Human, chimp lineages interbred after splitting, study sugge

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Roger Bagula

Posted: Sat Dec 30, 2006 1:54 pm

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http://www.world-science.net/othernews/060517_hybridfrm.htm

Human, chimp lineages interbred after splitting, study suggests

May 17, 2006
Courtesy The Broad Institute of MIT and Harvard
and World Science staff

Probably the most shocking aspect of Darwin’s theory of evolution has
always been its implication that we descend from ape-like ancestors. But
that idea may be easy to stomach compared with new findings.

Skull of "Toumaï" or Sahelanthropus tchadensis, thought to be the
earliest fossil from the human family tree. If the results of a new
study are correct, it could have come from a time when the chimp and
human lineages had begun to split, but were still interbreeding.
(courtesy M.P.F.T.)
A study has concluded that human and chimp ancestors may have interbred
for a long time after their two lineages began to split apart
evolutionarily.

The research also found the final separation was more recent than
previous research suggested.

“The study gave unexpected results about how we separated from our
closest relatives, the chimpanzees,” said David Reich of the Broad
Institute of Harvard University and the Massachusetts Institute of
Technology in Cambridge, Mass.

Reich is senior author of a paper detailing the findings, published in
the May 17 online edition of the research journal Nature.

“Something very unusual happened at the time of speciation,” he added.

Speciation, the evolutionary branching off of new species from existing
ones, is the key mechanism that creates new species, according to
evolutionary theory. Since chimps are our closest relatives, our
speciation from them would be the pivotal event that put us on the road
to humanhood.

Previous genetic studies have focused on the average genetic difference
between human and chimpanzee across their genomes.

By contrast, the new study scrutinized the variation in evolutionary
history across the whole human genome. In theory, some regions of the
genome should be “older” than others, the researchers explained. That
is, different regions should have characteristics traceable to different
times in the evolutionary history of the common ancestors of humans and
chimps.

This analysis led to three surprising conclusions, the scientists said:

* The time from the beginning to the end of the splitup ranges over more
than 4 million years across of the genome. In other words, the date of
the divergence seems different depending on where in the genome you
look—suggesting the process may have been gradual, and marked by
interbreeding.
* The youngest genomic regions are surprisingly recent, no more than 6.3
million and probably no more than 5.4 million years old. This would
suggest the final speciation itself occurred on the same time frame,
more recently than scientists previously thought.
* The X chromosome, which contributes to sexual characteristics, falls
almost completely at the more recent end of the time frame.

Chromosome X’s young age is a “smoking gun” for interbreeding, said Eric
Lander, a co-author of the paper and director of the Broad Institute.

Interbreeding is known to produce strong pressure for evolutionary
change—called selective pressure—in sexual characteristics, the
scientists said. That, they added, could explain the chromosome’s young age.

The researchers said their estimate for the time of the final splitup is
more recent than previous figures based on studies of the famous Toumaï
fossils, widely thought to be the oldest from the human family. Those
previous estimates put the divergence time at between 6.5 million and
7.4 million years.

The Toumaï fossil may itself be “more recent than previously thought,”
said the institute’s Nick Patterson, one of the authors of the new
study. “But if the dating is correct, the Toumaï fossil would precede
the human-chimp split. The fact that it has human-like features suggests
that human-chimp speciation may have occurred over a long period with
episodes of hybridization between the emerging species.”

Hybridization, or interbreeding, is thought to play a common role in
plant speciation, but not usually in animals. However, the apparent lack
of such events among animal species, Reich said, “may simply be due to
the fact that we have not been looking for them.”

johnwl4@aol.com

Posted: Sat Dec 30, 2006 2:30 pm

Guest

Roger Bagula wrote:

Quote:

Hi, Roger,

The ideas here may indeed be difficult for some to stomach, namely,
that occasionally a human ancestor and a chimp ancestor were able to
stomach each other.( Cool

Personally, I never concern myself with the
sex habits of individuals who lived 4 million years ago, except to
the extent it affects my genome.
Cheers
John GW

John Roth

Posted: Sun Dec 31, 2006 11:29 am

Guest

johnwl4@aol.com wrote:

Quote:

Roger Bagula wrote:
http://www.world-science.net/othernews/060517_hybridfrm.htm

Human, chimp lineages interbred after splitting, study suggests

May 17, 2006
Courtesy The Broad Institute of MIT and Harvard
and World Science staff

Probably the most shocking aspect of Darwin's theory of evolution has
always been its implication that we descend from ape-like ancestors. But
that idea may be easy to stomach compared with new findings.

