I picked this book up after wanting to follow up on a topic I touched upon last spring and summer, that of modernity and cultural complexity in Africa. (I've focused on the Akan culture in West Africa primarily because this is the culture with which I am familiar.)
Samuel Obeng's broadly premised book tells us about African (Akan) politeness and cultural complexity and, by comparison, allows us to reflect on the many cultural communication styles outside of Africa.
Conversation among friends, legal discourse, discussion with elders and political dissent are some of the communications which are analyzed. Use of metaphor, hyperbole, irony, avoidance, and many other devices are illustrated. The author does an excellent job of showing how indirectness and politeness function in Akan society to permit communication while maintaining dignity, peace and social cohesion.
'Folklorist Alan Lomax spent his career documenting folk music traditions from around the world. Now thousands of the songs and interviews he recorded are available for free online, many for the first time. It's part of what Lomax envisioned for the collection — long before the age of the Internet.'
As I listened, I was especially engaged, hearing about Lomax's vision and passion:
'"Alan scraped by the whole time, and left with no money. He did it out of the passion he had for it, and found ways to fund projects that were closest to his heart."'
'Money is still tight. But that never stopped Alan Lomax, and it hasn't deterred Anna Lomax Wood, either. "He believed that all cultures should be looked at on an even playing field," she says. "Not that they're all alike. But they should be given the same dignity, or they had the same dignity and worth as any other. "'
Much of Lomax's Collection is contained at The American Folklore Center at the Library of Congress. There's a nice write up on Lomax there which describes his life's work and some of his beliefs:
'Alan Lomax believed that folklore and expressive culture are essential to human continuity and adaptation, and his lifelong goal was to create a public platform for their continued use and enjoyment as well as a scientific framework for their further understanding. His desire to document, preserve, recognize, and foster the distinctive voices of oral tradition led him to establish the Association for Cultural Equity (ACE), based in New York City and now directed by his daughter, Anna Lomax Wood.'
"Although Africa is the origin of modern humans, the pattern and distribution of genetic variation and correlations with cultural and linguistic diversity in Africa have been understudied. Recent advances in genomic technology, however, have led to genomewide studies of African samples. In this article, we discuss genetic variation in African populations contextualized with what is known about archaeological and linguistic variation. What emerges from this review is the importance of using independent lines of evidence in the interpretation of genetic and genomic data in the reconstruction of past population histories."
"In a recent issue of PNAS, Scheinfeldt et al. maintained that, although Fulani mtDNA is consistent with a West African origin, the linguistic and nonrecombinant portion of the Y chromosome (NRY) supports a Middle Eastern origin for this population. Although this is their opinion, the linguistic and genetic evidence fails to support this conclusion."
"The Fulani speak a Niger-Congo language. They probably came to West Africa from Nubia. Welmers explained that the Niger-Congo homeland was in the vicinity of the upper Nile valley, not Niger Basin. The archaeological evidence supports this view, indicating that only in the past 3 ky did people begin to occupy the Niger Basin."
3. Reply to Winters: The Origin of the Fulani Remain Unknown
Laura B. Scheinfeldt, Sameer Soi, and Sarah A. Tishkoff
Published online 2010 August 3
"We would like to first point out that we never interpreted any genetic data in our review article to support a Middle Eastern or European origin for the Fulani. We agree with Winters that the Fulani do not originate from the Middle East or Europe. Furthermore, we do not maintain that there is a predominance of Eurasian markers in the Fulani; we merely point out that there is some evidence of shared recent ancestry (i.e., gene flow) between the Fulani and Eurasian populations based on the presence of particular mtDNA (J1b, U5, H, and V) and NRY (R-M173) haplogroups, and the T-13910 European-specific lactase persistence allele in the Fulani. The combined linguistic and genetic data, however, support an African origin for the Fulani, as we discuss in our work. "
(Link) French documentary film, 50 minutes, Eric Elléna and Clara Ott Produced by Yadé French Connection, Available as a vodeo.tv pay to view download.
"Central and West Africais experiencing apopulation explosion thathas been accompaniedinrecent years by strong growth in the need for foodandmeat.Meanwhile,the situation oftraditional herdsmen,whoprovide much of the red meatconsumed bythe population of largecities,has deterioratedalarmingly.
"The first impacted arethe millions of herdsmen who belong to the Fulaniethnic group who originate inNubia.From Mauritaniato Sudan,thesenomadic or transhumantshepherds, with their remarkable expertise in a flexibleandautonomous form of herding, grace theentireSahel regionwiththeir herds ofzebu cattleand sheep.
