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:

P { margin-bottom: 0.08in; direction: ltr; color: rgb(0, 0, 0); widows: 2; orphans: 2; }P.western { font-family: “Times New Roman”,serif; font-size: 10pt; }P.cjk { font-family: “Times New Roman”,serif; font-size: 10pt; }P.ctl { font-family: “Times New Roman”,serif; font-size: 10pt; }

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

 

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

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

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

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

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

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

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

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

References:

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

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

See also: Were the Etruscans after all Native Italians?

 

Linguist Jürgen Untermann has died

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

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

 

Were the Etruscans after all native Italians?

Etruscan sarcophagus (CC by Ecelan)

A new study casts doubt on the Anatolian origin theory of Etruscan origins.

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

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

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

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

Abstract

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

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

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

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

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

Among the study’s conclusions are:

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

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

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

Villanovan urn (CC by Sailko)

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

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

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

 

Genetic isolates from Friuli

Just a quick mention of this paper on selected rare populations of Friuli because I totally fail to see the angle of interest in this paper, yet, together with other data may be of interest for European population genetics… potentially.

Tõnu Esko et al., Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity. European Journal of Human Genertics, 2012. Open access → LINK [doi: 10.1038/ejhg.2012.229]

Abstract


Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country’s complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145 000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate.

Fig. 2 Model-based mapping convergence with SPA. Label position indicates the (a) specific PC1 and PC2 coordinate values for each individual and (b) the mean PC1 and PC2 coordinate values for each population. For (a, b), the colors have a following meaning: (1) dark blue color: a homogeneous fraction of the FVG population; a blue color: more general fraction of the FVG population; a red color: other Italian samples; a violet color: Basques; an orange color: Slovenians; and green color: all other populations. For (a, b), the following population abbreviation labels are used: AT, Austrians; BA, French Basques; BG, Bulgarians; BO, Borbera; CA, Carlantino; CL, Clauzetto; CH, Swiss; CZ, Czechs; GR, Germans; ER, Erto; ES, Spaniards; FR, French; HU, Hungarians; IL, Illegio; IT, Italians; JW_A, Ashkenazy Jews; JW_S, Sephardic Jews; OR, Orcadians; RE, Resia; RO, Romanians; SA, Sardinians; SA_, Sauris; SMC, San Martino del Carso; SI, Slovenians; TU, Tuscans. The extra abbreviations: N, northern; S, southern; I, a more homogeneous sub-population; G, a more general sub-population.

 

Italian haploid genetics (messy paper)

This study is rather chaotic and poorly presented with potentially interesting but very confusingly reported data Italian paternal and maternal lineages, after we wade through the hyper-obsolete and sometimes sloppy nomenclature they use and the many bugs in the presentation of the data.

Their attempt to say anything of the autosomal genetics is rather useless, confusing and pointless however and will not be discussed here.

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

Abstract

Background

According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country.

Methods/Principal Findings

A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers.

Conclusions/Significance

Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.

As the data is so poorly presented, I decided to rework it all myself. This is the mtDNA map (made recycling figs. 1 and 4 on a map of Italy):

Italian mtDNA – on Brisighella 2012 – click to expand

We can see that the apportions of haplogroups are generally in agreement with what we can find in Western Europe, showing some minor but evident differences in the South: high frequency of J, more T and X than in the North and Center, less W, H and V, presence of rare lineages in the N* and M* categories.

However warning must be made that the Northern and Central pie charts are so exactly identical that it looks like an error was made (and either one was copied twice). I don’t have time right now to research this so obvious error, checking the supp. material and what not, but be warned that there is a bug (this bug is reproduced here from fig. 1 as-it-is).

Southern highlight populations (Salentine Greeks and Lucerans, a town where Sicilian Muslims where deported to in the Middle Ages) appear to be very similar to Southern Italians in general. Instead the Ladins appear to retain a more Paleolithic-looking mtDNA pool, dominated by H, U and V. However notice that K (often considered a Neolithic haplogroup) is not mentioned separately from its parent U.

I did the same with Y-DNA, however here the difficulty is in the horribly chosen nomenclature:

Italian Y-DNA – on Brisighella 2012 – click to expand

Before you jump to any conclusion from the map above, you must note that the haplogroups are all poorly described. I checked ISOGG present day nomenclature and annotated fig. 3 (in grey) so we can get a more clear idea of what they are trying to describe:

Fig. 3 of Brisighella 2012 Phylogeny of Y-chromosome SNPs and haplogroup frequencies in different Italian populations. (annotated by Maju) – click to expand –

Notice also apparent inconsistencies on the labeling, notably how R1* becomes R1b3 (sic) among Ladins, Lucerans and Salentine Greeks.

In truth it’s very difficult to get anything straight from this paper because there is such sloppiness in the presentation of the data that we can only end with a headache and greater confusion than when we started. 

Therefore I must renounce to make any attempt of analysis, sadly enough.

 

Epipaleolithic Sicilian had mtDNA haplogroup HV1

Besides sequencing this individual’s ancient DNA, the study focuses on discerning the earliest stable occupation of the island and the diet of its inhabitants.

Marcellino A. Manino et al., Origin and Diet of the Prehistoric Hunter-Gatherers on the Mediterranean Island of Favignana (Ègadi Islands, Sicily). PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0049802]

The authors argue that this occupation of Sicily could be the oldest stable one and that it happened because of the formation of a land bridge because of low sea levels soon after the Last Glacial Maximum (but actual bathymetries hardly support such land bridge, so soon after the LGM they needed boats again to cross the dangerous Strait of Messina). However some Aurignacian artifacts are known and believed to be of older chronology. 

They also argue that, based on the N/C isotopic ratios, these peoples had a mostly carnivore land-based diet. This leaves me quite perplex because the Nitrogen-15 values are much higher than those of foxes (a mostly carnivore animal) and that is usually considered a signature of feeding off sea mammals. 

Figure 3. Carbon and nitrogen isotope composition of bone collagen from Mesolithic humans and fauna of Grotta d’Oriente.

See also: Magdalenians did eat sea mammals (at my old discontinued blog Leherensuge).