Obsidian exchange in Neolithic Sicily and Sardinia (video)

Thanks to Theasparagus for noticing this quite interesting video-lesson on quite obviously seagoing peoples of the Central Mediterranean and their journeys to distant volcanic islands to obtain the valuable obsidian (sharper than a scalpel) and also to the mainland to trade it for whatever goods.

Neolithic DNA from Greece and NW Anatolia and their influence on Europe

This is a most interesting study that brings to us potentially key information on the expansion of European Neolithic and the formation of modern European peoples.

Zuzana Hofmanová, Susanne Kreutzer et al., Early farmers from across Europe directly descended from Neolithic Aegeans. PNAS 2016. Open access → LINK [doi:10.1073/pnas.1523951113]

Abstract

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

Uniparental DNA

One of the most important findings is that the two Epipaleolithic samples from Theopetra yielded mtDNA K1c, being the first time in which haplogroup K has been detected in pre-Neolithic Europe. Sadly enough these two individuals could not be sequenced for full genome. 

The other five individuals are all Neolithic (three early, two late) and did provide much more information.

• Rev5 (c. 6300 BCE): mtDNA X2b
• Bar31 (c. 6300 BCE): mtDNA X2m, Y-DNA G2a2b
• Bar8 (c. 6100 BCE): mtDNA K1a2
• Pal7 (c. 4400 BCE): mtDNA J1c1
• Klei10 (c. 4100 BCE): mtDNA K1a2, Y-DNA G2a2a1b (same as Ötzi's)

I color coded their abbreviated names according to the usage in the study's many maps, for easier reference: green shades are for Greece (Western Macedonia), red shades for Turkey (Bursa district). It is also very convenient to get straight their real geography because many of the map-styled graphs are not precise at all about that:

Fig. 1.

North Aegean archaeological sites investigated in Turkey and Greece.

Autosomal DNA affinities

This is probably the most interesting part. There is a lot about it in the supplementary information appendix but I find that the really central issue is how they relate to each other (or not) and to other ancient and modern Europeans. I reorganized figs S21 and S22 to better visualize this:

Ancient samples compared to each other and other ancient samples ("inferred proportions of ancestry")

Ancient samples compared to modern Europeans ("inferred proportions of ancestry")

So what do we see here? First of all that the strongest contribution of known Aegean Neolithic peoples on mainline European Neolithic is from Bar31, which is from NW Anatolia, and not from Greece. Bar8 is a less important contributor but may have impacted particularly around the Alps (Stuttgart-LBK, modern North Italians).

This goes against most archaeology-based interpretations, which rather strongly suggest a Thessalian and West Macedonian origin of the Balcanic and, therefore, other European branches of the mainline Neolithic of Aegean roots, and do instead support some sort of cultural barrier near the European reaches of the Marmara Sea. Of course we lack exhaustive sampling of Greek Neolithic so far, so it might be still possible that other populations from Thessaly or Epirus could have been more important. However the lack of Anatolian-like influence on the Western Macedonian Neolithic until c. 4100 BCE, makes it quite unlikely.

So it seems that, once again, new archaeogenetic information forces us to rethink the interpretative theories based on other data.

However we do see a strong influence of Greek Neolithic and particularly the oldest sample, Rev5, in SW Europe, very especially among Basques, who seem to have only very minor Anatolian Neolithic ancestry, unlike everyone else relevant here. This impact is also apparent in Sardinia and to some extent North Italy (but overshadowed in these two cases by the one from Anatolia, particularly Bar31).

There are also similar analyses for other four ancient samples (Lochsbour, Stuttgart, Hungary Neolithic and Hungary Bronze) but they don't provide truly new information, so I'm skipping them here. As I said before, there's a hoard of analyses in the SI appendix, enjoy yourselves browsing through them and feel free to note in the comments anything you believe important.

A synthesis of the various "inferred proportions of ancestry" analyses is anyhow shown in fig. 3:

Fig. 3. (click to expand)

Inferred mixture coefficients when forming each modern (small pies) and ancient (large pies, enclosed by borders matching key at left) group as a mixture of the modern-day Yoruba from Africa and the ancient samples shown in the key at left.

The fractions may be misleading however, especially for the ancients. For example: Lochsbour (a total outlier among the ancients in this study) appears best correlated with Pal7 but in fig. S24 it is clear that does no correlate with any Neolithic sample at any significant level. But in general terms it can give a good idea of where does ancestry, particularly for modern samples, come from.

Note: elsewhere someone was being a crybaby about the Polish sample (may well be an error) or the Kalmyk sample (who are obviously most related to East Asians, not used here) but those are minor issues.

Of course there's a lot more to learn from the remains of the ancients. Let's keep up the good work.

