Morphological and mtDNA analysis of Mezzena mandible

 

I've written about late Neandertals becoming more AMH-like, and a new study on an Italian specimen that postdates the arrival of AMH in Europe lends some further support to that idea.
The Mezzena jaw has Neandertal mtDNA and shares a number of morphological traits with other Neandertals, but its overall shape places it within the cluster of modern humans  (triangles; figure on the left). Notice also that Qafzeh 9 (Q9) and Shkul V (SV) are also within the cluster of modern humans, and Spy 1 (a Neandertal) is actually closer to modern humans than to other Neandertals.
From the paper:

The position on the scatter plot of our specimen of interest, Mezzena, has been calculated a posteriori. Unsurprisingly, the Mezzena mandible does not present any particular affinities with mid-Pleistocene specimens. It is most similar to AMHs being positioned within the H. sapiens cloud of points and the DFA classifies the specimen with modern humans (Table S7). Especially its shape is similar to that of Ohalo II and to a lesser extent to the recent modern human specimen China5. However, it should be noted that its position also indicates affinities with some Neanderthal specimens: the late Neanderthal Spy 1 and Saint-Césaire, the Near-East specimens Tabūn II and Amud 1, and to a lesser extent the classic Neanderthals La Ferrassie 1 and Guattari III (Figure 2).

According to the authors:

In this light, we can interpret the position of the Mezzena mandible which stands within the modern human shape space, while presenting strong shape similarities with some Neanderthal specimens. Such a conflicting taxonomical position is not surprising, considering the geological age of the mandible [30]. Indeed, numerous late Neanderthals such as Spy 1, Saint Césaire and the Near-East mandibles Amud 1 and Tabun II possess hints of a chin (i.e. tuber symphyseo) though not a true modern human morphology [37], [51]. Late Neanderthals lived in area where AMHs might have been already present [2], [23], [52], while the Levantine fossils are displaying a less derived Neanderthal morphology [35], [36]. 

Therefore, in our view, this change in morphology of the mandibular chin among the fossils of Mezzena and other late Neanderthals could have been the result of a small degree of interbreeding with AMHs.

It would be interesting to sequence Mezzena to confirm the existence of AMH admixture.
PLoS ONE 8(3): e59781. doi:10.1371/journal.pone.0059781
Possible Interbreeding in Late Italian Neanderthals? New Data from the Mezzena Jaw (Monti Lessini, Verona, Italy)
Silvana Condemi et al.
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.
Link

Revised timescale of human mtDNA evolution (Fu et al. 2013)

 

An important new paper has just appeared in Current Biology. It is very exciting for a couple of reasons:

• The paper uses the idea of branch shortening to infer dates for the mtDNA phylogeny. Briefly, if one counts differences between a present-day sample P and an ancient sample A, one can get a sense of when their most recent common ancestor X, lived. But PX and PA are not equal: PA is shorter, because A has "missed" a few thousand years of evolution (depending on its age). If we know the age of A (and this can be reliably known by direct dating for many samples), then we can infer the time of X.

Looking at the ages of many haplogroups, I don't see any that immediately strike me as inconsistent with recent published age estimates based on modern mtDNA alone, such as those from the Copernican reassessment paper. In any case, this is an exciting new application of an idea that will yield good dates for haplogroup ages in the future. For example, it could be used to date Y-chromosome lineages as well, when high-quality sequences of ancient human Y-chromosomes become available.

• The paper also presents a number of new and exciting ancient DNA samples:

Please note that the "Cro Magnon" sample is actually revealed to be non-ancient in the study; that is another utility of the "branch shortening" idea, since it can demonstrate that purported very old samples are in fact fairly recent.
Note the important new samples from Dolni Vestonice, Oberkassel, Continenza, all of which are Paleolithic Europeans and all of which belong, without exception to subgroups of haplogroup U. It appears that Europe was indeed dominated by this haplogroup down to Mesolithic times, with a sharp discontinuity with early Neolithic Europeans.
The only outlier in the European context is Paglicci Str. 4b which is assigned to haplogroup H1. However:

Using this criterion, we excluded Paglicci Str. 4b from further analysis as the rate of C to T misincorporation at the 50 end was only 8.8%, thus making an ancient origin for the DNA in this sample uncertain [14].

