Anthropology.net

The latest issue of the Proceedings from the National Academy of Science journal hosts a Out of Africa: Modern Human Origins special feature for free online. I recommend you check it out.

September 22nd, 2009 Cover of the PNAS Out of Africa: Modern Human Origins Special

• Editorial by Richard G. Klein, “Darwin and the recent African origin of modern humans.”
• Perspective by Ian Tattersall, “Human origins: Out of Africa.”
• Perspective by Timothy D. Weaver, “The meaning of Neandertal skeletal morphology.”
• Research Article by J. J. Hublin, “The origin of Neandertals.”
• Research Article by Michael P. Richards and Erik Trinkaus, “Isotopic evidence for the diets of European Neanderthals and early modern humans.”
• Research Article by John F. Hoffecker, “The spread of modern humans in Europe.”
• Research Article by G. Philip Rightmire, “Middle and later Pleistocene hominins in Africa and Southwest Asia.”
• Research Article by Francesco d’Errico, et al., “Additional evidence on the use of personal ornaments in the Middle Paleolithic of North Africa.”
• Research Article by Michael DeGiorgio, et al.,”Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa.”

Unfortunately, I have not yet had the time to read any of these papers but they I reckon they should be somewhat enlightening.

Speaking of the Johansons and fossils …

Earlier this year, I’ve blogged about the 2009 Human Evolution Leakey Symposium at Stony Brook that I went to. For more about that blog post, click here.

The symposium, entitled “Hobbit in the Haystack: Homo floresiensis and Human Evolution” can now be streamed live through the Stony Brook website. The website also includes previous Human Evolution Leakey symposia. Click here to watch.

Thanks to Afarensis: Anthropology, Evolution and Science for the heads up!

Originally posted on The Prancing Papio

Many have written how the term ‘junk DNA’ is an imperfect one, and how junk DNA may have a tangential role in evolutionary changes. A new study published in Science visits this topic, specifically focusing on repetitive non-coding sequences in and around promoter regions of the human genome. The authors of this study have published their findings under the title, “Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability.”

DNA Packaging

The findings concluded that the repeats affect the activity of neighboring genes by way of how tightly the downstream DNA is wrapped around a complex of proteins collectively called a nucleosomes. A nucleosome is one of the half dozen packaging features of the eukaryote genome which allows a genome that is 3 billion base pairs long or 6 feet in length to be squeezed into a tiny little nucleus. About 167 basepairs wrap around one nucelosome. DNA that is more wrapped around a nucleosome is harder to be activated, and thus otherwise non-coding/junk tandem repeats of sequences determine how tightly the local DNA is wrapped around these protein complexes.

The extra cool finding about this paper is that the tandem repeats are very unstable, as you possibly could tell from the title. The authors found out that the number of repeats changes a lot during DNA replication, as if the DNA pol III exonucleases don’t bother proof-reading these areas! These changes affect the local DNA packaging, which in turn alters gene activity. In this way, unstable junk DNA is one of the faster acting mechanisms in altering gene activity with each cellular division.

As an extra step, the researchers conducted a experiment investigating the impact of these tandem repeats on yeast cells. They found out that when a repeat is present near a gene, it is possible to select yeast mutants that show vastly increased activity of this gene. But, when the repeat sequences were removed, this fast evolution was impossible.

So what does this all mean for human evolution? Well, unstable pieces tandem repeats of ‘junk’ non-coding DNA are one of the many ways of regulating gene expression and honing on when a gene’s activity can enable organisms like humans to quickly adapt to changes in their environments.

Vinces, M., Legendre, M., Caldara, M., Hagihara, M., & Verstrepen, K. (2009). Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability Science, 324 (5931), 1213-1216 DOI: 10.1126/science.1170097

The upcoming issue of Science will be publishing the announcement of a newly discovered 1.2 million-year-old female Homo erectus pelvis. The fossil was found in 2001 at the Gona Study Area in the Afar region Ethiopia. Excavations were completed in 2003.

The 1.2 million year old female Homo erectus pelvis from Gona, Ethiopia

Sileshi Semaw, the leader of the Gona Project, said that the birth canal of this pelvis is 30% larger than earlier estimates based on the 1.5-million-year-old juvenile male pelvis of KNM-WT 15000 (Turkana Boy) found in Kenya. I don’t have an early copy of the paper, but if this is true, this find will make us reevaluate our estimations of Homo erectus growth and development. Current theories, based upon estimations of the existing male skeleton from Kenya, suggested Homo erectus produced babies with only a limited neonatal brain size, and experienced rapid brain growth while still developmentally immature. But as you may know, male and female primate pelvic girdles are extremely different. This new pelvis also tells us of some interesting differences in stature and gait.