Large monolith found underwater near Pantellaria (Sicily)

A large human-made monolith has been discovered underwater in the Pantellaria shoal, submerged since the end of the Ice Age.

E. Lodolo & Z. Ben-Avraham. A submerged monolith in the Sicilian Channel (central Mediterranean Sea): Evidence for Mesolithic human activity. Journal of Archaeological Science, 2015. Freely accessible → LINK [doi:10.1016/j.jasrep.2015.07.003]

Other source: Pileta de Prehistoria. 

While it is hard to argue that the monolith is not man-made, as it has three holes of the same size in non-random positions, I would take with a pinch of salt the claim that the would-be standing stone or menhir has been there since the 10th millennium BCE, when the shoal was flooded by seawater. 

Instead I would consider the following scenarios as plausible:

1. The land could have been at higher absolute altitude in the past and sunk because of local techtonics. It is, we must not forget, a very active geological area.
2. The monolith could have just sunk when being transported on a ship of some sort between islands. The ship, made of wood and ropes would leave no obvious trace.

So I'd rather imagine the stone to have been produced in the Chalcolithic Megalithic context that has some relevance in the area, very especially the fascinating case of Maltese Megalithism, which spans between 3600 and 700 BCE.

Sicilian haploid genetics in the Mediterranean context

A new study takes a look at Sicilian haploid genetics in its wider geographical context.

Stephania Samo et al., An Ancient Mediterranean Melting Pot: Investigating the Uniparental Genetic Structure and Population History of Sicily and Southern Italy. PLoS ONE 2014. Open access → LINK [doi:10.1371/journal.pone.0096074]

Abstract

Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.

No particular haplogroup is dominant in the island in the Y-DNA side and, although H has some clear prevalence among mtDNA haplogroups, it is actually well under the normal European levels for this common haplogroup.

Table 1. Age estimates (in YBP) of STR and HVS variation for the most frequent haplogroups in Sicily and Southern Italy.

Y-DNA

We can see how the following patrilineages are more common: J2a (16%), G2a (12%) and E1b1b1a1b1a (10%) and R1b1a2a1a2 (9%). R1a1a (5%), J1 (5%) R1b1a2a1a1 (4%) and J2b (4%) are less common instead.

Fig, S2(a) - Principal Component Analysis (PCA) based on haplogroup frequencies for Y-chromosome (a) (...). Population codes as in Table S1. Colour codes for geographic affiliations as in the legends at the bottom-left of each plot. Legend abbreviations: NAFR: North-Africa, LEV: Levant, BALK: Balkans, SSI: Sicily and South-Italy, NCI: North-Central Italy, IBE: Iberian Peninsula, GER: Germany.

There is an interesting tendency in Agrigento (AG) towards Lebanon (which in this graph includes all the LEV category), while other areas of Sicily and Southern Italy (Lecce, Cosenza, Enna) tend instead towards the Aegean (Pho, Smy). These tendencies could be interpreted (at least partly) in terms of historical colonization events by Phoenicians and Greeks. Catania instead tends towards Central-North Italy, maybe reflecting its important role under Roman rule and a historical colonization in the times of Augustus.

The Southern Italian towns of Matera (Basilicata) and Campobasso (Molise) also show a tendency towards the Northern Balcans (represented by Serbia here). 

The authors confirm previous impressions of a West-East Y-DNA duality in the Mediterranean that divides Italy:

When comparing SSI with Mediterranean reference populations, Y-chromosome results (Figure 1 and Figure S2) revealed a clear-cut genetic differentiation between the North-Western vs. the Central- and South-Eastern Mediterranean genetic pools (as confirmed by both sPCA G-test and AMOVA F_CT statistically significant tests). These results are consistent with our previous study about Italy [12], in which we detected a discontinuous paternal genetic structure, clearly separating the South-Eastern and the North-Western parts of the Italian Peninsula. Here this pattern appears extended to the whole Mediterranean Basin, particularly suggesting a shared genetic background between South-Eastern Italy and the South-Eastern Mediterranean cluster from one side, and between North-Western Italy and the Western Europe from the other side (Figure 2).

Mitochondrial DNA

The main matrilinages of Sicily are H (28%) T (13%), J (10%) and HV(xH) (5%). U5 is also well under the usual European frequencies with just 3% of prevalence. 

While the AMOVA statistical significance tests say that PC2 in the following graph is not really significant. However PC1 is still relevant, I understand.

Fig S1(b) - Principal Component Analysis (PCA) based on haplogroup frequencies for (...) mtDNA (b). Population codes as in Table S1. Colour codes for geographic affiliations as in the legends at the bottom-left of each plot. Legend abbreviations: NAFR: North-Africa, LEV: Levant, BALK: Balkans, SSI: Sicily and South-Italy, NCI: North-Central Italy, IBE: Iberian Peninsula, GER: Germany.

