Showing posts with label U5. Show all posts
Showing posts with label U5. Show all posts

September 04, 2014

Y chromosomes and mtDNA of early farmers from Hungary

A new preprint has just appeared on the bioRxiv. It's free to read so I'll just summarize some results. First:
The haplotype of the Mesolithic skeleton from the Croatian Island Korčula belongs to the mtDNA haplogroup U5b2a5 (Dataset S3). The sub-haplogroup U5b has been shown to be frequent in pre-Neolithic hunter-gatherer communities across Europe [28–30,32,33,45,46]. 
But:
Contrary to the low mtDNA diversity reported from hunter-gatherers of Central/North Europe [28–30], we identify substantially higher variability in early farming communities of the Carpathian Basin  including the haplogroups N1a, T1, T2, J, K, H, HV, V, W, X, U2, U3, U4, and U5a (Table 1). Previous studies have shown that haplogroups N1a, T2, J, K, HV, V, W and X are most characteristic for the Central European LBK and have described these haplogroups as the mitochondrial ʻNeolithic packageʼ that had reached Central Europe in the 6th millennium BC [36,37]. Interestingly, most of these haplogroups show comparable frequencies between the STA, LBKT and LBK,
N1a is the "signature group" of the LBK based on previous publications and now it seems that it was also found in the Starcevo culture of Hungary. The mtDNA PCA plot (right) shows clearly that the Hungarian farmers are very similar to the German ones so it seems that the LBK is a direct outgrowth of the Carpathian Neolithic; some earlier models of "demic diffusion" argued that Neolithic farmers spread slowly across Europe, picking up hunter-gatherer ancestry as they went along, but now it seems that at least in the Hungary->Germany part of this journey interaction with hunter-gatherers was minimum.

mtDNA change over time in Europe is pictured in Figure 3 (left) showing a shared haplotype analysis. The Y-chromosome data genetic distance is shown on the right and shows the Balkan-Anatolian-Caucasian-Mesopotamian relationship of the early farmer Y-chromosomes. Practically, this is due to haplogroup G2a (and especially G2a2b), which has turned up in lots of ancient European farmers (including the famous Iceman):
Three STA individuals belong to the NRY haplogroup F* (M89) and two specimens can be assigned to the G2a2b (S126) haplogroup, and one each to G2a (P15) and I2a1 (P37.2) (Dataset S3, S5). The two investigated LBKT samples carry haplogroups G2a2b (S126) and I1 (M253). Furthermore, the incomplete SNP profiles of eight specimens potentially belong to the same haplogroups; STA: three G2a2b (S126), two G2a (P15), and one I (M170); LBKT: one G2a2b (S126) and one F* (M89) (Dataset S5).
I believe this is the first ancient finding of haplogroup I1 which attains a peak in modern Swedes. This might be useful to those who have tied this to Germanic migrations because of this, as it was already in Central Europe with the earliest farmers.

Interestingly:
Surprisingly, Y chromosome haplogroups, such as E1b1b1 (M35), E1b1b1a1 (M78), E1b1b1b2a (M123), J2 (M172), J1 (M267), and R1b1a2 (M269), which were claimed to be associated with the Neolithic expansion [23–25], have not been found so far in the 6th millennium BC of the Carpathian Basin and Central Europe. Intriguingly, R1a and R1b, which represent the most frequent European Y chromosome haplogroups today, have been reported from cultures that emerged in Central Europe during the 3rd/2nd millennium BC, while a basal R type has been reported from a Palaeolithic sample in Siberia [60] in agreement with a proposed Central Asian/Siberian origin of this lineage. In contrast, G2a has not been detected yet in late Neolithic cultures [42,43]. This suggests further demographic events in later Neolithic or post-Neolithic periods.
A cautionary tale against over-reliance on modern distributions to trace ancient origins.

Also:
Considering the entire set of 32 published NRY records available for Neolithic Europe thus far, the low paternal diversity is indeed quite remarkable: G2a is the prevailing haplogroup in the Central European and Carpathian Basin Neolithic, and in French and Iberian Neolithic datasets [36,40,41]. There are only two exceptions, namely one E1b1b (V13) [41] individual from the Avellaner cave in Spain (~5,000-4,500 BC), and two I2a [40] individuals from Treilles, France (~3,000 BC).


biorxiv http://dx.doi.org/10.1101/008664

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

Anna Szécsényi-Nagy et al.

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis has not been revealed yet. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (7th/6th millennium BC) from the Carpathian Basin and south-eastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early farming south-eastern European and Carpathian Basin cultures on Central European populations of the 6th-4th millennium BC. Our comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through south-eastern Europe and the Carpathian Basin into Central Europe. Our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting patrilineal descent system and patrilocal residential rules among the early farmers.

Link

December 24, 2013

Europeans = Neolithic farmers, Mesolithic hunter-gatherers and "Ancient North Eurasians" (etc.)

A new preprint on the bioRxiv reports ancient DNA from a Mesolithic European hunter-gatherer from Luxembourg whose mtDNA was published a few years ago and a Neolithic European LBK farmer from Germany, as well as several Mesolithic hunter-gatherers from Sweden.

The Luxembourg sample is similar to the Iberian La Brana samples and the Swedish Mesolithic samples are similar to Swedish Neolithic hunter-gatherers. The LBK farmer is similar to Oetzi and a Swedish TRB farmer and to Sardinians. The authors also study the recently published Mal'ta Upper Paleolithic sample from Lake Baikal and find that it is part of an "Ancient North Eurasian" population that also admixed into West Eurasians on top of the Neolithic/Mesolithic mix.

The authors' proposed model and admixture estimates:



It seems that the estimates go all the way to "almost pure" Early European farmer ancestry but "West European Hunter-Gatherer" and "Ancient North Eurasian" ancestry isn't found unmixed in any modern populations. The model seems to agree with Raghavan et al. that Karitiana are "Mal'ta"-admixed but also finds the most basal Eurasian ancestry in the European Neolithic farmer. The authors write:
The successful model (Fig. 2A) also suggests 44 ± 10% “Basal Eurasian” admixture into the ancestors of Stuttgart: gene flow into their Near Eastern ancestors from a lineage that diverged prior to the separation of the ancestors of Loschbour and Onge. Such a scenario, while never suggested previously, is plausible given the early presence of modern humans in the Levant25, African-related tools made by modern humans in Arabia26, 27, and the geographic opportunity for continuous gene flow between the Near East and Africa28
The Swedish/Luxembourg Mesolithic hunter-gatherers are all mtDNA-haplogroup U and Y-chromosome haplogroup I, so again no R1a/R1b in early European samples.

An interesting finding is that the Luxembourg hunter-gatherer probably had blue eyes (like a Mesolithic La Brana Iberian, a paper on which seems to be in the works) but darker skin than the LBK farmer who had brown eyes but lighter skin. Raghavan et al. did not find light pigmentation in Mal'ta (but that was a very old sample), so with the exception of light eyes that seem established for Western European hunter-gatherers (and may have been "darker" in European steppe populations, but "lighter" in Bronze Age South Siberians?), the origin of depigmentation of many recent Europeans remains a mystery. Ancient DNA continues to surprise at every turn.

UPDATE (4/4/2014): a new version of the preprint.

bioRxiv doi: 10.1101/001552

Ancient human genomes suggest three ancestral populations for present-day Europeans

Iosif Lazaridis et al.

Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.

Link

December 14, 2013

Ancient mtDNA from Rössen culture in Wittmar, Germany

Archaeological and Anthropological Sciences December 2013

Ancient DNA insights from the Middle Neolithic in Germany

Esther J. Lee et al.

Genetic studies of Neolithic groups in central Europe have provided insights into the demographic processes that have occurred during the initial transition to agriculture as well as in later Neolithic contexts. While distinct genetic patterns between indigenous hunter-gatherers and Neolithic farmers in Europe have been observed, it is still under discussion how the genetic diversity changed during the 5,000-year span of the Neolithic period. In order to investigate genetic patterns after the earliest farming communities, we carried out an ancient mitochondrial DNA (mtDNA) analysis of 34 individuals from Wittmar, Germany representing three different Neolithic farming groups (ca. 5,200–4,300 cal bc) including Rössen societies. Ancient DNA analysis was successful for six individuals associated with the Middle Neolithic Rössen and observed haplotypes were assigned to mtDNA haplogroups H5, HV0, U5, and K. Our results offer perspectives on the genetic composition of individuals associated with the Rössen culture at Wittmar and permit insights into genetic landscapes in central Europe at a time when regional groups first emerged during the Middle Neolithic.

