Accelerated rate of evolution in SSU rDNA of Nematoda

Kerstin Hoef-Emden kerstin.hoef-emden at uni-koeln.de
Thu Feb 26 17:31:11 EST 2004


Hi,

Wurff, Andre vander <Andre.vanderWurff at wur.nl> wrote:

> We are wrestling to explain the finding that recently derived nematodal
> clades have a significant higher rate of evolution that older clades
> (Relative rate tests). In fact, we witness an increase in evolutionary
> rate from primitive clades towards more recently derived clades.

Is it also obvious from the phylogenetic trees? Which gene(s) or DNA
fragments did you use? May the acceleration of evolutionary rates indicate
speciation processes?

> 1. Can anyone help us in finding an explanation for this phenomenon ?

Often an acceleration of substitution rates was accompanied by a change in
life style, e.g. a change from free-living to endosymbiontic life style, a
change from photosynthesis to heterotrophy etc. In endosymbionts and
organelles also a bias toward increased A+T contents was found.

Are these younger nematodal lineages endosymbiotic, did they change habitat=
,
did they become asexual ....?

> (e.g. relevant articles/opinions/vicariance/life hostory traits ?)

a few refs:

Moran NA (1996). Accelerated evolution and Muller's ratchet in endosymbioti=
c
bacteria. PNAS 93: 2873-2878

Nedelcu A (2001). Complex patterns of plastid 16S rRNA gene evolution in
nonphotosynthetic algae. J. Mol. Evol. 53: 670-679

dePamphilis CW, Young ND, Wolfe AD (1997). Evolution of plastid gene rps2 i=
n
a lineage of hemiparasitic and holoparasitic plants: many losses of
photosynthesis and complex patterns of rate variation. PNAS 94: 7367-7372

Lynch M (1997). Mutation accumulation in nuclear, organellar, and
prokaryotic transfer RNA genes. Mol. Biol. Evol. 14: 914-925

Charlesworth D, Morgan MT, Charlesworth B (1993). Mutation accumulation in
finite outbreeding and inbreeding populations. Genet. Res. 61: 39-56

> 2. Do we have to correct for this in a phylogenetic analysis (in
> MP/Bayesian/NJ trees) ?

If not corrected, the long branches may cause LBA artefacts. In ML and NJ:
run analyses always with a gamma distribution. It does not really account f=
or
taxon-specific accelerated rates, but by including a site-specific rate
variation, the problem will be mildered. If you use Modeltest to choose the
evolutionary model fitting best the data, it will presumably anyway come up
with an evolutionary model with a gamma distribution.

In MrBayes: settings to invgamma+covarion

In MP: presumably difficult




Best wishes,

Kerstin Hoef-Emden

--=20

Dr. Kerstin Hoef-Emden=09=09=09Gyrhofstr. 15
Universit=E4t zu K=F6ln=09=09=0950931 K=F6ln
Botanisches Institut=09=09=09Germany
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