Natural Selection Not The Only Proces...

Natural Selection Not The Only Process That Drives Evolution

Posted in the Evolution Debate Forum

“Fear is One's Weakness”

Since: Jan 14

Weakness is Anothers Strength

#1 Jan 22, 2014
The researchers identified fast evolving human genes by comparing our genome with those of other primates. However, surprisingly, the patterns of molecular evolution in many of the genes they found did not contain signals of natural selection. Instead, their evidence suggests that a separate process known as BGC (biased gene conversion) has speeded up the rate of evolution in certain genes. This process increases the rate at which certain mutations spread through a population, regardless of whether they are beneficial or harmful.

http://www.sciencedaily.com/releases/2009/01/...
The Dude

Birkenhead, UK

#2 Jan 23, 2014
Yes, there's multiple mechanisms for evolution. In other news, the sky is blue. For anyone else who hasn't caught up.

““You must not lose faith ”

Level 5

Since: Jun 11

Location hidden

#3 Jan 23, 2014
It would however be good to see the actual paper in plos.

http://en.wikipedia.org/wiki/Gene_conversion

Is afterall not a straightforward definition.

““You must not lose faith ”

Level 5

Since: Jun 11

Location hidden

#4 Jan 23, 2014
http://www.nature.com/ng/journal/v36/n2/full/...

Meiotic gene conversion has an important role in allele diversification and in the homogenization of gene and other repeat DNA sequence families1, 2, 3, 4, 5, sometimes with pathological consequences6, 7. But little is known about the dynamics of gene conversion in humans and its relationship to meiotic crossover. We therefore developed screening and selection methods to characterize sperm conversions in two meiotic crossover hot spots in the major histocompatibility complex (MHC)8 and one in the sex chromosomal pseudoautosomal pairing region PAR1 (ref. 9). All three hot spots are active in gene conversion and crossover. Conversion tracts are short and define a steep bidirectional gradient centered at the peak of crossover activity, consistent with crossovers and conversions being produced by the same recombination-initiating events. These initiations seem to be spread over a narrow zone, rather than occurring at a single site, and seem preferentially to yield conversions rather than crossovers. Crossover breakpoints are more broadly diffused than conversion breakpoints, suggesting either differences between conversion and crossover processing after initiation or the existence of a quality control checkpoint at which short interactions between homologous chromosomes are preferentially aborted as conversions.

““You must not lose faith ”

Level 5

Since: Jun 11

Location hidden

#5 Jan 23, 2014
Fear is not Real wrote:
The researchers identified fast evolving human genes by comparing our genome with those of other primates. However, surprisingly, the patterns of molecular evolution in many of the genes they found did not contain signals of natural selection. Instead, their evidence suggests that a separate process known as BGC (biased gene conversion) has speeded up the rate of evolution in certain genes. This process increases the rate at which certain mutations spread through a population, regardless of whether they are beneficial or harmful.
http://www.sciencedaily.com/releases/2009/01/...
There is considerable current interest in establishing haplotype maps of the human genome and in understanding how such processes as recombination can influence haplotype structures28. Approaches include the exploration of models of crossover distribution that can account for observed haplotype block structures29, 30. What is missing from this modeling is the inclusion of gene conversion as an additional process that can lead to haplotype diversification. The present work provides the first step in determining basic parameters of meiotic gene conversion in the human genome and suggests that interallelic conversion in hot spots has the potential to profoundly affect haplotype diversity, but only at an extremely localized level, in the hot spots themselves.

The darn things they keep renaming with every paper on it.

““You must not lose faith ”

Level 5

Since: Jun 11

Location hidden

#6 Jan 23, 2014
http://www.plosgenetics.org/article/info:doi/...
A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes
John A. Capra equal contributor, Melissa J. Hubisz equal contributor,
Dennis Kostka, Katherine S. Pollard , Adam Siepel
Published: August 15, 2013
DOI: 10.1371/journal.pgen.1003684

See human origin on malaria and south-pacific population.
GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood

““You must not lose faith ”

Level 5

Since: Jun 11

Location hidden

#7 Jan 23, 2014
http://mbe.oxfordjournals.org/content/early/2...