Link

June 11, 2013

mtDNA from Late Bronze Age West Siberia (Stary Sad)

From the paper:
All of the samples studied have a different sequence of mitochondrial DNA HVR I (Table). An analysis of haplotype structure enabled its attribution to five mitochondrial DNA haplogroups: western Eurasian U2e, U5a, T and eastern Eurasian C and A10. A mixed gene pool structure combining mitochondrial DNA groups typical of human populations from western and eastern parts of Eurasia, have been ascertained for all ancient Western-Siberian forest-steppe human populations that we have studied to date (Pilipenko, 2010).
The authors identify two components in the population: (i) the "indigenous" mixed population of West Eurasian (U2e+U5a) and East Eurasian (A10+C), and (ii) the intrusive Andronovo (Fedorovka) (T). They also hint about a special article on the autochthony of the A10 lineages in the region. We now seem to have fairly good data about the existence of a wide West/East Eurasian interaction zone from eastern Europe to Siberia, and it would certainly be interesting to see when this zone was first formed; in any case, it seems clear that at least in the central-northern parts of Eurasia admixture between East and West has been going on for a while.

The more interesting question is where did the mtDNA haplogroup-T in Fedorovo groups come from? In Europe, for which we have the best data, T makes its appearance with early Neolithic groups, but it's difficult to imagine that this was the source of T in West Siberia. I would not be surprised if the entrance of T into the boreal zone occurred via the Caucasus, although Grigoriev derives them "from the Near East through Iran and Central Asia into the Irtish basin." Ancient DNA reveals the gradual appearance of new players in both Europe and West Siberia, but their ultimate source(s) and migratory paths remains elusive.

Related:

Archaeology, Ethnology and Anthropology of Eurasia Volume 40, Issue 4, December 2012, Pages 62–69

An Analysis Of Mitochondrial Dna From The Pakhomovskaya Population Of The Late Bronze Age, Western Siberia

V.I. Molodin et al.

This article presents the results of an analysis of mitochondrial DNA extracted from bone samples from Stary Sad – a burial ground representing the eastern variant of the Late Bronze Age Pakhomovskaya culture in the Baraba forest-steppe, Western Siberia. Comparison with mitochondrial DNA data from earlier populations of the region and also with archaeological facts, points to the origins of the Pakhomovskaya people. Certain components of their gene pool were evidently derived from the local pre-Andronovo populations, others from the actual Andronovo (Fedorovka) population and also from later immigrants. In this article an integrative reconstruction based on biological and cultural facts is proposed.

Link

January 01, 2013

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

July 14, 2012

Population strata in the West Siberian plain (Baraba forest steppe)

Also from the Population Dynamics in Prehistory and Early History (2012) volume, this is an awesome ancient DNA study which dissects a succession of archaeological cultures stretching from the beginning of the metal ages to the beginning of the Iron Age in a small region of West Siberia. As the authors write:
Our work is devoted to the analysis of human migration processes that occurred during the Bronze Age (4th–early 1st millennium BC) in the forest steppe zone between the Ob and Irtysh rivers (about 800 km from west to east). This area, known as Baraba forest steppe, stretches over 200 km from the taiga zone in the north to the steppes in the south.
The careful examination of the sequence of cultures, combining ancient mtDNA and physical anthropology paints a very compelling picture of the changes that occurred in the span of a few millennia in the Baraba forest steppe. The authors give the map on the left, with the caption: "Fig. 5 | Location of ancient human groups with a high frequency of mtDNA haplogroups U5, U4 and U2e lineages. The area of Northern Eurasian anthropological formation is marked by yellow region on the map (References: 1 Bramanti et al., 2009; 2Malmstrom et al., 2009; 3 Krause et al., 2010; 4 this study)".


The northern Eurasian anthropological formation actually combines eastern and western Eurasian features and may correspond to the Proto-Uralic type. Researchers have clashed about the origins of this population element, with some considering it a third Eurasian race that evolved independently of Caucasoids and Mongoloids, others assigning it to a much diverged branch of one of the two major Eurasian races, and still others considering it the product of admixture between east and west.


All indications are that the type, unlike the Caucasoid-Mongoloid mixtures that took place in Central Asia in the last 2 millennia, is of more ancient vintage, and represents an anthropological element that was indeed of Caucasoid-Mongoloid origins, but in the rather remote past. The authors write with respect to the most ancient periods:

In contrast to the occupation of the southern region of West Siberia, modern humans arrived in the Ob-Irtysh interfluve relatively late, at the end of the Pleistocene, about 13–14 thousand years ago (Okladnikov, Molodin, 1983; Petrin, 1986). The absence of burials dating back to this period in the region does not allow us to conduct a biological investigation of this earliest population. The most ancient anthropological material available is from the Neolithic period (4th–5th millennium BC). 
And, what of the earliest available material?
The anthropological analysis of the material allowed us to detect a specific craniological type in the Baraba population, which was assigned to one of the anthropological formations discovered by V.V. Bunak in 1956 through the analysis of Neolithic materials from the northern forest zone of the East European Plain. Bunak called it the “northern Eurasian anthropological formation” (Bunak, 1956).

This anthropological type developed in a zone that is intermediate to the geographic areas occupied by the classic Caucasoids and the Mongoloids. The exists substantial anthropological evidence showing a wide geographic distribution of this anthropological formation: from the Trans-Urals forest and the Barabian province of Western Siberia in the east to Karelia and the Baltic in the west (Chikisheva, 2010).
The mtDNA evidence seems to support the anthropological assessment:
We have analyzed 18 mtDNA samples from the Ust-Tartas population to date (Fig. 3). The results obtained thus far allow us to draw several preliminary conclusions about the genetic background in the region in the beginning of the Bronze Age. By the Early Metal Period the mtDNA pool structure was already mixed and consisted of both Western and Eastern Eurasian haplogroups in nearly equal proportions. The eastern Eurasian mtDNA cluster was represented by Haplogroups A, C, Z, D, which are most typical of modern and perhaps ancient populations located in the east of the region studied. Haplogroups C and D were predominantly represented by widely distributed root haplotypes. A lineage of Haplogroup A that was detected in two Ust-Tartas samples represents a subcluster that is apparently characteristic of West Siberia and the Volga-Ural Region. The observed presence of Haplogroup Z lineages with a high frequency in the Ust-Tartas group was unexpected, since these lineages are nearly absent in the gene pool of modern indigenous West Siberian populations.

It is worth noting that the Western Eurasian mtDNA haplogroups in the Ust-Tartas series were represented only by Haplogroup U lineages, and specifically by the three subgroups – U2e, U4, U5a1. These results are in agreement with previous data indicating that Haplogroup U lineages (particularly Subgroups U5 and U4) predominated in Eastern, Central and Northern European hunter-gatherer groups from 14000 to 4000 years ago (Bramanti et al., 2009; Malmstrom et al., 2009), and possibly in earlier periods (Krause et al., 2010). The geographic area within which this genetic feature is observed appears to be broad (Fig. 5). Apparently, Baraba was near the eastern periphery of this area.
We now have evidence of the zone of U dominance extending from Iberia in the west and all the way to Lake Baikal in the east. But, this zone is not homogeneous: its western, European, end appears to have lacked the East Eurasian lineages, while starting from Ukraine and to the East the U types were supplemented by the Mongoloid lineages.

But, there was structure within the U zone itself: according to Lillie et al. (same volume) in Ukraine during the 6th millennium BC, the West Eurasian types were represented by U1 and U3, a different mix than in the Baraba forest steppe, and haplogroup T was also present, while of the Mongoloid haplogroups only C was present.

