News on South Africa’s Hominins: Berger’s Rising Star Expedition

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This November, a team funded by National Geographic and led by Lee Berger of the University of Witwatersrand in Johannesburg made a huge find. 1200 hominin skeletal elements were recovered from a South African cave, representing at least 12 individuals. Human remains are pretty rare, and this one site contains more human fossil material than the rest of South Africa combined, according to Berger.  While I’m sure the researchers have their hunches, they have so far been cryptic about species attribution. Dates have also yet to be determined for the collection.

Only months passed between the original discovery of the cave and the excavation of the remains. Berger quickly mobilized a 60 person team and secured funding from National Geographic to conduct a field season (the team came to be called the Rising Star Expedition). Though the remains had been in the cave for perhaps millions of years, it was impossible to know if they would survive another rainy season, which was fast approaching in November.  Unlike most other fossils of the same antiquity these were sitting in loose sediments, which are easier to excavate than breccia but could likely make the bones more fragile.

In order to access the chamber with the fossils, scientists must squeeze through a seven inch opening.  While it has been suggested that the cave opening be widened, Berger doesn’t think a cave that has been forming for millions of years should be updated so that the project directors can stand over the finds. For this reason, small-bodied paleoanthropologists and archaeologists were recruited from all over the world to participate in the fieldwork. In fact, because of size, Berger sent his 15 year old son Matthew in to verify there were in fact human remains in the preliminary stages of the project.

Lee Berger with A. sediba. Photo credit Eloff.

Lee Berger with A. sediba. Photo credit Eloff.

While the finds coming from this project are remarkable, the way in which Berger has been directing the project has been equally fantastic. Typical fossil finds (see recent post on Ardi, for an example) are guarded for years, sometimes over a decade. Frequently only select researchers are able to access the material and data, which makes it difficult for publications to be critiqued or built on by other scientists.  Berger has gone the opposite direction, making fossils less his and more open-access. He already set the stage for this type of protocol with A. sediba, which was published in 2010 shortly after being unearthed.

Transparency and collaboration wasn’t enough for leaders of the Rising Star Expedition, though. Last week, they announced a call for applications to work on the fossil material, especially for early-career scientists.  Successful applicants will have their expenses covered to travel to South Africa for the month long project, which is guaranteed to generate some high-impact publications.  This type of cooperative research is unheard of, and will provide significant opportunities for future generations of paleoanthropologists.  If I didn’t specialize in stone tools, my application would’ve already been in.

The work of Berger’s team is commendable, and they will undoubtedly out produce most other proprietary, territorial paleoanthropologist in both quantity and quality. It will be interesting to see what else the cave yields next season, since literally only centimeters on the surface of a relatively small area have been scratched.

Matthew Magnani

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Ramidus Returns

Ardipithecus ramidus (Ardi) is back. In 2009, the skeleton discovered by Tim White’s team in the mid-90s was published in full. Dated to approximately 4.4 million years old based on volcanic stratigraphy, ramidus was found in the Middle Awash river valley in Ethiopia. The most complete individual, over 40% of a female skeleton, had the brain approximately the size of a chimp and exhibited a similar level of facial prognathism. Hand and foot morphology pointed to an arboreal creature, most notably a divergent big toe that would make many primates proud.

However, ramidus exhibits a bunch of other traits which seemed derived in the direction of Homo, which is what the authors of the study are pushing. These traits include reduced canines, and aspects of the foot and pelvis which could indicate a level of at least facultative bipedalism.  Critics argue that it is possible that these traits were present in many apes of the time period around the human-chimp split, and that chimps rather than humans moved away from these adaptations.

Ardipithecus ramidus from White et al. 2009

Ardipithecus ramidus from White et al. 2009

The new study published in PNAS furthers the original argument made by the discoverers that Ardi is in fact a hominin.  In particular, the reconstructed basicranium was observed in the study, led by William Kimbel of Arizona State University. Kimbel and his team demonstrate that like Homo and Australopithecus, Ardi had a short basicranium, and a relatively anteriorly placed foramen magnum. The placement of the foramen magnum, in particular, is particularly important in determining whether or not a species was bipedal. Along with the broadening of the cranial base, came notable modifications/shifting of tympanic elements and other foramena.  In short, the authors put forward the argument that because of the age of ramidus, it is possible to say that these types of changes in the cranial base were some of the earliest derivations towards Homo.

