Anthropology.net

We’ve covered the mitochondrial genome of the Denisova individual 2 years ago, back in March 2010. For those not familiar with the Denisova hominin, this specimen represents an archaic human species present at least 41,000 years ago – coexisting with Neandertals and modern humans in the Altai Mountains of Siberia. The species is represented by a tooth and phalange.

A draft of the genome was released shortly afterwards in December, 2010. Today, after 30-fold coverage of the genome using Illumina GAIIx sequencing platform, the complete genome was released. It is free to download and use on Amazon Web Services… weighing in at 160gb.  I can imagine a lot of interesting comparisons can be made with this dataset and am happy the researchers made it available to the public.  There’s a caveat though, you can use the data but however agree that you cannot publish your findings until the researchers at Max Planck first get a stab at it.

By Jay Fancher

Oil transformed Dubai in the 1970s. The city now boasts the world's tallest building, giant malls, and some two million residents, who depend on desalinated seawater and air-conditioning—and thus on cheap energy—to live in the Arabian desert. (Credit: Jens Neumann/Edgar Rodtmann/NATIONAL GEOGRAPHIC)

To paraphrase Carl Sagan, science has a way of deflating human conceits.  Anthropology reveals that humans are special – just not for many of the reasons proposed throughout our history.  Thanks to biology, astronomy, and geology, we now know that:

• Modern humans are one species among many, not the pinnacle of all creation.

• We’re not the center of the universe; our planet orbits a fairly average star.

• We haven’t been around since the beginning of time – far from it.

On a 4.5-billion-year-old planet, with a 3.5-billion-year history of life, anatomically-modern Homo sapiens only go back about 200,000 years.  We’re brand new, a tiny blip on the geologic time scale!  Despite this, a new National Geographic article explores the possibility that the “Anthropocene” may have already begun.  Here is a brief excerpt:

Enter the Anthropocene—Age of Man It’s a new name for a new geologic epoch—one defined by our own massive impact on the planet. That mark will endure in the geologic record long after our cities have crumbled…Probably the most obvious way humans are altering the planet is by building cities, which are essentially vast stretches of man-made materials—steel, glass, concrete, and brick. But it turns out most cities are not good candidates for long-term preservation, for the simple reason that they’re built on land, and on land the forces of erosion tend to win out over those of sedimentation.

The author of the article, Elizabeth Kolbert, graciously agreed to an interview with Anthropology.net.  The text of our discussion, conducted via e-mail, follows:

Fancher: The greatest strength of anthropology is its all-encompassing view of humanity.  We’re proud of this breadth, frequently describing our work as the study of all people, in all times, and all places.  But, as you state in your article, stratigraphers take an extremely long view – the entire 4.5-billion-year history of Earth.  How can students of the human past benefit from this geological perspective?

Kolbert: I’m not sure I have a good answer for this.  As all anthropologists know, we are a young species.  So human history doesn’t tell us much about earth history.  What is particularly alarming about a lot of recent discoveries in geology is that you have to go way, way back – i.e., tens of millions of years – to find analogues for some of the things we are doing today, like, for example, acidifying the oceans.

Fancher: I was surprised to read that our proudest technological achievements might not be easy to recognize in the geological record.  It’s humbling to think that urban centers will ultimately be as fleeting in the geological record as short-term hunter-gatherer camp sites are in the archaeological record.  Despite our human desire to leave huge, everlasting monuments, is it better not to be noticed in the geological record?

Kolbert: Well, it’s not clear that we will be noticed, because it’s not clear there’s going to be anything around to notice us.  But we will be noticeable.  And certainly from the standpoint of the other organisms on earth, it would be a lot better if our impact were not so obvious.

Fancher: Some issues of scientific classification appear to have little practical relevance.  For example, the debate over whether Pluto qualifies as a planet or not.  In your article, Dutch chemist Paul Crutzen concludes that the value of the Anthropocene classification goes far beyond textbook revisions.  Can you elaborate on the meaning of the Anthropocene?

