Anthropology.net

Tomorrow’s issue of the high impact & widly cited journal Cell hosts this paper, “A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing (DOI:10.1016/j.cell.2008.06.021)” First author, Richard Green, says that this genome is essentially without error. The genome comes from the Vindija 33.16 specimen, a 38,000 year old Neandertal from Croatia, of which around 0.3 grams of bone was extracted and mtDNA isolated.

Vindija Cave, Croatia

Serre et. al. sequenced the HVR1 region of the mtDNA of the Vindija 33.16 sample in 2004, and Richard Green et al. sequenced 2414 bp of mtDNA sequence from this sample in the famous 2006 paper, “Analysis of one million base pairs of Neanderthal DNA.” Like the 2006 paper, 454 sequencing was used in the current paper because it doesn’t rely on cloning, and yet provides 34.9 fold coverage.

I won’t get into the nitty gritty details of the sequencing protocol, but here’s some of the conclusions of the mitochondrial genome analysis. Comparing the assembled 16,565 base pair Neandertal mtDNA sequence to the 16,568 base pair Cambridge reference mtDNA sequence (rCRS) showed that there are 206 differences, of which 195 are transitions and 11 are transversions).

To assess the evolutionary relationship between modern humans and this Neandertal, the authors compared this Neandertal mitochondrial genome to 53 different mtDNAs of extant humans as well as a bonobo and chimpanzee. They estimated the divergence time of the Neandertal mitochondrial genome by using the 6-8 million year old divergence time of chimpanzees. They estimate a 660,000 year old divergence time between humans and Neandertals, with a 95% credibility interval of 520,000–800,000 years ago.

COX2 Protein Sequence Differences between Neandertal and Modern Humans in Structural Context

The subunit 2 of cytochrome c oxidase (COX2), an enzyme that functions in the electron transport chain, of modern humans exhibits four amino acid substitutions compared to the Neandertals. While the authors don’t know the implications of these subsitutions, they do consider this interesting,

“…because mtDNA is inherited without recombination, and because the Neandertal mtDNA falls outside the variation of modern human mtDNA, this single modern human observation represents a reversion to the ancestral state seen in Neandertals and chimpanzees. Thus, these four amino acid substitutions occurred in the relatively short period after the divergence of Neandertal and extant human mtDNAs and before the most recent common ancestor of current human mtDNAs. The observation of four nonsynonymous substitutions on the modern human lineage, and no amino acid changes on the Neandertal lineage, stands in contrast to the overall trend of more nonsynonymous evolution in Neandertal protein-coding genes, and deserves consideration.”

How does Green know that the genome is without error? In other words, how do we know contamination ain’t an issue? 454 sequencing generates,

“a high average coverage of the random sequence reads in combination with amplification and sequencing of positions where coverage is low, or where longer nucleotide homopolymers may cause base calling problems, make us confident that the error rates from both these sources are low.”

The authors estimate at most, modern DNA contamination is 0.5%.

I’d be really interested to see the sequences of Neandertals prior to the last Ice Age, when population sizes were relatively larger and the genetic diversity would be larger. DNA from Neandertals that were around 110,000 years ago would be great, because, what we have now, is from few individuals that were around glaciation would affect the observed mutations. Some of you may point me 2006 Current Biology paper by Orlando et al. where the authors were able retrieve 123 bp of the mtDNA HVR-1 from the molar of a 10-12 year-old Neandertal child from Scladina cave, Belgium… but that’s a very short region piece of DNA from an individual well inside the glaciation period… But I don’t know of any 110,000 year old Neandertal specimens off the top of my head.

Two papers have come out this week that refine our understanding of the agricultural revolution in the Neolithic Near East. The first is actually an advance copy, “Population Based Re-sequencing Reveals that the Flowering Time Adaptation of Cultivated Barley Originated East of the Fertile Crescent,” published in the journal Molecular Biology and Evolution, in which the researchers sequenced 184 samples of the Ppd-H1 gene of barley.

Barley

Ppd-H1 is a circadian clock gene, one that affects variation in flowering time. The authors identified a unique haplotype due to a SNP called SNP48, which causes early flowering in long days. Specifically a cytosine at SNP48 is associated with early flowering in long days, whereas a thyamine at SNP48 is not associated with early flowering in long days. Effectively this SNP allows for the plant to grow where the growing season is short and with a dry summer. Early domesticators of barley would have selected for this SNP to create a more versatile, flexible barley crop.

They next sought to identify where this SNP originated from. So they did a phylogenetic analysis of the Ppd-H1 gene and traced down the origins of domesticated barley to Iran. Here’s the unrooted tree:

A Phylogenetic Tree of the Barley Ppd-H1 Gene

Is this surprising? No, it is not. 8,000 year old sites in Iran like Ali Kosh have yielded evidence of domesticated barley. And if you’ve ever had ash-e jo, an Iranian barely soup — you’d know the Iranians and barley have had a very intimate history. But, this finding is extremely fascinating because it correlates a phenotype with artificial selection that can be traced to the region of the world where it originated from.

While we’re discussing domestication cultures in the Middle East, a new paper has come out in the journal Nature which extends the domestication of cattle by 2,000 years earlier than previously thought. I must disclaim that I haven’t read the full paper, because my VPN access to my institution’s library seems to be broken, so I’m running this summary off this National Geographic news article. The paper, for those with access, is “Earliest date for milk use in the Near East and southeastern Europe linked to cattle herding.”

