitle
A whole-genome phylogeny of the family Pasteurellaceae.
pubmed:affiliation
Sackler Institute of Comparative Genomics, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA.
pubmed:publicationType
Journal Article