Neandertal/Denisovan Ancestors Interbred With Unknown Hominin

As if the tangle of early archaic Homo sapiens relationships couldn't get any more confusing, evidence has now surfaced that the ancestors of both the Neandertals and Denisovans interbred with a hominin only known from its DNA signature.  From the University of Utah, through Science Daily:

For three years, anthropologist Alan Rogers has attempted to solve an evolutionary puzzle. His research untangles millions of years of human evolution by analyzing DNA strands from ancient human species known as hominins. Like many evolutionary geneticists, Rogers compares hominin genomes looking for genetic patterns such as mutations and shared genes. He develops statistical methods that infer the history of ancient human populations.

According to the article, Rogers performed a study that argued that Neandertals and Denisovans separated earlier than has previously been suggested but that his evidence for this was thin.

The new study has solved that puzzle and in doing so, it has documented the earliest known interbreeding event between ancient human populations -- a group known as the "super-archaics" in Eurasia interbred with a Neanderthal-Denisovan ancestor about 700,000 years ago. The event was between two populations that were more distantly related than any other recorded. The authors also proposed a revised timeline for human migration out of Africa and into Eurasia. The method for analyzing ancient DNA provides a new way to look farther back into the human lineage than ever before.

"We've never known about this episode of interbreeding and we've never been able to estimate the size of the super-archaic population," said Rogers, lead author of the study. "We're just shedding light on an interval on human evolutionary history that was previously completely dark."

According the Rogers, the DNA evidence puts the final nail in the coffin of the complete Out-of-Africa replacement model of modern human origins:

The researchers also proposed there were three waves of human migration into Eurasia. The first was two million years ago when the super-archaics migrated into Eurasia and expanded into a large population. Then 700,000 years ago, Neanderthal-Denisovan ancestors migrated into Eurasia and quickly interbred with the descendants of the super-archaics. Finally, modern humans expanded to Eurasia 50,000 years ago where we know they interbred with other ancient humans, including with the Neanderthals.

This was likely something like Homo antecessor.  As is also true with the Chinese evidence, this evidence suggests that throughout human evolutionary history, there has never/rarely been a time when these groups of archaic and early modern Homo sapiens could not/did not interbreed. As J. Lawrence Angel once said “When two groups of people meet, they may fight, but they will always mate.”

The Science Advances article is open access. 

http://dx.doi.org/10.1126/sciadv.aay5483

DNA Proteins Revealing Information About Human Evolution

Since the advent of population genetics and modern techniques to examine DNA, research has focused on, first, Mitochondrial DNA and then nuclear DNA.  Now we have another weapon in our arsenal.  Matthew Warren of Nature News relates new research done on palaeoproteomics.  This is the study of proteins found in fossilized human ancestors.  How is this possible, you ask?

Some time in the past 160,000 years or so, the remains of an ancient human ended up in a cave high on the Tibetan Plateau in China. Perhaps the individual died there, or parts were taken there by its kin or an animal scavenger. In just a few years, the flesh disappeared and the bones started to deteriorate. Then millennia dripped by. Glaciers retreated and then returned and retreated again, and all that was left behind was a bit of jawbone with some teeth. The bone gradually became coated in a mineral crust, and the DNA from this ancient ancestor was lost to time and weather. But some signal from the past persisted.

Deep in the hominin’s teeth, proteins lingered, degraded but still identifiable. When scientists analysed them earlier this year, they detected collagen, a structural support protein found in bone and other tissues. And in its chemical signature was a single amino-acid variant that isn’t present in the collagen of modern humans or Neanderthals — instead, it flagged the jawbone as belonging to a member of the mysterious hominin group called Denisovans. The discovery of a Denisovan in China was a major landmark. It was the first individual found outside Denisova Cave in Siberia, where all other remains of its kind had previously been identified. And the site’s location on the Tibetan Plateau — more than 3,000 metres above sea level — suggested that Denisovans had been able to live in very cold, low-oxygen environments.

As the author notes, this kind of research has opened many other doors that, up until now, have been shut to researchers. The realization that proteins have much longer staying power than DNA could radically reshape our understanding of human evolution:

Previously, scientists had recovered proteins from 1.8-million-year-old animal teeth and a 3.8-million-year-old eggshell. Now, they hope that palaeoproteomics could be used to provide insights about other ancient hominin fossils that have lost all traces of DNA — from Homo erectus, which roamed parts of the world from about 1.9 million to 140,000 years ago, to Homo floresiensis, the diminutive ‘hobbit’ species that lived in Indonesia as recently as 60,000 years ago. By looking at variations in these proteins, scientists hope to answer long-standing questions about the evolution of ancient human groups, such as which lineages were direct ancestors of Homo sapiens.