Kolbert: Officially, we live in the Holocene, or “wholly recent” epoch.  The Anthropocene translates basically as the man-made epoch.  It’s an acknowledgment that humans, rather than what are sometimes quaintly called “the great forces of nature,” have become the driving force on the planet.

Fancher: How might recognition of a geological epoch called the Anthropocene influence human behavior?

Kolbert: I end the piece with a quote from Paul Crutzen, the Nobelist who coined the term.  Crutzen says, “What I hope is that the term ‘Anthropocene’ will be a warning to the world.”  I think what he means by that is: we are now in the driver’s seat.  Unfortunately, we don’t really know how to operate the vehicle.  So we’d better think about what we’re doing very carefully.

Many thanks to Elizabeth Kolbert for writing such a thought-provoking article, and for agreeing to this interview.  Enter the Anthropocene – Age of Man is part of National Geographic magazine’s year-long coverage of the global human population reaching 7 billion.

What do you think about the possibility of a geological epoch called the Anthropocene?

Carol Ward1, William Kimbel, and Donald Johanson have published a paper in Science on the arch seen in a newly discovered fourth metatarsal of Australopithecus afarensis (AL 333-160). A lot of the popular press are publishing misleading headlines that this proves bipedalism in australopithecines. No, we’ve known they were bipedal — we just didn’t have a true idea as to what extent they were bipedal. So a find like this helps investigate the degree of bipedalism.

AL 333-160 left fourth metatarsal in dorsal, lateral, medial, plantar, and proximal views.

How does this tell us how bipedal A. afarensis were?

) Box plots of angular relations of the proximal and distal metatarsal ends to the diaphysis in chimpanzees, gorillas, humans, and AL 333-160.

If you’ve ever had the pleasure of visiting a podiatrist, you’d know flat feet are not conducive to bipedalism. The two-way arch helps support upright walking and distribute recoil force. Other great apes like, chimps and gorillas have flatter feet than us. The authors of this paper confirmed this by comparing the fourth metatarsal of chimps, gorillas, and humans to AL 333-160.

On all their comparisons, AL 333-160 fell within range of humans. There were some occasions where there’s a lot of gray area which I’ll address later. Nonetheless, to the right you can see the best comparison, in my opinion, which the comparison of the arch of the diaphysis of the bone between the two species. You can have a look at the rest of the figures here.

The problem I am seeing here is that this metatarsal is not Lucy’s (AL 288-1). AL 333 is designated to fossils from the site where the “First Family” came from and not the same  locality as AL 288. Nonetheless, they are not the same individual. Kimbel is quoted in the BBC News, saying,

“Lucy’s spine has the double curve that our own spine does,” Professor Kimbel said.

“Her hips functioned much as human hips do in providing balance to the body with each step, which in a biped of course means that you’re actually standing on only one leg at a time during striding.

“The knees likewise in Lucy’s species are drawn underneath the body such that the thighbone, or femur, angles inwards to the knees from the hip-joints – as in humans.

“And now we can say that the foot, too, joins these other anatomical regions in pointing towards a fundamentally human-like form of locomotion in this ancient human ancestor.”

This is a flawed association to make; a form of what I would call confounding bias. We don’t have Lucy’s 4th metatarsal to see what it looks like and unfortunately we don’t have the rest of the this specimens skeleton to say it looked like Lucy’s. In fact, we have very little australopithecine appendicular and skeletons other than AL 288-1 (most notable are AL 129-1 and STS 14). So how can Kimbel say that the foot joins other anatomical regions when we don’t know what the other regions really looked like?

