A Fourth Unknown Early Human Lineage?

A couple of days ago, Nature published a comparison of the genome of a 50,000-year-old Neandertal woman with those of modern humans and Denisovans. The group revealed evidence of interbreeding among at least 4 species of early humans.

Family tree of the four groups of early humans living in Eurasia 50,000 years ago and the gene flow between the groups due to interbreeding. Image credit: Kay Prüfer et al.

Neandertals and Denisovans diverged 300,000 years ago, both of which eventually died out, they left bits of their genetic heritage because they occasionally interbred with modern humans. It is estimated about 1.5 – 2.1% of modern non-African’s can be traced to Neandertals and for Denisovans, only about 6% of Oceanic populations like aborigines, New Guineans, and about 0.2% of Han populations show footprints.

The genome comparisons show that Denisovans interbred with a mysterious, fourth group of early humans also living in Eurasia at the time. That group had split from the others more than a million years ago, and may have been the group of human ancestors known as Homo erectus, which fossils show was living in Europe and Asia at the time.

This current study also indicates that this female Neandertal was highly inbred. She was the daughter of a very closely related mother and father who either were half-siblings who shared the same mother, an uncle and niece or aunt and nephew, a grandparent and grandchild, or double first-cousins. Further analyses suggest that the population sizes of Neandertals and Denisovans were small and that inbreeding may have been more common in Neanderthal groups than in modern populations.

 

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A New Twist in the Neandertal Lineage

Just in from Atapuerca, northern Spain: mitochondrial DNA has been retrieved from the bones of Homo heidelbergensis.

The Sima de los Huesos, or pit of bones, has been a treasure trove of human remains, and has yielded a minimum number of 28 individuals dating to at least 300,000 years ago. This type of preservation and concentration of human remains is rare—most excavations are lucky to turn up a stray hominin tooth every couple of seasons.

Homo heidelbergensis cranium number five from the Sima. Photo by José-Manuel Benito Álvarez

Homo heidelbergensis cranium number five from the Sima. Photo by José-Manuel Benito Álvarez

Not to mention mitochondrial DNA typically does not have such a long shelf-life. After a successful attempt at analyzing cave bear DNA from the Sima, researchers decided to risk portions of valuable human remains for testing. The MtDNA did turn out to be viable, and the provided some seriously unexpected results.

The Heidelberg femur that yielded the mtDNA. Image from Meyer et al. 2013.

The Heidelberg femur that yielded the mtDNA. Image from Meyer et al. 2013.

The outcome of the mtDNA analysis demonstrates that the Sima matrilineal tree shares its roots with Denisovan populations, a group of archaic humans discovered recently in Siberia. Previously it would have been expected that the Sima Heidelberg mitochondrial genome would share most affinities with Neandertals.

So what exactly does this mean for our current understanding of human evolutionary models?

The findings imply that the Sima hominins share a common ancestor with Denisovans rather than Neandertals. For a long time, the Heidelberg population of the Sima was looked at as a group of hominins en route to becoming Neandertals—now the picture isn’t as clear.

It is possible that the Sima hominins are a distinct line of humans that later contributed genetically to Denisovans. This wouldn’t however explain the morphological traits they exhibit which are consistent with Neandertals, and would mean the same traits evolved in two separate contexts.

It is also possible that the Sima population was ancestral to both Neandertals and Denisovans. This answer would require further explanation for why the genomes of Neandertals differ significantly from the recently sequenced genome, though.

Right now, there isn’t one answer.  As DNA processing methodology gets better and better, the picture of what was going on will become more evident. We’ve only begun to scratch the surface of what was really going on, and it’s going to get a lot more complicated before it gets any clearer.

