February 28, 2013

Northern Marianas was first colonized from Philippines

Lapita pot from Tonga (source)
The first known colonists of Tinian (Northern Marianas) were people coming from Luzon and using a kind of red painted pottery which is also found in Northern Luzon, Philippines, similar to  Lapita (Island Melanesia, Polynesia).

However these people seem to have arrived to the Marianas a century or two before the Lapita carriers (precursors of Oceanic languages) reached Melanesia, according to Peter Bellwood.

Source and more details: Islands Business (interview with Bellwood), via Pileta.


See also:

February 27, 2013

Maize was common in Peru 5000 years ago

It has been confirmed, after decades of debate, that the people of coastal Peru did not just live on fishing but also on farming.

Jonathan Haas et al., Evidence for maize (Zea mays) in the Late Archaic (3000–1800 B.C.) in the Norte Chico region of Peru. PNAS 2013. Pay per view (for six months) → LINK [doi: 10.1073/pnas.1219425110]

Abstract

For more than 40 y, there has been an active discussion over the presence and economic importance of maize (Zea mays) during the Late Archaic period (3000–1800 B.C.) in ancient Peru. The evidence for Late Archaic maize has been limited, leading to the interpretation that it was present but used primarily for ceremonial purposes. Archaeological testing at a number of sites in the Norte Chico region of the north central coast provides a broad range of empirical data on the production, processing, and consumption of maize. New data drawn from coprolites, pollen records, and stone tool residues, combined with 126 radiocarbon dates, demonstrate that maize was widely grown, intensively processed, and constituted a primary component of the diet throughout the period from 3000 to 1800 B.C.

See also: Science Daily.

Iberian script of Iruña-Veleia

A new study of the Iberian script findings withing the (partly disputed but most likely very real) ostraka graffiti at Iruña-Veleia (Basque-Roman city of Antiquity on which I have written extensively in the past) is freely available online.

Antonio Arnaiz-Villena & Diego Rey, Iberian-Tartessian scripts/graffiti in Iruna-Veleia (Basque Country, North Spain): findings in both Iberia and Canary Islands-Africa. International Journal of Modern Anthropology 2012. Freely accessibleLINK

Abstract

760 officially recognized scripts on ceramics from Iruña-Veleia excavated by the archaeology firm Lurmen S.L. (approximately between years 2002-2008)have been analyzed. A number of these ceramics contains scripts which may be assimilated to Iberian/Tartessian writings. This number may be underestimated since more studies need to be done in already available and new found ceramics. This is the second time that Iberian writing is found by us in an unexpected location together with the Iberian-Guanche inscriptions of Lanzarote and Fuerteventura (Canary Islands). On the other hand, naviform scripting, usually associated to Iberian rock or stone engraving may have also been found in Veleia. Strict separation, other than in time and space stratification, between Iberian and (South) Tartessian culture and script is doubted.

Source: Ama Ata[es].

Riel-Salvatore on the reality and hype of Upper Paleolithic burials

From A Very Remote Period Indeed:

On the variability of Upper Paleolithic burials: Hype, facts and fiction (and Neanderthals?)

A new study of mine (written with Claudine Gravel-Miguel of ASU) is getting a bit of press, and I really want to write a post on AVRPI to serve as a proper companion piece to it, since the narrative in the press is already slipping away from what the paper actually says. In short, our paper does not say that Upper Paleolithic burials were not more sophisticated than those of Neanderthals. Rather, it emphasizes how heterogeneous Upper Paleolithic burials are (a point I recently also mentioned in relation to 'Venus' figurines), and that many of them were fairly simple. As a result, we need to be very careful about using exceptionally lavish as representative of Upper Paleolithic burials as a whole, as emphasized in the official CU Denver press release "Early human burials varied widely," which is a bit meta, being illustrated as it is by... one of the Sungir burials, arguably some of the fanciest Upper Paleolithic burials known!

Man in an Upper Paleolithic burial in Sunghir, Russia. The site is approximately 28,000 to 30,000 years old. 
Not a typical Upper Paleoilthic burial!

... continue reading at A Very Remote Period Indeed.

February 23, 2013

Algerian haploid genetics

This new study has particular interest for data miners willing to dig in the supplemental materials. It also has some other points of interest that I will discuss below and its general approach is loosely alright. However there are many nuances to be discussed in depth on the very complex NW African genetic landscape in which their tentative conclusions seem to lack enough depth of analysis (who grabs too much, squeezes little). Hence the complexity is too big for me to go issue by issue offering a criticism, so I will leave most of that open for the discussion, if the readers wish so.

Asmadan Bekada et al., Introducing the Algerian Mitochondrial DNA and Y-Chromosome Profiles into the North African Landscape. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0056775]


Mitochondrial DNA

The mtDNA landscape of Algeria and Northwest Africa is dominated (using HVS-I only to estimate it) by R-CRS ("H/HV" in table S2) with levels of 18-34% (29% in Algeria) almost comparable to Western Europe (~45%). This fraction we know from previous studies to be composed almost only by H1, H3, H4 and H7, all them attributed by Cherni to be originated (judging on diversity) in SW Europe (Iberia, France). Along with them HV0/V (7% in Algeria, 5-9% regionally) must be mentioned as also plausibly to be from that part of Europe (4-7%).

Another notable lineage is U6 (typical and most diverse in NW Africa), which reaches frequencies of 11% in Algeria (somewhat less in neighboring countries). Outside this area is only notable in Levant (~1%) and Iberia (~1,4%).

M1 reaching 7% in Algeria (~1-4% elsewhere in NW Africa, <1% in Europe and Highland West Asia, 1.2% in Levant, 2.4% in Peninsular Arabia) is also very much worth a mention, especially because the authors find an specifically NW African node centered in Algeria (HT2):

Figure 3. Reduced median network relating HVS-1 sequences of subhaplogroup M1.
(...) Black circles correspond to haplotypes observed in Algeria, whereas grey triangles pentagons correspond to lineages found in Egypt. Haplotype observed both in Algeria and Egypt are indicated using a black triangle. Grey circles indicate haplotypes observed in other geographical regions. (...)

