For what they were... we are

Ancient Minoan mtDNA

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

Early Minoan jar
(CC by Wolfgang Sauber)

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

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

Abstract

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

From the paper (emphasis mine):

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Echoes from the past (May 17 2013)

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

Some interesting news I cannot dedicate much effort to:

Human intelligence not really linked to frontal lobe.

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

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

Early hominin ear bones found together in South Africa.

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

New hominin site in Hunan (China).

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

The five human teeth

Neanderthal workshop found in Poland.

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

Ancient Eastern Europeans ritually killed their pets to become warriors.

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

Ancient log boat found in Ireland.

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

Maya pyramid destroyed in Belize... to get gravel

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

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

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

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

Constructors invade major archaeological site in Istanbul with heavy machinery

2013-05-17T20:10:00.000+02:00

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

2013-05-17T19:43:00.000+02:00

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?

2013-05-17T16:56:00.002+02:00

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

2013-05-17T16:31:00.001+02:00

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

2013-05-17T16:08:00.000+02:00

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

2013-05-17T15:40:00.000+02:00

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

2013-05-12T16:14:00.000+02:00

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).

Strontium data shows that Aldaieta remains are mostly local Basques - but some immigrants too

2013-05-11T13:39:00.001+02:00

Certain historians have in the past claimed that Southern Basques arrived from the North in the Middle Ages (Spanish school) or vice versa, that Northern Basques arrived from the South in exactly the same period (French school). The evidence for either hypothesis was nearly zero but that does not seem to deter certain kind of minds more concerned about defending their own biased version of history than about knowing and discussing the facts.

Your truth not, Truth.
And come with me in search of it,
yours keep it for yourself.

Antonio Machado

Luis Ángel Ortega et al., Strontium isotopes of human remains from the San Martín de Dulantzi graveyard (Alegría-Dulantzi, Álava) and population mobility in the Early Middle Ages. Quaternary International 2013. Pay per view → LINK [doi:10.1016/j.quaint.2013.02.008]

Abstract

Strontium isotope analysis of human remains from San Martín de Dulantzi (Alegría-Dulantzi, Álava, Spain) graveyard has been used to establish mobility patterns during the Early Middle Ages. Some archaeological human remains had Germanic grave goods. Through radiogenic strontium isotope analysis, local origin individuals and immigrants were differentiated. Archaeological human bone samples exhibit 87Sr/86Sr = 0.70779–0.70802 values similar to domestic fauna isotope composition, indicating local origin of individuals or long residence time in the region. Comparing these data with tooth enamel values, two groups of immigrants from distinctive geological environment were established. The Dulantzi population constituted mainly a local society with influxes of immigrants. The foreign individuals are distributed through the studied period of time, suggesting that migration movements were limited in number. Isotopic signatures indicating mainly local individuals, linked to grave goods with archaeological attribution to Germanic origin, question the previous ethnic paradigm.

Fig. 7. Isotope variation of the studied samples. Grey area corresponds to the variation range in local waters (Fernández de Ortega, 2007). Dashed line indicates the average isotope ratio of soil at the site. Doted line corresponds to the average for the bones. Green and blue areas indicate immigrants from different geological environments.

At the time of writing this entry, Luis Ortega had uploaded a pre-print version of the paper at Academia.edu.

The site was argued to imply immigration because of the grave goods (pottery, weapons, belt buckles), which are similar to those found elsewhere in the Basque Country in that period and which are much more similar to Frankish or Aquitanian similar items than to Iberian ones (then under Visigothic rule). The period of the cemetery includes the 6th and, much more densely, 7th centuries CE.

Duchy of Vasconia, 8th century (CC by myself)

The Duchy of Vasconia was founded by the Merovingian Franks in 602 as a march against Basque tribes, then effectively independent. In 628 Charibert, brother and heir of Dagobert, was appointed as Duke after the successful Basque rebellion of 626, and in 635 a massive Frankish army took control of most of the country but defeated in Zuberoa (Soule). Another rebellion in 643 erased all Frankish control and established an independent state, since 660 in personal union with Aquitaine (in medieval times the romanized area between the Garonne and the Loire with capital in Toulouse).

Meanwhile the Visigoths of Toledo had established another march by the name of Duchy of Cantabria in the southern frontier, briefly conquering what is now Southern Navarre in 621 and founding the city of Oligitum (Olite). The fact that the Bishop of Pamplona was absent from Visigothic Councils at Toledo between 589 to 684 evidences that the Goths never conquered anything relevant further North than this town.

With this historical context it seems somewhat logical that Southern Basques had greater relations with the Franks and, particularly, the wider region of Aquitaine (both Novempopulania, now Gascony and the Northern Basque Country, and medieval Aquitaine between the Garonne and the Loire), however nothing seems to suggest widespread immigration.

Neither do the results of this study, which however show half a dozen individuals apparently from outside (two groups).

It is interesting to recall that a previous study on ancient mtDNA on the same cemetery (Alzualde 2006, PPV - but available at Academia.edu), found three individuals with the lineage U2 and two with M1c, both apparently exotic in the Basque Country. U2 is relatively common (5%) in the area of Perigord-Limousin (Dubut 2004), while M1c is deemed North-West African. However the vast majority of lineages belongs to haplogroups normal among Basques since early Neolithic times, and in apportions consistent with local continuity.

However the similitude between Basque and Aquitanian genetic pools does not allow for easy discernment, reason why this isotopic study is particularly important to confirm the local origins of most of the Aldaieta medieval population.

Thanks to Ama Ata[es], which made me aware of this study.

Askondo cave art is 25,000 years old

2013-05-11T12:07:00.000+02:00

The rock art of Askondo cave (Mañaria, Biscay, Basque Country) has been dated to c. 25,000 years ago. The materials used for the artworks (red paint and engraving) cannot be dated directly but a bone fragment encrusted in the wall provided an age of c. 23,800 years BP (C14-AMS) belonging therefore to the Gravettian period.

