Another Mystery Ancestor Joins The Group

Science Daily has a story on genetic work done by researchers at Cornell University and Cold Spring Harbor Laboratory that suggests that there is, as yet, another unnamed ancestor to the modern human line. They write:

In the new paper, the researchers developed an algorithm for analyzing genomes that can identify segments of DNA that came from other species, even if that gene flow occurred thousands of years ago and came from an unknown source. They used the algorithm to look at genomes from two Neanderthals, a Denisovan and two African humans. The researchers found evidence that 3 percent of the Neanderthal genome came from ancient humans, and estimate that the interbreeding occurred between 200,000 and 300,000 years ago. Furthermore, 1 percent of the Denisovan genome likely came from an unknown and more distant relative, possibly Homo erectus, and about 15% of these "super-archaic" regions may have been passed down to modern humans who are alive today.

The paper is available in PLoS Genetics, which means that it is free to the public.  The above-description makes it sound like bootstrapping on stilts.  Here is a paragraph from the paper, itself, that describes the process:

In this paper, we describe a powerful and highly general new method, called ARGweaver-D, that samples ancestral recombination graphs (ARGs) [18–20] conditional on a generic demographic model, including population divergence times, size changes, and migration events. After introducing ARGweaver-D, we present simulation studies showing it can successfully detect Nea→Hum introgression, even when using a limited number of genomes, and that it also has power for older migration events, including Hum→Nea, Sup→Den, and Sup→Afr events. Finally, we apply this method to modern-day Africans and ancient hominins, and characterize both new and previously reported cases of introgression between humans and archaic hominins.

Okay, it still sounds like bootstrapping on stilts.  I am not sure how you can do a simulation to detect older migration events when that is what you are looking for in the first place.  What exactly is an ancestral recombination graph, you ask?  From a previous paper on this subject:

It is possible to capture these complex relationships using a representation called the ancestral recombination graph (ARG), which provides a complete description of coalescence and recombination events in the history of the sample. However, previous methods for ARG inference have not been adequately fast and accurate for practical use with large-scale genomic sequence data. In this article, we introduce a new algorithm for ARG inference that has vastly improved scaling properties. Our algorithm is implemented in a computer program called ARGweaver, which is fast enough to be applied to sequences megabases in length. With the aid of a large computer cluster, ARGweaver can be used to sample full ARGs for entire mammalian genome sequences.

The best data we have suggests that Neandertals and African archaics split some 600 ky ago when a group of Homo ergaster migrated out of Africa and took up residence in western Europe, leading to branching events that eventually included H. antecessor and the Neandertals.  This is supported by this research, which found about 7% introgression into the Neandertal genome of archaic H. sapiens.  The surprise was that 1% of the Denisovan genome likely came from an, as yet, undiscovered hominin.  

Increasingly, there is evidence that considerable interbreeding occurred throughout the middle to late Pleistocene, continuing through the interbreeding that occurred in China and Europe.  As I wrote about the 105-130 ky old Chinese Xuchang skulls:

These two Chinese skulls stand at the crossroads of these population movements. While showing clear Neandertal characteristics, they also express modern traits, possibly reflecting mixing with the late, modern human arrivals represented by the recent modern human finds at Daoxian. Yet they also express a clear link to ancient East Asian populations. The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well. As Chris Davis of China Daily News put it: “One big happy family.”

This likely represents only a small part of the vast scope of population mixing. I will be curious to see where the ARG research leads.

Homo erectus 200,000 Years Older Than We Thought

UPI has a story about a discovery in South Africa of a Homo erectus infant that is 200 ky older than the oldest known specimen currently in existence.  From the original Science article: 

Fossil hominins from South Africa are enriching the story of early human evolution and dispersal. Herries et al. describe the geological context and dating of the hominin-bearing infilled cave, or palaeocave, at a site called Drimolen in South Africa (see the Perspective by Antón). They focus on the age and context of a recently discovered Homo erectus sensu lato fossil and a Paranthropus robustus fossil, which they dated to ∼2.04 million to 1.95 million years ago. This makes Drimolen one of the best-dated sites in South Africa and establishes these fossils as the oldest definitive specimens of their respective species ever discovered. The age confirms that species of Australopithecus, Paranthropus, and early Homo overlapped in the karst of South Africa ∼2 million years ago

The goofy thing about this is that, in East Africa,  early Homo was still running around and out-competing the robust australopithecines (Paranthropus).  The fossil was uncovered and described over a five year period at the site of Drimolen, which is part of the UNESCO World Heritage Site in South Africa that contains the important fossil sites of Swartkrans and Sterkfontein. 

From the UPI story:

“One of the questions that interests us is what role changing habitats, resources, and the unique biological adaptations of early Homo erectus may have played in the eventual extinction of Australopithecus sediba in South Africa,” said study co-author Justin Adams, researcher at Monash University's Biomedicine Discovery Institute.
“Similar trends are also seen in other mammal species at this time. For example, there are more than one species of false sabre tooth cat, Dinofelis, at the site -- one of which became extinct after two million years,” Adams said. “Our data reinforces the fact that South Africa represented a truly unique mixture of evolutionary lineages -- a blended community of ancient and modern mammal species that was transitioning as climates and ecosystems changed.”

