Re: Paper: Adaptive Evolution of Conserved Noncoding Elements in Mammals

One more nail in the puffed-up (or overinflated), needlessly uninspiring
(and to me 'tyresome' :>) attitude of scientists who have (at least in the
past) asserted themselves by rolling the jargon that calls CNCs "junk-DNA"
off their tongues all too often;
And one more blow scored for those more freewheeling scientists and amateur
Evolutionary Philosophers That have thought that Evolution Pictured
Tentatively as partly proceeding through 'Equilibrium Punctuation' Tells
the truth better.
;-)
P
"Robert Karl Stonjek" <rstonjek@xxxxxxxxxxxxxx> wrote in message
news:fbta1t$h5k$1@xxxxxxxxxxxxxxxxxxxxxx
Adaptive Evolution of Conserved Noncoding Elements in Mammals

Su Yeon Kim 1, Jonathan K. Pritchard 2

1 Department of Statistics, The University of Chicago, Chicago
2 Department of Human Genetics, The University of Chicago
Conserved noncoding elements (CNCs) are an abundant feature of vertebrate
genomes. Some CNCs have been shown to act as cis-regulatory modules, but
the
function of most CNCs remains unclear. To study the evolution of CNCs, we
have developed a statistical method called the "shared rates test" to
identify CNCs that show significant variation in substitution rates across
branches of a phylogenetic tree. We report an application of this method
to
alignments of 98,910 CNCs from the human, chimpanzee, dog, mouse, and rat
genomes. We find that 68% of CNCs evolve according to a null model where,
for each CNC, a single parameter models the level of constraint acting
throughout the phylogeny linking these five species. The remaining 32% of
CNCs show departures from the basic model including speed-ups and
slow-downs
on particular branches and occasionally multiple rate changes on different
branches. We find that a subset of the significant CNCs have evolved
significantly faster than the local neutral rate on a particular branch,
providing strong evidence for adaptive evolution in these CNCs. The
distribution of these signals on the phylogeny suggests that adaptive
evolution of CNCs occurs in occasional short bursts of evolution. Our
analyses suggest a large set of promising targets for future functional
studies of adaptation.

Source: PLoS [Open Access]
http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0030147

Posted by
Robert Karl Stonjek




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