Personally, I doubt there was any mtDNA haplogroup H in pre-Neolithic Europe, as the first author of this paper has also argued for in a previous one.
There is also a new sample from Boshan; it is probably too early to detect a pattern, but it is nonetheless noteworthy that it also belonged to mtDNA haplogroup B like the much earlier sample from Tianyuan.
Finally, the paper also discusses the issue of the mutation rate, noting that the divergence between Eurasian (M+N) and African (L3) mtDNA is much later than that inferred for autosomal DNA using new and "slow" de novo autosomal mutation rates. In my opinion there are two possible interpretations for this: one that there's something wrong with the slow rates, while another is that the earlier divergence using autosomal DNA may be a consequence of inflation due to admixture events in Africa.
Current Biology doi:10.1016/j.cub.2013.02.044
A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes
Qiaomei Fu et al.
Summary
Background
Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought.
Results
Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62–95 kya.
Conclusions
Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population divergence times, they can provide valid upper bounds. Our results exclude most of the older dates for African and non-African population divergences recently suggested by de novo mutation rate estimates in the nuclear genome.
Link

Etruscan mtDNA origins (Ghirotto et al. 2013)

Etruscan mtDNA origins (Ghirotto et al. 2013)

From the paper:

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.

and:

As for the second question, the IM analysis shows that indeed there might have been a genealogical link between modern Tuscans and the inhabitants of what Herodotus considered the Etruscans’ homeland, Western Anatolia. However, even under the unrealistic assumption of complete reciprocal isolation for millennia, the likely separation of the Tuscan and Anatolian gene pools must be placed long before the onset of the Etruscan culture, at least in Neolithic times; if isolation was incomplete, the estimated separation must be placed further back in time. Consistent with this view is the observation that Etruscan and Neolithic mtDNAs are close to each other in the two-dimensional plot of Figure S4C; however, a formal test would be necessary to draw firm conclusions from the simple observation of a genetic similarity. Separation times were very close when estimated both using a sample from Western Anatolia, and an expanded sample including individuals from much of Anatolia, and so the choice of the Anatolian population does not seem to affect the results of this analysis.

As always with estimates in years, the choice of mutation rate may affect results, but I am reasonably confident that this particular result does not depend on such issues. From the paper:

For these tests we chose the mutation rate (μ) estimated from the data in the previous ABC analyses (very close to the figure accounting for the time-dependency of the mitochondrial molecular clock [13], μ = 0.003). Tests were also run using the value incorporating a correction for the effects of purifying selection [23] (μ = 0.0014), always finding that it results in a further increase of the estimated separation times (Figure S7B). Only assuming very high mutation rates, at least twice as large as estimated in Henn et al. [13], was it possible to obtain separation times less than 5,000 years (Figure S7B). With both Anatolian samples, any degree of gene flow after separation between the ancestors of Tuscans and Anatolians resulted in more remote separation times.

A couple of observations:

If Etruscans did originate in Anatolia then presumably the historical Etruscans were not descended entirely from them but from a mixture of pre-Etruscans with the incoming population. So, it would seem that the inferred dates are incompatible with a folk migration model of Etruscan origins, but not necessarily with a model that accommodates admixture (e.g., initial mtDNA gene pool separation c. 8,000 years ago with the onset of the Neolithic + later admixture during the Bronze Age). On the other hand, the close similarity between Etruscan and Central European Neolithic mtDNA is a good argument for (mostly) continuity in this case.