Matthew Magnani

 

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HSV-1 Phylogenetics As A Model for Human Migrations

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 World map featuring the geographic location of the 6 HSV-1 clades with respect to human migration. Each clade — or variant — is depicted by a roman numeral inside a circle. Land migration is depicted by yellow lines and air/sea migration is shown by the pink line. (Kolb, Brandt, et al/PLoS)

World map featuring the geographic location of the 6 HSV-1 clades with respect to human migration. Each clade — or variant — is depicted by a roman numeral inside a circle. Land migration is depicted by yellow lines and air/sea migration is shown by the pink line. (Kolb, Brandt, et al/PLoS)

This has been done before using H. pylori as a model, but it is remarkable nonetheless to see how innovative researchers are in using different models to track human migration patterns… this time with HSV 1 or human simplex virus 1.

For the study, which is published in the open access journal PLoS ONE, the researchers compared 31 strains of HSV-1 collected in Africa, Europe, Asia, and North America. They then mapped patterns of mutations using high-capacity sequencing and to reconstruct cladograms. They were able to support what anthropologists and molecular geneticists have already — that humans originated in Africa, spread out into Europe and Asia, and then ultimately crossed the Beringia “land bridge” into North America.

 Phylogenetic network — Clade I includes European/North American strains, Clade II comprises East Asian strains and III, IV, V and VI are East African. HSV-2 was used as an outgroup. Splitstree 4 was used to generate the network. The viral isolates are colored according to country of origin and are as follows: U.S.A: light blue, U.K.: dark blue, China: red, South Korea: purple, Japan: orange, and Kenya: green. (Kolb, Brandt, et al/PLoS)

Phylogenetic network — Clade I includes European/North American strains, Clade II comprises East Asian strains and III, IV, V and VI are East African. HSV-2 was used as an outgroup. Splitstree 4 was used to generate the network. The viral isolates are colored according to country of origin and are as follows: U.S.A: light blue, U.K.: dark blue, China: red, South Korea: purple, Japan: orange, and Kenya: green. (Kolb, Brandt, et al/PLoS)

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D4500 & D2600, A Complete Skull from Dmanisi, Georgia

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The face of Skull 5. Credit: Guram Bumbiashvili, Georgian National Museum

The face of Skull 5. Credit: Guram Bumbiashvili, Georgian National Museum

A complete 1.8 million year old skull found from Dmanisi, Georgia could be evidence that early hominids are actually all members of a single species. Researchers published their analysis in Science today and argue that the skull’s combination of primitive and more evolved features, such as a small braincase (546 cubic cm) with a large prognathic face.., Similar morphological affinities with the earliest known Homo fossils from Africa, which make it difficult to classify by now accepted definitions of early hominid species.

The Role Of Climate On African Stone Age Technology

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Nature Communications published an article in May, 2013 that just now caught my eye. The paper’s title, “Development of Middle Stone Age innovation linked to rapid climate change,” lays down a solid understanding of what the authors found… The one line summary of the article is: the authors observed that very abrupt changes in rainfall in South Africa, about 40,000 – 80,000 years ago, correlated with the development of new technologies.

Stone tools known as bifacial points recovered from Blombos Cave, South Africa. They were made during the Middle Stone Age, about 75,000 years ago, by anatomically modern humans. Scale bar: 1 cm (0.4 inches). CREDIT: Courtesy of Christopher Henshilwood, University of the Witwatersrand

Stone tools known as bifacial points recovered from Blombos Cave, South Africa. They were made during the Middle Stone Age, about 75,000 years ago, by anatomically modern humans. Scale bar: 1 cm (0.4 inches).
CREDIT: Courtesy of Christopher Henshilwood, University of the Witwatersrand

The global climate of last million years varied between glacial and interglacial periods. These changes occurred about every 100,000 years. But within these long-term periods there have been shorter blips of climate changes, sometimes happening in the span of just a few decades. During these short blips, variations of up to 10ºC in the average temperature of the polar regions are caused by changes in the Atlantic ocean circulation, which ultimately affected rainfall in southern Africa.