Early hominid female pelvic anatomy is basically unknown, in fact we don’t really have much data, really only Lucy’s fragmented pelvis, the 3.2 million year old Australopithecus afarensis. So I’m interested in reading more about this fossil and what it has to tell us of Homo erectus anatomy and early human evolution. I guess I gotta wait until the paper appears in Science. Expect a post about it as soon as I get my hands on the paper.

LB1 (Homo floresiensis)

I watched that NOVA special on Homo floresiensis last night. It was extremely well done. The producers covered a lot of angles, interviewed many key players, presented the information in a clear manner and kept it entertaining. I wish more anthropology related documentaries would use this show as a template.

In lieu of resonating more noise in the echo chamber, I’ll pass you onto John Hawks‘ minute by minute review of the show. But I do want to say the show really effectively addressed some of the critics of the Flores hobbit, including me, by reminding us that evolution is not linear. And even though we’ve seen a linear pattern in previous hominid brain size growth patterns and associated archaeological complexity, it is possible a smaller brained hominid also evolved simultaneously. If I were teaching a paleoanthropology class, I would show this documentary for sure.

For those of you who couldn’t watch it, it is online now in both Quicktime and Windows Media formats. Watch it.

The role of copy number variations (CNVs) has been explained before. In 2006 I discussed the identification of 355 CNVs in the chimpanzee genome, later in 2007 a study fished out human lineage-specific CNVs by comparing them to ones found in chimpanzees, and lastly, this year, another study suggested that CNVs may account for much more genetic variation among individuals than we’ve previously thought. This week the journal Genome Research published a paper which is the largest comparison of CNV differences between human and chimpanzee genomes. The authors specifically sought to identifying regions that have been duplicated or lost during evolution of the two lineages.

Colocalization of CNVs and SDs in the human and chimpanzee genomes

The paper, “Copy number variation and evolution in humans and chimpanzees,” reports on using whole genome tilepath microarrays for the high-throughput identification of these chromosomal deletions and duplications. The arrays had 28,708 DNA clones on them and the DNA from 30 unrelated chimpanzees and 30 unrelated people of African ancestry were used in this comparative genomic screening. Why Africans? Well the  genetic diversity in Africans, especially sub-Saharan populations, is comparable to that of Western chimpanzees. In order compare large scale (kilobase) genetic variation, have populations that both exhibit inherit diversity already knocks out one variable.

DNA was isolated and hybridized to the arrays. Experiments were duplicated. CNVs were validated by FISH and PCR. The authors and reported that each individual had an average of 70 to 80 CNVs. CNVs of genes that genes involved in the inflammatory response and cell proliferation – are more commonly duplicated or deleted and also occur in both species very frequently in orthologous genomic regions, suggesting a tight association to homologous intrachromosomal segmental duplications. Some examples are APOL1, APOL4, CARD18, IL1F7, IL1F8 and are completely deleted from chimp genome. In humans, APOL1 is involved in immune response to the Trypanosoma brucei parasite, transmitted by the tsetse fly, that causes sleeping sickness. IL1F7 and CARD18 play a role in regulating inflammation: therefore, there must be different regulations of these processes in chimpanzees.

Of particular interest is the identification of a CNV: CCL3L1. When compared to chimpanzees, humans have far fewer copies of this gene. Deletions in CCL3L1 have been associated with increased susceptibility to HIV infection. Another gene, TBC1D3, involved in cell proliferation, was reduced in number in chimpanzee compared to human. On average, there were eight copies in humans sampled, but apparently only one in all chimpanzees and this difference. This difference is argued to have been driven by selection.

SNPs are usually the goto comparative genomic marker for most comparative genetic studies. In this situation CNVs were the star. CNVs can have more impactful phenotypic effects than SNPs — where a SNP may alter the shape a final protein makes or alter the promoter sequence, duplications of a gene can lead to more proteins produced. Deletions in copy numbers can also down size the amount of protein produce, affecting the biochemical pathways the product is involved in. So are CNVs more important thant SNPs or other forms of genetic variation? No. They are one of the many structural elements that need to be studied to completely understand the variomes present within human populations and between humans and related species.