That things did happen in Italy in the last 5,000 years can be inferred on the basis of the Iceman's genome. It will certainly be interesting to extract Y chromosomes and/or autosomal DNA from some of these Etruscan samples.

A different issue that may bias dates upwards is the occurrence of East Eurasian mtDNA in current Anatolian Turks. It is not clear by how much this would affect age estimates (this admixture is low, sub-10%, but from a population that split off from West Eurasians perhaps more than 40kya); it would nonetheless be useful to repeat the experiment after either (i) purging the Anatolian sample of lineages likely to have introgressed into the population in medieval times, or (ii) using a different West Asian sample other than that of Anatolian Turks.

In any case, it's great to finally have the genetic characterization of a historical European people, and hopefully more samples will follow both from Italy (at least from those who practiced inhumation) and elsewhere.

PLoS ONE 8(2): e55519. doi:10.1371/journal.pone.0055519

Origins and Evolution of the Etruscans’ mtDNA

Silvia Ghirotto et al.

The Etruscan culture is documented in Central Italy (current Tuscany and Northern Latium, formerly known as Etruria) between the 8th and the 1st century BC. Questions about the Etruscans’ origins and fate have been around for millennia. Herodotus and Livy regarded them as immigrants, respectively from Lydia, i.e. Western Anatolia, or from North of the Alps, whereas for Dionysius of Halicarnassus they were an autochthonous population [1]. Previous DNA studies, far from settling the issue, have raised further questions. The Etruscans’ mitochondrial DNAs (mtDNAs) appear similar, but seldom identical, to those currently observed in Tuscany [2], [3]. Assuming reasonable effects of genetic drift and mutation, these levels of resemblance proved incompatible with the notion that modern Tuscans are descended from Etruscan ancestors [4], [5]. Explanations for this result include the (extreme) possibility that the Etruscans became extinct, but also that their modern descendants are few and geographically dispersed, or that the ancient sample studied represents a small social elite rather than the entire population [4]. As for the Etruscans’ origins, ancient DNA is of little use, because pre-Etruscan dwellers of Central Italy, of the Villanovan culture, cremated their dead [1], and hence their genetic features are unknown. DNAs from modern humans and cattle in Tuscany show affinities with Near Eastern DNAs, which was interpreted as supporting Herodotus’ narrative [2], [6], but in these studies modern Tuscans were assumed to be descended from Etruscan ancestors, in contrast with ancient DNA evidence [5]. The claim that systematic errors in the Etruscan DNA sequences led to flawed genealogical inference [2], [7] is not supported by careful reanalysis of the data [8].

Link

Aztec conquest of Xaltocan led to population replacement

Aztec conquest of Xaltocan led to population replacement

This study represents a good example of how ancient DNA analysis can supplement traditional archaeology. Issues of population replacement/continuity are often encountered in archaeology, especially when there are traditions of conquest/resettlement, or such events might be hypothesized by changes in the material record.

But, such events are often difficult to interpret, because people living through periods of turmoil might have a tendency to exaggerate their importance, while culture is malleable and may shift without large-scale population replacement.

Am J Phys Anthropol DOI: 10.1002/ajpa.22152

The Genetic Impact of Aztec Imperialism: Ancient Mitochondrial DNA Evidence From Xaltocan, Mexico 

Jaime Mata-Mıguez et al.

In AD 1428, the city-states of Tenochtitlan, Texcoco, and Tlacopan formed the Triple Alliance, laying the foundations of the Aztec empire. Although it is well documented that the Aztecs annexed numerous polities in the Basin of Mexico over the following years, the demographic consequences of this expansion remain unclear. At the city-state capital of Xaltocan, 16th century documents suggest that the site's conquest and subsequent incorporation into the Aztec empire led to a replacement of the original Otomí population, whereas archaeological evidence suggests that some of the original population may have remained at the town under Aztec rule. To help address questions about Xaltocan's demographic history during this period, we analyzed ancient DNA from 25 individuals recovered from three houses rebuilt over time and occupied between AD 1240 and 1521. These individuals were divided into two temporal groups that predate and postdate the site's conquest. We determined the mitochondrial DNA haplogroup of each individual and identified haplotypes based on 372 base pair sequences of first hypervariable region. Our results indicate that the residents of these houses before and after the Aztec conquest have distinct haplotypes that are not closely related, and the mitochondrial compositions of the temporal groups are statistically different. Altogether, these results suggest that the matrilines present in the households were replaced following the Aztec conquest. This study therefore indicates that the Aztec expansion may have been associated with significant demographic and genetic changes within Xaltocan.