Signs of modern human culture - symbolic artifacts from around 75,000 years ago unearthed from Still Bay at Blombos Cave, South Africa: a) bifacial foliate point, b) bone tool, c) engraved ochre, d) shell beads, e) engraved bone. Credit: Christopher Henshilwood

Signs of modern human culture – symbolic artifacts from around 75,000 years ago unearthed from Still Bay at Blombos Cave, South Africa: a) bifacial foliate point, b) bone tool, c) engraved ochre, d) shell beads, e) engraved bone. Credit: Christopher Henshilwood

By analyzing river delta deposits, the researchers of this paper have pieced together how rainfall patterns varied in southern Africa over the last 100,000 years. Every millimeter of sediment core corresponds to 25 years of sedimentation. The ratio of iron to potassium in the layers is a record of the sediment carried by rivers and of the rainfall throughout the period. With that the authors were able to see patterns in the climate… As the South African climate changed rapidly towards more humid conditions, the northern sub-Saharan Africa experienced widespread droughts, and the Northern Hemisphere entered phases of extreme cooling.

The reconstruction of the rainfall over 100,000 years shows a series of spikes that occurred between 40,000 and 80,000 years ago. These spikes show rainfall levels rising sharply over just a few decades, and falling off again soon afterwards, in a matter of centuries. The climate changes coincided with abrupt emergence of material culture and modern behaviour such as the beginnings of symbolic expression, the making of tools from stone and bone, jewellery and the first agricultural settlements. And in turn, the end of certain stone tool industries of the period coincides with the onset of a new, drier climate.

Climate change during the Middle Stone Age in Southeast Africa

Climate change during the Middle Stone Age in Southeast Africa

The findings confirm one of the principal models of Palaeolithic cultural evolution, which correlates technological innovation with the adoption of new refuges and with a resulting increase in population and social networks.

 

Light Warlpiri, A Newly Discovered Australian Mixed Language

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Linguist Carmel O’Shannessy wrote to the journal Language of a newly discovered language, Light Warlpiri. Her correspondence, “The role of multiple sources in the formation of an innovative auxiliary category in Light Warlpiri, a new Australian mixed language,” documents 300 people in a remote desert community about 644 kilometres from Katherine, a town in Australia’s Northern Territory, speaking in a striking auxillary system. She believes it emerged in the 1970’s and 80’s.

The language draws on traditional Warlpiri, which is spoken by about 6,000 people in indigenous communities scattered throughout the Tanami Desert along with Kriol, an English-based Creole language spoken in various regions of Australia; and English. In the Warlpiri language, words can be placed in any order, and grammatical interpretations are based on suffixes that are attached to the nouns. And the imported words have changed meanings so that the structure of the auxiliary model is not the same as they were in the source languages. O’Shannessy explains,

“In Light Warlpiri, you have one part of the language that mostly comes from English and Kriol, but the other grammatical part, the suffixing, comes from Warlpiri.”

Another distinction of the newfound language is a word form that refers to both the present and past time, but not the future. For example, in English, “I’m: refers to “I” in the present tense, but Light Warlpiri speakers created a new form, such as “yu-m,” which means “you” in the present and past time, but not the future.

“That structure doesn’t exist in any of the languages that this new code came from, which is one of the reasons we see this as a separate linguistic system, even though it comes from other languages that already exist,

Here’s an interesting example. Blue words in this color are from Warlpiri, and those in that are red are from English or Kriol. Green colored words are for the creative auxiliary system and verbal structure.

De-m run back rarralykaji-kirra jarntu an yapa-wat ngapa-kujaku.
“The dog and the people run back to the car to get out of the rain.”

Simulating The Social Brain Hypothesis

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An Oxford University team of two led by Tamás Dávid-Barrett published an open access paper in the Proceedings of the Royal Society B testing the social brain hypothesis. In a nutshell, the social brain hypothesis was created by the other author of this paper, Robin Dunbar, who theorized in 1993 with anthropologist Leslie Aiello, that intelligence among humans is a function of surviving and reproducing in large and complex social groups and not solving ecological problems.