This paper is based upon a chemical analysis of 2,200 milk jugs from sites across Turkey, southeastern Europe, and the Middle East. 8,500 year old vessels from northwestern Turkey have high levels of milk fat embedded in the walls. Lead author, Richard Evershed, thinks that cow herders in northwest Turkey were the first milk users, but not necessarily drinkers, because the jugs indicate that they were used to store butter, yogurt, or cheese. Furthermore, the lactose tolerance genotype didn’t appear until 7,000 years ago — 1,500 years after these jugs were being used. Ultimately the significance of this is that people were herding cattle for their milk and using it indirectly — processing milk way before for lactose intolerance problems were resolved.

Jones, H., Leigh, F.J., Mackay, I., Bower, M.A., Smith, L.M., Charles, M.P., Jones, G., Jones, M.K., Brown, T.A., Powell, W. (2008). Population Based Re-sequencing Reveals that the Flowering Time Adaptation of Cultivated Barley Originated East of the Fertile Crescent. Molecular Biology and Evolution DOI: 10.1093/molbev/msn167

According to this press release, a new paper reports on the discovery of a 10,000 year old SNP on the Y-chromosomes of men from Tanzania and southern Africa. It will be appearing in PNAS‘ online early edition tomorrow (DOI: 10.1073/pnas.0801184105). The SNP is thought to have originated in eastern Africa,

“The team analyzed Y chromosomes from men in 13 populations in Tanzania in eastern Africa and in the Namibia-Botswana-Angola border region of southern Africa. They discovered a novel mutation shared by some men in both locations, which implied those men had a common ancestor. Further analysis showed the novel mutation arose in eastern Africa about 10,000 years ago and was carried by migration to southern Africa about 2,000 years ago. The mutation was not found in Bantu-speakers, suggesting that a different group – Nilotic-language speakers – first brought herds of animals to southern Africa before the Bantu migration.

This new genetic evidence correlates well with pottery, rock art and animal remains that suggest pastoralists – herders who migrated to new pasture with their flocks – first tended sheep and cattle in southern Africa around 2,000 years ago. The genetic finding also helps explain linguistic similarities between peoples in the two regions.”

You may know that previous research based upon archaeology, skeletal morphology, linguistics and mtDNA has suggested that prehistoric people in eastern and southern Africa were virtually isolated between 30,000 and 1,500 years ago, with only two known migrations between the regions during that time frame. One of the authors of this paper, Brenna Henn, acknowledges this over at the Spitton. She writes,

“Our new genetic study, while still supporting the archaeological record for the timing and place of the origins of pastoralism in sub-Saharan Africa, puts a new twist on the current thinking. It suggests that a small group of men actually migrated into southern Africa about 2,000 years ago. These men probably married into local hunter-gatherer populations, contributing their livestock and cultural knowledge of pastoralism.”

About a week ago, I read and posted on a summary piece on cultural evolution research in PLoS Biology. The reviewer introduced me to Simon Kirby‘s work, which I found remarkable. Kirby and colleagues setup an experiment, one that observed the evolution of an artificial language from a set of random terms to an ordered, naturally adapting system in ways that assured its reproduction.

I didn’t know when Kirby was to publish his work, but lo and behold in this week’s issue of PNAS, I saw “Cumulative cultural evolution in the laboratory: An experimental approach to the origins of structure in human language,” by Simon Kirby, Hannah Cornish, and Kenny Smith. The experiment involved showing subjects illustrations that were associated with nonsense words.

The subjects were asked to play a game of Memory, by trying to recall the terms with the illustrations. Regardless of the accuracy of their recollections, the associated terms were used as a foundation of the group’s subsequent language training. This was done over and over, and low and behold, detectable patterns began emerging. Terms began to be used to describe whether an illustration pictured horizontal movement or a bouncing object. The following graphs document the transmission error and measure of structure over each generation:

Transmission Error & Measure of Structure versus the Number of Generations

Clearly there’s some pattern forming. But, Kirby and team understood that these emerging languages were simplistic and limited. So the team switched it up a bit, and discarded duplicate words. This represented a sort of selection, which gave structure and allowed the language to be remembered. Throughout 10 generations, the grammar of laboratory language went from meaningless, ad-hoc bunch of words into an expressive mode of communication. The speakers didn’t change, it was the change in the meanings behind the terms. The following graphs document the transmission error and measure of structure over each generation with selection:

Transmission Error & Measure of Structure versus Number of Generations with Selection

So how did the subjects screen out their own linguistic predispositions? Most humans are exposed to at least one language, which would clearly bias them and affect their abilities to give structure to a set of gibberish. In other words, the ‘selection’ applied could have been favoring structures that matched existing languages.

Kirby said that’s not really a concern, because that languages that emerged in his experiments do not have much in common with the extant languages. And since the emerging languages resembled those from computer models, which did not have preexisting languages to muddle up the waters, then we’re not to worry. Kirby concludes that the,

“The best explanation for our results is the cultural system ‘discovering’ adaptations for all aspects of the transmission bottleneck rather than merely mirroring the native language of our participants.”

Kirby, S., Cornish, H., Smith, K. (2008). Cumulative cultural evolution in the laboratory: An experimental approach to the origins of structure in human language. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0707835105