(snip)

Hi, Roger,

The ideas here may indeed be difficult for some to stomach, namely,
that occasionally a human ancestor and a chimp ancestor were able to
stomach each other.( Cool

Personally, I never concern myself with the
sex habits of individuals who lived 4 million years ago, except to
the extent it affects my genome.
Cheers
John GW

It must be a slow news day - this study came out some time ago.
There are a number of problems with it, as I remember. First,
genome dating is notoriously tricky; most dates have to be
regarded as little more than informed speculation unless they're
backed up by fossil evidence which is difficult to come by for
species that lived in jungles.

Then there's the notion that human-like characteristics in the
fossil mean that it's from the human side of the tree. That's
not particularly well founded; it might as well be from the
common ancestor, with the chimp side changing afterwards.
The lack of fossils makes it very hard to be confident.

Also, all of this came out before the Neandertal introgression
studies. Given the number of introgression events that Hawks
references in his latest theory paper, I find it hard to credit
the statement that "introgression is unknown among mammals."

Finally, none of this should come as a surprise: speciation
events don't happen at a single point in time. They happen
over an extended period as two populations gradually grow
farther and father apart until eventually they're incapable of
producing offspring. I've seen a reference that this period
seems to be between 1.5 and 5 my in apes and monkeys.

John Roth

Paul Crowley

Posted: Sun Dec 31, 2006 3:09 pm

Guest

"John Roth" <JohnRoth1@jhrothjr.com> wrote in message
news:1167578952.694252.157840@v33g2000cwv.googlegroups.com...

Quote:

johnwl4@aol.com wrote:
Roger Bagula wrote:
http://www.world-science.net/othernews/060517_hybridfrm.htm

Human, chimp lineages interbred after splitting, study suggests

May 17, 2006
Courtesy The Broad Institute of MIT and Harvard
and World Science staff

Probably the most shocking aspect of Darwin's theory of evolution has
always been its implication that we descend from ape-like ancestors. But
that idea may be easy to stomach compared with new findings.

(snip)

It must be a slow news day - this study came out some time ago.
There are a number of problems with it, as I remember. First,
genome dating is notoriously tricky; most dates have to be
regarded as little more than informed speculation unless they're
backed up by fossil evidence which is difficult to come by for
species that lived in jungles.

Fair enough.

Quote:

Then there's the notion that human-like characteristics in the
fossil mean that it's from the human side of the tree. That's
not particularly well founded; it might as well be from the
common ancestor, with the chimp side changing afterwards.

Drivel. The chimp niche has existed for
about 10 million years. There is no reason
why the animal in it should change. The
hominid branch from it was exremely peculiar.
The new taxon did not merely find a new
niche -- it developed a new method of
locomotion.

Quote:

The lack of fossils makes it very hard to be confident.

Nope. The problem is the lack of common
sense.

Quote:

More nonsense. The hominid taxon moved
into an exceedingly specialised niche --
which imposed HUGE pressures on its
members to change, adopt a new morphology
and acquire all manner of new traits. There
was no question of "the two populations
moving slowly apart". The 'intermediate
stages' in the development of this new form
of locomotion were barely viable.

All this was well understood in Darwin's
time. Although, as PA steadily moves
further and further back into the Dark Ages,
it has been forgotten, and the sort of crap
that you are coming out with here is now
close to the standard.

Paul.

