Breastfeeding improves IQ and other mental developments in children depending on duration

Again nurture (environment) seems to be much more important than nature (genetics) in what regards to human intelligence.

A new study show that not just the mere fact of breastfeeding but the duration of natural motherly nutrition (and maybe the emotional elements attached to it) is strongly correlated with IQ (but not memory and learning).

Mandy B. Belfort et al., Infant Feeding and Childhood Cognition at Ages 3 and 7 YearsEffects of Breastfeeding Duration and Exclusivity. JAMA Pediatrics 2013. Pay per view → LINK [doi:10.1001/jamapediatrics.2013.455]

Abstract

Importance  Breastfeeding may benefit child cognitive development, but few studies have quantified breastfeeding duration or exclusivity, nor has any study to date examined the role of maternal diet during lactation on child cognition.

Objectives  To examine relationships of breastfeeding duration and exclusivity with child cognition at ages 3 and 7 years and to evaluate the extent to which maternal fish intake during lactation modifies associations of infant feeding with later cognition.

Design, Setting, and Participants  Prospective cohort study (Project Viva), a US prebirth cohort that enrolled mothers from April 22, 1999, to July 31, 2002, and followed up children to age 7 years, including 1312 Project Viva mothers and children.

Main Exposure  Duration of any breastfeeding to age 12 months.

Main Outcomes and Measures  Child receptive language assessed with the Peabody Picture Vocabulary Test at age 3 years, Wide Range Assessment of Visual Motor Abilities at ages 3 and 7 years, and Kaufman Brief Intelligence Test and Wide Range Assessment of Memory and Learning at age 7 years.

Results  Adjusting for sociodemographics, maternal intelligence, and home environment in linear regression, longer breastfeeding duration was associated with higher Peabody Picture Vocabulary Test score at age 3 years (0.21; 95% CI, 0.03-0.38 points per month breastfed) and with higher intelligence on the Kaufman Brief Intelligence Test at age 7 years (0.35; 0.16-0.53 verbal points per month breastfed; and 0.29; 0.05-0.54 nonverbal points per month breastfed). Breastfeeding duration was not associated with Wide Range Assessment of Memory and Learning scores. Beneficial effects of breastfeeding on the Wide Range Assessment of Visual Motor Abilities at age 3 years seemed greater for women who consumed 2 or more servings of fish per week (0.24; 0.00-0.47 points per month breastfed) compared with less than 2 servings of fish per week (−0.01; −0.22 to 0.20 points per month breastfed) (P = .16 for interaction).

Conclusions and Relevance  Our results support a causal relationship of breastfeeding duration with receptive language and verbal and nonverbal intelligence later in life.

Related is also:

Dimitri A. Kristakis, Breastfeeding and CognitionCan IQ Tip the Scale? JAMA Pediatrics 2013. Pay per view → LINK [doi:10.1001/jamapediatrics.2013.470]

Extract

In the developed world, where the benefits of breastfeeding are not measured in terms of life or death or even serious morbidity, the question has been what benefits might motivate mothers to both initiate and sustain it consistent with the World Health Organization and American Academy of Pediatrics recommendations.^1- 2 The reduction of gastroenteritis, otitis media, and atopic eczema in the first year of life is supported by a strong evidence base.³ While these are important and desirable outcomes, none in and of themselves have dramatic public health consequences, particularly beyond early childhood. On the other hand, the connection between breastfeeding and cognition has lifelong and widespread implications. Whether a causal linkage between the two exists has long been debated, in part, because most existing studies are observational and have failed to adjust for maternal IQ. Given the known association between educational attainment or intelligence and breastfeeding, failure to adjust for maternal IQ may confound any observed effects on infants.

The study by Belfort et al⁴ in this month’s issue of JAMA Pediatrics, although observational, has many notable strengths including controlling for maternal intelligence, as well as features of the home environment that promote cognitive function. Assuming these findings are in fact robust, what are the public health implications?

A synthesis of the findings is also available at Science Daily. They explain that the association with motherly fish intake mentioned in the first abstract is not statistically significant. They also quote the authors as saying:

In summary, our results support a causal relationship of breastfeeding in infancy with receptive language at age 3 and with verbal and nonverbal IQ at school age. These findings support national and international recommendations to promote exclusive breastfeeding through age 6 months and continuation of breastfeeding through at least age 1 year.

Christakis in turn emphasizes that while the absolute distinction between breastfeeding and bottle feeding is important (in the USA only 70% of  White mothers and only 50% of Black ones initiate breastfeeding at all), a major problem is the lack of persistence of this natural form of nutrition, caused mostly by social and labor pressures, including the absurd stigma against breastfeeding in public, not so long a common sight. Only 35% of European-American and a mere 20% of African-American mothers still breastfeed by their baby's age of six months. He says:

Breastfeeding in public should be destigmatized. Clever social media campaigns and high-quality public service announcements might help with that. As with lead, some of these actions may require legislative action either at the federal or state level. Let's allow our children's cognitive function be the force that tilts the scale, and let's get on with it.

See also: 

• Breatsfeeding vastly improves brain development in early infancy
• Not more than 2% of educational attainment can be attributed to genes
• Emotional care or neglect of young children decisive for brain size, intelligence
• Epigenetics and IQ variability
• Intelligence genes more elusive than Higgins' boson
• Breastfeeding greatly increases IQ

A review of haplogroup N (Y-DNA)

Haplogroup N (Y-DNA) is spread from the Baltic to the South China Sea being one of those rare genetic links between East and West Eurasia (other than ultimate common ancestry) and one of the two Y-DNA lineages which expanded across the Northern Eurasian continent (the other one being Q).

