A genetic legacy of North Africa: mtDNA U6 under the microscope

An excellent new study on mtDNA haplogroup U6 has been published this week:

Bernard Sechel et al., The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents. BMC Evolutionary Biology 2014. Open access → LINK [doi:10.1186/1471-2148-14-109]

Abstract (provisional)

Background

Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia.

Results

Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent.

Conclusions

The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.

Figure 1 Surface maps, based on HVI frequencies (in o/oo), for total U6 (U6), total U6a
(Tot U6a), U6a without 16189 (U6a), U6a with 16189 (U6a-189), U6b'd, U6c, U6b and U6d.

U6 can be considered a somewhat strange haplogroup. While it is derived from U (and hence from R and N), which has an Asian origin, it seems to have expanded from NW Africa, more specifically from the Northern mountainous areas of the Moroccan state, a country known as Rif or in the native Tamazigh language Arif (of which Rif is an Arabized version), not the usual place one tends to imagine as the origin of any human expansion wave. 

Actually there is at least one important cultural expansion from that area: the Oranian or Iberomaurusian culture of the Mid-to-Late Upper Paleolithic. To some extent at least the expansion of this lineage is probably associated to this ancient culture. 

Whatever the case, U6 is not a common haplogroup: its highest peak in frequency is in the Canary Islands (16%), followed by North-West Africa (5-9%). Then come Portugal and its insular colonies, as well as Cape Verde and Ethiopia (~3%) and then there is some scatter in Spain, West Africa, NE Africa and peninsular Arabia (~1%), as well as in some other parts of Europe, Africa and West Asia (<1%). 

On the other hand it is one of the four basal branches of the major West Eurasian haplogroup U (U5 and U2'3'4'7'8'9 are more common, while U1 is even rarer and less studied), so understanding U6 seems important to better understand its parent lineage. 

Therefore this new study with its great wealth of detail and care is much welcome.

Chronological estimates and expansion patterns of U6

It may surprise you that I am even in tentative agreement with the chronological estimates for U6 and its subclades, listed in tables 2 and 3. But it is for a good reason: they make sense (assuming a reasonable CI). And the fact that they seem to make sense is probably because the authors took great care to calibrate the ages for this lineage, using as main (but not only) reference a Canadian derived lineage that seems to be a colonial founder effect. 

Anyhow all these dates should be considered as center-points of a variably wider range of possibilities, the so-called confidence interval (CI) or error margin (em). If we do that, as we should, we get the "power" to stretch the figures forth and back as need be to some extent without losing consistency, and that alone should be enough to get the estimates fit better with the material evidence (archaeology mostly). 

The authors actually mention some of those CIs in a lengthy section dedicated to explore the possible patterns of U6 spread in Africa and elsewhere.

Interestingly they suggest that the first radiation of U6 took place from NW Africa in largely eastwards direction, belonging almost necessarily to the Iberomaurusian (Oranian) culture:

This first African expansion of U6a in the Maghreb was suggested in a previous analysis [6]. This radiation inside Africa occurred in Morocco around 26 kya (Table 2) and, ruling out the earlier Aterian, we suggested the Iberomaurusian as the most probable archaeological and anthropological correlate of this spread in the Maghreb [6]. Others have pointed to the Dabban industry in North Africa and its supposed source in the Levant, the Ahmarian, as the archaeological footprints of U6 coming back to Africa [7,9]. However, we disagree for several reasons: firstly, they most probably evolved in situ from previous cultures, not being intrusive in their respective areas [42-44]; second, their chronologies are out of phase with U6 and third, Dabban is a local industry in Cyrenaica not showing the whole coastal expansion of U6. In addition, recent archaeological evidence, based on securely dated layers, also points to the Maghreb as the place with the oldest implantation of the Iberomaurusian culture [45], which is coincidental with the U6 radiation from this region proposed in this and previous studies [6].

Some millennia later, U62 appears to expand in Ethiopia, while, as mentioned, U6a1 does the same in Europe (mostly Western Iberia) and other sister lineages do the same in NW Africa itself.

A second wave of radiation corresponds to the early Holocene:

Basic clusters like U6b, U6c and U6d also emerged within a window between 13 to 10 kya (Table 2). U6b lineages spread from the Maghreb, through the Sahel, to West Africa and the Canary Islands (U6b1a), and are also present from the Sudan to Arabia, but not detected in Ethiopia. In contrast, U6c and U6d are more localized in the Maghreb. Further spreads of secondary U6a branches are also apparent, going southwards to Sahel countries and  reaching West Africa (U6a5a). Autochthonous clusters in sub-Saharan Africa first appeared at around 7 kya (U6a5b), coinciding with a period of gradual desiccation that would have obliged pastoralists to abandon many desert areas [52]. Consequently, no more U6 lineages in the Sahel are detected, while later expansions continued in West Africa (U6a3f, U6a3c, and U6b3) and the Maghreb with an additional spread to the Mediterranean shores of Europe involving U6b2, U6a3e, U6a1b and U6a3b1.