If anything there is some discrepancy between Y-DNA tendencies and those of mtDNA. For example the "Phoenician" Agrigento in the Y-DNA graph, looks "Iberian" or "Tuscan" in the mtDNA one. 

The authors believe that mtDNA lineages could be older than Y-DNA ones in many cases:

Y-chromosome results however contrast with the lack of statistical support to the sPCA global structure observed for mtDNA diversity, excepted for a similar NW-SE genetic pattern identified by sPC1 (Figure 3). The common South-East to North-West pattern in the distribution of genetic variation across the European and Mediterranean domain, could be interpreted as reflecting the same SE to NW genetic cline extensively reported in literature for the whole of Europe [71]–[74]. However, the general lack of statistical support to the global structure observed for mtDNA markers suggests a higher homogeneity for maternal than paternal genetic pools in the Mediterranean genetic landscape. These results could be ascribed to older population events and/or different demographic and historical dynamics for females than males. (...) In fact, whereas the different continental and within continental contributions to the current SSI genetic pool appeared to be more equally distributed on the maternal side (despite a noteworthy contribution of Levantine females), the paternal counterpart appeared to be clearly affected by South-Eastern Mediterranean, mainly Balkan [Aegean], males.

See also:

• Italian haploid genetics
• Italian and Sardinian autosomal genetics
• Italian complex ancestry

Diversity and legacy of ancient European farmers

Two new Swedish papers, published almost simultaneously, add important extra information and, of course, also some more questions to the previous analysis of European ancestry by Lazaridis et al. (see here, here and here). They are:

Evangelia Dasakali, A late Neolithic Iberian farmer exhibits genetic affinity to Neolithic Scandinavian farmers and a Bronze Age central European farmer. Paper IV of the greater collection Archaeological Genetics - Approaching Human History through DNA Analysis. Acta Universitatis Upsaliensis, 2014. Freely accessible PDF → LINK [ISBN 978-91-554-8816-1]

Pontus Skoglund, Helena Malström et al., Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers. Science 2014. Pay per view (supp. info. freely accessible) → LINK [doi:10.1126/science.1253448]

I must say that it seems a bit odd that, being colleagues of the same university, Dasakali and Skoglund/Malström have decided to publish such two strongly related studies separately. But, well, whatever...

The first study briefly compares the genome of a Chalcolithic Iberian farmer from El Portalón (Atapuerca) to modern Europeans and some previously published ancient genomes, mostly Neolithic but also one from Epipaleolithic Iberia (La Braña).

The study is just a very short synthesis and lacks detail but provides this PCA graph:

On it's own, it already provides evidence of ancient European farmers not being as homogeneous as the  Lazaridis sample (n=3 but all from near the Alps) may suggest. The Iberian sequence deviates more towards modern Italy than the Alpine ones (here represented only by Ötzi), who tend to cluster towards modern Sardinians. Also the Gökheim sequence from Southern Sweden, the only clearly Megalithic sample so far to be studied, clusters with Basques. But Gökeim is better addressed in the Skoglund paper in fact.

This is because Skoglund & Malström use more samples from Neolithic Scandinavia: four from the Gökheim site (Megalithic and Funnelbeaker farmers) and six from Götland's Pitted Ware late semi-foragers of the Baltic (probably with partial Eastern European roots).

The results are more directly visualized and comparable with those Dasakali and Lazaridis in the Principal Component Analysis:

Fig. 1. Population structure and genetic affinities of ancient Eurasians. (A) Ancient individuals were projected on principal components computed on 57 modern-day Western Eurasian groups. (...)
Notice that ancient samples are projected on the modern PCA, what explains especially the anomalous position of Mal'ta 1 (MA1), which is actually much more divergent from all modern Europeans. SF11 = Stora Förvar 11.

Obviously not all is just a simple PCA, together we find these heatmaps that help us to better understand the affinities of the ancient farmers:

Fig. 1. Population structure and genetic affinities of ancient Eurasians. (...)
(C) Shared genetic drift between Western Eurasian populations and Ajvide58, a Neolithic hunter-gatherer from Scandinavia.
(D) Shared genetic drift between Western Eurasian populations and Gökhem2, an early farmer from Scandinavia.

In fact Gökheim 2 shares a bit more genetic drift with Sardinians than with Basques, an that's probably the reason why she is located rather towards Spain and Italy in the PCA, even if they don't share greater genetic drift with these than with Basques and Sardinians (PCAs can be misleading). However the shared drift is probably less than among Alpine farmers, owing largely to Gökheim's greater aboriginal hunter-gatherer admixture.