The cave of Askondo (← aitz-ondo = near the rock) was believed to be a destroyed site but recent archaeological research has shown the opposite: that there is a lot to be researched in that cave, which has a surprising sedimentary depth of at least 6 m and that has already become, thanks to its artwork, in the third more important Paleolithic site of Biscay, after Santimamiñe and Arenaza caves.

Source: Bizkaia.Net.

Archaeologists: Dakar rally in Chile is a crime against patrimony

2013-05-11T11:51:00.001+02:00

The College of Archaeologist of Chile has risen their voice against the Rally Dakar 2014 (which is not anymore held in Africa after much controversy but in South America) because it impacts and destroys many archaeological sites.

According to the Chilean archaeological guild the rally is a clear crime under the article 38 of law 17288, which should be persecuted by the Council of Defense of the State (CDE). However this entity "has its hands tied" because the Rally is promoted by the National Sports Institute (IND).

The Council of National Monuments (CMN) has documented not less than 207 archaeological sites damaged by previous editions of the rally up to 2012 (all rallies since 2009 have gone through Chilean, as well Argentine and sometimes Peruvian lands).

Since 2009 five legal actions have been initiated against this destructive competition, all of which have been dismissed by the courts.

Source[es]: Diario de Antofagasta (via Paleorama).

Praileaitz cave to have even less protection

2013-05-11T11:35:00.001+02:00

The new law of coasts passed by the conservative Spanish government and allowing construction only 20 meters from the coast (it used to be 100m), a scandal on its own right, will have direct effects on the already extremely fragile protection of the cave of Praileaitz, located within an active quarry and holding evidence of human existence from the Magdalenian period but also, we know now, from Neanderthal times some 100-120 Ka ago.

Years ago, the (then unelected) Western Basque Government limited the protection area to just 65m, considered by all experts wildly insufficient (Jean Clottes asked for 500m, for example), however a tribunal ruled later that 50m was enough. This new law allows for constructions and economic activities (such as the quarry) to take place just 20m away from the cave galleries, what may be very damaging.

There are possible mechanisms to counter this legislation but require of a political will that so far has been lacking or rather negative, hostile.

The utmost fragility of the cave is very apparent in this air view highlighting the archaeological sites near the controversial quarry:

Source: Caminando por Iberia

Some ornamental findings and archaeological works at Praileaitz (Bertan)

Sources[es]: Gara, Caminado por Iberia, Bertan, Amigos de Praileaitz.

Update (May 11): a report (in Spanish language) on the Mousterian and new Magdalenian findings from Praileaitz can be read at Noticias de Gipuzkoa (via Pileta).

Echoes from the past (May-9-2013)

2013-05-09T13:00:00.000+02:00

I am getting updated with a rather long backlog, so I will speed things up placing here in nearly telegraphic style the informative snippets that require less work. This does not mean that they are less interesting, not at all, just that I have to adapt to that elusive quality of time...

Middle Paleolithic

Toba supervolcano only had short-term climate effect → BBC.

Research on Lake Malawi's sediments shows that the climate-change effect of the catastrophic eruption was limited. Droughts previously believed to be from that period have been revised to be from at least 10,000 years before, corresponding to the end of the Abbassia Pluvial rather than to Toba super-eruption.

Upper Paleolithic

Altai rock art and early astronomy from 16,000 BP → Siberian Times, Daily Mail.

Sunduki (Khakassia), here there are what are surely the oldest rock art of Northern Asia, representing people hunting or interacting among them, which are from just centuries ago, however other petroglyphs are apparently much older like this horse:

Prof. Vitaly Larichev (Institute of Archeology and Ethnography, Russian Academy of Sciences) has detected a whole astronomical structure implemented in the landscape.

He claims to have found 'numerous ancient solar and lunar observatories around Sunduki'.

'This square pattern of stones on the ground shows you the place', he told visiting author Kira Van Deusen. 'I knew there would be an orientation point, but we had to search through the grass for a long time to find it.

'Now look up to the top of that ridge. You see a place where there is a crack between the rocks? If you were here on the summer solstice, you would see the sun rise right there. Or you would if you were here 2,000 years so. Now the timing is slightly differen'.

High on one cliff wall is a rock engraving showing dragon heads in one direction, and snake heads in the other.

'If the sun were shining, we could tell the time,' he said. 'In the morning the shadow moves along the snake's body from his head to his tail, and in the afternoon it comes from the other direction along the dragon.

'From the same observation point you can determine true north and south by sighting along the mountains'.

Neolithic

Vietnam: early cemetery dug in Thahn Hoa → Australian National University.

Some 140 human remains of all ages have been unearthed at the site of Con Co Ngua, estimated to be 6-4000 years old. Cemeteries of this size and age were previously unknown in the region. The site has also revealed a dearth of artifacts.

The people were buried in fetal position with meat cuts of buffalo or deer.

Chalcolithic

India: 4000 y.o. stone tools unearthed in Bhopal (Madhya Pradesh, Narmada river) → India Today.

Details:

Some of them are decorated with aquatic animals.
150x200 m. mound in Birjakhedi
Terracotta game pieces
Pottery (incl. jars, pots, dishes)
Stone and ivory beads

Bell Beaker rich lady's burial unearthed in Berkshire (England) → Wessex Archaeology.

The middle-aged woman wore a necklace of tubular golden beads, amber buttons on her clothes and a possible lignite bracelet. She was accompanied by a bell-shaped beaker of the "corded" type (oldest and roughest variant, of likely Central European inception).

The chemical signature of the gold beads is coherent with deposits from Southern Britain and SE Ireland.

Giza pyramid construction's logistics revealed → Live Science.

Caesar beat the Gauls.

Was there not even a cook in his army?

