For what they were... we are

Mellars 2013: second round

2013-06-18T18:56:00.002+02:00

As I mentioned before, I have already got copies of the controversial study by Paul Mellars et al., which argues for a very late colonization of Eurasia. It includes some aspects not dealt with in the first round, when I could only access the supplemental material.

Paul Mellars et al., Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. PNAS 2013. Pay per view (6-month embargo) → LINK [doi:10.1073/pnas.1306043110]

Maybe the most important is the very striking visual comparison between proto-LSA African microlithic industries and post-UP South Asian microlithic ones:

While it is maybe easy to dismiss the patterns drawn on ostrich shells in Africa and South Asia as not really looking the same at all and therefore likely coincidence, the visual comparison of the industries is much harder to reject. It does indeed pose a mysterious apparent link similar to others that are hard to explain like the similitude between Chatelperronian and Gravettian (not so long ago treated together as "Perigordian") or the hammering insistence by some rather marginal academics on the similitudes between the SW European Solutrean culture and the (much more recent) North American Clovis industry.

Sure: impressive and intriguing. But when it comes to chronology the Mellars hypothesis seems to fail terribly. While the African microliths are pre-LSA and therefore from before ~49,000 years ago in all cases, the South Asian ones only show up mostly since c. 34-38,000 years ago, more than ten millennia later. Mellars makes this figure 40-35 Ka and then just 40 Ka for the following graph, which in fact misrepresents Petraglia's model and data in a key issue (see below):

It must be emphasized here that Petraglia's data and model, at least for what I know it, implies an hiatus between c. 110 Ka and c. 80 Ka BP, hiatus for which there is no archaeological data of any kind in South Asia. Therefore neither side graph should suggest continuity to the past before ~80 Ka, allowing at most for a highly hypothetical dotted line (as in Petraglia 2010):

Also there is nothing in Petraglia's work that could suggest discontinuity at the Toba ash layer, as suggested by Mellar's version, rather the opposite: continuity is very apparent in Jwalapuram:

Jwalapuram industries (from Petraglia 2007)

Quite conveniently Mellars ignores Petraglia's data again, which suggest continuity before and after microlithism in Jurreru Valley and then also finds a transition towards UP ("blade and bladelet", as well as "backed artifacts") technologies since c. 34 Ka BP.

But regardless, I'm pretty sure that Prehistory-savvy readers have already noticed a major issue in all this chronology: we are talking of dates that are almost 20,000 years after the colonization of West Eurasian by H. sapiens with "Aurignacoid" technologies, which are dated to before 55 Ka BP in Palestine (OSL), to c. 49 Ka BP in Central Europe and to c. 47 Ka BP in Altai (C14 calibrated).

And those who are also familiar with Eurasian population genetics are by now shaking their heads in disbelief and claiming to heaven and hell alike. Because West Eurasians derive, at a late relative date, from Tropical Asians and therefore, if our core ancestors were already separated before 55 Ka BP, there is just no room for the Tropical Asian (and Australasian) expansion that must have preceded the Sapiens colonization of the West Eurasian Neanderlands.

(Those unfamiliar with the basics of Eurasian population genetics, see here).

So there is no way that the Out of Africa migration could be dated to just c. 55 Ka BP, as Mellars does (after grabbing hard the burning nail of conjectural coastal sites now under the sea, which would have to account for some 15-20,000 years of Eurasian prehistory on their own).

In fact it is also impossible from the viewpoint of Australian chronology, which again needs to go after the settlement of Tropical Asia but surely before that of West Eurasia.

So, regardless of the striking visual comparison between African and Indian industries, which is no doubt the "bunny in the hat" here, the Mellars hypothesis simply doesn't stand.

Was there another cultural (surely not demic) flow from Africa to South Asia c. 40-35 Ka BP? Maybe. Or maybe it is just one of the many hard-to-explain coincidences in stone industry design. But whatever it is, it just cannot be the Out-of-Africa migration, unless one is ready to accept that Aurignacian and related European rock art, as well as Australian rock art, for example, are the product of archaic homo species (something that I am sure that Mellars won't admit to: it just goes against his "modern human behavior" prejudices). And, even then, it just doesn't add up either.

PS- Petraglia himself finds Mellar's alternative model untenable. From ABC Science (emphasis mine):

... Professor Michael Petraglia, an archaeologist from the University of Oxford disputes Richards' and Mellars' argument.

Petraglia says there's not enough evidence to rule out an earlier colonisation before the eruption of Mount Toba.

"The research reported by Mellars and colleagues is riddled with problems," he says.

Petraglia says that the similarity between tools used in Africa 60,000 years ago and those from Asia dating to around 35,000 years ago is not a consequence of direct migration.

"These toolkits are separated in time by more than 20,000 years and distances exceeding several thousand miles."

He questions the evidence supporting a migration along the coast. He says that surveys of ancient shorelines have not revealed any evidence for human settlements anywhere along the Indian Ocean shore between 55,000 and 50,000 years ago.

He also says genetic dating should be treated cautiously.

"Most geneticists will admit that genetic dating of the out-of-Africa event is tenuous, at best. Published genetic ages for out-of-Africa range anywhere between 45,000 to 130,000 years ago.

Petraglia says his team is currently conducting archaeological fieldwork in Arabia, India and Sri Lanka they expect will show that the story of human dispersal from Africa is complex.

"What we can agree on is that little research in these key geographic regions has been conducted and much more evidence needs to be collected to support or refute the different theories," says Petraglia.

Mellars challenges the 'early out of Africa' model

2013-06-11T15:38:00.001+02:00

~~I do not have yet access to this potentially key paper, so first of all I want to make an appeal here to share a copy with me (→ email address). Thanks in advance~~. Update: got it (thanks to all who shared, you people are just great!) I will review it again as soon as possible.

Update (Jun 18): complementary review of the full paper now available here.

Abstract

It has been argued recently that the initial dispersal of anatomically modern humans from Africa to southern Asia occurred before the volcanic “supereruption” of the Mount Toba volcano (Sumatra) at ∼74,000 y before present (B.P.)—possibly as early as 120,000 y B.P. We show here that this “pre-Toba” dispersal model is in serious conflict with both the most recent genetic evidence from both Africa and Asia and the archaeological evidence from South Asian sites. We present an alternative model based on a combination of genetic analyses and recent archaeological evidence from South Asia and Africa. These data support a coastally oriented dispersal of modern humans from eastern Africa to southern Asia ∼60–50 thousand years ago (ka). This was associated with distinctively African microlithic and “backed-segment” technologies analogous to the African “Howiesons Poort” and related technologies, together with a range of distinctively “modern” cultural and symbolic features (highly shaped bone tools, personal ornaments, abstract artistic motifs, microblade technology, etc.), similar to those that accompanied the replacement of “archaic” Neanderthal by anatomically modern human populations in other regions of western Eurasia at a broadly similar date.

A review has been published at Live Science.

South Asian artifacts from ~30-50 Ka BP.

By "genetic evidence" they obviously mean "molecular clock" nonsense, so it is not evidence at all but mere speculation. However I am indeed very interested in knowing in detail what they mean by "archaeological evidence", because they seem to get into direct confrontation with much accumulated evidence, first and foremost all of Petraglia's research in both India and Arabia but also with the quite strong evidence for pre-60 Ka human presence in Australia and growing evidence for pre-60 Ka modern humans in SE Asia (in some cases even as old as 100 Ka).

It must be said that Paul Mellars has been criticized before a lot for several reasons but very especially for his adherence to the quite speculative "modern human behavior" conjecture and, relatedly, bigotric attitudes against Neanderthal intellectual capabilities, based on nothing too solid. Therefore I'm generally skeptic about what Mellars has to say on this matter because this kind of conclusion is what one would expect from him.

However Mellars is certainly a distinguished academic and, even if prejudiced and stuck to his own old-school and somewhat Eurocentric interpretations, he knows his trade as archaeologist and prehistorian. So he may be onto something, even if it is not exactly what he wants us to believe.

For example, it is not impossible that this research may have, unbeknown to the authors, found evidence of a secondary OoA wave (maybe related to the spread of Y-DNA D and mtDNA N?) or even a distinctive evolution in Southern Asian technology prior to the expansion of Western Eurasia.

It is interesting that they suggest that the 80-60/50 Ka toolkits of India would have been made by Neanderthals, when they are not describing them at all as Mousterian, the almost exclusively Neanderthal techno-culture, or Mousterian-related.