"Today, asthe regions in which they have traditionally herded areaffected byrecurrent droughtandanuncontrolled expansionofagricultural areas,their freedom of movement,accessto waterand pastureis madeincreasinglydifficult during the dry season.Consideredaffluent,theyare neglected bygovernments,ordiscriminated against by racketeering farmersand local authorities,attacked byhighwaymenand distressed by the competition fromsubsidizedmeat,imported from Europeand Latin America.
"In Senegal andChad,breedersandresearchersare sounding thecall to protect against unjust lawsof the market in order to preserve an economic sector which isvitalfor West Africa.Will this ancient, flexible, environmentally friendly form of meat production, rich in lessons for our modern society, prosper and continue? Or will it be allowed to disappear in the faceof globalization, climatic hazards and economic uncertainties?"
Le cri d'appel des pasteurs peuls La révolution de l'élevage aura-t-elle lieu?
"L'Afrique centrale et occidentale vit une explosion démographique qui s'est accompagnée dans ces dernières années d'une forte croissance de ses besoins en nourriture et donc en viande. Dans le même temps, la situation des éleveurs traditionnels, qui fournissent l'essentiel de la viande rouge consommée par la population des grandes villes, s'est dégradée de façon inquiétante.
"Les premiers touchés sont les millions d'éleveurs peuls appartenant à la grande ethnie originaire de Nubie. De la Mauritanie au Soudan, ces bergers nomades ou transhumants, au savoir-faire remarquable et aux formes d'élevage souples et autonomes, ont mis en valeur des régions sahéliennes entières grâce à leurs troupeaux de zébus et de moutons.
"Aujourd'hui, alors que leurs régions de prédilection sont frappées par des sécheresses à répétition et par une extension incontrôlée des zones agricoles, leur liberté de mouvement, d'accès à l'eau et aux pâturages est rendue de plus en plus difficile en saison sèche. Considérés comme des nantis, ils sont délaissés par les gouvernements, discriminés ou rackettés par agriculteurs et les autorités locales, attaqués par les bandits de grand chemin et concurrencés par la viande subventionnée, importée d'Europe et d'Amérique Latine.
"Au Sénégal et au Tchad, chercheurs et éleveurs lancent un cri d'appel pour protéger des lois injustes du marché une filière économique, vitale pour l'Afrique. Va-t-on laisser disparaître, dans le contexte de la mondialisation, une forme d'élevage performante, flexible et respectueuse de l'environnement, riche d'enseignements pour nos sociétés modernes, de plus en plus soumises aux aléas climatiques et aux incertitudes économiques ?"
"On the basis of the data and analyses presented by Green et al. and Reich et al., it appears that a simple out of Africa hypothesis with no admixture does not give the full picture of human origins. As sequencing technology improves and additional archaeological discoveries are made, we should be able to gain a more detailed understanding of what now seems to be the mosaic ancestry of the human genome."
Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroups
Viktor Černý, Verónica Fernandes, Marta D Costa, Martin Hájek, Connie J Mulligan, and Luísa Pereira
"Chad Basin, lying within the bidirectional corridor of African Sahel, is one of the most populated places in Sub-Saharan Africa today. The origin of its settlement appears connected with Holocene climatic ameliorations (aquatic resources) that started ~10,000 years before present (YBP). Although both Nilo-Saharan and Niger-Congo language families are encountered here, the most diversified group is the Chadic branch belonging to the Afro-Asiatic language phylum. In this article, we investigate the proposed ancient migration of Chadic pastoralists from Eastern Africa based on linguistic data and test for genetic traces of this migration in extant Chadic speaking populations."
Dienekes, the pseudonym of an unknown anthropology blog author, publishes today PCA plots of human populations against Denisovans, Neanderthals and Chimpanzees. (link)
In the first plot, humans cluster tightly, reflecting their remarkable homogeneity.
In Dienekes' second plot, he claims to "zoom in" on the little blob of humans on the first plot. I have good eyesight and cannot quite see how the "zoomin" of the second plot is taken directly from the "blob" at the center of the first plot.
It's true that the little cluster of humans in the first plot is somewhat multimodal. Those who have been following developments in genetic anthropology won't be surprised that Africans and Non-Africans cluster closely, but separately. Clearly, there are many early humans who didn't make it through events of the last 100,000 years. Additionally, there is evidence of separate low level (<4%) admixture events for Africans and Non-Africans that may account for some of the multimodality. The wiki page on archaic human admixture touches on the relevant references.