Phylogenetic Patterns of GC-Biased Gene Conversion in Placental Mammals and the Evolutionary Dynamics of Recombination Landscapes

Nicolas Lartillot*,1,2

Deriving a model of the substitution process at putatively neutral nucleotide positions from population-genetics arguments, and accounting for among-lineage and among-gene effects, we propose a reconstruction of the variation in gBGC intensity at the scale of placental mammals, and of its scaling with body-size and karyotypic traits. Our results are compatible with a simple population genetics model relating gBGC to effective population size and recombination rate. In addition, among-gene variation and phylogenetic patterns of exon-specific levels of gBGC reveal the presence of rugged recombination landscapes, and suggest that short-lived recombination hot-spots are a general feature of placentals. Across placental mammals, variation in gBGC strength spans two orders of magnitude, at its lowest in apes, strongest in lagomorphs, microbats or tenrecs, and near or above the nearly neutral threshold in most other lineages. Combined with among-gene variation, such high levels of biased gene conversion are likely to significantly impact midly selected positions, and to represent a substantial mutation load. Altogether, our analysis suggests a more important role of gBGC in placental genome evolution, compared with what could have been anticipated from studies conducted in anthropoid primates.

““You must not lose faith ”

Level 5

Since: Jun 11

Location hidden

#9 Jan 23, 2014
Given that neither selectionist nor mutational
models provide satisfactory explanations for the
origin of GC-rich isochores, we focused on
a third possible hypothesis: biased gene conversion
(54). This model originates from work
by Brown & Jiricny (20), who noted that the
GC-bias of the mismatch repair machinery
might lead to a gene conversion bias favoring
GC-alleles (gBGC). A few years later,
Holmquist (64) and Eyre-Walker (40) proposed
the hypothesis that gBGC could be responsible
for the evolution of GC-rich isochores. One
strong prediction of this model is that sequences
subject to a high level of recombination should
be GC-rich. And indeed, the analysis of human
sequences demonstrated a genome-wide
positive correlation between crossover rate and
GC-content (r2 = 0.15 at the Mb scale)(48,
80).

further reading:
http://isites.harvard.edu/fs/docs/icb.topic88...
This gene was
recently translocated into the pseudoautosomal
region of the X chromosome, where the rate of
crossover is extremely high. This translocation
was followed by a strong acceleration in substitution
rates (111) and a very strong increase
of its GC-content at both coding and noncoding
sites

Biased Gene Conversion and
the Evolution of Mammalian
Genomic Landscapes
Laurent Duret1,∗ and Nicolas Galtier2 2009

““You must not lose faith ”

Level 5

Since: Jun 11

Location hidden

#12 Jan 23, 2014
RELAX

The fact that the GC-bias and the
accelerated evolution affected not only coding
sites but also silent sites clearly shows
that this pattern is not driven by positive selection.
The nonsynonymous/synonymous rate
ratio is generally increased during GC-biased
episodes, consistent with a gBGC-induced relaxed
selective pressure. Analyzing 46 nuclear
genes in Triticeae (wheat and relatives),
Haudry et al.(60) reported a higher nonsynonymous/
synonymous ratio in outcrossing
than in selfing species. The reverse pattern
would be theoretically expected under selective
models because of the reduced efficacy
of purifying selection in selfers. Noting that
the effect was stronger in GC-enriched and
in high-recombining genes, these authors invoked
gBGC as a potential explanation: gBGC
is efficient in outcrossers, but not in selfing
organisms, which are mainly homozygous.
Accordingly, the gBGC-induced substitution
load would explain the elevated rate of fixation
of nonsynonymous mutations in outcrossers.
Although these recent results warrant confirmation,
they strongly suggest that gBGC,
when active, can significantly (and negatively)
affect the evolution of functional genomic
elements, in human and in other
species.

Indeed, in some cases, gBGC overcomes purifying
selection and leads to the fixation of deleterious
AT → GC mutations (52, 53). Thus,
recombination hotspots might constitute the
Achilles heels of our genome.

from page 303 a summation.

““You must not lose faith ”

Level 5

Since: Jun 11

Location hidden

#13 Jan 23, 2014
http://gbe.oxfordjournals.org/content/4/7/787...

All relevant papers together looking at GB content and chromosome size.

““You must not lose faith ”

Level 5

Since: Jun 11

Location hidden

#14 Jan 23, 2014
http://imgpublic.mci-group.com/ie/PCO/AllAbst...
O3 page 12
de novo genes , a, tug of war over dominance over the sequence between old and new ones, overlapping the old frame. Old ones are under stronger purifying selection.

