Long Live the 25th March, 1821

Long Live the 28th October, 1940

Long Live the 25th March, 1821

Long Live the 25th March, 1821

Long Live the 28th October, 1940

Long Live the 25th March, 1821

China's Great Flood and the rise of the Xia dynasty

From a related story: Massive flood may have led to China's earliest empire:

Many cultures trace their origins to the hazy horizon where history meets legend. In China's case, that blurry line occurs sometime between 2200 B.C.E. and 2000 B.C.E., when a legendary hero named Yu tamed Yellow River flooding and earned a mandate to become the founding emperor of the Xia dynasty, the country's first. That’s the story according to texts written long after the fact, and many Chinese believe their civilization started with emperor Yu. But archaeologists have been unable to find convincing evidence for either the flood or the Xia dynasty itself. 

... 

The massive flood “provides us with a tantalizing hint that the Xia dynasty might really have existed," says David Cohen, an archaeologist and co-author at National Taiwan University in Taipei. The devastating flood could have inundated settlements even a thousand or more kilometers downstream, he says, and created chaos from which a new political order emerged. This sequence of events neatly fits the legend of Yu controlling the flooding by dredging channels to confine the Yellow River and its tributaries. This feat, the ancient texts say, allowed him to claim a mandate as the first emperor of the Xia dynasty.  

The timing is curiously coincidental. Around 1900 B.C.E., Cohen says, Chinese society was transitioning from the Neolithic to the Bronze age. The date also correlates with what is called the Erlitou culture, which is known from palace buildings and bronze smelting workshops discovered near Zhengzhou, about 2500 kilometers downstream from Jishi Gorge. Many scholars have argued that Erlitou is a manifestation of the elusive Xia dynasty, but a link is not firmly established.

Science 05 Aug 2016: Vol. 353, Issue 6299, pp. 579-582 DOI: 10.1126/science.aaf0842

Outburst flood at 1920 BCE supports historicity of China’s Great Flood and the Xia dynasty

Qinglong Wu

China’s historiographical traditions tell of the successful control of a Great Flood leading to the establishment of the Xia dynasty and the beginning of civilization. However, the historicity of the flood and Xia remain controversial. Here, we reconstruct an earthquake-induced landslide dam outburst flood on the Yellow River about 1920 BCE that ranks as one of the largest freshwater floods of the Holocene and could account for the Great Flood. This would place the beginning of Xia at ~1900 BCE, several centuries later than traditionally thought. This date coincides with the major transition from the Neolithic to Bronze Age in the Yellow River valley and supports hypotheses that the primary state-level society of the Erlitou culture is an archaeological manifestation of the Xia dynasty.

Link

British Celts have more steppe ancestry than British English

An interesting tidbit in a preprint about blood pressure genes:

We consistently obtained significantly positive f4 statistics, implying that both the modern Celtic samples and the ancient Saxon samples have more Steppe ancestry than the modern Anglo-Saxon samples from southern and eastern England. This indicates that southern and eastern England is not exclusively a genetic mix of Celts and Saxons.

Southeastern England is genetically very homogeneous. If the people there were a mix of ancient Celts and Saxons you'd expect them to be intermediate between modern Celts (who should have more Celtic ancestry than the modern English) and ancient Saxons (who should have more Saxon ancestry than the modern English).

But, it seems that the English have less steppe ancestry than both modern Celts and ancient Saxons, so they're not really intermediate. My guess is that the English have Norman ancestry that the Celts don't. While the original Normans were Scandinavians with presumably lots of steppe ancestry, I'd be surprised if the post-1066 Normans that settled England were not already heavily admixed with the "French" and so had less steppe ancestry than the modern British Celts from Wales and Scotland.

bioRxiv http://dx.doi.org/10.1101/055855

Population structure of UK Biobank and ancient Eurasians reveals adaptation at genes influencing blood pressure

Kevin Galinsky et al.