G. H. Perry, F. Yang, T. Marques-Bonet, C. Murphy, T. Fitzgerald, A. S. Lee, C. Hyland, A. C. Stone, M. E. Hurles, C. Tyler-Smith, E. E. Eichler, N. P. Carter, C. Lee, R. Redon (2008). Copy number variation and evolution in humans and chimpanzees Genome Research, 18 (11), 1698-1710 DOI: 10.1101/gr.082016.108

It has been a while since I blogged anything on paleoanthropology. But once I saw John Hawks‘ post where he pointed out Elizabeth Culotta’s news piece in the latest Science on a new hominin femur from Galili, Ethiopia, I was excited. The femur was presented by Bence Viola to the Society of Vertebrate Paleontology, which meet for their annual get together about two weeks ago.

Galili, Ethiopia

Very recent argon-argon dating was done on, and Viola shared those to the Society. The bone is somewhere between between 4.38 million and 3.92 million years old. The bone indicates the individual was larger than lucy but isn’t complete. From what Culotta says, it seems as the distal end is broken off.

The anatomy of the head and neck of the femur suggest the owner was bipedal. But, the distribution of cortical bone around the femur is even. Arboreal primates have an even distirbution of cortical bone around the neck of the femora. The force of gravity and the weight of a bipedal individual causes a lot of stress on the lower half of the femoral neck. It has been observed that the cortical bone of femoral necks of bipedal hominids is thicker on the lower half, as a response to this stress. If you know anything about the debate between the Orrorin camp and the Ardipithecus camp, this should be all too familiar of a discussion.

I first read about hominid remains from Galili in this 2004 piece, which reported on the discovery of an almost complete lower right third molar (GLL 33) likely that of a male Australopithecus afarensis. Hawks pointed out a recent paper which describes the paleoecology of Galili — a open woodland to bushland ecosystem at a time when A. afarensis began replacing A. anamensis. So it is certainly possible that a semi-arboreal/bipedal hominids were navigating this terrain… But, Yohannes Haile-Selassie, who is also working on a 4 million years old hominid from Ethiopia, isn’t too convinced.

What do you think?

E. Culotta (2008). SOCIETY OF VERTEBRATE PALEONTOLOGY 68TH ANNUAL MEETING: Two Legs Good Science, 322 (5902), 670-671 DOI: 10.1126/science.322.5902.670b

Nature Genetics just published a brief correspondence on the evolution of promoter regions in the human genome. The basis of this study relies on the observation that 46% of promoter regions in the human genome have a higher number of nucleotide substitutions than corresponding introns. The authors don’t make the distinction that positive selection, relaxed constraint or mutation rate are the causes of this observation, but they suggest that they have been important to hominid evolution and the genetic diversity of humans.

If you don’t know what a promoter is, I’ll give you a quick run down. Promoters are regions of the genome that are upstream from genes. Regulatory elements such as transcription factors bind to these regions and either start the expression of the gene that is downstream or regulate expression. Any changes to these region can affect phenotypes related to the gene downstream. Between two populations with the exact same intronic sequence of a gene, a difference in the promoter region can have dramatic effects.

In this current paper, “Rapidly evolving human promoter regions,” the authors respond to a previous paper on the subject. They reanalyzed the alignments used by the previous paper. They asked whether each promoter region as a whole is evolving more rapidly than local intronic sequences. They find that almost all (569/575; 99%) of the promoter regions identified by the previous paper as containing positively selected sites have a higher average substitution rate than their paired intronic regions.

The previous authors say that positive selection is at play. They based this conclusion on positive selection on introns. But the current authors caution that promoters are unusual genomic regions, and cannot be compared to selection on introns. They simiply conclude that promoters have higher neutral substitution rates. The previous authors respond to this in this same issue of Nature Genetics. They defend that the current authors methodology “do[es] not affirm their contention that mutation is generally accelerated in primate promoters.” Either way, both teams have identified that promoter regions of the human genome are highly diversified. The reason why they are, is still unresolved, but these conclusions do fall in line with previous ones that I’ve covered here on Anthropology.net:

• Differences of gene expression between human populations
• Identifying Cis-Acting Elements that regulate Human Gene Expression
• Gene Regulation, the driving force in Human Evolution
• Understanding Adaptive Evolution in the Human Genome

Martin S Taylor, Tim Massingham, Yoshihide Hayashizaki, Piero Carninci, Nick Goldman, Colin A M Semple (2008). Rapidly evolving human promoter regions Nature Genetics, 40 (11), 1262-1263 DOI: 10.1038/ng1108-1262

Ralph Haygood, Olivier Fedrigo, Gregory A Wray (2008). Reply to “Rapidly evolving human promoter regions” Nature Genetics, 40 (11), 1263-1264 DOI: 10.1038/ng1108-1263

Bergmann’s rule is an observation that body mass of endotherms increases with altitude and colder climate. Neandertals fit this rule, their barrel chests and wide hips, indicate they had large bodies, and thus smaller surface area relative to their body mass. This feature made them comparatively inefficient at radiating their body heat off into the surrounding environment than smaller bodied hominins…. which is an advantageous trait to have in cold environments.

