A chronology of ancient Egypt

PNAS doi: 10.1098/rspa.2013.0395
An absolute chronology for early Egypt using radiocarbon dating and Bayesian statistical modelling

Michael Dee et al.

The Egyptian state was formed prior to the existence of verifiable historical records. Conventional dates for its formation are based on the relative ordering of artefacts. This approach is no longer considered sufficient for cogent historical analysis. Here, we produce an absolute chronology for Early Egypt by combining radiocarbon and archaeological evidence within a Bayesian paradigm. Our data cover the full trajectory of Egyptian state formation and indicate that the process occurred more rapidly than previously thought. We provide a timeline for the First Dynasty of Egypt of generational-scale resolution that concurs with prevailing archaeological analysis and produce a chronometric date for the foundation of Egypt that distinguishes between historical estimates.

Link

World map of Y-chromosome haplogroups

This map was posted on Wikipedia and while I would not vouch for all its details, it is nonetheless and impressive effort of visually summarizing what we know about worldwide Y-chromosome distribution.

I don't know if this type of visual representation is even possible: there are peoples like native Americans, or Bantu farmers where a single haplogroup dominates decisively, but most human groups show a mix of a variety of lineages at different frequencies. The wide distribution of haplogroup G for example -which occurs throughout west Eurasia, but is only dominant in the Caucasus and some populations of the Near East- could not be guessed from this map. The labeling of R1 as "NE Amerindian" is peculiar, given the likely introduction of this lineage with European colonists.

In any case, this pushes to the limit what is possible for map-making at this scale, and underscores the complexities of the present-day distribution of Y-chromosome haplogroups.

ISABS 2013 abstracts

From the book of abstracts (pdf):

MITOCHONDRIAL DNA AND PHYLOGENETIC ANALYSIS OF PREHISTORIC NORTH AFRICAN POPULATIONS

North Africa is located at a crossroad between Europe, Africa and Asia and has been inhabited since the Prehistoric time. In the Epipaleolithic period (23.000 years to 10.000 years BP), the Western North Africa has been occupied by Mecha- Afalou Men, authors of the Iberomaurusian industry. The origin of the Iberomaurusians is unresolved, several hypotheses have been forwarded. With the aim to contribute to a better knowledge of the Iberomaurusian settlement we analysed the mitochondrial DNA (mtDNA) of skeletons exhumed from the prehistoric site of Taforalt in Morocco (23.000-10.800 years BP) and Afalou in Algeria (11.000 to 15.000 BP -Algeria). Hypervariable segment 1 of mtDNA from 38 individuals were amplified by Real-Time PCR and directly sequenced. Sequences were aligned with the reference sequence to perform the mtDNA classification within haplogroups. Phylogenetic analysis based on mitochondrial sequences from Mediterranean populations was performed using Neighbor-Joining algorithm implemented in MEGA program. mtDNA sequences from Afalou and Taforalt were classified in Eurasiatic and North African haplogroups. We noted the absence of Sub-Saharan haplotypes. Phylogenetic tree clustered Taforalt with European populations. Our results excluded the hypothesis of the sub-Saharan origin of Iberomaurusians populations and highlighted the genetic flow between Northern and Southern cost of Mediterranean since Epipaleolithic period.

DISCONTINUITY SCREENING OF THE EARLY FARMERS’ MT-DNA LINEAGES IN THE CARPATHIAN BASIN

Discontinuous mitochondrial (mt) haplotype data between Central-Europe’s first farmers and contemporary Europeans have been described before. Hungary was a key-area of the Neolithisation, in the route of Neolithisation following the River Danube, and that was also the birthplace of the Linear Pottery Culture, which later colonised Western and Northern Europe. Neolithic and post-Neolithic human remains as well as contemporary population of Hungary is involved in our project to gain information on their mt-haplotype pattern and especially on the frequency of Asian haplotypes in the Carpathian Basin. HVS-I sequences from nt15977 to nt16430 of Neolithic specimens with sufficient mtDNA preservation among an extended Neolithic collection were analysed for polymorphisms, identifying 23 different ones. A novel, N9a, N1a, C5, D1/G1a, M/R24 haplogroups were determined among the pre-industrial Hungarians. The presence of Asian haplotypes in the ancient populations must be taken into consideration when reconstructing the population history of Europe and Asia, so a survey of the recent Asian haplotype frequency in Europe is unavoidable. The ancient and recent haplotype pattern of Hungary is definitely worth further investigation to test a theory on the continuous population history of Europe, wheter genetic gaps between ancient and recent human populations of Europe were more likely to be detected. 

ANTHROPOLOGIC AND MITOCHONDRIAL DNA ANALYSIS OF A MEDIEVAL GRAVEYARD FROM SOPOT (CROATIA)

Anthropologic and DNA analysis of human remains recovered from a graveyard in ©opot near Benkovac (Croatia) dating to the 14th/15th century was conducted in order to reconstruct the origin and life conditions of the people populating the region at that time. The dynamics of the population represented in this graveyard are important for understanding Croatian history because the deceased individuals were buried according to pagan ritual which was uncommon in a post Christianization period. Human remains from a total of 31 graves were analyzed, in which 47 individuals were found (9 female, 23 male and 15 children). Average age at death for adults was lower than expected (for female 28.9, male 32.4 years), suggesting that the living conditions of these individuals were poor. In addition, 10 antemortem traumas were visible on 6 adults, which is a higher rate than expected, and indicates potential violence within the population group. Finally, mitochondrial DNA (mtDNA) analysis was performed on hypervariable regions one and two for 46 of the individuals. Due to the age and condition of the remains, only 19 of the samples yielded full sequence profiles. Haplogroup analysis was performed for these 19 individuals, with the majority of the results falling within the most common groups in present-day Croatia. However, examination of the lesscommon haplogroups suggested a possible migration of individuals from Asia. Collectively, the physical and molecular results from this study provide evidence to suggest that individuals recovered from this gravesite are not from the current indigenous population.