As we head into the Bronze Age, the population of the region displayed signs of continuity:

The genetic analysis of the Odinovo and Krotovo groups (10 and 6 samples, respectively) (Fig. 3) did not reveal any differences between them and the previous Ust-Tartas group, such as the presence of new mtDNA haplogroups. The mtDNA pool structure was still mixed. The East Eurasian haplogroups were represented by the D, C, Z (in both the Odinovo and Krotovo groups) and A (in the Krotovo group) haplogroups. The East Eurasian lineages identified were phylogenetically close (lineages of haplogroups A, C, Z) or even identical (D haplogroup, 16223–16362 lineages) to the samples from the Ust-Tartas group. The West Eurasian part of the samples were represented by the U5a1 (Odinovo group) and U2e (Krotovo group) haplogroup lineages.  
Although only a small series of samples have been investigated thus far, the data obtained reveal continuity between the Odinovo and Krotovo populations and the earlier Ust-Tartas group. These findings are consistent with the autochthonous development of the Baraba populations during the Early and the beginning of the Middle Bronze Age, as well as with the anthropological evidence.  
It is during the Middle and Late Bronze ages that we begin to say the first intrusive lineage into the native population mix:
The anthropological analysis of the West Siberian Andronovo population shows at least four craniological types. Three types are related to the Palaeocaucasian race and are represented by proto-European anthropological type variants. The fourth, Mongoloid, component is autochthonous. The most intensive interactions between the Andronovo migrants and the indigenous populations apparently occurred in the Baraba forest steppe and the right bank of the upper Ob River (Chikisheva and Pozdnyakov, 2003).  
To investigate the putative impact of Andronovo migrants on the mtDNA pool structure of the indigenous populations in Baraba, mtDNA samples from the Late Krotovo (n=20) and Andronovo (n=20) groups in this region were analyzed (Fig. 3) and compared to recently published data (n=10) (Keyser et al., 2009) and our own unpublished data (n=6) on mtDNA lineages from West Siberian Andronovo populations located outside the Baraba forest steppe.  
The genetic influence of migrants can be detected by the appearance of a new mtDNA haplogroup that was absent in the populations preceding the migration wave. This new mtDNA haplogroup, a West Eurasian T haplogroup, was detected in the Late Krotovo population. The T haplogroup appears simultaneously (with a 15 % frequency) in the Krotovo and Andronovo groups, but was completely absent in all preceding Baraba populations. We therefore consider the appearance of the Haplogroup T-lineage as the most likely genetic marker of the Andronovo migration wave to the region.  
This assumption is confirmed by mtDNA studies of Andronovo groups from other West Siberian areas. Haplogroup T lineages were found, with a frequency of 25 %, in the samples (n=16) taken from two Andronovo groups from the Krasnoyarsk and upper Ob River areas.  
We also detected another remarkable feature in the mtDNA pool of the Andronovo group from Baraba. Most mtDNA samples belonged to haplogroups, such as the East Eurasian A and C haplogroups, that are typical of preceding Baraba indigenous populations. Still, these haplogroups were not found in the other West Siberian Andronovo groups. Apparently, the Andronovo group from Baraba assimilated the aboriginal Krotovo population, from which it obtained these East-Eurasian mtDNA haplogroups. Obviously, there was reciprocal genetic contact between the migrant and indigenous groups in the region. 

...

A small but informative series of mtDNA samples from the Baraba Late Bronze Age culture population (n=5) was analyzed (Fig. 3), revealing the presence of MtDNA lineages (East Eurasian A and C lineages) that mark the genetic continuity with aboriginal Baraba groups. At the same time, the series includes the Haplogroup-T lineage, which we believe marks the Andronovo migration wave to West Siberia. Our data is therefore consistent with the putative origin of the West Siberian Late Bronze Culture population as the result of interaction between the Baraba indigenous genetic substrate and the newly arrived group.
It is now clear that the Andronovo groups moving into the area possessed mtDNA haplogroup T and assimilated the locals with their U+East Eurasian mix. It is of course interesting that haplogroup T is the only non-U lineage found in the aforementioned study of Mariupol-type cemeteries from Neolithic Ukraine.

The earliest occurrence of haplogroup T is in the Pre-Pottery Neolithic B of the Near East (Tell Hallula), and this haplogroup appears all over the place in Neolithic Europe. While a recent article has suggested a pre-Neolithic dispersal of T subclades into Europe, on the basis of modern populations, this hypothesis is difficult to reconcile with the ancient DNA data.


Pending new discoveries, it appears likely that mtDNA haplogroup T represents a Neolithic entrant into the boreal zone of U dominance. This has, of course, substantial implications in the context of J.P. Mallory's concept of fault lines, as it demonstrates that the steppe populations did not evolve in isolation, but the dominant lineage in the Andronovo groups was a late entrant into the indigenous U-zone of the eastern European plain.


But, the story doesn't end here:

The analysis of mtDNA samples from the Chicha-1 population revealed some interesting patterns. Crucial changes in the composition of mtDNA haplogroups in the gene pool were observed as compared to the earlier Baraba groups studied (Fig. 3). Dominance of Western Eurasian haplogroups and the near absence of East Eurasian were observed. Additionally, several new West Eurasian haplogroups appeared in the region, including Haplogroups U1a, U3, U5b, K, H, J and W.  
The phylogeographic analysis suggests that the distribution and diversification centres of several of these mtDNA haplogroups and specific lineages are located on the west and south west of the Baraba forest steppe region, on the territory corresponding to modern-day Kazakhstan and Western Central Asia (Fig. 10). Apparently, the migration wave from the south strongly influenced the gene pool of the Baraba population in the transitional period from the Bronze to the Early Iron Age. The impact of the northern human groups was probably less evident in the south of the Baraba forest steppe, at least at the mtDNA level. 
The drastic appearance of a purely Caucasoid population at the Iron Age from a southern, east-Caspian origin perhaps corresponds to the arrival of the first steppe Iranians. The vector of proposed migration is reasonable, if we consider both the likely Indo-Iranian homeland east of the Caspian, as well as the literary evidence for Scythian mobility during this period.

All in all, this is commendable research which allows us to intuit a sequence of events:
  • An early mixture zone between Caucasoids and Mongoloids
  • The Bronze Age arrival of mtDNA-T bearing Andronovo groups, the first pastoralists entering the zone of U+East Eurasian boreal hunter-gatherers; these Caucasoid peoples admixed with the natives of the mixture zone.
  • The early Iron Age arrival of a full-blown set of Caucasoid mtDNA lineages from the south paving the way for the Iranian Scytho-Sarmatian period

Human migrations in the southern region of the West Siberian Plain during the Bronze Age: Archaeological, palaeogenetic and anthropological data


Molodin, Vyacheslav I. et al.


In this paper we present archaeological and anthropological data on human migrations in the Western Siberian foreststeppe region during the Bronze Age (4th–beginning of 1st millennium BC). These data, accumulated over forty years of intensive research in the region, are compared to new results showing the diversity of mitochondrial DNA (mtDNA) lineages in this region during that period (92 mtDNA samples from seven ancient human groups). Preliminary analyses have demonstrated the usefulness of ancient DNA in tracing and unravelling patterns of past human migrations.  


Link


Prehistoric populations of Ukraine: Migration at the later Mesolithic to Neolithic transition


Lillie, Malcolm C. et al.


This paper focuses on the identification of population movements during the Mesolithic and Neolithic periods in the Dnieper Basin region of Ukraine. We assess the evidence for migration from the perspective of individual life histories using a combination of palaeoanthropology/pathology, radiocarbon dating, stable isotopic studies of diet, and mtDNA. 


Link

January 30, 2012

AAPA 2012 abstracts (part 1)

Here are some interesting abstracts from the 81st Annual Meeting of the American Association of Physical Anthropologists.


Maternal marks of admixture in Cape Coloreds of South Africa.
KRISTINE G. BEATY1, DELISA L. PHILLIPS1, MACIEJ HENNEBERG2 and MICHAEL H. CRAWFORD1.
Previous studies of genetic diversity have suggested that the Cape Coloureds of South Africa are a highly admixed population with genetic roots from indigenous African groups including Khoisans, and the later arrival of Bantu speaking Xhosa farmers. Further genetic contributions came during European colonization of South Africa, which added to the inclusion of largely male European markers to the gene pool. Slaves from Indonesia, Malaysia, Madagascar and India are also thought to have contributed to the genetic makeup of this ethnic group. This study examines the maternal contribution of each of these groups to the genetic diversity of the Cape Coloreds through sequencing of the hypervariable region I of the mitochondrial DNA and through restriction fragment length polymorphism.
A total of 123 individuals were examined for this study. High frequencies of haplogroups L1 and L2 were found at 81.3 percent in this group (100 of the 123 individuals), which indicates that this group has a large African contribution to its mitochondrial makeup. Restrictions of the major European haplogroups identified nine individuals, 7.3 percent of the sample, belonged to haplogroups I and J. Five individuals (4.1 percent of the sample) belonged to the superhaplogroup M, indicating that Asian slaves did contribute to the maternal gene pool. The majority of maternal lineages in this Cape Coloured sample are African in origin, with some European influence and a small contribution from Asian maternal lineages.