While it is apparent to me and many others that the lineage originated in East Asia and expanded first Northwards to Siberia and later Westwards to Europe. I have found sometimes reluctance to accept this fact or difficulty understanding why. Some of the data of this paper may be of help in this regard. It is also a good exercise for those learning to understand how haploid genetics can be decoded into a meaningful pattern that reveals key parts of the untold history of peoples. 

Hong Shi et al., Genetic Evidence of an East Asian Origin and Paleolithic Northward Migration of Y-chromosome Haplogroup N. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0066102]

Abstract

The Y-chromosome haplogroup N-M231 (Hg N) is distributed widely in eastern and central Asia, Siberia, as well as in eastern and northern Europe. Previous studies suggested a counterclockwise prehistoric migration of Hg N from eastern Asia to eastern and northern Europe. However, the root of this Y chromosome lineage and its detailed dispersal pattern across eastern Asia are still unclear. We analyzed haplogroup profiles and phylogeographic patterns of 1,570 Hg N individuals from 20,826 males in 359 populations across Eurasia. We first genotyped 6,371 males from 169 populations in China and Cambodia, and generated data of 360 Hg N individuals, and then combined published data on 1,210 Hg N individuals from Japanese, Southeast Asian, Siberian, European and Central Asian populations. The results showed that the sub-haplogroups of Hg N have a distinct geographical distribution. The highest Y-STR diversity of the ancestral Hg N sub-haplogroups was observed in the southern part of mainland East Asia, and further phylogeographic analyses supports an origin of Hg N in southern China. Combined with previous data, we propose that the early northward dispersal of Hg N started from southern China about 21 thousand years ago (kya), expanding into northern China 12–18 kya, and reaching further north to Siberia about 12–14 kya before a population expansion and westward migration into Central Asia and eastern/northern Europe around 8.0–10.0 kya. This northward migration of Hg N likewise coincides with retreating ice sheets after the Last Glacial Maximum (22–18 kya) in mainland East Asia.

Hong Shi has previously produced very interesting materials and this is no exception, however I find the use of chronological guesstimates as if these would be objective findings and treated as part of the central discourse (and not the mere side note where they belong) a bit nauseating and a cause of confusion.

Figure 4. Proposed prehistoric migration routes for Hg N lineage.
(the pattern is correct but the dates are mere hunches, not any sort of objective facts)

Above we can see the reconstructed pattern of expansion of Y-DNA N in three phases. In my understanding the dates are not way off, although I can only imagine that there is still room for improvement, especially regarding the "red" phase. After all NO may have split c. 60 Ka ago and the main branch, O, c. 50 Ka BP - and not the mere 25-30 Ka that Shi calculated (in a previous study but mentioned again here).

But the really interesting part is not molecular-clock-o-logy but this:

Figure 3. Median-joining networks for sub-haplogroups of Hg N lineage using Y-STR alleles.

The diagnostic mutations used to classify the sub-haplogroups are labeled on the tree branches. Each node represents a haplotype and its size is proportional to the haplotype frequency, and the length of a branch is proportional to the mutation steps. The colored areas indicate the geographic origins of the studied populations or language groups.

Here we can appreciate, with the labyrinthine limitations of the use of (too few?) STR markers, the apparent structure of the various haplogroups and paragroups under N. We can also see the STR diversity in numerical terms:

Table 3. Y-STRs diversity of Hg N sub-haplogroups.

Sadly the category "Han Chinese" is almost useless and one wonders why Shi et al. changed from the North/South polarity in the key paragroup N* to such a confusing terminology in N1.

In any case, it is quite evident that N arose in South China, spread, already as N1 to NE Asia and, later, some of that N1 (N1c mostly but also some N1b) spread Westwards reaching to Finland and other Eastern European populations. In the haplotype graph we can appreciate a distinct European-specific branch within N1b.

Update (Jul 28): some new findings (not considered in the study) and updated nomenclature.

See comments' section for greater details. Special thanks to Palamede for his efforts in clarifying the matter.

Commercial testing company FTDNA has recently detected some new markers within haplogroup N1 that alter the phylogeny. A synthesis of these findings can be seen in this graph.

This new nomenclature was adopted by ISOGG but the study discussed here does not include it, using instead a 2011 nomenclature. Hence we must understand that:

• N* and N1* remain as such
• "N1a" (M128) is now known as N1c2a
• "N1b" (P43) is now N1c2b
• "N1c" (M46/Tat) is now N1c1

Therefore the N1 tree splits as:

• N1a (new clade, P189)
• N1b (new clade, L732)
• N1c (new clade including all previously named subhaplogroups)
• N1c1 (M46/Tat, former N1c)
• N1c2 (new clade, L666)
• N1c2a (M128, former N1a)
• N1c2b (P43, former N1b)

 

As far as I could gather, N1(xN1c) is so far only clearly represented by two FTDNA-tested singletons: a Slovakian (N1a) and someone of Polish surname (N1b1). However I may be missing some details. Whatever the case it is possible that, unless more samples show up in these groupings the tree may be later reverted to the original state (or something in between) because isolated individuals or families do not haplogroups make. 

Also it is important to understand that commercial DNA testing companies have very unbalanced samples, clearly dominated by people of NW European (and to lesser extent other European) ancestry, what is not too useful when discerning what is where, producing sometimes the false impression of greater European diversity just because of greater number of samples.

On the other, hand the Hong Shi data reported above clearly shows a great number (and diversity) of East Asians within N1*, so the most likely conclusion is that the few Europeans within N1* are mere erratics within clades of East Asian origin, surely brought Westward by the overall N1 tide. 