Link

Genomic history of Denmark

Genomic history of Denmark

An announcement from the GeoGenetics centre:

The Genomic History of Denmark.

The centre has received a 36 mill. DKK grant from Univ. of Copenhagen's dedicated 2016-program. Researchers from GeoGenetics in close cooperation with collegues from the National Museum of Denmark and institutes at the University of Copenhagen will make Denmark the first country in the world to map its evolutionary, demographic and health history - from the earliest settlers through to modern times.

DNA and proteins extracted from a Danish collection of archaeological skeletons from the Older Stone Age (5000-3000 BC) will be analysed in order to learn more about the Danish cultural heritage and health history.

Professor and director of the Centre for GeoGenetics Eske Willerslev is project leader.

Ancient DNA from Tianyuan Cave

Ancient DNA from Tianyuan Cave

Another new PNAS paper that hasn't yet appeared in the journal website. Still, from this description at ScienceNews this appears to be Very Important, as it pertains to a 40,000-year-old modern human, which, if I'm not mistaken is the oldest modern human tested so far:

Ancient DNA from cell nuclei and maternally inherited mitochondria indicates that this individual belonged to a population that eventually gave rise to many present-day Asians and Native Americans, says a team led by Qiaomei Fu and Svante Paabo, evolutionary geneticists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

The partial skeleton, unearthed in Tianyuan Cave near Beijing in 2003, carries roughly the same small proportions of Neandertal and Denisovan genes as living Asians do (SN: 8/25/12, p. 22), the scientists report online January 21 in the Proceedings of the National Academy of Sciences.

The Max Planck press release adds some information:

The genetic profile reveals that this early modern human was related to the ancestors of many present-day Asians and Native Americans but had already diverged genetically from the ancestors of present-day Europeans.

This is an important finding because some published demographic models had Europeans and East Eurasians diverging as recently as ~20 thousand years ago. It now appears that they did so already at around the time of the Upper Paleolithic revolution, when unambiguous evidence of modern humans across Eurasia exists.

UPDATE I: While we wait for this paper to appear on the PNAS website, it might be useful to wonder whether the Tianyuan sample might fall on the East Asian/Amerindian group or the more general "Ancestral South Indian" (ASI)/East Eurasian group.

According to current dating, haplogroup M itself is ~50 thousand years old, and most of the subclades therein coalesce to younger than 40ky times. It's possible that the Tianyuan sample dates from a period where ASI/East Asian differentiation had only just begun or was just about to begin.

The press release makes clear that Tianyuan was already "Asian" rather than generalized Eurasian, proving that East/West Eurasian differentiation had begun by ~40kya. It will be interesting to see whether it can be placed on a more specific "East Eurasian" group rather than a generalized "Asian" one.

UPDATE II: The paper is now online.

UPDATE III: From the paper:

Thus, it is related to the mtDNA that was ancestral to present-day haplogroup B (Fig. 1), which has been estimated to be around 50,000 y old (18) (50. 7 ka BP; 95% CI: 38.1–68.3 ka BP). We note that the age of the Tianyuan individual is compatible with this date.

So, it appears to be within macro-haplogroup N, with haplogroup B being, I think, a fairly unambiguously East Asian/Native American clade of the phylogeny. It will certainly be interesting to see how the much more successful -and younger- M subclades ended up dominating East Eurasia.