Paleoanthropologists are in a tough place. Inferring descent through morphology alone is tough, but it is all fossils really give us right now. This was just demonstrated in an even more recent case where H. heidelbergensis was demonstrated to be more closely related to Denisovans on its matriline than Neandertals, with whom they shared many morphological affinities. Going back millions of years doesn’t make it any easier, and we’re not going to be recovering 4.4 million year old DNA any time soon to help give answers. Till then here’s to the many personalities of paleoanthropology, who direct our understanding of human evolution with biology, anthropology, and sometimes a sprinkling of ego.

Matthew Magnani

A Higher Than Average Risk Of Diabetes Among Mexicans Linked To Neandertal Introgression

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Why do some populations have increased incidences of chronic disease? Why do blacks have hypertension more than whites? Why does a Mexican have 2.72 more the risk of having Type 2 Diabetes compared to a non-Hispanic person? A new paper published in Nature yesterday outlines a particularly interesting finding about rhetorical questions about metabolic disease… One that I’ll digest in this post.

David Altshuler and his colleagues conducted a GWAS comparing 8,214 Mexicans and other Latin Americans. They specifically had 3,848 people with type 2 diabetes and 4,366 non-diabetic controls. They compared over 9.2 million SNPs. They found a unique SNP, SLC16A11, that codes for a transmembrane transporter of monocarboxylates and triacylglycerols.

Graphical depictions of SLC16A11 haplotypes constructed from the synonymous and four missense SNPs associated to type 2 diabetes, with haplotype frequencies derived from the 1000 Genomes Project and SIGMA samples. AFR, African (n = 185); ASN, east Asian (n = 286); EUR, European (n = 379); MXL, Mexican samples from Los Angeles (n = 66). Frequencies from SIGMA samples are calculated from genotypes and represent either the entire data set (All) or only samples estimated to have ≥95% Native American ancestry (≥95 NA, n = 290; Supplementary Methods). Haplotypes with population frequency <1% are not depicted.

Graphical depictions of SLC16A11 haplotypes constructed from the synonymous and four missense SNPs associated to type 2 diabetes, with haplotype frequencies derived from the 1000 Genomes Project and SIGMA samples. AFR, African (n = 185); ASN, east Asian (n = 286); EUR, European (n = 379); MXL, Mexican samples from Los Angeles (n = 66). Frequencies from SIGMA samples are calculated from genotypes and represent either the entire data set (All) or only samples estimated to have ≥95% Native American ancestry (≥95 NA, n = 290; Supplementary Methods). Haplotypes with population frequency <1% are not depicted.

The authors found that why Mexican Americans are twice as likely to develop type 2 diabetes is because about 50% of the population carry the four amino acid substitution risk haplotype. In comparison, 20% of Asians have it, only 2% of Europeans carry the mutations, and no Africans. The risk for Type 2 diabetes for a Mexican increases from 13% to 19% if they inherit two copies of the mutations, but others the risk only increases to about 11% from 8%. They tend to carry this one sequence of DNA more than people with only African or European ancestry.

Why and where did this increased frequency of SLC16A11, come from? The haplotype sequence is highly divergent, with an estimated TMRCA of 799,000 years to a European haplotype. This date long precedes out of Africa but yet it’s not observed in Africa and rare in Europe. When the authors compared it to the published Neandertal genome and the Denisova genome, they found no similarities.

Denisova Pedal Phaylnx

But when they compared it to the unpublished genome of the Neandertal from Denisova Cave they found that individual was homozygous across 5 kb for the 5 SNP haplotype at SLC16A11, including all four missense SNPs, outlined above. This indiciates that the risk haplotype introgressed into modern humans via admixture with Neandertals.

The impact of Neandertal introgression is now well-known. Up to 4% of our genomes, for those of us who are non-African, have Neandertal sequences in them. Does this mean that Mexican’s have more than the average admixture? No. The authors write, 

“We note that whereas this particular Neanderthal-derived haplotype is common in the Americas, Latin Americans have the same proportion of Neanderthal ancestry genome-wide as other Eurasian populations.”

We know obesity and diabetes are two epidemics that are hand in hand. As SLC16A11 codes for a protein that transports lipids, any changes to its structure and function can change the amount of a type of fat which moves in and out of a cell. These findings suggest that some Mexicans and even Asians inherited a variant of SLC16A11 from Neandertals, which increases risk of type 2 diabetes.

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.

 

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.

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