Anthropology.net

Ever since December, I’ve been reading a lot of research about the genetics of human skin color variation. To date, many genes have been identified in the skin pigmentation biochemical pathway. This suggests that the evolution of human skin color is multifaceted. Some of the genes you may have heard of before are ASIP, MC1R (more info), SLC24A5, TYR, KITL, HERC2, and the OCA gene family. To add a layer of complexity, many different alleles of each gene exist and ultimately affect the functionality of the gene product in the pigmentation pathway. Projects like the HapMap initiative have identified that certain populations have unique distributions and frequencies of skin color alleles.

A new research paper shared by Razib and published in the open access PLoS Genetics journal reports on new human skin color alleles not identified before. The paper is titled, “A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation.” The authors of this paper scanned the genomes of over 10,000 people of European ancestry to find alleles associated with hair and skin color, using the Illumina HumanHap300 array. They were able to identify IRF4 and SLC24A4 as two loci highly associated with hair and skin color.

Within IRF4 and SLC24A4, two SNPs had the most statistically significant associations to pigmentation:

• The rs12896399 SNP is 15.5 kb upstream of the SLC24A4 gene, and was highly associated with light color. Almost 99% of Africans do not carry this allele, whereas there’s a 60:40 distribution among Europeans.
• The rs12203592 SNP is found in intron 4 of the IRF4 gene. It was strongly associated with pigmentation. This SNP is associated with a black to blonde or red change in pigmentation of hair. I want to point out that this SNP seems to be found exclusively in 17% of people with European ancestry — or at least that’s what two different tests have shown.

The authors were also able to identify three chromosomal regions adjacent to the previously known pigmentation genes: MC1R, OCA2, and MATP. Further work needs to be done to figure out what IRF and SLC24A4 do in the pigmentation pathway. We already know that SLC24A4 is very similar to SLC24A5 in sequence and is most likely a calcium and sodium antiporter protein. According to the authors, the gene product of IRF4 falls under a member of the interferon regulatory factor family of transcription factors that regulate genes in response to interferons (immune proteins) and other cytokines (signaling proteins). This factoid makes me wonder if IRF4 also regulates the transcription of many known pigmentation genes and also how integrated are immune response and skin coloration (hint: tuberculosis and light skin)?

Han, J., Kraft, P., Nan, H., Guo, Q., Chen, C., Qureshi, A., Hankinson, S.E., Hu, F.B., Duffy, D.L., Zhao, Z.Z., Martin, N.G., Montgomery, G.W., Hayward, N.K., Thomas, G., Hoover, R.N., Chanock, S., Hunter, D.J., Abecasis, G. (2008). A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation. PLoS Genetics, 4(5), e1000074. DOI: 10.1371/journal.pgen.1000074

I’m kinda surprised that this paper, “A study on the correlation between IL1RAPL1 and human cognitive ability,” hasn’t made many waves in the press nor in the blogosphere. Aside from being controversial, it is a pretty fascinating study. But, I’m not completely shocked many have abstained from mentioning it… Like the genetics of race, the genetics of intelligence is a topic many researchers aren’t willing to bet their academic careers on. Why? Because, it has been source for some pretty knee-jerk reactions.

Don’t believe me?

Remember what James Watson said last fall? To save grace, I’m not gonna reiterate his words… But I will mention that the consequences of Watson’s commentary are rather unforgettable. He lost a very prestigious career, and ended his successful reign in science on a bad note. I’m not defending beliefs like Watson’s, especially because what he said was expressed as subjective, inflammatory conjecture more than anything else, but I am curious about looking into how genetic predispositions affect intelligence and cognition.

I’ve done some reading on the topic and started many discussions about this topic, bringing up the correlations of higher than normal intelligence and the higher than normal incidences for many genetic diseases (like Tay-Sachs and hemophilia) in in Ashkenzai Jews as a case study. Time and time again, discussions have been shunned down. I’ve wondered why and I’ve come to think that people just don’t want to engage in this train of thought because of the possible repercussions it has. I worry that it has more to do with being politically correct than anything else.

That all being said, I’m very excited to have stumbled across this current paper from Dienekes. I wouldn’t have found it if it weren’t for his post. As you can tell from the title, this paper focuses on a correlation between a gene and cognition in humans. Please note how the authors are all Chinese academics, seems like folk in China people aren’t afraid to research this topic.

Anyhoot, the gene of interest, IL1RAPL1, is believed to function in binding of a kinase to a receptor. On Monday, I took an exam on this subject, looking into all the known different signal transduction mechanisms and receptor kinases were a major part of the test. Kinases are special proteins, enzymes that phosphorylate other proteins. In most common terms, a phosphorylated protein is an active one. Receptor kinases span the membranes of cells and receive extracellular stimulus to activate intracellular proteins. L1RAPL1 is expressed in muscle and brain tissue.

Previous studies have shown that individuals who have deletions or inversions of L1RAPL1 have a form of mental retardation. This indicates an important signaling pathway involved in cognition is lost when L1RAPL1 is knocked out, which is what got this group of academics to hone in on L1RAPL1 as a gene linked to cognition. To date, there has not been an investigation on the impact of the alleic variants of L1RAPL1 on cognition, which is the scope of this paper. The paper specializes in looking at relationship of L1RAPL1 polymorphisms (two microsattelites and two SNPs) with intelligence in population of Chinese kids. They also extended this study by looking a the effects of the polymorpisms on rats.

