While exploring the Paisley 5 Mile Point Caves in the Cascade Range of central Oregon, archaeologists may have found the earliest confirmed evidence for human habitation in North America, namely fourteen pieces of 14,300 year old human excrement. That’s right. Poop. The fossilized feces, or coprolites, are extraordinary in that besides probably being older than any artifacts thus far discovered on the continent, six of them appear to contain human protein and DNA. All of this provides a strong indication that humans were in North America at least a thousand years before the so-called Clovis people (named after the New Mexico site where distinctively-shaped rock spear points that gave the name to the prehistoric paleo-Indians were first found), who for years were thought to be the first humans to live here.

We’ve been aware of these shallow arid caves for 60 years, which had been carved into a hillside by a prehistoric lake, and have previously uncovered a variety of animal bones and several stone tools there. But in 2002, a team led by Dennis L. Jenkins, an archaeologist at the University of Oregon dug deeper into cave No. 5 and found the coprolites in question. They noted that few artifacts were found in the cave which implies that the occupant’s visits were somewhat brief and that the cave may have even served as a latrine of some sort.

In many ways, coprolites are ideal human remains for archaeologists. First, because indigenous people often are upset when their ancestors bones are excavated, but nobody gets upset to examining their feces. Second, since because bones calcify over time this makes it difficult to extract any viable DNA, while coprolites are full of cellular material that comes from the colon.

Jenkins says that studying the coprolites has allowed them to determine what these early Americans ate. “They certainly ate sage grouse and smaller animals," he noted. "I think we recovered some chipmunk bones from one of the coprolites.” Furthermore, there are residues from plant types that are still found close to the caves that have also been found in the coprolites. And with hundreds of more coprolites to be tested, there is still more information that can be uncovered, possibly including what sort of diversity was there in the first people entering America, such as how many different people and the ratio of males to females.

But to first verify that the coprolites were indeed from humans, Jenkins recruited some DNA experts to carry out multiple tests on the samples. The primary DNA analysis was carried out by Eske Willerslev and M. Thomas P. Gilbert of the Center for Ancient Genetics at the University of Copenhagen in Denmark. Besides confirming their human origin, Willerlev and Gilbert were also able to determine that the DNA found were from the founding genetic groups, or haplogroups, of present-day Native Americans. These same genetic patterns are also found among certain groups in eastern Asia and increase support for the theory that the first people came here by crossing the Bering Sea land bridge that at one time connected North America and Asia.

Yet the findings aren’t without their detractors. Noting that there were also non-human coprolites at the cave bottom, Vanderbilt University archeologist Thomas Dillehay (known for his excavations at Monte Verde in Chile, which indicate humans may have inhabited that region as long as 14,500 years ago) urges caution. He argues that since several of the fossilized feces “did not have human DNA, and some of them had canine, perhaps fox, DNA,” that the coprolites might have been contaminated by them. Jenkins dismisses this by noting that some of the coprolites contained human hair and human proteins, in addition to human DNA, so that if they had been left by canines, then they must have been canines that were eating humans (or humans eating the canines), which doesn't change the conclusion that people lived there 14,300 years ago.

A more serious challenge has been raised by one of the researchers who did the DNA testing of the coprolites, Dr. Gilbert, who worries that the coprolites could have been contaminated with younger human DNA by being urinated on by later Native Americans inhabitants. He also pointed out that not all the coprolites contain Native American DNA, and that this may be because they are all non-human and have been only identified as such because of contamination from being urinated on. His colleague, Dr. Willerslev, quickly rejects at least the latter possibility by observing that human proteins found in the samples rule out any contamination or leeching as the cause because it couldn’t provide enough human protein for the type of testing that was employed to have detected. Willerslev also mentioned that since only one Native American DNA sequence was associated with each coprolite, and that the sediment samples and animal bones (primarily horse and camel) only tested positive for animal DNA and negative for human DNA, indicates that contamination is an unlikely source for the Native American DNA found in the coprolites identified as coming from humans. Still, the results remain controversial until more testing can be done.

Further Reading:

Pre-Clovis Human DNA Found In 14,300-year-old Feces In Oregon Cave Is Oldest In New World

Fossilized Feces Tell Tale of Earliest Americans

Fossil Feces Is Earliest Evidence of N. America Humans

Fossilized feces found in Oregon suggest earliest human presence in North America

Evidence Supports Earlier Date for People in North America

The incredibly well-preserved remains of an ancient female mammoth calf, which died when only three or four months old, between 37 to 40,000 years ago and discovered in the Russian Arctic, has offered scientists with an unprecedented look into the inner structure of the prehistoric animal. The baby mammoth has been named Lyuba after its discoverer’s wife, reindeer hunter and herder Yuri Khudi, who made the discovery last May on the Yamal Peninsula in what is now the Yamalo-Nenetsk region in the Urals, a part of north-west Siberia that projects into the Kara Sea. The calf weighed only 50kg (110lbs.) and was just 130cm (4’3”) long and slightly less than 90cm (just under 3’) tall – basically the size of a large dog – and possessed nascent tusks no larger than a human finger. When found Lyuba was in such extraordinary condition that its eyes and trunk were still intact and a few patches of fur still remained on its body. Its only defect is that it is missing its tail, which appears to have been bitten off. And although nearly its entire shaggy coat of hair was gone, being that the skin was still completely intact and protecting her internal organs, modern-day microbes were prevented from contaminating them.