Still, I can't quite make out how the two graphs match. The first graph shows that the human cluster is skewed right toward Chimpanzees. In the "zoomed in" plot, Africans seem to be skewed downward and away from Chimpanzees, Denisovans and Neandertals. Yet, the optical illusion is enough for some commentators to think they are observing a "shift toward chimps" of some populations. It would be easy to laugh off Dienekes' amateurish analysis as harmless. However, his blog is widely read. Many of his readers are curious, but not equipped with the analytical skills to see the mistakes in his experiments. Sadly, experts in the field of genetics rarely speak out about Dienekes' biased publications.
While we're on the topic of bias, there's another area of genetic anthropology where I can see a less deliberate form of bias. That's in the area of sampling. More than one sixth of the world's population are African or of recent African origin (within the last five hundred years). However, in the world of genetic anthropology, you would never know it. Study after study show a diverse choice of Non-African samples invariably referenced against a tiny group of African samples. Perhaps this is because the African samples are not widely available. However, it is hard to see how we are going to be able to understand our Out-of-Africa origins when so little effort has been expended to obtain a diverse set of African samples. We will also not learn about migrations within Africa. Additionally, if Africans are going to benefit from genetic research, more attention needs to be paid to Africans as a diverse people, not a tiny reference blob of "Yorubans".
I'm sure that as more African DNA becomes available, genetic anthropology studies will make an effort to include a wider array of African samples. Hopefully, some of those genetic research dollars will make their way toward treating the diseases that Africans suffer from.
As to Dienekes, a more ethically based genetics blogosphere would have more researchers and the curious realize that the message he is presenting is often distorted and potentially clouded with an uninformed view of many Sub-Saharan African groups.
With the new release of Treemix, it is increasingly possible to attempt to map genetic drift and admixture within the human species. If you read through Joe Pickrell and Jonathan Pritchard's paper, you will see buried deep in the Supplementary Material, a test for robustness of the allele data sets they have chosen. It's a classic test of robustness against missing data. In this test, they infer that there must be missing data, as the admixture between Oceanian populations with Neanderthals and Denisovans appears with one allele data set, but not the other. The authors correctly reject any inferences that might be made for Oceanian populations with the given data sets.
With recent genetic discoveries, it is clear that low level admixture events with archaic hominids are present in most human populations, including Asians, Europeans, West Africans and Native Americans. These are low level events, but as they lie at the root of human synthesis, genetic inferences which do not contain enough data to map these early admixture events are likely not to be robust.
Other model vulnerabilities such as a lack of robustness against model inadequacy may also be present. Pickrell and Pritchard note that the Treemix algorithm depends on the assumption that human evolution is largely tree like. Because of this, the algorithm has trouble handling early admixture events such as early human-Neanderthal admixture.
Overall, Treemix appears to be a powerful tool, but it should definitely come with the label USER BEWARE.
R. Srivastava, Rajender Parsad and V. K. Gupta; Robustness Aspects of Experimental Designs, (Link)
"Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and muskox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian muskox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change."
In this paper, Joe Pickrell and Jonathan Pritchard announce a cool software package that plots genetic population relationships. They use the software to analyze populations of humans and dogs. For humans, it shows the continuous, linear process of genetic drift between populations, and also estimates the statistical likelihood of admixture between populations. Their plot demonstrates the effect of geography, with clear jump discontinuites between African, European, Central Asian, East Asian and Indigenous American populations. The authors also plot dogs, who, like humans, exhibit a pattern of genetic drift from wolf to German Shepherd. From that point onward, the dog pattern is very different from the human one, probably because at this point, humans started to take command of dog reproduction. It's interesting to consider that in the period before dog breeding, the wolf-Akita-Husky-Saluki-German Shepherd axis geographically tracks the human Mongolian-Burusho-European axis. It would be interesting to see some samples of indigenous South American dogs, if there were such a thing.
Using the software, the authors identify SNPs that diverge from the overall genome wide patterns. (See comments on Genomes Unzipped.) For humans, SNPs related to skin pigmentation and hair morphology diverge from the genetic drift patterns, indicating that those features are likely to be under selective pressure.
One further point of interest of this paper is that Palestinians, the Bedouin and Mozabites are indicated to be an offshoot of the Druze, a Northern Levant population. Publications, described in the posts The Origin of Y-chromozome Haplogroup J1 and The Bedouin, have previously suggested these relationships. The branching of Western European populations from the Near East has been suggested by Haak, et al and others.
Joseph K. Pickrell and Jonathan K. Pritchard
further comments on the Genomes Unzipped Blog (Link)
" Many aspects of the historical relationships between populations in a species are reected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and ancient Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com/."