Another similar theorem, Allen’s rule, summarizes the observation that endotherms from colder climates usually have shorter limbs compared to counterparts from warmer climates. Similar to Bergmann’s rule, shorter limbs keep blood and heat closer to the core of the body, reducing heat loss.

All this may sound like adaptionist mumbo-jumbo, but researchers have observed these adaptations to cold climate in other animals. Compare the profiles of polar bears, walruses, and mammoths to cheetahs, antelopes, and giraffes, and you’ll see how some of this makes sense.

Homo neanderthalensis from la Chapelle aux saints

Anyways, I digress. There are two different camps currently hashing out whether the Neandertal facial morphology is due to random genetic drift or a mix of archaic traits and climate influenced adaptations. One of the more hotly debated facial traits, the Neandertal nose, doesn’t quite fit what we expect to see in cold climate adapted species. The Neandertal nose is broad and wide, a feature seen in tropical climates. Physiologists have shown that narrow noses better warm the air being inhaled and prevent evaporation of water in such dry environments by recapturing moisture during exhalation. Wide noses dissipate heat very efficiently.

Some researchers, like Milford Wolpoff, have suggested that there’s a growth and development reason to why we don’t see narrow Neandertal noses. For example, the effects of large teeth and broad palates could have affected the reduction of the nasal aperture, and were most likely inherited traits from Pleistocene ancestors. In a new Journal of Human Evolution paper that Dienekes pointed out this week, researchers from the University of Iowa have investigated the relationships between nasal breadth, intercanine breadth, and facial prognathism. The paper is titled, “The paradox of a wide nasal aperture in cold-adapted Neandertals: a causal assessment.” They tested variants of the following hypothesis: Does the distance between the two upper canines correlated with nasal breadth in modern and archaic Homo?

Intercanine Breadth Measurement

Their sample set of modern humans included 119 crania of Bantu people and 112 crania of Western Europeans. The sample of human ancestors included 11 from the early Upper Paleolithic, 9 from the late Upper Paleolithic all coming from Eurasia. They also included 15 samples from the late Stone Age in Africa, and 14 Pleistocene Homo. Like I mentioned earlier, they measured the distance between the two canines, known as the ICB. In anatomical terms that’s the distance between the lingual tubercles of the maxillary canines, or the pointy parts of your vampire teeth. The lower facial prognathism (BPL) is a measurement of basion to prosthion. Upper facial prognathism (BNL) is a measurement of basion to nasion. Of course some fossils didn’t have all the measurements so predictions were made by least squares regression.

The authors conclude that intercanine breadth cannot fully explain nasal breadth from their sample set, which goes against what anatomist Gustav Schwalbe said in the later 1800′s and what E.V. Glanville reconfirmed in the late ’60s. They also note that the development of the anterior palatine bone does not affect the growth trajectory of the breadth of the nose. While, they do suggest that nasal breadth is affected by the ICB, the lower facial prognathism impacts nasal breadth more than any other trait.

They finally suggest that the plesiomorphic retention of a prognathic lower face is due to the extended time the premaxillary sutures remain open during development. This is lower face prognathism is not a derived trait, but rather a retention of archaic traits, seen in early humans. But that’s not to say the Neadertal nose never adapted to cold climates while the rest of their body did. Neandertals from colder climate have been characterized with a more narrow superior nasal dimensions, which have ultimately been linked to aspects of airflow dynamics.

N HOLTON, R FRANCISCUS (2008). The paradox of a wide nasal aperture in cold-adapted Neandertals: a causal assessment Journal of Human Evolution DOI: 10.1016/j.jhevol.2008.07.001

I mentioned the drawn out process of me trying to download this new paper, “Dynamics of Alliance Formation and the Egalitarian Revolution,” the other day. I’ve read it and although I found it to be a difficult and theoretically dense paper, I believe you should also read the open access piece if you have any interest in understanding how culture evolved and the possible mechanisms of egalitarian behavior early on in human evolutionary history. The paper’s first author is Sergey Gavrilets, a theoretical evolutionary biologist from the University of Tennessee, Knoxville. The other co-authors are also from the same institution.