Lyuba was originally sent to Jikei University in Japan for analysis where it was subject to computer tomography scanning (a sophisticated three-dimensional imaging procedure comparable to that used by doctors to examine patients) and returned to Russia back in February. The researchers discovered that she was fed on milk and died with a full stomach. Further, her airways and digestive system were clogged with what appears to be silt, leading the scientists to think that she drowned. The scanning revealed no evidence of injuries or fractures.

More importantly, as the deputy director of the Russian Academy of Science’s Zoological Institute (located in St. Petersburg), Alexi Tikhonov, who headed the team investigating Lyuba, noted: “We could see for the first time how internal organs are located inside a mammoth… Her internal organs were well preserved - the heart was seen distinctly with all its ventricles and atria, as well as the liver and its veins.” Tikhonov said that he believes that Lyuba “is the best preserved specimen not only of the mammoth but of any prehistoric animal.”

Tikhonov feels that her contribution to science will be far more important than first thought. “If we take samples of Lyuba's tissues by biopsy, without unfreezing her, there is a big chance we can obtain promising results in genetics and microbiology,” he said. “I believe the genetic map (of the mammoth) will be decoded within a year or two. As for (Lyuba's) practical use, we will have discovered methods of decoding the genetic map of any extinct prehistoric animals.”

Lyuba’s body is currently being preserved in a container that maintains sub-zero temperatures so as to prevent her from decomposing. She is scheduled to be sent to Salekhard, the capital of the Yamalo-Netnetsk region where she was discovered, where she will be exhibited in a special glass case this summer.

Further Reading:

Baby mammoth reveals ancient secrets: Prehistoric animal's genetic map could be decoded within two years

Preserved Mammoth Calf Yields New Information

Originally posted by rogue06

While exploring the Paisley 5 Mile Point Caves in the Cascade Range of central Oregon, archaeologists may have found the earliest confirmed evidence for human habitation in North America, namely fourteen pieces of 14,300 year old human excrement. That’s right. Poop. The fossilized feces, or coprolites, are extraordinary in that besides probably being older than any artifacts thus far discovered on the continent, six of them appear to contain human protein and DNA. All of this provides a strong indication that humans were in North America at least a thousand years before the so-called Clovis people (named after the New Mexico site where distinctively-shaped rock spear points that gave the name to the prehistoric paleo-Indians were first found), who for years were thought to be the first humans to live here.

We’ve been aware of these shallow arid caves for 60 years, which had been carved into a hillside by a prehistoric lake, and have previously uncovered a variety of animal bones and several stone tools there. But in 2002, a team led by Dennis L. Jenkins, an archaeologist at the University of Oregon dug deeper into cave No. 5 and found the coprolites in question. They noted that few artifacts were found in the cave which implies that the occupant’s visits were somewhat brief and that the cave may have even served as a latrine of some sort.

In many ways, coprolites are ideal human remains for archaeologists. First, because indigenous people often are upset when their ancestors bones are excavated, but nobody gets upset to examining their feces. Second, since because bones calcify over time this makes it difficult to extract any viable DNA, while coprolites are full of cellular material that comes from the colon.

Jenkins says that studying the coprolites has allowed them to determine what these early Americans ate. “They certainly ate sage grouse and smaller animals," he noted. "I think we recovered some chipmunk bones from one of the coprolites.” Furthermore, there are residues from plant types that are still found close to the caves that have also been found in the coprolites. And with hundreds of more coprolites to be tested, there is still more information that can be uncovered, possibly including what sort of diversity was there in the first people entering America, such as how many different people and the ratio of males to females.

But to first verify that the coprolites were indeed from humans, Jenkins recruited some DNA experts to carry out multiple tests on the samples. The primary DNA analysis was carried out by Eske Willerslev and M. Thomas P. Gilbert of the Center for Ancient Genetics at the University of Copenhagen in Denmark. Besides confirming their human origin, Willerlev and Gilbert were also able to determine that the DNA found were from the founding genetic groups, or haplogroups, of present-day Native Americans. These same genetic patterns are also found among certain groups in eastern Asia and increase support for the theory that the first people came here by crossing the Bering Sea land bridge that at one time connected North America and Asia.