I have some difficulties judging before reading the whole study. However the supplemental material (quite extensive) is freely accessible and for what I can see there:

They dedicate much text to attempt to justify a particular version of mainstream "molecular clock" hypothesis, which are clearly broke in my understanding. The kind of arguments "rebated" are more or less what I have been putting forward since many years ago. Ironically their "molecular clock" estimates make N and R much older than M, what I absolutely oppose (just count mutations downstream of the L3 node).
No real attention is given instead to the geographical structure/distribution of major mtDNA haplogroups, only mentioned in relation to "molecular clock" speculations.
The criticism of the African affinity of the Jwalapuram (Jurreru Valley) cores (Petraglia 2007) focuses on dismissal of any possibility of comparison, rather than on alternative comparisons.
Another "criticism" is that there is no apparent connection between Jwalapuram and the Nubian Complex (why there should be any?, it is not the only East African techno-culture, nor the only group that shows indications of traveling to Arabia in the Abbassia Pluvial).
Also it is "criticized" that the most comparable African culture, Howiesons Poort) is not recorded before c. 71 Ka BP (what IMO may indicate late cultural dispersals to Southern Africa from East Africa, for example, but, hey!, Mellars is fencing off balls like crazy at his conservative goal).
They find clear similitudes between Indian and African microlithic industries (apparently related to the development of "mode 4" in both areas, as well as in West Eurasia). Indian industries are dated to c. 38-40 Ka BP, while African ones are dated to c. 49 Ka BP (Kenya) or later. However West Eurasian ones have dates as old as 55 Ka BP (not for Mellars, who remains stuck in older date references which he describes as ∼40–45 ka [calibrated (cal.) before present (B.P.)]), what really suggest that we are talking here not of the "out of Africa" but of the West Eurasian colonization process (necessarily from further into Asia, genetic phylo-geographic structure demands) with offshoots to the nearby regions.
Another element of late Africa-India "similitude" they find is "the remarkable, double bounded criss-cross design incised on ostrich eggshell", dated in India (Patne) to at least ∼30 ka (cal. B.P.), much earlier in South Africa. For Mellars this is beyond the range of either pure coincidence or entirely independent and remarkably convergent cultural evolutionary processes. Hmmm, really? Or are we before a clear case of wishful thinking as happens with the Solutrean-Clovis relationship hypothesis? Isn't it 30 Ka BP anyhow well beyond any reasonable expectations for the OoA time frame, including Mellar's own conjectures?
Mellars accepts the paradox that the geographical limits of these highly distinctive microblade and geometric microlithic technologies are confined to the Indian subcontinent, with no currently documented traces of these technologies in regions farther to the east. And then makes up excuses for it, such as biological and cultural bottlenecks caused by "founder effects", mysteriously leading to a loss or simplification of cultural and technological know-how, as well as fininding new and contrasting environments (in the same latitudes?!)
Even in the case of Arabian colonization, Mellars shows to be in a very defensive attitude, admitting only to the reality of the Palestinian sites with clearly modern skulls, as well as to the area of Nubian Complex colonization (on whose peculiarities he insists a lot, as if it would be the only expression of the wider MSA techno-complex), disdaining all the other MSA colonization areas and, often ill-defined, variants.

In brief, for what I could see in the supplemental material, along with some potentially interesting references to the relative cultural community spanning from East Africa to South Asia at the time of emergence of "mode 4" industries, it seems that Mellars and allies are essentially putting the cart (their models) before the horses (the facts), what is bad science.

In 2008, Zilhao and d'Errico angrily accused Mellars of being an obsolete armchair prehistorian (different words maybe, same idea). Back in the day I was tempted to support Mellars but nowadays I must agree that he is clearly stuck in a one-sided interpretation of prehistory whose time is long gone. Whatever the case I welcome the debate and can only hope that will help to produce even more evidence to further clarify the actual facts of the Prehistory of Humankind.

55 million years old evolved primate fossil

2013-06-10T16:28:00.002+02:00

A small early Tarsiiforme specimen, named Archicebus achilles, lived some 55 million years ago in what is now Central China, it has been known from a recently discovered fossil (right).

This primate was already an ancestor of modern tarsiers, then just diverged from the line leading to us Anthropoidea, what comes to support the theories that suggest an old origin of the primate lineage, possibly c. 85 Ma ago, still in the Cretaceous era, when T. rex and all the famous Hollywood dinosaurs still roamed the Earth.

And this has of course implications as well for the origin of mammals, popularly believed to be in a very early stage of their evolution in that period... but maybe much more diversified than some pop documentaries want us believe.

Until now the oldest known primate was Plesiadapsis, a proto-lemur that may look maybe more like a squirrel than a primate (at least to my eyes). Plesiadapsis is from the same time as Achicebus, c. 55-58 Ma ago.

Primate phylogenetic tree (from Wikipedia) with the aprox. placement of Archicebus

Ref. X. Ni et al. The oldest known primate skeleton and early haplorhine evolution. Nature. Vol. 498, June 6, 2013, p. 60. doi:10.1038/nature12200.

HERC2 haplotypes, phylogeny and frequencies

2013-06-09T14:25:00.001+02:00

Palisto at Kurdish DNA has a most interesting report of his own production on the eye color gene HERC2, its variant haplotypes, their phylogeny and their frequency in West Eurasian and Pakistani populations.

Based on Kurdish haplotypes, he developed the following phylogeny:

All branches produce dark eye color, excepted the two colored in blue, which are associated with light eye color.

The defining transitions from branch#3 to branch#1 are rs1129038 and rs12913832 (demonstrated to cause blue eyes in 99% of cases) while the transition to branch#2 is found at rs11636232.

He also produced haplotype frequency tables for the two light eye color haplotypes (here the one sorted by branch#1 frequencies):

	Branch#1	Branch#2
Brahui	2%	2%
Balochi	8%	2%
Balochi	12%	6%
Kalash	12%	16%
Sardinian	16%	4%
Palestinian	18%	3%
Burusho	18%	12%
Basque	19%	21%
Italians	25%	19%
Adygei	26%	6%
Orcadian	28%	41%
Galician	30%	17%
French	32%	30%
Russians	36%	46%
Italians	42%	27%
Swedes	42%	54%
Germans	46%	33%
Danes	52%	32%
Austrian	55%	28%
Swiss	69%	25%

In West Asia and Pakistan (the most plausible ancient origin of the trait), we see how the ancestral #1 variant is generally dominant, with the only exception of the Kalash, reaching the highest frequencies (18%) among the Burusho and Palestinians, among the studied populations.

This pattern is continued (at overall quite higher frequencies) in Central Europe, Denmark, Italy and Galicia, with peak among the Swiss (69%). Instead the derived haplotype #2 seems dominant among Swedes, Russians and Orcadians. French and Basques are balanced for both types.

See also:

Eye and skin pigmentation genetics: Cape Verdeans as informative population
Causes of skin and hair color variance in Europeans remain undetermined (includes data for eye color)

Breatsfeeding vastly improves brain development in early infancy

2013-06-08T21:37:00.000+02:00

Nature vs nurture? Where genetics often fail to explain most differences in cognitive development in a satisfactory manner, environmental causes instead show outstanding importance.

A very clear case is breastfeeding, which not only provides the best nutrition for babies but also key emotional support. And new research only emphasizes this.

From Science Daily:

The research found that by age 2, babies who had been breastfed exclusively for at least three months had enhanced development in key parts of the brain compared to children who were fed formula exclusively or who were fed a combination of formula and breastmilk. The extra growth was most pronounced in parts of the brain associated with language, emotional function, and cognition, the research showed.

(...)

The study showed that the exclusively breastfed group had the fastest growth in myelinated white matter of the three groups, with the increase in white matter volume becoming substantial by age 2. The group fed both breastmilk and formula had more growth than the exclusively formula-fed group, but less than the breastmilk-only group.

"We're finding the difference [in white matter growth] is on the order of 20 to 30 percent, comparing the breastfed and the non-breastfed kids," said [lead researcher Sean] Deoni. "I think it's astounding that you could have that much difference so early."

Ref. (pay per view): Sean C.L. Deoni, Douglas C. Dean, Irene Piryatinksy, Jonathan O'Muircheartaigh, Nicole Waskiewicz, Katie Lehman, Michelle Han, Holly Dirks. Breastfeeding and early white matter development: A cross-sectional study. NeuroImage, 2013; DOI: 10.1016/j.neuroimage.2013.05.090

Caribbean autosomal ancestry

2013-06-08T20:58:00.001+02:00

Battle of Vertières (Haiti 1803)

A very interesting study on Caribbean populations' autosomal ancestry is in the oven (pre-publication at arXiv).

Andrés Moreno Estrada et al., Reconstructing the Population Genetic History of the Caribbean. arXiv 2013 (pre-pub). Freely accessible → LINK [ref. arXiv:1306.0558v1]

Abstract

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean.

The most synthetic graph is the following one:

Figure 1: Population structure of Caribbean and neighboring populations. A) On the map, areas in red indicate countries of origin of newly genotyped admixed population samples and blue circles indicate new Venezuelan (underlined) and other previously published Native American samples. B) Principal Component Analysis and C) ADMIXTURE [12] clustering analysis using the high-density dataset containing approximately 390K autosomal SNP loci in common across admixed and reference panel populations. Unsupervised models assuming K= 3 and K=8 ancestral clusters are shown. At K=3, Caribbean admixed populations show extensive variation in continental ancestry proportions among and within groups. At K=8, sub-continental components show differential proportions in recently admixed individuals. A Latino-specific European component accounts for the majority of the European ancestry among Caribbean Latinos and is exclusively shared with Iberian populations within Europe. Notably, this component is different from the two main gradients of ancestry differentiating southern from northern Europeans. Native Venezuelan components are present in higher proportions in admixed Colombians, Hondurans, and native Mayans.

