Monthly Archives: May 2013

Italian complex ancestry

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 accessLINK [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.


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

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.
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.
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?

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 accessLINK [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:
  1. Southern area (dominated by the pink component): including Zeeland, North Brabant, Limburg, South Holland, much of North Holland and, counterintuively, Western Overjissel.
  2. Northern area (dominated by the yellow component): including Friesland, Gröningen, Drenthe and the eastern areas of Gelderland and Overjissel.
  3. 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

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.

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Posted by on May 29, 2013 in blogging, general strike


Chinese neolithic site of Tianluo Mt.

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.
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Posted by on May 29, 2013 in archaeology, China, East Asia, Neolithic


Neanderthals weaned their babies between 9 and 18 months of age

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

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
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Posted by on May 29, 2013 in intelligence, mind, psychology


Ancient West Siberian mtDNA

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 accessLINK
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).