So in essence the conclusions of the paper remain unchallenged.

Madagascar inhabited long before Austronesian arrival

These findings revolutionize the understanding of the prehistory of the island, until now believed to have remained uninhabited until the arrival of peoples of Austronesian stock some 1500 years ago (with some scattered evidence of earlier inhabitation but nothing too conclusive). New archaeological data pushes back the first colonization period to some 4000 years ago, a time when Malayo-Polynesian culture was still restricted to, roughly, the Philippine archipelago.

Robert E. Deward et al., Stone tools and foraging in northern Madagascar challenge Holocene extinction models. PNAS 2013. Pay per view (6-month embargo) → LINK [doi:10.1073/pnas.1306100110]

Abstract

Past research on Madagascar indicates that village communities were established about AD 500 by people of both Indonesian and East African heritage. Evidence of earlier visits is scattered and contentious. Recent archaeological excavations in northern Madagascar provide evidence of occupational sites with microlithic stone technologies related to foraging for forest and coastal resources. A forager occupation of one site dates to earlier than 2000 B.C., doubling the length of Madagascar’s known occupational history, and thus the time during which people exploited Madagascar’s environments. We detail stratigraphy, chronology, and artifacts from two rock shelters. Ambohiposa near Iharana (Vohémar) on the northeast coast, yielded a stratified assemblage with small flakes, microblades, and retouched crescentic and trapezoidal tools, probably projectile elements, made on cherts and obsidian, some brought more that 200 km. 14C dates are contemporary with the earliest villages. No food remains are preserved. Lakaton’i Anja near Antsiranana in the north yielded several stratified assemblages. The latest assemblage is well dated to A.D. 1050–1350, by 14C and optically stimulated luminescence dating and pottery imported from the Near East and China. Below is a series of stratified assemblages similar to Ambohiposa. 14C and optically stimulated luminescence dates indicate occupation from at least 2000 B.C. Faunal remains indicate a foraging pattern. Our evidence shows that foragers with a microlithic technology were active in Madagascar long before the arrival of farmers and herders and before many Late Holocene faunal extinctions. The differing effects of historically distinct economies must be identified and understood to reconstruct Holocene histories of human environmental impact.

Notice that this colonization is also older than the Bantu expansion and therefore these settlers must have been pre-Bantu peoples of East African roots.

Source: Al-Hakawati

The sites are located in the North tip of the island, what is consistent with arrival through Comoros, the most natural route between East Africa and Madagascar, which  requires the sailing of some 190 miles (~350 Km) of open sea.

Otherwise the narrowest extent of the Mozambique Channel, between Angoche and Tambohorano, is of some 460 Km. The small island or Juan de Nova (uninhabited except for a military garrison) lies to the south of this other potential sailing route.

The toolkit found in the key site of Lakaton'i Anja includes many microliths, as well as some larger tools, made of chert and obsidian. This last must have been brought from far away, as there are no sources of the volcanic glass in Northern Madagascar.

An important point is that these new dates show that human inhabitation did not kill the Malagasy megafauna right away but that instead humans and giant animals shared the environment without immediate catastrophic consequences, which would only happen in the last two millennia.

Partial source: Rhett A. Buttler, Madagascar occupied by humans 2,500 years earlier than previously thought, Wild Madagascar (via Pileta).

Homo sapiens from Central China dated to 81-101 Ka BP

I just received notice (h/t David) of this most important finding and dating:

Guanjun Shen et al., Mass spectrometric U-series dating of Huanglong Cave in Hubei Province, central China: Evidence for early presence of modern humans in eastern Asia. Journal of Human Evolution 2013. Pay per view → LINK [doi:10.1016/j.jhevol.2013.05.002]

Abstract

Most researchers believe that anatomically modern humans (AMH) first appeared in Africa 160-190 ka ago, and would not have reached eastern Asia until ∼50 ka ago. However, the credibility of these scenarios might have been compromised by a largely inaccurate and compressed chronological framework previously established for hominin fossils found in China. Recently there has been a growing body of evidence indicating the possible presence of AMH in eastern Asia ca. 100 ka ago or even earlier. Here we report high-precision mass spectrometric U-series dating of intercalated flowstone samples from Huanglong Cave, a recently discovered Late Pleistocene hominin site in northern Hubei Province, central China. Systematic excavations there have led to the in situ discovery of seven hominin teeth and dozens of stone and bone artifacts. The U-series dates on localized thin flowstone formations bracket the hominin specimens between 81 and 101 ka, currently the most narrow time span for all AMH beyond 45 ka in China, if the assignment of the hominin teeth to modern Homo sapiens holds. Alternatively this study provides further evidence for the early presence of an AMH morphology in China, through either independent evolution of local archaic populations or their assimilation with incoming AMH. Along with recent dating results for hominin samples from Homo erectus to AMH, a new extended and continuous timeline for Chinese hominin fossils is taking shape, which warrants a reconstruction of human evolution, especially the origins of modern humans in eastern Asia.

In other words: strong material evidence is quickly piling up in favor of a Homo sapiens "fast" colonization of Southern Asia (and as far NE as Hubei!) around 100 or at least 90 Ka BP. 

See also:

• Middle Paleolithic industries of African affinity of the Thar Desert go back to c. 96 Ka ago
• East Asian jaw from 100,000 years ago is 'modern human'

Refined Basque-centric mitochondrial lineages

A new study has located some mitochondrial lineages that seem to be specific of Basques and nearby populations.

