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.

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 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.

"Single Evolving Lineage of Early Homo"

This was reported a month or so back.  A new fossil has been described from the site of Dmanisi, the 1.8 million year-old site in the Russian republic of Georgia.  The skull is almost totally complete and, with associated jaw, is one of the best examples of early Homo in existence.  From the abstract of the Lordkipanidze et al¹ article:

The Dmanisi sample, which now comprises five crania, provides direct evidence for wide morphological variation within and among early Homo paleodemes. This implies the existence of a single evolving lineage of early Homo, with phylogeographic continuity across continents.

The idea of a single, evolving lineage is the closest you will get to someone admitting that there might be anagenetic speciation going on here. It also suggests a wide range for early Homo that extended from eastern Africa, across the upper coast, and across the strait of Gibraltar. There is evidence of early Homo at Orce, in Spain and Pirro Nord, in Italy from around 1.6 to 1.3 million years ago. No actual hominin remains exist at these sites but the stone tools that have been found found match, generally, those found at Dmanisi. Not a smoking gun but close.

What is intriguing about this is that it is not a huge intellectual leap that is making these hominins move.  The newly-described Dmanisi skull has a cranial capacity of 546 cubic centimeters, barely 100 more than the late australopithecines.  The morphological diversity also has people interested.  From the Science Daily story:

According to [Christophe] Zollikofer, the reason why Skull 5 is so important is that it unites features that have been used previously as an argument for defining different African "species." In other words: "Had the braincase and the face of the Dmanisi sample been found as separate fossils, they very probably would have been attributed to two different species." Ponce de León adds: "It is also decisive that we have five well-preserved individuals in Dmanisi whom we know to have lived in the same place and at the same time." These unique circumstances of the find make it possible to compare variation in Dmanisi with variation in modern human and chimpanzee populations. Zollikofer summarizes the result of the statistical analyses as follows: "Firstly, the Dmanisi individuals all belong to a population of a single early Homo species. Secondly, the five Dmanisi individuals are conspicuously different from each other, but not more different than any five modern human individuals, or five chimpanzee individuals from a given population."

the differences between the East African and Eurasian fossils then could be just regional variation in an evolving polytypic species. This kind of explanation certainly gives the "lumpers" a leg up and, if this explanation is the best one going, calls into our question the splitting that we have applied to other species. Is it, instead, appropriate to sink such taxonomic forms such as Homo heidelbergensis, Homo ergaster, Homo rudolfensis and Homo habilis, all of which exhibit considerable size and shape dimorphism, into one species: Homo erectus which now has taxonomic precedence?

¹A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo David Lordkipanidze, Marcia S. Ponce de León, Ann Margvelashvili, Yoel Rak, G. Philip Rightmire, Abesalom Vekua, and Christoph P. E. Zollikofer Science 18 October 2013: 342 (6156), 326-331.

Two Hominin Species Running Around At 1.9 Mya

Meave Leakey and some colleagues¹ have unearthed and described some new fossil hominins from Koobi Fora that seem to confirm that, yes, there were two very different critters running around 1.8 to 1.9 million years ago on the plains of eastern Africa. From the Turkana Basin Institute:

Found within a radius of just over 10 km from 1470’s location, the three new fossils are dated between 1.78 million and 1.95 million years old. The face KNM-ER 62000, discovered by field crew member Elgite Lokorimudang in 2008, is very similar to that of 1470, showing that the latter is not a single “odd one out” individual. Moreover, the face’s well-preserved upper jaw has almost all of its cheek teeth still in place, which for the first time makes it possible to infer the type of lower jaw that would have fitted 1470. A particularly good match can be found in the other two new fossils, the lower jaw KNM-ER 60000, found by Cyprian Nyete in 2009, and part of another lower jaw, KNM-ER 62003, found by Robert Moru in 2007. KNM-ER 60000 stands out as the most complete lower jaw of an early member of the genus Homo yet discovered.

The skull being referenced (heavily throughout the press release) is that of KNM-ER 1470, discovered by Richard Leakey in 1972 and dated to 1.9 million years ago. 1470 has a very flat face and is large, so much so that when it was discovered and compared to the Homo habilis material that Richard's dad, Louis Leakey and Napier and Tobias were pulling out of the ground, it was felt that it represented a new species, Homo rudolfensis.