Roger Bagula

Posted: Sun Dec 31, 2006 3:34 pm

Guest

http://www.playfuls.com/news_003498_Human_Chimpanzee_Differences_Are_Studied.html
Human-Chimpanzee Differences Are Studied
Research

Avatar06:39 PM, December 20th 2006
by Editorial Staff

A U.S. study suggests the genetic differences between chimpanzees and
humans might be much more substantial than has been thought.

Scientists at Indiana University-Bloomington have determined
approximately 6 percent of human and chimp genes are unique to each
species, taking into account a fact other genetic studies do not -- the
genes that aren't there.

Indiana University computational biologist Matthew Hahn, who led the
study with researcher Jeffery Demuth, said the study does not dispute
the commonly reported 1.5 percent nucleotide-by-nucleotide difference
between humans and chimps.

"Both estimates are correct in their own way," Hahn said. "It depends on
what you're asking. There isn't a single, standard estimate of variation
that incorporates all the ways humans, chimps and other animals can be
genetically different from each other."

The scientists also surveyed gene families common to both humans and
chimps and observed in the human genome a significant increase in the
duplication of genes that influence brain functions.

That, said Hahn, suggests duplication and loss of genes plays a bigger
role in human evolution than changes within single genes.

The study appears in the inaugural issue of Public Library of Science ONE.

© 2006 UPI

Roger Bagula

Posted: Sun Dec 31, 2006 3:38 pm

Guest

94% or 99%?... or less or more? There seems to be little agreement
even among experts in the field.

http://www.chinapost.com.tw/news/archives/taiwan/20061222/98129.htm
Chimpanzee gene study may help find cures for human diseases

2006/12/22
TAIPEI, CNA

The results of a recent analysis of chimpanzee genes may be helpful in
developing cures for hepatitis B and C, as well as acquired
immunodeficiency syndrome (AIDS) and Alzheimer's disease, sources at
Taiwan's National Health Research Institutes (NHRI) said yesterday.

The research paper was published online in November by the scientific
journal Genome Research.

The principal author, Chen Feng-chi, an assistant researcher in NHRI's
Division of Biostatistics and Bioinformatics, said that humans and
chimpanzees are closely related to each other genetically and have 99
percent of genes in common. However, some diseases that are extremely
dangerous to humans have altogether no effect on chimpanzees -- and that
one percent variance may hold the key to answering such a difference.

For instance, life-threatening complications in the later stages of
hepatitis B and C are common in human patients. However, such symptoms
never occur in chimpanzees.

The human immunodeficiency (HIV) often leads to AIDS in humans, while
there are only a few cases in which HIV in chimpanzees develops into
AIDS. And chimpanzees never get Alzheimer's disease, even in old age.

After close comparisons were made between humans and chimpanzees on
7,000 genes related to biological functions, the team found that humans
have an additional 840,000 gene deletions and insertions in genetic
sequencing, which may lead to the development of the diseases.

Gene deletions and insertions are very similar in the analogy of a word,
for example "vocabulary, " that is spelt correctly as "vocabulary"in the
chimpanzee genetic sequence,but spelt "vocbulary" or "vocaebulary" in
humans, Chen explained.

Chen noted these deletions and insertions may alter the expression of
genes and interfere with the functions of RNA and protein, thus creating
an environment in which certain human-specific diseases develop.

If a single or a series of deletions and insertions are proved to be
related to certain diseases such as hepatitis B/C, AIDS, or Alzheimer's
disease, then modifying these alterations may "close the door" and stop
the disease from developing, Chen said.

Roger Bagula

Posted: Sun Dec 31, 2006 3:44 pm

Guest

Quote:

http://chronicle.uchicago.edu/061207/neanderthals.shtml
Humans, Neanderthals share common ancestry, yet have nothing in common
after evolutionary split of two species
By Catherine Gianaro
Medical Center Public Affairs

In the most thorough study of the Neanderthal genome to date, scientists
suggest an early human-Neanderthal split. The two species have a common
ancestry but do not share much else after evolving their separate ways,
wrote the authors of a recent study that appears in the Thursday, Nov.
16 issue of Science. In addition, the authors reported no evidence of
genetic admixture between Neanderthals and humans.