In their sample, the L1RAPL1 of 332 children (50:50 male to female), aged 5-14 years old, was screened. The genotype of each child’s L1RAPL1 variant was identified using PCR. In the population, roughly 90% were heterozygotic in the DXS1218 microsattelite variant of L1RAPL1 . Microsattelites are simple repeats of nucleotides in a sequence of DNA, I outlined one way they come about here. The other microsattelite, DXS9896 was present as heterzygotic alleles in 87% of the kids.

Two SNPs are also looked at. 89% of the kids had an A nucleotide in the rs6526806 SNP, where the other 11% had a G. 42% of the kids had one version of the rs12847959 SNP, the other 58% had another version. The authors did not mention what effect these polymorphisms had on the gene, but did indicate they all fall in the intron of the gene — a non-coding region that is spliced out.

The kids were asked to take several cognitive tests that tested their memory, concentration, perception, and verbal abilities. Three of the polymorphisms listed above had effects on memory and concentration. Those that had longer DXS1218 microsattelite variants had lower IQ scores. Similarly, kids with longer DXS9896 mircosattelites also had lower IQ scores. One of the SNPs, rs12847959 showed that individuals that had the CC genotype in the SNP had higher IQ scores compared to those that had the CG genotype. The p-values for all were pretty strict, suggesting that the differences are statistically significant.

I find the results pretty cool. Those with longer introns seem to have reduced IQ scores. Those with a difference in 1 base pair also seem to have differences in IQ scores. Now, what do lower IQ scores have to do with intelligence? Can we say low IQ scores equal dumber people? Many people will say no. IQ tests have often been criticized for not being an adequate screens of intelligence, but they are one of the only ways to systematically and uniformly exam some degree of memory, concentration, perception, and verbal abilities. I find the use of them kinda flawed because the children screen in this study were from different ages, if they all came from the same age group, I would say there would be more structure. I know I was much more intelligent at age 14 than I was at age 5… my parents may disagree though.

I want to also outline that L1RAPL1 is one of the 8,000 or so genes expressed in the human brain, all of which have some function the brain and ultimately in cognition. Thus, intelligence is very much an epistatic trait and we can’t just say alleles of L1RAPL1 are the only player in determining cognitive abilities. Perhaps a wider genome wide association/linkage disequilibrium study will begin to identify all the genetic players affecting intelligence.

GAO, X., XI, G., NIU, Y., ZHANG, S., FU, R., ZHENG, Z., ZHANG, K., LV, S., HE, H., XUE, M. (2008). A study on the correlation between IL1RAPL1 and human cognitive ability. Neuroscience Letters DOI: 10.1016/j.neulet.2008.03.084

Thank you, Kambiz, for letting me introduce my new book to the Anthropology.net community.

The story behind The Genius of Kinship is an interesting one. In 1991, then a student of history at the St. Petersburg State University, I wrote a course paper on the traditional social organization of the Shoshone Indians as could be gleaned from ethnographies and trappers’ accounts. Why would a Russian student be interested in the Shoshone Indians is an entirely different story to be told on a different occasion. Let’s just say I was researching Shoshone Indians because they were not widely known in the Russian ethnological literature. My advisors apparently noticed my interest in pre-industrial social structures, and recommended that I explored Shoshone Indian kinship structure in greater detail next year. I poured over literature on kinship studies in Russian, French and English for a few months and then looked at Shoshone kinship again. I was struck by their logical consistency and by the fact that this elegant simplicity was not mentioned anywhere in the basic literature on kinship. Typical case studies came from Australia, Southeast Asia, Oceania, Sino-Tibetan languages, but not from North America.

I thought that was puzzling: kinship studies, as we all know, were founded in the mid-19th century by the American lawyer, Lewis Henry Morgan, on the basis on Iroquois and other North American Indian tribes/nations. The birth of kinship studies coincided with the birth of anthropology as a romantic quest for the origins of Western civilziation. But by the end of the 20th century American Indian kinship structures are nowhere that prominent. Possessed by a pioneer’s zeal, I ventured into kinship terminologies around the world and initially amassed a database of over a thousand kinship nomenclatures from many linguistic families. In 1997, I defended my research as a Ph.D. dissertation at the Peter the Great Museum of Anthropology and Ethnology in St.Petersburg, and in 2001 I published it as a book entitled The Phenomenon of Kinship. Without a particular premeditation, I followed in Morgan’s early footsteps when he wrote The Systems of Consanguinity and Affinity of the Human Family (1870) and conceived of kinship terminologies as a source of information about ancient human population dispersals. (Morgan as a famous social evolutionist emerged with the publication of Ancient Society in 1877 when he attempted to explain the diversity of human kinship structures as a matter of stages in the progressive maturation of humankind.) Over and over again, I caught myself thinking that American Indian kinship structures are unique and can provide a missing link for the evolution of Old World kinship structures.