Sergio Cardoso et al., The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0067835]

Abstract

The European genetic landscape has been shaped by several human migrations occurred since Paleolithic times. The accumulation of archaeological records and the concordance of different lines of genetic evidence during the last two decades have triggered an interesting debate concerning the role of ancient settlers from the Franco-Cantabrian region in the postglacial resettlement of Europe. Among the Franco-Cantabrian populations, Basques are regarded as one of the oldest and more intriguing human groups of Europe. Recent data on complete mitochondrial DNA genomes focused on macrohaplogroup R0 revealed that Basques harbor some autochthonous lineages, suggesting a genetic continuity since pre-Neolithic times. However, excluding haplogroup H, the most representative lineage of macrohaplogroup R0, the majority of maternal lineages of this area remains virtually unexplored, so that further refinement of the mtDNA phylogeny based on analyses at the highest level of resolution is crucial for a better understanding of the European prehistory. We thus explored the maternal ancestry of 548 autochthonous individuals from various Franco-Cantabrian populations and sequenced 76 mitogenomes of the most representative lineages. Interestingly, we identified three mtDNA haplogroups, U5b1f, J1c5c1 and V22, that proved to be representative of Franco-Cantabria, notably of the Basque population. The seclusion and diversity of these female genetic lineages support a local origin in the Franco-Cantabrian area during the Mesolithic of southwestern Europe, ~10,000 years before present (YBP), with signals of expansions at ~3,500 YBP. These findings provide robust evidence of a partial genetic continuity between contemporary autochthonous populations from the Franco-Cantabrian region, specifically the Basques, and Paleolithic/Mesolithic hunter-gatherer groups. Furthermore, our results raise the current proportion (≈15%) of the Franco-Cantabrian maternal gene pool with a putative pre-Neolithic origin to ≈35%, further supporting the notion of a predominant Paleolithic genetic substrate in extant European populations.

I'd say that the finding of these three lineages is in itself the interesting part. The molecular-clock-o-logical speculations are something that as, you know, I tend to ignore. However these seem to be almost invariably just fractions of the realistic dates when properly calibrating, so if the authors get a 10 Ka date, then we can be reasonably sure that it is a minimum date and that the likely actual date can well be twice that figure (although in the case of mtDNA this may depend on each particular branch, as these are very unequal). 

Another important note is that the authors rather studied the sub-Pyrenean isthmic region rather than the original Franco-Cantabrian region, which corresponds mostly to what is now Southern France. I am always rather skeptic about attributing to Basques exclusively the legacy of this wider Paleolithic region and I want to insist that Southern France's peoples (Gascons, Occitans, Perigordians and all others south of the Nantes-Lyon line) be studied in depth and detail along Basques, Cantabrians and Asturians. At the very least this study has an important Gascon sample (Bearn, Bigorre and Chalosse), although it is from the areas closest to the Basque Country.

In a previous study by the same team (2011), they detected apparent Basque (or is it Gascon?) centrality of lineages J1c and U5b. In this study they refine those findings by locating some sublineages that are more clearly Basque-specific: J1c5c1 and U5b1f. They also spotted another Basque-centric haplogroup within V: V22. 

Figure 1. Maximum parsimony trees of haplogroups U5b, J1c and V including the three autochthonous lineages U5b1f, J1c5c1 and V22.
These trees are extracted from the maximum parsimony phylogenetic tree of 76 complete mtDNA sequences of the Franco-Cantabrian region shown in detail in Fig. S1. Mutations are displayed along the branches. All mutations are transitions unless a suffix specifies a transversion (A, C, G, T). Recurrent mutations within the complete phylogeny of the Franco-Cantabrian area are underlined. The prefix ‘‘@’’ indicates a back mutation. Mutational hotspot variants such as 16182, 16183, or 16519, or a variation around position 310 or 523–524, as well as length heteroplasmies were not considered for the phylogenetic reconstruction. All the samples are colored according to their geographic origin, as shown in the legend. For phylogeny construction, five previously published mitogenomes belonging to subhaplogroups U5b1f (JX286537 and DQ156208), J1c5c1 (JQ702776 and JQ704051) and V22 (HQ384212) were included (GenBank accession numbers in the tree). German ethnicity was declared for sample JX286537 in GenBank; however, maternal ancestry in southwestern Europe cannot be ruled out owing to the absence of lineage U51bf in populations outside the Franco Cantabrian area (see Tables S2 and S3). French B.C. refers to samples from the French Basque Country.

As for the apportions, table S3 provides them for U5b1f and J1c5c1, however I could not find anywhere the frequencies of V22 nor other lineages (although there is a list of lineages on a reduced sample in table S1). Sorted by frequency:

U5b1f:

1. Lapurdi: 24.1%
2. NE Navarre: 23.6 %
3. Zuberoa: 17.7%
4. NW Navarre: 17.0%
5. North Navarre: 15.2%
6. Chalosse (Dax district): 15.0%
7. Bearn: 12.5%
8. Gipuzkoa: 11.8%
9. SW Gipuzkoa: 9.5%
10. Bigorre: 9,5 %
11. Low Navarre: 8,2%
12. Central-West Navarre: 7.8%
13. Burgos (Castile): 4.2%
14. La Rioja: 3.8%
15. Biscay: 3.6%
16. Zaragoza (Aragon): 2.5%
17. Catalonia: 0.7%
18. Araba: 0.05%

Not detected in: West Biscay (Enkarterriak), Pas Valley, Cantabria, (North?) Aragon, Madrid, Perigord-Limousin.

So this U5b1f lineage seems concentrated around the Western Pyrenees with a highest density axis between, say, Baiona (Bayonne) and Zangoza (Sangüesa). It is a most important lineage in that core Eastern Basque and Southern Gascon area with frequencies above 5% and reaching almost to 25% in some cases.