For easier understanding of the U6 phylogeny and its sometimes hard to interpret migration patterns, I made up the following graph, based on the supplemental material of this study:

U6 phylogeny, color coded by regions:

• North Africa
• Europe
• Tropical Africa
• West Asia
• intermediate colors: equal weight between two regions, black: undecided
• italic type: unnamed lineages

I must say that, I have some doubts about the exact origins of several subhaplogroups, notably:

• U6a is so diverse in some branches that it is difficult to identify it as unmistakably of NW African origin. NW Africa still gets the greatest weight (3/7) but not a clear majority.
• In U6b Tropical African lineages weight 4.5/10, while NW African ones weight only 3/10. It is a good candidate for expansion from the "Wet Sahara" indeed.
• In U6c1 European and NW African lineages weight exactly the same, although I guess that it may be reasonable to imagine Andalusian U6c1c as derived from North Africa.

However overall U6, as well as its derived lineages U6b'd and U6c clearly originated in NW Africa, so I understand that, when unclear, NW Africa gets the benefit of doubt for the derived origins.

Bayesian modeling in lighter news (humor)

From Saturday Morning Breakfast Cereal:

Autosomal modeling getting closer to archaeological facts by doubling effective mutation rate

Interesting try at autosomal DNA nuclear clock-o-logy. Not quite it yet but interesting nevertheless because it approximates much better what seems to be the reality, based on archaeological data, than previous attempts.

Stephan Schiffels & Richard Durbin, Inferring human population size and separation history from multiple genome sequences. Pre-published at bioRxiv, 2014. Freely accessible → LINK [doi:http://dx.doi.org/10.1101/005348]

Abstract

The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.

Based on Figure 4c:

Figure 4: Genetic Separation between population pairs
(...) (c) Comparison of the African/Non-African split with simulations of clean splits. We simulated three scenarios, at split times 50kya, 100kya and 150kya. The comparison demonstrates that the history of relative cross coalescence rate between African and Non-African ancestors is incompatible with a clean split model, and suggests it progressively decreased from beyond 150kya to approximately 50kya. (...)

This comparison reveals that no clean split can explain the inferred progressive decline of relative cross coalescence rate. In particular, the early beginning of the drop would be consistent with an initial formation of distinct populations prior to 150kya, while the late end of the decline would be consistent with a final split around 50kya. This suggests a long period of partial divergence with ongoing genetic exchange between Yoruban and Non-African ancestors that began beyond 150kya, with population structure within Africa, and lasted for over 100,000 years, with a median point around 60-80kya at which time there was still substantial genetic exchange, with half the coalescences between populations and half within (see Discussion). We also observe that the rate of genetic divergence is not uniform but can be roughly divided into two phases. First, up until about 100kya, the two populations separated more slowly, while after 100kya genetic exchange dropped faster. We note that the fact that the relative cross coalescence rate has not reached one even around 200kya (Figure 4c) may possibly be due to later admixture from archaic populations such as Neanderthals into the ancestors of CEU after their split from YRI [29].

Follows their population size estimates:

Figure 3: Population Size Inference from whole genome sequences
(a) Population size estimates from four haplotypes (two phased individuals) from each of 9 populations. The dashed line was generated from a reduced data set of only the Native American components of the MXL genomes. Estimates from two haplotypes for CEU and YRI are shown for comparison as dotted lines. (...)

A serious problem I have with this graph is that the gradual bottleneck affecting Eurasian-plus populations does not begin to recover within this simulation before c. 40 Ka. That doesn't seem good enough because by that time the Asian population must have expanded at least moderately, as they had colonized all the continent and even Australasia by that date. 

This means that there is a lot of refining still to be done to the methodology, because there should be signal of expansion in Asia much earlier than 40 Ka and not more and more apparent decrease of the population size, what is totally inconsistent with the ongoing colonization of a whole continent. 

I could try to double again the rates to get a more consistent Asian expansion age of c. 80 Ka but that should push the Eurasian-plus bottleneck to a much earlier date, 600 Ka ago, what is simply nonsensical. So the only possible conclusion is that the algorithm is far from realistic and still needs a lot of work.

Non-Bantu East Africans belong to the proto-Eurasian cluster:

Our results suggest that Maasai ancestors were well mixing with Non-African ancestors until about 80kya, much later than the YRI [Yoruba]/Non-African separation. This is consistent with a model where Maasai ancestors and Non-African ancestors formed sister groups, which together separated from West African ancestors and stayed well mixing until much closer to the actual out-of-Africa migration.

South Asians exchanged a lot with West Eurasians before Neolithic:

.... the GIH [Gujarati emigrants to Texas] ancestors remained in close contact with CEU [NW European emigrants to Utah] ancestors until about 10kya, but received some historic admixture component from East Asian populations, part of which is old enough to have occurred before the split of MXL.

Figure 4: Genetic Separation between population pairs
(...) (d) Schematic representation of population separations. Timings of splits, population separations, gene flow and bottlenecks are schematically shown along a logarithmic axis of time. (...)

