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 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?

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:

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.

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.

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

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 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

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:

1. The monosyllabic root theory of Lakarra is too daring. The available evidence does not support this in most cases.
2. 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.
3. All reconstructions are purely theoretical.
4. Abusive self-citation, often of unpublished materials. Lakarra almost never cites other authors than himself.
5. 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.
6. Frequent changes in the etymologies, revealing extreme insecurity and improvisation in Lakarra's own thought.
7. 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.
8. 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.
9. 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.
10. It does not even consider dialectal variation. Lakarra invariably uses only the modern standard form (Euskara Batua), totally ignoring the well attested dialectal variation.
11. 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.
12. Some proposed evolutions are absolutely incredible. For example:
    *goi-bar ('up-down') > *gwibar > *bi-z-bar > bizkar (anat. back, geog. hill, mountain).
13. 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].
14. Breaches the principle of regularity when we consider Basque dialects.
15. 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.
16. Sometimes misinterprets words. For example atseden (to rest, turn off, breath, satisfy) is mistranslated by Lakarra as to die.
17. 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.
18. 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.
19. 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

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)

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

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.

Constructors invade major archaeological site in Istanbul with heavy machinery

Archaeologists working in one of the most important archaeological sites of Europe, Yenikapı (Istanbul, Turkey), an emergency dig that has been extended for years as it became obvious that it is a treasure of archaeological evidence spanning many ages, saw their work interrupted and damaged by an impromptu invasion of heavy machinery. The site is meant to be one of the major nodes in the ambitious Marmaray subway project but is under archaeological research since 2004. 

Archaeologists working at the site have released a written statement to attract public attention to the incident. “An excavation has been carried out in Yenikapı as part of the Marmaray Subway Project for eight years as ordered by the Fourth Regional Board of Protection of Cultural and Natural Assets. The importance of the contributions that this excavation has made to the cultural life of İstanbul is already well known by the public. This excavation has been defined by world authorities as one of the most important excavations made during the century. The ongoing excavation activities do not block the construction of the Marmaray project because the work is being conducting at a place that is planned to be a parking lot. This excavation is the site of the Port of Theodosius, which dates back to the fourth century. The site is also in a residential area dating back to the Neolithic Age. On May 11, 2013, bulldozers went onto the site and started to destroy these historically important remnants. This is a crime under the current Constitution's Article 63 concerning the conservation of historical, cultural and natural wealth, and this is against international agreements signed by Turkey,” they said.

Source: Today's Zaman.

The human colonization of Australia and Near Melanesia

Continuing with the joint series of articles on the expansion of Homo sapiens, David Sánchez published last week an interesting piece[es] on the original colonization of Australia and Papua at Noticias de Prehistoria - Prehistoria al Día, which I'll try to synthesize here.

Earliest evidences of human occupation of Australia and Near Melanesia (all before 30 Ka BP)

Maybe the most interesting detail is that Lake Mungo 3 has dates that clearly establish a colonization of the continent at least 60,000 years ago:

81.000 +- 21.000 U (Uranium series)
62.000 +- 6.000 ESR/U (Electron spin resonance/Uranium)
61.000 +- 2.000 OSL (Optical Stimulated luminiscence)
40.000 +- 2.000 OSL (Optical Stimulated luminiscence)

The sites of Nauwalbila I and Malakunanja II have provided similar dates: 60-50 Ka BP (OSL) and 61,000 BP +9,000/-13,000 (TL) respectively. So we can safely discard the conservative approach that only allowed for at most 50 Ka as earliest colonization boundary for the Oceanian continental landmass. 

The depiction of a Genyornis, giant duck-like bird extinct before 40 Ka, in Australian rock art ago also supports a very early date for the settlement of Australia. In Highland Papua human presence is also confirmed to at least 49 Ka ago, as I reported in 2010.

Naturally the settlers must have arrived by sea, the most commonly accepted candidate for such a vessel is a humble raft still used by some Papuan populations and which has parallels in Southern Asia (also still in use in some places):

Such a journey was attempted with a similar but larger raft, equipped with a simple sail named Nale Tasih 2. This craft had no trouble in reaching the continental platform of Australia from Timor in just six days and they actually managed to reach the modern Australian coast, although they desisted of beaching by night in the middle of a storm in an area infested by the largest crocodiles on Earth, being evacuated by the coastguard instead (the barge was later recovered in perfect state).

'Eurasian' language macro-family or just another bluff?