Bertolt Brecht (A Worker reads History)

Now we know that at the very least the famed early pharaohs Khafra, Khufu and Menkaure, who ordered the massive pyramids of Giza to be built as their tombs did have some cooks in charge of feeding the many workers who actually built them, stone by stone.

These workers were housed in a village some 400 meters south of the Sphinx, known as Heit el-Ghurab. In this place archaeologists have found a cemetery, a corral with apparent slaughter areas and piles of animal bones. Based on these, researchers estimate that more than 2,000 kilograms of meat were eaten every day during the construction of Menkaure's pyramid, the last and smallest one of the three geometric mounds.

The figures estimated for such a logistic operation border disbelief: 22,000 cows, 55,000 sheep and goats, 1200 km² of grazing land (roughly the size of Los Angeles or 5% of the Nile Delta), some 3500 herders (adding up to almost 20,000 people if we include their families).

A curious detail is that most of the beef was destined to the building of the overseers, while the common workers were mostly fed sheep or goat instead. Another settlement to the East of apparently local farmers ate most of the pork. There were also temporary tent camps closer to the pyramids.

Iron Age

Late Indus Valley Civilization was overcome by violence → National Geographic.

Harappa (CC by Shephali11011)

The Late Indus Valley Civilization (Cemetery H cultural layer, usually attributed to the Indoeuropean invasions) was, unlike in previous periods, quite violent, new evidence highlights.

The evidence from the bones also highlights the arrival of many non-local men, who apparently married local women. But the most shocking element is the striking evidence of widespread violence:

The skull of a child between four and six years old was cracked and crushed by blows from a club-like weapon. An adult woman was beaten so badly—with extreme force, according to researchers—that her skull caved in. A middle-aged man had a broken nose as well as damage to his forehead inflicted by a sharp-edged, heavy implement. Of the 18 skulls examined from this time period, nearly half showed serious injuries from violence ...

Gaming pieces of Melton Mowbray (England) → Science Daily.

Excavation of a hillfort at Burrough Hill revealed ancient gaming pieces, among other materials.

Funerary chamber found near the original location of the Lady of Baza (Andalusia) → Paleorama[es].

(CC by P.A. Salguero Quiles)

The tomb has an access gate and is estimated to be from the 5th or 4th centuries BCE (Iberian culture) and, unlike most burials of the time, the corpse was not incinerated.

The finding highlights the need for further archaeological work in all the hill but the severe budgetary cuts threaten this development.

Baza (Granada) hosts a dedicated archaeological museum inaugurated in 2011.

Tocharian mummy buried with marijuana hoard → Paleorama[es].

Some 800 grams of the psychedelic plant, including seeds, were found at the burial place of a Tocharian man, presumably a shaman, at Yanghai (Uyghuristan), belonging to the Gushi culture and dated to at least 2700 years ago. The plant belongs to a cultivated variety.

Some of the oldest cannabis evidence are also from that area (Pazyrk culture c. 2500 years ago) and also from Nepal (Mustang, similar dates). Later in Southern Central Asia it was used in combination with opium and ephedra, from where soon migrated to South Asia and many other parts of Eurasia.

Genetics

New device radically reduces costs and time in DNA extraction → Science Daily.

Researchers from the University of Washington and NanoFacture Inc. have developed a device, which looks like a kitchen appliance, able to extract DNA from tissues (like saliva or blood) in minutes at low cost and without using the toxic chemicals habitual in the field.

The prototype is designed for four samples but can be scaled for the lab standard of 96 samples at once.

8th Congress on the Antiquity of the Basque Language

2013-05-01T16:28:00.004+02:00

From Jatorriberri (bilingual: Basque-English):

8th. Congress on the Antiquity of the Basque Language. “Mythology: A Science for Analyzing the Past”.

The presentations will be held in Lazkao, Gipuzkoa the Saturday 25th. of May of 2013

Juan Inazio Hartsuaga: Fossil Words.
Roslyn M. Frank: Looking for attributes and cognitive tracks in the figure of fourteen, within and out from Euskal Herria.
Felix Zubiaga: Dramatic performance of a Sumerian-Basque tale.
Xabier Renteria: Basques of older times: Mythological vision of the world and pre-Indo-European Basque language.
Visit to the: Joxemiel Barandiaran's Museum
Jorge Oteitza gogoratuz. Notions of pre-Indo-European Basque philology
Antonio Laguardia: Iberian writings and the hieroglyphs from the 8th to the 29th Century B.C.
Presentation of new books. The DNA of Euskera, Studies of Iberian toponyms, The origin of Basques, The antiquity of words - Etymological Basque dictionary
Iruña-Veleia: What is new?

Registration: Congress outline and registering information can be found in the

following address: euskararenjatorria@gmail.com

There are other bilingual articles in the Jatorriberri newsletter.

Brotherton 2013: cherry-picking the evidence for mtDNA H

2013-04-27T15:25:00.000+02:00

Unlike the conceptually akin paper by Fu 2013 (PPV - discussed here), this one is very neatly explained and allows no doubts on how they reached their conclusions. Another thing is to agree with the method being good enough to provide for any conclusions at all. It is still an interesting study on the evolution of mtDNA lineage H in the specific context of the Elba-Saale region of Germany.

Paul Brotherton et al., Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nature Communications 2013. Pay per view → LINK. [doi:10.1038/ncomms2656]

Abstract

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

Let's deal with the interesting part first and then with their impossible molecular clock speculations.

All the samples used in this study belong to haplogroup H as you can see in table 1. This does not allow to consider the overall apportion of H in each population, for which we would need to go to the original studies. For example in the region's LBK samples, H was just some 20% of the total, what alone talks of a population that was not at all like the modern one, never mind N1a. On the opposite side of the spectrum are the Bell Beaker (BBC) samples, where H made up 88% of the total (Adler 2012, discussed here), again non-modern but a possible source of H increase in frequency.