The authors comprise scientists from the University, the Lawrence
Berkeley National Laboratory, the U.S. Department of Energy’s Joint
Genome Institute and the Max Planck Institute for Evolutionary
Anthropology in Germany.

The study helps explain the evolutionary relationship between Homo
sapiens and Neanderthals (Homo neanderthalensis), and it “signifies the
dawn of Neanderthal genomics,” according to the authors.

“Humans went through several key stages of evolution during the last
400,000 years,” said study author Jonathan Pritchard, Professor in Human
Genetics, who led the Chicago team that analyzed the sequencing data.
“If we can compare human and Neanderthal genomes, then we can possibly
identify what the key genetic changes were during that final stage of
human evolution.”

Another author of the recent Science paper, Svante Pääbo of the Max
Planck Institute, sequenced Neanderthal mitochondrial DNA in 1997, and
first suggested that Neanderthals did not make a substantial
contribution to the modern human gene pool. This new study, headed up by
Edward Rubin of the Lawrence Berkeley National Laboratory, reinforces
that long-debated theory.

“While unable to definitively conclude that interbreeding between the
two species of humans did not occur,” Rubin said, “analysis of the
nuclear DNA from the Neanderthal suggests the low likelihood of it
having occurred at any appreciable level.”

According to the authors, “If Neanderthal admixture did indeed occur,
then it would manifest in our data as an abundance of low-frequency
derived alleles in Europeans where the derived allele would match
Neanderthal. No site in the data set appears to be of this type.”

However, Pritchard said, “We do not exclude the possibility of modest
levels of genome admixture. Pritchard’s team suggests that humans and
Neanderthals shared a common ancestor about 706,000 years ago, and that
the human and the Neanderthal ancestral populations split around 370,000
years ago. (Researchers found some genetic variation between the two
species, which the team attributes to the ancestral population.) Both
lines co-existed in Europe and western Asia until about 30,000 years ago.

The team used DNA extracted from a 38,000-year-old Neanderthal specimen
from Vindija, Croatia. They recovered 65,250 base pairs of the
Neanderthal’s 3 billion total base pairs and utilized traditional
sequencing technologies used in the Human Genome Project as well as a
new method called parallel pyro-sequencing to clone and insert missing
fragmented DNA and create a library of Neanderthal DNA.

Unlike the libraries used to sequence the human genome, which contained
only human DNA fragments, the Neanderthal DNA library is riddled with
contamination from microbes, which lived off the nutrients in the
Neanderthal remains, and from humans handling the Neanderthal specimen.

However, the scientists performed a variety of studies to confirm that
the vast majority of the human-like sequence in the library was indeed
Neanderthal and not just contamination from human bone collectors and
laboratory workers.

The researchers then verified the authenticity of the Neanderthal
sequence by comparing it to the human and chimpanzee genomes. This
revealed multiple locations where the Neanderthal sequence matched more
closely to the genomes of the chimpanzee than to the human. Using the
comparison of the Neanderthal to the human and chimp genomes enabled the
investigators to estimate the human-Neanderthal divergence timeline.

The scientists also used data from the HapMap genome project to
understand the relationship between modern human diversity and the
Neanderthal sequence. Their analysis showed that the Neanderthal
sequence could not have come from any modern human population.

The study suggests that Neanderthal and human genomes are greater than
99.5 percent identical, which leaves less than 0.5 percent of the
Neanderthal genome that will attract much attention. Many of the
biological differences between modern humans and Neanderthals will be
encoded at specific sites, which is why the researchers were able to
analyze enough data without having to sequence the entire Neanderthal
genome.

Authors of the paper are: Pritchard, Graham Coop, a Postdoctoral Scholar
in Human Genetics, and Human Genetics student Sridhar Kudaravalli; Joe
Alessi, Feng Chen, Darren Platt and Doug Smith of the DOE’s Joint Genome
Institute; Rubin and James Noonan of the Lawrence Berkeley National
Laboratory and the Joint Genome Institute; and Pääbo and Johannes Krause
of the Max Planck Institute.