MATERNAL GENETIC PROFILE OF A NORTHWEST ALGERIAN POPULATION

The North African population gene pool based on mitochondrial DNA (mtDNA) polymorphisms has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. Recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North- South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the continent. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population. mtDNA sequences analysis was performed on the regulatory hypervariable segment I region (HVSI). Haplogroup diagnostic mutations were analyzed using PCR-RFLPs and/or SNaPshot multiplex reactions. Of all North African populations, Eurasian lineages are the most frequent in Algeria (80%) while sub-Saharan Africa origin accounts for the remaining (20%). Within them, the North African genetic component U6 and M1 count for 20%. Indeed, the U6 haplogroup, highly distributed in Northwestern African populations, show a high frequency in Algeria (11.83%), while, the M1 frequency (7.1%) raises an anomalous peak in its decreasing Northeast - Northwest gradient. Moreover, the high frequency of HV subgroups (38.33%) point to direct maritime contacts between the European and North African western sides of the Mediterranean. Besides, the most common western H subgroups, H1 (47.8%) and H3 (10.1%), represent 60% of H lineages. These frequencies and HV0 (7.5%) lie well within the observed Northwestern to Northeastern African decreasing gradients.

MATERNAL GENETIC VARIATION OF THE SLOVENIAN POPULATION IN A BROADER EUROPEAN CONTEXT AND COMPARED TO ITS PATERNAL COUNTERPART

Slovenia is a European country situated at the crossroads of main European cultural and trade routes. It is geographically more linked to Central Europe, but history draws it closer together to its ex-Yugoslavian, Southeast European (SEE) neighbors. Slovenian maternal heritage has not been analyzed since 2003 and our aim was to analyze SNP markers of 97 Slovenian mtDNAs in high resolution to see where this population fits according to its maternal genetic variation. We compared the Slovenian sample with the neighboring SEE populations, as well as with other published European population datasets. Also, we compared the obtained mtDNA variation results with the available Slovenian Y chromosome data to see how these two uniparental marker systems correspond to each other. In the PC plot based on mtDNA haplogroups frequencies, Slovenian population has an outlying position mostly due to the increased prevalence of J (14.4%) and T (15.4%) clade and especially because of the abundance and diversity of J1c samples in Slovenia, represented with 8 haplotypes and in a percentage of >11%. Although in an outlying position, Slovenian mtDNA variation still shows a certain degree of affinity to SEE. On the contrary, Slovenia’s paternal genetic heritage yielded results that correspond to the population’s geographic location and groups Slovenian population considerably closer to Central European countries, based on increased prevalence of Northern/Central European R1a-M198 and decreased frequency of Balkan-specific I2a2-M423. Such differences in maternal and paternal marker systems could indicate that Slovenian genetic variation was influenced by sex-biased demographic events.

AN ASIAN TRACE IN THE GENETIC HERITAGE OF THE EASTERN ADRIATIC ISLAND OF HVAR

The Island of Hvar is situated in the central eastern Adriatic, and its relatively small rural population has been reproductively isolated thought history. Therefore, founder effects, genetic drift and inbreeding have had significant role in the shaping of current genetic diversity of Hvar Islanders. We analyzed Y-chromosome SNP markers of 412 Hvar islanders in high resolution, with the aim to investigate the current paternal genetic diversity. We found a relatively high frequency (6.1%) of unrelated male samples belonging to the Q*-M424 haplogroup, which is unusual for European populations. Interestingly, a previous study showed 9 individuals from Hvar with mitochondrial haplogroup F, which is almost absent in Europe. Both findings could indicate a certain connection with Asian populations, where these haplogroups are most common. This might be a result of several migratory events in the history, one of which could be linked to the ancient Silk Road, the other a consequence of the arrival of the Slavs, following the Avars, to the eastern Adriatic in the 6th century or due to the expansion of the Ottoman Empire in 16th to 18th century. The presence of these rare mitochondrial and Y-chromosome lineages are an example of founder effect and random genetic drift which, in this small island with a high degree of isolation and endogamy, had a strong impact on shaping the genetic diversity of the population. 

GENETIC PORTRAIT OF THE BESERMYAN ETHNIC GROUP BASED ON MTDNA HAPLOGROUP STUDY

Besermyan are a small ethnic group living in the Volga-Ural region of Russia. They belong to Finno-Ugric language group, but speak a special dialect. There are some Bulgar-Chuvash borrowings in their adverb vocabulary that are absent in other dialects of the Udmurt language. Besermyan live in the northwestern part of modern Udmurtia in the Cheptsa basin. In 2002 their number was about three thousand. The Besermyan origin is a very interesting issue. There is a view that the endonym Besermyan (beserman) is derived from the Turkic word which means flMuslim« in Arabic. This hypothesis, along with their language, hints at the origin of this ethnic group; however the genetic portrait of Besermyan has not been described yet. In our study we used the data of mitochondrial DNA (mtDNA) HVSI sequencing from 98 Besermyans representing 10 villages in Udmurtia Republic of Russia. The prevalence of Western Eurasian mtDNA lineages (91.7%) over Eastern Eurasian ones (9.2%) was shown in the studied population which is consistent with the structure of mtDNA pool of Finno-Ugric ethnic groups of the Volga-Ural region. Some Eastern Eurasian lineages in Besermyan are represented by haplogroups D4b, A4b and Z1a which are also common in Udmurts. It is important to note though that the share of Western Eurasian component in Udmurts according to previous study by Bermisheva et al. (2002) is about 74.5% so mtDNA haplogroup distribution in Besermyans is closer to other Finno-Ugric people of the Volga-Ural region: Mordvins and Maris.

