Anthropology.net

This morning Dienekes pointed out a new paper in the open access journal PLoS Genetics on polygyny and its impact on human genetic variation. Razib followed suite, providing a more in depth review of the study. I recommend you check out both. In this post, I’m also gonna have a stab at reviewing the paper since it has an important anthropological impact.

The paper, “Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity,” is authored by some people you may have heard of, such as Michael Hammer and Jeffrey Wall among others. Like many population geneticists, they isolated the problems and limitations of previous studies which investigated genetic diversity of humans from only markers on the mitochondrial DNA and non-recombining portion of the Y chromosome genome. They proposed that markers on the autosomal genome, including the X sex chromosome, will provide a more insightful understanding.

So they compared the genetic variation among 40 independent loci on the X chromosome and autosomes in 90 individuals from six different populations. 20 loci on the X chromosome and 20 on the autosomes were picked from non-coding regions of the genome.

Why wasn’t there a more even distribution of sites across the whole genome? Well, the authors specifically sought to seek out the impact of sex-specific processes, such as mating patterns, in shaping genomic patterns of variability. Both Razib and Dienekes do an excellent job in explaining this, but I’ll snip what Razib wrote since it is more clear in my mind:

“Assuming equal numbers of males and females in any given generation you expected a ratio of diversity of 0.75 between the X and the autosomes; remember that the number of copies of X circulating within the population are reduced by 25% because males carry only one copy, while women carry two.”

In other words, the X chromosome is present in two copies in females and a single copy in males. We all know that. We expect that the other chromosomes will show more genetic diversity than the X chromosome in a population with an equal number of breeding males and females because they are inherited equally by both sexes from each parent. In a populations with an unequal number of breeding males to females, we should see something different. Actually, we expect to see more genetic diversity on the X chromosome than on the other chromosomes in areas where men don’t get to pass on their genes, while most women do.

The authors’ samples included individuals from Africa, such as the Biaka of the Central African Republic, the Mandenka from Senegal, and the San from Namibia were included. Outside of Africa, the French Basque, the Han Chinese and Melanesians were also sampled. Roughly 210kb of DNA was sequenced from each of these individuals, and a basic statistical summary of the nucleotide diversity in six human populations was conducted. Comparing the observed nucleotide diversity on the X chromosome to the chromosomes showed that there was more genetic differences in the X chromosome than would be expected if equal numbers of males and females tended to mate.

Even though I explained this in two paragraphs above, polygyny could be the only reason why we see such results. Some men just didn’t get a chance to pass on their genes. The authors even made sure to rule out background selection, changes in population size and sex-specific migration in their conclusion. Only the process of polygyny could account for the sex ratio skew and resulting patterns of genomic variation. By this process, fewer unique male genes are being passed into the next generation.

In the same issue, a very similar paper was also published that I don’t think many other people noticed. A separate team of academics applied this multilocus approach to the genetic diversity of Central Asia. It is published under the title, “Sex-Specific Genetic Structure and Social Organization in Central Asia: Insights from a Multi-Locus Study.” Their sample included 10 populations of bilineal agriculturalists and 11 populations of patrilineal herders from West Uzbekistan to East Kyrgyzstan. Bilineal means that there’s an even migration of men and women while patrilineal means there’s an uneven migration of women to their husband’s location. In total, their sample size represents 780 healthy adult men from 5 ethnic groups: Tajiks, Kyrgyz, Karakalpaks, Kazaks, and Turkmen. They conclude that the number of reproductive individuals is likely to be higher for women among patrilineal populations.

Both these studies show that the organization and structure of patrilineal populations is the likely cause of the observed genetic patterns, where men tend to father children with more females than females do with males despite institutionalized monogamy.