As expected, Mexicans and most Colombians and Hondurans cluster mostly between Europeans and Native Americans, while Cuban, Dominicans and Haitians do between Europeans and Africans instead, with Puerto Ricans and some Colombians and Hondurans showing tripartite ancestry.

A most notable issue is that the bulk of Caribbean Latin American ancestry from Europe forms a distinctive component that the authors suggest is a founder effect from the early colonization almost 500 years ago but that I feel that deserves a closer look.

The authors provide also the full ADMIXTURE results for up to K=15, with cross-validation data, what is certainly appreciated by this blogger.

Figure S3:
ADMIXTURE metrics at increasing K values
based on Log-likelihoods (A)
and cross-validation errors (B)
for results shown in Figure S2.

Using table B, the best fit is K=7:

From Fig. S2 (ADMIXTURE results)

Here we see a generic Mediterranean presence in Europe of the "black" component. Would it be just a simple reflection of European structure, then we should expect that the European component in Latin Americans would be c. 70% "red" and just 30% "black". But nope, not even in Cubans, who are the ones with the most recent European input overall (because it was a colony until a century ago).

This may indeed have the explanation that the authors suggest: that it is the result of a "recent" founder effect some 500 years ago in the early moments of the Castilian conquest and colonization of America. But still something does not ring correct. At the very least I have some doubts.

An alternative possibility that should be eventually tested could be that what we identify as "European" ancestry is in fact something European-like but not exactly European, for example North African and/or Jewish ancestry. There could be various sources for this trans-Mediterranean flow into America: on one side it has often been speculated (but never really proven) that a lot of Muslim and Jewish converts migrated to the colonies in the hope to escape the Inquisition. A major problem here is that most Muslim Iberians should be identical or nearly identical in ancestry other Iberians (Jews were not numerous enough probably anyhow).

But another interesting possibility is that many North Africans (including Canarian Aborigines or Guanches) may have been enslaved early on to supply the plantations of the Caribbean. Initially the excuse for slavery was not "racial" (an Illustration development in fact) but "religious". There are known many Papal edicts insisting that Canarian converts would not be enslaved, something that the Portuguese (first colonial power in the archipelago) did anyhow again and again. It is plausible (but ill-documented) that North African conquest campaigns and raids by Portugal first and Castile later would also capture many slaves in those areas, slaves that would probably end up in America in many cases, where they may have been emancipated eventually, becoming part of the Mestizo backbone of the Castilian colonial empire.

I know I am speculating a bit here but it is an interesting alternative to explore. In this regard I really miss North African control populations, because they would shed light on this intriguing matter.

Another issue the paper explores is the origin of African ancestry, finding that the oldest ancestry is mostly from westernmost Africa (Mandenka, Brong as reference populations), while more recent ancestry is mostly from the Nigeria-Angola arc (Yoruba, Igbo, Bamoun, Fang and Kongo).

The study also tries to reconstruct population history but some of their results are perplexing and highly unlikely.

Figure 3: Demographic reconstruction since the onset of admixture in the Caribbean. We used the length distribution of ancestry tracts within each population from A) insular and B) [not shown] mainland Caribbean countries of origin. Scatter data points represent the observed distribution of ancestry tracts, and solid-colored lines represent the distribution from the model, with shaded areas indicating 68.3% confidence intervals. We used Markov models implemented in Tracts to test different demographic models for best fitting the observed data. Insular populations are best modeled when allowing for a second pulse of African ancestry, and mainland populations when a second pulse of European ancestry is allowed. Admixture time estimates (in number of generations ago), migration events, volume of migrants, and ancestry proportions over time are given for each population under the best-fitting model. The estimated age for the onset of admixture among insular populations is consistently older (i.e., 16-17) compared to that among mainland populations (i.e., 14).

The really perplexing issue here is that in Haiti and Cuba particularly, the latest and quite notable arrival of African ancestors corresponds to a mere four generations ago, what means (as the approx. generation length is of c. 30 years, not longer because then the earliest European arrival would be before Columbus' feat) a mere 120 years ago, i.e. around 1890.

The reality is that Haiti became independent in 1791-1804 and no relevant demographic inflow has happened since then. Similarly the last major batch of slaves to Cuba (from Spain, where slavery was being outlawed, as well as from Haiti itself) was in the earliest 19th century (however slavery would not be abolished in Cuba until 1884, although human trade was declared illegal in 1835 under British pressure).

Therefore there must be an error of some sort in these reconstructions, which generate more recent African inflows that are realistically possible.

Sago trees were important in Neolithic Guangxi

2013-06-08T18:28:00.001+02:00

What did SE Asians eat before the spread of rice farming?

Xiaoyan Yang et al., Sago-Type Palms Were an Important Plant Food Prior to Rice in Southern Subtropical China. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0063148]

Abstract

Poor preservation of plant macroremains in the acid soils of southern subtropical China has hampered understanding of prehistoric diets in the region and of the spread of domesticated rice southwards from the Yangtze River region. According to records in ancient books and archaeological discoveries from historical sites, it is presumed that roots and tubers were the staple plant foods in this region before rice agriculture was widely practiced. But no direct evidences provided to test the hypothesis. Here we present evidence from starch and phytolith analyses of samples obtained during systematic excavations at the site of Xincun on the southern coast of China, demonstrating that during 3,350–2,470 aBC humans exploited sago palms, bananas, freshwater roots and tubers, fern roots, acorns, Job's-tears as well as wild rice. A dominance of starches and phytoliths from palms suggest that the sago-type palms were an important plant food prior to the rice in south subtropical China. We also believe that because of their reliance on a wide range of starch-rich plant foods, the transition towards labour intensive rice agriculture was a slow process.

Reconstructing human demographic history from IBS segments

2013-06-07T12:56:00.002+02:00

Figure 1. An eight base-pair tract of identity by state (IBS).

Identity-by-state (IBS) segments are those located between any two SNPs (polymorphisms, letters that vary among individuals). According to this new paper, they seem to be evolutionarily neutral and therefore their length, modified by recombination events each new generation, is a good trail to reconstruct human demographic history.

Kelley Harris & Rasmus Nielsen, Inferring Demographic History from a Spectrum of Shared Haplotype Lengths. PLoS Genetics 2013. Open access → LINK [doi:10.1371/journal.pgen.1003521]

Abstract

There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.

The most interesting graph, synthesizing the result for standard HapMap European and African proxy samples is figure 7. However I have major issues with the age estimates, which seem to be half what is needed to be realistic according to archaeological and other genetic data (unlineal haplogroup history, for example). Therefore I have annotated it with a revised timeline, so it fits better with the objective data:

Figure 7. A history inferred from IBS sharing in Europeans and Yorubans.
This is the simplest history we found to satisfactorily explain IBS tract sharing in the 1000 Genomes trio data. It includes ancient ancestral population size changes, an out-of-African bottleneck in Europeans, ghost admixture into Europe from an ancestral hominid, and a long period of gene flow between the diverging populations.
(Right margin annotations by Maju).

Indeed the simplest revision of the time-scale was to double it. I guess it can be refined a bit more than that, maybe pushing it a bit further into the past, but the alternative time-scale I propose fits closely enough with known archaeological data like the time of the OoA to Arabia and Palestine or the spread of Acheulean (and therefore H. ergaster, common ancestor of Neanderthals and H. sapiens) out of Africa c. 1 Ma ago to illustrate that the reconstruction seems pretty much correct overall but fails when estimating the dates (because of scholastic-autistic academic biases that are too common in the field of human population genetics).

Update: even Dienekes agrees, on his own well documented reasoning, with a x2 mutation rate being necessary for the above graph.

Ancient Jomon mtDNA from Japan

2013-06-02T15:52:00.002+02:00

Udege family

There is some debate about the connection between the Jomon period (Japan's ceramic but pre-agricultural period, extending between c. 16,000 to 2300 years ago) and the Ainu, as well as Ryukyuans and other peoples, including mainstream Japanese. A new study provides some extra bits of information to fuel the debate:

Hideaki Kanzawa-Kiriyama et al., Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan. Anthropological Science 2013 (advance publication). Open access → LINK [doi:10.1537/ase.121113]

The researchers sequenced ancient mtDNA from Jomon remains from a shell mound of Sanganji (Fukushima), which produced two M7a2, one N9b2 and one (incomplete) N9b* sequences.

Referring to previous similar studies as well, they produced the following tables:

From this data it would appear that the ancient Jomon people would be most closely related to modern Udegey (or Udege) from the Amur region of Eastern Siberia (with the possible exception of the Kanto Jomon, who may be closest to Ryukyuans instead).