For a short run-down on the material from this time period, go to my BioLogos post, The Human Fossil Record, Part 7: The Rise of Early Homo.

Anyhow, these new fossils add a new level of what Bernard Wood² calls “complexity.” For quite some time, 1470 existed in its own little world, with no fossil remains being similar to it in size or in shape. Questions began to rise about the veracity of its reconstruction and its provenance. These new fossils fit 1470 to a “T” and it now seems clear the 1470 does, in fact, represent a different form than that represented by skulls like ER 1813, which is small and gracile and gives support to the idea that there were two competing species of hominin on the landscape even before Homo erectus/ergaster arrived on the scene some two hundred thousand years later. Below, on the top is KNM-ER1813 and below it is KNM-ER 1470















As you can see, there is considerable difference in overall size and robusticity between the two and when the new material is compared to the mandible KNM-ER 1802, which is similar to 1813, there is a considerable mismatch. What remains to be seen is where Homo ergaster came from.

¹Leakey, M. G., Spoor, F., Dean, M. C., et al. (2012). New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo. [10.1038/nature11322]. Nature, 488(7410), 201-204.
http://www.nature.com/nature/journal/v488/n7410/abs/nature11322.html#supplementary-information

²Wood, B. (2012). Palaeoanthropology: Facing up to complexity. Nature, 488(7410), 162-163.
http://dx.doi.org/10.1038/488162a

Middle Pleistocene Hominin Height

Science Daily has a story on work being done with the material from the Sima de los Huesos cave at Atapuerca. 27 complete long bones have been discovered there and from these, it has been possible to estimate the height of Homo heidelbergensis. Science Daily writes:

The results suggest that both men and women in the Sima de los Huesos population were on average slightly higher than Neanderthal men and women. "Neither can be described as being short and both are placed in the medium and above-medium height categories. But, both species featured tall individuals," assured the experts.

The height of these two species is similar to that of modern day population of mid-latitudes, like in the case of Central Europe and the Mediterranean.

The humans who arrived in Europe during the Upper Palaeolithic era, Cro-Magnons or anatomically modern humans, replaced the Neanderthal populations. They were significantly taller than other human species and their average height for both sexes was higher, falling in the very tall individual category.

Height remained the same for some 2 million years.

We know from the remains at Turkana that, at least for some individuals, height close to that of modern humans had been achieved by 1.3 million years ago.This probably reflects (amongst other things) a massive increase in protein in the diet, which would come about by increased hunting, something present in late African Homo ergaster. More pieces of the puzzle.

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New BioLogos Post is Up

My new post on early Homo is up at BioLogos. As always, comments are welcome here and there.

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Nature News Story on Au. sediba

Nature News has a story on the Australopithecus sediba skeleton described by Lee Berger and colleagues.  Ewen Callaway writes:

At around 420 cubic centimetres, A. sediba 's puny brain compares to those of other Australopithecus specimens and chimpanzees. But a high-resolution synchrotron scan of the brain's impression on the skull shows enlarged frontal areas that are normally associated with humans and linked to higher cognitive abilities, such as planning. A. sediba's pelvis also looks wider than those of other australopiths, raising doubts about the idea that the human pelvic shape evolved to accommodate large-brained babies. "Whatever is driving a relatively human-like shape of the pelvis, it is not a big brain," says Berger. The orientations of its leg and ankle bones suggest that A. sediba walked upright, and its nearly complete ankle resembles that of a human. But its long arms, and some features of its feet and shin bones, are similar to those of a chimpanzee. Taken together, these features suggest that A. sediba was adapted for both bipedalism and tree-dwelling.

This is a wonderful mosaic. As I wrote yesterday, though, it is not clear where it fits. There are three possibilities: A. africanus gives rise to A. sediba and A. habilis and A. rudolfensis.  Here, the two species of early Homo have been demoted and all three have transitional characteristics that represent a general trend toward modernity (after Walker and Wood).