The pattern suggests an Egypt-centered expansion for this lineage, however notice that East African M1 was not considered. 

Synthesis of mtDNA haplogroups or paragroups found in NW Africa at frequencies >2.5% (see table S2 for details and the many low frequency lineages as well), nomenclature as in table S2 (but some annotations in [square brackets] by me), frequencies for Algeria first (in brackets NW African range):
  • HV/H[R-CRS]: 28.8% (17.9-34.2%)
  • HV0/HV0a/V: 6.7% (4.6-8.3%)
  • R0a: 0.8% (0.8-3.2%)
  • U3*: 3.2% (1.1-3.2%)
  • U6a[U6a*]: 1.9% (1.9-7.8%)
  • U6a1'2'3: 9.4% (2.6-9.4%)
  • K*: 1.6% (0.7-4.8%)
  • T1a: 3.5% (0.0-5.6%)
  • T2b*: 1.9% (0.0-2.2%)
  • J[*]/J1c/J2[*]: 3.8% (1.3-3.8%)
  • M1[*]: 7.3% (0.7-7.3%)
  • L3b[*]: 0.3% (0.3-2.8%)
  • L3b1a3: 1.3% (0.0-2.8%)
  • L3e5: 1.6% (0.0-2.9%)
  • L2*: 0.5% (0.0-4.1%)
  • L2a[*]: 0.8% (0.0-3.2%)
  • L2a1*: 1.3% (0.7-4.8%)
  • L2a1b: 1.3% (0.8-3.5%)
  • L2d: 0.0% (0.0-2.8%)
  • L1b*: 3.0% (2.7%-9.0%)
Notice that in nearly all cases L(xM,N) highest frequency correspond to West Sahara. The exceptions are L2a* (Tunsian "Andalusians") and L3e5 (Tunisians), suggesting maybe a local NW African deep rooting rather than ancient or recent flows from Tropical Africa. There are other lineages in the low frequency range in similar situation.

For this and other reasons I decided to color-code the list above according to my best guess about the origin of each lineage: NW African in deep red, Tropical African in brown, Egyptian in light brown, West Asian in green and European in blue. Unclear cases I left in black type.


Y chromosome DNA

Algerian and NW African Y-DNA is overwhelmingly dominated by E1b1b1b (M81), reaching 44% in Algeria (44-67% in the region), which is a NW African specific lineage. The second most important lineage by frequency is J1 (M304) with 22% in Algeria (0-22% in the region, 6-22% if we exclude Libya). None of the rest of the lineages reaches 7%, excepted E1b1b1c (M123) but only in West Sahara (11%, elsewhere it is very minor).

List of Y-DNA haplo-/paragroups with frequencies above 2.5% anywhere in NW Africa follows (based on table S6). Same notation as with mtDNA (Algerian frequency first, NW African range in brackets):
  • E1a (M33): 0.6% (0.0-5.3%)
  • E1b1[*] (P2): 5.2% (0.7-38.6%)
  • E1b1b1[*] (M35): 0.6% (0.0-4.2%)
  • E1b1b1a4 (V65): 1.9% (0.0-4.8%)
  • E1b1b1b (M81): 44.2% (44.2-67.4%)
  • E1b1b1c (M123): 1.3% (0.0-11.1%)
  • F[*] (M89): 3.9% (0.0-3.9%)
  • J1 (M267): 21.8% (0.0-21.8%)
  • J2a2 (M67): 3.9% (0.0-3.9%)
  • R1b1a (V88): 2.6% (0.9-6.9%)
  • R1b1b1a1b[*] (U198): 2.6% (0.0-2.6%)
  • R1b1b1a1b1 (U152): 2.6% (0.0-2.6%)

For more diverse samples of NW African Y-DNA (from previous studies), Wikipedia has a nice table.

I would like to highlight the problematic of J1 in Africa in general (including NW Africa). While there is no reasonable doubt that J1 as a whole originated in West Asia, it is found at rather high frequencies in East/NE Africa (Sudan, the Horn, Upper Egypt) and NW Africa with only very limited (at best) company by J2. Instead West Asian populations show a much more balanced apportion of the two major J sublineages, even in Saudi Arabia the J1:J2 proportion is of 8:3, almost 2:1. We do see this kind of apportioning in Lower Egypt, suggesting a "recent" (Neolithic or later) demic colonization from West Asia but we see exactly but nowhere else in Africa, where J1 is found always much more frequently than J2 (if the latter is found at all). 

In my understanding this excludes colonization from West Asia after the Pre-Pottery Neolithic B, which seems the most plausible scenario for the spread of "Highlander" J2 into "Lowland" West Asia (probably dominated by J1 initially). So J1 in Africa (excepted Lower Egypt) cannot be argued easily to be of "recent" Neolithic, much less Semitic or Arab origin: it must be older. 

Also Ethio Helix commented in this very interesting discussion at his blog that Tofanelli 2009 found low diversity on NW African J1. However, to my knowledge, nobody has looked at NE/East African J1 diversity nor a proper study has been done on the substructure of this lineage in Africa. This leaves wide open the possibility that NW African J1 has a NE African origin, surely related to the expansion of Capsian culture or internal African Neolithic flows. 

While this matter is not properly addressed, researchers will oversimplify and imagine J1 as simply West Asian influx. It is ultimately of course but I strongly suspect that it has a secondary and distinct NE African center at the Nile basin and this is being totally ignored. 


Comparisons

This study offers several rough comparisons with nearby regions (but not West Africa), however they oversimplify some stuff (the already mentioned Y-DNA J1 or assigning all mtDNA L(xM,N) to East Africa, when it seems obvious that some lineages may be deeply rooted in NW Africa or others probably come from West Africa). For whatever it is worth anyhow, here there are two such questionable comparisons:

Table 2. Geographic components (%) considered in Y-chromosome and mtDNA lineages.

Figure 2. Graphical relationships among the studied populations.
PCA plots based on mtDNA (a) and Y-chromosome (b) polymorphism. Codes are as in Supplementary Tables S2 and S6.