When I came to the U.S. in 1997 as a Ph.D. student in Anthropology at Stanford, I faced another puzzling irony of history: it’s not just American Indian kinship structures that have been eclipsed from the anthropological agenda, American anthropologists were not doing kinship studies at all. As Sylvia Yanagisako said upon learning about my Russian research, “But nobody does this stuff here anymore.” Truth be told, she herself was part of a “revival” of kinship studies in the U.S. in the late 1980s but more along the lines of gender, with “kinship” being scowled at as a spurious Victorian invention. For some inexplicable reason, she was sceptical of kinship systems, structures, lineages, and especially terminologies. Speaking to other feminist professors at Stanford’s Department of Anthropology (later Department of Cultural and Social Anthropology) such as Jane Collier and Carol Delaney, I couldn’t figure out where all the good old kinship studies went. Where were Lowie, Kroeber, Radcliffe-Brown, Malinowski, Fortes, Levi-Strauss, Dole, Murdock, Tax, Scheffler, Lounsbury, Dumont, Allen, Barnes, Trautmann, Tyler, Kronenfeld, componential analysis, generative analysis, equivalence-rule analysis and other proud representatives of the anthropological tribe? Yanagisako, Delaney and Collier all referred me back to David Schneider who allegedly “proved” that “kinship” was a malignant excresecence on the body of the discipline manifesting all the imaginable vices from racism and colonialism to the masculine bias.

It didn’t make much sense: coming out of a former Soviet country with all its anti-racism and anti-colonialism and anti-capitalism-with-its-severe-exploitation-of-women-and-children, I still felt okay about kinship. Of course, it’s a tough field, not for everyone, but anthropology and kinship are inseparable. You can critisize, develop new theories, change paradigms, but still groom the central concept of the discipline. That’s how I felt.

Across the Main Quad at Stanford, another group of American anthropologists was setting up a different anthropology department called “Anthropological Sciences.” Jim Fox was teaching anthropological linguistics, Joanna Mountain population genetics, Merritt Ruhlen Greenberg’s multilateral comparison, Bill Durham general evolution. There was no kinship studies either, but at least Tom Trautmann once came in with a talk, Hill Gates asked me about the Russian kinship theorist, Mikhail Kryukov, and Joanna Mountain heard about African “segmentary lineages.” Needless to say, the Anthropological Sciences people were very much into out-of-Africa theory of human evolution. Correspondingly, they were supporters of Clovis-I in the Americas. I took classes with Joanna Mountain and worked in her genetics lab. She was a student of Luca Cavalli-Sforza. I also heard wonderful presentations from Richard Klein on African fossils, Peter Underhill on Y chromosome, Marcus Feldman and Lev Zhivotovsky (a Russian geneticist from Moscow) on autosomal markers, and Joe Greenberg on the peopling of the Americas. When Greenberg passed away in 2001, Christie Turner flew in from Arizona for the memorial conference, only to reiterate the “consensus” between his odontology and Greenberg’s linguistics as a rock-solid proof of a recent origin of American Indians. (By 2005, Matsumura and Hudson in “Dental Perspectives on the Population History in Souteast Asia” //
American Journal of Physical Anthropology 127 deconstructed Turner’s celebrated Sundadonty category as a result of relatively recent admixture, thus depriving his general theories of much of their power.) In 1997-1998, Tom Dillehay’s Monte Verde was coming into spotlight, and John Rick grudgingly accepted Dillehay’s dates, with a caveat that “Tom probably mixed up the strata” but now it’s too late to disprove his Monte Verde tome.

So, I was caught in a cross-fire: on the one hand, feminists and post-structuralists “proved” that kinship studies was the unfortunate invention of the confused Cro-Magnon male; on the other hand, archaeology and genetics from across the Quad “proved” that humans came from Africa some 50,000 BP and peopled the Americas no earlier than 11,500 BP (okay, 12,500 BP but Dillehay must have confused the layers). In 1986, Greenberg tried to endorse the latter view linguistically with his tripartite division of American Indian languages into Amerind, Na-Dene and Eskimo-Aleut. (This classification was eventually rejected by the actual specialists in American Indian languages, and with it went down the linguistic counterpart of the out-of-Africa model.) But there was a gap between molecular genetics and linguistics, namely demography, social structure, marriage practices, residence patterns and kinship terminologies. Only this sociocultural bit of evidence could imbue our human origins story with necessary realism. I thought kinship studies could definitely furnish this missing link, and whether human kinship is about “biology” or about “culture” was an utterly secondary matter. I was contemplating terms like “idenetics” and “gignetics” (from Greek gigno ‘to give birth’, a cognate of gen-) to dub this mature state of kinship studies in the 21st century.

Human origins and dispersals research in the 1980s-1990s was driven by “physical” disiplines, those being archaeology/paleontology and genetics. Sociocultural data, meaning linguistics, kinship systems, mythology, were lagging behind. As late as 1980, Robert Austerlitz published a paper in a highly-specialized linguistics periodical called Ural-Altaische Jahrbucher calling attention to the fact that American Indians harbor much more linguistic diversity than the Old World. In 1992, Johanna Nichols published Linguistic Diversity in Space in Time and concluded that our perspective on early human languages comes from America and Australia/Oceania and not from Africa and Europe. Sociocultural anthropology was supposed to contribute kinship studies to the growing interdisciplinary effort, but it forsook it for the sake of abstract ethical polemics. This is all the more bizarre and unfortunate, since anthropology had been working with worldwide databases of kinship terminologies and forms of social organization long before blood groups were discovered, never mind mtDNA sequenced. (In 1967, Murdock sampled 800 kinship terminologies for the patterns of sibling nomenclature that gave a pretty good overall resolution of what patterns are found on what continents.) And the futility of post-modernist moralizing was vividly manifested “across the Quad,” where any reflexivity was tantamount to heresy. Both versions of anthropology looked equally sterile to me.