Just a few short years ago, it was thought that Australopithecus sediba might be ancestral to early Homo based on the characteristics of its hands, pelvis and the proximity of stone tools to the Rising Star Cave.  This was an idea championed by Lee Berger, but it now seems likely that it was another, earlier form that gave rise to Homo erectus. 

Here is the photo of DNH134, taken by Jesse Martin, Reanud Joannes-Boyau, and Andy I. R. Herries

EarthSky: Twenty years of discoveries changing story of human evolution

EarthSky has an interesting article that summarizes twenty years of human evolution discoveries.  They write:

Perspectives on our own species have also changed. Archaeologists previously thought Homo sapiens evolved in Africa around 200,000 years ago, but the story has become more complicated. Fossils discovered in Morocco have pushed that date back to 300,000 years ago, consistent with ancient DNA evidence. This raises doubts that our species emerged in any single place.

This century has also brought unexpected discoveries from Europe and Asia. From enigmatic “hobbits” on the Indonesian island of Flores to the Denisovans in Siberia, our ancestors may have encountered a variety of other hominins when they spread out of Africa. Just this year, researchers reported a new species from the Philippines.

All of these discoveries point to the idea that there was considerable population mixing throughout the Middle to Late Pleistocene not just in Africa but throughout the Old World. We know that it took place in China around 120,000 years ago by the evidence from Linjing.  These particular hominins have characteristics found in modern humans, Neandertals and Homo erectus.

Interestingly, the idea that our species did not originate in any single place was an idea pursued by Rachel Caspari almost two decades ago, at a paper given at one of the American Association of Physical Anthropologists conventions.  At the time, it was still thought that the “Out of Africa” replacement model was still the best explanation for modern human origins.We now know that it is not.

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.

On the Heels of the Discovery of Homo luzonensis...

A new study from the journal Cell suggests that there were multiple migrations of individuals into Southeast Asia with the Denisovan genome.  Here is the summary from Cell.

Genome sequences are known for two archaic hominins—Neanderthals and Denisovans—which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.

These data, in combination with the new Luzon material further suggest that the population interrelationships in Southeast Asia were complex, with considerable mixing between Denisovans, archaic Homo sapiens, eastward-migrating Neandertals and who knows how many other groups. We know from the material in China that the fossil material of even 100 thousand years back exhibits multiple origins.  As I noted about the Xuchang hominins at the time:

These two Chinese skulls stand at the crossroads of these population movements. While showing clear Neandertal characteristics, they also express modern traits, possibly reflecting mixing with the late, modern human arrivals represented by the recent modern human finds at Daoxian. Yet they also express a clear link to ancient East Asian populations. The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well. As Chris Davis of China Daily News put it: “One big happy family.”

The presence of the hominins in Luzon, as well as the new research reported here suggests that this complexity comprised all of East Asia.

New Species of Hominin Found in Phillipines

From a story in UPI:

At the completion of excavations on the island of Luzon, scientists had unearthed several teeth, part of a thigh bone, and a few hand and foot bones. The fossils comprise the "the earliest direct evidence of a human presence in the Philippines," according to the latest study.

The fossilized bones, dated to between 67,000 and 50,000 years ago, feature a mix of anatomical characteristics, some that recall more primitive hominins and others similar to those of more modern human species.

Callao Cave is toward the northern tip of Luzon. The corresponding article from Nature seems to indicate that the fossil remains from this cave are “all over the map.”  The premolars indicate size and shape affinities to later Homo, while some of the characteristics are australopithecine (!).  This is also true of the hand elements. 

Although we have found human fossil remains in East Asia for some time (1896 on), there are large gaps in our knowledge, especially from the first appearance of Homo erectus to the advent of modern humans.  These fossils, while giving us more  information than we had, muddy the waters a bit.  Once upon a time, Grover Kranz (RIP) tried to convince me that australopithecines could be found in East Asia, but his evidence was based on a badly crushed occipital bone. 

It is clear from the presence of H. floresiensis and the current evidence that primitive traits were being retained in some groups but, as the authors point out, we need quite a bit more fossil material to make any definitive assessments. 

Homo erectus Was Lazy??

A short piece in PhysOrg links to an article in PLoS that argues that, when faced with the opportunity to make Acheulean tools out of really good raw materials at a site in what is now Saudi Arabia, the local Homo erectus group took the easy way out and made them out of whatever was lying around.  From the PhysOrg piece: “New archaeological research from The Australian National University (ANU) has found that Homo erectus, an extinct species of primitive humans, went extinct in part because they were 'lazy'.”

First off, the first paragraph is nothing short of idiotic. There is absolutely no evidence whatsoever that Homo erectus went extinct because they were lazy. They colonized huge sections of Asia and were integral to the appearance of early modern humans in the area.They might have disappeared from this particular area of Saudi Arabia but that is all.  Also from PhysOrg:

"At the site we looked at there was a big rocky outcrop of quality stone just a short distance away up a small hill.

"But rather than walk up the hill they would just use whatever bits had rolled down and were lying at the bottom.

"When we looked at the rocky outcrop there were no signs of any activity, no artefacts and no quarrying of the stone.

"They knew it was there, but because they had enough adequate resources they seem to have thought, 'why bother?'".

This is in contrast to the stone tool makers of later periods, including early Homo sapiens and Neanderthals, who were climbing mountains to find good quality stone and transporting it over long distances.