COSMOPOLITAN CENTRAL ASIA: TAJIK MTDNA TRACES THE EASTWEST MOVEMENT OF ANCIENT NOMADS 

Tajikistan is a country in the mountains of southeast Central Asia. Due to its isolation, mtDNA variation in the Tajiks has been fragmentary studied on a limited number of samples. In 1997 saliva samples were collected from unrelated Tajiks across Tajikistan. After long-term preservation DNA was extracted from 2 mm FTA discs. Due to degradation mtDNA was amplified using the primary and secondary PCRs with nested primers in the multiplex format. The origin of 91 mitochondrial genomes from Tajikistan traced from western Eurasia (62.6%), eastern Eurasia (25.3%), south Asia (11.0%), and North Africa (1.1%). Significant population structure in the distribution of these mtDNA lineages was revealed within the regional groups in Tajikistan. The mtDNA variation was compared between the Tajiks and 45 populations of Eurasia. Pairwise Fst comparisons and the correspondence analysis revealed non-significant differences between the Tajik and Uzbek populations. Although both nations speak languages belonging to different linguistic groups, this result corresponds to their cultural and economic proximity. Surprisingly, after the Uzbeks, the Tajik mtDNA pool most closely resembles to the Ossetians, an Indo-Iranian people from the North Caucasus. The Tajiks also display intensive gene flow and admixture with some other populations of Central Asia and the Iranian Plateau living along the centers and crossroads of the earliest civilizations and belonging to different linguistic groups including the Uyghur, Kazakh, Karakalpak, Turkmen, Pathans, Iranian Arabs, and Gilaki. This study demonstrates an impact of ancient nomad migrations and invasions on the distribution of mtDNA variation in Eurasia. 

EAA 2013 abstracts

The bioarchaeology of the neolithic Carpathian Basin

By the beginning of the 6th Millennium cal BC, the first farmers reached the Carpathian Basinwhere the last transition to food production and sedentary life took place. The early neolithic groups became restructured both in their cultural and genetic composition in the 6th and 5th Millennium BC, affected by at least five major Northern Balkan impulses. The western part of the area became a major communication zone, mediating between South Eastern and Central Europe. Our working group has been focusing on this early population history of Eastern Hungary and of Transdanubia, developing and comparing ancient DNA, stable isotope, osteological and archaeological data gained from not less than 600 neolithic skeletons (6000–4300 cal BC).  

In the session we would like to give an account of the DNA and stable isotope (SR, N, C) analysis, carried out within the frames of a three-year interdisciplinary project funded by the German Research Foundation along with the co-evaluation of these results with osteology and zooarchaeology, as well as giving a comparative interpretation of this data within our present socioarchaeological knowledge.

The megalithic past of the Bronze Age kurgans of the North Pontic Region 

The Early Bronze Age (EBA) burial mounds (kurgans) in the western part of the North Pontic Region (NPR) display a tendency to be erected over earlier megalithic ritual constructions. The initial purpose of these megalithic structures might have been cosmology-related. In succeeding time periods the initial astronomic purpose could have been forgotten and these megalithic sites became designated at sacred places suited for distinguished burials. Megalithic elements comprising the initial constructions became incorporated into the subsequent burials. The Revova kurgan from western NPR is one such construction. It was erected over a megalithic structure in a shape of a tortoise with the stone elements of the construction being astronomically aligned. An assembly of disarticulated human remains deposited in the center of the construction dated to the Eneolithic (4200 BC). On the other hand, the layout of stones comprising the “Tortoise” appears to most accurately line up with the movement of celestial objects as they appeared on the sky around 6300 BC. Mitochondrial DNA lineage extracted from the remains was characteristic to the Mesolithic/Neolithic hunter-gatherer populations from northern Europe as well as Bronze Age groups from south Siberia. 

The spread of domestic pig in the central and Eastern part of the Romanian territory described by the ancient mithochondrial DNA

Previous genetic analysis showed the presence of two different haplotypes for domestic pigs from 11 different sites in the South-Eastern part of Romania: the Near-Eastern haplotype ANC-Y1-5A, for 18 individuals, and ANC-Aside european haplotype, for 8 individuals. This study reveals the genetic signature for other 52 samples (5000–3500 BC, from 7 archaeologic sites) covering the central and Eastern parts of Romania. After the DNA extraction, PCR, and sequencing, no ANC-Aside haplotype was found, but, apart from the Near-Eastern ANC-Y1-5A haplotype, identified in the majority of domestic pig samples, the european ANC-Cside haplotype (generally identified in the wild boars), was also found in three domestic pigs from Poduri, Ghigoiesti and Trusesti. The wide spread of the wild boar with the ANC-Cside haplotype not only on the entire Romanian territory, but also, as previously shown, in it’s close proximity, and the emergence of this genetic signature in both wild and domestic pigs from three different sites could support the idea of a local domestication of the wild boar after 4500 BC, in this specific area.

The genetic make-up of the Linear Pottery culture

The Linear Pottery culture (LBK) is one of the first Central European Neolithic farming cultures marking the transition from a hunter-gatherer to a farming lifestyle. The LBK is thought to have originated from Early Neolithic cultures in the Carpathian Basin from where it extended across Europe over a vast distribution area spanning from the River Rhine to the Ukraine. Consequently, its role during the process of Neolithisation in Central Europe is subject of a long-standing debate in archaeology, anthropology and human genetics. Ancient DNA studies have provided direct insights into Mesolithic and Neolithic mitochondrial diversity indicating genetic discontinuity between Central Europe’s autochthonous hunter-gatherers and LBK populations. Comprehensive population genetic analyses utilizing large databases of present-day populations have disclosed genetic affinities of the LBK to the modern-day Near East, Anatolia and the Caucasus, supporting genetic influx from this region into Central Europe at the advent of farming and explaining the apparent genetic discontinuity between foragers and farmers. We will summarize the inferences that have been drawn from 108 LBK data to provide an overview of genetic diversity of the first farming communities in Central Europe, which represents an invaluable genetic perspective for the discussion of the Neolithic in the Carpathian Basin.