We must keep in mind all the time that in this study only H is considered, with all the derived pros and cons.

Maybe the most interesting result is therefore the comparison with modern populations done in fig. 2a:

Figure 2 | Population affinities of select Neolithic cultures. (a) PCA biplot based on the frequencies of 15 hg H sub-haplogroups (component loadings) from 37 present-dayWestern Eurasian and three ancient populations (light blue:Western Europe; dark blue: Central and Eastern Europe; orange; Near East,Caucasus and Anatolia; and pink: ancient samples). Populations are abbreviated as follows: GAL, Galicia; CNT, Cantabria; CAT, Catalonia; GAS, Galicia/Asturia; CAN, Cantabria2; POT, Potes; PAS, Pasiegos; VIZ, Vizcaya; GUI, Guipuzcoa; BMI, Basques; IPNE, Iberian Peninsula Northeast; TUR, Turkey; ARM, Armenia; GEO, Georgia; NWC, Northwest Caucasus; DAG, Dagestan; OSS, Ossetia; SYR, Syria; LBN, Lebanon; JOR, Jordan; ARB, Arabian Peninsula;ARE, Arabian Peninsula2; KBK, Karachay-Balkaria; MKD, Macedonia; VUR, Volga-Ural region; FIN, Finland; EST, Estonia; ESV, Eastern Slavs; SVK, Slovakia; FRA, France; BLK, Balkans; DEU, Germany; AUT, Austria, ROU, Romania; FRM, France Normandy; WIS, Western Isles; CZE, Czech Republic; LBK, Linear pottery culture; BBC, Bell Beaker culture; MNE, Middle Neolithic.

BBC (Bell Beaker) and LBK (Linear Pottery Culture) are clear-cut cultures in this graph. However MNE (Middle Neolithic) is a pooled agglomeration of several not too related cultures from the Late Neolithic and Early and Middle Chalcolithic. So, using the haplogroup vectors (grey), I remapped its unlikely components:

Fig. 2a annotated by Maju: green "MNE" cultures, grey: other cultures. Dotted circles just for reference.

Suddenly the mirage of modernity and homogeneity in MNE's H collapses, very specially for Salzmünde (2/2 H3) but really also for the other components of the MNE pool: Rössen (directly derived from LBK) appears here as Balcano-Estonian and similar to Bronze Age Sardinia, Schöningen (derived from Rössen) appears Norman French and close to the original LBK pool, the first Kurgan culture in Central Europe, Baalberge, is the only one really close to the MNE dot but its closest modern relatives are NE Iberians (IPNE), while its successor Salzmünde is "hyper-Iberian" much as Bell Beaker after them - however the intermediate Corded Ware, C.W., leans back to the right and appears Catalan.

No conclusions can be inferred from this, for that we'd need to compare whole genetic pools and not just H, which is minority in most ancient samples but for whatever is worth... I made yet another annotated version of this graph:

Fig. 2a annotated by Maju: changes in Central European mtDNA H composition along time (arrows).

I considered here Rössen as different from Schöningen, as Rössen or Epi-Rössen persisted in much of Germany and nearby Alpine areas for long, but feel free to draw or imagine it differently.

Whatever the case the appearance is of gradual "modernization" or "Germanization" of haplogroup H culminating in Baalberge, followed by an "Iberization" of the haplogroup pool in the Middle and Late Chalcolithic, coincident roughly with the expansion of Megalithism and Bell Beaker and just mildly countered by Indoeuropean expansion from the East (Corded Ware, Unetice). Here they mention six Unetice H sequences but, judging on Adler 2012, H was very very rare in this culture at least in the Elbe-Saale area (1/31).

Beyond this I doubt that the paper can provide us with any more enlightenment.

Molecular-clock-o-logy

It does provide for some false leads however.

The authors use this Elbe-Saale limited ancient mtDNA evidence to construct a "molecular clock":

Another major advantage of the temporal calibration points provided by ancient hg H mt genomes is that the data allow a relatively precise estimate of the evolutionary substitution rate for human mtDNA. The temporal dependency of evolutionary rates predicts that rate estimates measured over short timespans will be considerably higher than those using deep fossil calibrations, such as the human/chimpanzee split at ~6 million years.

6 million years?! Where have you been in the last five years, Paul? Ahem...

It doesn't really matter but it illustrates the reactionary scholastic inertia that plagues the Academia, very especially in the field of population genetics.

What matters is that they continue as follows:

(...) The rate calibrated by the Neolithic and Bronze Age sequences is 2.4 x10⁻⁸ substitutions per site per year (1.7–3.2x10⁻⁸; 95% high posterior density) for the entire mt genome, which is 1.45 (44.5%) higher than current estimates based on the traditional human/chimp split (for example, 1.66 x10 ⁻⁸ for the entire mt genome and 1.26x 10⁻⁸ for the coding region). Consequently, the calibrated ‘Neolithic’ rate infers a considerably younger coalescence date for hg H (10.9–19.1 kya) than those previously reported (19.2–21.4 kya for HVSI, 15.7–22.5 kya for the mt coding region or 14.7–22.6 kya when corrected for purifying selection).

What matters is that by cherry-picking only some sequences of ancient mtDNA H, they are denying themselves (and the rest of us by extension) a realistic calibration of the haplogroup. What happened with the Cantabrian Magdalenian and Epipaleolithic Basque H? What happened with Epipaleolithic Karelian H? Never mind Sunghir's Gravettian H17'27 or Taforalt's massive pool of R*-CRS, most likely H1 (Kéfi 2005), which may be more questionable but never rejected without direct negative evidence.

In other words: they are cherry-picking the evidence. They could argue that the Elbe-Saale data was the only one readily available for them to sequence in full or whatever and that therefore the evidence was cherry-picked by Destiny... but that would not justify in any case the arrogance of their conclusions: they should have been much more humble and admit that this evidence is only part of all the ancient mtDNA H (known or suspected), some of which is clearly much older and therefore much more relevant.