Maybe this particular population was stressed in some way. Maybe the tools that they made were good enough to get done what they needed. Who knows. It is a huge inference, though, that because they didn't use the raw materials that were better that they were “lazy.”  The last sentence of the abstract reads thus:

The Acheulean hominins at Dawadmi were strong and skilful, with their adaptation evidently successful for some time. However, these biface-makers were also technologically conservative, and used least-effort strategies of resource procurement and tool transport. Ultimately, central Arabia was depopulated, likely in the face of environmental deterioration in the form of increasing aridity.

This sentence alone belies the opening, “lazy” paragraph of the PhysOrg story.  More junk journalism. 

New Chinese Material Pushes the Exit From Africa to 2.1 mya

Nature is reporting research on new Chinese material that strongly suggests that the Georgian site of Dmanisi is not the earliest location to which migration out of Africa went.  Here is the abstract:

Considerable attention has been paid to dating the earliest appearance of hominins outside Africa. The earliest skeletal and artefactual evidence for the genus Homo in Asia currently comes from Dmanisi, Georgia, and is dated to approximately 1.77–1.85 million years ago (Ma)1. Two incisors that may belong to Homo erectus come from Yuanmou, south China, and are dated to 1.7 Ma2; the next-oldest evidence is an H. erectus cranium from Lantian (Gongwangling)—which has recently been dated to 1.63 Ma3—and the earliest hominin fossils from the Sangiran dome in Java, which are dated to about 1.5–1.6 Ma4. Artefacts from Majuangou III5 and Shangshazui6 in the Nihewan basin, north China, have also been dated to 1.6–1.7 Ma. Here we report an Early Pleistocene and largely continuous artefact sequence from Shangchen, which is a newly discovered Palaeolithic locality of the southern Chinese Loess Plateau, near Gongwangling in Lantian county. The site contains 17 artefact layers that extend from palaeosol S15—dated to approximately 1.26 Ma—to loess L28, which we date to about 2.12 Ma. This discovery implies that hominins left Africa earlier than indicated by the evidence from Dmanisi.

For the new site sequence data, we don't have any hominin remains so we don't know exactly what these folks looked like but the tools are very primitive.  A section from a companion piece reads thus:

The identity of their makers is, for now, unclear: no hominin bones have been recovered at Shangchen. “We would all love to find a hominin — preferably one with a tool in its hand,” says Dennell. Homo erectus is one possibility, because some of the earliest members of this species were found at Dmanisi. But Dennell thinks that the Shangchen toolmakers belonged to an earlier species in the genus Homo.

Petraglia and Rezek both say that the age of the tools — not to mention the possibility that hominins arrived in China even earlier than the 2.12-million-year mark — suggests that the toolmaker was a species such as Homo habilis. This relatively small-brained hominin is thought to have been confined to Africa between around 2.4 million to 1.4 million years ago.

Jungers holds open the possibility that the Shangchen toolmaker was a species of Australopithecus, a group of more ape-like hominins to which the iconic fossil Lucy belongs. So far, all Australopithecus fossils have been discovered in Africa.

Before his death, Grover Krantz argued for the presence of Australopithecus in East Asia but could never get anyone to come on board with him. Everyone was pretty content to label what was coming out of the ground as Homo erectus.I think it would be a stretch if the hominins from Shangchen were australopithecines since we don't see any advanced species of Australopithecus in East or North Africa between 2 and 2.5 mya.  In fact, Au. boisei drops out around 2.1, likely out-competed by early Homo.

Nonetheless, something was making stone tools in China at 2.1 mya and that is “Yuuuuge” news. 

Daniel Everett: Homo erectus Could Speak and Make Boats

Bentley University Global Studies professor Daniel Everett argues that Homo erectus could speak and had the ability to make ocean-going vessels.  The Guardian has the story:

“Oceans were never a barrier to the travels of Erectus. He travelled all over the world, travelled to the island of Flores, across one of the greatest ocean currents in the world,” said Daniel Everett, professor of global studies at Bentley University, and author of How Language Began. “They sailed to the island of Crete and various other islands. It was intentional: they needed craft and they needed to take groups of twenty or so at least to get to those places.”

While Everett is not the first to raise the controversial possibility that H. erectus might have fashioned some sort of seagoing vessel, he believes that such capabilities mean that H. erectus must also have had another skill: language.

“Erectus needed language when they were sailing to the island of Flores. They couldn’t have simply caught a ride on a floating log because then they would have been washed out to sea when they hit the current,” said Everett, presenting his thesis at the meeting of the American Association for the Advancement of Science in Austin. “They needed to be able to paddle. And if they paddled they needed to be able to say ‘paddle there’ or ‘don’t paddle.’ You need communication with symbols not just grunts.”

It is pretty clear that Homo erectus hunted, at least in some fashion, could control fire and evidence seems to be accumulating that they hafted spears and, at least late in the range, the European variant set up rudimentary complex settlements.

There is, naturally, skepticism that any hominin form prior to Neandertals were sea-going: 

But others say that there is little evidence that H. erectus was a sophisticated seafarer, let alone had a language. “I don’t accept that, for example, [Homo] erectus must have had boats to get to Flores,” said Chris Stringer, head of human origins at the Natural History Museum in London. “Tsunamis could have moved early humans on rafts of vegetation.”

Before dismissing that idea out of hand, remember that it is the best one going to explain how the New World Monkeys got where they are, since Africa and South America had parted ways some 180 million years prior to their arrival.