See also:

Screw stoppers of Upper Paleolithic Dordogne

While not really a novelty, I bet that most readers have never heard of this (I had no idea myself admittedly). David Sánchez discusses this week at his (Spanish language) blog Noticias de Prehistoria - Prehistoria al Día the existence of several most intriguing conic screw pieces found in Gravettian and Magdalenian sites from Dordogne (Aquitaine, French Republic), a district that (because of its great density of findings and cultural centrality for Middle and Late UP European prehistory) I have sometimes dubbed the Paleolithic Metropolis of Europe.

Drawing of two ivory (?) stoppers from Combe-Capelle and Fourneau du Diable
(from Don's Maps, ultimately from S. Lwoff 1968)

Stopper of bone (?).
First reported as
from Laugerie-Haute
but apparently the
same as above (bottom),
from Forneau du Diable.
What are these magnificent pieces of Paleolithic craftsmanship? Apparently they are nothing else that that waterskin stoppers. Don's Maps suggest (scroll down) that the waterskin's neck hole would be made with a long bone hollow piece (just get out the marrow and tie it tightly to the skin's neck with a couple of thin ropes after performing two grooves on the external surface of the bone piece), then just apply the screw stopper forcing the bone (which is hard but somewhat flexible) to adapt to it. Naturally the inner groove would be created as you repeat the process once and again, surely having to push a little more each time (the bone tends to expand somewhat under the internal pressure).

Why are they conical and not cylindrical like modern ones? Surely because the same stopper (hard high quality work) was expected to serve many different waterskins, with different neck sizes. Also the very process of creation of the neck's perfect fit requires of an initial process of expansion for which a cylindrical stopper was not fit.

It never ceases to amaze the ingenuity and creativity of our Paleolithic ancestors, right?


Sources: Noticias de Prehistoria[es], Don's Maps.



Update (Jan 7 2014):

I just got feedback from Don Hitchcock (the author of Don's Maps and main ultimate source for this entry) saying that he found that the photographed stopper and the second drawn ones are the same (from Forneau du Diable and not Laugerie-Haute, as originally reported), complaining that the artist 'gilded the lily' more than a little with regard to the perfection of the screw thread.

I fear he must be right because some details in the handle are very similar. It is a bit disappointing but I believe that the original hypothesis about their use as stoppers stands anyhow. 


Update (Jan 10):

Don Hitchcock has updated his page on the Paleolithic tools with other two example of water bag stoppers. These don't seem to have any clear spiral design in the screw but at least one uses instead parallel groves.

To the right: ivory stopper from Laugerie Haute Est.

Below: ivory stopper from Brassempouy (Aurignacian):


Bronze Age cremation necropolis found in Romania

A large and informative necropolis dating to c. 1300 BCE has been found at Păru (Banat, Romania).
“Particularly important are the graves that shed new light on the funerary ritual at the end of the Bronze Age in north-eastern Banat. It was found that the dead were deposited on a pyre where items from the funerary trousseau were also burned.” This included “a table-altar of clay on which they brought funerary offerings, stone grinders and various pots that were used for the funeral banquet. Modern methods of radioactive carbon dating method shows that the necropolis at Păru dates between 1300 and 1200 BC” Ph.D. Florin Drasovean told  www.tion.ro.
“In terms of inventory, there were discovered pots that were used in the funeral banquet and various fragments of altars, on which the deceased was cremated. Subsequently, the funeral was done in circular pits of 1 meter diameter, grouped in nests, probably because individuals came from the same family,” explained Professor Drasovean.

Part of the excavated necropolis

Contextualizing


This cremation funerary fashion is also found further West, where it is most strongly associated to the Urnfield culture (as well as others more or less related ones), later, in the Iron Age, cremation is also associated to stone circle burials in Scandinavia and the Pyrenees. Therefore one could fathom that the transition between the Bronze and Iron Age in Europe North and West of the Balcans could well be described also as the Age of Cremation, even if (of course), there are also many areas where such practice never caught up.



Ancient Cantabrian fortified town: conquered and burned by Rome

Paleorama[es] has an interesting article on how the Ancient Cantabrian castro (fortified town) at Monte Ornedo, located in the modern municipality of Valdeolea (Cantabria, near Palencia, Spain) was captured in fierce battle by the Roman legions in a key battle of the Cantabrian Wars, burned and on top of the remains a Roman fort was built instead (Octaviolca?)



The aboriginal castro covered 19 Ha (=190,000 m², ~47,000 acres), being the largest of its kind known in all Ancient Cantabria. Many brooches (fibulae), characteristic of the indigenous horsemen's clothing are concentrated near the main gate, suggesting that a key episode of the battle took place there. Around the castro, the Romans built their characteristic siege fortifications. Caligae sole nails, tent holding pins and weapons have been found all over the place, including a dagger with silver decorations and even a catapult fire projectile.

After the capture the Romans built there their own fort. First a campaign one with earth walls and then another more consolidated one with stone walls. Milestones defining the pastures assigned to the Legio IV Macedonica from those of the nearby town of Iuliobriga further North have also been found.


See also:

February 18, 2013

Submerged rock art from Papua

In the World-famous diving paradise of Raja Ampat, just West of the Bird's Head peninsula of Papua (aka New Guinea), there is more than one of the greatest biodiversity areas of the planet. It has been found recently that off the shore of Misool, one of the major islands of the archipelago, there is also abundance of beautifully conserved Paleolithic murals.


The now submerged rock art is found in 13 different sites (so far), most of them sharing an intriguing pattern of location:
  • a large and rather high cliff;
  • a cavity, cave, overhang or hole around the foot of the cliff;
  • a main coloured (red-yellow to red-brown) wide strip pouring out, or reaching down to the cavity;
  • a (facultative) step-bank (coral or karst platform) at the foot. 
The art was obviously above the water level until the sea flooded all that area at the end of the Ice Age. 

Sources: World Archaeological Congress, Stone Pages' Archaeonews.



Update (Feb 24): after being down for days, causing perplexity among some readers and myself, the WAC source site is up again. Exactly as it was four days ago. Just in case this time I'll upload the images here. 

