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

From: Robert Karl Stonjek (rstonjek_at_bigpond.net.au)
Date: 12/23/04 

Date: Thu, 23 Dec 2004 17:51:56 +0000 (UTC)

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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:=20
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 =CE=B3-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 =CE=B3-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:=20
phylogenetic supertrees, prokaryotic phylogeny, taxonomic congruence, =
phylogenomics, molecular evolution=20

Abstract and Full text links at The Royal Society
http://www.journals.royalsoc.ac.uk/link.asp?id=3DHNAFDHG6X5XBWJL4

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
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<DIV>
<DIV>
<DIV>Does a tree-like phylogeny only exist at the tips in the=20
prokaryotes?<BR><BR>Christopher J. Creevey A1, David A. Fitzpatrick A1, =
Gayle K.=20
Philip A1, Rhoda J. Kinsella A1, Mary J. O'Connell A1, Melissa M. =
Pentony A1,=20
Simon A. Travers A1, Mark Wilkinson A2, James O. McInerney</DIV>
<DIV><BR>A1 Bioinformatics and Pharmacogenomics Laboratory, Department =
of=20
Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, =

Ireland<BR>A2 Department of Zoology, The Natural History Museum, =
Cromwell Road,=20
London SW7 5BD, UK<BR><BR>Abstract: <BR>The extent to which prokaryotic=20
evolution has been influenced by horizontal gene transfer (HGT) and =
therefore=20
might be more of a network than a tree is unclear. Here we use supertree =
methods=20
to ask whether a definitive prokaryotic phylogenetic tree exists and =
whether it=20
can be confidently inferred using orthologous genes. We analysed an =
11-taxon=20
dataset spanning the deepest divisions of prokaryotic relationships, a =
10-taxon=20
dataset spanning the relatively recent =CE=B3-proteobacteria and a =
61-taxon dataset=20
spanning both, using species for which complete genomes are available.=20
Congruence among gene trees spanning deep relationships is not better =
than=20
random. By contrast, a strong, almost perfect phylogenetic signal exists =
in=20
=CE=B3-proteobacterial genes. Deep-level prokaryotic relationships are =
difficult to=20
infer because of signal erosion, systematic bias, hidden paralogy and/or =
HGT.=20
Our results do not preclude levels of HGT that would be inconsistent =
with the=20
notion of a prokaryotic phylogeny. This approach will help decide the =
extent to=20
which we can say that there is a prokaryotic phylogeny and where in the=20
phylogeny a cohesive genomic signal exists.</DIV>
<DIV><BR>Keywords: <BR>phylogenetic supertrees, prokaryotic phylogeny, =
taxonomic=20
congruence, phylogenomics, molecular evolution </DIV>
<DIV>&nbsp;</DIV>
<DIV>Abstract and Full text links at The Royal Society</DIV>
<DIV><A=20
href=3D"http://www.journals.royalsoc.ac.uk/link.asp?id=3DHNAFDHG6X5XBWJL4=
">http://www.journals.royalsoc.ac.uk/link.asp?id=3DHNAFDHG6X5XBWJL4></=
DIV>
<DIV>&nbsp;</DIV>
<DIV>Comment:</DIV>
<DIV>I can still remember back when 'networks' were just called =
'Bushes'.&nbsp;=20
Perhaps the current US political landscape has irretrievably soiled the=20
term?</DIV>
<DIV>&nbsp;</DIV>
<DIV>Posted by<BR>Robert Karl Stonjek</DIV></DIV></DIV></BODY></HTML>

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