I think there is likely not enough evidence to know one way or another if Homo erectus could sail the high seas and had speech, although the only skeletal evidence that we have for that part of the anatomy suggests not. 

Modern Humans Came Out of Africa Earlier Than Thought and Did So Multiple Times

If you have been studying human evolution, this story is not new.We have suspected for some time that humans migrated out of Africa in waves, beginning with Homo heidelbergensis, up through archaic Homo sapiens and, now, modern Homo sapiens.  As the story notes, there have likely been multiple migrations of Homo sapiens, as well. 

From the story in Science Daily:

A review of recent research on dispersals by early modern humans from Africa to Asia by researchers from the Max Planck Institute for the Science of Human History and the University of Hawai'i at Manoa confirms that the traditional view of a single dispersal of anatomically modern humans out of Africa around 60,000 years ago can no longer be seen as the full story. The analysis, published in the journal Science, reviews the plethora of new discoveries being reported from Asia over the past decade, which were made possible by technological advances and interdisciplinary collaborations, and shows that Homo sapiens reached distant parts of the Asian continent, as well as Near Oceania, much earlier than previously thought. Additionally, evidence that modern humans interbred with other hominins already present in Asia, such as Neanderthals and Denisovans, complicates the evolutionary history of our species.

Here is the graphic from the story:

 
What is only hinted at in the article is that when these waves of moderns came out of Africa, they interbred with the archaic hominins that they encountered. Further, this genome was remarkably stable, since there is genetic evidence that there was at least 500 thousand years of separation between them.Also missing from the story is the range of variation that these hybridizations display.  For example, as noted by the triangle on the map, the Xuchang fossils from China seem to show a mix of modern, Neandertal and late Homo erectus morphologies.  As I noted at the time:

The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well.

The other peculiar thing about the graphic is that there seems to be no migration pattern through the strait of Gibraltar. This seems odd since this is likely at least one of the routes that were taken by H. ergaster between 1.5 and 2.0 mya, and since it is thought that the Levallois tool technology comes from the Middle Stone Age of Africa, this would have been a likely route of introduction.  There may have been a barrier of sorts, suggested by the fact that the latest surviving Neandertals are from Spain. 

New Jebel Irhoud Date Causes Rethink of Chinese Dali Skull

Newsweek (Yes, that Newsweek) has a story on the reexamination of the Chinese Dali cranium, in light of the revised dates for the Jebel Irhoud skulls.  Kastalia Medrano writes:

Known as the Dali skull, it was discovered nearly 40 years ago in China’s Shaanxi province. It belonged to a member of the early hominin species Homo erectus. Its facial structure and brain case are intact, despite being dated to around 260,000 years ago. The Dali skull is so old that archaeologists initially didn’t believe it could share features with the modern Homo sapiens.

But Xinzhi Wu of the Chinese Academy of Sciences in Beijing believed that due to the overwhelming physical similarities, Homo erectus must have shared DNA with Homo sapiens. After decades of this idea being dismissed by mainstream academia, Wu and a colleague, Sheela Athreya of Texas A&M University, recently reanalyzed the Dali skull and found it may force us to rewrite our evolutionary history after all. It’s incredibly similar to two separate Homo sapiens skulls previously found in Morocco. “I really wasn’t expecting that,” Athreya told New Scientist.

If we’d found only the Moroccan skulls, and not the Dali skull, it would make sense to keep believing all modern humans evolved in Africa. But the similarities show that early modern humans may not have been genetically isolated from other parts of the world, like what we know today as China.

“I think gene flow could have been multidirectional, so some of the traits seen in Europe or Africa could have originated in Asia,” Athreya told New Scientist.

Okay, now the nuts and bolts.Dali has always been thought to occupy that rarified space between Homo erectus  and early modern Homo sapiens.  It was always thought to be between 200 and 250 kya, and optically-stimulated luminescence dating (a variant of thermoluminescence) places it between 258 and 267 kya.  My analyses of the skull suggested that it was, in no way, shape or form, a modern human but it did not tend to cluster with the Neandertals in terms of head shape.  Athreya and Wu have done an extensive multivariate analysis and conclude (from the article, likely behind a paywall:

When just the facial skeleton is considered, Dali aligns with Middle Paleolithic H. sapiens and is clearly more derived than African or Eurasian Middle Pleistocene Homo. When just the neurocranium is considered, Dali is most similar to African and Eastern Eurasian but not Western European Middle Pleistocene Homo. When both sets of variables are considered together, Dali exhibits a unique morphology that is most closely aligned with the earliest H. sapiens from North Africa and the Levant.

These results add perspective to our previous view of as Dali a “transitional” form between Chinese H. erectus and H. sapiens. Athough no taxonomic allocation is appropriate at this time for Dali, it appears to represent a population that played a more central role in the origin of Chinese H. sapiens. Dali's affinities can be understood in the context of Wu's Continuity with Hybridization scenario and a braided-stream network model of gene flow. Specifically, we propose that Pleistocene populations in China were shaped by periods of isolated evolutionary change within local lineages at certain times, and gene flow between local lineages or between Eastern and Western Eurasia, and Africa at other times, resulting in contributions being made in different capacities to different regions at different times.

