Genomewide diversity in the Levant (Haber et al. 2013)

Razib points me to a new paper (and its associated data, consisting of Christian, Druze, and Muslim Lebanese).
Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture
Marc Haber et al.
The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period. Genetic and archeological studies present solid evidence placing the Middle East and the Arabian Peninsula as the first stepping-stone outside Africa. There is, however, little understanding of demographic changes in the Middle East, particularly the Levant, after the first Out-of-Africa expansion and how the Levantine peoples relate genetically to each other and to their neighbors. In this study we analyze more than 500,000 genome-wide SNPs in 1,341 new samples from the Levant and compare them to samples from 48 populations worldwide. Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region. Cultural changes within the last two millennia appear to have facilitated/maintained admixture between culturally similar populations from the Levant, Arabian Peninsula, and Africa. The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations. Consequently, Levant populations today fall into two main groups: one sharing more genetic characteristics with modern-day Europeans and Central Asians, and the other with closer genetic affinities to other Middle Easterners and Africans. Finally, we identify a putative Levantine ancestral component that diverged from other Middle Easterners ~23,700–15,500 years ago during the last glacial period, and diverged from Europeans ~15,900–9,100 years ago between the last glacial warming and the start of the Neolithic.
Link

Connections between Indus Valley and Mesopotamia

 

Of interest from the paper:

Based on this distribution of values, it would appear from our preliminary analysis that almost half of the individuals sampled from the Harappa cemetery have isotope values outside the local baseline (0.7158-0.7189). Most of these individuals have values below the Harappa range. In addition, there are at least three non-local individuals with higher values, including one with an extremely isotope ratio that cannot be from the Harappa region. A more detailed discussion of the Harappa samples will be presented in a future publication on the Harappa cemetery, but it is clear that many of what appear to be local individuals at Harappa are females and they are associated in burial with nearby males who are clearly not local. These preliminary patterns require further testing before major conclusions can be proposed, but it does suggest that they represent a unique population of people from multiple regions of the Indus valley or beyond.

Journal of Archaeological Science
Volume 40, Issue 5, May 2013, Pages 2286–2297
A new approach to tracking connections between the Indus Valley and Mesopotamia: initial results of strontium isotope analyses from Harappa and Ur
J. Mark Kenoyer et al.
Exchange and interaction between early state-level societies in Mesopotamia and the Indus Valley during the 3rd millennium BC has been documented for some time. The study of this interaction has been dominated by the analysis of artifacts such as carnelian beads and marine shell, along with limited textual evidence. With the aid of strontium, carbon, and oxygen isotopes, it is now possible to develop more direct means for determining the presence of non-local people in both regions. This preliminary study of tooth enamel from individuals buried at Harappa and at the Royal Cemetery of Ur, indicates that it should be feasible to identify Harappans in Mesopotamia. It is also possible to examine the mobility of individuals from communities within the greater Indus Valley region.
Link

Y chromosome and mtDNA study of modern Middle Eastern populations (Badro et al. 2013)

Y chromosome and mtDNA study of modern Middle Eastern populations (Badro et al. 2013)

I will just briefly comment on the occurrence of L3* mtDNA in the Near East. This is a critical haplogroup because of its age of ~70ky. If all L3* in the Near East represents African migrants, then only the M and N macrogroups appeared in Eurasia, and a good case can be made for a "late" OoA event.

On the other hand, it is quite possible that some of the L3* in the Near East does not represent recent admixture, but rather native forms of L3 with deep ancestry in the region. If that is the case, then the Near East will emerge as the origin of L3, with M, N representing Out-of-Near East-into-Eurasia founders, and the various L3*(xM, N) representing Out-of-Near East-into-Africa founders.

It is difficult to say at present what will turn out to be the case. Ancient DNA has the potential of resolving this issue, because if L3*(xM, N) in Eurasia is really recent (e.g., associated with Islamic/Arab dispersals spanning Africa and Eurasia), then it ought to be missing from the earliest genetic layers.

Also of interest the geographical distribution of Y-haplogroups; nothing much new here, but still useful as a reference:

PLoS ONE 8(1): e54616. doi:10.1371/journal.pone.0054616

Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations 

Danielle A. Badro et al.

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

Link

2,400BC golden mask of Thracian king

2,400BC golden mask of Thracian king

Bulgarian archaeologist Georgi Kitov holds a 2,400-year-old golden mask he discovered Thursday in the tomb of a Thracian king in Shipka, Bulgaria. The solid gold mask “has no comparison in the world,” said Kitov, who believes it may depict the image of King Seutus III.

Toronto Star. Aug. 21, 2004. 01:00 AM.

Golden mask `sensational'
Artifact unearthed in Bulgaria

Find may depict ancient king

SHIPKA, Bulgaria—A Bulgarian archaeologist has unearthed a 2,400-year-old golden mask in the tomb of an ancient Thracian king — a find he says is unrivalled in the study of classical antiquity.

"It is sensational," said Georgi Kitov, who found the mask Thursday near the village of Shipka, 200 kilometres east of Sofia.

He believes it may depict King Seutus III, a 5th century BC leader of the Thracians, the dispersed tribes who once lived in parts of what is now modern-day Bulgaria, Romania, Macedonia, Turkey and Greece.

Kitov said the mask "has no comparison in the world," and may be a more significant find than the Mask of Agamemnon, the Greek hero described by Homer in the Iliad. It's one of the most famous images of Greek antiquity, and the centrepiece of the National Archaeological Museum in Athens.

"The Mask of Agamemnon was made of gold foil and weighs only 60 grams, while this mask weighs 690 grams (24 oz.) and is of solid gold," Kitov said.

The burial place was covered with six stone slabs, each weighing at least two tonnes. The king's remains have not yet been found, but excavations at the tomb continue.

The Thracians lived on the fringes of the Greek and Roman civilizations, often intermingling and clashing with the more advanced cultures until they were absorbed around 45 AD. Archaeological finds have provided most of what is known of the culture.

mtDNA of ancient central Asians

mtDNA of ancient central Asians

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

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

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

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

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

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

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

Link (pdf)