Bell Beaker child burials and their gender identity in the light of DNA analysis

The DNA analysis of 53 child burials from the Bell Beaker cemetery at Hostice-I produced data on 21 sexed individuals. Out of 14 burials with male gender attributes were 12 individuals biologically male and two determinate as women. Cases of girls that were brought up as boys probably existed in 3rd Millennium BC burial customs. Out of seven children buried in the female position only 1 was actually biological female (juvenile 15–20 years) and 6 male (2 juvenile 15–19/20 years). That means four boys (aged 3–4, 7, 8–12, 15) were in fact buried as women. Such a result is in line with known demographic unbalance within Beaker cemeteries. Most young girls were not buried at the communal cemetery and considerable number of boys were buried in the female fashion. This is rather high number of cases when the masculine attributes were downplayed in the burial customs and it is hard to interpret whether they were boys supposed to be brought up as women or they had yet no right to act as men, unlike some other sub-adult boys, perhaps members of families with ascribed hereditary warrior status. It almost seems that some young boys were socially considered to be girls, perhaps until ceremonial rite of passage, social initiation of some kind.

Ancient Human DNA – A problem of interpretation

The problem with ancient human DNA is not contamination with modern human DNA any more. This still happens, but aDNA scientists can now recognise it and deal with it. The problem is with the overinterpretation of results. Only a few mitochondrial and Y chromosome aDNA sequences may be obtained from a burial assemblage, but these are interpreted in a population genetics framework which incorporates DNA sequences obtained from present day populations. This type of analysis ignores the possibility that social structures can affect genetic outcomes, as is seen in traditional societies and has recently been recognised by evolutionary geneticists. Societies practising patrilocal exogamy versus endogamy have been studied and the mtDNA and Y chromosomal haplotype diversity analysed. Patrilocal societies show high mtDNA diversity while Y haplotype diversity is reduced. Endogamous societies do not show the reduction in Y diversity, but mtDNA diversity is maintained. Ancient DNA results from several Neolithic sites can therefore be interpreted to identify the type of social structure present. Patrilocal exogamy is the most parsimonious interpretation and this is corroborated by Sr isotope studies from LBK sites.

 Ancient DNA discloses multiple migrations into Central Europe during the Neolithic

The Central European Neolithic is characterised by a succession of differentiated archaeological cultures indicating a period of fundamental cultural change. A recurrent question in archaeology and anthropology is whether cultural change in prehistory was accompanied by variation in the gene pool of associated populations. Ancient DNA studies based on mitochondrial DNA revealed a discontinuity between Central Europe’s autochthonous hunter-gatherers and their early farmers and between the latter and the present-day population, suggesting further migration events after the initial Neolithisation. However, to date little attention has been drawn to cultural and potentially population changes in subsequent Neolithic periods. To investigate this issue, we conducted a large chronological study including a succession of nine cultures from the Mittelelbe-Saale region, Saxony-Anhalt, Germany to reconstruct a detailed temporal profile of cultural and genetic diversity in Central Europe. The presented diachronic study spans overall 3,950 years from the beginning of the Neolithic period and the introduction of producing subsistence strategies ~5,500 BC to the appearance of structured chiefdoms in the Early Bronze Age ~2,200–1,550 BC. This transect through time identified multiple population dynamic events during the Neolithic, which involved genetic influx from various regions in Europe.

 Ancient DNA and isotope analysis of the Starčevo graves at Alsónyék-Bátaszék

Between 2006 and 2009 at Alsónyék-Bátaszék a settlement with 26 graves of the Starčevo culture were unearthed. More than 400 various features belonged to this early Neolithic period on an extension of 80 hectares. The archaeological findings underline the significance of Alsónyék-Bátaszék, which is to date the largest Starčevo site uncovered in present-day Hungary. We analysed the 26 Starčevo burials from Alsónyék from ancient DNA and stable isotopic aspects, involving them in our three-year bioarchaeological Neolithic project. The excellent DNA preservation made it possible to gain reproduced mitochondrial DNA results from all skeletons, and we could additionally type the Y chromosome in 5 of the male individuals. The strontium (87Sr/86Sr) and oxygen (δ18Op) isotopic data obtained an insight into the mobility and kinship system of the population. The carbon (δ13C) and nitrogen (δ15N) isotope analyses of the skeletons supported a basis for a diet reconstruction, supplementing the archaeozoological proceedings of the site. Our results from the Alsónyék-Bátaszék Starčevo specimens, dated between ca. 5800-5500 cal BC, denote a milestone of the early Neolithic bioarchaeological studies in Transdanubia.

 6–5th millennium BC cultural changes in Western Hungary tested by ancient DNA

Western Hungary (Transdanubia) was one of the key regions at the process of Neolithisation in Central Europe. The Starcevo culture, representing the earliest farmers on this region, settled down at latest 5750 cal BC south of the Lake Balaton. It had a major role in the formation of the Linearbandkeramik culture in Transdanubia. The following Sopot, Lengyel cultures of the late Neolithic and Early Copper Age Transdanubia show repeated cultural influences from the Balkan, besides local extant cultural traditions. 

The focus of our study is the process of these cultural changes in Transdanubia, in the view of ancient DNA, investigating mitochondrial and Y chromosomal lineages and markers. A total of 292 skeletons were sampled and processed, with an overall success rate of 89% for mitochondrial DNA. Comparing the mitochondrial and Y chromosomal results with other published data and evaluating them with population genetic analyses, we gained a peerless insight into the population history of Western Hungary. 