Overall their population tree makes good sense, except for the apparently too recent dates for nearly all the events and very especially for the intra-Eurasian split. There are no doubt confounding factors acting here. Probably if MXL (Native American component) were excluded, the West-East split could be moved backwards in time.

They heavily rely on the MXL Native American element to calibrate the clock, what makes sense on the surface. But  the fact that Native American origins are themselves a mix of West/South Eurasian and East Asian origins may be tricking them. In the tree, MXL derives from East Asians and it actually should be, we know for a fact, intermediate between East Asia and West/South Eurasia, something that is not reflected at all and that is almost certainly altering the picture.

But, as said above, there are more corners, some quite prominent, to be polished in all the modeling process until a future version of it can be acknowledged as a reliable "clock" (emphasis on reliable, because some people put way too much faith on these rough approximations, what is clearly an error).

On mutation rates:

Our results are scaled to real times using a mutation rate of 1.25×10-8 per nucleotide per generation, as proposed recently [16] and supported by several direct mutation studies [14-16]. Using a value of 2.5×10-8 as was common previously [44, 45] would halve the times. This would bring the midpoint of the out-of-Africa separation to an uncomfortably recent 30-40kya, but more concerningly it would bring the separation of Native American ancestors (MXL) from East-Asian populations to 5-10kya, inconsistent with the paleontological record [25, 26].

In short: using the usual scholastic mutation rates would have been nonsensical. Doubling them was common sense needed to achieve minimal coherence with observed reality (how many times have I said that?) It is obviously not enough but it was something needed in any case.

13,000 years old Mexican remains confirm genetic continuity from Paleoamericans

New ancient mtDNA from an underwater cave in Yucatan confirmed that there are no obvious differences between the so-called Paleoamericans and modern Native Americans.

James C. Chatters et al., Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans. Science Magazine 2014. Pay per view → LINK [doi:10.1126/science.1252619]

Abstract

Because of differences in craniofacial morphology and dentition between the earliest American skeletons and modern Native Americans, separate origins have been postulated for them, despite genetic evidence to the contrary. We describe a near-complete human skeleton with an intact cranium and preserved DNA found with extinct fauna in a submerged cave on Mexico’s Yucatan Peninsula. This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.

The Hoyo Negro girl, whose skeleton was preserved underwater for millennia, after she apparently fell into the cave and died as consequence, belonged to haplogroup D1, one of a handful found in modern Native Americans (all them within A, B, C, D and X2). 

The radiocarbon date for the skeleton is c. 12,800 BP, while the upper limit of her death (inferred from calcite formation on the bones, dated via thermoluminiscence) is of c. 12,000 BP. 

Overall there are already four mtDNA and two Y-DNA Paleoamerican sequences from the 13-10,000 BP bracket, all of which fit perfectly with modern Native American DNA. See map to the right.

This underlines that anthropometric estimates are not really reliable to determine ancestry, at least in the long run, because there has been much speculation about these not supporting continuity between the first settlers of America (Paleoamericans) and modern Native Americans, however ancient DNA consistently supports continuity. 

One thing is the genotype and another the phenotype. And although they are somehow related for the greatest part, this relationship is not always straightforward, at least with our current knowledge.

See also: Ancient DNA from Clovis culture is Native American (also Tianyuan affinity mystery

South Asian first Neolithic and its relation with West Asia

Informative compilation of dates for West and South Asian Neolithic sites.

Kavita Kangal et al., The Near-Eastern Roots of the Neolithic in South Asia. PLoS ONE 2014. Open access → LINK [doi:10.1371/journal.pone.0095714]

Abstract

The Fertile Crescent in the Near East is one of the independent origins of the Neolithic, the source from which farming and pottery-making spread across Europe from 9,000 to 6,000 years ago at an average rate of about 1 km/yr. There is also strong evidence for causal connections between the Near-Eastern Neolithic and that further east, up to the Indus Valley. The Neolithic in South Asia has been far less explored than its European counterpart, especially in terms of absolute (¹⁴C) dating; hence, there were no previous attempts to assess quantitatively its spread in Asia. We combine the available ¹⁴C data with the archaeological evidence for early Neolithic sites in South Asia to analyze the spatio-temporal continuity of the Neolithic dispersal from the Near East through the Middle East and to the Indian subcontinent. We reveal an approximately linear dependence between the age and the geodesic distance from the Near East, suggesting a systematic (but not necessarily uniform) spread at an average speed of about 0.65 km/yr.

We must be warned that the study dwells on statistical data, mostly ¹⁴C and other archaeological dates and not in pottery typology and such. So there are probably a lot of nuances to be added to what the authors conclude. However the study is a major effort to systematize West and South Asian Neolithic dates (details in the extensive supplementary materials) and that must be acknowledged as very useful on its own.

Fig. 2 synthesizes the findings of this study:

Figure 2. A linear envelope fit to the data using the weighted dates yields the average Neolithic dispersal speed km/yr.