I illustrated this problem using their fig. 1a:

Fig. 1a, annotated by Maju.
(Note: one of the "Magdalenian" H* sequences from North Iberia is actually Epipaleolithic, my error)

In orange color I have marked an alternative minimal "molecular clock" extrapolation using the La Chora H6 sequence (Hervella 2006 open access). This is minimal because I'm assuming this sequence to be underived H6, if it'd be derived (what I don't know), the estimate would be even larger.

I have annotated all the sequences I am aware of ancient confirmed (unquestionable) mtDNA H. There are many more that are very likely, and in many cases older (see maps), but not yet confirmed.

So well, molecular-clock-o-logical pseudoscience again. It's a pity that otherwise respectable scientists pay tribute to this academic fetish.

The molecular clock hypothesis has never been proven, being a mere statistical construct, and it has many problems particularly in mitochondrial DNA, where branches are dramatically unequal, obeying to either: (a) randomness, (b) differential adaptive fitness or (c) ancient population dynamics (variable drift results depending on population size). I discussed some of that here and also here.

I beg here to population geneticists to be more serious and careful and not try to push their ideas against the available evidence. That is not proper of scientists but belongs to the field of ideological propaganda.

Update: La Chora Magdalenian H6 is probably H6a1, with implications for the age estimate of H.

All known H6 of Iberia and all or most of Western Europe is H6a1, while the "famous" Central Asian H6 (very minor overall) is all H6(xH6a), which is also relatively important in Eastern Europe. See Álvarez Iglesias 2009 (open access), especially Supp. Table 3. H6a(xH6a1) has only been detected so far in Austria (oversampled - I miss data from France again).

Brotherton's H6 only sample (Corded Ware) is H6a1a. Álvarez Iglesias did not test for this phylogenetic level, hence would show in his data as H6a1 but he did test for H6a1a1, only found precisely in Cantabria.

So the La Chora H6 Magdalenian sequence can be:

H6(xH6a): extremely rare in Western Europe modernly
H6a: reported in Austria only (modern sample)
H6a1: most common in Western Europe and especially North Iberia
H6a1a: like Brotherton's Corded Ware sequence
H6a1a1: found only in Cantabria modernly, it seems
etc. (PhyloTree allows for some other options)

I already discussed the possible age (using molecular clock theory, calibrated) of H if La Chora H6 would be H6-root. But, considering that H6b and H6c seem to be Eastern European or Central Asian, it seems more reasonable to think it is H6a or downstream of it. What would be the age range of H for the other possible assignations of La Chora's H6, would it be tested for coding region mutations? Let's see:

If H6a-root: 47,500 to 24,500 years ago (median: 36,000 BP)
If H6a1: 73,200 to 34,800 years ago (median: 54,000 BP)

Of course I do not really think that the molecular clock can be easily applied, if at all, to mtDNA, because the rarity of accumulating mutations poses way too many challenges. But if it had to be applied, as Brotherton, Fu, their teams and some amateurs seem to think, then we'd have to test the La Chora and La Pasiega (and Sunghir and others) for coding region mutations in order to have the most valid calibration points.

Otherwise is like the blind man who touched the trunk of an elephant and imagined it was like a snake.

Synthesis of the Spanish-language series on the expansion of H. sapiens (2)

2013-04-24T18:36:00.001+02:00

One of the reasons I have been a bit too saturated and maybe not writing as much as usual is that I am collaborating in a series in Spanish language for the blog Noticias de Prehistoria - Prehistoria al Día.

I already mentioned last month the initial article[es] of the series by David Sánchez, which dealt with the African Middle Paleolithic (MSA, Lupembian, Aterian, etc.) We have not been idle in the meantime but actually wrote a number of other articles that may well be of your interest:

Breve introducción a la genética de poblaciones (Brief introduction to population genetics), by me.
La primera expansión del Homo sapiens en África desde el punto de vista de la genética (The first expansion of Homo sapiens in Africa from the viewpoint of genetics), by me.
La llegada a Arabia y Palestina (The arrival to Arabia and Palestine), by me.
La expansión de Homo sapiens por Asia Meridional desde la perspectiva arqueológica (The expansion of Homo sapiens through Southern Asia from the archaeological viewpoint), by David.

There is still a lot to do for the series to be complete but the time for a synthetic review in this blog is quite overdue. I will skip the brief intro to population genetics on the belief that most readers here have a decent idea, but the other three articles ask for due mention.

Expansion of H. sapiens in Africa (genetic viewpoint)

This is something that complements David's analysis of the African MP and that to a great extent I dealt with already at my former blog Leherensuge. I like graphs and maps because they often tell more than just words:

Basic mtDNA tree of Humankind
Branch length is proportional to coding region mutations from root per PhyloTree v.15 (L0k excepted)

We can see in this graph two main "moments" of diversification or expansion:

The L0 and L2-6 nodes, followed soon by the L1 and L0a'b'f'k nodes
The L0a'b'f, L0d and L2'3'4'6 nodes

The latter may well be calibrated with the archaeological evidence for the arrival of H. sapiens (MSA) to Southern Africa (L0d), which may be as old as 165 Ka but shows a clear increase in density since c. 130 Ka. I'd rather lean for the later date, that is roughly coincidental with the beginning of the Abbassia Pluvial, which must have provided good opportunities for expansion also in more northernly latitudes (the other nodes).

The first expansion is harder to estimate but c. 160 Ka. is a time in which we can see some of the first signs of expansion of our species within Africa (Jebel Irhoud and the already mentioned first Southern African MSA) so it is a tentative date.

The geography of both expansions should be as follows (based on the raw data of Behar 2008):

Approx. geography of the first expansion of H. sapiens
(Purple dotted area indicates the max. likelihood for 'mtDNA Eve' location)

Approx. geography of the second expansion of H. sapiens

I also mentioned the expansion of L3, which preludes the migration Out of Africa, but this was already discussed in this entry.

