Anthropology.net

One of the pieces to appear in the latest Science is Constance Holden’s synopsis of the core issues discussed at last week’s meeting of the National Human Genome Research Institute: defining geographic populations, handling interpretations of race (especially as as a sociopolitical term), and phrasing results of population genetic studies.

I paid cursory attention to the etymological aspects of the piece. Yes, I know Amerindian isn’t how some Native Americans want to be identified as, and there are some problems with figuring out where European populations end and where Asian populations begin. But I’m hopeful, as more individual genomes are sequenced and released, that genetic patterns can better define populations than cultural and geographic categories have in the past. We don’t necessarily have to rephrase terms or agree on new ones, but can possibly use biological terms, such as allele frequencies, as defining characteristics of populations.

Holden also reviews a discussion on interpretations of fitness — i.e. how some of the public may interpret Carlos Bustamante’s recent Nature paper, where he concluded that European-Americans had more deleterious gene mutations than African-Americans. Does that mean there’s some sort of superiority? No, but that doesn’t mean the public won’t interpret it like that. Should scientists hold back on their reporting their results or sugar coat them just to prevent the public from over analyzing them? I don’t think so.

The must read part of this news piece, especially for anyone news piece for anyone interested in the current state of population genetics and molecular anthropology, is the heated debate between Bruce Lahn and Celeste Condit, a professor of speech communication at the University of Georgia, Athens. Bruce Lahn, as you may know reported 4 years ago that selection in mutations of two genes (ASPM & microcephalin) regulating brain development is more common in Eurasians than in Africans. Condit argued that Lahn’s results have a political message embedded, a common mistake that many uneducated critics of population genetics repeat. We’ve had similiar misconceptions raised on Anthropology.net. Lahn retored back that some…

“are almost like creationists” in their unwillingness to acknowledge that the brain is not exempt from selection pressures.”

Oh snap! The whole meeting didn’t seem to be fruitless though, most agreed that suppressing freedom of reporting results as they are observed in the name of political correctness is not conduicive to the scientific method.

C. Holden (2008). PERSONAL GENOMICS: The Touchy Subject of ‘Race’ Science, 322 (5903), 839-839 DOI: 10.1126/science.322.5903.839a

Tomorrow’s issue of Science hosts lots of interesting papers, one of which is titled, “A Test of Climate, Sun, and Culture Relationships from an 1810-Year Chinese Cave Record,” and reports on the analysis of a 1.2-meter-long stalagmite from Wanxiang Cave in northern China. The analysis tells us that the rock holds records of waning Asian monsoon rains around 1,100 years ago. The dry spell was due to weakening of the sun, possibly from a sunspot, and this climate change is thought to have been what brought down the Tang dynasty.

Map of Wanxiang Cave, China

Stalagmites are calcium carbonate mounds which form from dripping groundwater. Chemical analysis of this Wanxiang stalagmite told the researchers that there’s a lot of uranium and exceptionally low clay-borne thorium. That allowed them to do a uranium-thorium radiometric dating of the layered deposits down to an interval of 2.5 years. With such accuracy, the authors were able to calculate precise dates for variations in the stalagmite’s oxygen isotope composition. Oxygen isotope levels reflect variations in rainfall near the cave. The isotope levels match that of drought conditions.

Comparing this result to Chinese historical records of rainfall, the authors matched the chemical analysis to the written record. Furthermore, previously published climate record from a lake on the southern coast of China also confirm this. This 9th-century dry period is also thought to be what also doomed the Mayan civilization. Poor rainfall affected crops and the carrying capacity of each civilization.

P. Zhang, H. Cheng, R. L. Edwards, F. Chen, Y. Wang, X. Yang, J. Liu, M. Tan, X. Wang, J. Liu, C. An, Z. Dai, J. Zhou, D. Zhang, J. Jia, L. Jin, K. R. Johnson (2008). A Test of Climate, Sun, and Culture Relationships from an 1810-Year Chinese Cave Record Science, 322 (5903), 940-942 DOI: 10.1126/science.1163965

Today’s issue of Nature has a brief essay on the role of language in cultural evolution. The authors touch up on a lot basics, such as anatomical localization of brain activity related to language and tool making, FOXP2, and how language has helped humans pass on cultural information more effectively than any other form of communication. Overall, it is a well written review that I want to pass on.