MClark

Posted: Sun Dec 31, 2006 4:25 pm

Guest

"Paul Crowley" <slkwuoiutiuytciuyik@slkjlskjoioue.com> wrote in message
news:eZTlh.17179$j7.337136@news.indigo.ie...

Quote:

"John Roth" <JohnRoth1@jhrothjr.com> wrote in message
news:1167578952.694252.157840@v33g2000cwv.googlegroups.com...

johnwl4@aol.com wrote:

[GASP! monkey boinkin']

Quote:

Finally, none of this should come as a surprise: speciation
events don't happen at a single point in time. They happen
over an extended period as two populations gradually grow
farther and father apart until eventually they're incapable of
producing offspring. I've seen a reference that this period
seems to be between 1.5 and 5 my in apes and monkeys.

More nonsense. The hominid taxon moved
into an exceedingly specialised niche --
which imposed HUGE pressures on its
members to change, adopt a new morphology
and acquire all manner of new traits. There
was no question of "the two populations
moving slowly apart". The 'intermediate
stages' in the development of this new form
of locomotion were barely viable.

All this was well understood in Darwin's
time. Although, as PA steadily moves
further and further back into the Dark Ages,
it has been forgotten, and the sort of crap
that you are coming out with here is now
close to the standard.

Slip off your meds over the holidaze Pauly?
What on god's-green-earth would you know about
it anyway? You openly confess to never reading
any scientific journals and widely disparage those
who do. Knowing what PA is all about is easily
the most unattainable goal for you that you could
possibly set for yourself. Why do you persist in
embarrassing yourself by your continued harangues?

Come on, answer the question.

Quote:

Paul.

--
"For whosoever quoteth scripture endlessly
hath neither job nor hobby." II Mumbleonians 4:19

johnwl4@aol.com

Posted: Sun Dec 31, 2006 6:32 pm

Guest

Roger Bagula wrote:

Quote:

The researchers then verified the authenticity of the Neanderthal
sequence by comparing it to the human and chimpanzee genomes. This
revealed multiple locations where the Neanderthal sequence matched
more closely to the genomes of the chimpanzee than to the human. Using
the comparison of the Neanderthal to the human and chimp genomes
enabled the investigators to estimate the human-Neanderthal divergence
timeline.

http://chronicle.uchicago.edu/061207/neanderthals.shtml
Humans, Neanderthals share common ancestry, yet have nothing in common
after evolutionary split of two species
By Catherine Gianaro
Medical Center Public Affairs

In the most thorough study of the Neanderthal genome to date, scientists
suggest an early human-Neanderthal split. The two species have a common
ancestry but do not share much else after evolving their separate ways,
wrote the authors of a recent study that appears in the Thursday, Nov.
16 issue of Science. In addition, the authors reported no evidence of
genetic admixture between Neanderthals and humans.

The authors comprise scientists from the University, the Lawrence
Berkeley National Laboratory, the U.S. Department of Energy's Joint
Genome Institute and the Max Planck Institute for Evolutionary
Anthropology in Germany.

The team used DNA extracted from a 38,000-year-old Neanderthal
specimen
from Vindija, Croatia. They recovered 65,250 base pairs of the
Neanderthal's 3 billion total base pairs and utilized traditional
sequencing technologies used in the Human Genome Project as well as a
new method called parallel pyro-sequencing to clone and insert missing
fragmented DNA and create a library of Neanderthal DNA.

Authors of the paper are: Pritchard, Graham Coop, a Postdoctoral Scholar
in Human Genetics, and Human Genetics student Sridhar Kudaravalli; Joe
Alessi, Feng Chen, Darren Platt and Doug Smith of the DOE's Joint Genome
Institute; Rubin and James Noonan of the Lawrence Berkeley National
Laboratory and the Joint Genome Institute; and Pääbo and Johannes Krause
of the Max Planck Institute.

Believe the Green group got a million base pairs.
REgards
John GW

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