Mouth bacteria changed with civilization... for worse

A premise of Primitivism, which is not really a doctrine or philosophy but more like realistic approach to the human condition, is that our evolutionary past is shaped almost totally by hunter-gathering. That we are basically hunter-gatherers in a jump or maybe formal suit. Why? Because some 95% of the biological history of Homo sapiens, as a formed species is one of hunter-gathering, not of productive economy nor civilization. This percentage can be extended to maybe 99.5% if we consider the whole history of the genus homo, etc. And that is a lot. 

Do I digress? Well, maybe not so much after all. The evolutionary news today is in any case that the bacterial ecosystems in our mouths have been degenerating since Neolithic, and then again with Industrialization. As Not exactly rocket science (a National Geographic blog written by Ed Yong) explains the bacteria in our mouth is not all hostile but, at least for hunter-gatherers, often balanced: some bacteria may attack our teeth but then others protect and even repair them. Much like the better known bacteria of our guts, there is a general balance in which, naturally at least, symbiosis with the human needs tends to dominate. After all those bacteria live in our mouths and therefore need it to exist in good shape: they may not be exactly "aware" of their own needs or the benefits of harm they bring to us but evolution fixes it in the long run, of course. 

Epipaleolithic foragers from Poland with a rather thick plaque, plaque that retained in millennial hibernation the bacteria of their mouth, have provided evidence of Prehistoric hunter-gatherers having a healthy, balanced mouth bacterial ecology. 

Instead Medieval English, who were already eating many carbohydrates from cereals, illustrate with their plaque the beginning of mouth bacterial decadence. There are a total of 34 studied remains between these two dates, illustrating that this change happened exactly with the Neolithic Revolution.

The members of the modern research team used their own mouths as reference for the modern bacterial environment. The results were rather depressing: industrialization has created many refined, unbalanced, foods (white cereals and sugar especially) that cause our mouths to be the boon of dentists.
We are what we eat
(source)

A similar kind of bacterial ecology decadence was observed in a previous study between the guts of Burkinabe farmers' children and those of Italian urban ones. The latter have ecosystems dominated by well-fed firmicutes, associated to obesity.

Reference paper:  Christina J. Adler et al., Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nature 2013. Pay per viewLINK [doi:10.1038/ng.2536]

February 16, 2013

Genetic origin of East Asian thicker hair, denser sweat glands

The single origin of these regional phenotype traits has now been tracked to a single allele of gene EDAR (Wikipedia, SNPedia), specifically to its variant EDAR370A, typical of East Asians, using a genetically modified mouse model.

Yana G. Kamberov, Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell 2013. Pay per viewLINK [10.1016/j.cell.2013.01.016]

Summary

An adaptive variant of the human Ectodysplasin receptor, EDARV370A, is one of the strongest candidates of recent positive selection from genome-wide scans. We have modeled EDAR370A in mice and characterized its phenotype and evolutionary origins in humans. Our computational analysis suggests the allele arose in central China approximately 30,000 years ago. Although EDAR370A has been associated with increased scalp hair thickness and changed tooth morphology in humans, its direct biological significance and potential adaptive role remain unclear. We generated a knockin mouse model and find that, as in humans, hair thickness is increased in EDAR370A mice. We identify new biological targets affected by the mutation, including mammary and eccrine glands. Building on these results, we find that EDAR370A is associated with an increased number of active eccrine glands in the Han Chinese. This interdisciplinary approach yields unique insight into the generation of adaptive variation among modern humans.

As the summary mentions, it has also been suggested that the variant influences tooth morphology, although this could not be demonstrated in the mouse model. 


The mutation was found in a gene for ectodysplasin receptor, or EDAR, part of a signaling pathway known to play a key role in the development of hair, sweat glands and other skin features. While human populations in Africa and Europe had one, ancestral, version of the gene, most East Asians had a derived variant, EDARV370A, which studies had linked to thicker scalp hair and an altered tooth shape in humans.

The ectodysplasin pathway is highly conserved across vertebrates -- the same genes do the same thing in humans and mice and zebrafish. For that reason, and because its effects on skin, hair and scales can be observed directly, it is widely studied.

This evolutionary conservation led Yana Kamberov, one of two first authors on the paper, to reason that EDARV370A would exert similar biological effects in an animal model as in humans. The HMS research fellow in genetics developed a mouse model with the exact mutation of EDARV370A -- a difference of one DNA letter from the original, or wild-type, population. That mouse manifested thicker hair, more densely branched mammary glands and an increased number of eccrine, or sweat, glands.

The authors argue for a selective pressure but I find hard to imagine which one could it be. Therefore I rather lean again towards a random founder effect. 

Unless... notice that in the figure accompanying the summary also mammary gland density is shown as increased, what could result in improved nutrition for babies, what would indeed be selected for (assuming the rest of effects are neutral or quasi-neutral).

Anyhow, linking it obliquely to the previous entry (on Neanderthal admixture in East Asians), I have often wondered about the origins of straight hair in general, because it is obviously not ancestral in our species (all "Aboriginal African" populations have thinly curled hair, as do some non-Africans, especially remote Tropical populations like Papuans or Andamanese) and my main hypothesis is that it could be a Neanderthal genetic influence, possibly selected because of less intense need of head ventilation (for which thinly curled "African" hair seems best) and more intense need instead of protection against cold and rain. The thick hair East Asian variant might in this case be just the extreme variant of a more widespread Neanderthal introgression. Just food for thought.


Update (Feb 20): Razib Khan also finds the suggested "selection sweep" dubious, and his discussion of this paper is very interesting to read.

An interesting detail that I could not gather clearly from the abstract is that the allele causes (at least in mice) smaller breasts and not just denser mammal glands.

But surely the most interesting item is this map of the frequencies of the EDARV370A allele through the World, being very much and quite strictly limited to the peoples displaying what is classically described as the Mongoloid phenotype:


An intriguing issue is also the lack of it in Europe, even among peoples of well-known Siberian/East Asian low-level admixture (Northern Russians). I'm tentatively imagining some sort of "racist selection" against the trait among those peoples, as it expresses an exotic, possibly not favored (to put it mildly), very apparent phenotype. Food for thought.