Yet the findings aren’t without their detractors. Noting that there were also non-human coprolites at the cave bottom, Vanderbilt University archeologist Thomas Dillehay (known for his excavations at Monte Verde in Chile, which indicate humans may have inhabited that region as long as 14,500 years ago) urges caution. He argues that since several of the fossilized feces “did not have human DNA, and some of them had canine, perhaps fox, DNA,” that the coprolites might have been contaminated by them. Jenkins dismisses this by noting that some of the coprolites contained human hair and human proteins, in addition to human DNA, so that if they had been left by canines, then they must have been canines that were eating humans (or humans eating the canines), which doesn't change the conclusion that people lived there 14,300 years ago.

A more serious challenge has been raised by one of the researchers who did the DNA testing of the coprolites, Dr. Gilbert, who worries that the coprolites could have been contaminated with younger human DNA by being urinated on by later Native Americans inhabitants. He also pointed out that not all the coprolites contain Native American DNA, and that this may be because they are all non-human and have been only identified as such because of contamination from being urinated on. His colleague, Dr. Willerslev, quickly rejects at least the latter possibility by observing that human proteins found in the samples rule out any contamination or leeching as the cause because it couldn’t provide enough human protein for the type of testing that was employed to have detected. Willerslev also mentioned that since only one Native American DNA sequence was associated with each coprolite, and that the sediment samples and animal bones (primarily horse and camel) only tested positive for animal DNA and negative for human DNA, indicates that contamination is an unlikely source for the Native American DNA found in the coprolites identified as coming from humans. Still, the results remain controversial until more testing can be done.

Further Reading:

Pre-Clovis Human DNA Found In 14,300-year-old Feces In Oregon Cave Is Oldest In New World

Fossilized Feces Tell Tale of Earliest Americans

Fossil Feces Is Earliest Evidence of N. America Humans

Fossilized feces found in Oregon suggest earliest human presence in North America

Evidence Supports Earlier Date for People in North America

Given its recent age, did it have 9/10th ribs, 9/10th eyes, 9/10th limbs, and 9/10th hair? In fact did it look 9/10ths like an elephant? If not then this has nothing to do with evolution.


Dang. Read one post and replied to another.

Here goes again.

Given its age, was it 9/10ths of a poo? If not then this has nothing to do with evolution.

(The one above is for the mammoth post.)


Thanks Rogue for pointing this out.

Sheesh. First I reply to a 3 year old post. Now this. I shall retire for a bit. Go and bath the dog or something. Might go out and make some mud-pies with the grandkids.



Regards, Roland

This doesn’t actually constitute a fossil find, but rather an analysis of some fossils, but I’m going to put it here anyway.

Researchers at Oxford University in England and Stony Brook University in New York, USA have concluded that, after analyzing fossil teeth from extinct relatives of elephants that lived some 37 mya, these elephant ancestors lived in freshwater swamps and rivers similar to the way modern day hippopotami do. The scientists studied the chemical signatures preserved in the teeth from two different creatures, the Moeritherium, which stood between 74 to 107cm (about 29-42”) tall at the shoulder, or the size of a modern tapir, and the Barytherium, which was much larger being only a bit smaller than a modern elephant and possessing tusks more like a hippos than an elephant’s. The teeth from these Eocene mammals were discovered in northern Egypt’s Faiyum region, which today is a desert but in ancient times was a sub-tropical shallow estuary or coastal system.

Still, just because the teeth were found in such a location didn’t prove that animals actually lived there for it was entirely possible that their bodies had merely washed up there after their deaths. This is why the researchers examined the patterns of different oxygen and carbon atoms, or isotopes, found in the teeth’s enamel and compared the ratios of these isotopes with those found in both aquatic and terrestrial mammals from the same time period in an effort to investigate the lifestyle and diet of the creatures. Carbon isotopes retain signatures of the creature’s diet, whereas oxygen isotopes supplied information about the local water sources. The results indicate that Moeritherium and Barytherium were largely aquatic and grazed on freshwater vegetation in rivers or swamps. Their diet was in fact very similar to that of fully aquatic animals, but they were definitely not completely aquatic since their bones demonstrate that they walked around and put weight on their feet and lacked they adaptations like a stream-lined body or flipper-like fins.

Still this raises serious doubts about the theory that elephants have evolved from fully terrestrial ancestors and have always had this kind of a lifestyle. Scientists were aware that elephants are related to modern aquatic creatures like manatees (also known as sea cows) and dugongs due to DNA evidence, but previously there had never been any ancient elephant ancestor that lived primarily in the water. Now there appears to be an evolutionary link. “I think it’s the first real evidence that there is a semi-aquatic lineage to the elephants,” said Alexander Liu, a graduate student in paleobiology at Oxford University and co-author of the study. “It's something that people have expected but not been able to actually show.”

Liu also is intrigued with the possibility that proboscideans (the order under which elephants are classified) might present evidence of being the first terrestrial mammal that became aquatic and then at some point returned to the land. But it isn’t clear how or why these elephant ancestors would have left their largely aquatic lifestyle for life on land. One theory holds that it could have been due to a cooling event at the end of the Eocene which could have led to the drying up of rivers and swamps, forcing the animals out on to the land. Liu recognizes that “there’s little real evidence yet to suggest that’s true,” but that, “we've got an awful lot of pieces in the puzzle; if we could find one more example of an aquatic or semi-aquatic elephant that would be extremely convincing.”