As a true patriot of Stanford’s Anthropology, I escaped the split of the department into Cultural and Social Anthropology and Anthropological Sciences by migrating for two quarters to the University of Chicago. I listened to terrific Terry Turner on the Kayapo, the late Kostas Kazazis on Indo-European historical linguistics and Balkan dialectology, flamboyant Michael Silverstein on evidentiality, and cowboy-hatted Ray Fogelson (once Yanagisako’s professor at the University of Washington) on American Indian studies and psychological anthropology. I saw legendary Marshall Sahlins from behind and narrowly missed Eric Hamp and Paul Friedrich. And lo and behold, Tom Dillehay himself was there teaching “Andean Prehistory” for half-a-year from the University of Kentucky. For his class, I wrote a paper suggesting that a crucial piece is missing from our human origins research (namely, kinship systems and related linguistic typology), that the out-of-Africa theory is quick and premature, and that if we look closely at American archaeology we won’t be able to see the exact process by which an adventurous group of Siberian hunters colonized the Americas. Symptomatically enough, Cavalli-Sforza assumed a relatively recent entry into the Americas in order to substantiate his claims of an African origin of modern humans; genetically, American Indians and Africans are polar opposites, hence, if we know that America was peopled late, then we can be sure that Africa was the cradle. Looking at Pleistocene archaeology with a critical eye leads one to believe that the data can’t exactly justify using America as an inverted yardstick for Africa. Clovis tools are found everywhere in the Americas but not in Siberia; microblades are found everywhere in Siberia from 20,000 BP but in America they never penetrated south of the Vancouver Island.

Dillehay gave me an A-, and put me in touch with a fellow out of California by the name of Alvah (Pardner) Hicks who’s been trying for a good decade to convince people to look at America as a possible homeland of modern humans. Hicks was in the midst of the 1990s hoopla around the peopling of the America: he attended conferences, dated skulls in South America, corresponded with Tad Schurr, Dave Meltzer and Lou Binford, buttonholed Lyle Campbell and Emoke Szathmary and summarized a myriad of human origins-related scholarly articles for the Mother Tongue readership (kinda doing blogging before blogging became popular). He tried his best to at least make people consider the possibility that American Indians could have migrated into Siberia at the end of the Ice Age. (Franz Boas talked about it a hundred years ago after the Jesup expedition.) But scholars simply refused to listen to Hicks: he brought to the table wacky ideas and he didn’t have a Ph.D. Nevertheless, Dillehay put me in touch with Hicks probably because I had one extra Ph.D. to give away.

When I returned to Stanford in 1999, I rushed to the library to update my kinship terminological database. The Russian library resources are no match for the Stanford ones, and the several years I spent at Green library comparing kinship terminologies from America, Africa, Oceania, Australia and Eurasia were totally worth it. I dug into obscure Brazilian Ph.D. theses, old French dictionaries of rare Austroasiatic languages and Joe Greenberg’s own collection of African language studies. In the end, I assembled a database of some 2500 languages, diligently assembled a comprehensive bibliography and screened this sample for a bunch of typological markers, such as self-reciprocal terminology, “Crow-Omaha,” sibling nomenclature, formal morphology, etc. Some of these typological/polysemic markers were well-known in the literature, others I had to describe anew. When the ordeal was over, I realized that my initial findings were reinforced and bolstered. American Indian kinship terminologies are archaic, while African kinsip terminologies are transformed.

This is the central thesis of The Genius of Kinship. But it’s not the only one. I introduce the reader into the history of kinship studies within and outside of anthropology, compare the ideas about kinship held by Morgan, Darwin and Lyell and conclude (very much in a post-structuralist vein) that our 19th century ideas about human kinship influenced our ideas about human origins. We looked into archaeology and paleontology for answers to the questions of where we came from, while outright dismissing evidence from living human populations (language, kinship, folklore). We were interested in what was left behind in a garbage pit, not in what was passed down to the next generation. We sought our origins in Neandertals, while letting American Indians pass into oblivion. We bypassed American Indian linguistic diversity and grammatical uniqueness and declared them a “recent” population in virtue of the fact that no fossil hominids were ever found in the Americas.

The Genius of Kinship is not meant to be an advocacy for an out-of-America theory of human origins and dispersals. This is a gigantic task. Rather, it’s a revival of kinship studies in anthropology in conjunction with the recent advances in linguistics, psychology, sociology and historiography, a nitty-gritty typological analysis of a large sample of kin terminologies and its application to the prehistory of such accepted language families as Na-Dene, Austronesian and others. One of the results of this revival is a suspicion that the 150 years of finagling with anthropological knowledge (are Indians savages? shall we continue with kinship or shall we switch to gender? only archaeology can furnish reliable data, let’s look at Neandertals, languages are too difficult to comprehend, while we need something tangible to look at, etc.) has resulted in a confused picture of human origins and dispersals in which fundamental assumptions remain unproven, while every new piece of evidence is either swept under the carpet or instantly reinterpreted to fit the consensus.

For instance, the original mtDNA paper, namely “Radiation of Human Mitochondrial DNA Types Analyzed by Restriction Endonuclease Cleavage Pattern” published by Johnson, Doug Wallace and Cavalli-Sforza in the Journal of Molecular Evolution 19 (1983) clearly showed that American Indians have the highest frequency of the ancestral human mtDNA “morph combination” (That was a restriction-site analysis, but still it provided a foundation for all subsequent research, the only difference being that at some point the tree was flipped around and the Africans were declared the oldest population.) The tree topology in this early paper bears close resemblance to the map of human blood types, with American Indians being preponderantly type O. Now, match Johnson et al. (1983) with Ward et al.’s (1992) intriguing paper on extensive mtDNA diversity among the Nuu-Chah-Nullth exceeding that of African !Kung, and ponder as to why American Indians are widely considered to be a young population. In order to explain away an inconvenient fact, Ward et al. had to resort to an argument that American Indians brought this diversity with them from Siberia. Now that pre-Clovis coprolites attest to the antiquity of mtDNA A and B lineages in North America (see Gilbert et al. Science 320 [5877], 2008), even The Onion is smart enough to ridicule Ward et al.’s logic when it writes: “How can we be sure that some ancient nerd didn’t just carry an already thousand-year-old petrified turd with him when he crossed over the land bridge from Asia?”

