In a message dated 10/9/00 7:37:02 PM Eastern Daylight Time,
sejones@iinet.net.au writes:
<< HX>What about nuclear DNA mutation rates?
It was the New Scientist article (based on a SCIENCE journal report) that
I quoted so if Huxter has any questions about the use of mtDNA rather
than nuclear DNA his dispute is with those journals.
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I have no dispute, I was just curious if any mention of nuclear DNA mutation
rates had been mentioned. It appears that 1) they were not and 2) you are
unfamiliar with the concept of using nuclear DNA in molecular clock
calculations. Do you know why mtDNA is preferrentially used in such studies?
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My understanding is that the molecular clock hypothesis is based on the
*neutral* mutation rate. Mitochondrial DNA is therefore used instead of
nuclear DNA because mtDNA is thought to be selectively neutral since it
does not code for any phenotypical features.
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Actually, there isn't really "a" molecular clock hypothesis, at least not
insofar as it focuses on mt or nuclear DNA. The MCH was originally aimed at
proteins, way back in the early 1970s, and nuclear DNA has been used as far
back as the late 1980s (if not sooner). Your understanding is apparently
limited.
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But if Huxter knows of any molecular clock studies based on "nuclear DNA
mutation rates", perhaps he can post it to the List?
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Sure Steve. Why, doing a simple medline search produced 8 hits on Primates
alone. A sampling:
==============
Mol Phylogenet Evol 1999 Nov;13(2):348-59 Related Articles, Books, LinkOut
Molecular phylogeny of Old World monkeys (Cercopithecidae) as inferred from
gamma-globin DNA sequences.
Page SL, Chiu Ch, Goodman M
Department of Anatomy and Cell Biology, Wayne State University School of
Medicine, Detroit, Michigan 48201, USA.
DNA sequence data of the nuclear-encoded gamma1-gamma2-globin duplication
region were used to examine the phylogenetic relationships of 16
cercopithecid (Old World monkey) species representing 12 extant genera. ...
Local molecular clock divergence time estimates were used as a yardstick in a
"rank equals age" system to propose a reduction in taxonomic rank for most
clades within Cercopithecidae.
======================
J Mol Evol 1997;44 Suppl 1:S121-32
Molecular evidence from the nuclear genome for the time frame of human
evolution.
Easteal S, Herbert G
Human Genetics Group, John Curtin School of Medical Research, Australian
National University, Canberra, Australia.
Evolutionary divergence times can be inferred from molecular distances if a
molecular clock can be assumed and if the substitution rate can be estimated.
...This range of substitution rates implies a divergence time of humans and
chimpanzees of 4.0-3.6 million years ago. This postdates the occurrence of
Ardipithecus ramidus and the earliest occurrence of Australopithecus
afarensis, suggesting that the common ancestor of humans and chimpanzees was
bipedal and that the trait has been lost in chimpanzees rather than gained in
humans.
===========================
Mol Phylogenet Evol 1992 Jun;1(2):97-135
Reexamination of the African hominoid trichotomy with additional sequences
from the primate beta-globin gene cluster.
Bailey WJ, Hayasaka K, Skinner CG, Kehoe S, Sieu LC, Slightom JL, Goodman M
Department of Molecular Biology and Genetics, Wayne State University School
of Medicine, Detroit, Michigan 48201.
Additional DNA sequence information from a range of primates, including 13.7
kb from pygmy chimpanzee (Pan paniscus), was added to data sets of
beta-globin gene cluster sequence alignments that span the gamma 1, gamma 2,
and psi eta loci and their flanking and intergenic regions. This enlarged
body of data was used to address the issue of whether the ancestral
separations of gorilla, chimpanzee, and human lineages resulted from only one
trichotomous branching or from two dichotomous branching events.... Support
for this human-chimpanzee clade is statistically significant at P = 0.002
over a human-gorilla clade or a chimpanzee-gorilla clade. An analysis of
expected and observed homoplasy revealed that the number of sequence changes
uniquely shared by human and chimpanzee lineages is too large to be
attributed to homoplasy. Molecular clock calculations that accommodated
lineage variations in rates of molecular evolution yielded hominoid branching
times that ranged from 17-19 million years ago (MYA) for the separation of
gibbon from the other hominoids to 5-7 MYA for the separation of chimpanzees
from humans. ...
========================
Science 1986 Oct 10;234(4773):194-6 Related Articles, Books
Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in
the molecular clock.
Vawter L, Brown WM
The discovery that the rate of evolution of vertebrate mitochondrial DNA is
rapid, compared to the rate for vertebrate nuclear DNA, has resulted in its
widespread use in evolutionary studies. Comparison of mitochondrial and
nuclear DNA divergences among echinoid and vertebrate taxa of similar ages
indicates that the rapid rate of vertebrate mitochondrial DNA evolution is,
in part, an artifact of a widely divergent rate of nuclear DNA evolution.
This disparity in relative rates of mitochondrial and nuclear DNA divergence
suggests that the controls and constraints under which the mitochondrial and
nuclear genomes operate are evolving independently, and provides evidence
that is independent of fossil dating for a robust rejection of a generalized
molecular clock hypothesis of DNA evolution.
===========================
There are others, and I know of at least two more that will be coming out
within a few months looking specifically at humans. There is a review paper
that compares nuclear DNA molecular clock dates with dates inferred from the
fossil record and there is a remarkable congruence between the two. I can
dig up the ref if you'd like.
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HX>Do we just ignore that much larger amount of information
See above. It was the above scientific journals who Huxter is claiming is
"ignore that much larger amount of information". I just posted what New
Scientist said.
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I see. I thought maybe you could formulate your own opinion. I didn't
realize that you were simply a 'reporter' for this list, busily scribbling
down and quoting what others have written...
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And anyway, what "larger amount of information" is that exactly?
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Surely you recognize that the nuclear genome is many orders of magnitude
larger than the mitochondrial genome?
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HX>because if we put a certain spin on reality,
I am glad Huxter said "we"! Claims about putting a "spin on reality" cut
both ways.
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It is a shame you cut out the context of my quote. I understand creationists
of all stripes have a distinct tendancy to do so such that a statement can
appear to mean something it originally did not.
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HX>the YEWC framework looks peachy?
What is the "YEWC framework"?
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It is a typo. You see, on my keyboard, the 'w' and the 'e' are next to each
other, and when typing hurriedly one can often hit more than one key at a
time. Not doing a spell check allows them to slip through. But I'm glad you
paid such close attention.
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If it is anything to do with YEC then Huxter is barking up the wrong tree
on two counts:
1. I am an *old*-Earth creationist; and
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Well, pardon me. Either way, it seems that your 'concerns' about the mtDNA
molecular clock are a bit on the weak side.
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2. the issue is the antiquity of *man* not the antiquity of the Earth.
>>
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Same thing.
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