Arrival to Arabia and Palestine

While most of the entries I am doing for this series deal with the genetic aspects, in this case I worked mostly with the archaeology, recycling many materials that are readily available in this blog and achieving the following synthetic map (recycling one by Armitage 2011) as central element of the article:

In addition to reviewing the archaeological discoveries of the last few years (and few older ones) I also discussed the issue of Neanderthal admixture, which most likely happened in this phase, and the possibility of some L(xM,N) lineages found in Arabia being from this period (see here).

Synthesis of Asian Prehistory

The last article so far in the series, authored by David Sánchez, has been published just today and is a very good visual review of the complex archaeological record of most of Asia in the period that interests us (most Middle Paleolithic with marginal mention of the earliest UP of West Asia, Siberia and neighboring areas, which will be reviewed more in depth in later articles). Probably the maps say it all, although we must understand that they only consider the best known sites:

Prior to Toba event (120-74 Ka BP)
(open circles: human remains, dots: other archaeological sites)
(notice that the date of Narmada hominin is most unclear, what is not reflected in the map)

Blue: 74-45 Ka BP
(stars: Neanderthal sites, open circles: other human remains, dots: archaeological sites, black: previous map)

Red: 45-35 Ka BP
(stars: neanderthal sites, open circles: other human remains, dots: archaeological sites, black & blue: previous maps)

Green: later expansion of H. sapiens in Northern Asia
(stars: Neanderthals, open circles: other human remains, dots: other archaeological sites, black, blue & red: previous maps)

I must say that the design of the maps is not quite the way I would have done myself but is still interesting. Very especially I miss lots of info on post-Toba South Asia. Also the Altai transition is not really well explained in my understanding. On the other hand East Asia is full of details and the overall picture of the archaeology of the Eurasian expansion is well described nonetheless.

PS- from the commentaries by David at his blog, it seems clear that he gives for granted the occupation of South Asia after Toba and therefore he did not consider it important to mark any more recent sites in the subcontinent.

OSL dating: Brazilian site is 22,000 years ago

2013-04-22T18:35:00.000+02:00

Toca da Tira Peia is the new name of American prehistory, providing an OSL date for the layer of scattered stone tools of c. 22,000 years BP. Located near the also controversial Pedra Furada site, the date seems to give some support to those who dare to think outside the box on the early peopling of America.

Christelle Lahaye et al., Human occupation in South America by 20,000 BC: the Toca da Tira Peia site, Piauí, Brazil. Science 2013. Pay per view → LINK [doi:10.1016/j.jas.2013.02.019]

Abstract

When and how did the first human beings settle in the American continent? Numerous data, from archaeological researches as well as from palaeogenetics, anthropological and environmental studies, have led to partially contradictory interpretations in recent years, often because of the lack of a reliable chronological framework. The present study contributes to the establishment of such a framework using luminescence techniques to date a Brazilian archaeological site, the Toca da Tira Peia. It constitutes an exemplary case study: all our observations and measurements tend to prove the good integrity of the site and the anthropological nature of the artifacts and we are confident in the accuracy of the luminescence dating results. All these points underline the importance of the Toca da Tira Peia. The results bring new pieces of evidence of a human presence in the north-east of Brazil as early as 20,000 BC. The Toca da Tira Peia thus contributes to the rewriting of the history of the peopling of the American continent.

There are slightly older sites in North America, however they are all surrounded into some degree of controversy: Topper in South Carolina is dated to c. 23,000 cal-BP (C14) while some sites in Alberta, located in the Mackenzie "ice-free corridor" have also dates under the LGM layer (i.e. > 21 Ka BP).

There's actually nothing impossible about such early dates in my understanding.

Australian Burrup Peninsula's rock art is 30,000 years old

2013-04-22T11:39:00.003+02:00

The open air engravings have managed to survive thanks to the extremely low erosion rates produced by the hardness of the rock combined with the local climate.

The petroglyphs have been dated using the isotope beryllium-10. Based on current evidence, the archaeologists say, the occupation of the peninsula cannot be dated to before c. 42,000 years ago.

Source: Australian Geographic.

Spring near Stonehenge occupied since Epipaleolithic

2013-04-22T11:32:00.003+02:00

(CC by Jeffrey Pfau)

The spiritual relevance of Amesbury may well stem from a much older time than Neolithic or Chalcolithic. Recent research at a spring not far from Stonehenge has got radiocarbon dates of c. 7500 years ago, some three millennia before the building of the world-famous monument, and up to 4,700 BP, when the megalith was already in use.

The low budget research project led by David Jacques of Open University, who had spotted the site, known as Vespasian's Camp, just a mile north of Stonehenge, in air photos a decade ago. The site had never been researched before.

The findings imply some sort of continuity between the Epipaleolithic and Late Neolithic (i.e. Chalcolithic), although the details have yet to be systematized.

Source: BBC News (includes video).

Ardipithecus ramidus' skull is hominin

2013-04-22T11:13:00.000+02:00

Ardi's skull reconstructed
(CC by T. Michael Keesey)

I recently mentioned that Sahelanthropus tchadiensis 'Toumaï' was quite clearly within the hominini biological tribe, i.e. in the line leading to us and not anymore in the one leading to chimpanzees and bonobos. Now I have to echo the claim that a more recent being, Ardipithecus ramidus 'Ardi' also seems to have skull characteristics that place it in the hominin group.

While the relevance of Toumaï's grouping is much greater, because it help us to clarify the issue of Pan-Homo divergence dates, which seems to be of the order of c. 8-13 million years ago (Langergraber 2012), the case of Ardi is not without interest anyhow in the understanding of human evolution.