Or, take Edward Vajda’s recent discovery of a linguistic connection between an isolated Siberian language, Ket, and Na-Dene in North America. The system of verbal prefixes is better preserved in Na-Dene than in Ket, the Ket sibling terminology is radically transformed from its Na-Dene prototype (The Genius of Kinship, p. 325). Or, the fact that the Kets’ neighbors, the Selkups and the Evenkis have a subtype of the purely American Indian mtDNA haplotype A2 (Tamm et al. Beringian Standstill and the Spread of Native American Founders. PLoS One, September 2007, no. 9). Isn’t it a genetic illustration of Boas’s and Hicks’s “back-migration”? While we find traces of American Indian genes in Siberia, the reverse isn’t true: we haven’t found such a close variant of a Siberian gene in the Americas. Or, if one reads Russian and opens up Vladimir Napolskikh’s dissertation on the Earth-Diver myths in America and Siberia, a simple scheme shows that all the archaic variants of this widely-spread motif are in North America, while all the derived ones are in Siberia.

There’s a puzzling contradiction in our data (if this data is looked at through unbiased interdisciplinary lenses), namely that “physical” disciplines such as archaeology/paleontology find lots of support for out-of-Africa, while “ideational” disciplines such as linguistics and kinship studies have Africa as a secondary spread zone and not a homeland. Which data should we trust? Can we ever hoe to build a robust theory on the basis of archaeology’s always-fragmentary-and-accidental evidence? Or, as Eldridge ad Gould famously claimed, such a theory can only be built on the basis of data coming from living biota? How do we now that the currently popular out-of-Africa interpretation of mtDNA and Y chromosome data is not simply a theoretically possible scenario and and the adaptation of a new system of information to suit the existing archaeological/paleontological consensus but a true description of unique population events? All our population genetic maps show the world at 1492, when Africa was probably genetically most diverse, but by 2008 America is arguably the most diverse continent: what scenario of human evolution would we develop hundreds of years from now provided that we wouldn’t know upfront that America was peopled from Europe, Asia and Africa after 1492? We dismissed America as a “New World” and its inhabitants as an Asian offshoot back in the 16th century, which is long before any scientific evidence has been accumulated, but can we reject the possibility that our modern archaeological, genetic, linguistic and ethnological data is consistent with two opposite “single-origin” scenarios? If so, can we rationally adjudicate between the two scenarios without demolishing one as “wacky” and then using the rubble to lionize the other?

Got to hand it to Blaine Bettinger, of the Genetic Genealogist, for catching this news on GenomeWeb Daily New. In a nutshell, it is a report of what Svante Pääbo‘s talked about at the Biology of Genomes meeting at Cold Spring Harbor Laboratory. Pääbo, if you don’t know, is one of the main researchers behind sequencing the Neandertal genome. He’s spent a lot of his life perfecting the recovering and sequencing of ancient DNA, from Egyptian mummies to ice-age bears.

In late 2006, he was a co-author of a paper reporting that he and his team have sequenced 1 million bases of the Neandertal genome. The paper, “Analysis of one million base pairs of Neanderthal DNA,” was generally well received. But a PLoS Genetics paper titled, “Inconsistencies in Neanderthal Genomic DNA Sequences,” found a lot of problems with results and raised concerns that a lot of the issues are possibly due to modern human DNA contaminants and/or a high rate of sequencing errors. Pääbo has looked into this and in his talk,

“mentioned that about 10 percent of the DNA library they initially sequenced consisted of modern human DNA. But over the last two years, they have been guarding against contamination by generating DNA libraries in a clean room and by barcoding the Neandertal DNA.”

He and his team have also been able to sequence the complete Neandertal mitochondrial genome. They didn’t do this just one time. They did it 35 times, which not only increases the accuracy of the sequence by conferring it many more times, but also weeds out the possibility contamination exists. This has been possible because Pääbo has utilized pyrosequencing, a newish method developed by 454 Life Sciences. Pyrosequencing can handle several contiguous sites in parallel, whereas traditional chain termination methods can’t.

The completed mitochondrial genome of the Neandertal is approximately 16 kilobases long and differs from the Cambridge Reference Sequence of the modern human mitochondrial genome at 133 positions. Blaine has tried to seek out the actual sequence, but with little luck. I hope that they will soon put up the sequence on GenBank for us to play around with!

I recently got an email from German Dziebel letting me know that he’s recently published his book titled, “The Genius of Kinship,” in English. The book explains American Indian kinship systems, and synthesizes ethnographic, linguistic and population genetic lines of evidence to discuss kinship organization. I do not yet have a copy of the book to review, but am curious to read it because criticizes the Out-of-Africa theory and outlines a new model of human origins and dispersals. As you may know, we have had many recent discussions on linguistic and genetic evidence behind the peopling of the Americas, so to read someone has a different take on it all seems very intriguing.