Ancient DNA reveals the population origin of the Eastern Xinjiang.
SHIZHU GAO2, HONGJIE LI1, CHUNXIANG LI1 and HUI ZHOU1,3.
Connecting with the Turpan Basin, the Eurasia steppe and the Gansu Corridor, the Eastern region of Xinjiang has played a significant role in the history of human migration, cultural developments, and communications between the East and the West. The population origin, migration and integration of this region have attracted extensive interest among scientists.
In order to research the population origin and movement of the Eastern Xinjiang, genetic polymorphisms studies of the Hami population were conducted. The Hami site is located in the East of Tian-Moutain in Xinjiang, dating back to the Bronze-early Iron Age. Archaeological studies showed that the culture of the Hami site possessed features from both the East and the West. Ancient mtDNA analysis showed that A, C, D, F, G, Z and M7 of the Eastern maternal lines, and W, U2e, U4, and U5aof the Western maternal lines were identified. Tajimas’D test and mismatch distribution analysis show that the Hami population had experienced population expansion in recent time. The demographic analysis of haplogroups suggests that the populations of the Northwest China, Siberia and the Central Asia have contributed to the mtDNA gene pool of the Hami population.
Our study reveals the genetic structure of the early population in Eastern Xinjiang, and its relationships with other Eurasian populations. The results will provide valuable genetic information to further explore the population origin and migration of Xinjiang and Central Asia.


Analysis of Chuvash mtDNA points to Finno-Ugric origin.
ORION M. GRAF1, STEPHEN M. JOHNSON1, JOHN MITCHELL2, STEPHEN WILCOX3, GREGORY LIVSHITS4 and MICHAEL H. CRAWFORD1.
A sample of 92 unrelated individuals from Chuvashia, Russia was sequenced for hypervariable region-I (HVR-I) of the mtDNA molecule. These data have been verified using RFLP analysis of the control region, revealing that the majority exhibit haplogroups H (31%), U (22%), and K (11%), which occur in high frequencies in western and northern Europe, but are virtually absent in Altaic or Mongolian populations. Multidimensional scaling (MDS) was used to examine distances between the Chuvash and reference populations from the literature. Neutrality tests (Tajima’s D (-1.43365) p<0.05, Fu’s FS (-25.50518) p<0.001) and mismatch analysis, which illustrates unimodal distribution, all suggest an expanding population.
The Chuvash speak a Turkic language that is not mutually intelligible to other extant Turkish groups, and their genetics are distinct from Turkic-speaking Altaic groups. Some scholars have suggested that they are remnants of the Golden Horde, while others have advocated that they are the products of admixture between Turkic and Finno-Ugric speakers who came into contact during the 13th century. Earlier genetic research using autosomal DNA markers indicated a Finno-Ugric origin for the Chuvash. This study examines uniparental mitochondrial DNA markers to better elucidate their origins. Results from this study maintain that the Chuvash are not related to Altaic or Mongolian populations along their maternal line, thus supporting the “Elite” hypothesis that their language was imposed by a conquering group —leaving Chuvash mtDNA largely of Eurasian origin. Their maternal markers appear to most closely resemble Finno-Ugric speakers rather than Turkic speakers.


An ancient DNA perspective on the Iron Age “princely burials” from Baden-Wurttemberg, Germany.
ESTHER J. LEE1, CHRISTOPH STEFFEN1, MELANIE HARDER1, BEN KRAUSE-KYORA1, NICOLE VON WURMB-SCHWARK2 and ALMUT NEBEL3.
During the Iron Age in Europe, fundamental social principles such as age, gender, status, and kinship were thought to have played an important role in the social structure of Late Hallstatt and Early Latene societies. In order to address the question of kinship relations represented in the Iron Age “princely burials” that are characterized by their rich material culture, we carried out genetic analysis of individuals associated with the Late Hallstatt culture from Baden-Wurttemberg, Germany. Bone specimens of thirty-eight skeletal remains were collected from five sites including Asperg Grafenbuhl, Muhlacker Heidenwaldle, Hirschlanden, Ludwigsburg, and Schodeingen. Specimens were subjected to DNA extraction and amplification under strict criteria for ancient DNA analysis. We successfully obtained mitochondrial DNA (mtDNA) control region sequences from seventeen individuals that showed different haplotypes, which were assigned to nine haplogroups including haplogroups H, I, K, U5, U7, W, and X2b. Despite the lack of information from nuclear DNA to infer familial relations, information from the mtDNA suggests an intriguing genetic composition of the Late Hallstatt burials. In particular, twelve distinct haplotypes from Asperg Grafenbuhl suggest a heterogeneous composition of maternal lineages represented in the “princely burials”. The results from this study provide clues to the social structure reflected in the burial patterns of the Late Hallstatt culture and implications on the genetic landscape during the Iron Age in Europe.


Genetic snapshot from ancient nomads of Xinjiang.
HONGJIE LI1, SHIZHU GAO2, CHUNXIANG LI1, YE ZHANG1, WEN ZENG3, DONG WEI3 and HUI ZHOU1,3.
Nomads of the Eurasian steppes are known to have played an important role in the transfer commodities and culture among East Asia, Central Asia, and Europe. However, the organization of nomadic societies and initial population genetic composition of nomads were still poorly understood because of few archaeological materials and written history.
In this study, the genetic snapshot of nomads was emerged by examining mitochondrial DNA and Y-chromosome DNA of 30 human remains from Heigouliang (HGL) site in the eastern of Xinjiang, which dated 2000 years ago and associated to the nomadic culture by archaeological studies. Mitochondrial DNA analysis showed that the HGL population included both East Eurasian haplogroups (A, C, D, G, F and Z) and West Eurasian haplogroups (H, K, J, M5 and H). The component of Eastern haplogroups is dominant. The distribution frequency and Fst values of Eastern haplogroups indicated the HGL population presented close genetic affinity to the nearby region modern populations of Gansu and Qinghai, while those of western haplogroups showed similar with Mongolia and Siberia populations. The results implied various maternal lineages were introduced into the HGL population. Regarding the Y chromosomal DNA analysis, nearly all samples belonged to haplogroup Q which is thought to be the mark of the Northern Asian nomads. We identified paternal kinship among three individuals at the same tomb by Y-STR marker.
Combined with archaeological and anthropological investigations, we inferred that the gene flow from the neighboring regions was possibly associated with the expansion of Xiongnu Empire.


Vikings, merchants and pirates at the top of the world: Y-chromosomal signatures of recent and ancient migrations in the Faroe Islands.
ALLISON E. MANN1, EYDFINN MAGNUSSEN2 and CHRISTOPHER R. TILLQUIST1.
The Faroe Islands are a small archipelago in the North Atlantic Ocean. With a current population of approximately 48,000 individuals and evidence of high levels of genetic drift, the Faroese are thought to have remained highly homogeneous since the islands were settled by Vikings around 900CE. Despite their geographic isolation, however, there is historical evidence that the Faroese experienced sporadic contact with other populations since the time of founding. Contact with Barbary pirates in the seventeenth century is documented in the Faroes; there is also the possibility of modern migrations to work in the highly productive fishery. This study set out to distinguish the signal of the original founders from later migrants. Eleven Y-chromosomal STR markers were scored for 139 Faroese males from three geographically dispersed islands. Haplotypes were analyzed using Athey's method to infer haplogroup. Median-joining networks within haplogroups were constructed to determine the phylogenetic relationships within the Faroese and between likely parental populations—Danish, Irish, and Norwegians. Dispersal patterns of individuals around Faroese haplogroups suggest different times of haplotype introduction to the islands. The most common haplogroup, R1a, consists of a large node with a tight network of neighbor haplotypes, such that 68% of individuals are one or two mutational steps away. This pattern may represent the early founder event of R1a in the Faroes. Other distributions, especially of non-Scandinavian haplotypes, document more recent introductions to the islands. The overall pattern is one of a strong founder effect followed by minor instances of later migrations.



Date estimates for major mitochondrial haplogroups in Yemen.
DEVEN N. VYAS1, VIKTOR ČERNÝ2, ALI AL-MEERI3 and CONNIE J. MULLIGAN1.
Yemen occupies a key location as the first stop for anatomically modern humans on a theoretical southern migration route out of Africa. If modern humans did pass through Yemen during the first migrations out of Africa and if they left modern-day descendants, we would expect to see deep divergences in the Yemeni mitochondrial gene tree. Alternatively, if modern humans passed through Yemen but did not leave modern-day descendants or if Yemen was not on the path of these ancient migrations, we would expect more recent dates to be associated with Yemeni mitochondrial haplogroups.
Using 44 previously sequenced mitochondrial genomes as well as 24 newly sequenced mitochondrial genomes from samples collected throughout Yemen, several methods were used to estimate divergence dates of major Yemeni haplogroups including L2, M, R0a and HV. Specifically, phylogenetic trees were generated using MrBayes and maximum likelihood methods. Bayesian and ρ statistic based methods were used to estimate dates of Yemeni haplogroups and these dates were compared with each other, previously published dates for these haplogroups, approximate dates of climatic change that might be expected to correlate with population expansions, and estimates based on archaeological and paleontological evidence for the first migrations out of Africa. These comparisons are intended to cover the range of possible haplogroup divergence dates with respect to the history of early modern humans in southern Arabia.