Our study may give an additional help to prehistoric archaeology, for a better understanding of the nature of cultural changes, supporting it with a new type of evidence, in order to see Transdanubia as a mediating area between South East and Central Europe.

Why Europeans gained 11cm in height in a century

The paper's conclusion:

The main findings in this article can be summarized as follows. New data show that average male height in Europe increased by about 11 cm in the century from the 1870s—representing an unprecedented improvement in health status. In northern and middle European countries there was a distinct quickening in the pace of advance in the period spanning the two world wars and the Great Depression, which largely predates the modern medicine and national health services. In southern Europe height increased fastest in the postwar period. There is evidence of a concave health production function, but the effects of inequality are not robust. Education had a positive effect on height and family size a negative effect, consistent with the quality-quantity trade-off. The evidence suggests that improvements in the disease environment, as reflected in infant mortality, is the single most important factor driving the increase in height. This accounts for much of the acceleration during the transwar period. Social services and health systems made a modest contribution to the overall increase in height. One reason is that education and expenditure on social services seem to be substitutes. Transport infrastructure also contributed to health and height, especially in the prewar era. But a substantial part of the overall upwards trend in height is not explained—in the absence of infant mortality, about a half. There are other important factors that are not easily measured, including medical advances and practices, and especially better parental knowledge of the effects of nutrition and hygiene on children’s health.

Oxf. Econ. Pap. (2013)
doi: 10.1093/oep/gpt030

How have Europeans grown so tall?

Timothy J. Hatton

Increases in human stature are a key indicator of improvements in the average health of populations. In this article I present and analyse a new data set for the average height of adult male birth cohorts, from the mid-nineteenth century to 1980, in 15 European countries. In little more than a century average height increased by 11 cm—representing a dramatic improvement in health. Interestingly, there was some acceleration in the period spanning the two world wars and the Great Depression. The evidence suggests that the most important proximate source of increasing height was the improving disease environment as reflected by the fall in infant mortality. Rising income and education and falling family size had more modest effects. Improvements in health care are hard to identify, and the effects of welfare state spending seem to have been small.

Link

Multiple sources of European barley

This seems to parallel quite well with my hypothesis of a secondary expansion into Europe of the component I've labeled "West Asian", after the early Neolithic. From the paper:

The wild progenitor of barley, Hordeum spontaneum, is typically a winter-germinating species, responsive to day length (Turner et al. 2005), but recent work (H. Jones et al. 2008) has demonstrated that the non-responsive allele also occurs in wild barley in Israel, Jordan and Iran, in regions where this allele is favoured by the climatic conditions. There is strong evidence to suggest that the non-responsive allele in European cultivars (Group A) is genetically more similar to the allele in Iranian wild barleys than to the allele in wild barleys from Israel and Jordan.

and:

 Detailed genetic comparisons between groups A, B and C (H. Jones 2008; H. Jones et al. 2008) suggest that Group A represents a more recent introduction of day-length non-responsive barley into Europe, rather than the selection of non-responsiveness from within populations that diffused into Europe in the Early Neolithic. In addition, three of the nine principal groups identified on the basis of the neutral SSR markers (groups 1–3) are genetically closely related and very similar in their phenotypic characteristics. They are located in north-west and Central Europe (Figure 3b), and are made up almost entirely of  day-length non-responsive barleys (98 per cent) with a spring growth habit (98 per cent) (H. Jones et al. 2011). The distinctiveness of the landraces making up groups 1–3 suggests that the responsive/non-responsive difference between Southern and Northern Europe is not simply a reflection of current selective pressure but rather is one aspect of a more fundamental genetic difference between barley populations. These day-length non-responsive cultivars have therefore been interpreted as representing a later spread of barley into Northern Europe from the eastern part of the Fertile Crescent or beyond. This raises the issue of when they spread into Europe and whether or not they were introduced via the same route as the initial  spread of agriculture.

and:

A possible channel for the introduction of day-length non-responsive barley into Northern Europe from the east at this time could have been through early exchange networks with metal-working communities of south-eastern Europe (Sherratt 1976; Bogucki 1999: 220–21). The Chalcolithic societies of the Balkans also maintained connections further east with the west Eurasian Steppes, Anatolia, and the Caucasus in the fifth and early fourth millennia, and copper was exchanged from west to east across the steppes north of the Black Sea (Kohl 2007: 31–39). Day-length non-responsive barley could, therefore, have travelled from east to west along the same route, north of the Black Sea via the Caucasus or, perhaps more likely given its agricultural nature, south of the Black Sea through Anatolia, possibly via a coastal route around the Black Sea, and then from the Carpatho-Balkan metallurgical region into Northern Europe (Figure 3b). A similar suggestion has been made for the later appearance of the oil plant Lallemantia, which was apparently introduced into Europe in the third millennium BC, possibly along the same trade routes as tin-bronzes (Valamoti & Jones 2010). 

Antiquity Volume: 87 Number: 337 Page: 701–713

DNA evidence for multiple introductions of barley into Europe following dispersed domestications in Western Asia

G. Jones et al.

It has long been recognised that the Neolithic spread across Europe via two separate routes, one along the Mediterranean coasts, the other following the axis of the major rivers. But did these two streams have a common point of origin in south-west Asia, at least with regard to the principal plant and animals species that were involved? This study of barley DNA shows that the domesticated barley grown in Neolithic Europe falls into three separate types (groups A, B and C), each of which may have had a separate centre of origin in south-west Asia. Barley was relatively rarely cultivated by the early Linearbandkeramik farmers of Central and Northern Europe, but became more common during the fifth and fourth millennia BC. The analysis reported here indicates that a genetic variety of barley more suitable for northern growing conditions was introduced from south-west Asia at this period. It also suggests that the barley grown in south-eastern Europe at the very beginning of the Neolithic may have arrived there by different routes from two separate centres of domestication in south-west Asia. The multiple domestications that this pattern reveals imply that domestication may have been more a co-evolutionary process between plants and people than an intentional human action.