Andrew (at his blog) leads me to this interesting criticism by Sally Thomason of the much fabled study about a supposed new language macro-family including the most unlikely Eurasian languages such as Dravidian, Indoeuropean and "Eskimo" (sic). 

The original paper by Mark Pagel et al. proposes that a reduced core of 23 words are "ultraconserved", allowing them to formulate their hypothesis only on them (totally substandard even for the more generous mass-comparison approach). 

When Thomason looks at the raw data she finds that of the 23 words, only 2 have consensual proto-words in Altaic, for example, all the rest having several alternatives, of which Pagel and co. cherry-picked this or that one with the sole criterion of the convenience for their speculation. 

Never mind that Altaic, as defined in that database of Starostian inspiration, includes Japonic and Koreanic, something nowadays essentially discarded. 

Also the attribute of ultraconservation, foundation for the Pagel hypothesis, is challenged by Thomason, who finds that only 6 or 7 words of the 23 are conserved from Proto-Indoeuropean into English, a very low rate considering that English vocabulary is overwhelmingly of Indoeuropean origins (be them Germanic, Old French or some other variant).

In other words and in French: rien de rien; nothing at all worth the media hype that the Pagel paper has achieved... in the short run.

New sublineages in Y-DNA haplogroups A3 and B2a

Improving the knowledge of African genetics.

Rosaria Scozzari et al., Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0049170]

Abstract

One hundred and forty-six previously detected mutations were more precisely positioned in the human Y chromosome phylogeny by the analysis of 51 representative Y chromosome haplogroups and the use of 59 mutations from literature. Twenty-two new mutations were also described and incorporated in the revised phylogeny. This analysis made it possible to identify new haplogroups and to resolve a deep trifurcation within haplogroup B2. Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.

Figure 1. Revised topology of the deepest portion of the human MSY tree.

The names of the mutations genotyped are indicated on the branches (green, mutations from the paper by Karafet et al. [14]; black, mutations from the paper by Cruciani et al. [16]; red, previously undescribed mutations, see text). For the sake of clarity, the internal structure of haplogroups B-M108.1 (2 branches) and B-50f2(P) (8 branches) is not shown (black triangles). The phylogenetic position of mutations mapping within haplogroup CT is shown in Figure S1. Dashed lines indicate putative branchings (no positive control available). The microsatellite intermediate allele DYS449.2, that was found to delineate new phylogenetic structure in human Y chromosome haplogroup tree [42], was not observed in 19 Y*(xBT) and 4 B chromosomes analyzed.

Notice that the nomenclature per ISOGG is right now as follows:

• A1b-V148 is now known as A0
• A1a-V4 retains the name A1a
• A2-V50 is A1b1a
• A3-M32 is A1b1b
• A3a-M28 is A1b1b1
• A3b-M144 is A1b1b2

See ISOGG for more details.

South Arabian genetic refugium

This is not about the L(xM,N) lineages but about the Eurasian ones like R0a or R2.

Jeffrey I. Rose et al., Tabula rasa or refugia? Using genetic data to assess the peopling of Arabia. Arabian Archaeology and Epigraphy, 2013. Pay per view → LINK [doi:10.1111/aae.12017]

Abstract

This paper provides a broad overview of the current state of archaeogenetic research in Arabia. We summarise recent studies of mitochondrial DNA and lactase persistence allele -13915*G in order to reconstruct the population histories of modern Arabs. These data, in turn, enable us to assess different scenarios for the peopling of the Peninsula over the course of the Late Pleistocene and Early Holocene. The evidence supports the posited existence of Arabian refugia, although it is inconclusive which (e.g. Persian Gulf basin, Yemeni highlands and/or Red Sea basin) was/were responsible for housing ancestral populations during the Last Glacial Maximum. Synthesising genetic and archaeological data sets, we conclude that a substantial portion of the present South Arabian gene pool derives from a deeply rooted population that underwent significant internal growth within Arabia some 12,000 years ago. At the same time, we interpret the disappearance of Nejd Leptolithic archaeological sites in southern Arabia around 8000 years ago to represent the termination of a significant component of the Pleistocene gene pool.

Rose uploaded the full paper at Academia.edu. Very much worth a careful read because it is a rare case of paleogenetics being done by a researcher who is primarily an archaeologist and who knows well the material Prehistory of which he's talking about, at all moments seeking to reconcile archaeological and genetic evidence and not, as way too often happens, creating genetic-only models with absolutely no material foundations and unavoidably clashing with prehistoric reality.  