See, the n of this sample is 1. Looking at the intervals in the figures, especially Fig 3 & 4, there a a significant amount of variation in humans and chimpanzees that overlap. Chimps aren’t bipedal but we are. So imagine you are a paleoanthropologist way in the future looking at one metatarsal of a now-current then-ancient chimpanzee way and comparing it to a humans — surely you could make the same conclusion as these three have. And herein lies the big issue with sensationalism… as is the problem often in paleoanthropology, we just don’t have many comparative samples but people want definitive conclusions.

Ward, C., Kimbel, W., & Johanson, D. (2011). Complete Fourth Metatarsal and Arches in the Foot of Australopithecus afarensis Science, 331 (6018), 750-753 DOI: 10.1126/science.1201463

Hans-Peter Uerpmann of the University of Tubingen has lead a team excavating the Jebel Faya site in the United Arab Emirates, right near the Straits of Hormuz. They’ve found 125,000 year old stone tools that look like early modern human tools from East Africa around the same time. They’ve published their findings in today’s Science, under the title, “The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia.”

The current understanding is what we know as anatomically modern humans (AMH) originated in Africa about 250,000 years ago. The oldest Home sapiens, known as H. sapiens idaltu, was found to be 160,000 years old, found at the Middle Awash site in Ethiopia. Then between 80k-100k years ago, modern humans began appearing in the middle east, as remains from sites like the Qafzeh cave in Israel have yielded. Most agree that AMH stayed in Africa and about 140,000 years ago they began migrating out. There was an exception, a colonization remained or failed in Israel about 100,000 years ago.

One of the hand axes from Jebel Faya, UAE (Photograph courtesy Science/AAAS)

These hand axes, pictured above, show a pattern of flaking distinct from that made by Neandertals and also dissimilar to those by ~100,000 year old Israeli tools. They are two sided and very similar to stone tools seen only in early Africa.

What this means is early humans left Africa 20,000 years earlier than thought. Just how did they do it? 130,000 years ago, there was a window of climate change. They figured this out by using luminescence dating to determine the age of sand grains buried with the stone tools. Luminescence dating is a technique that measures naturally occurring radiation stored in the sand. The data showed that 130,000 years ago, the Arabian Peninsula was relatively more warm which caused more rainfall, turning it into a series of lush habitable land. During this period the southern Red Sea’s levels dropped and was only 2.5 miles or 4 km wide. This offered a brief window of time for humans to easily cross the sea and cross the Peninsula to opposing sites like Jebel Faya.

Does this study tell us that modern humans left Africa, into Arabia and out from there? It is most certainly a possibility. However, these axes could be of an abandoned migration like the site in Israel I’ve mentioned. I say that because no genetic clade, be it from mitochondrial, Y-chromosome, or somatic genome, shows an earlier divergence of modern humans from Africa earlier than 60,000 years ago. At the very minimum a find like this tells us humans left Africa a bit sooner than we thought, but does not really tell us that these were the humans that helped seed the Eurasia.

Armitage, S., Jasim, S., Marks, A., Parker, A., Usik, V., & Uerpmann, H. (2011). The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia Science, 331 (6016), 453-456 DOI: 10.1126/science.1199113

Neandertals have long been touted as a species with “hyperarctic” adaptations. Their stout proportions and shortened distal limb segments are often explained to conserve heat. Similarly, the Neandertal cranium is traditionally said to be cold adapted. An article released on December 22^nd in the Journal of Human Evolution challenges these traditional notions, specifically those about Neandertal nasal adaptations.

The Neandertal nasal apparatus has conventionally been cited as cold adapted mainly because of the enlarged sinuses. The authors of this article, among them Chris Stringer, cite evidence that larger sinuses are not in fact typical of cold weather mammalian species.

Through observation of human populations and studies on other mammals, cold weather is more highly correlated with smaller sinuses. That is, animals from more northerly locations typically have smaller sinus cavities. As an example taken from lab studies, rats raised in colder conditions also show smaller sinus cavities.