Link

Nuclear sequences of mitochondrial origin and gene flow in Pleistocene Africa

I haven't read this, but the idea of looking at looking at nuclear sequences of mitochondrial origin (numt) as a way of testing for archaic admixture seems interesting to me. Human mtDNA has a relatively shallow coalescence (less than 200 thousand years), with Neandertal mtDNA being a clear outgroup, and Denisovan mtDNA being an even more remote outgroup. If modern humans admixed with archaic ones (having mtDNA lineages much more remote than "Eve"), then the evidence may have been lost (due to drift) in mtDNA, but may have been preserved in the autosomes.

Anthropologischer Anzeiger, Volume 70, Number 2, July 2013 , pp. 221-227(7)

Hominin evolution and gene flow in the Pleistocene Africa

Ovchinnikov, Igor V.

Africa demonstrates a complex process of the hominin evolution with a series of adaptive radiations during several millions of years that led to diverse morphological forms. Recently, Hammer et al. (2011) and Harvati et al. (2011) provided integrated morphological and genetic evidence of interbreeding between modern humans and unknown archaic hominins in Africa as recently as 35,000 years ago. However, a genetic evidence of hybridization between hominin lineages during the Lower and Middle Pleistocene epochs is unknown and the direct retrieval of DNA from extinct lineages of African hominins remains elusive. The availability of both nuclear and mitochondrial genome sequences from modern humans, Neanderthals, and Denisovans allows collecting nuclear DNA sequences of mitochondrial origin (numts) inserted into the nuclear genome of the ancestral hominin lineages and drawing conclusions about the hominin evolution in the remote past. The mtDNA and numt analysis uncovered a deep division of mtDNA lineages that existed in African hominins in the Middle Pleistocene. The first cluster included the human and Neanderthal-like mtDNA sequences while the second consisted of DNA sequences that are known today as mtAncestor-1, a nuclear fossil of the mtDNA, and the Denisova mtDNA isolated from a bone and a tooth found in southern Siberia. The two groups initially diverged 610,000-1,110,000 years ago. Approximately 220,000 years after the primary split, the Denisova - mtAncestor-1 mtDNA lineages mixed with the mtDNA pool of an ancestral population of Neanderthals and modern humans. This admixture after the profound division is demonstrated by the transposition of the Denisova-like mtDNA sequence into the nuclear genome of an ancestor of Neanderthals and modern humans. This finding suggests the matrilineal genetic structure among the Middle Pleistocene hominins as well as the existence of gene flow between African hominin lineages. Through paleogenomic analyses, it is impossible to exclude the theory that population structure and gene flow in African hominins influenced the admixture pattern observed in the nuclear genomes of non-Africans.

Link

European hunter-gatherers acquired pigs with Near Eastern and European mtDNA

This is a nice demonstration of transfer of domesticated animals from Neolithic farmers to European hunter-gatherers. (Red=European, Yellow=Near Eastern).

Related: Ottoni et al. (2012).

Nature Communications 4, Article number: 2348 doi:10.1038/ncomms3348

Use of domesticated pigs by Mesolithic hunter-gatherers in northwestern Europe

Ben Krause-Kyora et al.

Mesolithic populations throughout Europe used diverse resource exploitation strategies that focused heavily on collecting and hunting wild prey. Between 5500 and 4200 cal BC, agriculturalists migrated into northwestern Europe bringing a suite of Neolithic technologies including domesticated animals. Here we investigate to what extent Mesolithic Ertebølle communities in northern Germany had access to domestic pigs, possibly through contact with neighbouring Neolithic agricultural groups. We employ a multidisciplinary approach, applying sequencing of ancient mitochondrial and nuclear DNA (coat colour-coding gene MC1R) as well as traditional and geometric morphometric (molar size and shape) analyses in Sus specimens from 17 Neolithic and Ertebølle sites. Our data from 63 ancient pig specimens show that Ertebølle hunter-gatherers acquired domestic pigs of varying size and coat colour that had both Near Eastern and European mitochondrial DNA ancestry. Our results also reveal that domestic pigs were present in the region ~500 years earlier than previously demonstrated.

Link

Population growth and deleterious mutations

Genetics doi: 10.1534/genetics.113.153973

Population Growth Inflates the Per-Individual Number of Deleterious Mutations and Reduces Their Mean Effect

Elodie Gazave et al.

This study addresses the question of how purifying selection operates during recent rapid population growth such as has been experienced by human populations. This is not a straightforward problem because the human population is not at equilibrium: population genetics predicts that, on the one hand, the efficacy of natural selection increases as population size increases, eliminating ever more weakly deleterious variants; on the other hand, a larger number of deleterious mutations will be introduced into the population and will be more likely to increase in their number of copies as the population grows. To understand how patterns of human genetic variation have been shaped by the interaction of natural selection and population growth, we examined the trajectories of mutations with varying selection coefficients using computer simulations. We observed that while population growth dramatically increases the number of deleterious segregating sites in the population, it only mildly increases the number carried by each individual. Our simulations also show an increased efficacy of natural selection, reflected in a higher fraction of deleterious mutations eliminated at each generation, and a more efficient elimination of the most deleterious ones. As a consequence, while each individual carries a larger number of deleterious alleles than expected in the absence of growth, the average selection coefficient of each segregating allele is less deleterious. Combined, our results suggest that the genetic risk of complex diseases might be distributed across a larger number of more weakly deleterious rare variants.