Oppenheimer 2012: the scholastic ouroboros of repeating the usual 'molecular clock' errors

Last year Stephen Oppenheimer published yet another article on the mitochondrial DNA tree and his vision of the molecular clock applied to the human matrilineages.

Stephen Oppenheimer, Out-of-Africa, the peopling of continents and islands: tracing uniparental gene trees across the map. Philosophical Transactions of the Royal Society B, 2012. Freely accessible → LINK [doi:10.1098/rstb.2011.0306]

The centerpiece of the article is fig.2, a mtDNA tree with his "molecular clock" estimates of the ages of the haplogroups. Sadly it has a major problem: the resulting dates have a horrible fit with all the archaeological and paleoclimatic evidence and even with the most recent estimates for the Pan-Homo split. 

Much of the article (all section 1.b) is dedicated to attempt to justify his so-called "calibration" methods, which are in the end based on a self-reference: Soares 2009, of which Oppenheimer was co-author and which was calibrated assuming a Pan-Homo split age of 5-6 Ma. 

In annoyingly pointless circular reasoning, Oppenheimer manages now to estimate the  Pan-Homo split at 6.5 Ma using the Soares 2009 "molecular clock" rates.

All these Pan-Homo split age guesstimates are horribly wrong, because Sahelanthropus tchadiensis (c. 7 Ma ago) was already in the Homo line (and not anymore in the Pan one) and also because several other authors have estimated the Pan-Homo divergence age to be at least 8 Ma old, and maybe as ancient as 13 Ma (Langergraeber 2012).

Sadly the Academy remains stuck and Oppenheimer is no exception but rather the opposite. This is his fig. 2 with my rough corrections in red after proper recalibration of the Pan-Homo split age:

This does not mean that the red colored dates provided here are necessarily the correct ones, although in many cases they do seem to fit much better with the archaeological and paleoclimatic data, especially at the lower ranges. It is merely a simple "first aid" correction to Oppenheimer's necessarily incorrect estimates. 

Other factors must be taken into account, for example I do not believe for a second that M is older than African L3 branches, which show only one or, in one case, two coding region mutations downstream of the L3 node, while M is three mutations downstream and N five. Oppenheimer seems determined to count HVS mutations for example and to estimate age counting from the present forms (which could well be frozen in time for many many millennia because of "drift out" phenomena if the population was large enough but not too large, which would tend to freeze the hegemonic lineages in my modeling tests, while removing any novel ones). 

I do not propose any alternative "molecular clock" for mtDNA because I feel that it poses way too many issues because of irregular branch length. Maybe in the future some brilliant geneticist (or maybe mathematician?) will be able to posit a reasonably good refurbished "molecular clock" for mtDNA but at the moment I know of no one. 

I'm just stating the obvious: what Oppenheimer is selling is necessarily wrong.

Bronze Age Sweden imported its copper

Dienekes' Anthropology Blog mentions this week several papers that dwell in the nature of the Nordic Bronze Age, specifically in Southern Sweden. It turns out that the copper used by the Nordic smiths was not local in almost all cases but imported from elsewhere in Europe (Sardinia, Iberia, Auvergne, Tyrol and British Islands) or even West Asia (Cyprus). This imported copper was exchanged by essentially amber, it seems, an export product of the Nordic area since the Chalcolithic. Nothing is said about the tin needed to make bronze but most likely it came from SW Britain and/or NW Iberia, as these were the two main producers of the strategic metal in old times.

Of the three mentioned papers only one is freely accessible, and also quite interesting to read:

Nils-Axel Mörner & Bob G. Lind, The Bronze Age in SE Sweden Evidence of Long-Distance Travel and Advanced Sun Cult. Journal of Geography and Geology 2013. Open access → LINK [doi:10.5539/jgg.v5n1p78]

Abstract

The Bronze Age of Scandinavia (1750-500 BC) is characterized by the sudden appearance of bronze objects in Scandinavia, the sudden mass appearance of amber in Mycenaean graves, and the beginning of bedrock carvings of huge ships. We take this to indicate that people from the east Mediterranean arrived to Sweden on big ships over the Atlantic, carrying bronze objects from the south, which they traded for amber occurring in SE Sweden in the Ravlunda-Vitemölla–Kivik area. Those visitors left strong cultural imprints as recorded by pictures and objects found in SE Sweden. This seems to indicate that the visits had grown to the establishment of a trading centre. The Bronze Age of Österlen (the SE part of Sweden) is also characterized by a strong Sun cult recorded by stone monuments built to record the annual motions of the Sun, and rock carvings that exhibit strict alignments to the annual motions of the Sun. Ales Stones, dated at about 800 BC, is a remarkable monument in the form of a 67 m long stone-ship. It records the four main solar turning points of the year, the 12 months of the year, each month covering 30 days, except for month 7 which had 35 days (making a full year of 365 days), and the time of the day at 16 points representing 1.5 hour. Ales Stones are built after the same basic geometry as Stonehenge in England.