Whether that level of resolution will ever be possible remains to be seen, especially given that the modus operandi of modern palaeontology is focused on clade relationships. It will be interesting to see.

A Good Video on Radiometric Dating

Joy Walters has a video on BioLogos that explains in layman's terms why radiometric dating is sound and how hominin/hominid fossils have been dated. Go watch!

A New Species of Hominin Coeval With Lucy?

Great Googlymoogly! A new discovery has been made in the Afar triangle that indicates that a similar species of Australopithecus that was not A. afarensis lived alongside them. Science Daily writes:

“The Burtele partial foot clearly shows that at 3.4 million years ago, Lucy’s species, which walked upright on two legs, was not the only hominin species living in this region of Ethiopia,” said lead author and project leader Dr. Yohannes Haile-Selassie, curator of physical anthropology at The Cleveland Museum of Natural History. “Her species co-existed with close relatives who were more adept at climbing trees, like ‘Ardi’s’ species, Ardipithecus ramidus, which lived 4.4 million years ago.”

There is nothing to dictate that there were no intermediates between Ar. ramidus and Au. afarensis or that there were not several hominins on the landscape at this point. We know that there were two species of Ardipithecus. It is possible that this represents a descendent of Ar. ramidus or a descendent of a species that lived at the same time as Ardi and gave rise to a hominin that was more arboreal in nature. Until we have more to go on, it will be hard to construct any relationships that are even provisional.

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Geologically Recent Ape in Europe

Deutsche Welle world has an interesting story about dental remains that have been discovered in Europe that put Miocene apes in the region as recently as 7 million years ago. According to the story:

"The latest data have shown that contrary to the hominids in Western and Central Europe (with the exception of the insular Oreopithecus), hominids from the Eastern Mediterranean may have lived up to 8 to 7.5 [million years ago], preadapted to the more open biotopes of the Balkan-Iranian zoographic province," the team wrote.

What is important to note about this story (and it threw me for a minute) is that the author is using the newer phylogenetic systematics-driven definition of “hominid.” In this scheme, “hominids” are now at the family level and include us and all of the great apes and “hominins” (us and our ancestors) are at the sub-family level.

A problem, voiced by one of the excavators, is, of course, that it is just one tooth, so we cannot say too much about it. Still, it is interesting if it bears up.

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Gibbons and Siamangs Booted off the Island

Science Daily has a story about a new Primate phylogenetic tree that has been derived from sequencing 54 genetic regions in 186 species. Over the course of the last twenty years or so, with the advent of the genetic revolution, there has been a wave of new information about the higher apes that has allowed us to break them out of their “grade” of higher apes and place them more accurately taxonomically.


It now appears that gibbons and siamangs (Hylobates, Nomascus and Symphalangus) are monophyletic with respect to the clade that includes gorillas, chimpanzees, orangs and us. I have reproduced the relevant part of the image in the PLoS article to the left. About them, the authors of the article write:

The eight species included in this study form three clades that coincide with genus designation (absent is Hoolock; nodes 64–69) that diverged rapidly 8.9 MYA. Moreover, Nomascus species appear more recent than Symphalangus and Hylobates, with node divergence dates estimated at less than 1 MY (Table 3, Table S9, Figure 2). Thus, Hylobatidae exhibits episodes of rapid divergence perhaps related to excessive genome re-organization and warrants additional investigation.

Another piece of the puzzle.

Hat Tip to Bill Myers.

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Not Out of the Trees?

The Independent has a story about research indicating that our earliest human precursors might not have been as arboreal as originally thought. Michael McCarthy writes:

Humanity's immediate predecessors may have had trouble climbing trees, research suggests – so they may not have been as ape
-like as many experts believe.

Scientists have arrived at this conclusion after making a close study of the way chimpanzees scale trees – virtually vertically and with ease – and then comparing chimpanzee ankle joints with those of hominins, humans' ancestors.