In combination with the Xuchang remains, the reanalysis of this skull suggests that, indeed, there is a long and complex interrelationship between different hominin groups that dates back some 400 thousand years. From the paper:

In the braided-stream network model, evolutionary change in China was the result of a shifting network of gene flow among distinct regional Chinese populations, as well as between Chinese and Western Eurasian populations. These were not isolated evolutionary lineages; gene flow both within China and between Eastern Eurasia, Western Eurasia and Africa was intermittent and could explain the similarities in aspects of the neurocranium found here between Dali and Western Eurasian Middle Pleistocene humans. Gene flow would best be described as a braided stream network with periods of isolated evolutionary change within a local lineage at times, and periods of gene flow between local lineages or paleo-demes at other times, resulting in contributions being made in different capacities to different regions at different times.

It is pretty clear that our simplistic models of Recent African Replacement and Multiregional Evolution need to be reworked. It is becoming more apparent that what we are looking at either a polytypic species with a huge geographical range or a syngamion of related species that intermixed regularly. The Xuchang skulls were, apparently, not unique.

Why Is Homo floresiensis Still Such a Mystery?

Cosmos Magazine has an article by Debbie Argue, biological anthropologist from Australian National University, about Homo floresiensis and why it has been a struggle to accurately and adequately place this hominin within the framework of human evolution.

 Here was the initial assessment:

Peter Brown and colleagues originally proposed two competing hypotheses about the origins of H. floresiensis. One is that the species is an early hominin similar to the earliest identified in the Homo genus. The fossils for these species are known only from Africa and are between one and two million years old. This implies that the ancestors of H. floresiensis could have got to Flores Island in the vicinity of a million years ago and survived there until at least 60,000 years ago.

Their alternative hypothesis was that H. floresiensis is a dwarfed descendant of Homo erectus, which is the only known non-sapiens hominin to once have existed in Indonesia. Its remains have been found on the island of Java. According to this view, the dwarfing of H. erectus was an evolutionary response to being isolated on an island with a limited food supply. Just as the Asian elephant evolved into the dwarfed Flores stegodon after becoming marooned on the island, H. erectus could have met a similar fate.

It was also proposed that this hominin might have expressed microcephaly.  This idea failed to explain other aspects of the skeleton, however, such as its diminutive height (around 3 feet), long arms and feet and primitive skull features. Here is an image of H. floresiensis compared to a modern human, who had been running around the landscape for at least 100k years while H. floresiensis was extant.

This all saw at least some resolution with the discovery and description of some remains  on another areas of the island Flores that were very similar to the H. floresiensis remains but dated to some 600 thousand years earlier than the remains in Liang Bu.  This lent more credence to the idea that H. floresiensis was, in fact, an offshoot of Homo erectus.

So, Argue, along with Colin Groves, Bill Jungers and Mike Lee, performed statistical tests (this story does not say which kind, a peculiar omission) on a number of different hominin species, comparing them to H. floresiensis.  What did they find?

We therefore hypothesise that H. floresiensis shared a common ancestor with H. habilis. We do not know who that ancestor was or when it lived, but it would have to be older than the oldest H. habilis specimen known, so older than 1.75 million years. The implication is that the H. floresiensis ancestor evolved before that time in Africa, dispersed from that continent, and arrived on Flores earlier than 700,000 years ago, judging by the age of the jaw and teeth found at Soa Basin. This represents a hitherto unknown movement of very early hominins out of Africa.

Presently, the earliest evidence for hominins outside of Africa come from Europe, the Near East and Asia, and date to between 1.5 and 1.8 million years ago. Argue's hypothesis would suggest that H. floresiensis appearance in east Asia represents a separate migration out of African sometime either before or after the wave that saw Homo erectus show up in Trinil and Sangiran, in Indonesia.

Questions still abound as to why this species never saw the evolutionary trajectory that other hominins went through in terms of cranial expansion, increase in height and changes in brachial and crural indices. On the other hand, if evolution proceeds through what we have termed systematics, then advanced traits will show up in related species and if the ancestors of H. floresiensis were cut off, they would just go on their merry way.  We know that such a pattern holds for H. naledi, in South Africa, which coexisted with archaic Homo sapiens, in some way, shape or form. 

The article ends on a very peculiar note, in which she suggests the remote possibility that H. floresiensis is still alive out there, somewhere:

Could the Hobbit still exist in the wild mountain forests of Flores? When H. floresiensis was announced, the media picked up on the local folklore that small human-like creatures roam the forests. Descriptions of sightings are well recorded and quite detailed. The similarity to H. floresiensis is intriguing. But most researchers would say ‘show me the bones!’

This reminds one of the stories involving the Yeti/Sasquatch/Abominable Snowman, which likely derive from the finding of the bones of the Miocene ape Gigantopithecus, which was close to ten feet tall, when standing.  Is H. floresiensis still out there?  Probably not, but I am sure that the cryptozoologists haven't given up hope. 

Genetic Model Identifies Paranthropus boisei as Vector For Transmission of Herpes Virus

CNN (usual caveats) reports on a study that identifies Paranthropus boisei as the likely transmission vector of genital HSV-1.  From the story:

Herpes has been around a long time, to say the least.

Ancient chimpanzees genetically passed oral herpes (herpes simplex 1, or HSV-1) to the earliest humans millions of years ago when our lineage split. And we almost missed out on catching that other scourge, genital herpes (HSV-2) -- almost. Unlike HSV-1, HSV-2 didn't make the leap to early humans on its own.