The Sanganji sample is included pooled into Tohoku Jomon

The Ainu, it must be said, are next in line after the Udege, and I wonder if recent admixture may be distorting their relation. Another issue is that in such an extensive period of almost all the Holocene and even some millennia into the Pleistocene, there may have been flows and variability also within the Jomons (the Sanganji shell mound is dated to c. 4000-2500 BP, for example).

Whatever the case, it seems clear that N9b was an important matrilineage among ancient Jomon peoples, while M7a (now most common among Ryukyuans) was present but less common, with the Sanganji sample being rather exceptional in this.

Not more than 2% of educational attainment can be attributed to genes

2013-06-02T14:58:00.000+02:00

Correction: a reader indicates that ~2% is the amount of influence from the addition of many SNPs (often with a tiny estimated impact each), while ~0.2% is the amount of influence estimated for each of the three most influential SNPs, not together. I stand corrected (but still a very small influence).

While the authors express themselves hopeful that this proportion will increase in the future, so far only three SNPs have been found with a clear correlation to educational attainment, representing 0.2% of all genetic influence. When they consider a linear polygenic score from all measured SNPs, they can't still measure more than an elusive 2% of putative genetic causes for these differences.

Cornelius A. Rietveld et al., GWAS of 126,559 Individuals Identifies Genetic Variants Associated with Educational Attainment. Science 2013. Pay per view → LINK [doi:10.1126/science.1235488]

Abstract

A genome-wide association study of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490. Three independent SNPs are genome-wide significant (rs9320913, rs11584700, rs4851266), and all three replicate. Estimated effects sizes are small (R2 ≈ 0.02%), approximately 1 month of schooling per allele. A linear polygenic score from all measured SNPs accounts for ≈ 2% of the variance in both educational attainment and cognitive function. Genes in the region of the loci have previously been associated with health, cognitive, and central nervous system phenotypes, and bioinformatics analyses suggest the involvement of the anterior caudate nucleus. These findings provide promising candidate SNPs for follow-up work, and our effect size estimates can anchor power analyses in social-science genetics.

Seriously, if they could find no more than an elusive ~2% in more than 100,000 individuals... how do they expect to ever find any more?

Let's be honest: there is only very limited genetic influence on intelligence and cognitive or educational attainment, because, after all what genes do with the brain is to lay out the hardware, so to say, with all the software (but surely a basic emotional-instinctual ROM) being the product of environmental interaction. It's possible that there is minor variance in the hardware (genetics) and maybe even more in its initial configuration (basic epigenetics) but, the same that most desktop computers can do the same things, with less important variability, human brains can too (unless somehow damaged).

Some 7% modern humans retain ape-like fexible feet

2013-06-02T14:40:00.002+02:00

A very curious story this one: a study performed on 398 visitors of Boston Museum of Science revealed that one of every thirteen people retain flexible characteristics in their feet, reminiscent of our ape cousins.

Most of us have very rigid feet, helpful for stability, with stiff ligaments holding the bones in the foot together.

When primates lift their heels off the ground, however, they have a floppy foot with nothing holding their bones together.

This is known as a midtarsal break and is similar to what the Boston team identified in some of their participants.

Source: BBC.

New Acheulean date in Europe: 800,000 to one million years ago

2013-06-02T14:35:00.002+02:00

St. Acheul's namesake biface
(CC by Didier Descouens)

A new date obtained in the Catalan site of Boella confirms very old presence of Acheulean stone technology (and therefore, inferred, of Homo ergaster, common ancestor of Neanderthals and our species) in SW Europe, up to one million years ago.

In 2009 it was also reported comparably old dates for this key techno-culture in SE Iberia, specifically c. 780,000 BP in Zamborino (Andalusia) and 900,000 BP in Cueva Negra (Murcia). So this date should not be any surprise, however it confirms the overall scenario for a very old Acheulean in the Iberian peninsula.

Acheulean technology, usually associated with H. ergaster, appeared first in Africa c. 1.6 Ma ago, and spread to Palestine c. 1.4 Ma ago, with South Asian and Iberian sites following in antiquity (surely both older than 800,000 BP).

Source: CEICS.

Basque linguistics: Frank criticizes Lakarra

2013-06-02T14:07:00.000+02:00

I mentioned recently how the pope of Basque linguistics, Joseba Lakarra, is being more and more criticized. Here however I will briefly discuss another such criticism.

Frank, Roslyn M. 2011. Repasando a Joseba Lakarra: Observaciones sobre algunas etimologías en euskera a partir de un acercamiento más cognitivo (Reviewing Joseba Lakarra: Observations on some etymologies in Basque language from a more cognitive approach). ARSE 45: 17-64. Available at Academia.edu (in Spanish only).

On one side the alleged Latin/Romance alleged etymologies by Lakarra are self-exposed as a total fraud. Some self-explanatory examples:

turpe (Lat. foul, dirty) → *durpe → *burde → urde (pig, boar; metaphorically only: dirty - the common word for dirty is zikin)
timor (Lat. fear) → … *dirbur → *birdur → bildur (more commonly beldur: fear¹)
hierba (Sp. grass, herb) > *erbar > *berar > belar / bedar (grass, there's actually a real Latin/Romance derived word: zerba = herb)
caninu (from. Lat. caninus: rel. to dogs) → *ahinu → *ahiun → *ha.in → hagin (molar)
*(la)grima (Sp. lágrima: tear; grima: coll. pity) > *girma > *girna > *nirga > nigar (more commonly negar: cry, tears, negar egin: to cry, to express emotion by tears)

One of the many problems with this last 'etymology' is that Basque language hates double consonants (with the exceptions: tx [ch], ts, tz) and that therefore the hypothetical *grima would become *girima or *kirima first of all, again unattested.

But in general all the Lakarran hypothetical etymologies are self-defeating, needing of several unlikely intermediate variants, each of them extremely unlikely, and would not stand any minimally serious scrutiny. The problem is that there is very little of that.

Another criticism is that he uses almost only his own work, often not even published, as evidence of his own conclusions. This is mere pseudoscience but somehow he gets away with it.

Other issues that Lakarran conjectures (calling that 'garbage in - garbage out' speculation "theory" would be way too generous) pose are grammatical. Unlike the late North American linguist Larry Trask, who establishes that Basque has primarily a SOV grammatical structure, for Lakarra the proto-Basque had no grammar whatsoever: no SOV, no ergative, no agglutination, no verbal inflections... In other words: for Lakarra proto-Basque speakers were probably not even human yet, but that proto-Basque is only estimated to have existed some 3000 years into the past, so...

For Lakarra, proto-Basque would not be agglutinative but isolating. This isolating characteristic of some languages is actually restricted to East Asia (the most notable example is Chinese, especially classical Chinese). However real Basque has a clear agglutinative tendency, what seems highly inconsistent with Lakarra's formulation.

The bulk of the study however only touches Lakarrism somewhat obliquely, dwelling in some depth on the etymology of hatzapar² (animal claw), which Lakarra forces to derive from Sp. garra (same meaning) but Frank considers 100% Basque, deriving from the more widespread hatzamar (i.e. the toe that means ten, the big toe), and the grammaticalization of gai, originally ability, able, potential (also matter, substance) but now inserted in many words like zerga(i)tik (why, from zer(en)-gai-tik) or -gale (feeling of the prefix: edagale: thirsty, etc.)

The study ends with a criticism of the group Monumenta Linguae Vasconum, which is led by said Joseba Lakarra (and co-participated by Blanca Urgell, Gidor Bilbao, Ricardo Gómez, Julen Manterola Agirre, Mikel Martínez and Céline Mounole). This group is preparing, at the snail pace of a mere 500 words per year, with public financing, an etymological dictionary of the Basque language, which will be no doubt founded only on Lakarra's own speculations. Since 2007 Lakarra is member of the Academy of the Basque Language, Euskaltzaindia, what means that his work is de facto being backed by this influential organism.

_________________________________________________

Notes (my own ideas):

¹ Beldur (fear) surely derives from bel(tz): black in fact, possibly: *bel-adur: black humor.

² I would also consider *hatz-adar (toe-horn, toe's horn) as possible origin of both forms.

Synthesis of the early colonization of Asia and Australasia by Homo sapiens (haploid genetics)

2013-06-01T19:19:00.000+02:00

Continuing with the joint series in Spanish language with David Sánchez at his blog Noticias de Prehistoria, I have just written an article on the early expansion of Homo sapiens in Asia and Australasia after the "out of Africa" migration.

I have in the past explored this matter on this blog and its predecessor but there has been some time since I did it the last time. Therefore it may be interesting to share a synthesis of this updated review with the readers of For what they were...

As usual the review is built upon geographic reconstructions and an overly simple "molecular clock", in the case of mtDNA only (which is the base of the interpretation), that merely counts coding region mutations from the most recent common ancestor (the L3 node), using the latest version of PhyloTree (build 15).