The hominins lived between 1.5 and 4.1 million years ago, a relatively short time after proto-humans and chimpanzees split from a common ancestor (generally thought to have been between four and eight million years ago). Many experts have argued that this ancestor was probably quite chimpanzee-like, and as a result it has been widely assumed that the earliest humans were ape-like, too.

Given what we know about the bipedalism of Ardipithecus and Australopithecus afarensis, this doesn't seem to me to be too much of a surprise. It is quite possible that bipedality evolved due to selective pressures for a more terrestrial lifestyle, perhaps because they were being out competed by the precursors of modern chimpanzees.

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Cold Weather and Bigger Brains

Bob Holmes of the NewScientist has a report on brain size and hominid evolution, in which it is hypothesized that modern human brains could only expand when the air temperature was cold enough to allow for adequate heat dissipation—a glacial maximum for example. He writes:

For all its advantages, the modern human brain is a huge energy glutton, accounting for nearly half of our resting metabolic rate. About a decade ago, biologists David Schwartzman and George Middendorf of Howard University in Washington DC hypothesised that our modern brain could not have evolved until the Quaternary ice age started, about 2.5 million years ago. They reckoned such a large brain would have generated heat faster than it could dissipate it in the warmer climate of earlier times, but they lacked evidence to back their hypothesis.

Now hints of that evidence are beginning to emerge. Climate researcher Axel Kleidon of the Max Planck Institute for Biogeochemistry in Jena, Germany, modelled present-day temperature, humidity and wind conditions around the world using an Earth-systems computer model. He used these factors to predict the maximum rate at which a modern human brain can lose heat in different regions. He found that, even today, the ability to dissipate heat should restrict the activity of people in many tropical regions (Climatic Change, vol 95, p 405).

One of the big questions surrounding the research is whether or not the climate data has the kind of resolution that is necessary to support the hypothesis:

Given the timescales involved, it may be near-impossible to match definitively the onset of an ice age with speciation, but a 1.5 °C drop is consistent with the cooling climate of the time, says Middendorf.

It is an intriguing idea and bears more investigation but I suspect it may be one of many variables driving brain size expansion at the time.


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Dating Hominids Based on What the Animals at the Sites Ate

ScienceDaily has a story on how to date fossil hominid sites based on the dental remains of the animals that lived around them. As the story relates:

Florent Rivals is the main author and a researcher from the Catalan Institute for Research and Advanced Studies (ICREA), attached to the IPHES in Tarragona. "For the first time, a method has been put forward which allows us to establish the relative length of the human occupations at archaeological sites as, up until now, it was difficult to ascertain the difference between, for example, a single long-term occupation and a succession of shorter seasonal occupations in the same place", he explained to SINC.

In the study, recently published in the Journal of Human Evolution, the researchers analyze the dental wear of the ungulates (herbivorous mammals) caused by microscopic particles of opaline silica in plants. These marks appear when eating takes place and erase the previous ones. This is why they are so useful.

This almost qualifies as a taphonomic technique and to have it as an extra tool in trying to figure out how these people lived and what they ate is good news.



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After All, If You Can't Laugh at Yourself...

The June 4 issue of Current Biology contains a study indicating that laughter goes back beyond the ape-human split. The article, in Thaindian reports:

“This study is the first phylogenetic test of the evolutionary continuity of a human emotional expression,” said Marina Davila Ross of the University of Portsmouth in the United Kingdom.

“It supports the idea that there is laughter in apes,” she added.

To reach the conclusion, researchers analysed the recorded sounds of tickle-induced vocalizations produced by infant and juvenile orangutans, chimpanzees, gorillas, and bonobos, as well as those of human infants. A quantitative phylogenetic analysis of those acoustic data found that the best “tree” to represent the evolutionary relationships among those sounds matched the known evolutionary relationships among the five species based on genetics.

The researchers said that the findings support a common evolutionary origin for the human and ape tickle-induced expressions.They also show that laughter evolved gradually over the last 10 to 16 million years of primate evolutionary history.

But human laughter is nonetheless acoustically distinct from that of great apes and reached that state through an evident exaggeration of pre-existing acoustic features after the hominin separation from ancestors shared with bonobos and chimps, about 4.5 to 6 million years ago, Davila Ross says.

Uh, not 4.5 to 6 mya. Not if Orrorin and Sahelanthropus represent incipient hominids. More like 9 to 10 mya. Still, it is nice to know we share such a stress-reducing behavior.