From Science News:

By examining 79 skull bases of chimps, gorillas, modern humans and ancient hominids, Kimbel’s group identified relationships among anatomical landmarks that distinguish apes from people and hominids. The researchers estimated the total length of A. ramidus’ skull bottom and found that it fell within a range characteristic of hominids, not apes.

As in more recent members of the Australopithecus genus, such as the 3.2-million-year-old partial skeleton nicknamed Lucy, Ardipithecus ramidus displays a relatively short, humanlike skull base, Kimbel said.

A new 3-D analysis of Ardi’s previously reconstructed pelvis, also presented April 11 at the anthropology meeting, finds a mix of monkey, ape and hominid characteristics. Although not confirming a consistently upright gait, this version of Ardi’s hips doesn’t undermine her proposed hominid status, said Nicole Webb of City University of New York, who led the research.

As for Ardi’s disputed mode of travel, she probably had a two-legged gait “but didn’t use her hands much while upright,” said Caley Orr of Midwestern University in Downers Grove, Ill., who didn’t participate in the new research.

While Ardipithecus ramidus is dated to c. 4.4 Ma BP, there is another specimen of the same genus, Ardipithecus kadabba, dated to c. 5,7 Ma.

Ref. AAPA 2013 meeting (abstracts):

W. Kimbel et al. Ardipithecus ramidus and the evolution of the human cranial base.
N. Webb et al. An analysis of the Ardipithecus ramidus pelvis reconstruction using 3D geometric morphometric techniques.

Fu 2013: new ancient mtDNA sequences and "molecular clock" madness

2013-04-18T16:11:00.000+02:00

It took me quite a while to get time to look at this study in some depth and when I finally did I must say I was rather disappointed. In any case the popular demand makes necessary to discuss it.

Qiaomei Fu et al., A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes. Current Biology 2013. Pay per view → LINK [doi:10.1016/j.cub.2013.02.044]

The study has two aspects: one, of great interest, which is the sequencing of a number of ancient remains, the other a complex and quite poorly explained and rendered speculation on how these sequences could be used to produce a refined molecular clock.

Ancient mtDNA sequences

Most of the sequences used by Fu et al. in their molecular clock speculations are new and that part is very interesting:

I have highlighted in lime green the new sequences, otherwise also noted by the marker b. It is of note that the "Crô-Magnon 1" sequence produced a C14 age of just a few centuries, being therefore removed from the collection. Other Crô-Magnon 1 remains produced no useful data.

The authors also decided to discard as possibly contaminated the UP sequence from Pagicci Str. 4b. I have highlighted in red why they decided to do so: because the C→T misincorporation rate, characteristic of ancient remains, is too low, what makes contamination at least a serious probability.

So we have as new data for the Upper Paleolithic landscape in Europe that the people of Dolni Vestonice carried lineages U* (found also in Swabian Magdalenian) and U8, in the line of haplogroups K, U8a (Basque) and U8b (Eastern Mediterranean). Also some late UP and Epipaleolithic sequences from Oberkassel (Low Rhineland, Germany), Loschbour (Luxemburg) and Continenza (Abruzzo, Italy) are U5b variants, consistent with other findings from various parts of Europe. In Paglicci (Apulia, Italy), another sequence yielded U2'3'4'7'8'9, surely an extinct variant of the ancestor of U8 and U2 (among other lineages). No radiocarbon date is available for any of the Italian remains.

In East Asia, Boschan, with B4c1a, provides one of the first Epipaleolithic sequences for the region.

Molecular clock madness

The authors seem to intend, or so declare, to refine the molecular clock estimates by means of using these sequences as intermediate calibration references. Here I get the first big question: with all the literature on ancient DNA, why only these sequences? No idea.

Then the contradictions arise. I believe that I have synthesized the most obvious ones in the following marginal annotations (in red) to their molecular clock estimates:

Furthermore, the authors claim in the text that U5 is the oldest branch to diverge from U, however their TRMCA figure is of only 34.4 Ka BP (coding region), while Kostenki 14 has an age of 38 Ka BP and already carried U2, what really makes this claim extremely unlikely: U2 and its ancestor U2'3'4'7'8'9 should be considered the oldest U sublineage.

I do not understand either why they force age estimates for many lineages for which they have no working aDNA references and instead desist of estimating the age of lineages for which they have several calibration points, like U2'3'4'7'8'9 or B4'5 (aka B).

In brief: the claims of this paper on molecular-clock-o-logy are ill-explained, confusing, incoherent... a total mess. The raw data on ancient mtDNA is however good looking and of doubtless interest.

Central European Bell Beaker mtDNA: 88% H

2013-04-15T21:22:00.000+02:00

Bell beaker from Hungary (source)

This doctoral thesis by Christina J. Adler is a most important study on the formation of the modern genetic pool (and hence population) in Central Europe. Previously we knew of data from the Paleolithic (U*), Epipaleolithic (U5, U4) and Earliest Neolithic (much more diverse but not yet modern in any sense). Then we had a huge blank until Urnfields (late Bronze), when the genetic pool seemed to be modern already.

This thesis (found via Eurogenes) fills in the blanks at least to some extent.

Christina Jane Adler, Ancient DNA studies of Human Evolution. University of Adelaide (thesis), 2012. Freely accessible → LINK

The thesis is, as usual in this kind of studies, extremely long; even the abstract is too long to copy here. Just to mention that the hard data (graphs, tables) is from page 96 on, although there are some other aspects in the text that deserve mention.

Critically Adler could research the ancient mtDNA of Bell Beaker and Únětice culture populations from several German sites, adding important information about the genetic pools of the Late Chalcolithic and Early Bronze Age. She also goes over previous studies on the same area.