The result for mtDNA are the following five maps:

Map 1: the expansion of L3 sublineages from Africa to South Asia. Molecular time: L3+0 to L3+3.

The big M star indicates the large M star-like explosion upon arrival to South Asia.

Map 2 represents the molecular time L3+4 (=M+1). There is an evident expansion in South Asia but also into SE Asia.

The presence of M29'Q in Papua must be taken with some caution, as always that a single lineage is involved, what has low statistical significance.

Map 3 represents the molecular time L3+5, which corresponds to the coalescence of haplogroup N, as well as many M sublineages. There is a slowing down in the number of nodes sprouting at this "time", so I would estimate it to correspond with Toba supervolcano (c. 74 Ka BP).

Map 4 represents the molecular time L3+6, which corresponds with the coalescence of R. The rhythm of expansion recovers and the colonization of Australasia seems by now quite statistically significant.

Map 5 represents the molecular time L3+7, which shows the first indications of expansion to NE Asia and Western Eurasia (the Neanderlands), while expansion in South Asia continues very strong (this dynamism of South Asian M lineages may explain why N and R had a limited impact in the subcontinent).

I stopped here because I did not want to stretch too much the potential of my simplified molecular clock method, surely more likely to err as we move away from the reference point (L3 node) but the tendencies outlined in map 5 clearly continue and even increase at later "moments".

I also made a rough age estimate of the various maps, assuming map 2 to correspond to Jwalapuram (since c. 80 Ka BP) and map 5 to the earliest Aurignacoid cultures (Emirian, since c. 55 Ka BP or maybe a bit earlier). The result is:

Arrival to South Asia: c. 93-83 Ka BP
First expansion: c. 85-75 Ka BP
Slowing down of the expansion (Toba) and N node: c. 77-67 Ka BP
Reactivation of the expansion and clear arrival to Australasia: c. 69-59 Ka BP
Expansion to less hospitable areas (NE Asia, the Neanderlands): c. 61-51 Ka BP

It is in any case a rough (yet quite coherent) estimate: there is no genetic equivalent of radiocarbon or other physical methods of age calculation.

I did not even try to make any time approximation for Y-DNA, whose expansion I just split in two phases. First what could well be the overall process of expansion from Africa into Tropical Asia (roughly comparable to mtDNA maps 1, 2 and 3):

And then the later expansions, divided in two maps for clarity (they should be roughly simultaneous processes):

General expansion of macro-haplogroups C and D (Y-DNA)

General expansion of macro-haplogroup F and its major descendant MNOPS (highlighted in a lighter, fuchsia shade).

The continuous arrows in these two maps should correspond in essence to mtDNA maps 4 and 5 and even later in time. The dotted arrows merely indicate some important but late processes since at least 30 Ka BP up to the Late Neolithic.

In all maps there is some uncertainty about the exact coalescing location of each clade or node but overall they should be at least approximate. Particularly uncertain are the original locations of mtDNA N and Y-DNA C and MNOPS but should all have coalesced somewhere between Varanasi and Guangzhou, so to say.

I also mentioned the Denisovan or Homo erectus admixture in Australasia and nearby islands but I will not dwell on it here again.

See also:

Italian complex ancestry

2013-05-31T11:28:00.000+02:00

This paper is probably the most detailed study of the haploid genetics of Italy to date, considering both Y-DNA and mtDNA.

Alessio Boattini, Begoña Marínez Cruz et al., Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0065441]

The study contains very ample data for both uniparental lineages and confirms that the origins for Italians are very complex. However their conclusions on the alleged sex-bias are totally founded on the very unreliable "molecular clock" methodology, which I will ignore in this review, focusing instead on regional affinities and similar groupings.

Y-DNA

After toying a bit with table S1 for easier visualization, I took the following snapshot:

Regions:
NW (I): Piamonte, Liguria, Lombardia
NE (II): Veneto, Friuli-VJ,
BOL (III): Bologna (or Emilia-Romagna if you dare to generalize from a single sampling point)
TUS (IV): Tuscany
C (Central, V): Lazio, Umbria, Marche,
S (South, VI): Campania, Basilicata, Apulia, Abruzzi, Molise
SIC (VII): Sicily
SAR (VIII): Sardinia

I changed the names of the regions from cryptic Roman numerals. Frequencies are highlighted if >2.5% overall or >5% regionally. All the rest is the same.

In order to more easily visualize the data, I made the following synthesis:

Labels for R1b are based on previous analysis based on Myres 2010 (quick map link).

Most Italian R1b (27% of all patrilineal ancestry) belongs to the Southwestern clade, dominant (within R1b) in Iberia, France, Switzerland, Ireland... and Italy, and also very important in Great Britain, West and Southern Germany and Scandinavia. In Italy (as in Switzerland and Croatia), this clade is dominated by R1b-U152 (Alpine clade, sometimes also dubbed "Celtic"), which is also common in France and other places. Much less important is the "Irish" clade R1b-L21 (again common in France, as well as in Great Britain) which has however a notable peak in Bologna (10%). The presence of the Pyrenean clade R1b-SRY2627 is rather anecdotal (somewhat more common in NW and Sardinia). This grouping shows a clear strongest influence (almost 50%) in the Northwestern arch (NW, Bologna and Tuscany), with much lower frequencies elsewhere. This distribution does not look too "Celtic" to my eyes, I must say.

Second in importance within R1b is what I labeled as "Euro-root", most of which (6.9% of all patrilineages) belongs to R1b-M269(xP311). This paragroup connects more clearly with the Balcans and maybe West Asia, and is (coherently) somewhat more common to the South and less so in the NW.

Other R1b variants, which are likely to be mostly R1b-V88, are rare except to some extent (3.7%) in Sardinia, where this haplogroup was first identified.

The allegedly Indoeuropean haplogroup R1a1a displays a very strange pattern for such attribution, being completely absent in the Northeast (NE, BOL), where we would have expected it to be common, as it is for example in nearby Slovenia. Instead the greatest frequencies are in the South and Center of Italy, what suggests that there is still a lot to understand about the origin and dispersal of this lineage.

It is also notable the presence of I(xI2a), which I labeled "other NE European", although maybe "North, Eastern and SE European" would have been more correct. Within it, the allegedly "Nordic" haplogroup I1 (very common in Sweden), reaches c. 10% in NE Italy (NE, Bologna), again raising questions about the origin of this lineage as well as of all I (which I tend to consider of Ukrainian/Romanian Paleolithic origin).

The other half of the Italian Y-DNA should be of Eastern Mediterranean origins, be them in West Asia or the Balcans. I have divided this group into two categories: on one side what I label "Cardium Neolithic", all three haplogroups being attested in ancient DNA of this culture in Mediterranean Iberia/France, and on the other the rest, which is not attested but should also have arrived from the same broader region, either in the Neolithic wave or later ones (Bronze, etc.)

All three "Cardium Neolithic" clades are well represented in Italy, being the most notable G2a (11.1%), followed by E1b-V13 (7.8%) and then I2a (only 4.1% overall but a bulging 39% in Sardinia - also having the greatest I2b apportion: 2.4%). The most plausible origins of these three Neolithic lineages are respectively Anatolia (G2a), Greece-Albania (E1b-V13) and the former Yugoslavian Adriatic regions (I2). Italy surely acted as trampoline for their expansion Westward some 7500 years ago.

The "Other West Asian" category includes all other E1b-M78, E1b-M123 (both with ultimate origins in NE Africa but arriving to Europe almost necessarily via West Asia and the Southern Balcans), other G, as well as all J, L and T. The most notable of these lineages is J2a (11.4%, with strongest impact in Sicily, Central and NE Italy), followed by E1b-M123, which made an impact especially in Sardinia (6.1%) and L (major in NE Italy: 8.2%). They may all be localized Neolithic founder effects but uncertain. Of this group only J2 (J2a?) made some impact further West, reaching >5% in some parts of Iberia.

Overall African lineages (the rest of E) seem to have impacted more notably in Sicily (6.4% overall), however the characteristic NW African E1b-M81 also left some mark in Bologna (3.4%).

Some mention deserves also the rare F*, which has a rather Northern distribution in Italy, quite similar to that of R1b-SW.

Figure 1. Spatial Principal Component Analysis (sPCA) based on frequencies of Y-chromosome haplogroups.
The first two global components, sPC1 (a) and sPC2 (b), are depicted. Positive values are represented by black square; negative values are represented by white squares; the size of the square is proportional to the absolute value of sPC scores.