Other scientists urge caution though. Speaking specifically about Moeritherium, William Sanders of the University of Michigan’s Museum of Paleontology praised the new study for providing compelling evidence that it was indeed semi-aquatic. “Paleontologists have thought for nearly a century that moeritheres were at least semi-aquatic, hippo- or sea cow-like in their overall adaptations and lifeways,” he noted. Yet Sanders also pointed out that this does not mean we should automatically assume an aquatic ancestry for modern elephants or even presuming that all ancient proboscideans were aquatic. “[Moeritherium is a] very specialized animal that may have been off the main line of evolution from that which led to elephants,” he said.


Further Reading:

Ancient elephants loved water: Study finds that ancestor spent most of its time in rivers and swamps

Elephant ancestors lived like hippos, fossils suggest

Elephant 'had aquatic ancestor'

Ancient Elephant Ancestor Lived in Water, Study Finds

Meet the Prehistoric Elephantopotamus

OK, this one is major league cool

A team of researchers led by Jack D. Griffith, Kenan Distinguished Professor of microbiology and immunology at the University of North Carolina at Chapel Hill’s School of Medicine have discovered 253 myo cellulose microfibers in samples taken from salt deposits found 2000’ below the surface, beneath the U.S. Department of Energy’s Waste Isolation Pilot Plant (WIPP), an underground nuclear waste depository in the deserts of southern New Mexico near the city of Carlsbad. Cellulose is the tough, resilient material that is the major structural element of plant matter, and is one of the most plentiful biological materials on Earth, with plants, algae and bacteria producing approximately 100 gigatons per year. Prehistoric forms of cellulose were created by cyanobacteria, the blue-green algae and bacteria still found in almost every imaginable environment on land and in the oceans, which is known to have been present on Earth 2.8 bya. In a statement released by Dr. Griffith, the age of the cellulose microfibers make them “the oldest native macromolecules to date to have been directly isolated, visualized and examined biochemically.” Previously, the most ancient evidence of biological material was from fragments of ancient protein found in some Tyrannosaurus Rex fossils dating back to around 68 mya.

Along with the cellulose, the researchers also found some possible ancient DNA. “We did see some ancient DNA in the salt, but not a lot, and we have to continue experiments to try to verify that it is ancient DNA,” said Dr. Griffith who is also a virology professor at the UNC Lineberger Comprehensive Cancer Center, which is where the salt samples retrieved from the WIPP were studied. Being that they still need to confirm whether or not the DNA is actually ancient, this likely means there is concern the samples may have been contaminated with modern DNA somewhere along the line from extraction to being tested in the lab.

Further, Dr. Griffith said that he thinks looking for cellulose in salt deposits is an excellent way to search for life on other planets because of how tough cellulose is. He said that “in looking for evidence of life on Mars, for bacteria or higher plants that existed on Mars or other planets in the solar system, then looking for cellulose in salt deposits is probably a very good way to go. Cellulose appears to be highly stable and more resistant to ionizing radiation than DNA. And if it is relatively resistant to harsh conditions such as those found in space, it may provide the ideal ‘paper trail’ in the search for life on other planets.”

The research by Griffith and four co-authors was published as the cover story in the April issue of the journal Astrobiology.

Further Reading:

Mine Yields 253-Million-Year-Old Cellulose

Ancient organism found in rock salt

For the paper trail of life on Mars or other planets, find cellulose

Last year, while he waited for his colleagues at a natural history museum located in the mostly rural southern state of Chipas, Mexico, Greg Dietl, an adjunct professor in Cornell's Department of Earth and Atmospheric Sciences and director of collections at the Cornell-affiliated Paleontological Research Institution in Ithaca, New York, noticed something unusual in one of the museum’s display cases. It was the fossil of a large crab dating back 67-69 mya that had an oversized right claw. Why this caught his attention is because crabs with different sized claws were thought to have only come about some 20 million years later, during the early Cenozoic.

When the museum staff discovered Dietl and his associates making a fuss over the fossilized crab, they proceeded to bring out a second crab of the same species, Megaxantho zogue, from a storage room in the back of the museum, unquestionably demonstrating the fossil was not some kind of fluke.

What’s more, aside from the asymmetrical claws, Megaxantho also had a curved tooth-like projection on the movable finger of the larger claw, which is yet another specialized adaption useful in peeling snail shells open that was also thought to have come about much later. “I was really excited when I found it. The fossil re-opens the question of the role crabs played in the well-documented restructuring of marine communities that occurred during the Mesozoic era,” exclaimed Dietl. He hopes the discovery will encourage other researchers to look for more examples of these curved tooth structures from the Late Cretaceous period.