UPDATE IV: The TreeMix analysis clearly places Tianyuan within the Asian group, but does not resolve whether Papuans are an outgroup to East Asians/Tianyuan:

I guess that is expected (see my UPDATE I), since Tianyuan dates from a period where within-Asia differentiation had only just begun or was about to begin.

UPDATE V: With respect to sharing of alleles with archaic Eurasian hominins, the Tianyuan sample is within the modern range of variation.

PNAS doi: 10.1073/pnas.1221359110

DNA analysis of an early modern human from Tianyuan Cave, China

Qiaomei Fu et al.

Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (~30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.

Link

Ancient mtDNA from Santimamiñe Cave

Ancient mtDNA from Santimamiñe Cave

I see press releases and news stories on this cave from time to time, but I haven't actually located any published studies. If anyone is aware of more information, feel free to leave a comment.

Genetic research reveals that current population of Urdaibai probably descended from cave dwellers at Santimamiñe

The comparison of DNA extracted from a Homo sapiens who inhabited the Santimamine Cave (in the Basque province of Biscay) some 4,000 years ago, and from 6 other bone remains found in the same cave, with the DNA of 158 persons currently living in the surrounding Urdaibai region, has shown that current individuals have maternal lineages very similar to the archaeological remains. The findings enable putting forward the hypothesis that the current population is descended from the ancient denizens of the Santimamine Cave. 

... 

The research received funding from the Department of Culture of the Provincial Government of Bizkaia, as well as from the Urdaibai District Authority. Once the research in Urdabai is concluded, it is hoped that, shortly, it will be extended to other regions of the Basque Country, using new studies of funerary sites from the same period and from other eras (the Copper Age, the Bronze Age, etc.) thus enabling extending the knowledge we currently have on the special characteristics of the Basque population. This populational group has sparked enormous scientific interest for its distinctive characteristics regarding the preservation of its pre-Indo-European language and its relative isolation from the influence of other peoples and cultures.

Multiplex determination of eye and hair color

Multiplex determination of eye and hair color

From the paper:

Sample S24 represents a controversial case from the Benedictine Abbey in  Tyniec near Krakow. During the work undertaken in the crypt of the St. Peter and Paul  church belonging to the Abbey, 17 skeletons of alleged abbots were found. The burial was  dated to the period of the 12th to 14th centuries. Unexpectedly, the anthropological  examination revealed that two skeletons may be of female origin, which indeed was  confirmed by DNA analysis (data not shown), while only male monks were expected. One of the two DNA samples was sufficiently preserved to enable analysis of other nuclear markers  (data not shown) and was used here for HIrisPlex analysis. The mysterious woman was  predicted to have dark blond/brown hair (accuracy of 78.5%) and brown eyes (accuracy of 90.4%), (Table 2 and Figure 2B). 

... 

Two medieval  skeletons were found under the floor between the chancel and the nave of the church. Based  on historical markers the grave was dated to originate from the 14th century. Further  anthropological examinations indicated that the S25 male died at the approximate age of 60,  whereas the S26 male was approximately 75 years old at the time of death. It is alleged that  the skeletons belong to members of the Teczynski family, representing noble Polish magnates  of medieval times. The tooth collected from the deeper burial (S25) was found to be seriously  affected by decay, which was reflected by a very low DNA concentration (3 pg/µl) and  incomplete autosomal and Y chromosome STR profiles (NGM and Yfiler). Complete  mtDNA HVI and HVII profiles were generated in both teeth (data not shown). From these  data it was possible to conclude that both skeletons are of male origin and are unrelated in  both maternal and paternal lines. From the partial HIrisPlex profile ascertained from S25 we  successfully inferred blue eye colour (P = 0.899, accuracy of 95.6%), but hair colour could  not be inferred because of missing genotypes at three DNA variants (N29insA, rs1805005,  rs2228479). The sample S26 revealed a prediction of blond hair colour (P = 0.784) together  with a light hair colour shade (P = 0.918) concluding that the individual had light blond hair  (accuracy of 69.5%). Eye colour prediction of S26 revealed blue eyes (P = 0.919, accuracy of  97.4%) (Table 2).