Mitochondrial DNA

Being too large and detailed I did not take a picture of table S7, which neatly displays the mtDNA data. The most notable lineages anyhow are the following ones:

HV*: 4.1% (notable in NW: 6.8%)
H*: 11.1% (widely distributed)
H1*: 10.4% (common except in NE, highest in Sardinia: 18.6%)
H1a (5.7% in Bologna)
H2 (7.7% in Tuscany)
H3: 3.9% (10% in Sardinia, 8.6% in Bologna)
H5: 4.3% (more notable in NW, Tuscany, Center)
T1a: 3.4% (9.3% in NE)
T2b: 3.4% (8.6% in Sardinia)
J1c: 3.9% (6.2% in NW, 14.3% in Bologna)
J2a (5.1% in Sicily)
J2b (7.1% in Sardinia)
U5a: 3.7% (most important in Central region, NE and Bologna)
U5b (7.1% in Sardinia)
K1a: 4.4% (most important in NE, Bologna, Tuscany and Center)

I also attempted a synthesis here, although some may disagree with my labels (I'm a bit in doubt myself in some particular cases, admittedly):

Let me explain the why of the labels and groupings:

Paleo1 corresponds to what some extremists consider the only valid Paleolithic lineages in Europe, i.e. those sequenced in Central and Eastern European "foragers" (excluding Sunghir's H17'27). I'm particularly uncertain about U8b: U8 has been sequenced in Paleolithic Europeans but U8b is closest to K and both are found also in West Asia.
Paleo 2 corresponds to the lineages that appear to spread, at least partly, from SW Europe, some of which (H6, H1b, H*) have been sequenced among pre-Neolithic hunter-gatherers.
Paleo/Neo is a category of lineages I am uncertain about:

HV* has been sequenced in Italian foragers but some of it may also have arrived with Neolithic
V appears to have similar origins to the SW European H lineages but it has only been sequenced in aDNA since Neolithic, so...
Other H: I was simply unwilling to ponder each of the many small lineages' possible origins.

Neo is the category of most likely lineages of Neolithic or post-Neolithic arrival. I have doubts especially about K, which is first sequenced in aDNA in Neolithic Syria/Kurdistan and spread clearly within Neolithic flows, however its phylogenetic connection with U8 makes me doubt about its ultimate origins and flows.
Exotic includes those clades of quite clear origin outside West Eurasia/Mediterranean basin (mostly Siberian lineages): they are quite rare even considered together*.
The categories in cursive are just groupings of the previous, as per description.

One of the aims of these groupings was to check if the molecular-clock-o-logical claims of the paper made any sense. It seems not. Italian mtDNA, like the Y-DNA seems split by about half between likely Paleolithic European clades (of possible post-Paleolithic arrival to Italy in many cases) and likely Neolithic ones. Regional variation does exist but it's not too remarkable. For example if we take the Neo row, it seems that the South of the Peninsula (S) was a bit more influenced by Neolithic or post-Neolithic flows, but the difference with the less influenced area (NW) is of just some 12 percentile points. This pattern is mirrored in reverse by the Paleo 1+2 row.

However if we take the Paleo 1 row, we see a pattern which does not seem consistent with Paleolithic continuity, at least to my eyes, with the highest frequency in the NE (open to migrations from Balcans and Central Europe), followed by the Central region and Sardinia. It rather seems to correspond, at least in part, to migrations from those regions: Balcans and Central Europe.

But, as always, your take.

Figure 3. Spatial Principal Component Analysis (sPCA) based on frequencies of mtDNA haplogroups.
The first two global components sPC1 (a) and sPC2 (b) are depicted. Positive values are represented by black squares; negative values are represented by white squares; the size of the square is proportional to the absolute value of sPC scores.

_____________________________

* On second thought (mini-update), the overall frequencies of "Siberian" lineages are not so negligible in two regions: Sicily and Central Italy, where they amount to >3% taken together. I'm wondering if this may be symptomatic of Roman slave trade, which is known to have Eastern Europe as its main source of slaves after its consolidation as Empire (also in the Middle Ages).

Dutch: single or dual population?

2013-05-31T06:35:00.001+02:00

A recent study deals with the autosomal structure (or lack of it) of the population of the Netherlands.

Oscar Lao et al., Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history. Investigative Genetics 2013. Open access → LINK [doi:10.1186/2041-2223-4-9]

They studied the autosomal DNA of almost 1000 anonymous male donors from the Netherlands. Interestingly the lowest cross-validation value was at K=1, what indicates that the Dutch (Frisians included) are a very homogeneous population, that the most accurate result of their splitting into several components produced only one such component.

Supp. fig. 3-A

K=2 and K=3 however produce similarly low scores, however the researchers preferred to study K=5, which makes a shallow valley between its neighboring values. Probably not the best idea but nevertheless the overall result is similar to what they get at K=3.

Supp. Fig. 3b (ADMIXTURE clustering)

K=2 is very intriguing because only a few scattered individuals fall totally (just two) or partly within the second cluster. These individuals persist in their distinctiveness through the whole series. I wonder if they are people with non-European ancestry (no way to know because they are anonymous donors and as far as I could discern ancestry information was not requested from them).

K=3 is what I would consider the most usable K-level, with similar cross-validation score to the lowest one (K=1) and displaying two widely represented clusters (plus the anomalous one mentioned before). However the authors preferred to work on K=5, which, luckily enough, is quite similar to K=3 in the essentials, also showing two basic components (yellow and pink):

Figure 4 Admixture analysis of the Dutch samples. A) Pie chart map of the genome-wide ancestry assignment in the 54 Dutch subpopulations estimated with 10 independent runs by ADMIXTURE [26] using K = 5 assumed parental populations. B) Individual ancestry estimated by ADMIXTURE using K = 5. C) Ternary plot of subpopulations using the three.

If we ignore the ubiquitous orange component and the minor ones, we can appreciate that the country has two distinct areas:

Southern area (dominated by the pink component): including Zeeland, North Brabant, Limburg, South Holland, much of North Holland and, counterintuively, Western Overjissel.
Northern area (dominated by the yellow component): including Friesland, Gröningen, Drenthe and the eastern areas of Gelderland and Overjissel.
Transitional area: Utrecht and parts of Gelderland and North Holland.

Frisian language today
(CC by ArnoldPlaton)

The authors go to great lengths to try to explain this structure but they do not seem to reach any strong conclusion. I'm not any expert in Dutch history but a tentative explanation may be that, roughly, the yellow-dominated areas correspond more strongly to the areas of Low German/Frisian presence and/or some of their prehistoric precursors (often prehistoric cultures of Low Germany tended to be distinct to those further South).

Low Saxon area (NL)
(CC by Gebruker:Grönneger 1)

While Dutch and the related Limburgish dialect are part of the wider Low Franconian category (descending from Frankish Germanic and historically spoken around the Rhine), most of the yellow-dominated regions belong to distinct historical language areas: Frisian and Low German, which are both believed to derive (together with English) from the same ancestral Ingaevonic branch of West Germanic. This historical and prehistorical duality may well explain the modern genetic duality in its fundamentals, if not the genetic boundary in detail.

Your take in any case.

Approx. Germanic dialectal areas some 2000 years ago
Red: North Sea Germanic (Ingaevonic)
Orange: Wesser-Rhine Germanic (Istvaeonic)
→ full legend
(CC by Hayden120)

On strike next 24 hrs

2013-05-30T00:02:00.002+02:00

This blog will be on strike for all the day of May 30th (CET), as a general strike against the bankster doctrine of "austerity for the poor, massive profits for the rich" has been called in the Southern Basque Country.

More details here.

Chinese neolithic site of Tianluo Mt.

2013-05-29T22:37:00.003+02:00

Hemudu culture pottery
(CC by Editor at Large)

A 10-year long campaign of digs at the site of Tianluo Mountain (Zhejiang, China) has come to an end and will provide abundant information on the Hemudu culture, being considered the best preserved site of this Neolithic population.

The site, accidentally discovered in an attempted well drill, was once a village with walls, food stores, paddy fields and even piles of rice husks, as well as ladders made from a single piece of wood, big houses for ritual activities, wood-carved ritual wares with birds, and wooden swords.

The local government invested more than 10 million yuan in a shelter to protect the site, which has been open to visitors since 2007.

Source: China Daily.

Neanderthals weaned their babies between 9 and 18 months of age

2013-05-29T22:24:00.001+02:00

Or at least one of them did.

The finding is the product of detailed analysis of milk tooth formation in one infant Neanderthal from Scladina cave (Belgium) and comparison with many monkey teeth. The researchers concluded that the barium accumulation in the teeth correlates tightly with breastfeeding and gives information on this with almost a day of precision.

This Neanderthal kid was exclusive breastfed up to the age of nine months and then had another nine months of gradual weaning, eating also other foods, as well as its mother's milk.

This is probably much more than the average breastfeeding in our modern societies but less than it has been documented among some hunter-gatherers like Bushmen, who may well partly breastfeed their children for up to four years, what acts as (unsafe) contraceptive. Chimpanzees seem to breastfeed their infants for some 5.3 years, while non-civilized humans (H. sapiens) have ranges of around 2.4 years instead.

Sources: Science Daily, Paleorama[es].