Michael F. Hammer, Fernando L. Mendez, Murray P. Cox, August E. Woerner, Jeffrey D. Wall, Dmitri A. Petrov (2008). Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity PLoS Genetics, 4 (9) DOI: 10.1371/journal.pgen.1000202

Laure Ségurel, Begoña Martínez-Cruz, Lluis Quintana-Murci, Patricia Balaresque, Myriam Georges, Tatiana Hegay, Almaz Aldashev, Firuza Nasyrova, Mark A. Jobling, Evelyne Heyer, Renaud Vitalis, Molly Przeworski (2008). Sex-Specific Genetic Structure and Social Organization in Central Asia: Insights from a Multi-Locus Study PLoS Genetics, 4 (9) DOI: 10.1371/journal.pgen.1000200

Human mating systems are mediated by many different variables, from cultural preferences to religious alignments. In some places, people marry and mate within their class or ethnic group. But there are more subtle, almost subliminal conditions behind mating that often affect the outcome of genetic variation and evolution. While I was out of the country, a paper was published in PLoS Genetics which outlined one of these conditions — mate choice and the major histocompatibility complex.

If you haven’t taken an immunology or molecular biology course, you may not know what the major histocompatibility complex (MHC from now on) is. The MHC is the most gene dense region of the mammalian genome and encodes for a lot of proteins act which act as signposts on the cell. These proteins are a crucial part of the autoimmune system. These signposts identify cells as self or foreign to the immune system, ultimately making MHC’s a critical part of disease-resistance. As Dienekes summarized, the evolutionary implications are pretty profound,

“couples dissimilar in [MHC genotype] will produce heterozygous children that will be more capable of fighting disease.”

The three authors of, “Is Mate Choice in Humans MHC-Dependent?,” asked whether or not couples differ more or less in the MHC region of the genome they do across the entire genome? Their testing employed genome-wide genotype data and HLA types in a sample of Yoruban and a sample of European American couples. This allowed them to distinguish MHC-specific effects from genome-wide effects. The group examined whether husband-wife couples were more MHC-similar or MHC-dissimilar in comparison to random pairs of individuals.

Surprisingly, the African couples were not more MHC-similar nor MHC-dissimilar. But across the genome, they were more similar than random couples. How could this be? This could possibly be due to social factors, i.e. mating with genetically close individuals that are within social units, rather than with individuals from the entire population.

European American couples, however, were predominantly MHC-dissimilar. They were drastically so in comparison to the genome, supporting the hypothesis that the MHC influences mate choice in this population. Does this mean that there’s been some sort of evolutionary pressure for Europeans to have more heterozygosity at MHC loci? I’d venture to say yes, epidemics like the Black Plague severely affected European populations but that’s not to say African’s have been disease free. As you may know malaria has constantly been a problem. More studies need to be conducted in other African populations with different mating patterns to fully consider if biological traits like MHC genotype play a significant role beside social traits in the process of mating.

Raphaëlle Chaix, Chen Cao, Peter Donnelly, Molly Przeworski (2008). Is Mate Choice in Humans MHC-Dependent? PLoS Genetics, 4 (9) DOI: 10.1371/journal.pgen.1000184

Zooarchaeology is an anthropological sub-discipline which focuses on studying animal remains from archaeological sites. Animal remains can tell us a lot of about prehistoric peoples’ diets and behavioral tendencies as well as the ecological makeup of the area. A new PNAS paper investigates the zooarchaeological record of two Neandertal sites in Gibraltar, Vanguard and Gorham‘s Caves.

The paper, “Neanderthal exploitation of marine mammals in Gibraltar,” is authored by some familiar names such as Chris Stinger and J.C. Finalyson and Nick Barton, and the major conclusion is that the presence of mollusks, seal, dolphin, and fish from such sites suggests that Neandertals exploited a wide variety of foods — hammering yet another nail in the coffin of the Neandertals were dumb cavemen train of thought. John Hawks and Dienekes have both written that this research is yet another line of evidence in the modernization of Neandertal behavior.

The cave sites are part of the Gibraltar Caves Project, which began in 1994. Annual excavations followed the year after. The sites are located on the southeast side of the Rock, on Governor’s Beach. As far as I can tell, GPS coordinates were not provided. I’ve tried to track down the exact location of the sites but have found conflicting information. But the BBC has provided an image of the sites, by way of the Gibraltar Museum. The two sites are adjacent to each other and the Gibraltar Museum has dutifully also provided a prehistoric view of the sites when sea levels were much lower:

Gorham's & Vanguard Caves on Governor's Beach, Gibraltar.