The filled circles (red) and triangles (magenta) show the archaeologically dated sites from Iran and the Indus valley Civilization, respectively; filled circles (black) and open triangles represent sites with multiple and single ¹⁴C dates, respectively.

[Note: Gesher is one of the earliest PPNA sites, located in Northern Palestine].

The graph is a bit misleading because there are places in South Asia with ¹⁴C dates older than the apparent 7000 BP baseline (see Appendix in the study). Ayakagytma has several dates nearing 6000 BCE (i.e. ~8000 BP), while Merhgar is dated to as early as 8520 BCE (~10,500 BP), which overlaps the oldest sites of West Asia. These oldest Neolithic sites of South Asia are hardly recognizable in the graph, as they are shown as mere dots, whose only distinction is that they are ~3000 km away from Gesher. I had to investigate the Appendix to spot them.

The Merhgar ¹⁴C date is just one but it does not seem the authors felt compelled to discard it for any reason, so it should stand in principle.

Actually, rather than explain South Asian Neolithic as West Asian derived, the data in this study only offers an interesting overview of the dates but as such demonstrates nothing. Actually, if, as they argue, we are to consider always the oldest regional date (unless unreliable), then the expansion of Neolithic to South Asia was very fast. What was rather slow was its expansion within West Asia apparently.

Said that, there are many reasons to think that there was at least an important West Asian contribution to South Asian Neolithic, if nothing else because of the important presence of several important Western Y-DNA lineages (R1a, J), which seem somehow related to Neolithic spread, as well as the so-called "ANI" component, of clear West Asian affinity. Also many crops and animals were obviously imported from West Asia.

In this regard, a reader pointed to me weeks ago to a study that claims that sheep were independently domesticated in South Asia. However I found their conclusions far fetched so I never discussed it... until now.

Sachin Singh et al., Extensive Variation and Sub-Structuring in Lineage A mtDNA in Indian Sheep: Genetic Evidence for Domestication of Sheep in India. PLoS ONE 2013. Open access → LINK [doi: 10.1371/journal.pone.0077858]

What this study did find is a very specific founder effect of sheep lineages in India. However this cannot be accepted to be caused by an independent domestication but rather looks like a founder effect after domestication, which almost certainly owes to West Asia, where the ancestors of domestic sheep lives.

Figure 3. Neighbor-joining tree of domestic sheep based on 432 bp of control region mtDNA.
(A) Neighbor-joining tree of mtDNA sequences of Indian sheep (330) along with representative samples of five lineages (▲), namely; A, B, C, D & E. Indian sheep show three lineages, namely; A, B and C. (B) Neighbor-joining tree of mtDNA sequences of the Indian (330), Chinese (129), Central Asian, Caucasian and European (406), Portuguese (161), and West Balkan (60), sheep along with representative samples of five lineages (▲), namely; A, B, C, D & E . The sequences of wild Ovis species have been used as outgroups. MEGA 5 version 5.0.1.102 was used to construct the trees using Tamura-Nei model with 10,000 bootstrap. Numbers above a given branch represent bootstrap support for the branch as a percentage out of 10,000 re samplings.

Notice please how the root of the tree is at the bottom, where the various wild species of sheep are listed by their names. So the dominance of lineage A in South Asia surely owes to a founder effect and not local domestication.

Siberian genetics with focus on Yakutia

Informative study on the populations of Sakha Republic (Yakutia) and Siberia in general:

Sardana A. Fedorova et al., Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia. BMC Evolutionary Biology 2014. Open access → LINK [doi:10.1186/1471-2148-13-127]

Abstract

Background

Sakha – an area connecting South and Northeast Siberia – is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia.

Results

We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia.

Conclusions

Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.

The matrilineal mitochondrial DNA pool is dominated by  C4, C5, D4 and D5, with some instances of other lineages (see fig. 1). All these and most of the rest are common Siberian lineages of East Asian roots. 

In the odd zone, the extremely rare haplogroup R3 has been found among North Yuhaghirs in this study (previously only in Jordan that I know with any certainty). They mention that R3 and R1 are derived from the same root, sharing two coding region mutations, and therefore they proceed to rename R3 as R1b. R1 is an also rare Indian matrilineage. 

The patrilineal Y-DNA pool (see fig. 2) is massively dominated by N1c, which also dominates most Uralic-speaking peoples. This is unusual for a Turkic-speaking population but it was known since long ago. Other still important lineages are C2 (former C3, typical of NE Asia and some North American populations), N1b and R1a. Some instances of I, E1b1b1, J, O, F and L are also reported. C2 is more important among the Northern (non-Turkic) populations of Sakha Republic, reaching to 30-40%.

On the autosomal DNA pool, the heatmat (fig. 4) shows that among all sampled populations the Selkup are particularly isolated. Koryaks and Chukchis from the far NE Siberia form a small cluster of their own and so do Shors and Kets (West Siberians). Native American populations also show great individual isolation in comparison with most Eurasians.