Ref. Christine Austin, Tanya M. Smith, Asa Bradman, Katie Hinde, Renaud Joannes-Boyau, David Bishop, Dominic J. Hare, Philip Doble, Brenda Eskenazi, Manish Arora. Barium distributions in teeth reveal early-life dietary transitions in primates. Nature, 2013; DOI: 10.1038/nature12169

IQ related to ability to supress peripheral information

2013-05-29T22:09:00.000+02:00

Or in other words: to focus on what is most important.

An experiment performed at the University of Rochester confirmed previous findings of more intelligent people (measured by IQ) being more able to correctly identify in which direction moving bars drifted at the center of a screen. However they also made a new discovery: high IQ people were less able than lower IQ-scoring individuals to correctly identify this movement when the bars occupied all the screen, contrary to expectations.

They suspect that this makes sense after all, because it may reflect an ability of more intelligent people to suppress peripheral information to the benefit of their focus, having a less noisy mental processing overall.

Other tested sensory measures such as color discrimination have produced only lower correlation scores.

Source: Science Daily.

Ref. Michael D. Melnick, Bryan R. Harrison, Sohee Park, Loisa Bennetto, Duje Tadin. A Strong Interactive Link between Sensory Discriminations and Intelligence. Current Biology, 2013; DOI: 10.1016/j.cub.2013.04.053

Ancient West Siberian mtDNA

2013-05-22T21:58:00.001+02:00

Kristiina called my attention recently to this open access article on the ancient mtDNA of a district of South-Western Siberia known as Baraba.

V.I. Molodin et al., Human migrations in the southern region of the West Siberian Plain during the Bronze Age: Archaeological, palaeogenetic and anthropological data. Part of a wider book published by De Gruyter (2013). Open access → LINK

Fig. 1 - click to expand

Quite interestingly we see in the data that before 3000 BCE this part of Western Siberia (see locator map at the right) shows already signs of West-East admixture, much earlier than Central Asia did.

This fact is consistent with the apparently old admixture detected among the Khanty in autosomal DNA and also with the Epipaleolithic presence of East Asian mtDNA (C1) in NE Europe and the putative Siberian origins of the Uralic family of languages and Y-DNA haplogroup N in NE Europe.

Fig. 2 (left) | Chronological time scale of Bronze Age Cultures from the Baraba region
Fig. 3 (main) | Phylogenetic tree of 92 mtDNA samples obtained from the seven Bronze Age cultural groups from the Baraba region. Color coding of the groups as in Figure 2

The Ust-Tartas culture is part of the wider Combed Pottery culture, usually thought to be at the origins of Uralic peoples in NE Europe and Western Siberia, and shows an almost balanced apportion of Eastern lineages (C, Z, A, D) and Western ones (U5a, U4, U2e), suggesting that the process of admixture was by then already consolidated.

However the Odinovo cultural phase shows a change in this trend, with a clear hegemony of Eastern lineages (notably D) and almost vanishing of Western ones. Trend that continues in its broadest terms in the Early Krotovo phase.

Odinovo is part of the wider phenomenon known as Seima-Turbino, initiator of the Bronze Age in wide parts of Northern Asia and believed to be original of Altai. However the lineages do not correspond at all with the Altaian Bronze Age genetic pool, fully Western in affinity, excepted those from Mongolian Altai, which are all D. Hence the apparent demic replacement happening in this period must have been from the Mongolian part of Altai or some other region and not the core Altai area.

The oriental affinity of Early Krotovo is instead caused by a more diverse array of lineages (less D more CZ and A), which is interpreted materially as reflecting migrations from Northern Kazakhstan (Petrovo culture). However, as mentioned before the known mtDNA pool of Central Asia in that period is completely of Western Affinity, so we must in principle discard Kazakhstan as the origin of the probable demic flows.

Let me here mention that the authors insist on continuity through these three phases, however I see a very different picture in the same data, with Western lineages almost vanishing with Odinovo and Eastern ones clearly changing in frequency well beyond reasonable expectations on random fluctuations.

It is only in Late Krotovo when Western lineages reappear in significant numbers, probably reflecting, now yes, migrational flows from the South. This trend is clearly reinforced in the Andronovo, Baraba Late Bronze and transition to Iron Age phases, suggesting growing influence from Andronovo culture (early Indo-Iranians).

Basque language: a criticism of Joseba Lakarra

2013-05-22T20:46:00.000+02:00

Further correction to authorship (Jun 2): Euskararen Jatorria as a whole collectivity are the authors of this study (see comments in their entry), so it's not anonymous but collective (yet the various individual co-authors are not named anywhere).

Original article edited in order to clarify authorship:

Euskararen Jatorria collective have recently published a paper in which they criticize the excessive reliance of Basque language studies on the work of Prof. Joseba Lakarra, whose shadowy control of the Basque Academy on this matter is most worrying, notably since his key defamatory intervention against the extraordinary finds of Iruña-Veleia, which challenge to some extent the foundations of his work.

Sadly for many readers of this blog, the new study is published only in Spanish and Basque languages. In spite of that I feel the need to briefly discuss it here.

Euskararen Jatorria (collective work), Joseba Lakarra a examen. Sobre el Diccionario Histórico Etímologico Vasco. Euskararen Jatorria 2013. Freely accessible → LINK 1 (Spanish), LINK 2 (Basque)

The paper begins with a pondered praise of Lakarra's efforts to go beyond Mitxelena's paradigms. However they feel that he should also be much more self-critical and humble and ready to back when he's clearly wrong, what he does not. A key concern is that the Academy of Basque Language (Euskaltzaindia) and University of the Basque Country are focused on a major work: the creation of an etymological dictionary, which will be founded almost only on Lakarra's work, what could well be a total disaster and waste of resources if he is mostly wrong.

Naturally Lakarra is the director of the project himself. While a few other authors (Tovar, Trask) are cited in Lakarra's magnum opus project, they are almost only mentioned in a negative manner. The result can therefore be foreseen as a monument to Lakarra's own vanity.

Nothing new in fact, as Lakarra is infamous for citing almost exclusive his own works, often unpublished, what is not accepted as a healthy academic praxis anywhere... except in his own feudal domain, it seems. This problem of self-citation is discussed in section 4 of this paper.

The criticisms of Lakarra's work can be synthesized following the structure of the study:

The monosyllabic root theory of Lakarra is too daring. The available evidence does not support this in most cases.
There is no process of critical revision. This makes Lakarra models mere hypothesis or conjectures and not at all proven theories. Larry Trask did not include a single root by Lakarra in his own etymological dictionary. Michael Morvan and J.B. Orpustan frontally rejected Lakarra's ideas.
All reconstructions are purely theoretical.
Abusive self-citation, often of unpublished materials. Lakarra almost never cites other authors than himself.
No systematization. Lakarra's model has never been systematically described, something that the professor seems to prefer, as it allows him for unlimited freedom in his ramblings.
Frequent changes in the etymologies, revealing extreme insecurity and improvisation in Lakarra's own thought.
Abusive use of typological comparativism. Even if systematically criticizes comparativism, because he only believes in internal reconstruction for the case of Basque, he constantly relies in grammatic comparison with other unrelated languages.
Incoherence with the reality of languages 3000 years ago. For Lakarra, Basque in that time only had the most rudimentary vocabulary and grammar, while the reality we know is that all languages were as complete as they are today, and therefore (proto-)Basque must have been as well.
Monosyllabic root theory has serious issues. Words like lur (earth, land, soil) are ancestrally monosyllabic for Lakarra, however they are attested in bisyllabic forms like luur or luhur, suggesting that it is in fact a shortening of longer ancient words. There are many other such cases.
It does not even consider dialectal variation. Lakarra invariably uses only the modern standard form (Euskara Batua), totally ignoring the well attested dialectal variation.
It ignores Aquitanian toponymy. For example eihar for Lakarra derives from Lat. cremare, while it is attested as such []eihar in Aquitaine c. 87 CE.
Some proposed evolutions are absolutely incredible. For example:
*goi-bar ('up-down') > *gwibar > *bi-z-bar > bizkar (anat. back, geog. hill, mountain).
Some etymologies suffer of serious anachronisms. For example, bazter (edge, corner, riverside; secondarily: field, land, place) is made by Lakarra to derive from Lat. praesaepe via Castilian Spanish pesebre and a claimed intermediate word presepre (actually unattested). Sp. pesebre is attested only 130 years after Basque bazter is. [I believe that bazter is actually present in an ancient Iberian text from Mula, Murcia, see note below].
Breaches the principle of regularity when we consider Basque dialects.
Ignores Basque culture. For example hogi (bread) is for Lakarra derivate from hor (dog) and -gi (-gi/-ki common for meat kinds), meaning in his mind originally something like dog-meat. This is simply absurd... but so are so many things around this peculiar individual in his ivory tower.
Sometimes misinterprets words. For example atseden (to rest, turn off, breath, satisfy) is mistranslated by Lakarra as to die.
Does not help at all to the reconstruction of Aquitanian onomastics. Nothing at all in Lakarra's work helps the understanding of this key ancient reference of Basque studies.
Risk of unitary or monolithic thought. Lakarra's single-handed effective domination of Basque philology in the Western Basque Country has almost stopped independent research altogether. His followers limit themselves to make comments to his theories without daring to think independently, much less being critical.
Conclusions. Warning on the use of public funds for the vanity project of this man, who is no doubt fallible.