Gorham’s Cave site indicates three distinct occupations. There’s an Upper Palaeolithic occupation with dates spanning 26-30,000 years before the present (BP). There’s another distinct layer containing the youngest Middle Palaeolithic and dated at around 31-32,000 BP, and a third, older Middle Palaeolithic layer which is underneath. This older layer is dated to 45,300 ± 1,700 years BP. Vanguard Cave shows similar patterns with radiocarbon dates of 45,000 years BP and similar lithic assemblages.

Cut marks from a Mediterranean Monk Seal finger bone found in Vanguard Cave

Vangaurd Cave has yielded evidence of Mediterranean monk seal (Monachus monachus) phalanxes with cut marks and lots of mollusk shells. The minimum number of mollusks found isn’t provided but the authors do say that a particular layer was dominated by mollusk shells. Additionally the concentration of knapping debris and Mousterian stone tools, along with a hearth, from this layer suggest that Neandertals were having a prehistoric cioppino feast.

Additional remains of ibex, red deer, boar, bear, along with dolphins birds, tortoises indicate that these prehistoric people were exploiting a wide variety of food sources. Roughly 50% of the animal remains were cut or burned, and a lot of the rest show percussion marks and fractures. Compared to Neandertals from Northern Europe, who sustained a diet of big game meat such as mammoth, deer and horse, these guys from Governor’s Beach had a different diet. Stringer told the BBC that these caves tell us that we can’t generalize Neandertals.

C. B. Stringer, J. C. Finlayson, R. N. E. Barton, Y. Fernandez-Jalvo, I. Caceres, R. C. Sabin, E. J. Rhodes, A. P. Currant, J. Rodriguez-Vidal, F. Giles-Pacheco, J. A. Riquelme-Cantal (2008). From the Cover: Neanderthal exploitation of marine mammals in Gibraltar Proceedings of the National Academy of Sciences, 105 (38), 14319-14324 DOI: 10.1073/pnas.0805474105

Mark Stoneking is a population geneticist at the Max Planck anthropology powerhouse. He uses genetics to study the origin, relationships, structure and migration patterns of human populations. He’s written up a review of the origins of humans in the journal EMBO Reports under the title, “Human origins. The molecular perspective.” I’ve tried to get access to it, but my library doesn’t have a subscription and I’m not really willing to dish out $18 to buy the 4 page paper. I rather buy a book with that sort of cash.

But Dienekes seems to have read it and he’s found the illustration of the different models of human evolution interesting. I’ve decided to share the image with you. Dienekes also discusses Stoneking’s understanding of Carleton Coon, the physical anthropologist who wrote “The Origin of Races” in 1962, which was thwarted by the big boys of the time, Sherwood Washburn and Ashley Montagu and further discredited with Lewontin‘s 1972 conclusion that there’s more differences within groups than between.

We’ve come a long way since then. With DNA chips able to detect many SNPs and with the lower costs of genetic screening, we can assess the genetic diversity of more people. Datasets are growing and patterns are emerging. We’re now able to isolate distinguishable genetic differences in places like Europe. In the past, I’ve argued that with these higher resolution and more ubiqutious technologies available, we shouldn’t be falling back on Lewontin’s Fallacy anymore. Saying a biological component to race doesn’t exist just doesn’t cut it anymore.

I’m back to internet land a bit earlier than expected and even though I’ve got several thousand unread items in my RSS reader, hundreds of emails and photos to sort through, I’ve stumbled upon some really interesting news first shared by Dienekes that I just had to pass on: A reconstruction of a Neandertal’s face using DNA and morphometrics.

Physical anthropologists often argue that the bones tell us how an organism looked like. Based off the morphology of the bones, we can estimate the structure of faces and bodies. Forensic anthropologists use this to help put a face to the remains of a decomposed murder victims. Paleoanthropologists have also used this technology to illustrate how human ancestors may have looked like. But we haven’t been able to strictly rely on morphometrics to illuminate the color of a person’s skin or hair. There’s just too much variation in skeletal morphology to make such correlations.

Advances in ancient DNA analysis like last year’s identification of a Neandertal carrying the allele for red hair, have helped us pinpoint more finer details in the phenotype of prehistoric human ancestors that can’t be resolved by measurements of bones alone. In a hodepodge synthesis of morphometerics and genetics, the National Geographic has analyzed the remains of 43,000 year old cannibalized Neandertals and created an image of what a Neandertal may have looked like.