Update (March 22 2014): Kevin Brook mentions this database, which shows the "East Asian" C allele present in some other populations than the ones reflected in the map above, notably some South Asians (rather high frequencies in some cases) but also (at very low frequencies) in some Africans, West Asians and Eastern Europeans. At the very least it is an interesting counter-point.

More Neanderthal admixture details

The main conclusion of this new study seems to be that East Asians have normally more Neanderthal admixture than South or West Eurasians. Also the Maasai from East Africa have been shown to have minor Neanderthal admixture, consistent with the also minor Eurasian genetic component they have.

Jeffrey D. Wall et al., Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans. Genetics 2013. Freely accessible at the time of writing thisLINK [doi: 10.1534/genetics.112.148213]

Abstract

Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

There is a sentence in page 8 in which the authors claim that:

By using the high coverage Denisova genome, we are able to show that the admixture rate into East Asians is 40% higher than into Europeans.

However I fail to see it in the D-statistic graphs, which show less than 15% more Neanderthal admixture in Eastern Asians than in Europeans (on average and discounting error margins, which strongly overlap). It may be therefore another case of hair-splitting.

Instead the evidence of weak Neanderthal admixture (via minor Eurasian  genetic influence) in the Maasai of East Africa seems more solid: while error margins of Maasai and Luhya do overlap, the main blocs do not.

Figure 3. Summary of significance tests for average values of D. Positive values indicate that the second sequence is more similar to the Neanderthal genome than the first sequence. In all parts, the box plots indicate the range of D values obtained for pairs of individuals from the populations indicated. Parts A and B are box plots of individual D statistics computed for each individual from the specified population compared with each Yoruban. The p values are from the randomization test, Test 1, of significant differences in the average D values for different pairs of populations. Parts C and D show box plots of individual D statistics computed for every pair of individuals in the specified populations. The p values are from the randomization test, Test 2, of significant differences of the average D from 0. See also Table 2.

It is surely convenient to look carefully at all the data, including the supplementary materials, before jumping to any strong conclusions. Among them I found more interesting fig. S1:

Figure S1: Box plot of the D-statistics for Analyses A and B for the set (Afr, X), where X was any of the non-African populations, CEU or TSI (Europeans, green), CHB or JPT (East Asians, blue), or GIH (South Asian, pink) (PDF, 222 KB).

As we can see here, the error margins continue overlapping very strongly, but, assuming that we can jump to conclusions based on the norm (thick black line), which is assuming some risks indeed but also the only way to (tentatively) agree with the authors' conclusion of greater Neanderthal admixture among East Asians, then the causes should be:
  1. Founder effect among East Asians, known to have less overall genetic diversity and suspected to have undergone some extra (mild?) bottleneck at their ancient origins.
  2. Low-level African (and surely also early OoA residuals from West Asia) admixture among West Eurasians, notably Tuscans (TSI) in these samples but also to some extent all Europeans (incl. CEU). This has the effect of increasing genetic diversity but also of slightly diluting Neanderthal admixture. The control here are Indians (GIH), which show slightly more Neanderthal admixture than Europeans (but are still closer to these than to East Asians also in this aspect).
Indians (who don't seem to have any post-OoA African admixture, unlike Europeans and West Asians, who have it at variable low levels) suggest that factor #2 (dilution) weights only somewhat and therefore that factor #1 (East Asian founder effect) must be considered the main one instead. 

But, unless someone can point me where I am wrong, I fail to see neither the alleged 40% excess Neanderthal admixture in Orientals nor why would these results question the single admixture episode (or period) at the origins of migration out of Africa (OoA).

To finish this entry, it must be mentioned that the authors could only detect at most the tiniest fraction of Denisovan admixture among the sampled populations (i.e. nothing relevant and with no regional differences). However they did not research, admittedly, the South China populations suggested to have slight more Denisovan input by  Skoglund and Jakobsson 2011.


See also:

February 15, 2013

Guest article by Gail Tonnesen: Comments on “Origins and Evolution of the Etruscans’ mtDNA”

When discussing a recent revision of the ancient Etruscan mtDNA sequences, it became evident that haplogroup assignation was not really being dealt with by the authors, so Gail Tonnesen has dug on the matter further:

Comments on “Origins and Evolution of the Etruscans’ mtDNA”


In an analysis of Etruscan mtDNA Ghirotto et al. (2013) evaluated haplotype diversity in 30 samples of ancient remains from Etruscan burials that date to between 700-200 BCE. However, the authors did not identify haplogroups for these ancient remains. Analysis of the mtDNA data by haplogroup could provide additional insight into relationships among the ancients samples and to modern populations in the region, so we attempted to identify haplogroups for the 30 ancient mtDNA haplotypes listed in Table S1 of Ghirotto et al. These include 14 samples tested by Ghirotto et al. (2013), and 16 samples tested by Vernesi et al. (2004).



Ghirotto et al (2013) reported results in the mtDNA the control region at markers 16024-16384. Results were reported relative to the revised Cambridge Reference Sequence. These results should be sufficient to identify those haplogroups that have defining mutations in this region. We compared the ancient mtDNA haplotypes to Phylotree version 15. Seven of the haplotypes appear to be U5, however, the U5 defining mutation 16270 was identified in only two of these seven samples. Key defining mutations for U5 subclades that should be present were not identified in several of these samples. For example, samples Hap4 and Hap5 both appear to be U5a2a (based on the combination of 16114a and 16294). U5a2a should also have mutations at 16256, 16270 and 16526, but the test results did not report any of these 3 mutations in Hap4, and only found 16256 was reported in sample Hap5. Reversions at marker 16270 occur infrequently in U5, and it is possible that some of the ancient mtDNA samples could have a reversion at 16270, however, the probability is extremely low that that 5 of 7 samples would have this relatively rare reversion. Thus, based on these probable U5 samples, the reported results for the ancient mtDNA samples appear to have a high error rate of missed markers in their results.

Eight of the samples appear to be JT, based on the mutation at 16126. Two of the samples might be H1b based on the mutation at 16356. We were unable to identify haplogroups for any of the remaining 13 samples. Six of the samples are CRS, but given an apparent high rate of missed identification of 16270 in most of the apparent U5 samples, it is not possible to predict haplogroup for the CRS samples.