Wikipedia article on Tęczyński family.

Investigative Genetics 2013, 4:3 doi:10.1186/2041-2223-4-3

Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains

Jolanta Draus-Barini

Abstract (provisional)

Background

DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing persons, disaster victims or family relationships. They may also provide useful information towards unravelling controversies that surround famous historical individuals. Retrieving information about a deceased person's externally visible characteristics can be informative in both types of DNA analyses. Recently, we demonstrated that human eye and hair colour can be reliably predicted from DNA using the HIrisPlex system. Here we test the feasibility of the novel HIrisPlex system at establishing eye and hair colour of deceased individuals from skeletal remains of various post-mortem time ranges and storage conditions.

Methods

Twenty-one teeth between 1 and approximately 800 years of age and 5 contemporary bones were subjected to DNA extraction using standard organic protocol followed by analysis using the HIrisPlex system.

Results

Twenty-three out of 26 bone DNA extracts yielded the full 24 SNP HIrisPlex profile, therefore successfully allowing model-based eye and hair colour prediction. HIrisPlex analysis of a tooth from the Polish general W[latin small letter l with stroke]adys[latin small letter l with stroke]aw Sikorski (1881 to 1943) revealed blue eye colour and blond hair colour, which was positively verified from reliable documentation. The partial profiles collected in the remaining three cases (two contemporary samples and a 14th century sample) were sufficient for eye colour prediction.

Conclusions

Overall, we demonstrate that the HIrisPlex system is suitable, sufficiently sensitive and robust to successfully predict eye and hair colour from ancient and contemporary skeletal remains. Our findings, therefore, highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including ancient DNA studies, for the prediction of eye and hair colour of deceased individuals.

Link

Y-chromosome and mtDNA of Henri IV

Y-chromosome and mtDNA of Henri IV

A recent paper had determined the Y-chromosome haplotype of Louis XVI of France from a handkerchief preserving his blood after his execution. A new study looks at the mummified head of Henri IV, the first Bourbon King of France. Even though only a limited number of Y-STRs were successfully typed, they match those of Louis XVI, who belonged to the not-so-frequent-anymore haplogroup G2a. So, while we cannot be entirely sure that the two Y-chromosomes were related in a genealogical time frame, the evidence is consistent with their known genealogical relationship and with the attribution of the two samples (mummified head/blood) to the respective kings.

Also of interest, Henri IV's mtDNA haplotype:

The majority of the clones generated show an U5b* mtDNA haplotype defined by three nucleotide changes at positions 16239T 16270T 16311C (see Supplementary material). The three HVR1 diagnostic positions were confirmed in two different amplifications of the L16185-H16378 HVR1 fragment, proving that the results are reproducible. This mtDNA haplotype is present so far in one single individual from France (originally published in [10]) in an in-house database of 22,807 published European sequences, and it is absent in all people involved in the laboratory analysis.

 If I followed the trail of ancestry correctly, this matrilineage leads all the way to a Tochter von Egisheim in the 11th century.

Forensic Science International Available online 30 December 2012

Genetic comparison of the head of Henri IV and the presumptive blood from Louis XVI (both Kings of France)

Philippe Charlier et al.

A mummified head was identified in 2010 as belonging to Henri IV, King of France. A putative blood sample from the King Louis XVI preserved into a pyrographically decorated gourd was analyzed in 2011. Both kings are in a direct male-line descent, separated by seven generations. We have retrieved the hypervariable region 1 of the mitochondrial DNA as well as a partial Y-chromosome profile from Henri IV. Five STR loci match the alleles found in Louis XVI, while another locus shows an allele that is just one mutation step apart. Taking into consideration that the partial Y-chromosome profile is extremely rare in modern human databases, we concluded that both males could be paternally related. The likelihood ratio of the two samples belonging to males separated by seven generations (as opposed to unrelated males) was estimated as 246.3, with a 95% confidence interval between 44.2 and 9729. Historically speaking, this forensic DNA data would confirm the identity of the previous Louis XVI sample, and give another positive argument for the authenticity of the head of Henri IV.