November 01, 2011

Y-haplogroups E-V13 and G2a in Neolithic Spain

I have not read the paper, so I can't comment in detail. Two quick comments:
  • The discovery of G2a is added to the finds from Treilles, Derenburg, and the Alps. It is now virtually certain that the Neolithic transition in much of Europe, both inland, and coastal involved G2a-bearing men.
  • The discovery of E-V13 in Spain is unexpected on a number of different reasons: there is relatively little of it there now; it had previously been associated with the inland route of the spread of agriculture, as well as the spread of the Greeks to Sicily and Provence, or Roman soldiers at a much later date.
While this Neolithic E-V13 may well have come from the Balkans, and the common ancestor of the very uniform present-day Balkan cluster may have lived after this Spanish find, it is now certain that E-V13 was established in Europe long before the Bronze Age. This highlights the need to avoid Y-STR based calculations on modern populations for inferring patterns of ancient history, and not to conflate TMRCAs with "dates of arrival": "In short: a particular TMRCA is consistent with either the arrival of the lineage long before and long after the TMRCA in a particular geographical area."

At least for now, three of the major players of the European genetic landscape (E-V13, G2a, and I2a) have made their Neolithic appearance. Hopefully, as more ancient DNA is published, and even from later dates, more of them will turn up.

I will comment more when I get to read the paper.

UPDATE I:

From the paper:
For the six male samples, two complete and four partial Y-STRs haplotypes were obtained (Table 3). They allowed classification of individuals into two different haplogroups: G2a (individuals ave01, ave02, ave03, ave05, and ave06, which seem to share the same haplotype) and E1b1b1 (individual ave07). The four markers chosen to confirm belonging to these haplogroups (Y-E1b1b1-M35.1, Y-E1b1b1a1b-V13, Y-G2-M287, and Y-G2a-P15) were typed with a rate of 66%, which permitted confirmation that four males were G2a and one was E1b1b1a1b (Table 3).

Analysis of shared haplotypes showed that the G2a haplotype found in ancient specimens is rare in current populations: its frequency is less than 0.3%(Table S3). The haplotype of individual ave07 is more frequent (2.44%), particularly in southeastern European populations (up to 7%). The Ave07 haplotype was also compared with current Eb1b1a2 haplotypes previously published (10–14). It appeared identical at the seven markers tested to five Albanian, two Bosnian, one Greek, one Italian, one Sicilian, two Corsican, and two Provence French samples and are thus placed on the same node of the E1b1b1a1b-V13 network as eastern, central, and western Mediterranean haplotypes (Fig. S1).
The ancient remains all appeared to lack the common European lactase persistence genotype.

On the mtDNA:
Mitochondrial HVS-I sequences were obtained for the seven individuals and can be classified into four different haplotypes (Table 2). All are still frequent in current European populations (Table S1), and three of them were also found in ancient Neolithic samples (Table S2). These haplotypes permitted the determination that the individuals ave01, ave02, and ave06 belonged to K1a, ave04 and ave05 to T2b, ave03 to H3, and ave07 to U5 haplogroups.
The supporting information (pdf) has a lot of additional information.

PNAS doi: 10.1073/pnas.1113061108

Ancient DNA suggests the leading role played by men in the Neolithic dissemination

Marie Lacan et al.

The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a “multimarkers” approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.

Link

June 16, 2011

Y-chromosomes and mtDNA from medieval Aragonese Pyrenees

I don't see the full article in the journal site yet.

Croat Med J. 2011 Jun 15;52(3):336-43.

Genetic analysis of 7 medieval skeletons from the Aragonese Pyrenees.

Nunez C, Sosa C, Baeta M, Geppert M, Turnbough M, Phillips N, Casalod Y, Bolea M, Roby R, Budowle B, Martínez-Jarreta B.

Abstract

Aim. To perform a genetic characterization of 7 skeletons from medieval age found in a burial site in the Aragonese Pyrenees. Methods. Allele frequencies of autosomal short tandem repeats (STR) loci were determined by 3 different STR systems. Mitochondrial DNA (mtDNA) and Y-chromosome haplogroups were determined by sequencing of the hypervariable segment 1 of mtDNA and typing of phylogenetic Y chromosome single nucleotide polymorphisms (Y-SNP) markers, respectively. Possible familial relationships were also investigated. Results. Complete or partial STR profiles were obtained in 3 of the 7 samples. Mitochondrial DNA haplogroup was determined in 6 samples, with 5 of them corresponding to the haplogroup H and 1 to the haplogroup U5a. Y-chromosome haplogroup was determined in 2 samples, corresponding to the haplogroup R. In one of them, the sub-branch R1b1b2 was determined. mtDNA sequences indicated that some of the individuals could be maternally related, while STR profiles indicated no direct family relationships. Conclusions. Despite the antiquity of the samples and great difficulty that genetic analyses entail, the combined use of autosomal STR markers, Y-chromosome informative SNPs, and mtDNA sequences allowed us to genotype a group of skeletons from the medieval age.

Link

February 11, 2011

Mesolithic mtDNA haplogroup U5a from Luxembourg

Yet another U5a from pre-Neolithic Europe.

From the paper:
Le squelette mésolithique découvert à Reuland-
Loschbour (Fig. 1-2) est conservé au Musée national
d’histoire naturelle de Luxembourg, sous le numéro
20.5.1943. L’inhumation « LSB1 » de l’Homme de
Loschbour est une sépulture primaire datée d’environ 6 000 ans BC (Before Christ), par mesures radio - chronologiques sur le crâne [OxA-7338 : 7 205+/- 50BP (Before Present) soit 6 220-5 990 cal BC] et sur les 2 côtes d’aurochs accompagnant le squelette [GrN- 7115 : 7 115+/-45BP soit 6 070-5 890 cal BC].
This was a 1.6m tall, hyperdolichocephalic, robust, ~60kg male, with an age of 34-47 years. As the authors correctly point out:

Les haplogroupes U5 (65 %) et U4 sont les plus communs (>80%) parmi les chasseurs-cueilleurs d’Europe centrale et orientale (BRAMANTI et al. 2009). L’Homme de Loschbour, d’haplogroupe U5a, fait parfaitement le lien entre ceux-ci et l’Homme de Gough’s Cave (Cheddar Gorge, Somerset, Angleterre), daté de 7 150 BC et également d’haplogroupe U5a. Ces haplogroupes sont plus rares dans toutes ces régions, suite à l’arrivée des premiers agriculteurs de la Culture Linear Band Keramik (BRAMANTI et al. 2009), diffusant des Balkans, et probablement aussi pour d’autres raisons comme la dilution avec d’autres haplogroupes européens anciens présents au moins depuis l’expansion succédant au dernier maximum glaciaire. Actuellement, 11% de la population européenne globale appartiennent au clan U5. Les types U5, U5a et U5b ne représentent plus qu’environ 5 à 7 % de la population d’Europe occidentale, mais restent très fréquents (refuge ?) au Nord de l’Europe, principalement chez les Saami ou Lapons (40 % de la population), les Finlandais et les Estoniens ; ils ont également des représentants en Afrique du Nord (composante méridionale de l’expansion à la fonte des glaces ?) et au Proche Orient, probablement par migration inverse (voir MANCO 2009-2010 ; PONTIKOS 2010).

Bull. Soc. Préhist. Luxembourgeoise 31, 2009, 7-30.

De l’ocre sur le crâne mésolithique (haplogroupe U5a) de Reuland-Loschbour(Grand-Duché de Luxembourg) ?

Dominique Delsate, Jean Michel Guinet et Steven Saverwyns

Summary: A red colored area is present on the left portion of the frontal bone of the mesolithic man from Loschbour. After a preliminary report of the bio-anthropological study of the skeleton, with genetic typing of mitochondrial DNA, we present our attempts to determine the nature of the pigment, by the methods of Raman spectroscopy and elemental analysis by energy dispersive X-ray spectroscopy (EDX). Ochre is proven, and its presence is discussed.

August 18, 2010

Ancient Megalithic mtDNA from France

An extremely interesting paper, the first one on Megalithic remains, and a link between the Megalithic people and the early central European Neolithic Linearbandkeramik, where N1a was unexpectedly detected as a major component a few years ago. I'll probably have more to say on this after I read the paper.