Suggestive of a host-virus arms race.

Well that's one way to look at the male of the species, and his halting progress in spurts and bouts.

An invasion of RNA virussus, the entire mechanism of gBGC a residue thereoff?

Vertebrate adaptive immunity adapts plastically at the same timescale as viral evolution. Another reason to have spurts.
See pg 23

Koonin selection directed at prevention of malfunction rather than adaptive gain of function.
page 35

“It Is What It Is”

Level 2

Since: Jul 13

Alberta, Canada

#15 Jan 23, 2014
Evolution is the designing mechanism. Each species design is continuously changed over time by evolution to insure its survival in the changing environment and world.

“Do not bend, fold, staple or”

Level 9

Since: Jan 11

mutilate. Point down range.

#16 Jan 23, 2014
DarkBlue wrote:
Evolution is the designing mechanism. Each species design is continuously changed over time by evolution to insure its survival in the changing environment and world.
Evolution is the name of the process of change over time. It isn't a designer or the designer. You have never shown that and others have shown you why it is not so.

Where in Canada did you say you were from?

“It Is What It Is”

Level 2

Since: Jul 13

Alberta, Canada

#17 Jan 23, 2014
Not too far from you as the crow flies. You did say you were from Canada too didn't you?

“Do not bend, fold, staple or”

Level 9

Since: Jan 11

mutilate. Point down range.

#18 Jan 23, 2014
DarkBlue wrote:
Not too far from you as the crow flies. You did say you were from Canada too didn't you?
I moved. What was the city again?

“It Is What It Is”

Level 2

Since: Jul 13

Alberta, Canada

#19 Jan 23, 2014
DanFromSmithville wrote:
<quoted text>I moved. What was the city again?
Where did you move to? Was it a move for employment purposes or just for change?

“Do not bend, fold, staple or”

Level 9

Since: Jan 11

mutilate. Point down range.

#20 Jan 23, 2014
DarkBlue wrote:
<quoted text>
Where did you move to? Was it a move for employment purposes or just for change?
I moved from there to here. It was something. I am not really from Canada. I was just kidding you.

What city was that again? I don't think you said.

“It Is What It Is”

Level 2

Since: Jul 13

Alberta, Canada

#21 Jan 23, 2014
We have discussed where I live. You have admitted to being deceiving about where you live or lived. Is there a reason to your questions? Where is it that you now live and why is it you are so interested where I live? Sometimes there is a reason behind questions that can't be seen, so I am asking for your reason.

“Do not bend, fold, staple or”

Level 9

Since: Jan 11

mutilate. Point down range.

#22 Jan 23, 2014
DarkBlue wrote:
We have discussed where I live. You have admitted to being deceiving about where you live or lived. Is there a reason to your questions? Where is it that you now live and why is it you are so interested where I live? Sometimes there is a reason behind questions that can't be seen, so I am asking for your reason.
Don't get paranoid. I wanted you to remind me where in Canada you said you lived. You mentioned it before, I don't understand what the big deal is.

As to being deceiving I made a big joke of it when I mentioned that. If you couldn't figure out I was joking, you really need to relax.

Tell me when this thread is updated:

Subscribe Now Add to my Tracker

Add your comments below

Characters left: 4000

Please note by submitting this form you acknowledge that you have read the Terms of Service and the comment you are posting is in compliance with such terms. Be polite. Inappropriate posts may be removed by the moderator. Send us your feedback.

Evolution Debate Discussions

Title Updated Last By Comments
News Why Atheist Richard Dawkins Supports Religious ... 3 min Dogen 1,329
News "Science vs. Religion: What Scientists Really T... (Jan '12) 9 min Eagle 12 - 78,512
News Evolution vs. Creation (Jul '11) 1 hr Simon 222,156
News It's the Darwin crowd that lacks the facts in e... (Mar '09) 1 hr Science 162,986
Mathematicians PROVED evolution IMPOSSIBLE! 5 hr Dogen 779
News Atheism, for Good Reason, Fears Questions (Jun '09) Wed Science 32,431
News Nonsense of a high order: The confused world of... (Jan '17) Aug 5 yehoshooah adam 4,381
More from around the web