I thought it would be timely to revisit the raison d'etre for the word "linear" in the naming of this blog.
The observation of "linear" began with my post processing of ADMIXTURE results of whole genome datasets for Middle Eastern and European populations. That effort began in November and December of 2010. (here, for example.) What became apparent to me was that the ADMIXTURE data contained "components", "West Asian", "Southern European" and "Southwest Asian" that demonstrated an approximately linear genetic variation over geographic distance.
It happens that in the past I have looked at radio frequency data that is also analyzed using methods of linear approximation.
In looking for an explanation of linearity in the population data, I found the paper "The Coalescent in a Continuous, Finite, Linear Population" by J. Wilkins and J. Wakeley. (link)
Later, I stumbled on the Marcus W. Feldman 2008 Nobel lecture, in which he points out that human migration under the influence of serial founder effect yields an approximately linear genetic variation.
That's the reason for the word "linear" in the title. Serial founder effect, shaped by geography and climate, is the dominant effect in understanding human genetic variation.
More recently, I haven't spent much time analyzing ADMIXTURE data sets on this blog. I've certainly seen some very tempting whole genome data sets, but I have to confess that this is not my day job, so regretfully, there is not as much linear analysis on this blog as I would like.
In the last few months, I've looked at Neanderthals, as their small contribution to Eurasians (<4%) demonstrates that while serial founder dominates, other minor "discontinuous" contributions to the human genome also warrant consideration.
John Hawks posts recently on the Dalén et al. 2012 paper "Partial genetic turnover in neandertals: continuity in the east and population replacement in the west" . John is kind enough to post on his blog the Neanderthal phylogeny of the (unfortunately not open access) paper:
Figure 1 from Dalén et al. 2012. Original caption: "Figure 1. Phylogenetic relationships and geographic distribution of Neandertals. Recent (<48 kyr) western Neandertals are placed within a well defined monophyletic group (blue box), whereas specimens older than 48 kyr constitute a paraphyletic group together with eastern Neandertals (red box). The sampling locations for the specimens are shown with corresponding colour coding."
Close examination of the phylogeny suggests that a Neanderthal group migrated westward into Europe from the east sometime before 49kya and subsequently populated most of western Europe. Other Western European Neanderthal groups predating 49kya (those at Monte Lessini, Valdegoba and Scladina) seem not to have survived in Western Europe after 49kya and appear to have been replaced.
It helps to look at a map when pondering the implications of the phylogeny:
If there was migration and replacement, one has to wonder at the driving force behind it. The likelihood that Neandertal groups in Western Europe were under pressure during OIS 3 (MIS 3) due to climate has been suggested. John R. Stewart states:
"The cold-adapted mammals as a whole, such as the extinct mammoth and extant species like the reindeer and arctic fox, did not retreat from the north as the climate cooled like the Neanderthals."
"... Neaderthals were presumably a warmer-continental adapted species, based on their geographical distribution through time. Neanderthals seem to have been better-suited to the Mediterranean during the Late Pleistocene than to the more northern parts of Europe."
"The environmental changes that affected the earlier Late Pleistocene extinctions, including the Neandertals, contributed to the eventual disappearance of the steppe-tundra and all the later Late Pleistocene animals that relied upon it. The transition from Late Pleistocene to the Holocene may also have been similar to the changes that took place earlier at the approach of the LGM. Certainly, we have evidence for a reduction in carrying capacity through OIS 3 in the form of decrease in small carnivore occurances as well as a decrease of mammoth numbers on non-archaeological sites towards the LGM. The steppe-tundra appears to have reached a peak during the earlier part of OIS 3 and had deteriorated by the start of OIS 2, at the end of which it was replaced by the latitudinally banded vegetation zones of the Holocene still seen today. Therefore, the terminal Late Pleistocene extinctions may have been caused by the combination of the LGM together with the eventual warming and stabilising of the climate at the onset of the Holocene. It seems likely that other relatively large climate oscillations such as the Dryas events and other stadials may also have contributed."
Figure 1 of the Meerbeeck et al paper, which I posted a few days ago, describes extremely oscillatory climate in Europe after 50ka and throughout the remainder of the OIS 3. Specifically, there are mini ice ages at 48ka and 38ka which may be corrolated with the population narrowing of Neanderthals described in the Dalén paper. It is also interesting that there is a period of relatively stable but cooling climate from 55ka to 50ka, which could account for the range expansion of the "red box" Neanderthals into Western Europe in the period prior to 50ka.