Social Brain

In order to investigate their hypothesis, they looked at Encephalization Quotient is a measure of brain size relative to body size. The cat’s EQ of about 1, which is expected for its body size. But most primates have brains that are larger than expected for their body size. Chimps have an EQ of 2.5. Humans have almost three times as much, at around 7.5. Dolphins have an EQ of more than 5, and rats and rabbits are way down on the scale — below 0.4. Aiello and Dunbar published their findings, along with a run down in the fossil record, in the widely cited 1993 paper in Current Anthropology. They correlated that the larger a species’ group size, then the larger its brain—particularly the neocortex, the outer layers where most of the serious thinking goes on.

The current paper, “Processing power limits social group size: Computational evidence for the cognitive costs of sociality,” describes how the authors used agent-based modelling to serve up coordination problems to agents. Solving these problems required synchrony of behaviors, meaning each agent had to do the right thing and the right time in just the right way for the group to progress. In effect they simulated in computer models.

They found out that the viability of group size increased as calculation, or figuratively speaking cognitive, capacity increased. Furthermore, their simulations demonstrated the need for complex language through the situations where group size increased and the agents had to switch to deeper information processing strategies that allowed them to differentiate among their problems.

I like research like this, however I do not appreciate how it is digested and regurgitated in the press. The press is running headlines like “Big brains developed big brains to deal with society,” implying that evolution has some goal or some design. This is not true. It is true however, sociality is a selective pressure. And to be social required large frontal lobes, but is not the sole region for human intelligence.

What’s Wrong With Anthropology?

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In December, I linked up Ann Gibbons’ article in Science about anthropology’s poor reception in the scientific community. I forgot to mention that months before that, in August, Kiplinger named anthropology “the worst major for your career.” Two months later, Forbes followed suite and ranked “anthropology and archaeology,” as the No. 1 on its list of “worst college majors.”

Suffice to say, 2012 was a tough year for anthropology, but at least we were number #1 in something! But all kidding aside, increased discussion is a positive outcome from all this criticism. What needs to be done is to increase the worth of studying anthropology.

In April of this year, Ty Matejowsky and Beatriz M. Reyes-Foster, two anthropologists from the University of Central Florida, wrote a guest column in the Orlando Sentinel, on the issue of the lack of “cool” factor in cultural anthropology. They have an empowering message,

Anthropologists need to take better ownership of our brand. The complexity of anthropological concepts such as “culture,” “power” and the “global” should not dissuade anthropologists from engaging in meaningful public discourse.

A couple of days ago, Savage Minds tackled the Orlando Sentinel guest column, saying our problem with our field is not just due to how we sell or brand ourselves, but in actuality how we conduct our work.

And last week, in the AAA blog post Anthropology News continued this discussion. Jennifer Long wrote, “Anthropology’s Response to Finding Jobs for Its Undergraduates.” Her approach general cites that anthropology is rather incestuous. Often those interested in anthropology gain positions within universities as researchers, which creates a bubble. She advocates for an experiential approach, to branch out and apply our field elsewhere… Much like Robin Nagle, an anthropologist-in-residence at the New York City Department of Sanitation. Robin has recently written about trash and how our lives revolved around it. The book is titled, “Picking Up: On the Streets and Behind the Trucks with the Sanitation Workers of New York City,” and Collector’s Weekly interviewed her about it and the NY Times covered a book review about it.

With all this discussion about what’s wrong with anthropology, I want to turn to you, the readers and hear what you think is wrong with the field. Please feel free to comment and let us know what you find issue with the field — is it a branding problem; is it a problem with branching out and how we work?

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Chactún – A Newly Discovered Mayan City

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Last FridayIvan Sprajc led a group of researchers to a site in Campeche, a province in the western Yucatán peninsula, that he initially identified via stereoscopic aerial photographs. He and his group found the ruins of an enormous 54 acre (22 hectares) city, full of artifacts.

Archaeologist Ivan Sprajc led an international team of experts to study the Maya site. CREDIT: National Institute of Anthropology and History

Archaeologist Ivan Sprajc led an international team of experts to study the Maya site.
CREDIT: National Institute of Anthropology and History

The city is named Chactún. Chactún was occupied during the Late Classic Maya period, which spans roughly A.D. 600 until A.D. 900. Some interesting finds include three monumental complexes with the remains of pyramids — one 75 feet (23 meters) high. In addition, they’ve identified ball courts, plazas, homes, altars, bits of painted stucco and stone slabs known as stele. One stele refers to an apparent ruler named K’inich B’ahlam.