Otherwise there are three major clusters: West/South/Central Eurasians, East Asians and Siberians, who generally also cluster with East Asians.

Some of this is also apparent in the PCA (fig. 5) although not as neatly:

PCA of the native populations of Sakha in the context of other Eurasian and American populations.

Maybe more illustrative is the ADMIXTURE analysis:

ADMIXTURE plots. Ancestry proportions of the 758 individuals studied (from 55 populations) as revealed by the ADMIXTURE software at K = 3, K = 4, K = 6, K = 8, and K = 13.

The analysis reveals, from K=6 upwards, the following clusters: West Eurasian (dark blue), South Asian (green), East Asian (orange, also light green at K=13) and several Siberian and Native American specific clusters (yellow, light and dark brown, red, etc.)

The persistance of the blue West Eurasian component in Aleutians and Greenlanders should raise some eyebrows. However, Greenlanders do not really cluster with West Eurasians in the heatmap, so this is almost certainly an artifact that indicates that a much greater K-depth should be achieved in order to properly classify this most diverse human sample. Thirteen clusters are obviously not enough.

Oldest Cappadocian Neolithic site changed swiftly from hunting to herding

Reconstructed home entrance
(credit: Kvaekstad)

Aşıklı Höyük (Aksaray province) is the oldest known Cappadocian Neolithic site, located to the Northeast of the famous Çatalhöyük.

The site was inhabited since c. 9000 BCE, having a diet based on varied wild meat sources. But c. 8200 BCE the meat became almost exclusively that of sheep and goats, whose remains increased around this date from less than 50% (presumably wild) to around 90% of all meat sources, indicating that the community had become dependent on them, almost certainly because of transition to herding.

Not just that, young male sheep and goats make up the bulk of those remains, indicating the typical lamb culling proper of agricultural economies. Also analysis of the archaeo-dung indicates that the animals were kept captive in the settlement itself.

Altogether, these findings suggest the people in this area shifted from hunting to herding in just a few centuries.

Importantly, everything suggests that there was no immigration to the area: just a local change of economic paradigm. The homes were built just in exactly the same fashion as the previous ones, using their remains as foundations (typical of "tells", artificial hills formed by this long term continuity in habitation).

It is unclear from the source if they were involved in farming yet but it seems apparent that it was sedentarism what caused the economic change.

I find notable and needed to be mentioned that the life expectancy of men and women in Aşıklı Höyük was extremely unequal, with the latter dying often in their early 20s and showing signs of hard work, while the former generally survived to their 50s. Class inequality have also been proposed, considering the relative lack of burials compared to expected population size - however this last is controversial.

Sources: Live Science, Wikipedia.

Bell Beaker: very interesting e-book

Michael points me to this very interesting compilation of articles freely available to read online (or to purchase as PDF for a small amount, or even as true book) dealing with the complexities of the Bell Beaker phenomenon in Europe. The articles are mostly in English and French, although there is also one in German.

Several authors, Similar but Different. Bell Beakers in Europe. Edited by Janus Czebrezsuk. Sidestone Press 2014 → LINK

It would be quite worthless that I would try to make any synthesis of such an extensive and plural work on such a complex and hotly debated topic. But I must say that I find most interesting the attempts to describe the regional differences of this phenomenon and very especially the fact that, West of the Rhine and North Sea and South of the Alps, the phenomenon is always found inside previously existing cultural contexts, often as minority element. Therefore the pre-existing division between collective burials' Europe (Megalithic mostly) and single burials' one (Kurgans in essence) stands for most of the timeline and geographic extent of this cultural phenomenon, which no doubt highlights the increased European interactivity of the Late Chalcolithic. 

Hence it is important to establish the regional structure (not strict but notable anyhow) of the Bell Beaker phenomenon and that is indeed addressed by several of the articles. For example, Marc M. Vander Linen proposes the following five regions:

Of these only the Eastern region is single burial senso stricto, all the rest retaining their ancestral practices, which were collective burial in most cases (although this changes gradually in some areas as time passes until the "funerary collectivism" eventually vanishes as the Bronze Age hits in). 

In this map by Marie Besse of the so-called "common ware" (no or very little decorated beakers and similar pots, specific of continental Europe) we can also see much of the collective/single burial dichotomy.

Anyhow, notice that, with limited exceptions, bell beakers are not dominant in most regions and that most burials lack them. One of the main exceptions is Portuguese Estremadura, where beakers are found almost in every burial. However in nearby Alentejo, more rural and much less cosmopolitan, the opposite is true.

Enjoy the read.

North African and West Asian affinity in Europe

Ryan mentioned this rather interesting study from a year ago on IBD trans-Mediterranean affinities of Europeans.

Laura R. Botigué et al., Gene flow from North Africa contributes to differential human genetic diversity in southern Europe. PNAS 2013. Freely accessible by now → LINK [doi:10.1073/pnas.1306223110]

Abstract

Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.

