Sago trees were important in Neolithic Guangxi

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

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

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

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

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

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

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.