This image is from the southeast complex at the newfound Maya city called Chactún. CREDIT: National Institute of Anthropology and History

This image is from the southeast complex at the newfound Maya city called Chactún.
CREDIT: National Institute of Anthropology and History

Unlike other large Mayan cities, Chactún has never been studied by archaeologists before. I’m eager to see what comes from this city, and what insights it provides. Other interesting methods to find archaeological sites have been used in the past, which I’ve written about here, here and here.

A 120,000 Year Old Neandertal from Krapina who had Fibrous Dysplasia

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The internets are buzzing about the news of the earliest known bone tumor on record, predating others by more than 100,000 years. The tumor has been found on the left rib of a 120,000 year old Neandertal from Krapina, Croatia. The original paper is published under the title, “Fibrous Dysplasia in a 120,000+ Year Old Neandertal from Krapina, Croatia” in the journal PLoS ONE.

In the world of pathology, there are many terms to describe growth such as metaplasia, hypertrophy, neoplasia, hyperplasia and dysplasia. Dysplasia defines abnormal growth where cell differentiation is delayed. If a cell is committed to of one of the three germ lines, say ectodermal, a dysplastic cell of that lineage would then remain a ectodermal precursor and not differentiate into the nervous tissue or skin appendage it was programmed to become.

Bone is composed of two types of tissue, compact and trabecular. Compact bone is the dense, outside structure while trabecular or spongy bone is the fibrous layer that you often do not see. Fibrous dysplasia, therefore refers to the abnormal maturation of trabecular bone. Fibrous dysplasia is a benign, non-hereditary process. It was first described in the 1942 by Lichtenstein and Jaffe. The disease process may be localized to a single bone (monostotic) or multiple bones (polyostotic). Up to 80% of cases are monostotic.

Polyostotic fibrous dysplasia can occur as a part of McCune-Albright syndrome. McCune-Albright Syndrome often affects unilateral bones with ipsilateral café-au-lait spots on the skin, and endocrine disturbances such as precocious puberty. Fibrous dysplasia has also been reported in association with other endocrine dysfunctions such as hyperthyroidism, hyperparathyroidism, acromegaly, diabetes mellitus, and Cushing syndrome as well as an associated abnormality in Neurofibromatosis type II. Malignant transformation of fibrous dysplasia is very infrequent, with reported prevalences ranging from 0.4% to 4%.

We know that fibrous dysplasia is caused by a somatic mutation in the GNAS1 gene on chromosome 20q13.2-13.3. GNAS1 encodes the alpha subunit of the stimulatory G protein, Gsα. As a consequence of this mutation, there is a substitution of amino acid arginine in position 201 of the genomic DNA in the osteoblastic cells, by amino acid cysteine (R201C) or histidine (R201H). The abnormal G1 protein stimulates cAMP. Furthermore, proto-oncogene levels of C-fos and periostin are raised in fibrous dysplasia. Consequently, the osteoblasts expressing this mutation have a higher rate of DNA synthesis, leading to the formation of a disorganized fibrotic bone matrix with primitive bone formation, and lack of maturation to lamellar bone.

Figure 1. Krapina 120.71 in a caudal view (a). The large lesion is located above the tubercular facet and extends laterally. The trabeculae have been destroyed and the cortex appears expansive. The thin cortical bone forming the superior surface of the cavern was broken away postmortem. (b) Krapina 120.6 shows the normal pattern of bony trabeculae in the medullary space. The surface irregularities are post-mortem. doi:10.1371/journal.pone.0064539.g001

Figure 1. Krapina 120.71 in a caudal view (a).
The large lesion is located above the tubercular facet and extends laterally. The trabeculae have been destroyed and the cortex appears expansive. The thin cortical bone forming the superior surface of the cavern was broken away postmortem. (b) Krapina 120.6 shows the normal pattern of bony trabeculae in the medullary space. The surface irregularities are post-mortem.
doi:10.1371/journal.pone.0064539.g001