Link

EURO-DNA test

EURO-DNA test

AncestryByDNA has released a EURO-DNA test which reports percentages of "Northern European," "Southeastern European," "Middle-Eastern," and "South Asian" admixture based on a 320 ancestry-informative markers (AIMs).

The ad-hoc choice of the four ancestral groups and the rather confusing commentary and/or anomalous results (Iberians on average ~16% "South Asian"?) may discourage many from taking the test, especially at a price tag of $399. Still, EURO-DNA is a step towards personalized genetic archaeology, even though the theoretical assumptions and methodology leave much to be desired at this stage.

Update:

If you start with the a priori breakdown into 4 groups, then each individual will have 4 numbers that add up to 100%. One could just as easily have used a "Southwestern European", "Northeastern European", "Middle Eastern" and "South Asian" breakdown, and again each individual would have 4 numbers adding up to 100%.

The trick is to start with a collection of individuals, remove identifying tags and cluster them, thus identifying the real genetic components in the population, if any such components can be detected. This was the procedure followed by Rosenberg et al. [1]. In that analysis, wholly different clusterings emerged, with e.g., the specificity of Iberian Basques, who were allocated their own cluster, was discovered.



By contrast, an Iberian Basque taking the EURO-DNA test would perhaps get a score high in NOR/MED which however obfuscates the real genetic structure of the Basque population which is highly specific, as the Basques are an ancient ethnolinguistic isolate of the Iberian peninsula rather than the product of "admixture".

AncestryByDNA must show why its chosen four-group breakdown is used in lieu of other potential choices.

[1] Rosenberg et al (2002)

Update #2: Check out the comments for some additional information by Dr. Tony Frudakis of DNAPrint who is involved in the creation of EURO-DNA 1.0 and the AncestryByDNA tests.

Ancient DNA of Neolithic skeleton from NE Siberia

Ancient DNA of Neolithic skeleton from NE Siberia

A skeleton from northeastern Yakutia (east Siberia) dating to the Neolithic period (3,600 years BP) belongs to mtDNA haplogroup C and the combined mtDNA and autosomal analysis shows its similarity to modern east Siberian/Native American populations.

American Journal of Physical Anthropology (Early View)

Ancient DNA analysis of human Neolithic remains found in northeastern Siberia
François-Xavier Ricaut et al.

ABSTRACT

We successfully extracted DNA from a bone sample of a Neolithic skeleton (dated 3,600 ± 60 years BP) excavated in northeastern Yakutia (east Siberia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by sequencing of the hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The STR profile, the mitochondrial haplotype, and the haplogroup determined were compared with those of modern Eurasian and Native American populations. The results showed the affinity of this ancient skeleton with both east Siberian/Asian and Native American populations.
Link

mtDNA analysis of Neolithic Siberians

mtDNA analysis of Neolithic Siberians

This study shows that modern Siberians are partly descended from the Mongoloid Neolithic Siberians.

Anthropol Anz. 1998 Mar;56(1):1-6.

Siberian population of the New Stone Age: mtDNA haplotype diversity in the ancient population from the Ust'-Ida I burial ground, dated 4020-3210 BC by 14C.
Naumova O Y et al.