Link

The place of Armenian in the Indo-European language family

Journal of Language Relationship • Вопросы языкового родства • 10 (2013) • Pp. 85—137

The place of Armenian in the Indo-European language family: the relationship with Greek and Indo-Iranian*

Hrach Martirosyan

The main purpose of this paper is to present lexical correspondences that unite Armenian with Greek and/or Indo-Iranian. They include shared innovations on the one hand, and isolated lexemes on the other. These two lexical corpora — lexical innovations on an inherited basis and isolated words — can be placed within the same temporal and spatial framework. After the Indo-European dispersal Proto-Armenian would have continued to come into contact with genetically related Indo-European dialects. Simultaneously, it would certainly also have been in contact with neighbouring non-Indo-European languages. A word can be of a substrate origin if it is characterized by: (1) limited geographical distribution; (2) unusual phonology and word formation; (3) characteristic semantics. The material presented here, albeit not exhaustive, allows to preliminarily conclude that Armenian, Greek, (Phrygian) and Indo-Iranian were dialectally close to each other. Within this hypothetical dialect group, Proto-Armenian was situated between Proto-Greek (to the west) and Proto-Indo-Iranian (to the east). The Indo-Iranians then moved eastwards, while the Proto-Armenians and Proto-Greeks remained in a common geographical region for a long period and developed numerous shared innovations. At a later stage, together or independently, they borrowed a large number of words from the Mediterranean / Pontic substrate language(s), mostly cultural and agricultural words, as well as animal and plant designations. On the other hand, Armenian shows a considerable number of lexical correspondences with European branches of the Indo-European language family, a large portion of which too should be explained in terms of substrate rather than Indo-European heritage.

Link (pdf)

Y-chromosome haplogroup Q and Native Americans

PLoS ONE 8(8): e71390. doi:10.1371/journal.pone.0071390

The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q

Vincenza Battaglia et al.

Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.

Link

Pre-Viking colonization of Faroe islands

Quaternary Science Reviews Available online 17 July 2013

The Vikings were not the first colonizers of the Faroe Islands

Mike J. Church et al.

We report on the earliest archaeological evidence from the Faroe Islands, placing human colonization in the 4th–6th centuries AD, at least 300–500 years earlier than previously demonstrated archaeologically. The evidence consists of an extensive wind-blown sand deposit containing patches of burnt peat ash of anthropogenic origin. Samples of carbonised barley grains from two of these ash patches produced 14C dates of two pre-Viking phases within the 4th–6th and late 6th–8th centuries AD. A re-evaluation is required of the nature, scale and timing of the human colonization of the Faroes and the wider North Atlantic region.

Link

Oldest gaming tokens from Başur Höyük

Oldest Gaming Tokens Found in Turkey

Small carved stones unearthed in a nearly 5,000-year-old burial could represent the earliest gaming tokens ever found, according to Turkish archaeologists who are excavating early Bronze Age graves. 

Found in a burial at Basur Höyük, a 820- by 492-foot mound near Siirt in southeast Turkey, the elaborate pieces consist of 49 small stones sculpted in different shapes and painted in green, red, blue, black and white. 

"Some depict pigs, dogs and pyramids, others feature round and bullet shapes. We also found dice as well as three circular tokens made of white shell and topped with a black round stone," Haluk Saglamtimur of Ege University in Izmir, Turkey, told Discovery News.

This is a nice illustration of people's familiarity with several abstract geometrical shapes for the purposes of gaming.

Climate caused the Late Bronze Age collapse in the Eastern Mediterranean

PLoS ONE 8(8): e71004. doi:10.1371/journal.pone.0071004

Environmental Roots of the Late Bronze Age Crisis

David Kaniewski et al.

The Late Bronze Age world of the Eastern Mediterranean, a rich linkage of Aegean, Egyptian, Syro-Palestinian, and Hittite civilizations, collapsed famously 3200 years ago and has remained one of the mysteries of the ancient world since the event’s retrieval began in the late 19th century AD/CE. Iconic Egyptian bas-reliefs and graphic hieroglyphic and cuneiform texts portray the proximate cause of the collapse as the invasions of the “Peoples-of-the-Sea” at the Nile Delta, the Turkish coast, and down into the heartlands of Syria and Palestine where armies clashed, famine-ravaged cities abandoned, and countrysides depopulated. Here we report palaeoclimate data from Cyprus for the Late Bronze Age crisis, alongside a radiocarbon-based chronology integrating both archaeological and palaeoclimate proxies, which reveal the effects of abrupt climate change-driven famine and causal linkage with the Sea People invasions in Cyprus and Syria. The statistical analysis of proximate and ultimate features of the sequential collapse reveals the relationships of climate-driven famine, sea-borne-invasion, region-wide warfare, and politico-economic collapse, in whose wake new societies and new ideologies were created.

Link

Specialized bone tools made by Neandertals before the arrival of modern humans into Europe

PNAS doi: 10.1073/pnas.1302730110

Neandertals made the first specialized bone tools in Europe

Marie Soressia et al.

Abstract

Modern humans replaced Neandertals ∼40,000 y ago. Close to the time of replacement, Neandertals show behaviors similar to those of the modern humans arriving into Europe, including the use of specialized bone tools, body ornaments, and small blades. It is highly debated whether these modern behaviors developed before or as a result of contact with modern humans. Here we report the identification of a type of specialized bone tool, lissoir, previously only associated with modern humans. The microwear preserved on one of these lissoir is consistent with the use of lissoir in modern times to obtain supple, lustrous, and more impermeable hides. These tools are from a Neandertal context proceeding the replacement period and are the oldest specialized bone tools in Europe. As such, they are either a demonstration of independent invention by Neandertals or an indication that modern humans started influencing European Neandertals much earlier than previously believed. Because these finds clearly predate the oldest known age for the use of similar objects in Europe by anatomically modern humans, they could also be evidence for cultural diffusion from Neandertals to modern humans.