The specimen is Krapina 120.71, a 3 cm long, left rib fragment containing about 2/3rds of the neck, most of the tubercular facet and a small section of the shaft. It is thought to be rib 3-6. It was first unearthed between 1899 and 1905 in a cave known as the Krapina rock shelter in Croatia. This site held more than 900 Neandertal bones dating back 120,000 to 130,000 years ago. Many of the bones display signs of trauma, and a few show post-mortem cutting marks, perhaps indicating cannibalism or some sort of ritual reburial.

In the 1980s, University of Pennsylvania researchers X-rayed the entire collection. They published a book in 1999 showing each radiograph. Most of those X-rays were quite high-quality, but one exception was found in a little rib fragment which appeared “burned out.” That prompted the authors to return to the specimen. They adequately describe an osteolytic abnormality and offer differentials of chondroma, post-traumatic lesion and chronic osteomyelitis, but remain confident with their radiographic diagnosis of fibrous dysplasia via microCT scanning.

Bone lesions in the fossil and archaeological record are extremely rare for several reasons. Without adjacent soft tissue, it is hard to compare normal to abnormal. Furthermore, the decomposition process alters bone dramatically. Previously, the oldest known tumors came from Egyptian mummies and dated back only 4,000 years or so and a 1,600-year-old tumor containing teeth was found in the pelvis of an ancient Roman corpse. So to find a 120,000 year old Neandertal with a osteolytic lesion in the rib is significant.

What I find wrong with this publication is the spin; too often in our world of paleoanthropology do I see issue with people trying to put a particular bend to sell their otherwise interesting story as a sensational headliner. The press is running quotes from the senior author like,

“… indicates that Neanderthals were susceptible to the same types of tumors modern-day humans get, despite living in a remarkably different environment.

‘They didn’t have pesticides, but they probably were sleeping in caves with burning fires,’ says David Frayer, an anthropologist at the University of Kansas and the co-author…”

The problem with the above quotes stem from the conclusion,

“Finally, it is recognized that environmental changes wrought by humans, compounded by population expansion, have resulted in an increase the types and the intensification of the pollutants within the environment, many of which are directly associated with neoplastic disease and were not part of environments in the past [35]. Given these factors, most argue that cases of neoplastic bone disease are rare in prehistoric human populations [27]–[28]. It is against this background that the identification of a 120,000+ year old Neandertal with a primary osteolytic lesion is surprising and one that provides insights into the nature and history of the association of humans to neoplastic disease.”

Putting an emphasis that Neandertals lived in “cleaner” environments and still had susceptibility to the same types tumors is extremely short-sighted. There are most definitely some tumors with strong associations to environmental mutagens, such as tobacco consumption with mouth, throat and lung cancer or asbestos with mesotheliomas… To which I’d venture a hefty bet that Neandertals were not suffering from as much as modern humans are. So to use words like same types of tumors, or phrases like, “lived their lives basically the same way we did and basically with the same problems that we have,” is a stretch.

As explained earlier, fibrous dysplasia is caused a somatic mutation of the GNAS1 gene. Somatic mutations are acquired before birth, in utero, early in fetal development where DNA replication occurs at a rapid rate and errors can be made all throughout. The authors fundamentally neglect a discussion that most mutations are inherent problems in DNA replication, repair, tautomerism, depurination, deamination, and slipped strand mispairing.  A one-sided discussion that one benign bone lesion in one individual is indicative that prehistoric humans contracted the same cancers we do, despite environment, and had the same problems we have is incomplete.

Can we agree to just focus on the science and not extrapolate a faulted connection?

CITATION

Monge, J., Kricun, M., Radovčić, J., Radovčić, D., Mann, A., & Frayer, D. (2013). Fibrous Dysplasia in a 120,000+ Year Old Neandertal from Krapina, Croatia PLoS ONE, 8 (6) DOI: 10.1371/journal.pone.0064539

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