Figure 3, the median joining network, has the haplotypes connected in a way that is inconsistent with their probable relationship in the mtDNA phylogeographic tree. We recommend re-evaluating the median joining network using the probable phylogenetic relationships among the samples. We also recommend that the coding region be sequenced for these samples to better determine their haplogroups and subclades, especially for the 13 of the 30 samples whose haplogroup cannot be determined from the control region results. We also recommend sequencing control region more completely because important defining markers for several of the haplogroups tentatively identified here are found in the region from to nucleotide markers 16385 to 16569.

Based on the 17 samples for which we were able to predict haplogroups, JT and U5 are the most common haplogroups in the ancient Etruscans samples. These do not appear to be related individuals because there is considerable diversity in haplotypes among the JT and U5 samples. However, these results are uncertain because of the possibility that the some markers were not reliably detected in the ancient mtDNA samples. Additional testing of the coding region and re-testing of the control region are necessary to fully evaluate the ancient Etruscan samples in the context of ancient and modern populations.


References:

Ghirotto S, Tassi F, Fumagalli E, Colonna V, Sandionigi A, et al. (2013) Origins and Evolution of the Etruscans’ mtDNA. PLoS ONE 8(2): e55519.doi:10.1371/journal.pone.0055519

Vernesi C, Caramelli D, Dupanloup I, Bertorelle G, Lari M, et al. (2004) The Etruscans: a population-genetic study. Am J Hum Genet 74: 694-704.

Der Sarkissian's NE European ancient DNA formally published

This entry is a bit redundant because a previous version of this paper (presented as doctoral thesis) was already discussed in length months ago. Let us recall that this study provided the first confirmed (by coding region testing) mtDNA sequence belonging to haplogroup H in Northern Europe prior to the Neolithic*

Clio Der Sarkissian et al., Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe. PLoS Genetics, 2013. Open accessLINK [doi:10.1371/journal.pgen.1003296]

Abstract

North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.

As you may realize, the Sardinian sequences discussed also in the thesis are not part of this paper. Also the emphasis is on the presence of Oriental lineages (C*, C1, C5, D* and Z1a) in North-Eastern Europe prior to the Neolithic, which is, no doubt another element of interest.

Table 1. Results for mitochondrial DNA typing
Yuzhni Oleni Ostrov is in Karelia,Popovo in Northern Russia and Bol'shoy in Sápmi (Lapland)

As mentioned in the previous entry there is another (not shown) 13th century Sámi sample (Chalmny-Varre) which is totally modern in composition: dominated by haplogroup V7e and complemented by U5b1b1 and U5a1.

The simulations performed by the authors suggest that:

The model of genetic continuity between aUzPo and present-day Saami was found to fit the observed data better than the model of genetic continuity between aUzPo and present-day NEE.

The model also suggests that modern NE Europeans from the area (Russian, Finns and even to some extent Karelians and Volga-Ural peoples) are product of later migration from Central Europe, however they could not test this for the Saami because they could not find a plausible source population for them. 

This is maybe best visualized in figure 2:

Figure 2. Principal Component Analysis of mitochondrial haplogroup frequencies.

In this graph the Sámi look rather continuous with ancient locals but they show even more continuity with ancient Pitted Ware populations from the Baltic (aPWC, Chalcolithic semi-foragers with possible roots in Eastern European Neolithic) and related "foragers" from NE Poland and Lithuania (corresponding to various periods, even Chalcolithic in some cases), as well as more genuine pre-Neolithic hunter-gatherers from Germany (all them pooled as aHG).

It must be mentioned in any case that there is no single known case of haplogroup V in any pre-Neolithic sample (neither in Europe, nor anywhere else). And this one makes up the bulk of modern Sámi mtDNA pool.

____________________________________________________________________

Note:

* Other such strongly confirmed haplogroup H (mtDNA) sequences were also reported last year for Northern Iberia Paleolithic and Epipaleolithic remains. Many other Paleolithic sequences are suspect but have only been tested for the Hyper-Variable Region (HVS), which is often not conclusive for this haplogroup, causing in the recent past some people to (wrongly) reject the presence of this lineage, now the most common in Europe, before the Neolithic. Now we know that it did exist in both Northern and Southern Europe, although many questions remain on its commonality and history.

February 13, 2013

Large dolmen with 30 buried people discovered in Switzerland

Swiss archaeologists have unearthed in the Canton of Bern a large dolmen that must have been above the ground until the Late Middle Ages. The burial contains the remains of some 30 people, which will be studied also for DNA. 

The roof of the Megalithic monument was made from a large glacial boulder measuring 3x2x1 meters, which was the only part remaining visible and was not initially identified as such megalith. 

The dolmen upon excavation

Reconstruction of how it must have looked in the past

The cultural context of Megalithism in this part of Europe corresponds to the southwestern variant of late Danubian Neolithic, known as Horgen culture (c. 3400-2850 BCE, found in all Swabia). In this late period many Western Danubian peoples, as well as other cultures, adopted the Megalithic "collective" (clannic?) burial style, original from SW Europe, breaking away with the original Danubian traditions of simple individual burial in flexed position. However their settlements show continuity with the preceding Pfyn culture, which is widely considered Danubian. Their pottery was rough and influenced the post-Cardial culture of Cortaillod, later Saône-Rhône (French Switzerland and nearby parts of France), but their stone tools were well finished and often polished. Horgen culture collapsed with the arrival of the Kurgan (Indoeuropean) Corded Ware culture.




Sources: Swiss Info (video), Past Horizons, Asociación Los Dólmenes[es].

5000 years old temple found near Lima, Peru

Archaeologists have uncovered one of the oldest temples of America in El Paraíso, a rich archaeological site located 40 km northwest of Lima. 

The pyramidal structure is estimated to be c. 5000 years old (although awaiting radiocarbon dating), much much older than the Incas and rather contemporary of the pyramids of Egypt, for example. It confirms that the area of Lima was a ceremonial center for the ancient peoples of Peru.

The Temple of Fire, as it was nicknamed by the discoverers, contains a hearth at its center, which they suspect was a key part of their rituals. It is built of stone covered in fine yellow clay, which shows some indications of having been painted in red colors.

