Human, chimp lineages interbred after splitting, study suggests

[Roger Bagu]

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@Ao]

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.(8-) 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]

johnwl4@aol.com wrote:
> Roger Bagula wrote:
> > http://www.world-science.net/othernews/060517_hybridf-
> > rm.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.(8-)
> 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

[Roger Bagu]

http://www.playfuls.com/news_003498_Human_Chimpanzee_Differe-
nces_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 Bagu]

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 Bagu]

> 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 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.

[Johnwl4@Ao]

Roger Bagula wrote:
> > 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 P=E4=E4bo and
> Johannes Kra=
use
> of the Max Planck Institute.

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

[Paul Crowl]

"John Roth" <JohnRoth1@jhrothjr.com> wrote in message
news:1167578952.694252.157840@v33g2000cwv.googlegroups.com...
>
> johnwl4@aol.com wrote:
>> Roger Bagula wrote:
>> > http://www.world-science.net/othernews/060517_hybridfr-
>> > m.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.

> 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.

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

Nope. The problem is the lack of common sense.

> 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.

Paul.

[McLark]

"Paul Crowley" <slkwuoiutiuytciuyik@slkjlskjoioue.com> wrote
in message news:eZTlh.17179$j7.337136@news.indigo.ie...
> "John Roth" <JohnRoth1@jhrothjr.com> wrote in message news:-
> 1167578952.694252.157840@v33g2000cwv.googlegroups.com...
>>
>> johnwl4@aol.com wrote:

[GASP! monkey boinkin']

>> 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.

> Paul.

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