In lieu of a book review, I’ve asked Dr. Dziebel to guest blog here at Anthropology.net. He will hopefully host some discussions about his book and his involvement in anthropology. Dr. Dziebel has some remarkable academic achievements, he holds a Bachelors, Masters and PhD. in History from the Peter the Great Museum of Anthropology and Ethnology of the Russian Academy of Sciences in St. Petersburg. He also has a PhD in Anthropology from Stanford University and an Masters in Sociology from Central European University. He has also done field work on Karelian and Mordvinian populations in Russia.

I welcome Dr. Dziebel to the site and look forward to reading what he has to share with us.

Monte Verde, Chile is a very interesting archaeological site. First discovered in 1976, the site is about 500 miles south of Santiago and has yielded artifacts of a small settlement of 20 to 30 people living in a dozen huts along a small creek. Aside from artifacts, a wide variety of midden has also been unearthed from the site indicating these people survived on extinct species of llama, gomphotheres, shellfish, vegetables and nuts.

In 1979, Tom Dillehay conducted radiocarbon dating of the bones and charcoal found at Monte Verde. The results were shocking at the time. The dating of the organic materials was at 14,000 years before the present. This conflicted with other archaeological evidence of the settlement of North America, such as the artifacts that supported Clovis theory… none of which had dates earlier than 13,000 years ago. To have people living in Chile 14,000 years ago would have meant that people arrived in the Americas earlier than 13,000 years ago. Lots of people rejected the radiocarbon dating because of it challenged the Clovis theory. It wasn’t until 1997 that archaeologists reviewed the evidence, visited the Monte Verde site, and approved of the date.

Since then, lots of other evidence, such as genetics and more artifacts have helped provide more understandings on the mode and tempo of the peopling of the Americas. I’ve covered some of the recent evidence. If you’re interested in reviewing them, check out this collection of blog posts related to the peopling of the Americas.

Today’s Science has published a new report from Monte Verde, authored by Tom Dillehay and others. The paper, “Monte Verde: Seaweed, Food, Medicine, and the Peopling of South America,” announces the discovery of the remains of nine species of seaweed and algae found from hearths in Monte Verde. Radiocarbon dating of the layer yielded a date of 14,220 and 13,980 years ago… which is right in line with the 1979 dates.

The finding of seaweed and algae in Monte Verde is a curious one, and what makes this paper unique. See, Monte Verde is about 10 miles away from the ocean. The authors interpret that the seaweed and algae was of some value for the people of Monte Verde for them to haul it inshore… Perhaps it was used for food or medicine?

Who knows, really? What we can interpret from this evidence is that prehistoric people stuck to the shore. Sticking to the shore woulda made traveling throughout the Americas much more efficient, according to some scholars who subscribe to the coastal migration hypothesis. The general view of this hypothesis is that the early immigrants would have spread down the coast much faster than they could move inland because they could exploit familiar coastal resources more readily and get much of their food from the sea. Not much evidence has been found to support this hypothesis, partially because sea levels are 200 feet or so lower 14,000 years ago than they are right now. Any seaside sites would have been covered up as the ice melted after the last ice age. Finding seaweed from site like Monte Verde indicates that 14,000 years ago people relied on some sea life, and kept relatively close to the shore even though they established a rather permanent settlement inland.

From my personal experience with hiking the Santa Cruz mountains as well as working at an archaeological site in the Monterey Bay, I too have seen evidence that prehistoric peoples were relying heavily on sea life for food. Often, I’ve found mussel shells deep within the forest. I have also seen how people were regularly hunting fur seals from a rookery.

Dillehay, T.D., Ramirez, C., Pino, M., Collins, M.B., Rossen, J., Pino-Navarro, J.D. (2008). Monte Verde: Seaweed, Food, Medicine, and the Peopling of South America. Science, 320(5877), 784-786. DOI: 10.1126/science.1156533

There’s a new PLoS ONE paper making the rounds in the press today. The research behind it fits the kinda stuff you may see on Dienekes’ Anthropology Blog and sometimes on GNXP… it is basically an investigation on the attractiveness of a symmetrical face. The paper is published open access, under the title, “Symmetry Is Related to Sexual Dimorphism in Faces: Data Across Culture and Species.” It comes from psychologists and anthropologists in the U.K. and the U.S.

This subject is extremely interesting. The face has many functions in social behavior — moods are assessed from emotions expressed on the face. The face also functions as a billboard, advertising the quality of the mate. More attractive faces are often thought to be higher quality mates. Both symmetry and degree of sexual dimorphism have been linked to affect the attractiveness of human face shape.

In this study, subjects were given arrays of photos of 500 faces from people of European and African ethnicity as well as photos of non-human primates (macaques). About a third of the faces were male and the rest were females. The subjects were asked to judge for the most attractive face. The most attractive faces were then measured for symmetry. Symmetry was determined by measuring deviations from the midline, as well as measurements for the distance between the eyes. In total 6 measurements were made to assess bilateral symmetry.

The degree of sexual dimorphism was also measured. The distance between specific points, like the prominence of the cheekbone and ratios of the height of the jaw to the lower face height, lower face height to the face height and ratio of the width of the face to the height of the lower face were made. In all samples, symmetric males were ones who also had more masculine facial proportions and symmetric females had more feminine facial proportions. I’ve put up a figure that shows the highs and lows of attractive faces form their study.