Dubbed as Wilma, the NGS has created a documentary about the reconstruction process called the Neandertal Code, which airs Sunday, September 21st, 2008 at 9 p.m.

From what I can make of the anouncement, the reconstruction seems like more of an artistic endeavor than a scientific one. The skeleton was reconstructed based off of the bones of several female individuals, and when they didn’t have certain elements, male versions were scaled down. Also, it is uncertain what 43,000 year old specimens from this assembly of bones was used to figure out that this individual had red hair, fair skin and green-ish eyes. It is certainly possible that some elements came from darker Neandertals. Nevertheless, it is interesting to see how ancient DNA is being used to complement the reconstruction phenotypes of human ancestors.

Related to this, is an open access analysis of Neandertal brain size and development that has popped up in yesterday’s issue of PNAS. Using the remains of 3 Neandertal toddlers from Mezmaiskaya Cave in Russia and  Dederiyeh Cave in Syria, the authors of the paper conclude that the Neandertals shared similar brain sizes at birth to Homo sapiens, but brain growth rates during early infancy were higher which resulted in larger adult brain sizes but not necessarily earlier completion of brain development. I’ll try to give this paper a more thorough treatment once I take care of the mound of backlog. But you should check it out since it is free, “Neanderthal brain size at birth provides insights into the evolution of human life history.”

I don’t regularly make announcements about my life, but I wanted to let you that blogging here will be sparse because I’m leaving to Turkey to do some fieldwork. I should return in two weeks time, unless we find something that needs a bit more time or if the PKK and Turkish government have another flare up like they did earlier this year. Hopefully, the former rather than the latter will happen.

I’ll be doing paleoanthropology research, but unlike my field season last year in Ethiopia, I’ll be hitting much older localities — we’re talking about the Miocene not the Plio-Pleistocene. This means I’ll be looking for hominoids, not necessarily hominins. But I’ll be elated to find either, in fact I’ve been dreaming about finding something like last year’s Ouranopithecus turkae! I wouldn’t be disappointed to find a really old H. erectus, Neandertal.

I imagine I’ll be stumbling upon a lot of archaeological material too. I’ll try to document as much as I’m allowed to and put it up on my Flickr account when I can. I also imagine that internet connectivity will be limited in the field, as will my time and energy to loiter around online. That being said, I’ll see y’all later!

National Geographic News is running some press about the oldest skeleton found in the Americas, Eva de Naharon, at 13,600 years old. This would make her the oldest known human in the Americas, but as of now no peer reviewed journal has reviewed the research. The discovery of the skeleton, along with three others, were actually announced in a bulletin dated back to June on Mexico’s National Institute of Anthropology & History website.

Tulum, Mexico

The site is located in the Mexican state of Quintana Roo, which is on the Yucantan Peninsula. I’d map the actually cave but I can’t seem to track down a locality name nor any GPS information. Alls I know is that its somewhere near town of Tulum.

The lead investigator of the study is Arturo González, who says these particular remains have 10 teeth. Surprisingly, the skull morphology does not exhibit many affinities to northern Asian populations, you know like Siberians and the like. This conclusion comes from Alejandro Terrazas, of UNAM. Rather, the skull exhibits South Asian, almost Indian, like traits. No discussion nor description of what the actual traits are provided.

The remains have been dated via radiocarbon. But the remains have since been flooded over as the ice caps melted after the last glacial maximum. David Anderson says the saltwater that’s covered the remains affects carbon-14 dating. But the presence of elephants and giant sloths in the cave give some bio-chronological support to the date.

Photographing Eva de Naharon from Tulum, Mexico

So is this surprising? Yeah, but there have been signs pointing to a much older occupation of humans in the Americas. Recently, a genetic study suggested that the peopling of the Americas started around 17,000 years ago and a redating of Mexico’s Toloquilla footprints indicated that people may have been in or around central Mexico by 16,000 years ago. Furthermore, sites inside Chile have been redated to be as old as 14,200 years. But, should the radiocarbon dates hold, this will be the oldest American skeleton. You may know of Kennewick’s 9,300 years old date, but with Eva de Naharon antiqutity at 13,600 years, this maybe a significant find.