In general, like other early European farmers, Gökheim people seem to align best with Western Mediterranean peoples, particularly those with low paleo-Siberian (MA1) affinity, which are Basques and Sardinians. 

Judging on the PCA, there seems to be some diversity among them, with one being more extremely "Atlantic". It is very possible that in the Neolithic and Chalcolithic Atlantic Europe there were others like her (most Gökheim samples are female although I'm uncertain about this unnumbered one).

On the other hand, Pitted Ware sequences share greatest drift with modern Baltic peoples, including the oversampled Swedes but also with Eastern Baltics (Estonian, Finnish, Lithuanians). This last surely owes to the origins of this culture in Eastern Europe but in what regards to Sweden, it must imply that their kind of Eastern-like genetics were very strongly favored when the Kurgan macro-culture (Single Burials, part of the wider Corded Ware culture) took over the region c. 2500 BCE. Instead the ancient megalithic farmers quite obviously suffered a genocide in this part of the world.  

Overall, it seems obvious to me by now that Eastern European genetics distributed by the long-term Kurgan expansion (Indoeuropeans) must have been somewhat similar to aboriginal Western European hunter-gatherers but with greater paleo-Siberian affinities (MA1-like), which they also distributed by Europe for the first time.

For a wider comparison with World genomes, take a look at figures S3 and S4 please. In them we can see that Ajv58 is comparatively closer also to South Asians, Siberians and Native Americans, while Gök2 is instead relatively closer to Palestinians, Arabians and slightly to Egyptians too (not apparent in the above graph but certainly in the global one).

This is quite interesting because it directly relates to the mysterious "Basal Eurasian" element that Lazaridis et al. detected in their ground-breaking study, which is more clearly perceived as something "Palestinian", with whatever NE African and/or residual out-of-Africa element in it, which partly detaches the ancient farmers from the main Eurasian ("out-of-India") branch.

Some of all this is also quite apparent in the attempts of Skoglund & Malström to infer the ancestry of the various paleo-populations:

Fig. 2. (A) Sample locations of ancient human remains that are included in the population history model. (B) Admixture graph of population history fitted to ancient genomes showing more hunter-gatherer admixture in Neolithic Scandinavian farmers than in central European farmers (table S15).

The above "admixture graph" is identical in essence to fig. S6. However I find even more very interesting the fig. S7:

Fig. S7. A) Admixture graph of population history fitted to ancient genomes and two modern-day genomes from Europe. (...)

This alternative result has been produced by merely adding modern French and Sardinians to the analyzed pool and allowing for two extra admixture axes. The result is quite different:

Essentially the overall unity of all Europeans, ancient and modern is restored as a single derived branch distinct from the circum-Pacific populations. The deviation to "Basal Eurasianness" of Neolithic Europeans and Sardinians is instead largely explained by an admixture axis from the Dinka, which act as a proxy for whatever Red Sea area input in the early European Farmers. This is just as I expected and have tried to explain before, so I guess you understand why I do prefer this second admixture graph over the other.

In this sense, I feel that Skoglund & Malström could have done a bit better by testing more alternative models (different samples, different pre-definition of the admixture axes, etc.) but I guess it's good enough for their Swedish focus. Not so much for the pan-European one though. 

It is also very striking that the French sample appears unrelated to any of the ancient samples, be them farmers or not. Instead they show up as a branch of their own with proto-Sardinian admixture. This probably owes to the fact that neither of the sampled ancient populations is directly ancestral to the French, unlike what happens with Lochsbour, for which the French show the longest IBD segments, indicating a more direct ancestry. So I guess that we can take the French branch as being partly Lochsbour-like, plus whatever Eastern European (but not Scandinavian) extra ancestry the Celts, Romans and Germanic tribes brought with them (and of course the strong Neolithic element indicated as paleo-Sardinian admixture). Sadly the analysis strategy is not designed to provide us with such information here, but it can still be inferred if we consider all the available data.

Of course most modern samples show less drift because they are more cosmopolitan populations than the ancient ones, whose demographic base should be more like that of Australian aborigines, the only modern sample that shows a similarly high drift parameter. 

As concluding remarks, I wish to underline the greater aboriginal European (WHG or blue color) admixture in the Megalithic farmers of Gökheim, which resemble modern Basque genetics. It is very likely that more populations like those existed in the Megalithic axis from Southern Iberia to Southern Sweden, although naturally each one had its own peculiarities and we should not take Gökheim as any sort of ideal representative of such ancient Atlantic population but rather as one of its many likely subpopulations. 