UPDATE:

From the paper:
We reproducibly retrieved partial HVR-I sequences (nps 16,165 to 16,390) from three human remains (Prisse´ 1, 2, and 4, Table 1), one adult and two children deposited during different stages of use of the burial chamber. Corresponding sequences could be unambiguously assigned to haplogroups X2, U5b, and N1a (Table 2 and Supporting Online Information).
Haplogroup U5b subclusters are believed to have spread from central-southern Europe post-LGM. Haplogroup X2 is believed to have spread from the Near East and Mediterranean Europe; it is one of those mystery haplogroups that turn up in the Taklamakan desert as well as Native Americans. Together with the clearly invasive nature of N1a, these results are consistent with migrationism.

The authors write:
The widespread distribution of the N1a lineage in Early and Middle Neolithic northwestern Europe may indicate genetic continuity from Mesolithic populations.
This scenario would support a Mesolithic contribution to the earliest Neolithic of Atlantic Europe. This would imply that the N1a lineage was already common in
indigenous north European populations and that the spread of the Neolithic was principally the result of cultural diffusion. Although so far the N1a lineage has not
been encountered among late European hunter-gatherers in central and north Europe (Bramanti et al., 2009; Malmstro¨m et al., 2009), it is worth noting that less
than half of the hunter-gatherers’ paleogenetic data come indeed from the pre-Neolithic period (predating LBK expansion). Finally, no paleogenetic data currently
exist for the Mesolithic period in Western Europe. This prevents any conclusion being drawn about N1a occurrence during the Mesolithic period in those regions.
Of course we won't know if N1a occurred in France prior to the Neolithic until we test pre-Neolithic French samples. However, if N1a was present in France prior to the Neolithic, then why wasn't it present in central-northern Europe where substantial sample sizes exist? This would require a partition of pre-Neolithic populations of Europe, and also existence of N1a in both the Linearbandkeramik (that spread on a south-north vector) and in Mesolithic French. So, while we wait for pre-Neolithic Western Europeans to come up N1a, I'm willing to wager that they will not, and that N1a spread into France with the Neolithic or the later spread of Megalithic cultures.

Related:

American Journal of Physical Anthropology DOI: 10.1002/ajpa.21376

News from the west: Ancient DNA from a French megalithic burial chamber

Marie-France Deguilloux et al.

Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices.

Link

April 22, 2010

Origin and dispersal of mtDNA haplogroup U5 (Malyarchuck et al. 2010)

From the conclusion:
Genetic data obtained in this study allows the suggestion that during the LGM period, central European territories probably represented the area of intermingling between human flow from refugial zones in the Balkans, the Mediterranean coastline and the Pyrenees, as U5a and U5b gene flows occurred from there. Based on dating analysis of the U5 subclusters, it seems very likely that, despite the archaeological evidence testifying to the presence of humans in eastern Europe during the Ice Age, this part of Eurasia might have only been re-populated by modern humans at the end of the LGM, i.e. later than central Europe. In addition, U5b gene flow from central to eastern Europe become much more intense after the LGM. In general, we believe that molecular genetic data, in addition to archaeological and fossil evidence, are of significant use for resolving key questions regarding the interaction of human communities and climate.
The presence of mtDNA U2 in Russia (Kostenki) 30 thousand years ago, and the discovery of plentiful U5 in pre-farming populations is consistent with the scenario proposed by the authors. Now, if we find a U5 type in eastern Europe of e.g., Kostenki-age, the authors' hypothesis will be rejected. But, so far, the late (but pre-farming) time frame proposed by the authors is consistent with all our ancient European mtDNA sample points.

The sequence of events, as they now appear, include the earliest appearance of U2 in the eastern European plain (and possibly U4), the later appearance of U5, and then the advent of farming via the Balkans and Central Europe which brought the full suite of present-day Caucasoid haplogroups into the region.

PLoS ONE doi:10.1371/journal.pone.0010285

The Peopling of Europe from the Mitochondrial Haplogroup U5 Perspective

Boris Malyarchuk et al.

Abstract

It is generally accepted that the most ancient European mitochondrial haplogroup, U5, has evolved essentially in Europe. To resolve the phylogeny of this haplogroup, we completely sequenced 113 mitochondrial genomes (79 U5a and 34 U5b) of central and eastern Europeans (Czechs, Slovaks, Poles, Russians and Belorussians), and reconstructed a detailed phylogenetic tree, that incorporates previously published data. Molecular dating suggests that the coalescence time estimate for the U5 is ~25–30 thousand years (ky), and ~16–20 and ~20–24 ky for its subhaplogroups U5a and U5b, respectively. Phylogeographic analysis reveals that expansions of U5 subclusters started earlier in central and southern Europe, than in eastern Europe. In addition, during the Last Glacial Maximum central Europe (probably, the Carpathian Basin) apparently represented the area of intermingling between human flows from refugial zones in the Balkans, the Mediterranean coastline and the Pyrenees. Age estimations amounting for many U5 subclusters in eastern Europeans to ~15 ky ago and less are consistent with the view that during the Ice Age eastern Europe was an inhospitable place for modern humans.

Link

February 19, 2010

Y chromosomes and mtDNA in Bronze Age Tarim basin

This appears to be a published study by the same team which appeared in a recent National Geographic documentary on the Tarim mummies. The site of Xiaohe (of the current study) is earlier and to the southeast of Urumqi.

The finding that the Bronze Age population, like that of Krasnoyarsk Siberians belonged exclusively -as far as sampling allows- to Y-chromosome haplogroup R1a1 is extremely interesting as it raises the issue of when and how exactly the diverse extant Y-chromosome gene pool of Central Asia came about.

We can now confidently say that even at the early age of ~4ky BP an R1a1-bearing population of presumably western Eurasian origin had acquired a mixed mtDNA gene pool consisting of both west- and east-Eurasian mtDNA, which agrees with what was presented in the aforementioned documentary, in which many of the seemingly Caucasoid mummies had East Eurasian mtDNA.

From the paper:
The dominant haplogroup in the Xiaohe people was the East Eurasian lineage C, shared by 14 Xiaohe individuals who were associated with two different mtDNAhaplotypes (S1 and S2). According to the coding region 11969 A to G, all lineage C found in the Xiaohe people were further classified to subhaplogroup C4, which had D-loop group-specific polymorphisms at nucleotide positions (np) 16298 (T to C) and16327 (C to T) [18].

...

Besides the East Eurasian lineage, two West Eurasian mtDNA haplogroups H and K were found among the Xiaohe people. H lineage is the most common mtDNAhaplogroup in West Eurasia [20], but haplogroup H with a 16260T was shared by only nine modern people in Genbank, including one Italian, one German, one Hungarian,one Portuguese, one Icelander and four English people. Haplogroup K, a western Eurasian–specific haplogroup, is mainly distributed in Europe, central Asia, and Iran [20, 21]. However, haplogroup K with 16134T, found in the Xiaohe people, has not been found in modern people to our knowledge.

...

Among the Xiaohe people, three sequences with the unique HVRI motif 16189–16192–16311 formed a subcluster (Figure 2) and were not shared by modern people. [...] The results showed that they are related neither to the West Eurasian haplogroups UK, TJ, HV, R11and R1, nor to the East Eurasian haplogroups B and F. So we designated them as haplogroup R*temporarily. Another sequence with motif 16223–16304, shared by some people fromEast Asia, India, and Europe, was assigned to haplogroup M*.

The mtDNA results are interesting because they tie in with my theory of a boreal mtDNA-U zone which has recently found further support (and extended in time) with the mtDNA testing of Kostenki. Like the Krasnoyarsk Siberians the Caucasoid component in Xiaohe is light on U. Unfortunately, we don't have enough information to place the origin of this component in a particular region of West Eurasia.

A graphical display of this theory can be seen in Figure 5 from the paper (left). Sites 8, 9 and 3 (Lake Baikal and Xiognu) only have U5 "western" mtDNA, and, as I have argued in my previous post, represent the eastern edge of the "boreal zone" to which were added non-U bearing Caucasoids from the west.

As for the Y-chromosome results:
The Y chromosome haplogroup of the sevenmales were all assigned to haplogroup R1a1a through screening the Y-SNPs at M89,M9, M45, M173 and M198 successively. Haplogroup R1a1a is widely distributed inEurasia: it is mainly found in Eastern Europe, Central Asia, South Asia, Siberia,ancient Siberia, but rare in East Asia [22-24].
The authors address the origins of the admixture:
Given the unique genetic haplotypes and the particular archaeological culture, the
time of this admixture could be much earlier than the time at which the Xiaohe people were living at the site. This means that the time of their mingling was at least a 1000 years earlier than previously proposed.

...