Unfortunately for modern humans, millions of years ago, an early human ancestor was in the right place at the right time to catch HSV-2. And it might not have happened if it weren't for that meddling hominin species Paranthropus boisei, according to a new study in the journal Virus Evolution.

Why Paranthropus boisei, you ask? After all, P. boisei was not even on the main line of human evolution, coexisting with all manner of early Homo species at the same time, who likely out-competed them into extinction.  From the article, which is highly technical:

Paranthropus boisei would have been well placed to act as an intermediate host for HSV2. It most likely contracted the infection through hunting or more likely scavenging infected ancestral-chimpanzee meat. Processing (with or without tools) and consumption of raw meat would act as a simple path for ChHV1 to have crossed into P.boisei via open cuts or sores. Tropical refugia during hot dry periods may have driven chimpanzees into higher concentrations in certain areas, driving them into contact and competition with P.boisei and H.habilis as the margins of tropical forest blended into more open savannah-like habitats (Julier et al. 2017). Violent confrontation or hunting/scavenging and butchery practices would have provided a viable path of transmission for HSV2. Homo habilis remains have been recovered from the same layers as stone tools and bones carrying evidence of butchery, supporting a possible transmission–through-hunting/scavenging hypothesis for the initial anc-chimp to H.habilis transmission (Clarke 2012). Paranthropus aethiopicus, P. boisei, and P. robustus are associated with the Oldowan stone tool complex (De Heinzelin et al. 1999), and P.boisei explicitly with butchery (Domínguez-Rodrigo et al. 2013) lending support to the hypothesis that bushmeat hunting/scavenging and butchery may have led to the initial transmission of HSV2 to the hominins.

The entire exercise is very mathematical and relies on somewhat limited evidence of P. boisei behavior. It is, nonetheless, intriguing since it posits considerable interaction between the various hominin groups. 

Here is a mugshot of one of the perpetrators, the Zinj skull from Olduvai Gorge, found in 1959. 

Is Homo floresiensis a Sister Species of Homo habilis?

A short blurb in Science Magazine attempts to lay to rest one of the nagging questions in recent human evolution: where did the diminutive “hobbits” originate?  A report by the Australian National University suggests that Homo floresiensis is a sister species of Homo habilis. 

Data from the study concluded there was no evidence for the popular theory that Homo floresiensis evolved from the much larger Homo erectus, the only other early hominid known to have lived in the region with fossils discovered on the Indonesian mainland of Java.

Study leader Dr Debbie Argue of the ANU School of Archaeology & Anthropology, said the results should help put to rest a debate that has been hotly contested ever since Homo floresiensis was discovered.

"The analyses show that on the family tree, Homo floresiensis was likely a sister species of Homo habilis. It means these two shared a common ancestor," Dr Argue said.

"It's possible that Homo floresiensis evolved in Africa and migrated, or the common ancestor moved from Africa then evolved into Homo floresiensis somewhere."

Homo floresiensis is known to have lived on Flores until as recently as 54,000 years ago.

How do we know this?

Where previous research had focused mostly on the skull and lower jaw, this study used 133 data points ranging across the skull, jaws, teeth, arms, legs and shoulders.

Dr Argue said none of the data supported the theory that Homo floresiensis evolved from Homo erectus.

I think that it is passing peculiar that we have found absolutely nothing else like this in over 100 years of searching in this area, but who knows what these smaller islands have hidden in them. This also raises interesting questions. Since we know that early Homo got as far as Russian Georgia, is it possible they got as far as Flores? That's a long way.  Is it possible that incoming Homo erectus out-competed them in most places except for a few small refugia?  Also possible.   Hopefully more information will turn up to help us answer these questions.

Another Human Species in China?

The Christian Science Monitor and other outlets are reporting on a new find from Xuchang, China, that seems to possess intermediate traits between archaic and modern Homo sapiens:

In an article published Friday in the journal Science, the researchers note that the skull fragments date to the Late Pleistocene epoch, a time marked by the expansion of H. sapiens and the extinction of other species in the genus Homo. During the early part of that epoch, Neanderthals roamed Europe and western Asia while humans began to journey out of Africa. But fossil records of human species in Eastern Asia from that time period are thin, muddying the picture of that era for a substantial region of the planet.

The skulls found in China were found to bear very close resemblances to those of Neanderthals, including a very similar inner ear bone and a prominent brow ridge. But the brow ridge was much less pronounced than one would expect from Neanderthals, with a considerably less dense cranium, as one might expect in an early H. sapiens. Researchers also found that the skulls were large by both modern and Neanderthal standards, with a whopping 1800 cubic centimeters of brain capacity.

So where do they fit in the grand scheme of things?

"The overall cranial shape, especially the wide cranial base, and low neurocranial vault, indicate a pattern of continuity with the earlier, Middle Pleistocene eastern Eurasian humans. Yet the presence of two distinctive Neanderthal features ... argue for populational interactions across Eurasia during the late Middle and early Late Pleistocene," said Dr. Trinkaus in a statement.

This kind of population mixing makes sense. We already know that modern humans and Neandertals interbred in Europe and that the geographic range of Neandertals stretched from Portugal to Teshik Tash, in Russia and Shanidar Cave, in Iraq.