The other two are sold under mercantile schemes:

Johan Ling et al., Moving metals or indigenous mining? Provenancing Scandinavian Bronze Age artefacts by lead isotopes and trace elements. Journal of Archaeological Science 2013. Pay per view → LINK [doi:10.1016/j.jas.2012.05.040]

I.B. Gubanov, Grave Circle B at Mycenae in the Context of Links Between the Eastern Mediterranean and Scandinavia in the Bronze Age. Archaeology, Ethnology and Anthropology of Eurasia 2012. Pay per view → LINK [doi:10.1016/j.aeae.2012.08.011]

Ling's paper is the one indicating that Swedish copper had exotic Atlantic and Mediterranean origins, while Gubanov's highlights that amber from the Baltic is found in one Mycenaean grave (specifically Grave Circle B) and not in any known Minoan (Eteocretan) one. For him this means that bronze metallurgy and other associated elements like the quadruple spiral motif arrived with Mycenaean sailors in the Bronze Age. 

Grave Circle B is actually older than the much more famous Grave Circle A (the pseudo "Agamenon's Tomb"), although both belong to the Late Helladic I period (c. 1550-1500 BCE).

(public domain, credit: myself)

This chronology is interesting because it was roughly in those dates when SE Iberian El Argar civilization began its phase B, characterized by Greek influence in burials (pithoi). It is worth mentioning here that while these are the first findings of amber from Nordic Europe in the Eastern Mediterranean, such jewels were common in Iberia since c. 3000 BCE (beginnings of Chalcolithic period). 

It would seem therefore clear that Iberia was a pivotal area in this purported Scandinavian-Greek exchange. The question is: did the early Greek sailors actually reached Scandinavia themselves or were they rather just receiving products by mediation of Iberian traders with a long tradition of Atlantic (and Mediterranean) navigation?

It is probably a hard to answer question. But the studies point to some relevant cues, like the Swedish drawings of ships with rams and the presence of the (originally Mediterranean?) motif of the quadruple spiral, so similar to the Basque lauburu (four heads) icon (probably related to both the svastika and triskel). 

Figure 3.B. the spiral ornament from Sweden and Greece

This spiral icon is not Mycenaean in origin, having been found in Minoan Crete and Megalithic Malta (right), which are respectively older and a lot older than the Mycenaeans. The motif is not even exclusive of Europe, with very similar concepts found for example in the pottery of Western Mexico.

So while the similitude is striking, this evidence is not conclusive on its own. 

The Cypriot copper evidence alone is not enough evidence of Mycenaean presence in Scandinavia, very especially as Cyprus seems important, long before the Mycenaeans in the East-West Mediterranean connections. Cyprus used their own script (probably used for the native Eteocypriot language) up to the 4th century BCE and while Mycenaean presence in the island seems attested in the very late Bronze Age, the island was not a Mycenaean center at all but rather was under Hittite and Ugaritic influence instead.  

So we are left with the claim of rammed ships being coincident with the Mycenaean period. However what I find searching around are dates of c. 1700 BCE (Norway), very early in the Mycenaean chronology and some two centuries older than the single amber finding in Mycenae. It could indeed be a Mycenaean influence but how conclusive is it?

I have a vague memory of a Mycenaean ship (?) found years ago in the waters of Denmark or Germany, however I can't find anything searching online. Does anyone know something more detailed on the matter? This would be key evidence but I cannot trust my memory alone. 

So there seems to be some sort of interaction between the Eastern Mediterranean and Scandinavia but, as far as I can tell, specifically Mycenaean presence in the Far North is circumstantial rather than conclusive. 

Besides the issue of purported trade with the Mediterranean, there are some other interesting elements in Mörner & Lind 2013, notably the description of the Ales Stones ship-shaped megalith ("sun ship") as an astronomical calendar:

Not sure how new this is but it is a very interesting thing to know, right?



Update (May 17): Dispatches from Turtle Island has some interesting and realistic calculations on how long would take an ancient ship to sail from Greece to Sweden and back (c. 112 days, he estimates).