While we can appreciate the clinal decline in Iberia, lack of data for Gascony and most of the Paleolithic Franco-Cantabrian region (i.e. Southern France) leaves us without similar data for the northern cline, knowing only that in Perigord-Limousin is 0%. This last detail may explain why the haplogroup is contained within the wider Basque area, as Perigord (and not the Basque Country) was the true center of the Franco-Cantabrian region, a district I have dubbed sometimes "the metropolis of Paleolithic Europe". Rather than looking for signals of expansion from the Basque Country only, researchers should look for such signals of expansion from Perigord particularly (as well as the whole Franco-Cantabrian region, from Provence to Asturias and from the Loire to the Pyrenees). 

Haplogroup U among Basques and Pasiegos (from fig. S1)

J1c5c1:

1. Zuberoa: 4.8%
2. NW Navarre: 3.8%
3. Chalosse (Dax): 3.3%
4. Central-West Navarre: 3.1%
5. Low Navarre: 2.7%
6. North Navarre: 2.4%
7. Gipuzkoa: 2.2%
8. NE Navarre: 1.8%
9. Bearn: 1.8%
10. Lapurdi: 1.7%
11. Zaragoza: 1.2%
12. Araba: 1.0%
13. Biscay: 0.08%

Not detected in: SW Gipuzkoa, West Biscay (Enkarterriak), Bigorre, La Rioja, Burgos, Catalonia, Pas Valley, Cantabria, (North?) Aragon, Madrid, Perigord-Limousin.

Again the lineage, even if much less common, is concentrated around the Western Pyrenees, with a highest density axis from say, Leitza to Maule, spilling to Chalosse and Bearn by the NE but again reaching zero frequencies at Perigord-Limousin (and not knowing how it behaves in between). In Iberia, outside of the Basque Country, is only found in the city of Zaragoza. 

As happens with U5b1f, J1c5c1 quickly declines towards the West in the Southern Basque Country, what may be ground, especially if other lineages also follow this pattern, to consider two original Basque populations: one around the Western Pyrenees and another one around Biscay. This idea, while not commonly formulated, would not be new at all, for example F. Krutwig already suggested in the mid 20th century that Central-Eastern Basques had a Dinaric-like morphology (pseudo-Dinaric, because "true Dinarics" are supposed to be brachicephalic while Basques are usually mesocephalic, like most Europeans), while Biscayans would be rather dominated by the rare Dalic anthropometric type instead. Debatable, of course, but that's what we are here for, aren't we?

Haplogroup JT among Basques and Pasiegos (from fig. S1)

V22:

The study does not directly provide the frequency data for this lineage (they excuse themselves on technical HVS reasons, a very typical problem when working with HV lineages), so I had to work with supplemental table S1, where the HVS-I haplotypes and attributed haplogroups are listed (over a reduced sample of just 76 individuals). My synthesis is:

1. Low Navarre: 1/4 (25.0%)
2. Gipuzkoa: 2/10 (20.0%)
3. Biscay: 1/9 (11.1%)
4. West Navarre: 3/33 (9.1%)
5. Pas Valley: 1/19 (5.3%)

Not detected in Araba's single-person sample: 0/1.

I wouldn't dare to reach any strong conclusions with such small and irregular sample but it does look like the Northern Basque Country and Gipuzkoa have the highest frequencies, what suggests that maybe the lineage extends to the North into Gascony, etc. Unlike the previously discussed lineages in this case the decline towards the West is not as sharp.

Haplogroup R0 among Basques and Pasiegos (from fig. S1)

See also:

• Strontium data shows that Aldaieta remains are mostly local Basques - but some immigrants too
• Ancient DNA comparison supports continuity in the Basque Country
• More North Iberian Epipaleolithic mtDNA (and first Epipaleolithic nuclear DNA)
• Ancient mitochondrial DNA from the Basque Country and Cantabria: unmistakable mtDNA H in Magdalenian Cantabria
• Basque and Gascon Y-DNA survey
• Basque mtDNA
• Neolithic Basque (and Catalan, and Aragonese) mtDNA
• Basque autosomal genetics
• Basque-specific mtDNA lineages (preliminary to this study: J1c and U5b were detected as Basque-centric)
• Mitochondrial DNA of West Europe

Middle Paleolithic industries of African affinity of the Thar Desert go back to c. 96 Ka ago

Again Team Petraglia revealing fascinating evidence on the Middle Paleolithic dispersal of Homo sapiens, and one that fits well the genetic data (speculative "molecular clock" excluded), as well as with the climatic data.

James Blinkhorn et al., Middle Palaeolithic occupation in the Thar Desert during the Upper Pleistocene: the signature of a modern human exit out of Africa? Quaternary Science Reviews, 2013. Pay per view → LINK [doi:10.1016/j.quascirev.2013.06.012]

Abstract

The Thar Desert marks the transition from the Saharo-Arabian deserts to the Oriental biogeographical zone and is therefore an important location in understanding hominin occupation and dispersal during the Upper Pleistocene. Here, we report the discovery of stratified Middle Palaeolithic assemblages at Katoati in the north-eastern Thar Desert, dating to Marine Isotope Stages (MIS) 5 and the MIS 4–3 boundary, during periods of enhanced humidity. Hominins procured cobbles from gravels at the site as evidenced by early stages of stone tool reduction, with a component of more formalised point production. The MIS 5c assemblages at Katoati represent the earliest securely dated Middle Palaeolithic occupation of South Asia. Distinctive artefacts identified in both MIS 5 and MIS 4–3 boundary horizons match technological entities observed in Middle Palaeolithic assemblages in South Asia, Arabia and Middle Stone Age sites in the Sahara. The evidence from Katoati is consistent with arguments for the dispersal of Homo sapiens populations from Africa across southern Asia using Middle Palaeolithic technologies.