Related, Erin from the Spitton, shared news of the identification of a new language related SNP on the gene CNTNAP2. The paper which reports this is titled, “A Functional Genetic Link between Distinct Developmental Language Disorders,” and was published in the New England Journal of Medicine. I believe it is open access, I got to the full text with no problem. The authors hypothesized that neural pathways downstream of FOXP2 can also affect language impairment.

To identify possible downstream candidates that might be involved in typical SLI, the authors transfected a human brain cancer cell line (SH-SY5Y) to continually express FOXP2. FOXP2 is a transcription factor, meaning it is a controller of the expression of other genes. If it is mutated, it can’t regulate its targets properly and leads to different, sometimes mutant, phenotype. The used a type of test called the chromatin immunoprecipitation (ChIP) assay which identifies how and often where proteins, like the FOXP2 transcription factor, bind to specific regions of the genome. This is done by using specific antibodies that recognize a specific protein or a specific modification of a protein, in this situation anti-FOXP2 antibodies.

The ChIP assay showed that the FOXP2 transcription factor binds to a particular, novel region of interest, the first intron of gene CNTNAP2. When transcribed and translated, CNTNAP2 normally encodes for the protein CASPR2 — a protein that is localized and understood to function in the nodes of Ranvier on myelinated neurons. Of further interest, CNTNAP2 is expressed in the human cerebral cortex, specifically the orbital gyrus and superior frontal anlage, spanning the inferior and middle frontal gyri — all regions know to related to language cognition.

To make sure that FOXP2 was for sure targeting this region, and wasn’t mislead due to any conformational changes that came from the antibody it was complexed with, the authors did some PCR and sequencing and saw that this region of interest, intron 1, does have matching known consensus, binding sequence for FOXP2. They did some other tests that shows that this sequence is highly specific to FOXP2… all of which suggests that this site on CNTNAP2 is definitively a binding site for FOXP2 (CAAATT).

The authors next varied the amount of FOXP2 expression and tried to see if it affects the ultimate expression of CNTNAP2. They were able to show there is a correlation — CNTNAP2 transcript levels were lowest where there are higher levels of FOXP2, suggesting that FOXP2 down regulates CNTNAP2. We haven’t know about FOXP2-CNTNAP2 interactions before, because FOXP2-bound fragment of CNTNAP2 is outside of the classically defined regulatory regions that promoter based microarrays identify… So identifying this pathway is very commendable.

With this downstream candidate gene isolated the authors moved to see how polymorphisms in CNTNAP2 manifest language phenotypes. Their population sample was made up from children from 184 different families where at least one child had a specific language impairment (SLI). The children had wildtype FOXP2, but children who carried the guanine nucleotide at rs17236239 SNP on CNTNAP2 had worse scores on a test that measures their ability to reproduce nonsense words like “brufid” and “contramponist.”

Now don’t get me wrong, this SNP, rs17236239, ain’t on intron 1 — where FOXP2 binds. FOXP2 was used as bait to fish out what gene bites to it. When CNTNAP2 was figured out to be a new novel target of FOXP2, the authors tried to see if CNTNAP2 variations also affect language. And they do. What’s also of interest is that other SNPs in the same regaion that rs17236239 is found also have CNTNAP2 as been linked to delayed speech in children with autism.

I’m really impressed with this paper. It’s a gem. Well written and straight forward. I don’t regularly read papers of such caliber, to be honest… So I really appreciate when I do. The new language related gene is also very important as we begin to piece together the complex network of genes and proteins, anatomy and behaviors that have allowed us to have language and use it.