The admixture therefore
probably occurred elsewhere, before immigration into the Tarim Basin. The Xiaohe
people might well have been an admixture at the time of their arrival. Where did the
initial admixture occur?
To answer that question, the authors identify Afanasievo and other steppe cultures as related to the Xiaohe people. This is not very surprising as the Afanasievo people were described in the anthropological literature as prominent-nosed Caucasoids of western origin, although individual skulls show Mongoloid influences.

So, it's possible that the admixture took place in Siberia, and an already admixed population found its way to Xiaohe by ~4ky BP. The important question is: what happened to the male lineages of the eastern component of this population?

Years ago, I advanced a "pendulum" theory of migrations in Eurasia to explain the fact that quite often we find in the northern belt from Europe to China populations with typically Western/Eastern Y-haplogroups accompanied by the "opposite" (Eastern/Western) mtDNA.

According to my thinking, this is due to the patriarchal nature of mobile Eurasian societies (whether nomads or hunters) in which the "clan" maintains its Y-chromosome gene pool but incorporates foreign females. Thus, the absence of non-R1a1 chromosomes can be explained by the fact that non-R1a1 male individuals were not incorporated into the "western" tribe that made its way across Eurasia from Europe to China, but Eastern Eurasian-mtDNA bearing females were gradually absorbed; such would have been plentiful among the indigenous Mongoloid populations that lived east of the Urals since the Paleolithic.

Thus, at the eastern end of this migration, we ended up with an R1a1-pure/East Eurasian mtDNA-heavy population.

Years later, the pendulum of Eurasian migration swung backwards, with some of the Asian R1a1-bearing individuals returning towards Europe (starting with the Scythians) to meet their distant cousins, this time shedding whatever east Eurasian mtDNA gene pool they had acquired, for the regular west Eurasian mtDNA gene pool that would have been reinforced in the return journey.

BMC Biology doi:10.1186/1741-7007-8-15

Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age

Chunxiang L et al.

Abstract

Background
The Tarim Basin, located on the ancient Silk Road, played a very important role in the history of human migration and cultural communications between the West and the East. However, both the exact period at which the relevant events occurred and the origins of the people in the area remain very obscure. In this paper, we present data from the analyses of both Y chromosomal and mitochondrial DNA (mtDNA) derived from human remains excavated from the Xiaohe cemetery, the oldest archeological site with human remains discovered in the Tarim Basin thus far.

Results
Mitochondrial DNA analysis showed that the Xiaohe people carried both the East Eurasian haplogroup (C) and the West Eurasian haplogroups (H and K), whereas Y chromosomal DNA analysis revealed only the West Eurasian haplogroup R1a1a in the male individuals.

Conclusion
Our results demonstrated that the Xiaohe people were an admixture from populations originating from both the West and the East, implying that the Tarim Basin had been occupied by an admixed population since the early Bronze Age. To our knowledge, this is the earliest genetic evidence of an admixed population settled in the Tarim Basin.

Link

February 05, 2010

mtDNA in Iberian Northern Plateau

Am J Phys Anthropol doi:10.1002/ajpa.21252

Mitochondrial DNA patterns in the Iberian Northern plateau: Population dynamics and substructure of the Zamora province

Luis Alvarez et al.

ABSTRACT

Several studies have shown the importance of recent events in the configuration of the genetic landscape of a specific territory. In this context, due to the phenomena of repopulation and demographic fluctuations that took place in recent centuries, the Iberian Northern plateau is a very interesting case study. The main aim of this work is to check if recent population movements together with existing boundaries (geographical and administrative) have influenced the current genetic composition of the area. To accomplish this general purpose, mitochondrial DNA variations of 214 individuals from a population located in the Western region of the Iberian Northern plateau (the province of Zamora) were analyzed. Results showed a typical Western European mitochondrial DNA haplogroup composition. However, unexpected high frequencies of U5, HV0, and L haplogroups were found in some regions. The analyses of microdifferentiation showed that there are differences between regions, but no geographic substructure organization can be noticed. It can be stated that the differences observed in the genetic pool of the sampled area at regional level results from the mixture of different populations carrying new lineages into this area at different points in history.

Link

November 25, 2009

Sex-biased admixture in the Americas (Stefflova et al. 2009)


PLoS ONE doi:10.1371/journal.pone.0007842

Evaluation of Group Genetic Ancestry of Populations from Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas

Klara Stefflova et al.

Abstract

Background
Population history can be reflected in group genetic ancestry, where genomic variation captured by the mitochondrial DNA (mtDNA) and non-recombining portion of the Y chromosome (NRY) can separate female- and male-specific admixture processes. Genetic ancestry may influence genetic association studies due to differences in individual admixture within recently admixed populations like African Americans.

Principal Findings
We evaluated the genetic ancestry of Senegalese as well as European Americans and African Americans from Philadelphia. Senegalese mtDNA consisted of ~12% U haplotypes (U6 and U5b1b haplotypes, common in North Africa) while the NRY haplotypes belonged solely to haplogroup E. In Philadelphia, we observed varying degrees of admixture. While African Americans have 9–10% mtDNAs and ~31% NRYs of European origin, these results are not mirrored in the mtDNA/NRY pools of European Americans: they have less than 7% mtDNAs and less than 2% NRYs from non-European sources. Additionally, there is Additionally, there is less than 2% Native American contribution to Philadelphian African American ancestry and the admixture from combined mtDNA/NRY estimates is consistent with the admixture derived from autosomal genetic data. To further dissect these estimates, we have analyzed our samples in the context of different demographic groups in the Americas.

Conclusions
We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America. The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization. These data suggest that genomic data correlate well with historical records of colonization in the Americas.

Link

October 13, 2009

Migrationism strikes back

In 1939, Carleton Coon wrote the Races of Europe. In it, he used the "skulls and pots as migrations" paradigm of his times, to infer a number of Neolithic and post-Neolithic migrations into Europe. A map from the chapter on the Neolithic Invasions captures his conception of prehistory well:


This map was drawn before carbon dating had been invented. We now know much more about both the anthropology and archaeology of Europe. But, the main thrust of Coon's prehistorical narrative can be summarizes as arrows on a map, or, prehistory as a series of invasions. The closing paragraph from the Neolithic Invasions chapter sums up this view admirably:
Five invasions, then, converging on Europe from the south and east, brought a new population to Europe during the third millennium B.C., and furnished the racial material from which living European populations are to a large extent descended.
Today, carbon dating has pushed the arrival of the Neolithic to Europe into the 7th millennium BC, but, disregarding that detail, we can see that Coon thought that modern Europeans are primarily descended from Neolithic and post-Neolithic populations: farmers, seafarers and pastoralists from the south and east.

He did think that the Upper Paleolithic population had not disappeared completely, but the name he often used to describe them was survivors, which denoted quite clearly their limited contribution to the present-day population.

Acculturation & Demic Diffusion

After WWII, the arrows on a map paradigm was no longer in fashion. The transition from the old to the new prehistory did not happen overnight, but two new intellectual fashions gained ground: acculturation and demic diffusion.

The proponents of acculturation were motivated by a reaction to the pots and skulls paradigm. To the idea that the spread of a new pottery type, or a new type of skull morphology indicated the spread of a people across the map, they countered that (i) pottery could be exchanged, copied, and traded without the movement of people, and (ii) that conclusions based on typological old-style anthropology were unsupportable, and the limitless malleability of the human skull was affirmed.

In some respects, the acculturation hypothesis represented a valid response to the excesses of the pots and skulls tradition. But, they went a bit too far in presenting a picture of complete stasis, in which European people, seemingly fixed to the ground, participated only in "networks of exchange", only ideas and goods flowed, and all differences in physical type across long time spans were ascribed invariably to responses (genetic or plastic) to new technologies, but almost never to the introduction of a new population element.

Demic diffusion is not as extreme as the pure acculturation hypothesis, but it replaces the model of invasions and migrations represented by arrows with a purposeless random walk. Demic diffusion has been argued on both archaeological and genetic grounds.

When Cavalli-Sforza and colleagues collected genetic data on modern Europeans, and subjected them to principal components' analysis made possible by modern computers, they discovered that the first principal component of genetic variation was oriented on a southeast-northwest axis.

At roughly the same time, the widespread dating of Neolithic sites across Europe proved that there was a fairly regular advent of farming, with the earlier sites found in Greece, and the latest ones in the Atlantic fringe and northern Europe.

Demic diffusion was summoned to explain these phenomena. Neolithic farmers, the story goes, did not particularly want to colonize Europe. Europe was colonized as a side-effect of a random process in which farmers moved away from their parent's home, while their population numbers grew due to the increased productivity of the farming economy.