The ritual site is located close both to the coast and to the valley, allowing for it to interact with both the coastal fishing economy and the beginnings of agriculture in the interior, they say. The prehistorical period of this building is known as the Pre-Ceramic Age (c. 3600-1800 BCE). 

Sources: BBC, El Universo[es] (via Pileta).


Update: see the interesting comments below by Raimo Kangasniemi, who argues that several sites (Áspero, La Galgada, Caral, all them in Peru) are roughly contemporary of this one, indicating a growing dedication of resources to ritual/religious buildings already in the Pre-Ceramic Period V, also elsewhere.

February 11, 2013

Atlantic thermohaline currents nearly stopped in some cold spells of the Ice Age

That is what researchers claim in a new study:

Stephan P. Ritz et al., Estimated strength of the Atlantic overturning circulation during the last deglaciation. Nature Geoscience 2013. Pay per viewLINK [doi:10.1038/ngeo1723]

Abstract

The Atlantic meridional overturning circulation affects the latitudinal distribution of heat, and is a key component of the climate system. Proxy reconstructions, based on sedimentary 231Pa/230Th ratios and the difference between surface- and deep-water radiocarbon ages, indicate that during the last glacial period, the overturning circulation was reduced during millennial-scale periods of cooling. However, much debate exists over the robustness of these proxies. Here we combine proxy reconstructions of sea surface and air temperatures and a global climate model to quantitatively estimate changes in the strength of the Atlantic meridional overturning circulation during the last glacial period. We find that, relative to the Last Glacial Maximum, the overturning circulation was reduced by approximately 14 Sv during the cold Heinrich event 1. During the Younger Dryas cold event, the overturning circulation was reduced by approximately 12 Sv, relative to the preceding warm interval. These changes are consistent with qualitative estimates of the overturning circulation from sedimentary 231Pa/230Th ratios. In addition, we find that the strength of the overturning circulation during the Last Glacial Maximum and the Holocene epoch are indistinguishable within the uncertainty of the reconstruction.

Summary of thermohaline circulation (public domain, NASA)


In the North Atlantic the best known thermohaline current is the Gulf Stream, which effectively keeps Europe several degrees warmer than it would be otherwise, allowing a relatively dense population at latitudes unheard of elsewhere on Earth. This current was weak at best in the Ice Age. 

Notice that they say that they can find any difference between present day (Holocene epoch) and the Last Glacial Maximum, so it cannot be inferred, it seems, that the glaciation itself had anything to do with the thermohaline currents but only with  some particular cold spells of the late Upper Pleistocene, particularly the HE1 (c. 18-14.6 Ka ago) and the Younger Dryas (c. 10 Ka ago).

February 10, 2013

Linguist Jürgen Untermann has died

Surely one of the most important researchers of ancient Iberian languages and also of Italian ones, Jürgen Untermann has left his signature all around the bibliography regarding Iberian, Celtiberian and Italic languages. His life ended on February 7th 2013 at the venerable age of 84.



Source: Ama Ata[es], photo from Diario de Navarra.


February 8, 2013

Only two dates lead adventurous prehistorians to happily question late Neanderthal survival in Iberia

A recent paper has made the headlines all around questioning the, so far widely accepted, late Neanderthal survival in the Iberian Peninsula. I was so puzzled by the conclusions that I decided to hold back and await if I could muster some more information. Soon I was made to realize that the limelight-seeking authors only provided two new datings and could not even question at all some of the most relevant "late survival" dates like those from Gibraltar or the more recent one of very late Mousterian (22,000 BP) in a remote district of Cantabria (apparently not even known to the authors).

Rachel E. Wood et al., Radiocarbon dating casts doubt on the late chronology of the Middle to Upper Palaeolithic transition in southern Iberia. PNAS 2013. Pay per view (6 months embargo) → LINK [doi: 10.1073/pnas.1207656110]

Abstract

It is commonly accepted that some of the latest dates for Neanderthal fossils and Mousterian industries are found south of the Ebro valley in Iberia at ca. 36 ka calBP (calibrated radiocarbon date ranges). In contrast, to the north of the valley the Mousterian disappears shortly before the Proto-Aurignacian appears at ca. 42 ka calBP. The latter is most likely produced by anatomically modern humans. However, two-thirds of dates from the south are radiocarbon dates, a technique that is particularly sensitive to carbon contaminants of a younger age that can be difficult to remove using routine pretreatment protocols. We have attempted to test the reliability of chronologies of 11 southern Iberian Middle and early Upper Paleolithic sites. Only two, Jarama VI and Zafarraya, were found to contain material that could be reliably dated. In both sites, Middle Paleolithic contexts were previously dated by radiocarbon to less than 42 ka calBP. Using ultrafiltration to purify faunal bone collagen before radiocarbon dating, we obtain ages at least 10 ka 14C years older, close to or beyond the limit of the radiocarbon method for the Mousterian at Jarama VI and Neanderthal fossils at Zafarraya. Unless rigorous pretreatment protocols have been used, radiocarbon dates should be assumed to be inaccurate until proven otherwise in this region. Evidence for the late survival of Neanderthals in southern Iberia is limited to one possible site, Cueva Antón, and alternative models of human occupation of the region should be considered. 

From confidential personal communication with qualified prehistorians, I gather the following criticisms:
  • Achieving two new dates (out of eleven trials) is no major hit, even if useful.
  • The results have been oversimplified when presented to the media (and/or by the journalists themselves).
  • The new dates do not disprove that Neanderthals may have been there in later periods.
  • Any conclusions would need to wait for a more extended revision of dates.
  • Collagen preservation is much worse in Southern than Northern Iberia, what may actually imply some need for revision of dates towards more ancient ones (not just the Middle Paleolithic ones but also those from the initial Upper Paleolithic). This part is rather supportive but with due caution.
  • Dates should not be considered alone but in their stratigraphic and archaeological context.
  • The two sites have a very complex stratigraphy, what affects the interpretation of the new dates.
  • There may be pre-conceptions behind this exaggerated claim, such as attachment to the Finlayson model of Neanderthal collapse in Europe before the arrival of modern humans, which is surely wrong.
Also I will add on my own account that, unlike what has been published in some media, this result would not cast absolutely any doubt on the Neanderthal admixture episode, which must have happened not in Europe but, surely, in West Asia long before our ancestors set foot in Europe at all, just at the beginnings of the migration out of Africa (to Asia first of all, not to Europe) c. 125-90 Ka ago.