On the basis of analysis of mtDNA from skeletal remains, dated by 14C 4020-3210 BC, from the Ust'-Ida I Neolithic burial ground in Cis-Baikal area of Siberia, we obtained genetic characteristics of the ancient Mongoloid population. Using the 7 restriction enzymes for the analysis of site's polymorphism in 16,106-16,545 region of mtDNA, we studied the structure of the most frequent DNA haplotypes, and estimated the intrapopulational nucleotide diversity of the Neolithic population. Comparison of the Neolithic and modern indigeneous populations from Siberia, Mongolia and Ural showed, that the ancient Siberian population is one of the ancestors of the modern population of Siberia. From genetic distance, in the assumption of constant nucleotide substitution rate, we estimated the divergence time between the Neolithic and the modern Siberian population. This divergence time (5572 years ago) is conformed to the age of skeletal remains (5542-5652 years). With use of the 14C dates of the skeletal remains, nucleotide substitution rate in mtDNA was estimated as 1% sequence divergence for 8938-9115 years.


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mtDNA of ancient central Asians

mtDNA of ancient central Asians

An interesting new paper confirms the anthropological and archaeological picture of a westward spread of Caucasoids in Central Asia in early prehistoric times, followed by the spread of Mongoloids in the opposite direction during the 1st millennium BC. The Caucasoid-Mongoloid hybrid population resulting from these interactions is similar in terms of mtDNA with present-day Central Asians with some noted differences (e.g., presence of additional West Eurasian haplogroups). In the ancient samples, West Eurasian haplogroups H, HV, I, T*, T1, U*, U1, U5, U5a1 and W were represented:

• HV sequences have matches in the Central Mediterranean region
• H sequences are split between the common Cambridge Reference Sequence (CRS) found in many populations, and two other sequences found in the Central Mediterranean and the Caucasus
• The I sequence is present in a modern Central Asian and also in individuals from the Caucasus
• The W sequence is widespread in West Eurasia
• T* sequences are widespread in Europe, the Near East and the Central Mediterranean region
• T1 is widespread in West Eurasia, but also found sporadically in East Eurasia
• The U1a sequences are found in Turks, Armenians and Caucasians
• The U5a sequence has been found in an Egyptian
• The U5a1 sequence is frequent in the Caucasus and present in Europe, while a different U5a1 was reported previously in Mongolia

The East Eurasian haplogroups belong to A*, M*, M4 and G2:

• The M* sequence was observed in an Indian individual
• The M4 sequence has not been previously reported
• The G2 sequence is found in present-day China and Central Asia
• One A sequence is found in present-day Central Asians and Indians, while the other two have a motif found in a modern Chukchi

Most (78%) of the sequences are of West Eurasian (Caucasoid) origin, but before the 7th c. BC, East Eurasian (Mongoloid) sequences are absent, although they could be present up to 20.6% (p<0.05).
Proc R Soc Lond B Biol Sci. 2004 May 7;271(1542):941-7. 

Unravelling migrations in the steppe: mitochondrial DNA sequences from ancient central Asians.
Lalueza-Fox C et al.

This study helps to clarify the debate on the Western and Eastern genetic influences in Central Asia. Thirty-six skeletal remains from Kazakhstan (Central Asia), excavated from different sites dating between the fifteenth century BC to the fifth century AD, have been analysed for the hypervariable control region (HVR-I) and haplogroup diagnostic single nucleotide polymorphisms (SNPs) of the mitochondrial DNA genome. Standard authentication criteria for ancient DNA studies, including multiple extractions, cloning of PCR products and independent replication, have been followed. The distribution of east and west Eurasian lineages through time in the region is concordant with the available archaeological information: prior to the thirteenth-seventh century BC, all Kazakh samples belong to European lineages; while later an arrival of east Eurasian sequences that coexisted with the previous west Eurasian genetic substratum can be detected. The presence of an ancient genetic substratum of European origin in West Asia may be related to the discovery of ancient mummies with European features in Xinjiang and to the existence of an extinct Indo-European language, Tocharian. This study demonstrates the usefulness of the ancient DNA in unravelling complex patterns of past human migrations so as to help decipher the origin of present-day admixed populations.

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