The peopling of the Americas is one of my favorite subtopics in anthropology and Eva could shake things up especially if the carbon-14 wasn’t affected by saltwater and her physical traits are really south Asian-like. I guess we gotta wait until González and team excavate, clean up, and analyze Chan hol, the fourth skeleton at this site and submit their analyses to a journal.

The Sahul is the Australia-New Guinea continent, which is exposed during glacial maximums. If one were to take a satellite photograph of the Sahul during an ice age, you’d see more or less a complete island in the picture, one that spans from New Guinea to Australia and Tasmania. Kind of like the one to your right. Understanding the peopling of the Sahul is critical to understand human migrations and the peopling of Australia.

In the late ’70′s to the late ’80′s, most archaeologists thought that the Sahul was occupied by Late Pleistocene humans, somewhere around 45,000 years ago. A bit of a shake-up spurred about the exact timing of the occupation when older sites like the Devil’s Lair, Lake Mungo, Nauwalabila, Malakunanja, and Huon Peninsula were discovered.

Predictably, two camps emerged. One camp asserted that the Sahul was peopled around 60,000 years ago. The other camp held on the later date, contesting that their dates are based upon more reliable dating techniques, such as radiocarbon, luminescence, and uranium-thorium dating methods. They also contest that 45,000 year old artifacts better resemble the Out of Africa “package” that is represented elsewhere.

A new paper in the Journal of Human Evolution looks at the archaeological “package” from the earlier sites. The authors of the paper compare this archaeological record to the record of other Middle Stone Age sites in Africa, Europe, and Asia. Similar to genes, the displacement of artifacts occurs when new technologies and cultures influence existing ones. It can happen under different tempos — there can be a slow, gradual change of material culture or there can be rapid and punctual changes. There can even a mix of the two. In places like Europe, we see rather fast changes, as pre-existing populations like Neandertals were replaced by humans during the Middle to Upper Paleolithic transition.

To see whether or not the Sahul represents a slower change, Phillip Habgooda and Natalie Franklin have looked at the archaeological record of the Sahul. They’ve published their findings under the title, “The revolution that didn’t arrive: A review of Pleistocene Sahul.” I figure you can extract the main conclusion from this concise title. But I won’t stop there because Habgooda and Franklin have written up a rather thorough study. They specifically timed the rate of change in exchange networks, mining & quarrying, beads, ochre, art, burials, shellfish middens, grindstones, modified bone, and new lithic techniques.

For the section on exchange networks, they review the archaeological record of 20 sites. The trade of exotic materials for symbolic reasons, especially over long-distances, is understood to be a relatively modern behavioral trait. 40,000 years ago, the people who occupied the Sahul were moving shells and other materials long distances — in some cases 300 kilometers and in other cases to places like the little islands in the Bismarck Sea, which is north of Papau New Guinea.

Related to trade networks, mining and quarrying, also represents a modern trait as people specifically sought out certain rocks to fashion into tools and adornments. The record for mining emerges at a much more recent date: around 24,000 years ago. Take note of the discontinuity between these dates, because a rapid displacement of the Sahul should share similar dates among the different parts of the package looked at.

I shouldn’t really need to define why we consider personal adornments like beads, as modern. And in the Sahul, they are seen as 42,000 years ago. But other pieces of adornments, such as this limestone plaque from the Devil’s Lair appear only as early as 25,000 years ago. The role of ochre in art, rituals, and personal hygiene is also looked at. Similar to bead usage, ochre usage is seen as early as 42,000 years ago but not in an artistic and elaborate burial context until 2,000 years later. Complex rock art and symbolic burials are traits of modern humans and for them to not sync up with ochre usage and adornments make me wonder what was going on?

In general, resource exploitation is a modern human trait and by looking at the composition of middens and the number and specialization of grindstones, we can get an idea about when people started to change their lifestyles. In the Sahul, this didn’t start happening until around 30,000 years ago. Again, remember some other modern human traits are seen as early as 42,000 years ago but economic intensification didn’t happen until much later. Furthermore, modified bone tools, a hallmark of modern human behavior, is seen around 22,000 years ago but compound stone tools like adzes are seen as early as 40,000 years ago!