The new data (table 2) can be synthesized as follows:

Bell Beaker:

Quedlinburg XII: 3 H-CRS (H1?), 1 J
Rothenschirmbach: 2 H3, 1 H5
Alberstedt: 1 H-CRS (H1?)
Total (simplified): 7 H, 1 J

Únětice:

Quedlinburg VIII: 1 U5a1a, 1 U2, 1 U*, 1 H7a, 1 T1
Quedlinburg XII: 1 U5a1a
Quedlinburg XIV: 1 T2
Esperstedt: 2 I*, 1 I1, 1 U5a1, 1 U5b, 1 T2b, 1 T2*, 1 W, 1 X
Total (simplified): 4 U5, 3 I, 3 T2, 1 T1, 1 U2, 1 U*, 1 W, 1 X

This extremely high apportion of mtDNA H is almost unprecedented in ancient (and probably also modern) mtDNA samples, in Europe only the Portuguese Neolithic and Epipaleolithic samples by Chandler 2005 seem to be comparable in any way, suggesting that this most important European matrilineage may have expanded from Iberia in the Chalcolithic (aka Late Neolithic in some Anglosaxon literature) with either Megalithism, Bell Beaker or both.

It also seems to contradict the quite mainstream theory of Central European origins (post Corded Ware) of the Bell Beaker phenomenon and instead support the less popular Iberian origin theory. Until this very day I have been adherent to the Bohemian "Corded" origin theory (with some doubts) but today I have to admit that this genetic data weights heavily for the Iberian origin model, which in turn would fit very nicely with Venneman's Vasconic substrate theory.

Regardless of what I may think, Adler herself is clearly pushing for the Iberian origin model all along in her thesis, theory which she seems to find the best fit scenario.

Of course, the genetic landscape was not simply stabilized with Megalithism and Bell Beaker, more waves followed. The Western Indoeuropean Únětice culture seems to fit here as archetypal or potential source of other layers, resulting in modern genetic pools in many places (although as I have mentioned several times the Basque one seems stable since Early Neolithic). These Indoeuropean migrations (Tumuli, Urnfields, Hallstatt, La Tène, etc.) should explain the dilution of the extremely high apportion of H found in these Bell Beaker burials, as well as in Portugal (nowadays H is 40-50% in most of Western and Northern Europe).

The Únětice genetic landscape seems particularly interesting for including which is surely the oldest mtDNA I in Northern Europe (later very common in Viking Era Denmark). The only older case I know is again Early Neolithic Basque (same Paternabidea sample mentioned above) but I don't see any plausible relation.

PS- I know still have in the "to do" department the paper of Qiaomei Fu, "A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes", which several readers were so kind to send me a copy of weeks ago, encouraging me to write on it. My apologies but I'm on it and I promise to write a review this very week unless the sky falls on my head (or real life equivalent).

Southern Native American Y-DNA: no correlation with language, extensive info on haplogroup C3

2013-04-14T14:47:00.001+02:00

Genetics does not necessarily correlate with linguistic families. It often does not. This seems to be the case with Native Americans as well.

Lutz Roewer et al., Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans. PLoS Genetics 2013. Open access → LINK [doi:10.1371/journal.pgen.1003460]

Abstract

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.

There's only so much to say about language families and patrilineages: that they do not agree in any obvious way:

Table 1. Correlation between Y-SNP haplogroup and language class.

However the paper also address the interesting matter of NE Asian and Native American paragroup C3(xC3b), which is almost only found among Ecuadorean Natives (Kichwa and Waorani speakers). The only other known case among Native Americans, according to the authors, is an individual of Southern Alaskan native ancestry.

Figure 1. Origin of male native South American samples.
For each sampling site, its geographic location as well as the size (proportional to the circle area) and Y-SNP haplogroup composition of the respective sample are shown. Blue lines: major aquatic systems; dashed gray lines: current national boundaries.

Overall distribution of Y-DNA C3* (yellow), which I understand to mean C3(xC3b) for this study:

Figure 4. Prevalence of Y-SNP haplogroup C-M217 (C3*) around the Pacific Ocean.
Light blue: previous studies; dark blue: present study; yellow: relative frequency of C-M217 (C3*) carriers.

The most interesting information anyhow may be in the haplotype network:

Figure 5. Median-joining network of 167 different Asian and American Y-STR haplotypes carrying Y-SNP haplogroup C3* (from this and previously published studies).
The median-joining network is based upon markers DYS19, DYS389I, DYS389II-DYS389I, DYS390, DYS391, DYS392, DYS393 and DYS439 (see Materials and Methods for details). ALA: Alaskan; KOR: Korean; CHI: Chinese, including Daur, Uygur, Manchu; MON: Mongolian, including Kalmyk, Tuva, Buryat; ANA: Anatolian; INDO: Vietnamese, Thai, Malaysian, Indonesian, Philippines; JAP: Japanese; TIB: Tibetan, Nepalese; ALT: Altaian, including Kazakh, Uzbek; SIB: Teleut, Khamnigan, Evenk, Koryak; ECU: Ecuadorian, including Waorani, Lowland Kichwa, COL: Colombia, including Wayuu; RUS: Russian.

The network clearly shows that the Native American C3* haplotypes are mostly or totally related to a cluster of Altaian, Mongol and Chinese roots. The Altaian connection is particularly strong for all but one of the lineages. This is very much concordant with a proto-Amerind patrilineal origin in Altai (where NE Asian and American Y-DNA Q and mtDNA X2 variants surely originated in the early Upper Paleolithic) which traveled to Beringia via Mongolia or nearby regions, spreading the mode 4 (blade tech) to East Asia c. 30,000 years ago.

This is not the view of the authors but mine. The authors instead speculate with (i) a late wave or (ii) even naval contact between East Asia and South America. I find both hypothesis lacking merit and I lean for a founder effect model instead.

On the other hand, the C3b presence in NW North America, critically among Na-Dene speakers, may still represent a second wave: that of Na-Dene speakers, whose "recent" linguistic connections to Siberia (Yenisean family) have found strong support in the last years.