These conclusions further validate the notion that sexual dimorphism and symmetry in faces advertise mate quality. I kinda have an issue with how the authors are phrasing their results — they had two ethnic groups in their study but conclude that symmetry & dimorphism is attractive in all cultures. It is very probably that other cultures also share this sentiment, but it is over-stretching the results to say that this reaction is evident ALL cultures and species based off of two ethnic groups.

I’m also not too sure how the authors justify that sexual dimorphism and symmetry in the face provides evidence that there must be a biological mechanism linking the two traits during development. This could be because I really don’t know much about evolutionary psychology. There is without a doubt something going on psychologically that makes people associate symmetry and dimorphic faces as attractive, how that translates to mate quality is highly debatable. On a related sidenote, I find the data about our ability to find attractive primate faces also very interesting, the authors suggest that,

“the signaling properties of faces are universal across human populations and are potentially phylogenetically old in primates.”

Which indicates that there’s been some sort of selection in the primate lineage that has predisposed us to associate symmetrical, dimorphic faces as attractive.

Little, A.C., Jones, B.C., Waitt, C., Tiddeman, B.P., Feinberg, D.R., Perrett, D.I., Apicella, C.L., Marlowe, F.W., Reimchen, T. (2008). Symmetry Is Related to Sexual Dimorphism in Faces: Data Across Culture and Species. PLoS ONE, 3(5), e2106. DOI: 10.1371/journal.pone.0002106

The latest edition of the anthropology blog carnival Four Stone Hearth is now up at remote central, so fell free to head on over and check it out.

The next and 41st 4SH will be at Our Cultural World, on May 21st.

So, I got my hands on that mouth watering Nature paper I mentioned a couple days ago. It is titled, “Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution,” and it is probably the biggest anthropology news of this week. I’ve read it and it is dense. It really shouldn’t be so dense because what the authors ultimately did was a cladistic analysis on 17 of the most complete hominin fossil skulls. What really makes this study different is in the traits they have quantified and compared for their study. I’ll do my best to translate it into plain English.

First, let me define the methodology behind this paper, cladistics, also known as phylogenetics, is a way to organize entities. It can be used to organize really anything — such as tools like hammers, wrenches, pliers, etc. In this case, cladistics was applied on hominin species. Cladistics ultimately organizes things based on upon their ‘shared derived characteristics.’ Shared derived characteristics is an ambiguous term. It really means the traits that are seen in members of the same species, which are unique from other species, i.e. all orangutans have red hair whereas chimpanzees do not, making them different. When dealing with fossils, researchers can only compare and contrast measurements from the bones, such as the size of the brain case or the length of a bone.

I’ve written on several occasions how cladistic analysis works great for grouping different organisms that are really derived. It gets dicey when cladistics tries to resolve organization of organisms that show a lot of variation within one another, as seen in a recent discussion on H. floresiensis. The authors of this paper acknowledge this as a primary motivation for their research. They write,

“However, completion of cladistic analysis becomes problematic because, at lower taxonomic levels, most of observable variation is expressed as continuous changes of size and shape rather than in discrete identifiable structures.”

This problem arises when analyzing hominin fossils, especially fossils thought to be members of the genus Homo. All members of the genus Homo share a large number of derived morphological similarities, that make them different from australopithecines and other apes. What are they? A strictly bipedal adult stature and the largest brain size of all primates are a couple. But, because collections of Homo fossils show a lot of variation in the traits, it makes it difficult to validate such questions like if Homo neanderthalensis was more bipedal that H. heidelbergensis. This has made discerning what traits are unique to each species of Homo troublesome. The authors also acknowledge this. In their own words,

“these [discretization methods] disregard the continuous nature of many complex morphological traits.”

I’ll get to what that really means later in the next paragraph, but first let me also outline another related shortcoming in using cladistics to figure out what’s going on within Homo. See, in the process of trying to find discrete traits in each fossil hominid, researchers have often relied on quantifying multiple traits and presenting them as a univariant measurement. According to the authors, this “disregards the multivariant and geometric nature of form.”

Yesterday, I shared a perfect example of this problem — Yoel Rak identified several traits in the Neandertal mandible thought to be unique to them. He was pownced upon for disregarding that the Neandertal mandible size may have increased as a function of the expanding skull. This problem is not isolated to just Rak, it seems to be prolific within paleoanthropology. Functional traits are often separated from developmental traits, when in fact they are really integrated. The authors address ‘a logical approach’ to overcome this problem,

“treat integrated features as a single phylogenetic complex, and to treat the complex as if it were an independent character.”

The authors applied their approach, selecting four measurements of the skull that integrate functional and developmental traits. The four measurements the authors quantified are the flexure of the cranial base, facial retraction, neurocranial globularity, and the shape and position of the masticatory apparatus. If you’re curious to see exact what these measurements are, the authors provided a figure that illustrates them. I’m putting it right below this paragraph. These traits are believed to be constrained to evolve in a coordinated fashion, rather than independent from one another.

17 skulls were analyzed. John Hawks expressed beef with the sample size, but they are all very complete skulls. Folding in incomplete specimens woulda relied on inferring more missing measurements — which I don’t particularly think is the most conservative approach to figuring out hominid evolution. The 17 skulls are A.L. 444-2, Sts 5, KNMER-406, OH 5, SK 48, WT 17000, KNMER 1813, KNMER 3733, Zhoukoudian, D2700, Steinheim, Kabwe a.k.a. Broken Hill 1, Atapuerca 5, Gibraltar 1, La Chappelle-aux-Saints, and La Ferrassie 1. A skull of a gorilla, chimpanzee, and modern human were also included in the analysis.