The most interesting section is surely the one titled Long identical-by-descent haplotypes. Here the authors use long IBD readings to estimate "recent" genetic flows. However they cannot discern the direction of these flows, i.e. flows from Europe to West Asia and North Africa will look exactly the same as the reverse ones.

From fig. 2:
Haplotype-based estimates of genetic sharing between Europe and Africa show a significant latitudinal gradient where the highest sharing is in the Iberian Peninsula. Genetic sharing between geographic regions is represented as a density map of WEA estimates for 30 European populations where haplotypes are IBD with (A) Sub-Saharan Africa [not shown here, as it is comparatively very small and clearly related to the other clines], (B) North Africa and (C) the Near East. The Canary Islands are shown in the Lower Left. (...)

It seems obvious that North African affinity is concentrated in Iberia, especially in the Western half, what is consistent with previous data, and that West Asian affinity is concentrated in SE Europe. The Iberian extension of this one may be partly related to North African affinity (or not), as North Africans also have some clear West Asian affinity (as should be apparent from the Canarian inset).

I insist that directionality of this affinity is not clear. In the case of West Asian one, it seems plausible that most of it is caused by Neolithic inflows into Europe but in the case of the North African affinity cline, it probably represents bidirectional flows, because previous mtDNA and autosomal data show also quite apparent Iberian influx into North Africa, although the reverse flow is also real.

I find interesting the low levels of West Asian IBD affinity among Basques when compared with estimates of ancestry by early European farmers (EEF, partly West Asian themselves). In the map above Basques score just like other Atlantic populations in this element, yet in the Lazaridis study (see also here and here), Basques score quite high in EEF ancestry, much like the French, which in this graph are clearly higher in "recent" West Asian affinity. That makes me suspect that confounding factors may be at play and reinforces the notion of taking autosomal DNA statistical analyses with some care and try to contrast different approaches before reaching to conclusions.

Also interesting is fig. 3, which pinpoints the specific North African (or Arabian) regions which may show the strongest IBD affinities for the various European regions:

Fig. 3.

Population-specific estimates of haplotype sharing (in centimorgans) between North Africa and Europe. Estimates of W_EA (scaled by 100 for ease of presentation) between each European population (x axis) and each North African population and the Qatari are represented by colors and symbols. A substantial increase in haplotype sharing is detected between southwestern European populations and Maghrebi populations in comparison with the remainder of the European continent. The excess of sharing between the Near East and southern central and Eastern Europe is also noteworthy.

As expected,  NW Africa is the most common source-or-destination of Iberian long IBD affinities, instead Qatar or Egypt are most outstanding regarding Italy and SE Europe, what underlines that (North) African genetics in Europe arrived mostly via West Asia (Neolithic), with the notorious Iberian exception.

I just found my very old first Prehistory site as a Samoa hack

Yesterday I happened to run a simple quick test about how well this blog performs in Google ratings, so I made a search on "Chalcolithic Europe" (the kind of thing that I know brings up images from FWTWWA) with the result that this blog gave one hit among the top 10 in regular text search, and more than 30 hits in image search in the first page (including the first two ones, which come from the European aDNA page). 

This is the map that surprised me to find still around: Middle Bronze Age Europe/West Asia, c. 1500 BCE (not too exact in some details maybe? - well, still good enough).

 

Also many maps I did in the past for Wikipedia still rank high as well. 

That was cool to find out. But what really surprised me was to find my long gone GeoCities (former Yahoo! free hosting service) website online (→ LINK) and also ranking rather high in image search (for those words) because of one of my old maps. The site has not been available for many years because Yahoo! suspended its free hosting service but someone is making money out of my work with that site that is exactly how I left it, except for flashing publicity ads (oddly enough when Yahoo! managed the ads, which only they gained revenue from, not me, they were always empty boxes, very tellingly about this company's poor skill at marketing). 

The site can be found under its original GeoCities address except that it has the .ws extension instead of the .com one it used to have. Looking at this extension in Wikipedia, I learned that it means Samoa (West Samoa) and that:

The .ws country code has been marketed as a domain hack, with the .ws purportedly standing for "World Site" or "Web site", providing a "global" Internet presence to registrants, as it supports all internationalized domain names.

So some smart guy has hacked my old site (and probably many others) and is making money of its discrete appeal. 

At least in the "European Chalcolithic" search, the star is obviously the article about Atlantis, which attempted to interpret this legend, as well as the quite comparable Heraklean ones, in the context of the Bronze Mediterranean (in terms that I still consider perfectly valid). But there are also other interesting pages: a series of maps on Indoeuropean expansion, an incomplete Neolithic Europe map series (some of which were uploaded to Wikipedia back in the day but followed random fates afterwards), and an old self-made double map of European mtDNA haplogroups based on Simoni 2000 (yeah, that's quite old, but in those times, say 2007, info on mtDNA was scarce and scattered).

So what I'm going to do? Copy much of that in my PC and probably repost the best of it here in dedicated pages. It'd be totally hopeless to try to get the hacker to pay me a commission for his/her publicity earnings, more so when most of the material is explicitly donated to the public domain, and, in a sense, I feel even grateful for the chaotic effects of this hacking that has brought my old work back to the Web, although I lament I cannot edit the site anymore. 