Before the Indoeuropean consolidation of the Corded Ware period, these Atlantic farmers must have greatly contributed to at least a preliminary stage of "modernization" of the Central Europan (and possibly also others') genetic pool, as discussed in this entry. Notice also that the demographic expansion was much greater with Megalithism than with Corded Ware and Bell Beaker and that this applies in general terms to nearly all studied regions, with the main exception being Jutland. However in Scania (Southern Sweden), there is a clearly second demographic expansion with the arrival of Corded Ware. 

Sadly there is no direct comparison of modern Swedes as hypothetical admixture between Pitted Ware Chalcolithic foragers and Megalithic/Funnelbeaker farmers. It would have been interesting to know more details about that, especially if a third element from Germany, Poland or Russia is needed to explain their modern genetic pool, as I suspect, and in which apportions.

As for the Neolithic farmers, they were clearly somewhat more diverse than the Lazaridis study suggested, varying at least in their amount of "Basal Eurasian" and Western hunter-gatherer ancestry, and possibly also in other subtle aspects we still do not understand well, as suggested by El Portalón sample.
Their most direct legacy is in any case concentrated towards Southwestern Europe.

Italian haploid genetics (second round)

More than a year ago I commented (as much as I could) on the study of Italian haploid genetics by Francesca Brisighelli et al. Sadly the study was published with several major errors in the figures, making it impossible to get anything straight. 

I know directly from the lead author that the team has been trying since then to get the paper corrected but this correction was once and again delayed by apparent inefficiency of PLoS ONE's management, much to their frustration. Finally this week the correction has been published and the figures corrected.

So let's give this study another chance:

Francesca Brisighelli et al., Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage. PLoS ONE 2012 (formally corrected in February 2014). Open access → LINK [doi:10.1371/journal.pone.0050794]

 

Notice please that you have to read the formal correction in order to access the new figures, the wrong ones are still in the paper as such. 

The corrected figures are central to the study:

Figure 1 (corrected). Map showing the location of the samples analyzed in the present study and those collected from the literature (see Table 1).
Pie charts on the left display the distribution of mtDNA haplogroup frequencies, and those on the right the Y-chromosome haplogroup frequencies.

So now we know that the Northern mtDNA pie was duplicated in the original graph and that Central Italians are outstanding in R0(xH,V), which reaches 14% (probably most HV*), while they have some other peculiarities relative to their neighbors from North and South: some less U and no detected V. 

Other variations are more clinal: H decreases from North to South while J and T do the opposite.

Figure 3 (corrected). Phylogeny of Y-chromosome SNPs and haplogroup frequencies in different Italian populations.

In the Y-DNA side, the most obvious transition is between the high frequencies of R1b1a2-M269 (R1b3 in the paper) in the North versus much lower frequencies in the South. But also:

• J2 is notorious in the Central region (and also the South) but rare in the North.
• G frequencies in the South are double than those of Center and North.
• The same happens with lesser intensity regarding E1b1b1-M35 (E3b in the study).
• In contrast haplogroup I is most common in the North. However the Sardinian and sub-Pyrenean clade I2a1a-M26 (I1b2 in the paper), which is also the one documented in Chalcolithic Languedoc, is rare in all regions.

The study also deals with several isolated populations:

Figure 4. Haplogroup frequencies of Ladins, Grecani Salentini and Lucera compared to the rest of the Italian populations analyzed in the present study.

All them show large frequencies of mtDNA H relative to their regions. The Grecani Salentini do have some extra Y-DNA E1b1b1 (E3b) and J2, what may indeed underline their partial Greek origins. The Ladini show unusually high frequencies of R1b*(xR1b1a2) and K*(xR1a,R1b,L,T,N3), while the Lucerans are outstanding in their percentage of G.

I want to end this entry with a much needed scolding to the staff of PLoS ONE for their totally unacceptable original sloppiness and delay in the correction. And my personal thanks and appreciation to Francesca Brisighelli for her indefatigable persistence and enthusiasm for her work, which is no doubt of great interest.

Ancient Italian ape had human-like precission grip

Reconstruction of O. bamboli (Pavel Major / ICP)

Oreopithecus bamboli was primate species, surely a hominine (great ape excluding orangutans) that lived in Tuscany and Sardinia some 8.2-6.7 million years ago.

It has great interest regarding human evolution because it is the oldest known ape to have developed a pad-to-pad precision grip, a characteristic otherwise only found in the human genus.

This trait, hotly debated in the last decades, has been recently confirmed by researchers of the Catalan Institute of Paleontology Miquel Crusafont (ICP). It must be said however that this development is considered convergent evolution and not ancestral to our own precision grip.

O. bamboli fossil
(CC by Ghedoghedo)

I guess that much of the controversy is caused by the old hypothesis that argued that it was the precision grip itself which elicited human brain development, something that obviously did not happen with Oreopithecus.