What is as yet unknown is when, which and how many of these Neanderthal populations were absorbed into the populations of Homo Sapiens. Because no Neanderthal mitocondrial DNA was passed on to us, the answer to that question will have to come from whole genome sequences of Neanderthal samples. In any case, the answer cannot be far away.
John Hawks comments on the hoopla around the release of a book by Dennis Stanford and Bruce Bradley titled Across Atlantic Ice: The Origin of America's Clovis Culture. The researchers propose that Solutrean Hunters from Western Europe reached the east coast of North American during the the height of the Last Glacial Maximum. It's an interesting hypothesis. You can judge for yourself, based on Dennis Stanford's lecture on the topic back in 2008. I posted a link to his lecture last year, the fourth lecture in a superlative series of six.
C. J. Van Meerbeeck, H. Renseen, and D. M. Roche
Abstract: "Dansgaard-Oeschger events occurred frequently during Marine Isotope Stage 3 (MIS3), as opposed to the following MIS2 period, which included the Last Glacial Maximum (LGM). Transient climate model simulations suggest that these abrupt warming events in Greenland and the North Atlantic region are associated with a resumption of the Thermohaline Circulation (THC) from a weak state during stadials to a relatively strong state during interstadials. However, those models were run with LGM, rather than MIS3 boundary conditions. To quantify the influence of different boundary conditions on the climates of MIS3 and LGM, we perform two equilibrium climate simulations with the three-dimensional earth system model LOVECLIM, one for stadial, the other for interstadial conditions. We compare them to the LGM state simulated with the same model. Both climate states are globally 2 degrees C warmer than LGM. A striking feature of our MIS3 simulations is the enhanced Northern Hemisphere seasonality, July being 4 degrees C warmer than in LGM. Also, despite some modification in the location of North Atlantic deep water formation, deep water export to the South Atlantic remains unaffected. To study specifically the effect of orbital forcing, we perform two additional sensitivity experiments spun up from our stadial simulation. The insolation difference between MIS3 and LGM causes half of the 30–60degreeN July temperature anomaly (+6degreesC). In a third simulation additional freshwater forcing halts the Atlantic THC[thermohaline circulation], yielding a much colder North Atlantic region (−7degreeC). Comparing our simulation with proxy data, we find that the MIS3 climate with collapsed THC mimics stadials over the North Atlantic better than both control experiments, which might crudely estimate interstadial climate. These results suggest that freshwater forcing is necessary to return climate from warm interstadials to cold stadials during MIS3. This changes our perspective, making the stadial climate a perturbed climate state rather than a typical, near-equilibrium MIS3 climate."
"In our MIS3 climate simulations with the three-dimensional earth system model LOVECLIM, we find a warmer base climate than that of LGM simulated with the same model. Boundary conditions were different during MIS3 than at LGM, notably insolation, ice sheet configuration, atmospheric greenhouse gases and dust concentrations, all leading to a positive forcing. Our main findings are:
– With smaller Northern Hemisphere ice sheets, higher greenhouse gases and lower dust concentration, MIS3 mean annual temperatures are higher than LGM(globally +1.7degrees C for MIS3-sta and +2.0degrees C for MIS3-int).
– Orbital insolation forcing leads to enhanced Northern Hemisphere seasonality, with mainly warmer summers due to an increase of summer insolation, whereas winter insolation did not change substantially. Northern Hemisphere mean July temperature anomalies compared to LGM are +3.5degreesC for MIS3-sta (+5.7degrees C) between 30degrees N and 90degrees N) and +3.8degreesC for MIS3-int. The sensitivity of the MIS3 climate to insolation changes is relatively high (up to 1degrees C per 4Wm−2). June insolation is 39Wm−2 higher in MIS3-sta than in LGM, which explains about half (2.5degreesC between 30degrees N and 90degrees N) of the July temperature differences.
– If we add 0.3 Sv of freshwater to the North Atlantic Ocean in our stadial simulation, we shut down the Atlantic thermohaline circulation, leading to a much colder climate over Europe and the North Atlantic region. The annual mean temperatures in these two regions are 7.4 degrees C, respectively 6.9 degrees C colder than in MIS3-sta. The simulated cooling leads to a better temperature match with permafrost reconstructions over Europe regarding stadials than in our MIS3-sta simulation. This simulation compares to previous glacial simulations with shutdown thermohaline circulation, with freshwater forcing explaining most of the temperature difference."
Figure 1 of this paper, page 1149, merits the PDF download. It graphically illustrates the oscillatory nature of climate during MIS 3, compared to the LGM and the Holocene, which both present a much more stable climate.