You may know Gavrilets’ other piece on cultural evolution, the 2006 paper in which he and Aaron Vose built a mathematical model to test out the social brain hypothesis — creating situations where genes control brains which invent and learn strategies that are then used by individuals to gain advantage in competition for mates. He’s continued researching the evolution of social behavior, and in his most recent piece he and his team tackle the dynamics of coalition formation.

The observation that Gavrilets et al. make is that while our closest living evolutionary cousins form alliances and cooperate in groups, their social systems are extremely hierarchical. The most glaring example can be seen in a gorilla troop where a dominant silverback presides over a few adolescent males and a harem of females. The group dynamic is fluid throughout life history, but each member of the system ultimately plays a role in the dominance hierarchy.

But early human societies, such as the quintessential hunter-gatherer society, is generalized as being egalitarian. Prior to the agricultural revolution, hunting and gathering is thought to have been the only subsistence strategy deployed by early human cultures. Studying modern day hunter gatherers, ethnographers have noted that such societies distribute dominance much more equally and thus tend to be non hierarchical. Leaders are comparatively weaker than their subordinates which reverses the pyramid of power.

So why was there such a big behavioral shift during our evolutionary history? We may never know for sure. There are ideas floating around that all seem to suggest the lack of food and realization that cooperation, rather than competition, was more beneficial for overall survival. When food sources became more dependable, as seen after the Neolithic and the dawn of agriculture and pastoralism, is when we’ve seen a return to a traditional hierarchy.

Gavrilets and team created a complex model which ultimately relied on probability to solve problems. They simulated alliance formation among a group of individuals who had different fighting abilities. Their system distinguished between conflicts that existed only between pairs of individuals and conflicts that were composed of more than two individuals. In situations that conflicts existed solely between two individuals, a very structured hierarchy emerged, favoring the ones best able to fight for their interests. In situations that composed of more than two individuals, there was interference or a balance of power, where the hierarchy was biased towards one result over another.

With an increase of group size, Gavrilets et al. were able to see an increase in dyadic conflicts. When members of a group were aware of other conflicts, of which they were not directly related, there was also an increase of dyadic conflicts. Naturally, larger coalitions have a higher probability of winning a conflict and a positive outcome increased affinity between members of the coalition.

Again, this was a rather hard paper to read, and I’ve left out a lot of details. I’m a bit unclear about what was rewarded to drive forward the model, i.e. what were they fighting for? Some of you may write off models as being controversial and reductionist. You’re right. For starters, it is difficult to interpret methods and the data doesn’t seem like it factors in the interactions of so many different variables — some come from evolutionary, ecological, behavioral, and social factors and all acting simultaneously. It is also awkward to evaluate relevant time-scales, aside from generation turnover, and to figure out possible evolutionary dynamics.

But the model did show that the tendency towards egalitarianism is rapid — it consistently happened in the course of several generations. Under situations where all members of a group were a part of one alliance, where not all members were equal, they still remained united. But alliances weren’t permanent. They would phase and out of intensity. Outsiders were also a crucial part of keeping the dynamic alive.

Gavrilets and crew suggest that egalitarianism came along with changes in mating systems and influenced by primate mother-daughter bonding. They also noted that the emergence of language most definitely facilitates the formation of alliances. One last thing, the authors sent out a warning against considering modern day humans under such constraints, because when we join alliances, our decisions are strongly affected by how much we perceive to get out of the alliance versus the costs and risks of being a part of the alliance, which are factors not included in the model.

All aside, this model is informative but it is by no means the way human social behavior evolved. I’ve already outlined some of the caveats to modeling. To further supplement, there are exceptions to the rule that all hunter gatherer societies are/were egalitarian. Non-egalitarian hunter gatherer systems, such as the Haida, have been well documented by ethnographers. I also remember one of my anthropology professors telling me her accounts of living with outcasted Dassenach people. They were forced out of the pastoral lifestyle and into a hunting for crocodiles and fish one. But, they still retained the social structure despite the shift in subsistence.

Sergey Gavrilets, Edgar A. Duenez-Guzman, Michael D. Vose, Erik I. Svensson (2008). Dynamics of Alliance Formation and the Egalitarian Revolution PLoS ONE, 3 (10) DOI: 10.1371/journal.pone.0003293