Other traits of this species are quite different from our own or our australopithecine relatives. They probably walked upright but with different gait (unlike the more human-like Sahelanthropus, of similar age) and their feet were very much unlike ours, with a very open angle for the big toe (hallux).

It seems that their environment was swampy and not strictly forestal.

Sources[es/cat/en]: Pileta, Diari de Girona, Wikipedia.

Ref.: Sergio Almécija et al., The morphology of Oreopithecus bambolii pollical distal phalanx. AJPA 2014. Pay per view → LINK [doi:10.1002/ajpa.22458]

Italian complex ancestry

This paper is probably the most detailed study of the haploid genetics of Italy to date, considering both Y-DNA and mtDNA.

Alessio Boattini, Begoña Marínez Cruz et al., Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0065441]

The study contains very ample data for both uniparental lineages and confirms that the origins for Italians are very complex. However their conclusions on the alleged sex-bias are totally founded on the very unreliable "molecular clock" methodology, which I will ignore in this review, focusing instead on regional affinities and similar groupings.

Y-DNA

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

Regions:
NW (I): Piamonte, Liguria, Lombardia
NE (II): Veneto, Friuli-VJ,
BOL (III): Bologna (or Emilia-Romagna if you dare to generalize from a single sampling point)
TUS (IV): Tuscany
C (Central, V): Lazio, Umbria, Marche,
S (South, VI): Campania, Basilicata, Apulia, Abruzzi, Molise
SIC (VII): Sicily
SAR (VIII): Sardinia

I changed the names of the regions from cryptic Roman numerals. Frequencies are highlighted if >2.5% overall or >5% regionally. All the rest is the same.

In order to more easily visualize the data, I made the following synthesis:

Labels for R1b are based on previous analysis based on Myres 2010 (quick map link). 

Most Italian R1b (27% of all patrilineal ancestry) belongs to the Southwestern clade, dominant (within R1b) in Iberia, France, Switzerland, Ireland... and Italy, and also very important in Great Britain, West and Southern Germany and Scandinavia. In Italy (as in Switzerland and Croatia), this clade is dominated by R1b-U152 (Alpine clade, sometimes also dubbed "Celtic"), which is also common in France and other places. Much less important is the "Irish" clade R1b-L21 (again common in France, as well as in Great Britain) which has however a notable peak in Bologna (10%). The presence of the Pyrenean clade R1b-SRY2627 is rather anecdotal (somewhat more common in NW and Sardinia). This grouping shows a clear strongest influence (almost 50%) in the Northwestern arch (NW, Bologna and Tuscany), with much lower frequencies elsewhere. This distribution does not look too "Celtic" to my eyes, I must say.

Second in importance within R1b is what I labeled as "Euro-root", most of which (6.9% of all patrilineages) belongs to R1b-M269(xP311). This paragroup connects more clearly with the Balcans and maybe West Asia, and is (coherently) somewhat more common to the South and less so in the NW.

Other R1b variants, which are likely to be mostly R1b-V88, are rare except to some extent (3.7%) in Sardinia, where this haplogroup was first identified. 

The allegedly Indoeuropean haplogroup R1a1a displays a very strange pattern for such attribution, being completely absent in the Northeast (NE, BOL), where we would have expected it to be common, as it is for example in nearby Slovenia. Instead the greatest frequencies are in the South and Center of Italy, what suggests that there is still a lot to understand about the origin and dispersal of this lineage. 

It is also notable the presence of I(xI2a), which I labeled "other NE European", although maybe "North, Eastern and SE European" would have been more correct. Within it, the allegedly "Nordic" haplogroup I1 (very common in Sweden), reaches c. 10% in NE Italy (NE, Bologna), again raising questions about the origin of this lineage as well as of all I (which I tend to consider of Ukrainian/Romanian Paleolithic origin).

The other half of the Italian Y-DNA should be of Eastern Mediterranean origins, be them in West Asia or the Balcans. I have divided this group into two categories: on one side what I label "Cardium Neolithic", all three haplogroups being attested in ancient DNA of this culture in Mediterranean Iberia/France, and on the other the rest, which is not attested but should also have arrived from the same broader region, either in the Neolithic wave or later ones (Bronze, etc.)

All three "Cardium Neolithic" clades are well represented in Italy, being the most notable G2a (11.1%), followed by E1b-V13 (7.8%) and then I2a (only 4.1% overall but a bulging 39% in Sardinia - also having the greatest I2b apportion: 2.4%). The most plausible origins of these three Neolithic lineages are respectively Anatolia (G2a), Greece-Albania (E1b-V13) and the former Yugoslavian Adriatic regions (I2). Italy surely acted as trampoline for their expansion Westward some 7500 years ago.