The second scheme has A. africanus giving rise to A. sediba, which then goes extinct, and H. habilis and H. rudolfensis (in some fashion), one of which then gives rise to H. ergaster.  This posits that the traits present in both early Homo and A. sediba represent a general trend toward modernity. 

 

The third scheme has  A. garhi giving rise to early Homo with A. africanus giving rise to A. sediba, which then goes extinct.  The advantage of this is that A. garhi has modern-like limb proportions and is found in northeast Africa, not far from early Homo, while A. africanus and A. sediba are both found in south Africa.

 

Which one of these is right?  Are any of them right?  Who knows.  What we do know is that these critters have relationships to each other in some way, shape or form.  

Au. sediba Now Considered Possible Ancestor to Homo

New research is suggesting that the overall anatomy of Australopithecus sediba makes it the best candidate for being ancestral to Homo.  The article in Science Daily is quite long and delves into the specific traits that Lee Berger suggests are thought to evolving in the direction of Homo.  They write:

Lee Berger, the project leader from the University of the Witwatersrand in Johannesburg, South Africa, explains what these new findings mean for modern humans. "The many advanced features found in the brain and body, along with the earlier date, make it possibly the best candidate ancestor for our genus -- the genus Homo -- more so than previous discoveries, such as Homo habilis"
The age of the Au. sediba fossils has been constrained to about 1.977 million years, which predates the earliest appearances of Homo-specific traits in the fossil record. Until now, fossils dated to 1.90 million years ago -- and mostly attributed to Homo habilis and Homo rudolfensis -- have been considered ancestral to Homo erectus, the earliest undisputed human ancestor. But, the older age of these Au. sediba fossils raises the possibility of a separate, older lineage from which Homo erectus may have evolved.

This position seemed odd to me at first because there is already evidence of “early Homo” dating back to 2.3 million years ago. Then it occurred to me that this article makes a tacit assumption that is not stated: Homo habilis and Homo rudolfensis are not really Homo, but are Australopithecus. This is an argument that has been made by Alan Walker and Bernard Wood who suggest that, despite the size differential between H. rudolfensis and the late australopithecines, they are more similar than different.This levels the playing field and then Au. sediba simply becomes the branch of Australopithecus from which Homo sprung.

Taxonomy is a black art and we run the risk of tying too much significance to our taxonomic designations.  If we argue that Au. sediba gave rise to H. ergaster, despite the fact that there are already two species of Homo running around, it conjures up ideas of convergent evolution where an earlier australopithecine gave rise to Homo habilis and Au. sediba gave rise to Homo ergaster.  If, however we demote earliest Homo down to australopithecine status, the difficulties vanish “like the snows of yesteryear” as Isaac Asimov would say.  Look for this to be challenged as well. 

First Use of Fire in Europe Later Than Thought

New Scientist is reporting that examination of the earliest evidence of controlled fire in Europe has pushed it forward in time to around 400,000 years ago. Jessica Hamzelou writes:

To try to pin down the earliest evidence of controlled fire use, Paola Villa at the University of Colorado in Boulder, and Wil Roebroeks at Leiden University in the Netherlands re-examined the data from over 100 European sites. They were looking for evidence of fires that were unlikely to have occurred naturally – those in caves, for example – and for clues that fire had been used in a controlled way. These include activities such as making pitch: some early hominins made this sticky substance by burning birch bark and using it to glue pieces of flint to wooden handles to make stone tools easier to use.

She continues:

Although Villa and Roebroeks investigated only European sites, they think evidence of controlled fire use at a number of other sites is also up for debate. The Swartkrans site in South Africa is believed by some to contain 1.6 million-year-old evidence in the form of hundreds of charred bones. "But these might just have been sporadic natural fires that were taken advantage of," says Villa. In fact, just one site earlier than the 400,000 year mark has strong evidence of controlled fire use, the pair says: the 780,000-year-old Gesher Benot Ya'aqov site in Israel.

The earliest evidence in Asia is in the Homo erectus/ergaster site of Zhoukoudian, where it is estimated to be around 400 ky also. This does, indeed, suggest that early humans use of considerable resourcefulness without the use of fire. I am betting though, that even Spain during the Mindel and Riss glaciations was pretty cold. I would not be surprised if evidence was discovered that pushes the use of controlled fire back a bit.