Paper: Does a tree-like phylogeny only exist at the tips in the prokaryotes?

From: Robert Karl Stonjek (rstonjek_at_bigpond.net.au)
Date: 12/24/04 

Date: Fri, 24 Dec 2004 22:56:51 +0000 (UTC)

Does a tree-like phylogeny only exist at the tips in the prokaryotes?

Christopher J. Creevey A1, David A. Fitzpatrick A1, Gayle K. Philip A1,
Rhoda J. Kinsella A1, Mary J. O'Connell A1, Melissa M. Pentony A1, Simon A.
Travers A1, Mark Wilkinson A2, James O. McInerney

A1 Bioinformatics and Pharmacogenomics Laboratory, Department of Biology,
National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
A2 Department of Zoology, The Natural History Museum, Cromwell Road, London
SW7 5BD, UK

Abstract:
The extent to which prokaryotic evolution has been influenced by horizontal
gene transfer (HGT) and therefore might be more of a network than a tree is
unclear. Here we use supertree methods to ask whether a definitive
prokaryotic phylogenetic tree exists and whether it can be confidently
inferred using orthologous genes. We analysed an 11-taxon dataset spanning
the deepest divisions of prokaryotic relationships, a 10-taxon dataset
spanning the relatively recent γ-proteobacteria and a 61-taxon dataset
spanning both, using species for which complete genomes are available.
Congruence among gene trees spanning deep relationships is not better than
random. By contrast, a strong, almost perfect phylogenetic signal exists in
γ-proteobacterial genes. Deep-level prokaryotic relationships are difficult
to infer because of signal erosion, systematic bias, hidden paralogy and/or
HGT. Our results do not preclude levels of HGT that would be inconsistent
with the notion of a prokaryotic phylogeny. This approach will help decide
the extent to which we can say that there is a prokaryotic phylogeny and
where in the phylogeny a cohesive genomic signal exists.

Keywords:
phylogenetic supertrees, prokaryotic phylogeny, taxonomic congruence,
phylogenomics, molecular evolution

Abstract and Full text links at The Royal Society
http://www.journals.royalsoc.ac.uk/link.asp?id=HNAFDHG6X5XBWJL4

Comment:
I can still remember back when 'networks' were just called 'Bushes'.
Perhaps the current US political landscape has irretrievably soiled the
term?

Posted by
Robert Karl Stonjek