For whoever reads the site, please notice that most of that stuff is from around 2007. Although paid GeoCities still exists, the free hosting service was discontinued in 2009, and that was the time when all my work went down the toilet (I made a backup but it got eventually lost in an irreparable computer crash), until now. Long live Chaos!

Ancient Thracians, Ötzi and the origins of modern Europeans (another point of view)

A recent study has sequenced the DNA of an ancient Thracian woman but, for some reason, instead of looking at her comparison with modern Bulgarians and such, they have written a study that mostly goes about Ötzi "the iceman" and has not a single Bulgarian sample.

Martin Sikora et al., Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe. PLoS Genetics 2014. Open access → LINK [doi:10.1371/journal.pgen.1004353]

Abstract

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.

Notice please that, as the authors acknowledge, the DNA of the second Thracian individual, K8 may be contaminated:

the DNA damage pattern of this individual does not appear to be typical of ancient samples (Table S4 in [15]), indicating a potentially higher level of modern DNA contamination.

This does not seem to dissuade them to use it in the analyses.

Figure 1. Geographic origin of ancient samples and ADMIXTURE results.
(A) Map of Europe indicating the discovery sites for each of the ancient samples used in this study. (B) Ancestral population clusters inferred using ADMIXTURE on the HGDP dataset, for k = 6 ancestral clusters. The width of the bars of the ancient samples was increased to aid visualization.

Notice that, instead of attempting to model moderns on ancients, as would seem logical from the viewpoint of purported ancestry but would be incomplete for lack of a sufficiently large ancient sample or allow the ancient samples to "float freely" in the analysis, the researchers decided to force them into modern parameters what is still valid, because it indicates greater or lesser affinity to the various studied modern populations (among which there's not a single Balcanic sample, oddly enough). 

We can see that:

• Epipaleolithic Iberian Braña 1 approximates the French structure but is somewhat "more Basque" than these. 
• Neolithic Pitted Ware semi-forager Ajv70 (Gotland) approximates the Orcadians very well.
• Neolithic Megalithic/Funnelbeaker Gok4 (Southern Sweden) approximates North Italians. 
• Chalcolithic North Italian Ötzi (Iceman) is close to Sardinians but not quite the same ("more Basque" again).
• Iron Age Thracian commoner P 192-1 approximates Tuscans.
• I would ignore princely Thracian K8 because of the aforementioned contamination issues.

For completeness, I'm including here also fig. S1, which includes runs 1-8 of ADMIXTURE:

Fig S1- ADMIXTURE results for HGDP. Panels show the results for ADMIXTURE runs for k = 2 to k = 8 ancestral clusters on the HGDP individuals, and the corresponding cluster proportions inferred for the ancient samples.

Notice (see fig. S7) that K=3-5 are quite poor fits and therefore both should be ignored as meaningless. From K=6 onwards the scores slightly improve for all the ancient samples, however it must be said that K=2 is in general the best fit form most European populations, being most of the improvement in error score due to better approximation to West Asian samples. 

In most cases Basques have the lowest or one of the lowest fitness scores (except at K=5, where Basques are portrayed as a Russian-Sardinian mix, what is clearly a confounding artifact). Sardinians also have very low error scores but only from K=5 onwards, when the Sardinian component becomes apparent. The Iceman has very low error scores for all K values, while the Thracian samples have the greater ones, maybe owing to the lack of Balcanic samples.

For me these error results suggest that ancients are fine being just "unspecific Europeans" (K=2 blue), while the low error score for Basques and Sardinians surely underline that these are about the only modern populations which can be explained as simple Paleolithic-Neolithic mix, without need of a third Indoeuropean extra ancestry.

They also projected the ancient samples onto PCA plots of modern European populations:

Fig S2 - PCA results for HGDP. Panels show the results for PCA on the HGDP individuals for subsets of SNPs with data in the respective ancient sample. Each point represents an individual, with plot symbol and color indicating population of origin. The position of the ancient samples was inferred by projecting onto the PC space calculated using the modern samples only.

For some odd reason the PCAs are different in each case, even if the samples are the same (only moderns used, ancients are "projected" and should not affect the result). I have no explanation for this issue and I reckon I'm tempted to write to the authors asking for this unexpected complexity, which seems product of the projection itself altering the graph.

Whatever the case, the projection of the ancient samples, follows in general terms the patterns noted above for the ADMIXTURE graph:

• La Braña 1 projects between French and Basques.
• Ajv70 projects onto Orcadians, tending also towards France.
• Ötzi projects between Sardinians and Italians.
• Gok 4 with North Italians but not far from Basques.
• P 192-1 doesn't seem too akin to any specific modern population, although some French, Basques and Tuscans do approximate her.