Link

Indo-Europeans in Journal of Language Relationship

I had referred to this collection of papers before,  and now all the PDFs appear to be available free of charge.

This seems fairly interesting:

Language and archeology: some methodological problems.
1. Indo-European and Altaic landscapes

Anna Dybo

The article is the first part of a larger work that represents an attempt to systematize our
ideas on the natural environment and material culture of the Proto-Indo-Europeans. It is
based on a more or less complete selection of reconstructed words from the appropriate semantic areas and on their comparison with a similar selection performed for a protolanguage of similar time depth, whose speakers evidently inhabited a territory that was not
in contact with the Proto-Indo-European one — Proto-Altaic. In this part, only the words that
belong to the semantic field of landscape terms are analyzed. The main conclusion is that thehypothesis of a steppe environment is more applicable for the Proto-Altaic population,whereas for Proto-Indo-Europeans a mountainous region seems more appropriate. As for
the water bodies, for Proto-Indo-Europeans we should suppose the existence of a sea (or of a
very big lake), and for speakers of Proto-Altaic, the existence of very big rivers with season
floods

Mallory's article is also interesting as the latest public take on the PIE origins issue by the prominent champion of the Pontic-Caspian steppe hypothesis. It also alerted me to a study in Russian on the problem of Tocharian origins by Leonid Sverchkov. Sadly, I don't read Russian, but Mallory has a nice review of it in the Journal of Indo-European Studies, from which comes the following excerpt:

 The second section of the book investigates Central
Asia as a cultural historical region. It briefly summarizes the
major Palaeolithic influences, then provides more detail
about the Mesolithic cultures of the region before settling
down to a much more thorough description of the
Neolithic cultures, among which much time is devoted to
the Kelteminar culture that occupied a broad area of
Central Asia and which many earlier authors saw as critical
in explaining the origins of many of the neighboring
cultures, among which would be included the Afanasievo
culture of the Altay and Minusinsk Basin. The author
continues laying out the cultural-historical development of
Central Asia up to the early Middle Ages.
 The third part is titled ‘Tokharians and the IndoEuropean problem” and the archaeological evidence seen
earlier is then recast to provide arguments for a Central
Asian homeland for the Indo-Europeans. One of the
perennial problems with searching out the origins of any
particular Indo-European group is that all too often
proponents of a particular theory provide an isolated
‘solution’ divorced from the fact that it is only part of a
larger puzzle and its pieces must make joins with the rest
of the Indo-European world. I have termed this the ‘total
distribution principle’ and it is one of the tests of how
serious we should deal with any partial solution to IndoEuropean expansions. In attempting to meet this
principle, one can hardly criticize the author as his final
section is essentially a very detailed proposal for a ‘new’
Indo-European homeland in Central Asia. Geographically
situated not far from the earlier proposals of Gamkrelidze
and Ivanov, it does provide some legs to their general
positioning of the Indo-European homeland but in a novel
fashion. Sverchkov’s solution also embraces a series of
earlier suggestions or models but is truly his own in terms
of its implementation.
 Sverchkov’s solution is fundamentally a rejection of
those who would normally dismiss Central Asia as merely a
transition zone across which migrating populations passed
through. During the transition between the Mesolithic
and Neolithic we find a vast Keltiminar culture occupying
the entire region from the Urals and Caspian east to the
Altay, and north of the Kopetdagh and northern
Afghanistan. This region matches at least in areal extent
the type of homelands anchored in Europe such as those
who have sought the Urheimat in the area of the
Linearbandkeramik. To these Sverchkov also includes the
southern agricultural regions of Jarmo and later Jeitun
which would appear to lie outside the area normally
ascribed to other non-Indo-European languages (Semitic,
Elamite, Dravidian, Altaic, Uralic). This entire region then
functions as a broad Indo-European homeland. He suggests
that the westward movement of the Halaf culture accounts
for the separation of the Anatolian branch. The ProtoTocharians begin within the Jeitun region and moved
eastwards to arrive in Ferghana by the Bronze Age. The
archaeological discussion emphasizes the presence of
painted wares in both the Tarim Basin, especially in the
region where we find Tocharian B, and Ferghana, and
these persistent contacts are seen as indicating the spread
of the Tokharian languages. This pattern of Central Asian
contacts is seen even in the earliest cemeteries of the
region (Xiaohe, Gumagou) which, although lacking
ceramics altogether, possessed abundant evidence for bagshaped baskets which have been compared to the shape
and decorations of Kelteminar vessels. It might be noted
that precisely the same pot-to-basket argument has been
employed by those who support a connection between the
Tarim Basin and the steppelands.
 The other Indo-European languages are accounted
for by very early (Neolithic) movements from Central Asia
into the Pontic-Caspian region. The Ayderbol culture of
Kazakhstan, for example, is proposed as underlying the
formation of the Dnieper-Donets culture of the Ukraine
and as seen as the initial wave (roughly in the sense of
Marija Gimbutas) of the Italo-Celtic-Illyrians. The Neolithic
and Eneolithic developments of the Volga-Ural region are
under the Kelteminar aegis and yield the later GermanicBalto-Slavic branches. Out of the steppe cultures (Sredny
Stog and Khvalynsk) and the neighboring Maykop culture
he derives the Yamnaya which in the guise of the
Andronovo culture sets off the Aryanization of southern
Central Asia. Throughout this archaeological discussion the
author relates his theories to a variety of linguistic
proposals, e.g., Henning’s famous argument tying the
names of cultures on the frontiers of Mesopotamia with
those of the Tarim Basin

It seems that the PIE urheimat debate is alive and well.