_______________________________________________________________

Note on bazter: in the Ibero-Ionian text on lead from El Cigarralejo (Mula, Murcia - pictured), in line #7 it reads:

ZABARBAZDEŔKBIDEDENEDIZBEZANELAZ

Which I tentatively read in modern Basque as follows:

Zabal bazterrak bide denetik bezainelako; i.e. something like: such as the ample margins through the whole path. Uncertain particularly about the last word bezanelaz.

Other fragments of this piece, as well as of other Ibero-Ionian texts also sound terribly Basque-like, although of course not identical. Once I asked a friend from Ondarroa, native speaker of Basque, of his opinion on this text and, laughing, he replied: not from Ondarru but maybe from Lekitto (Lekeitio: the nearby town, which has a distinct dialect).

Ancient Minoan mtDNA

2013-05-17T22:01:00.004+02:00

Early Minoan jar
(CC by Wolfgang Sauber)

An ancient Minoan cave ossuary from Ayios Charalambos, Lasithi Plateau (around Mt. Ditke, Eastern Crete), dated to c. 2400-1700 BCE, has produced 37 valid mtDNA sequences (HVS-I).

Jeffrey R. Hughey et al., A European population in Minoan Bronze Age Crete. Nature Communications 2013. Open access → LINK [doi:10.1038/ncomms2871]

Abstract

The first advanced Bronze Age civilization of Europe was established by the Minoans about 5,000 years before present. Since Sir Arthur Evans exposed the Minoan civic centre of Knossos, archaeologists have speculated on the origin of the founders of the civilization. Evans proposed a North African origin; Cycladic, Balkan, Anatolian and Middle Eastern origins have also been proposed. Here we address the question of the origin of the Minoans by analysing mitochondrial DNA from Minoan osseous remains from a cave ossuary in the Lassithi plateau of Crete dated 4,400–3,700 years before present. Shared haplotypes, principal component and pairwise distance analyses refute the Evans North African hypothesis. Minoans show the strongest relationships with Neolithic and modern European populations and with the modern inhabitants of the Lassithi plateau. Our data are compatible with the hypothesis of an autochthonous development of the Minoan civilization by the descendants of the Neolithic settlers of the island.

From the paper (emphasis mine):

The majority of Minoans were classified in haplogroups H (43.2%), T (18.9%), K (16.2%) and I (8.1%). Haplogroups U5A, W, J2, U, X and J were each identified in a single individual.

Figure 2: Minoan mtDNA haplotypes in extant and ancient populations.
(a) Minoan mtDNA HVS-1 haplotypes shared with the modern or ancient populations. (b) Frequency distribution of the 15 shared Minoan haplotypes among the various modern and ancient population groups.

I find very interesting that of the six non-singleton shared HVS-I sequences, four match those of Central European Neolithic (ht 5, 11, 13 and 14, plus singleton ht 4). The total percentage of coincidences is smaller than with Southern Neolithic but this grouping only has two matches with Minoan common haplotypes (ht 11 and 14, plus singleton ht 4), not any striking match.

Among modern populations the best fits seem to be the Balcans, Turkey and Middle East, both with five non-singleton matches out of six possible ones (ht 20 is only found in Turkey, click to expand if you don't see it, while ht 8 is found in the Balcans and the Middle East).

So I would conclude that the Minoan sample fits well with a mix of Anatolian and Balcanic (or less likely Near Eastern) origin, after due founder effect, fitting also reasonably well with Danubian Neolithic and therefore with their likely (partial?) origins at the Balcanic Painted Ware Neolithic.

The greater pseudo-affinity with other populations, based only on overall frequency, seems to be inflated by four haplotypes only: ht 14 (the omnipresent CRS), ht 11 (apparently a common K variant), ht 4 (a relatively common T variant but only present in a single Minoan individual) and ht 12 (H5, again present only in an isolated case in the Minoan sample).

So let's please be careful and try not to mix quantity (frequency) with quality (relevant haplotype matches).

The paper also includes a principal component analysis with a more detailed array of populations:

One of the most intriguing facts here is the near-identity between Minoan and modern Lasithi Plateau populations. It would seem logical but Wikipedia describes an instance of ethnic cleansing and later repopulation by the Venetians (emphasis mine):

The fertile soil of the plateau, due to alluvial run-off from melting snow, has attracted inhabitants since Neolithic times (6000 BC). Minoans and Dorians followed and the plateau has been continuously inhabited since then, except a period that started in 1293 and lasted for over two centuries during the Venetian occupation of Crete. During that time and due to frequent rebellions and strong resistance, villages were demolished, cultivation prohibited, and natives were forced to leave and forbidden to return under a penalty of death. A Venetian manuscript of the thirteenth century describes the troublesome plateau of Lasithi as spina nel cuore (di Venezia) - a thorn in the heart of Venice. Later, in the early 15th century, Venetian rulers allowed refugees from the Greek mainland (eastern Peloponnese) to settle in the plain and cultivate the land again.

Is this totally wrong? A brutal error? Erudite vandalism? I cannot say (and would appreciate knowledgeable feedback).

A clear issue is that the current inhabitants of the plateau have a distinctive genetic signature in their Y-DNA, quite different from that of other Cretans, with much higher frequencies of R1b and R1a and much much lower frequencies of the most common Cretan lineage: J2a1. However they also almost lack the main mainland Greek haplogroup E1b, what suggests that the recolonization from Peloponnese story is not correct either.

Interestingly Cretan R1b, so important in Lasithi Plateau (almost 50%), is also largely derived from Western Europe (although the other half could be Balcanic), maybe via Italy, and cannot be ancestral to it (almost all the Western variant belongs to a derived subclade common in Italy, Central Europe and France: U152).

What is going on here then? I must admit that I do not really know.

Other very close populations in the PCA graph are Serbians (green star) and Bronze Age Sardinians (green rhombus). Take it as you wish. Bronze Age Sardinians are also top in the pairwise comparison table (the closest modern populations being Portuguese, Germans and Corsicans, also Neolithic Scandinavians). However these statistical analyses (both the PCA and the pairwise table) may well hide flaws (like the above mentioned confusion between quantity and quality), so I'd take them with the proverbial pinch of salt, as the confidence of the findings depends on the details of the methodology, not necessarily the best ones.

In any case, the general conclusions of the paper do not seem to be wrong: the Egyptian origin hypothesis is totally discarded and a Neolithic origin seems much more likely. However so many questions remain open...

Echoes from the past (May 17 2013)

2013-05-17T20:34:00.000+02:00

Some interesting news I cannot dedicate much effort to:

Human intelligence not really linked to frontal lobe.

New research highlights that the human frontal lobe is not oversized in comparison with other animals. Instead the human intelligence seems to be distributed through all the brain, being the network what really matters → Science Daily.

Ref. Robert A. Barton and Chris Venditti. Human frontal lobes are not relatively large. PNAS, May 13, 2013 DOI: 10.1073/pnas.1215723110

Early hominin ear bones found together in South Africa.

The three bones, dated to c. 1.9 Ma show intermediate features between modern humans and apes → PhysOrg.

New hominin site in Hunan (China).

The sediments of Fuyan cave, in which five human teeth (Homo erectus?) were found, along with plenty of animal ones, are dated to 141,700 (±12,100) years ago. → IVPP - Chinese Academy of Sciences.

The five human teeth

Neanderthal workshop found in Poland.

In Pietrowice Wielkie (Silesia), which is at the end of a major natural corridor from the Danubian basin → PAP.

Ancient Eastern Europeans ritually killed their pets to become warriors.

In the Bronze Age site of Krasnosamarkskoe (Volga region, Russia) more than 50 ritually pieced skulls of dogs have puzzled archaeologists, who have reached the conclusion, after researching Indoeuropean accounts from India, that the animals may have been killed in adulthood rituals: the boys who were to become warriors had to kill their most beloved pet in order to be accepted as such, and did so in a precise and macabre ritual → National Geographic.

Ancient log boat found in Ireland.

In the Boyne river, which was in the past a major artery of the island. Not yet dated: it could be from prehistoric times or the 18th century. → Irish Times.

Maya pyramid destroyed in Belize... to get gravel

2013-05-17T20:18:00.000+02:00

The machinery of a construction company has destroyed one of the most important archaeological treasures of Belize with the most idiotic possible purpose: to get gravel from it.

The pyramid of Nohmul was erected some 2300 years ago and are part of the most important patrimonial set of Belize, located not far from the Mexican border.

Belizean police claims to be investigating the incident and may lay charges against the vandals.