The "Other West Asian" category includes all other E1b-M78, E1b-M123 (both with ultimate origins in NE Africa but arriving to Europe almost necessarily via West Asia and the Southern Balcans), other G, as well as all J, L and T. The most notable of these lineages is J2a (11.4%, with strongest impact in Sicily, Central and NE Italy), followed by E1b-M123, which made an impact especially in Sardinia (6.1%) and L (major in NE Italy: 8.2%). They may all be localized Neolithic founder effects but uncertain. Of this group only J2 (J2a?) made some impact further West, reaching >5% in some parts of Iberia.

Overall African lineages (the rest of E) seem to have impacted more notably in Sicily (6.4% overall), however the characteristic NW African E1b-M81 also left some mark in Bologna (3.4%).

Some mention deserves also the rare F*, which has a rather Northern distribution in Italy, quite similar to that of R1b-SW.

Figure 1. Spatial Principal Component Analysis (sPCA) based on frequencies of Y-chromosome haplogroups.
The first two global components, sPC1 (a) and sPC2 (b), are depicted. Positive values are represented by black square; negative values are represented by white squares; the size of the square is proportional to the absolute value of sPC scores.

Mitochondrial DNA

Being too large and detailed I did not take a picture of table S7, which neatly displays the mtDNA data. The most notable lineages anyhow are the following ones:

• HV*: 4.1% (notable in NW: 6.8%)
• H*: 11.1% (widely distributed)
• H1*: 10.4% (common except in NE, highest in Sardinia: 18.6%)
• H1a (5.7% in Bologna)
• H2 (7.7% in Tuscany)
• H3: 3.9% (10% in Sardinia, 8.6% in Bologna)
• H5: 4.3% (more notable in NW, Tuscany, Center)
• T1a: 3.4% (9.3% in NE)
• T2b: 3.4% (8.6% in Sardinia)
• J1c: 3.9% (6.2% in NW, 14.3% in Bologna)
• J2a (5.1% in Sicily)
• J2b (7.1% in Sardinia)
• U5a: 3.7% (most important in Central region, NE and Bologna)
• U5b (7.1% in Sardinia)
• K1a: 4.4% (most important in NE, Bologna, Tuscany and Center)

I also attempted a synthesis here, although some may disagree with my labels (I'm a bit in doubt myself in some particular cases, admittedly):

Let me explain the why of the labels and groupings:

• Paleo1 corresponds to what some extremists consider the only valid Paleolithic lineages in Europe, i.e. those sequenced in Central and Eastern European "foragers" (excluding Sunghir's H17'27). I'm particularly uncertain about U8b: U8 has been sequenced in Paleolithic Europeans but U8b is closest to K and both are found also in West Asia.
• Paleo 2 corresponds to the lineages that appear to spread, at least partly, from SW Europe, some of which (H6, H1b, H*) have been sequenced among pre-Neolithic hunter-gatherers.
• Paleo/Neo is a category of lineages I am uncertain about: 
• HV* has been sequenced in Italian foragers but some of it may also have arrived with Neolithic
• V appears to have similar origins to the SW European H lineages but it has only been sequenced in aDNA since Neolithic, so... 
• Other H: I was simply unwilling to ponder each of the many small lineages' possible origins.
• Neo is the category of most likely lineages of Neolithic or post-Neolithic arrival. I have doubts especially about K, which is first sequenced in aDNA in Neolithic Syria/Kurdistan and spread clearly within Neolithic flows, however its phylogenetic connection with U8 makes me doubt about its ultimate origins and flows.
• Exotic includes those clades of quite clear origin outside West Eurasia/Mediterranean basin (mostly Siberian lineages): they are quite rare even considered together*.
• The categories in cursive are just groupings of the previous, as per description.

One of the aims of these groupings was to check if the molecular-clock-o-logical claims of the paper made any sense. It seems not. Italian mtDNA, like the Y-DNA seems split by about half between likely Paleolithic European clades (of possible post-Paleolithic arrival to Italy in many cases) and likely Neolithic ones. Regional variation does exist but it's not too remarkable. For example if we take the Neo row, it seems that the South of the Peninsula (S) was a bit more influenced by Neolithic or post-Neolithic flows, but the difference with the less influenced area (NW) is of just some 12 percentile points. This pattern is mirrored in reverse by the Paleo 1+2 row.

However if we take the Paleo 1 row, we see a pattern which does not seem consistent with Paleolithic continuity, at least to my eyes, with the highest frequency in the NE (open to migrations from Balcans and Central Europe), followed by the Central region and Sardinia. It rather seems to correspond, at least in part, to migrations from those regions: Balcans and Central Europe.

But, as always, your take.