But are Neandertal sinuses even large, as is typically maintained? The authors of this paper argue that there is nothing large about them. Through examination of Neandertal remains, the sizes of the frontal and maxillary sinuses actually fell within the range of Homo sapiens from temperate climates.

The Forbes’ Quarry Neandertal (left) and H. sapiens skulls. Frontal sinus in purple, maxillary sinus in red. Photo from Rae et al., 2010.

This study is very suggestive that Neandertal nasal anatomy is not due to cold weather adaptation. To be cold weather adapted, the sinuses would be smaller and not larger, as many anthropologists have maintained since the first remains were discovered. Not only are the sinuses not small, they are not large- which speaks to a larger problem. How many other basic assumptions do we take as fact just because they have been around for so long?

If not cold weather, what could have caused the differences in facial anatomy between H. neanderthalensis and H. sapiens? The authors of this paper do not offer many answers, but offer a couple of possibilities. Differences in masticatory stress (utilizing teeth as a tool, for example), or genetic drift are two potential reasons discussed.

This paper may be taking another step in overturning traditional understanding of Neandertals as a cold weather species. Generations of anthropologists have passed knowing that Neandertals differed in facial anatomy due to cold weather adaptation, unsubstantiated by data.

Rae, T.C., Koppe, T., Stringer, C.B. (2010).  The Neanderthal face is not cold adapted.  The Journal of Human Evolution. Article in Press.

FOXP2 is thought to be a language gene. It is highly conserved in most mammals but in humans there are two unique mutations in the protein caused by nucleotide substitutions at positions 911 and 977 of exon 7. It is thought to be a language gene because humans who have one FOXP2 copy have speech impediments and deficiencies in orofacial movement.

Now with all the progress in sequencing the genome of Neandertals, it seems like some anthropologists and biologists from Max Planck and institutions in France and Spain got curious about finding out the whether or not Neandertals have the same two mutuations as modern humans do in their FOXP2 gene.

Their work has been published today, in Current Biology under the following title, “The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals.” Thanks to one of our readers, Hugo, who sent me this paper I’ve had a chance to read this outstanding paper. Now, if you’ve been keeping track of the Neandertal genome project, I know what you’re thinking, “What about the inconsistencies with Neandertal sequences!?!”

Well the authors, Johannes Krause and team, were very careful about this from the beginning. They made sure the two bones from El Sidrón cave in Asturias were extracted under sterile condition. They also amplified the FOXP2 gene using Neandertal specific primers. That was done so that little to no modern human genes shoulda been targeted for amplification.

After a whole lot of cycles, sequencing, and alignment, the team found out that the Neandertals carried FOXP2 that was identical to that of present-day humans in the only two positions that differ between human and chimpanzee. Speicifcally, at position 911 on exon 7 of the Neandertal FOXP2, threonine is swapped for aspartic acid just like humans and also at position 977 of the Neandertal FOXP2, arginine replaces serine… just like in humans. Sending the samples to other lab to reproduce the experiments yielded the same results.

While the authors are a bit cautious, saying that the whole genome of the Neandertal will provide much more resolution in comparing FOXP2 genes, I do want to point out that this new finding messes up the results of Pääbo, who showed that the mutations in FOXP2 in modern humans were very recent, maybe less than 200,000 years ago in 2002. The authors kinda sorta challenge Pääbo’s conclusion,

“Leaving out the unlikely scenario of gene flow [between the two lineages], this establishes that these changes were present in the common ancestor of modern humans and Neandertals. The date of the emergence of these genetic changes therefore must be older than that estimated with only extant human diversity data, thus demonstrating the utility of direct evidence from Neandertal DNA sequences for understanding recent modern human evolution.”

So the common ancestor of Neandertals had this unique allele of FOXP2. Does that mean they had language capabilities? Does this mean Neandertals had language capabilities… I’d sure hope so because at this point in human evolution, erectines like Neandertals and their culture were widespread. Their ability to communicate in some higher form or another was crucial for their ubiquity in Europe and Asia.