While these crabs became extinct around 65 mya, these features would later evolve again in other crab species throughout the Cenozoic era, leading to present-day crabs. Dietl believes that the recurring evolution of these traits indicates that such power-augmenting adaptations may develop during times and places where food supplies are plentiful and accessible. I wish he would have gone into more detail on exactly why.

Megaxantho was found near the town of Ocozocoautla, which is located about 15 miles west of Tuxtla Gutierrez, the capital of Chipas.

Further Reading:

Researcher finds fossilized shell-breaking crab

Ho ho! Or should I say, "Bawk bawk!"

One of the predictable little YEC riffs over the past few years has been to wonder how "soft tissue" could be preserved within a Tyrannosaur femur that's over 65 million years old. Because, of course, YECs don't believe the world is even 10 K years old, much less 65 MY old... (Let's ignore the fact that Tyrannos have very large femurs, with very thick outer bony layers, and that in a quick enough depositional event, all that thick bone plausibly might have provided a protective environment in which some of the marrow material might have resisted complete degradation)...

Another such riff has been to reflexively question the evolutionary contention that birds-evolved-from-dinosaurs. Because, after all, no "transitionals" have ever been found and "macro"-evolution (by which YECs mean something very different than scientists) can ever occur.

Whoops! Now the YECs are once again hoist upon their own petard, for the very "soft tissue" evidence that they were wont to, er, crow over has now furnished confirmation for the dino-bird connection:

The latest evidence comes from an ancient femur bone unearthed in 2003 by Jack Horner of the Museum of the Rockies in the Hell Creek Formation, a fossil-packed area that spans Montana, Wyoming and North and South Dakota.

It seems some 68 million years ago, a teenage T. rex died and left behind a drumstick-shaped femur bone that today still contains intact soft tissue and the oldest preserved proteins discovered to date.

Though no genetic material was preserved, researchers were able to extract the proteins from the collagen tissues.

"The proteins are what carry out the function inside the cells and organs. So the protein does a lot of the work. That (protein) sequence was derived from DNA," Asara told LiveScience. In the case of T. rex's collagen, "it was responsible for making hard bone so that the dinosaur could stand."

By comparing the dino's protein sequences with those of 21 living organisms, a team of researchers say they have locked in the dinosaur-bird link.

"We determined that T. rex, in fact, grouped with birds — ostrich and chicken — better than any other organism that we studied," said researcher John Asara of Beth Israel Deaconess Medical Center and Harvard Medical School. "We also show that it groups better with birds than (with) modern reptiles, such as alligators and green anole lizards."

There are some other interesting tidbits in the same article, including a tighter dating of the K-T extinction event and the "shor[ing] up [of] the evolutionary link between the extinct mastodon and the modern-day elephant."

All these results are being published in the April 25 edition of Science.

Originally posted by Steviepinhead

Ho ho! Or should I say, "Bawk bawk!"

One of the predictable little YEC riffs over the past few years has been to wonder how "soft tissue" could be preserved within a Tyrannosaur femur that's over 65 million years old. Because, of course, YECs don't believe the world is even 10 K years old, much less 65 MY old... (Let's ignore the fact that Tyrannos have very large femurs, with very thick outer bony layers, and that in a quick enough depositional event, all that thick bone plausibly might have provided a protective environment in which some of the marrow material might have resisted complete degradation)...

Another such riff has been to reflexively question the evolutionary contention that birds-evolved-from-dinosaurs. Because, after all, no "transitionals" have ever been found and "macro"-evolution (by which YECs mean something very different than scientists) can ever occur.

Whoops! Now the YECs are once again hoist upon their own petard, for the very "soft tissue" evidence that they were wont to, er, crow over has now furnished confirmation for the dino-bird connection:


There are some other interesting tidbits in the same article, including a tighter dating of the K-T extinction event and the "shor[ing] up [of] the evolutionary link between the extinct mastodon and the modern-day elephant."

All these results are being published in the April 25 edition of Science.

Good job catching that story. I had noticed it earlier this week and thought it was a result of some rather late reporting of a similar story from last year – also reported in Science. The current paper appears to build on the earlier work. This new research matches predictions made from skeletal anatomy (biological morphology) and provides the first molecular evidence in support of the idea that birds are descended from dinosaurs and not more basal reptiles. Even though there were only something like six peptides and 89 amino acids recoverable from the Tyrannosaurus rex femur, the analysis of the data demonstrates that it looks like chickens are the closest living descendant is the chicken, though this may be subject to change as more species are entered into the genome databases. Still, this shows that molecular information like this can help to establish better evolutionary family trees between extinct and living organisms.

Yep, I was misled by the earlier result as well.

And there have been some critiques re possible contamination, the shortness of the sequence, etc.

But we're mostly just flagging these things to see what additional interest or discussion they might stir up...