Eörs Szathmáry, Szabolcs Számadó (2008). Being Human: Language: a social history of words Nature, 456 (7218), 40-41 DOI: 10.1038/456040a

S. C. Vernes, D. F. Newbury, B. S. Abrahams, L. Winchester, J. Nicod, M. Groszer, M. Alarcon, P. L. Oliver, K. E. Davies, D. H. Geschwind, A. P. Monaco, S. E. Fisher (2008). A Functional Genetic Link between Distinct Developmental Language Disorders New England Journal of Medicine DOI: 10.1056/NEJMoa0802828

If you’re a regular reader of Dienekes blog, you’d know he’s consistently raised concerns that calibrations of molecular clocks don’t quite fit the bill. Yesterday, he posted an addendum and shared a new paper in which authors advocate that molecular clock can be calibrated upon an archaeological context (not phylogeny-based) and human mtDNA estimates of dates of population and phylogenetic events should be adjusted to time-dependent mutation rate estimates.

I’m not gonna get into a rehashing of Dienekes’ post, I wouldn’t do as good of a job even if I did… but you should jump on over and read what he has to say and how he explains his criticisms of how the clock has been calibrated in the past. I want to spend some time in this post discussing some of the results of the paper he shared, “Characterizing the Time-Dependency of Human Mitochondrial DNA Mutation Rate Estimates,” in Molecular Biology and Evolution. The authors sought to establish genealogy-based estimates of the mtDNA mutation rate using both hypervariable and coding region data, they also wanted to figure out if multiple hits  affect the discrepancy between the different methods of mutation rate estimation.

So they setup new genealogy-based rates from 2,500 to 50,000 years ago using mtDNA from populations in the Canary Islands, Polynesia, Micronesia, North America, Taiwan, Indonesia, and Oceania. The populations were selected based upon relative isolation and the  available archaeological dates for the time of first human arrival, haplotypic data from neighboring regions, and indigenous haplotypes for that region.

The authors were able to calculate that the evolutionary mutation rate between approximately 2,500 and 50,000 years ago was much different than that from 50,000 to 6 million years ago. They suggest that since earlier mutation rates, ones based upon pedigrees, are not affected by the processes of
bottlenecks and selection, except for purifying selection on lethal alleles, they can’t weed out the effects demographic processes. Using their time-dependent approach they observe that molecular clock was accelerated for large Neolithic populations and is similar to the pedigree rate, but for the smaller Paleolithic hunter-gatherers it was much lower…. makes sense, as populations grow, variability accelerates.

B. M. Henn, C. R. Gignoux, M. W. Feldman, J. L. Mountain (2008). Characterizing the Time-Dependency of Human Mitochondrial DNA Mutation Rate Estimates Molecular Biology and Evolution DOI: 10.1093/molbev/msn244

Joyce Marcus has published a bold review in the Annual Review of Anthropology where she argues that anthropology must be willing to generalize — cultures must be compared and contrasted in order identify similarities in the ways cultures have responded to challenges. In other words, relativism has no place in trying to understand the evolutionary pattern to human social structure.

She further argues that such a comprehensive and comparative analysis of cultural evolution must be done with collaboration between ethnologists and archaeologists. She stresses the impact of archaeology has in investigating cultural evolution, using the transition to agriculture and animal domestication as a critical moment when we can see the emergence of institutions not seen in previous lifestyles. She further relates the relationship between ethnology and archaeology is analogous to that,

“… between zoology and vertebrate paleontology. Zoologists are able to study both muscle tissue and behavior at a level of detail unavailable to paleontologists. Paleontologists, however, can find the muscle attachments on fossil bones that provide evidence for specific muscles; they can then draw on the zoological literature both on those muscles and on the behavior they reflect. Paleontologists can also elucidate long-term trends and recover the skeletons of transitional species unknown to zoology; such fossils show us the order in which certain structures (and hence behaviors) arose. In an important sense, the fossil record is the proving ground for any theory of change based on comparisons of living species.”

In order for us to understand how cultures evolve, she’s very right, cultural anthropologists and archaeologists do need to collaborate. Hell, archaeologists even need to understand that they’re not just digging up cultural noise. Both disciplines need to agree upon a common terminology and see that cultures can be compared. But I don’t know if many cultural anthropologists are ready to hang up their relativist coats on the hanger just yet.

Joyce Marcus (2008). The Archaeological Evidence for Social Evolution Annual Review of Anthropology, 37 (1), 251-266 DOI: 10.1146/annurev.anthro.37.081407.085246