Possibly the most strikingly unmistakable evidence for a Homo sapiens affiliation of these findings is the Aterian-like tanged point, which is almost identical to another one found previously in Jwalapuram:

Fig. 4. 1) Tanged point from Jwalapuram 22 (adapted from Haslam et al., 2012); 2 & 3)
Tanged point from Katoati.

Not just Aterian: the, visually less obvious, Nubian technology is also present:

Two Levallois cores from S4 and one from S8 exhibit a mixture of distal divergent and lateral preparation of the flaking surface to produce a distale medial ridge resulting in the removal of prepared points (Fig. 3). These reduction schemes are consistent with descriptions of Nubian Levallois technologies (Rose et al., 2011; Usik et al., 2013).

...

A single flake from S4 presents a combination of distal divergent and lateral removals on the dorsal surface and a prior removal of a pre-determined pointed flake,indicative of the use of Nubian Levallois strategies (Fig. 3).

Table 2. I added at bottom (red) median OSL ages from table 1.

Zhirendong jaw

In synthesis: groups of unmistakably Homo sapiens with obvious African techno-cultural heritage were already within the modern boundaries of the Indian Federation around 96,000 years ago (CI: 109-83 Ka). This totally debunks Mellars' and Mishra's recent claims, the usual "molecular clock" nonsense (that so many people seems willing to believe at face value), and widens significantly the earliest plausible dates for the colonization of Asia (beyond Arabia-Palestine-Persian Gulf) making findings like Zhirendong jaw (the oldest non-Palestinian H. sapiens remains out of Africa, dated to c. 100,000 BP) much more credible.

Until today I was very much in doubt about accepting dates of c. 100,000 years ago for the Asian colonization but since right now I am adopting this model as the most likely one. In other words: it seems clear that the people already settled in Arabia and the Persian Gulf "oasis" did not wait for climatic pressure at the end of the Abbassia Pluvial to send them out in search of new lands: they did it when the pluvial period was still holding the arid gates of Asia open for them.

All the evidence adds up well now. 

_______________________________________

Note: the full paper was available at Academia.edu at the time of writing this:  HERE and HERE.

Indian Microlithic industry almost contemporary of Western initial UP and LSA

Mehtakheri toolkit

That is what a new study has found, albeit on just one date. Based on that they argue that the recent claim by Mellars et al. (see also here) about an extremely late date for the migration out of Africa (OOA) becomes more plausible.

Sheila Mishra et al., Continuity of Microblade Technology in the Indian Subcontinent Since 45 ka: Implications for the Dispersal of Modern Humans. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0069280]

However considering the pivotal role played by South Asia in the genetics of Humankind after the OOA it is still impossible that this microlithic industry corresponds with that process, because the migration and successive Eurasian expansion must:

1. Have minimal dates of well before 60-55 Ka ago, time when the presence of H. sapiens becomes undeniable from Palestine to SE Asia and Australia. 
2. Go at least largely through South Asia; because the distribution and basal diversity of mtDNA M and R, as well Y-DNA F demand it without any reasonable alternatives. 

The authors themselves acknowledge that the finding is inconclusive in this debate but they choose to lean for a revised Mellars-style interpretation on their own subjectivity.

Their hypothesis is not exactly like Mellars et al. These proposed an extremely late (c. 40-35 Ka BP) OoA, which would imply also extremely late colonization of East Asia and Australasia by Homo sapiens (via South Asia). In order to "explain" the lack East Asian blade-like technologies (necessary for the old professor's ideas about "modern human behavior") they proposed that the Eastern colonization was led by small populations who somehow lost the technology. But well, as I discussed back in the day, the hypothesis does not stand.

Mishra's revised hypothesis is somewhat more coherent (but still very unlikely): she proposes that East Asia and Australia were actually colonized with Middle Paleolithic technology (neither blades nor microblades) in the time demanded by archaeological data and that South Asia instead was not colonized by our species until c. 45,000 BP, possibly because there was some kind of intelligent archaic hominin (Hathnora?), which blocked the expansion of our species initially.

However the hypothesis is still plagued by problems:

1. As I said above, any model that dictates that South Asia was not central to the expansion of Homo sapiens in Eurasia and surroundings must be wrong: genetics demand otherwise. A settlement of South Asia that is posterior to that of East Asia, Papua and/or West Eurasia (other than the initial Arabian trailblazers or boaters) simply does not make any sense.
2. The African microblade technology is still quite older (70-60 Ka BP) than the South Asian findings and the similitude may well be a mirage or a matter of convergent evolution. Not the only time that people reinvent the same thing separated by time and space: look for example at Neolithic, which was developed at least in four separate regions of the World, maybe more; or look at the Solutrean style of retouch, used in many different Paleolithic cultures separated by time and space (Africa, Europe, America, etc.)
3. It would require that Homo sapiens would travel through Altai and all the evidence in this North Asian keystone region, a necessary corridor for transcontinental travel before the domestication of camels (or at the very least horses), indicates that it was inhabited by "archaic" hominids (Neanderthals, H. erectus/Denisovans) until c. 47 Ka BP, when industries related to those of West Asia and Europe show up (at later dates associated to H. sapiens remains).

The facts:

A C14 date was obtained for the site of Mehtakheri (near Barwah, Nimar region, Madhya Pradesh) annotated as: >42,900 BP, > 46,555 calBP, >45,028 - 48,081 (68% CI range for the calBP date). Another C14 date from the same site is much more recent (34,380 ± 991 calBP).