In any cladistic test outgroups must be established. Since we know gorillas and chimpanzees existed before the emergence of hominids, they were considered part of the outgroup — or the ancestral form to compare and constrast shared derived characteristics. Australopithecines, like members of the genus Paranthropus (KNMER-406, OH 5, SK 48, WT 17000) and Australopithecus (A.L. 444-2, Sts 5), were also considered in the outgroup because the scope of this study was to resolve the phylogeny of Homo. To reiterate, the function of establishing an outgroup in phlyogenetics is that the outgroup branched from the parent group before the other two groups branched from each other. Respectively, the ingroup (all the Homo skulls) are more closely related to each other than any single one of them is to the ‘outgroup.’

Casts of the skulls were digitized and the measurements were made. A Procrustes analysis was applied to normalize the data, removing variations in translation, rotation and scaling that woulda occurred in digitizing them. The statistical test used was a principal component analysis (PCA), a test that simplifies the variation described by many variables into a few. I kinda see a flaw in this, PCA has often been criticized for quantifying multiple traits and presenting them as a univariant measurement… a concern the authors raised in their introduction.

Anyways, two phylogenetic trees were constructed from the PCA, one applying a maximum parsimony algorithm and another applying a maximum likelihood algorithm. The parsimony algorithm organizes data based upon the premise of having least number of evolutionary changes. Maximum likelihood algorithm is much more statistically viable, it focuses on integrating probability — the normal distribution of a certain variable. Both trees constructed from the data were similar, differing only in the relative position of H. sapiens in relation to the complex H. erectus, H. ergaster, and H. rhodesiensis.

I’ve put the both figures of the tree on this post for you to evaluate. The top figure, a, is the parsimony tree and the bottom figure, b, is the likelihood tree. The coding may not be very straight forward… basically the recipe for deciphering the coding is the first capital letter represents the genus and the next three lower case letters represent the species. If you have any questions with that, comment here, and I’ll do my best to help you out.

The results aren’t very surprising. H. habilis is the ‘founder’ of the Homo clade. The press went wild over the conclusion Neandertals are distinct lineage from the H. erectus-sapiens lineage, which is misleading — we already have a lot of evidence supporting that. Something that’s worth pointing out is that H. heidelbergenis is more related to Neandertals than the H. erectus-sapiens group, which kinda makes sense, no H. erectus specimens have been found east of Turkey, to my knowledge, indicating that a group of Homo were unique to Europe, prior to the influx of H. sapiens — which could have been H. heidelbergenis.

Both trees show some curious organization in the australopithecines, they fail to form a monophyletic group, which is another hot debate in paleoanthropology. This indicates the australopithecines are paraphyletic. Both trees show that Australopithecus africanus is sister group of the genus Homo. This ain’t a very surprising conclusion because A. africanus was gracile and more like Homo… it is thought to have been a direct ancestor of modern humans and this kinda confirms it.

Even though the conclusions are not Earth shattering, I do want to point out that the scope of this paper was not to totally reorganize our understanding of human evolution. In fact, the authors advocate that paleoanthropologists be more cautious in considering what we measure, factoring that some traits need to be considered as modules. It is still possible to recover and reconstruct relevant phylogenetic signals from these modules. In their own words,

“valuable phylogenetic information is recovered from data sets that consider independence on a developmentally and functionally basis, and which preserve the multivariant and continuous nature of complex phenotypes.”

González-José, R., Escapa, I., Neves, W.A., Cúneo, R., Pucciarelli, H.M. (2008). Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution. Nature DOI: 10.1038/nature06891

A summary of Yoel Rak’s talk at the last month meeting of the Paleoanthropology Society in Vancouver, Canada has surfaced in a National Geographic news article from several days ago. Yoel Rak and William Hylander analyzed the anatomy of the Neandertal face and inferred what that coulda meant as far as Neandertal dietary behavior. Did they take quaint bites like a sophisticated aristocrat or were they ruthless wide mouth ogres? If you read the title of this post you’d know the answer to that.

Rak presented his findings, specifically focusing on how the forward-positioned molars and an unusually large mandibular notches allowed Neandertals to gape widely. I’ve put up a photo of La Ferrassie 1 to you right. La Ferrassie 1 is a Neandertal skull found in 1909 in France that shows both traits.

“The scientists believe the large space behind Neandertals’ molars created a geometry that allowed them to take extremely large bites… perhaps an adaptation to the size of the food Neandertals ate, the researchers said.”

This sort of conclusion reeks of adaptionist story telling. I remember reading a similar study that analyzed the form of a horse’s mouth and concluded that it is perfectly adapted to eat apples. Just silly to think of selection and adaptation this way. Anyone one else who shares this sentiment will also appreciate Alan Mann‘s snarky commentary, which really drives home the ridiculous nature behind this study. Mann said,

“They didn’t have to put a whole [animal] leg in their mouths.”

The news article goes on to express Mann’s opinion, on how the gape size expanded as a function of brain expansion.

“What has changed is the architecture that we begin to see in modern humans, where the face and the braincase have different kinds of structural relationships…This has produced a change in our ability to open our mouths.”

Recently, I introduced related studies that showed how Neandertals may have eaten plants and how form may not equal function in regards to hominin mastication anatomy. I have some concerns with both studies, but that doesn’t mean they don’t provide applicable criticisms towards Rak and Hylander’s conclusions on Neandertal dietary behavior.