Update (Feb 12): Basque prehistorian Joseba Ríos Garaizar inaugurates his new blog with an article[es] on this issue. He argues that the two new dates do not seem enough to revolutionize the whole understanding of Neanderthal periodization in SW Europe, especially with the recent re-dating of Saint-Césaire (which confirmed Neanderthal authorship of Chatelperronian and gives a date as late as c. 36 Ka BP, uncalibrated) and the various and also recent datings for Mousterian in the North of the Iberian Peninsula (Arrillor, Fuentes de San Cristobal, Esquilleu, Sopeña) all with dates more recent than 40 Ka BP (uncalibrated). In addition to these Axlor (Basque Country) has a Mousterian layer above another dated to c. 42 Ka BP (uncal.) and Lezetxiki is probably in the same situation. On top of those Mousterian layers many sites have their own Chatelperronian layer, of clear Neanderthal manufacture.

And then there are the already mentioned cases of the anomalous late Mousterian from Cantabria recently dated to 22 Ka BP and several Southern Iberian caves, including Gorham (Gibraltar), which appear also to be more recent than the dates managed by Wood et al.

Were the Etruscans after all native Italians?

Etruscan sarcophagus
(CC by Ecelan)
A new study casts doubt on the Anatolian origin theory of Etruscan origins.

As you may know, two main theories have been proposed for the origins of the ancient Italian civilization that taught Romans nearly everything, especially in the field of architecture: on one side that they were Bronze Age arrivals from Anatolia, maybe related to ancient Trojans, which had some support on art aesthetics, the historical presence of a close relative of Etruscan language in the island of Lemnos, some classical theories and, more recently, an ancient mtDNA study (Vernesi 2004), which found the mtDNA of ancient Etruscan aristocrats to be closest (by FST) to Turks than to any other studied population, excepted (by slight margin) modern Tuscans.

The main alternative theory proposes that Etruscans were a local development, what would be also consistent with an Anatolian genetic affinity because the Italian peninsula, including Tuscany, shows repeated waves of cultural influences from the Western Balcans first (Neolithic) and from the Aegean later on (Chalcolithic especially).

The debate seems however far away from reaching any strong conclusion, notably now that a new study revising Vernesi's data finds a different and rather puzzling set of affinities for ancient Etruscans.

Silvia Ghirotto et al., Origins and Evolution of the Etruscans’ mtDNA. PLoS ONE, 2013. Open accessLINK [doi:10.1371/journal.pone.0055519]

Abstract

The Etruscan culture is documented in Etruria, Central Italy, from the 8th to the 1st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed the hypervariable region of mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals from the Mediterranean basin. Comparing ancient (30 Etruscans, 27 Medieval individuals) and modern DNA sequences (370 Tuscans), with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the current inhabitants of Casentino and Volterra, but not to the general contemporary population of the former Etruscan homeland. By further considering two Anatolian samples (35 and 123 individuals) we could estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, and not as an immediate consequence of immigration from the Eastern Mediterranean shores.


The study finds that ancient Etruscan mtDNA is closest among modern populations (by FST) to Southern Germans and, following closely, a varied array of other Europeans (totally the opposite to Vernesi's findings), and rather not too close to Turks or other Eastern Mediterranean populations.

Annotated version of Fig. S3-B, FST distances of ancient Etruscan mtDNA
(red: 0.4-0.6, orange: 0.6-0.8, yellow: 0.8-1.0)
See also Fig. S4 (multidimensional scaling graphs)
= Click to expand =

Among ancient populations, ancient Etruscans are found to be closer to Neolithic farmers from Central Europe and then to ancient Lucchesi (from Lucca, including those from the Chalcolithic era, i.e. Eneolithic):

Fig. S4-C Multi Dimensional Scaling summarizing genetic affinities between the Etruscans and (...) (C) 9 ancient populations of Europe. Population labels and sample sizes are provided in Table S2 [Neo_Farm: Neolithic Central Europeans, Med: Medieval Tuscans]

Among the study's conclusions are:

A model of genealogical continuity across 2,500 years thus proved to best fit the observed data for Volterra, and especially Casentino, but not for another community dwelling in an area also rich with Etruscan archaeological remains (Murlo), nor (as expected) for the bulk of the current Tuscan population, here represented by a forensic sample of the inhabitants of Florence. Therefore, the present analysis indicates that the Etruscan genetic heritage is still present, but only in some isolates, whereas current Tuscans are not generally descended from Etruscan ancestors along the female lines.

Notice that this is always in relation to the ancient Etruscan mtDNA data, which comes from the tombs of aristocrats, not commoners. However they insist:

Because Medieval Tuscans appear directly descended from Etruscan ancestors, one can reasonably speculate that the genetic build-up of the Murlo and Florence populations was modified by immigration in the last five centuries.

Villanovan urn
(CC by Sailko)
An intriguing issue not considered apparently by the authors is the appearance of greatest genetic similitude with some populations of Central Europe. I would consider preliminarily that a possible line of interpretation of this data might be that the Etruscan elites might have arrived with the Urnfields expansion peoples (Indoeuropeans most probably) but were culturally and linguistically assimilated by the native substrate (proto-Etruscans did participate of the fashion of corpse incineration and burial of the charred remains in urns, which even led some to propose that they were Indoeuropeans in fact).

However this clashes with the fact that they also appear extremely close to Central European Neolithic peoples, which are not at all similar to modern nor Urnfields period Central Europeans. So I have to admit that a local Neolithic origin may be the most reasonable hypothesis with this data and that the irregular Central European affinities may have other explanation (such as local preservation of a mtDNA pool closer to Neolithic one than usual).


Update (Feb 15): Gail Tonnesen has researched in greater depth what haplogroups could the ancient Etruscans have specifically → LINK