They also obtained five of OSL dates for section 2 ranging from 41.6(±3.3) to 47.0(±4.9) Ka ago. Another date for this unit of 55.5(±5.8) was not used by the authors because it corresponds to an unstudied layer.

Section 3 has older dates (65-78 Ka) but it corresponds to the Middle Paleolithic.

The microlithic industry seems to continue in South Asia until the Iron Age, suggesting that Neolithic and later developments did not substantially alter the demography of the subcontinent. 

All this is very informative but the conclusions suggested don't seem to make any sense. It is much more logical to infer that H. sapiens left Africa with an MSA-like Middle Paleolithic toolkit that was not related to the Nubian culture (the dead horse being beaten once and again by both Mellars and Mishra) but to other ill-defined groups of possible South African affinity (as claimed by Petraglia). Insisting on the Nubian techno-complex, when we do not know it reaching beyond Dhofar (i.e. they did not reach the Persian Gulf "oasis", unlike Petraglia's trailblazers or Armitage's Jebel Faya findings) is taking the part for the whole, as if there was not already a much more widespread and diverse African Middle Paleolithic (MSA, Lupenbiense, Aterian) in those times already.

Instead these data may indicate a relation of some sort with West Eurasian Upper Paleolithic and African Late Stone Age, which are of roughly those dates. This tentative relationship does not imply migration but would just need some cultural contact. 

It would be interesting to know more about the MP-UP transition in the area around Arabia Peninsula in order to develop better theories on this tripartite interaction between the West Eurasian early UP, the African early LSA and the South Asian early microlithic industry. These very possible cultural interactions fit well within the wet phase of the Mousterian Pluvial (c. 50-30 Ka ago).


Update (Jul 11): "microliths" that are not microliths

I just looked for the first time at the technical issue of what is a microlith (~1 cm long, ~0.5 cm wide) and the published toolkits only seem to have one microlith senso stricto: the J4 point. All the rest have lengths of 2 cm or larger, often 5 cm or more.

The presence of some microlith-sized pieces (usually points) in early UP cultures is almost standard: Emirian, Chatelperronian, Aurignacian and Gravettian all them have occasional "microliths" (measured by size) an in all cases these are points, exactly as happens in Mehtakheri.

So these toolkits seem to have more relationship, if anything, with Western Eurasian early UP ones, which are roughly contemporary (Emirian is the only clearly older one).

Furthermore, archaeologist Millán Mozota sees even similitudes with Mousterian flaking style (see comments):

Bladelet flaking is a typical flaking strategy for this blank type (small pebbles). Specially if the raw material itself is of good enough quality.

It has been documented, for high quality quartz on Mousterian sites, like in Grotte Breuil and, if i recall correctly, other sites in that area of the Italian Peninsula.

Being also puzzled because the inventories described suggest a strong blade/bladelet component, instead of microblades. 

Ancient Native Americans related to modern ones

Sequencing of ancient Native American remains from British Columbia (Canada), dated to c. 5-6000 years ago, shows that many modern local natives are their apparent descendants or otherwise related.

Yinqiu Cui et al. Ancient DNA Analysis of Mid-Holocene Individuals from the Northwest Coast of North America Reveals Different Evolutionary Paths for Mitogenomes. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0066948]

Abstract

To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga’a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor–descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.

Figure 2. Phylogeny of complete mitochondrial genomes sequenced in this study.
Mutations are transitions unless specified. Transversions are indicated by an A, G, C, or T after the nucleotide position. Insertions are indicated by an “i”, deletions are indicated by a “d”, recurrent mutations are underlined, and mutations back to the rCRS nucleotide are designated by a “@”. The C stretch length polymorphism in region 303–315 was disregarded in the tree. The sample “Haida 9″ was analyzed in Schurr et al. (2012). All other samples were analyzed in this study.

Exercise causes epigenetic changes in fat cells

It seems more and more obvious than rather just burning fat, what exercise does against overweight is to alter the way the body works in more subtle pathways.

Tina Röhn et al., A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue. PLoS Genetics 2013. Open access → LINK [doi:10.1371/journal.pgen.1003572]

Abstract

Epigenetic mechanisms are implicated in gene regulation and the development of different diseases. The epigenome differs between cell types and has until now only been characterized for a few human tissues. Environmental factors potentially alter the epigenome. Here we describe the genome-wide pattern of DNA methylation in human adipose tissue from 23 healthy men, with a previous low level of physical activity, before and after a six months exercise intervention. We also investigate the differences in adipose tissue DNA methylation between 31 individuals with or without a family history of type 2 diabetes. DNA methylation was analyzed using Infinium HumanMethylation450 BeadChip, an array containing 485,577 probes covering 99% RefSeq genes. Global DNA methylation changed and 17,975 individual CpG sites in 7,663 unique genes showed altered levels of DNA methylation after the exercise intervention (q<0.05). Differential mRNA expression was present in 1/3 of gene regions with altered DNA methylation, including RALBP1, HDAC4 and NCOR2 (q<0.05). Using a luciferase assay, we could show that increased DNA methylation in vitro of the RALBP1 promoter suppressed the transcriptional activity (p = 0.03). Moreover, 18 obesity and 21 type 2 diabetes candidate genes had CpG sites with differences in adipose tissue DNA methylation in response to exercise (q<0.05), including TCF7L2 (6 CpG sites) and KCNQ1 (10 CpG sites). A simultaneous change in mRNA expression was seen for 6 of those genes. To understand if genes that exhibit differential DNA methylation and mRNA expression in human adipose tissue in vivo affect adipocyte metabolism, we silenced Hdac4 and Ncor2 respectively in 3T3-L1 adipocytes, which resulted in increased lipogenesis both in the basal and insulin stimulated state. In conclusion, exercise induces genome-wide changes in DNA methylation in human adipose tissue, potentially affecting adipocyte metabolism.