The remains are dated to Marine Oxygen Isotope Stage 5d or 5e, making them between 105 and 125 ky in age.  Here is a description of the neurocranium from the paper:

The large Xuchang 1 neurocranium closely approximates the shapes of those of Middle Pleistocene humans, especially eastern Eurasians (Fig. 2 and fig. S17). The vault height is low, similar to those of the Neandertals and the higher Middle Pleistocene vaults, and the low vault height is reflected in a low temporal squamous portion (figs. S27 and S28). It is also produced by the very flat midsagittal parietal arc. In contrast, the maximum cranial breadth is the largest known in the later Pleistocene (fig. S15), and it is securely based on an undistorted posterior cranium. Moreover, the widest point is low, on the temporal bones (fig. S17), as in most earlier crania, rather than on the parietal bones, as among Neandertals and most modern humans. In addition, the one complete mastoid process is short and slopes inward (fig. S17), rather than being longer and more vertical, as in modern humans and some Neandertals. These features combine to provide the cranium with an occipital profile similar to those of earlier human crania, contrasting with the rounded profiles of Neandertals and the laterally vertical ones of modern humans.

There are a few things that are immediately interesting about this. First, this skull is YUGE.  1800 cc is monstrous.  The average cranial capacity of modern humans is around 1450 cc and that of Neandertals, around 1550 cc.  Second, the low, flat cranium with the widest point on the temporal bones (just above your ears) are traits of Homo erectus, not modern humans or Neandertals, suggesting strongly that there was some sort of continuity from this group through to modern humans in this region.  Neandertals simply don't have those traits.  Nonetheless, the cranium clearly shows some Neandertal traits in the ear and rear of the vault.  This continuity is characterized by the authors thus: "This morphological combination, and particularly the presence of a mosaic not known among early Late Pleistocene humans in the western Old World, suggests a complex interaction of directional paleobiological changes and intra- and interregional population dynamics."  As more information becomes available, we will have a better idea of how this find fits in the east Asian evolutionary picture.  This is exciting.  Up until this point, we have had very few finds in China that fall within this general time frame, most notably the Dali and Mapa remains.  I will have to rework my section on human origins for the BioLogos site for this region. 

New Study on Homo naledi

Lauren Schroeder and colleagues have published a report on the skull of Homo naledi, in which they address the characteristics and attempt to place them in a taxonomic context, using morphometric analysis.  From the abstract:

Our results indicate that, cranially, H. naledi aligns with members of the genus Homo, with closest affiliations to H. erectus. The mandibular results are less clear; H. naledi closely associates with a number of taxa, including some australopiths. However, results also show that although H. naledi shares similarities with H. erectus, some distances from this taxon – especially small-brained members of this taxon – are extreme. The neighbor joining trees place H. naledi firmly within Homo. The trees based on cranial morphology again indicate a close relationship between H. naledi and H. erectus, whereas the mandibular tree places H. naledi closer to basal Homo, suggesting a deeper antiquity. Altogether, these results emphasize the unique combination of features (H. erectus-like cranium, less derived mandible) defining H. naledi. Our results also highlight the variability within Homo, calling for a greater focus on the cause of this variability, and emphasizing the importance of using the total morphological package for species diagnoses.

Another major finding of the study is that a grouping of H. naledi and specimens of Homo erectus "exceeds, in many instances, what we would expect if this grouping represented a single species."  Recall that we have zero idea how old this find is and, to the extent that this is possible, are trying to place this skull using only taxonomic analysis. Nonetheless, it gives us more information about this stage of hominin evolution and suggests that there was considerable variation of morphs running around during the transition from the australopithecines to early Homo. 

Of Stone Tools and Human Cognition

One of the things that is taught in human origins classes all over the world is that the earliest stone tools were likely made at the site of Dikika, and date to around 3.4 million years ago.  That perspective has now been called into question with the observation that monkeys can create exactly the same kinds of tools—by accident. Sarah Knapton, writing in the Telegraph has this:

In a discovery that calls into question decades of research, a band of wild bearded capuchin monkeys in Brazil were seen hammering rocks to extract minerals, causing large flakes to fly off.

Previously archaeologists believed the flakes were only made by humans through a process called ‘stone-knapping’ where a larger rock is hammered with another stone to produce sharp blade-like slivers which can be used for arrows, spears or knives.

The flakes were thought to represent a turning point in human evolution because they demonstrated a level of planning, cognition and hand manipulation that could not be achieved by other animals.

But the new research suggests that flakes can be made without any such foresight. In fact they can simply be made by accident.

“The fact that we have discovered monkeys can produce the same result does throw a bit of a spanner in the works in our thinking on evolutionary behaviour and how we attribute such artefacts,” said Dr Michael Haslam, lead of the Primate Archaeology project at the University of Oxford.

This is possible and it may be that some of the earliest “tools” aren't any such thing. When hominins started using tools in a concerted fashion has always been a large question in the evolutionary picture. It is very clear that by what we know as the Acheulean, manufactured by Homo ergaster, Homo erectus and Homo heidelbergensis, the hand axes are clearly human-made. Before that, maybe more research needs to be done to verify that what we think is human behavior actually is.  It is natural to want to impart human intelligence to our ancestors as far back as we can, in an effort to “humanize” them but, sometimes, this might be just wishful thinking.

Lauren Saville: The Importance of Teaching Human Evolution

Lauren Saville has written a post for NCSE titled "The Importance of Teaching Evolution."  Inevitably, the post deals not just with human evolution, but with climate change as well because, just as rejection of human evolution goes hand in hand with climate change skepticism on the right, acceptance of the two go hand in hand on the left.  So, why should we teach human evolution?