Clearly, this paper shows that the Sahul was gradually influenced by the modern human expansions out of Africa. Parts of the modern human package appear at different sites, separated spatially and temporally. The authors provide us with this poignant summary as well as an image depicting their results,

“Following initial colonization of the continent, terrestrial fauna are the dominant resources exploited, but freshwater shell middens are apparent around the palaeoriver and lake systems of southeast Australia. Long-distance transport and/or exchange networks are evident, as is collection and use of ochre for ritual behaviour (burial) and rock painting. Stone assemblages are dominated by retouched and unretouched flakes, but waisted hatchets are found in Papua New Guinea at this time. By 30,000 years BP, an expansion in resource exploitation may be signified by evidence of marine exploitation on islands off the northern coast of Sahul, the (possible) appearance of grindstones, and the intensive exploitation of macropods in southwest Tasmania. Flake-based stone tool assemblages are augmented by the introduction of ground stone hatchets in northern Australia and small thumbnail scrapers in southwest Tasmania. Personal ornaments in the form of shell beads are also present in northwestern Australia at this time. By 20–18,000 years BP the variety of personal ornaments has expanded to include bone beads, pendants, and notational pieces. Although there is evidence of painting of some form by 40,000 years BP, identifiable art does not appear until around 20,000 years BP. Flint mining is evident at this time, and the flake-based stone tool assemblages are supplemented with bone points made on macropod long bones in the southeast of the continent.”

Modern human behavioral traits in the archaeological record of the Sahul, emerged over a 30,000 year period, even though modern humans clearly had an early influence. The authors consider one possibility may have been that there was not a rapid colonization of the Sahul. I’ve thought about this some and think that differences in population densities and impact of new technologies, i.e. adoption rates amongst ‘stubborn’ populations affect rates of cultural change. Hell, look how long it has taken people to switch from Windows to Macs. ;-) Somethings may not have been useful to early peoples and may have not been taken up as readily, and adopted later under different pressures and considerations. What we can figure out is that what we consider the “package” is not necessarily and all or none indicator of modern human existance.

If you’re interested in understanding the peopling of the Greater Australia area, and wanna know more about Sahul sites, I recommend reading this paper. I got a bit annoyed by the over-usage of “package.” I know even though I used the phrase in similar manner — without directly defining it. But if you mentally replace it with other synonyms that work for you, the paper is much more digestible and chock full of information about the archaeology of early Austrialia, Papau New Guinea and adjacent areas.

P HABGOOD, N FRANKLIN (2008). The revolution that didn’t arrive: A review of Pleistocene Sahul Journal of Human Evolution, 55 (2), 187-222 DOI: 10.1016/j.jhevol.2007.11.006

Last month, I read and reviewed two papers that correlated the genetic and linguistic structure of European populations to their geographic locations. A new paper came out several days ago in Nature which announces a new model where the genetics of 3,200 Europeans is used to predict their country of origin, with an accuracy of a few hundred kilometers.

The paper, “Genes mirror geography within Europe,” comes from John Novembre and crew. They got their data from GlaxoSmithKline. 500,000 SNPs were compared and when they were plotted after two principle component analyses, the authors were able to see distinct clustering of geographically distinct populations. This is the image they provided.

Genetic & Geographic Separation of European Populations

Placing a map under this distribution shows how distinct the Iberian peninsula is from the Italian peninsula and within the ‘mixing pot’ French, German and Italian-speaking Swiss individuals are genetically separated. To touch on the accuracy issue again, with countries that had more individuals represented in the sample, this new method could pinpoint their origins to 310 kilometers. On average, the accuracy was able to identify an individual’s origins to 540km.

As P-ter of Gene Expression points out, the biggest restriction to this study is the array of SNPs on the GeneChip and the number of individuals sampled. With higher resolution GeneChips, ideally full genomes, and larger samples, we’ll be able see much more accurate genetic-geographic separations of populations.

John Novembre, Toby Johnson, Katarzyna Bryc, Zoltán Kutalik, Adam R. Boyko, Adam Auton, Amit Indap, Karen S. King, Sven Bergmann, Matthew R. Nelson, Matthew Stephens, Carlos D. Bustamante (2008). Genes mirror geography within Europe Nature DOI: 10.1038/nature07331