Figure 2. Analysis flowchart.

Table 3. Changes in adipose tissue DNA methylation in response to a 6 months exercise intervention. Significant CpG sites (q<0.05) with the biggest change in DNA methylation (>8%).

New evidence from Luristan reveals that Neolithic Revolution was almost simultaneous across the Fertile Crescent

Wild barley from Chogha Golan

The new sites, in the Southern Zagros mountain country of Luristan (Iran), evidence local development of agriculture between 12,000 and 9800 BP:

The plant remains found at the Chogha Golan site document more than 2,000 years of the region’s land use and represent the earliest record of long-term plant management in Iran, according to the researchers. The site’s excavation, which was conducted by archaeologists from the University of Tübingen and the Iranian Center for Archaeological Research between 2009 and 2010, shows that Chogha Golan’s early inhabitants cultivated wild barley, wheat, lentil and grass peas—and eventually domesticated emmer wheat—during their occupation, which began about 12,000 years ago.

“Plentiful findings of chaff remains of the cereals indicate that people processed their harvest within the sites they were living in,” Riehl said. “Mortars and grinding stones may have been used for turning the grain into some kind of bulgur or flour, which may have been further processed either by cooking or roasting.” (The author also notes, however, that chemical studies of the grinding tools showed that they were multi-purpose—not just for processing plant materials.)

Annotation on study's map. 
Earliest Neolithic areas in red (previously known) and in blue (new ones). Notice that Jarmo is not usually considered (against what the legend says) part of PPNA, but a different locally rooted culture altogether. There are doubts on whether PPNA was a productive or just Mesolithic cereal-gatherer economy.
Consolidated Neolithic: The green dotted line marks the max. extension of PPNB, which was not the only consolidated Neolithic culture: earliest Balcanic and South Asian Neolithic were already ongoing by that time (8th millenium BCE), while in Africa it should be not much more recent. In lowland Mesopotamia the sediments have so far hidden any cultural phase prior to the already highly developed Ubaid culture, the first known civilization.
East Asia and Papua had their own distinct Neolithic developments of similar time-frame.

Source: Past Horizons.

Ref. S. Riehl et al. Emergence of Agriculture in the Foothills of the Zagros Mountains of Iran. Science Magazine 2013. Pay per view → LINK [doi:10.1126/science.1236743]

HERC2 haplotypes worldwide study at Kurdish DNA

I must congratulate again Palisto of Kurdish DNA blog for his excellent work on the description of HERC2 haplotypes and their frequency across world populations. It is not a peer-reviewed academic paper but it could well be, and within the high quality sector.

Palisto, The color of the eyes: at least 17 HERC2 variants in Human gene pool. Kurdish DNA 2013. Freely accessible blog article → LINK

After initially detecting seven haplotypes in the Kurdish genetic pool (which were named ht1-7) and then studying these in the Eurasian gene pool, he decided to study the African haplotypes, largely in the "other" category, as well as comparing them all with the known Neanderthal and Denisovan sequences, at the very least to infer a root. The main result is this tree:

So the ancestral haplotype is ht13, found not just among Neanderthals and Denisovans, but also among scattered populations of H. sapiens both in Africa as in Eurasia-plus. 

From it hang ht8 (Homo sapiens, found in and outside Africa) and ht18 (Neanderthal-exclusive).

This main branch has two major sub-haplogroups, which I will label D and E for convenience (A would be ht13, B ht8, and C Neanderthal-only ht18). Haplogroup D (hts 11, 16 and 17) seems to have remained in Africa (only ht 11 was detected at low frequencies in Lebanon), while haplogroup E (all the rest) massively participated in the migration out of Africa (OoA).

However it must have done already in highly diversified form, as most named haplotypes are found at significant frequencies both outside and inside Africa. There are four exceptions only:

1. Ht9 is only found in Africa (with a minor Arabian exception), so this haplotype did not took part in the OoA.
2. Ht15 has not been found in Africa instead, so it is possible that it evolved already in Eurasia.
3. Ht2 and its descendant ht1 (both of which cause blue eyes, albeit in recessive manner) don't seem to exist in Africa either (with the exception of the HGDP San sample, which seems notably admixed with Europeans, at levels of almost 20%, not your typical Bushmen really), so again they probably arose already in Eurasia. 

These are the wider regional frequencies:

However at the original article there is a much more detailed list, which is probably more interesting to use when pondering each haplotype. For example the overall data for America is pretty much irrelevant, as it groups native peoples with mixed creole ones.

For example we can see that "blue eyes" ancestral haplotype ht2 looks like originated in West Asia, and it may also be the case of its descendant ht1. 

Ht 15 in turn may well have coalesced in Altai, from where it spread to mostly Native American peoples (represented by Mestizo Colombians). A similar pattern can be seen in ht14, however this must be original from Africa (the Biaka have it, as do Mozabites) and therefore it is found also in some other scattered populations like Cambodians, Sindhi, etc.

Something I wonder about is the low diversity displayed by East Asians in this haplotype. Or inversely, why did West Eurasians evolve so all non-African novel variants? While there is still some left to analyze in the ND box, it is very small in East Asia. I wonder if it has some relation with skin pigmentation pathways indirectly influencing this change somehow.