Originally posted by rogue06

Good job catching that story. I had noticed it earlier this week and thought it was a result of some rather late reporting of a similar story from last year – also reported in Science. The current paper appears to build on the earlier work. This new research matches predictions made from skeletal anatomy (biological morphology) and provides the first molecular evidence in support of the idea that birds are descended from dinosaurs and not more basal reptiles. Even though there were only something like six peptides and 89 amino acids recoverable from the Tyrannosaurus rex femur, the analysis of the data demonstrates that it looks like chickens are the closest living descendant is the chicken, though this may be subject to change as more species are entered into the genome databases. Still, this shows that molecular information like this can help to establish better evolutionary family trees between extinct and living organisms.

Good summary.

It's worth underlining a couple of points that are unclear or even actively misleading in popular reporting of this.

As I understand the matter, the real interest of this paper is in testing the preservation of collagen; not in testing the evolutionary relationships of animals.

The close association of a mastodon and elephant for example... not exactly earth shattering, is it! The significance is that it confirms the collagen could be preserved sufficiently well to do this kind of testing. If this association had NOT been obtained, it would not have falsified the elephant mastodon connection. It would have falsified the idea that collagen preserves well enough to be used for such testing.

It's the same with the T. rex and birds. This association is no surprise at all. We are already confident that T. rex would group with birds, and have alligators as an outgroup. Had the study returned anything else, it would actually have been falsifying the notion that collagen can be preserved over long time periods.

More seriously, T. rex was most definitely not the grand-daddy of chickens, as some headlines report. It is the great-greatⁿ-uncle; or better, a cousin. T. rex lived very late in the dinosaur age, when birds were already established.

New Scientist, which is not the most rigourous of science magazines, originally reported this under the headline: T. rex confirmed as great granddaddy of all birds. Thanks to howls of outrage from scientists and even reasonably well informed amateurs, this was quickly fixed, to read "T. rex kinship with chickens confirmed". The article is here. Note the contrast between the url, and the headline as it now appears in text!

In fact, the resolution of the data is not particularly good. They were only able to find small fragments (89 amino acids) and this was sufficient to put the T. rex in the same group as birds, with an alligator outgroup. It was not sufficient to put the T. rex as an outgroup from the two birds used in the study. This is plainly a case where (so far) molecular evidence is much weaker than the good old paleontological evidence. In fact, the data is not even enough to confirm birds as closely related to theropod dinosaurs; whereas fossil evidence has been able to pin it right down to maniraptors.

It would be useful if they could obtain molecular data from a number of different dinosaurs, as this would help confirm the placement of birds within the dinosaur family tree. I'm no expert, but I suspect this will present a problem. I think they'll need the tiny sequences obtained from fossils millions of years old to be from matching parts of the protein sequence. Even the data obtained with one dinosaur was not enough to resolve relationships between the dinosaur and the two bird sequences used. Comparing with modern animals is much easier, because we have a lot of sequence data available, and so it's easy to find the appropriate molecules.

It's interesting work opening up the possibility of getting molecular data for long extinct animals. The work confirm that the collagen does actually retain useful information. But it's not as yet likely to bring major new discoveries about actual evolutionary relationships.

Cheers -- Sylas

Originally posted by sylas

<SNIP>
More seriously, T. rex was most definitely not the grand-daddy of chickens, as some headlines report. It is the great-greatⁿ-uncle; or better, a cousin. T. rex lived very late in the dinosaur age, when birds were already established.

New Scientist, which is not the most rigourous of science magazines, originally reported this under the headline: T. rex confirmed as great granddaddy of all birds. Thanks to howls of outrage from scientists and even reasonably well informed amateurs, this was quickly fixed, to read "T. rex kinship with chickens confirmed". The article is here. Note the contrast between the url, and the headline as it now appears in text!
</SNIP>

Apparently not everyone got the memo.

From the Guardian: Our feathered friends are descended from T. rex

From the Sun: Dinosaur king became chicken They’ve since changed their title to “Tyrannosaurus pecks” but still left the subtitle of “BE careful who you call chicken – because the bird is actually descended from the fearsome Tyrannosaurus rex, say scientists.”

Good points, Sylas, and well laid out!

I suspect that recovering any "useable" collagen from 68 MYA is going to be a really exceptional case of preservation, but exceptional cases do occasionally crop up--as most of us recognize--and the ingenuity of the current crop of paleontologists is exceptional in itself.

Seeing these occasional cases of the genetic evidence and the paleontological evidence not just supporting/informing each other, but essentially merging into one another, is pretty cool...

Two new studies of Neanderthal (or Neandertal) teeth have given us a better look at these prehistoric hominid’s diet.