Figure 3. Spatial Principal Component Analysis (sPCA) based on frequencies of mtDNA haplogroups.
The first two global components sPC1 (a) and sPC2 (b) are depicted. Positive values are represented by black squares; negative values are represented by white squares; the size of the square is proportional to the absolute value of sPC scores.

_____________________________

* On second thought (mini-update), the overall frequencies of "Siberian" lineages are not so negligible in two regions: Sicily and Central Italy, where they amount to >3% taken together. I'm wondering if this may be symptomatic of Roman slave trade, which is known to have Eastern Europe as its main source of slaves after its consolidation as Empire (also in the Middle Ages).

Neanderthal mtDNA in alleged Italian hybrid from late Mousterian context

The alleged hybrid characteristics are only attributed to morphological data of the bones (the bulk of the paper), what is always subject of great debate. Otherwise most people would just think in terms of Neanderthal, as the individual from Monte Lessini is also from a Mousterian context. By this I do not mean there was no interbreeding in the Neanderthal direction, just that without clear genetic data, I fail to see such morphometric speculations as conclusive in any way.

S. Condemi et al., Possible Interbreeding in Late Italian Neanderthals? New Data from the Mezzena Jaw (Monti Lessini, Verona, Italy). PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0059781]

Abstract

In this article we examine the mandible of Riparo Mezzena a Middle Paleolithic rockshelter in the Monti Lessini (NE Italy, Verona) found in 1957 in association with Charentian Mousterian lithic assemblages. Mitochondrial DNA analysis performed on this jaw and on other cranial fragments found at the same stratigraphic level has led to the identification of the only genetically typed Neanderthal of the Italian peninsula and has confirmed through direct dating that it belongs to a late Neanderthal. Our aim here is to re-evaluate the taxonomic affinities of the Mezzena mandible in a wide comparative framework using both comparative morphology and geometric morphometrics. The comparative sample includes mid-Pleistocene fossils, Neanderthals and anatomically modern humans. This study of the Mezzena jaw shows that the chin region is similar to that of other late Neanderthals which display a much more modern morphology with an incipient mental trigone (e.g. Spy 1, La Ferrassie, Saint-Césaire). In our view, this change in morphology among late Neanderthals supports the hypothesis of anatomical change of late Neanderthals and the hypothesis of a certain degree of interbreeding with AMHs that, as the dating shows, was already present in the European territory. Our observations on the chin of the Mezzena mandible lead us to support a non abrupt phylogenetic transition for this period in Europe.

While there is little reason to doubt the Neanderthal attribution of these remains, the method of using only HVS-I is a bit antiquated and prone to errors and uncertainties. Follows table S10, with the genetic data (HVS-I) of this and other Neanderthal mtDNA sequences:

Table S10.

Fossil specimen	Country	mtDNA region	Length (bp)	Diagnostic Neanderthals trasversion in HVR1 according to	Reference
Feldhofer 1	Germany	Complete mtDNA	16565	16139 A/T 16256 C/A Insertion 16263 A
Feldhofer 2	Germany	Complete mtDNA	16565	16139 A/T 16256 C/A Insertion 16263 A
Mezmaiskaya	Russia	Complete mtDNA	16565	16139 A/T 16256 C/A Insertion 16263 A
Vindija 75	Croatia	HVR1	357	16139 A/T 16256 C/A Insertion 16263 A
Vindija 77	Croatia	HVR1	31	16256 C/A
Vindija 80 (33.16)	Croatia	Complete mtDNA	31	16139 A/T 16256 C/A Insertion 16263 A
Vindija 33.25		Complete mtDNA	16565	16139 A/T 16256 C/A Insertion 16263 A
Engis 2	Belgium	HVR1	31	16256 C/A
Le Chapelle-aux-Saint	France	HVR1	31	16256 C/A
Rochers de Villenueve	France	HVR1	31	16256 C/A
Scladina	Belgium	HVR1	123	16256 C/A
Monte Lessini	Italy	HVR1	378	16139 A/T 16256 C/A Insertion 16263 A
Monte Lessini Mandibula	Italy	HVR1	31	16256 C/A	This paper
El Sidron SD-441	Spain	HVR1	47	16256 C/A
El Sidron SD-1252	Spain	HVR1	303	16139 A/T 16256 C/A Insertion 16263 A
EL Sidron 1253	Spain	Complete MtDNA	16565	16139 A/T 16256 C/A Insertion 16263 A
Valdegoba	Spain	HVR1	303	16139 A/T 16256 C/A Insertion 16263 A
Teshik Tash	Uzbekistan	HVR1	190	16139 A/T 16256 C/A Insertion 16263 A
Okladnikov	Russia	HVR1	348	16139 A/T 16256 C/A Insertion 16263 A