From an early age we wonder where we come from; evolution explains that for us. From the amazing array of fossils that have been found in Africa, Asia, and Europe we can piece together our evolutionary lineage from Australopithecus to early Homo sapiens and explore the different species that branched off in between. By studying the fossil record we can understand when we began walking upright, by noting all the huge morphological changes that distinguish us from other great apes, such as our wide bowl-shaped pelvis, big toes in line with the rest of our feet and shorter arms. We can see when our brain size increased (when Homo erectus came about) and the subsequent huge change in our technology. As they say, the rest is history.

Tapping into our inherent curiosity about our history and origins is a great way to get students excited about science. Who does not want to know why we do the things we do and look the way we do? Learning about our own evolution helps students feel connected to science.

I would add that one of the reasons we should teach human evolution is because it places us in the wide pantheon of evolution on the earth, which began some 3.5 billion years ago. It gives us an idea of the vastness of time. Humans, in their (relatively) current form, have been around for almost 200 thousand years. Our genus has been around for over 2 million years. How long is that? If you started counting by ones out loud, it would take you twenty-two days of straight counting to get to two million.

To count to one billion would take you 31 years!!

Evolution has been going on for three and a half times that long. We are part and parcel of the grand design of life and should take joy in that.

H. floresiensis Not As Young or As Unique As We Thought

In other words, so much for the pathology argument.  Many news outlets, National Geographic being one of them, are reporting on new fossils that closely match those of Homo floresiensis that were found at Liang Bua Cave on the island of Flores in the late 1990s.  Adam Hoffman writes:

The 700,000-year-old human remains are the first found outside Liang Bua cave, the site on Flores that yielded the original hobbit fossils. The much older samples show intriguing similarities to H. floresiensis, including their small size, and so provide the best evidence yet of a potential hobbit ancestor.

“Since the hobbit was found, there have been two major hypotheses concerning its ancestry,” says Gerritt van den Bergh, an archaeologist at the University of Wollongong in Australia and a contributor to the work.

According to one theory, H. floresiensis is a dwarfed form of Homo erectus, an ancient human relative that lived in East Asia and parts of Africa until about 143,000 years ago. But other researchers think the hobbits evolved from even earlier, smaller-bodied hominins such as Homo habilis or Australopithecus.

“These new findings suggest that Homo floresiensis is indeed a dwarfed form of Homo erectus from Java, a small group of which must have gotten marooned on Flores and evolved in isolation,” van den Bergh says.

The article goes on to note that the competing argument, that the fossils of Liang Bua represent some kind of pathological condition, and that they maintained this condition for some 700 ky, is now untenable. Clearly this is a side-branch of human evolution.The other key finding is that they also had stone tools, specifically a “straightforward core and flake” technology. Further, the tools show a striking similarity to those found at Liang Bua, suggesting that there was remarkable cognitive "stability" in this population. 

The more we think we know about human evolution, the less, it turns out, that we do.  For now, the entire article is available from Nature for free here. 

Humans and Meat

New research by Dan Lieberman and Katherine Zink strongly supports what we have suspected for quite some time, that a substantial change in diet of early hominins led to rapid evolution in brain size and social structure.  Brian Handwerk of Smithsonian writes:

After measuring chewing and biting in modern humans, scientists found that a diet that includes one-third raw meat requires far less chewing and bite force exertion than meals of tubers alone. The researchers suggest that with the advent of stone tools, ancient human relatives were able to tenderize their food and make it far easier to chew and digest.

“An important step was just using a simple stone tool to cut our meat and bash our vegetables,” says Harvard University evolutionary biologist Daniel Lieberman.

The idea that fire allowed humans to cook their food and soften it that way has been around for quite some time and arguments usually point to the widespread use of fire toward the end of the Middle Pleistocene as the point where this begins to happen. This is the first time I have seen this argument extended to the early Pleistocene.The article continues:

“If I gave you a piece of raw goat, you would just chew and chew it, like a piece of bubble gum,” Lieberman explains. “Human teeth don't have the kind of shearing ability that, say, dogs' teeth have, and that is necessary to break down meat. With human chewing it just stays in a clump, and studies have shown how that makes digestion far less efficient.”

Cooking makes it easier to chew meat, but evidence suggests that the regular use of fire for cooking didn't pop up until perhaps half a million years ago—far later than the changes to H. erectus. Also, evidence from archaeological and paleontological research points to a spike in human meat consumption by at least 2.6 million years ago.

However, we have plenty of evidence that hominins had begun making stone tools some 3.3 million years ago. Those tools could have been used as pounders to tenderize foods, a practice seen in modern chimps. Flaked tools can also slice foods into easily chewable pieces or remove skin, cartilage and other bits that are harder to chew.

“It's not a coincidence that the oldest evidence for eating meat shows up around the same time as tools,” Lieberman says. “We know that the evolution of meat-eating basically required stone tools. And that had a huge effect on our biology.”

When my wife makes a dish involving chicken breasts, the first thing she does is pound them.  This makes it much softer and easier to eat. 

This is one of the principle reasons I tend to regard arguments in favor of vegetarianism somewhat warily. It is simply not in our nature or physiology to be that way. You can be one, if you wish, but that is not the natural state of things.