The first concerns research published in the Journal of Human Evolution by Richards et al. The team removed some fine powder from an upper right premolar from a Neanderthal whose remains are from 44-to-55,000 years old (late Mousterian)and unearthed from a now-collapsed rock shelter known as Jonzac in southwestern France, in order to conduct an isotopic dietary analysis. They focused on forms of the common chemical elements carbon and nitrogen of the extracted collagen, which are good indicators of an individual’s diet during the tooth development of later childhood. The work was conducted at the Department of Human Evolution at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany with the purpose of determining whether the isotopic evidence demonstrates that the primary source of protein was from animals as has been indicated by previous studies. For comparison the researchers also analyzed collagen from the bones of animal remains that had been discovered at Jonzac, including Steppe bison, aurochs, horses, reindeer and hyenas. They found that the Neanderthal’s isotopic values which show that its main source of protein was large herbivores, primarily the cattle and horses. It seems that the hyena consumed primarily the reindeer, which demonstrates distinct niches between the Neanderthal and hyena. This study confirms all earlier research done thus far on the Neanderthals found in Europe which shows they were highly carnivorous and fed primarily on large mammals. It also indicates this juvenile’s diet is similar to that of adult Neanderthals found elsewhere, which may indicate that even fairly young members of a Neanderthal group received a fairly high quality heavily carnivorous diet.

As Teresa Steele, third author of the report and assistant professor of anthropology at the University of California at Davis, notes “We assume that Neanderthals were eating some plant foods, but given the present evidence, these plant foods were not significant sources of protein.” But while the results of this isotopic dietary analysis was especially informative, still it can provide data only relevant to one part of their diet. New evidence presented by a team led by Amanda Henry a graduate student in hominid paleobiology at The George Washington University at the very recent Paleoanthropology Society meetings in Vancouver, Canada, is the first evidence that at least some Neanderthals seem to have made extensive use of plant resources whenever they had access to them as well.

The evidence of plant consumption comes in the form of microfossils of plant material that investigators found in the dental plaque of three teeth from an approximately 40 year old Neanderthal dated from 35,000 years ago and discovered half a century ago at the Shanidar cave, in the Zāgros Mountains of northeastern Iraq. “The formation of dental [plaque] traps the plant microfossils from food particles within the matrix of the plaque deposits, so the microfossils are protected and are a unique record of the plant foods put into the mouth,” Henry said. “So we can say with confidence that this individual Neanderthal ate plants.” Specifically she said that grass seeds, or grain were found in the enamel, but still cautions that more works needs to be done before issuing broad statements about Neanderthal diets can be issued. The isotopic study mentioned above wouldn’t detect microfossils in the enamel (it’s not what it’s designed for). I would think the fact of the significant geographic distance could well come into play here as well. And the test can’t determine if the Neanderthal ate plants only a few times or if it was a staple part of his diet. Several different tests on the same samples will have to be conducted in future studies to get a clearer picture.

Further Reading:

Isotopic dietary analysis of a Neanderthal and associated fauna from the site of Jonzac (Charente-Maritime), France Abstract

Neanderthals at Mealtime: Pass the Meat

Neandertals Ate Their Veggies, Tooth Study Shows

Originally posted by rogue06

While exploring the Paisley 5 Mile Point Caves in the Cascade Range of central Oregon, archaeologists may have found the earliest confirmed evidence for human habitation in North America, namely fourteen pieces of 14,300 year old human excrement. That’s right. Poop. The fossilized feces, or coprolites, are extraordinary in that besides probably being older than any artifacts thus far discovered on the continent, six of them appear to contain human protein and DNA. All of this provides a strong indication that humans were in North America at least a thousand years before the so-called Clovis people (named after the New Mexico site where distinctively-shaped rock spear points that gave the name to the prehistoric paleo-Indians were first found), who for years were thought to be the first humans to live here.

We’ve been aware of these shallow arid caves for 60 years, which had been carved into a hillside by a prehistoric lake, and have previously uncovered a variety of animal bones and several stone tools there. But in 2002, a team led by Dennis L. Jenkins, an archaeologist at the University of Oregon dug deeper into cave No. 5 and found the coprolites in question. They noted that few artifacts were found in the cave which implies that the occupant’s visits were somewhat brief and that the cave may have even served as a latrine of some sort.

In many ways, coprolites are ideal human remains for archaeologists. First, because indigenous people often are upset when their ancestors bones are excavated, but nobody gets upset to examining their feces. Second, since because bones calcify over time this makes it difficult to extract any viable DNA, while coprolites are full of cellular material that comes from the colon.

Jenkins says that studying the coprolites has allowed them to determine what these early Americans ate. “They certainly ate sage grouse and smaller animals," he noted. "I think we recovered some chipmunk bones from one of the coprolites.” Furthermore, there are residues from plant types that are still found close to the caves that have also been found in the coprolites. And with hundreds of more coprolites to be tested, there is still more information that can be uncovered, possibly including what sort of diversity was there in the first people entering America, such as how many different people and the ratio of males to females.

But to first verify that the coprolites were indeed from humans, Jenkins recruited some DNA experts to carry out multiple tests on the samples. The primary DNA analysis was carried out by Eske Willerslev and M. Thomas P. Gilbert of the Center for Ancient Genetics at the University of Copenhagen in Denmark. Besides confirming their human origin, Willerlev and Gilbert were also able to determine that the DNA found were from the founding genetic groups, or haplogroups, of present-day Native Americans. These same genetic patterns are also found among certain groups in eastern Asia and increase support for the theory that the first people came here by crossing the Bering Sea land bridge that at one time connected North America and Asia.