These results may be frustrating for those already too accustomed to the previous analysis of ancient autosomal DNA but we must not forget that, because of its huge size and complexity, autosomal DNA requires statistical analysis, which is highly susceptible to variations in sample strategy particularly, as well as to other not always well understood factors. Hence different points of view are generally complementary rather that outright contradictory.

Of some interest is also this TreeMix graph of modern populations and Ötzi:

Figure 3. Results of TreeMix analysis of the Iceman with 1000G/Sardinia.
Shown are maximum-likelihood trees and the matrices of pairwise residuals (inset) for a model allowing (A) m = 0 and (B) m = 3 mixture events. Large positive values in the residual matrix indicate a poor fit for the respective pair of populations. Edges representing mixture events are colored according to weight of the inferred edge.

It is notable the African low level admixture arrow at the root of the Euro-Mediterranean branch (the so-called "Basal Eurasian" element in Lazaridis 2013) and the East Asian component in Finns. Also sizable admixture from the West Eurasian root is apparent among Tuscans. Once these admixture axes are allowed for, the topology of the European tree changes significantly, showing a main split between Eastern Europeans (Finns) and Western/Southern ones.

Other similar trees are available in fig. S6.

No extra Neanderthal admixture in Ötzi

Contrary to some previous rough estimates, Ötzi does not appear to differ from other Europeans in Neanderthal ancestry at all. See figs. S9 and S10.

Moravian Bell Beaker in context

Bell Beaker Blogger mentions this week a lecture presentation on the Hostice I burial site of Moravia which I find quite interesting because it helps to contextualize the Bell Beaker phenomenon of that area.

Matějíčková, A. - Dvořák, P. 2014: Bell Beaker Culture in Moravia: 30 questions, 30 answers, 30 pieces of evidence. Based on the burial ground Hoštice-I. Beaker Days on Danube 2014. Bratislava and Vienna. (Lecture) → available at academia.edu

It's quite worth taking a look but, besides that, what I did was to create a synthetic map of the wider Eastern or Danubian Bell Beaker "province" and its relations with the other "provinces" of this cultural phenomenon of the Late Chalcolithic which I want to share here:

Red shaded area: Eastern or Danubian BB region per the main source
Slash lines: approx. extension of other Bell Beaker regions
Arrows: material relationships of Hostice I with regions other than the Danubian one (amber excepted)
Orange stars: sources of amber found in Hostice I
Black stars: main urban centers with Bell Beaker
Grey star: Amesbury/Stonehenge (non-urban center)

As reference for the wider context I used (mostly) the following "tutorial" source: Bell beakers from west to east (CONSEQUENCES OF AGRICULTURE, 5000-2000 B.C.)

Portuguese hemp strings: oldest evidence of the plant in Europe

Hemp has been widely used through history both for its great versatility: recreational drug, medicine, raw material for strings, cloth, paper and a lot of other uses. It is believed that the plant was first domesticated in China, maybe Taiwan, and its use in East Asia is widely documented. However there is only limited evidence on when it reached Europe, even if it was clearly known in Antiquity. 

The finding of hemp strings attached to a Palmela point and preserved thanks to the oxidization of copper (which is toxic) represents the oldest safe evidence for its use in Europe, dating to the Chalcolithic period ("last quarter of the 3rd millennium BC").

This amazing discovery took place at the Bela Vista 5 enclosure. A formal study is expected to be published soon. 

Source: Portuguese Prehistoric Enclosures.

Fig. 2.A. The three sizes of Palmela points.

Update (May 6): Bell Beaker Blogger points me to a most interesting experimental study (Carmen Gutiérrez Saez et al. 2010, in Spanish, freely accessible), where it is demonstrated that copper Palmela points were very effective as arrow points when properly forged (no recooking) and installed in the shaft (to 1/3 of the blade), at the very least the small and medium sizes. Smaller sizes were better for long distance shooting, whole larger ones for short distance damage (ensuring the kill).

He also mentions that the hemp would have made an excellent string for these bows, which were, based on prehistoric evidence, true longbows.

Palmela points were used together with flint ones, usually lighter, what is at the origin of the doubts on their effectiveness.

Amesbury has Epipaleolithic roots

Old map of Avesbury and the nearby hillfort

Recent field work at the town of Amesbury, specifically in Blink Meadow, has resulted in it being proclaimed in the media as "the oldest town in Britain". What it really means is that the site was occupied and had ritual significance before the Neolithic, since c. 8820 BP.

A possible reason for the magnetism of this location is that a nearby spring has the "magical" effect of turning some types of flint to a bright pink or fuchsia color. This is caused by certain algae but it must have appeared miraculous to ancient peoples. 

The district now proclaimed oldest continuously inhabited town in Britain has a large complex of ritual sites dating to the Chalcolithic period ("Neolithic" in British archaeo-slang).

It also includes a large Iron Age hillfort of unusual shape, inadequately named as "Vespasian's Camp". This fort which continued in use in the Roman period is suspected by many to be the real Camelot.

Pink colored flint pieces from Amesbury

Sources and more details: The Archaeology News Network, Express.

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