The process was not seen as one of population replacement, however. Rather, it was seen as a slow movement of a wave of advance, in which farmers mixed with hunter-gatherers, and some of them moved on to populate new lands beyond the farmer-hunter frontier. The model predicted that the technology would spread without large-scale population replacement, as the hunters' genes would make a substantial contribution to farmers' gene pools at the furthest end of their expansion.

The Paleolithic Europeans make a comeback

Bryan Sykes' The Seven Daughters of Eve was a popular treatment of a new wave of acculturation-minded scholarship whose more formal expression was the masterful Tracing European Founder Lineages in the Near Eastern mtDNA Pool by Martin Richards et al.

Whereas Cavalli-Sforza and his colleagues had looked at dozens of polymorphisms, their synthetic PC maps of Europe didn't come with dates or easy explanations. The observed clines in Europe may have been due to Paleolithic, Neolithic, or even recent historical events. While they were consistent with the Neolithic demic diffusion hypothesis, the possibility existed that they may have been formed either earlier, or later than the Neolithic.

The new approach by Sykes, Richards, and their colleagues, looked at just mtDNA, but due to its being inherited from mother to daughter without recombination, they could (i) estimate the age of the common ancestors of the "European mothers", (ii) study the patterns of geographical distribution of their descendants to infer when and where they may have lived. Hence, the various stories about Katrine, Ulrike, Helena, etc. in Sykes's book.

The conclusions of the new methodology were clear (at least to the authors' satisfaction):
This robustness to differing criteria for the exclusion of back-migration and recurrent mutation suggests that the Neolithic contribution to the extant mtDNA pool is probably on the order of 10%–20% overall. Our regional analyses support this, with values of 20% for southeastern, central, northwestern, and northeastern Europe. The principal clusters involved seem to have been most of J, T1, and U3, with a possible H component. This would suggest that the early-Neolithic LBK expansions through central Europe did indeed include a substantial demic component, as has been proposed both by archaeologists and by geneticists (Ammerman and Cavalli-Sforza 1984; Sokal et al. Sokal et al., 1991 RR Sokal, NL Ogden and C Wilson, Genetic evidence for the spread of agriculture in Europe by demic diffusion, Nature 351 (1991), pp. 143–144.1991). Incoming lineages, at least on the maternal side, were nevertheless in the minority, in comparison with indigenous Mesolithic lineages whose bearers adopted the new way of life.

The picture of continuity since the Paleolithic was further supported in the much briefer article by Semino et al. (pdf) on The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective. This study, based mostly on the observation of rough congruences of the European map with some Y-chromosome markers set the stage for most Y-chromosome work in Europe for the next decade.

In today's terminology, this paper suggested that, like mtDNA, most European Y-chromosomes were Paleolithic in origin, and belonged in haplogroups R1b, R1a, and I which repopulated Europe from refugia in Iberia, the Ukraine, and the Balkans, after the last glaciation. To this set were added Neolithic immigrants from the Middle East bearing haplogroups J, G, and E1b1b, and Northern Asian immigrants from the east bearing haplogroup N1c.

Unfortunately, we do not have Y-chromosome data of Paleolithic age to determine the veracity of this scenario. Given present-day distributions, we can be fairly certain of a European origin (but when?) of haplogroup I, of a non-European origin of haplogroup E1b1b (via North Africa or the Middle East), and of N1c. A non-European origin of the entire haplogroups J and G in West Asia also seems quite probable.

The house of cards collapses

The beauty of science is that new data can always falsify cozy and plausible scientific theories. In the case of European prehistory, this occurred due to a combination of craniometric, archaeological, and mtDNA data.

Pinhasi and von Cramon-Taubadel (2009) examined skulls from the early Central European Neolithic (Linearbandkeramik) and found them to be closer to Neolithic skulls from Balkans and West Asia, rather than the per-farming Mesolithic populations.
Our results demonstrate that the craniometric data fit a model of continuous dispersal of people (and their genes) from Southwest Asia to Europe significantly better than a null model of cultural diffusion.
The authors correctly identified their data as rejecting cultural diffusion, but their conclusion that they supported demic diffusion was not warranted as there was really no evidence that Neolithic groups were "transformed" by gradual slow admixture with hunter-gatherers in their march into Europe. Their data could just as easily be explained by plain migration.

Archaeologists also made a strong case for a rapid diffusion of the Neolithic in the Mediterranean. Neolithic settlements appeared suddenly, fully-formed, occupied regions abandoned by Mesolithic peoples, and spread not slowly, in a wave of advance, but rapidly, as a full-fledged colonization:
Thus it appears that none of the earlier models for Neolithic emergence in the Mediterranean accurately or adequately frame the transition. Clearly there was a movement of people westward out of the Near East all of the way to the Atlantic shores of the Iberian Peninsula. But this demic expansion did not follow the slow and steady, all encompassing pace of expansion predicted by the wave and advance model. Instead the rate of dispersal varied, with Neolithic colonists taking 2,000 years tomove from Cyprus to the Aegean, another 500 to reach Italy, and then only 500–600 years to travel the much greater distance from Italy to the Atlantic (52).
In a different study Vanmontfort et al. studied the geographical distribution of farmers and hunter-gatherers during first contact in Central Europe. This contact did not involve either adoption of farming by hunter-gatherers (as in the acculturation hypothesis), or admixture with hunter-gatherers (as in the demic diffusion/wave of advance model). Rather, agriculturalists and hunter-gatherers tended to avoid each other for 1,000 years after first contact!
To conclude, the following model can be put forward. During the 6th Millennium cal BC, major parts of the loess region are exploited by a low density of hunter–gatherers. The LBK communities settle at arrival in locations fitting their preferred physical characteristics, but void of hunter–gatherer activity. Evidently, multiple processes and contact situations may have occurred simultaneously, but in general the arrival of the LBK did not attract hunter–gatherer hunting activity. Their presence rather restrained native activity to regions located farther away from the newly constructed settlements or triggered fundamental changes in the socio-economic organisation and activity of local hunter–gatherers. Evidence for the subsequent step in the transition dates to approximately one millennium later (Crombé and Vanmontfort, 2007; Vanmontfort, 2007).
The "Paleolithic" case won a short-lived victory when Haak et al tested mtDNA from early Central European farmers, discovering that they had a high frequency of haplogroup N1a which is rare in modern Europeans. This finding was interpreted as evidence that the incoming Neolithic farmers were few in numbers and were absorbed with barely a trace by the surrounding Mesolithic populations who adopted agriculture. Acculturation seemed to have won the day! The case was, however, tentative, and hinged on the assumption that the Paleolithic Europeans -who had not been tested yet- would have a gene pool similar to that of modern Europeans.

When hunter-gatherer mtDNA was tested in both Scandinavia (by Malmström et al) and Central/Eastern Europe (by Bramanti et al.), it turned out that continuity from the Paleolithic was rejected. Hunter-gatherers were dominated by mtDNA haplogroup U, and subgroups U4/U5 in particular. None of the other lineages postulated by Sykes et al. as being "Paleolithic" in origin were found in them. Moreover, there was substantial temporal overlap between hunter-gatherer and farmer cultures, but farmers seemed to lack mtDNA typical of hunter-gatherers and vice versa. Confirming the archaeological picture of the two groups avoiding each other, it now seemed that there was little genetic contact between the two, at least in the early age. The Neolithic spread by newcomers; there was no acculturation of Mesolithic people; there was no slow process of admixture between farmer and hunter along a wave of advance.

The gap between contemporaneous farmer and hunter mtDNA gene pools was as large as that found between modern Europeans and native Australians! The whole controversy about the relative contributions of the Neolithic and Paleolithic in the modern European gene pool was found to be beside the point. The modern European gene pool did not seem to be particularly similar to either Paleolithic hunter or Neolithic farmer: it possessed any haplogroups completely absent in pre-Neolithic Europe. And, it did not have a high frequency of the N1a "signature" haplogroup of the Neolithic. Selection, migration, or a combination of both had reshaped the European gene pool from the Neolithic onwards.

Where things stand

We have come full circle. Once again, Paleolithic Europeans assume the status of survivors, as their typical lineages are observed in a small minority of modern Europeans. The evidence for widespread acculturation of European hunter-gatherers or their significant genetic contribution to incoming farmers along a wave of advance is just not there. Hunters and farmers possessed distinctive gene pools, and farmers expanded with barely a trace of absorption of hunter gene pools.

Clearly many details remain to be filled out. What does seem certain, however, is that dramatic events took place starting at the Neolithic, and that modern Europeans trace their ancestry principally to Neolithic and post-Neolithic migrants, and not to the post-glacial foragers who inhabited the continent.