Yet the findings aren’t without their detractors. Noting that there were also non-human coprolites at the cave bottom, Vanderbilt University archeologist Thomas Dillehay (known for his excavations at Monte Verde in Chile, which indicate humans may have inhabited that region as long as 14,500 years ago) urges caution. He argues that since several of the fossilized feces “did not have human DNA, and some of them had canine, perhaps fox, DNA,” that the coprolites might have been contaminated by them. Jenkins dismisses this by noting that some of the coprolites contained human hair and human proteins, in addition to human DNA, so that if they had been left by canines, then they must have been canines that were eating humans (or humans eating the canines), which doesn't change the conclusion that people lived there 14,300 years ago.

A more serious challenge has been raised by one of the researchers who did the DNA testing of the coprolites, Dr. Gilbert, who worries that the coprolites could have been contaminated with younger human DNA by being urinated on by later Native Americans inhabitants. He also pointed out that not all the coprolites contain Native American DNA, and that this may be because they are all non-human and have been only identified as such because of contamination from being urinated on. His colleague, Dr. Willerslev, quickly rejects at least the latter possibility by observing that human proteins found in the samples rule out any contamination or leeching as the cause because it couldn’t provide enough human protein for the type of testing that was employed to have detected. Willerslev also mentioned that since only one Native American DNA sequence was associated with each coprolite, and that the sediment samples and animal bones (primarily horse and camel) only tested positive for animal DNA and negative for human DNA, indicates that contamination is an unlikely source for the Native American DNA found in the coprolites identified as coming from humans. Still, the results remain controversial until more testing can be done.

Further Reading:

Pre-Clovis Human DNA Found In 14,300-year-old Feces In Oregon Cave Is Oldest In New World

Fossilized Feces Tell Tale of Earliest Americans

Fossil Feces Is Earliest Evidence of N. America Humans

Fossilized feces found in Oregon suggest earliest human presence in North America

Evidence Supports Earlier Date for People in North America

A bit of news that seems to go with the above…

Another study has come forth making the view that the so-called Clovis people were the first settlers in the Americas increasingly less tenable. A team led by Dr. Tom Dillehay, archaeologist and Distinguished Professor in the Department of Anthropology at Vanderbilt University in Nashville, Tennessee, has added further confirmation of the ancient age of the Monte Verde archaeological site in southern Chile about 800km (approximately 500mi.) south of the capital of Santiago, after carbon dating seaweed and marine algae samples of nine separate species (approximately 27 liters, or a tad over 7 gallons, worth) from the site at somewhere between 13,980 and 14,220 years old, confirming that the site was occupied some 1,000 years earlier than any other known human settlements in the Americas. Dillehay thinks that the seaweeds were used as both a food source and as medicine. Some of it was found in the remains of ancient hearths and some had been chewed into clumps, or "cuds," which may have been used for medicinal purposes. The types of seaweed samples recovered at Monte Verde are all good sources of iodine, iron, zinc and other nutrients as well as promoting cholesterol metabolism, bone strength and the body’s ability to fight infection. Indigenous people still use the same species to treat common health problems.

Interestingly, while some types of seaweeds found came from the coast, several others derived from a rocky inland bay located around 6-15km south of the settlement. The choice of seaweeds, and local land plants (primarily nuts and vegetables) also identified at the site, along with Monte Verde’s riverside location, indicate that the inhabitants had lived there long enough to develop a good understanding of both coastal resources and foods from the interior which allowed them to stay in the region year-round. This might imply that the early settlers moved south far more slowly than has been suggested by some – coming to terms with their current location, exploiting the interior resources of the hundreds of river basins descending from near-coast mountain ranges, before moving to another one. And as the discovery of human feces in the Oregon cave dated the same time testifies, people were moving much further inland than previously thought as well. Further, besides providing more evidence for the age of the Monte Verde site these new findings also support the coastal migration theory currently ascribed to by most scholars, which hypothesizes that people first entered the New World through the Bering land bridge more than 16,000 years ago and moved slowly down the Pacific Coast, exploiting a range of resources from kelp forests just off the coast.

Further Reading:

SLOWPOKE SETTLERS

First Americans thrived on seaweed

New Evidence From Earliest Known Human Settlement In The Americas

CHILE OR BUST: TRACING THE PATH OF THE FIRST AMERICANS

Earliest Known American Settlers Harvested Seaweed

Ancient seaweed chews confirm age of Chilean site

I love this line!

... so that if they had been left by canines, then they must have been canines that were eating humans (or humans eating the canines), which doesn't change the conclusion that people lived there 14,300 years ago.

Have you heard the discoveries of human and dinosaur bones in the same sedimentary layer? This is good evidence for creation.