Analyzing genetic differences between closely related populations can be a powerful way to detect recent adaptation. The very large sample size of the UK Biobank is ideal for detecting selection using population differentiation, and enables an analysis of UK population structure at fine resolution. In analyses of 113,851 UK Biobank samples, population structure in the UK is dominated by 5 principal components (PCs) spanning 6 clusters: Northern Ireland, Scotland, northern England, southern England, and two Welsh clusters. Analyses with ancient Eurasians show that populations in the northern UK have higher levels of Steppe ancestry, and that UK population structure cannot be explained as a simple mixture of Celts and Saxons. A scan for unusual population differentiation along top PCs identified a genome-wide significant signal of selection at the coding variant rs601338 in FUT2 (p=9.16×10-9). In addition, by combining evidence of unusual differentiation within the UK with evidence from ancient Eurasians, we identified new genome-wide significant (p less than 5×10-8) signals of recent selection at two additional loci: CYP1A2/CSK and F12. We detected strong associations to diastolic blood pressure in the UK Biobank for the variants with new selection signals at CYP1A2/CSK (p=1.10×10-19)) and for variants with ancient Eurasian selection signals in the ATXN2/SH2B3 locus (p=8.00×10-33), implicating recent adaptation related to blood pressure.

Link

Luwians vs. Hittites and Mycenaeans vs. Luwians

A rather imaginative reconstruction of the events surrounding the Sea Peoples and the ending of the end of the Bronze Age.

Jewish and Indian ancestry in the Bene Israel

PLoS ONE 11(3): e0152056. doi:10.1371/journal.pone.0152056

The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry
Yedael Y. Waldman , Arjun Biddanda , Natalie R. Davidson, Paul Billing-Ross, Maya Dubrovsky, Christopher L. Campbell, Carole Oddoux, Eitan Friedman, Gil Atzmon, Eran Halperin, Harry Ostrer, Alon Keinan

The Bene Israel Jewish community from West India is a unique population whose history before the 18th century remains largely unknown. Bene Israel members consider themselves as descendants of Jews, yet the identity of Jewish ancestors and their arrival time to India are unknown, with speculations on arrival time varying between the 8th century BCE and the 6th century CE. Here, we characterize the genetic history of Bene Israel by collecting and genotyping 18 Bene Israel individuals. Combining with 486 individuals from 41 other Jewish, Indian and Pakistani populations, and additional individuals from worldwide populations, we conducted comprehensive genome-wide analyses based on FST, principal component analysis, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing and allele sharing autocorrelation decay, as well as contrasted patterns between the X chromosome and the autosomes. The genetics of Bene Israel individuals resemble local Indian populations, while at the same time constituting a clearly separated and unique population in India. They are unique among Indian and Pakistani populations we analyzed in sharing considerable genetic ancestry with other Jewish populations. Putting together the results from all analyses point to Bene Israel being an admixed population with both Jewish and Indian ancestry, with the genetic contribution of each of these ancestral populations being substantial. The admixture took place in the last millennium, about 19–33 generations ago. It involved Middle-Eastern Jews and was sex-biased, with more male Jewish and local female contribution. It was followed by a population bottleneck and high endogamy, which can lead to increased prevalence of recessive diseases in this population. This study provides an example of how genetic analysis advances our knowledge of human history in cases where other disciplines lack the relevant data to do so.

Link

Long live the 25th March, 1821

Long Live the 28th October, 1940

Long Live the 25th March 1821

British origins (Leslie et al. 2015)

The long-awaited paper on the People of the British Isles has just appeared in Nature. I will update this entry with more information.

UPDATE:

The authors write:

Consistent with earlier studies of the UK, population structure within the PoBI collection is very limited. The average of the pairwise FST estimates between each of the 30 sample collection districts is 0.0007, with a maximum of 0.003 (Supplementary Table 1).

These are extremely small differences in the European (let alone global) context. So, the British are, overall, a very homogeneous population. This is what led the researchers to use methods such as ChromoPainter/ fineStructure/ Globetrotter that can squeeze out fine-scale population structure by exploiting linkage disequilibrium. Thus, the authors are able to detect 17 main clusters of the British.

Most of the clusters are geographical, but some span different regions (e.g., the "yellow circle" cluster). The elephant in the room is the "red square" cluster which spans Central/South England. The authors write:

There is a single large cluster (red squares) that covers most of central and southern England and extends up the east coast. Notably, even at the finest level of differentiation returned by fineSTRUCTURE (53 clusters), this cluster remains largely intact and contains almost half the individuals (1,006) in our study.

The authors then tried to infer the ancestry of the British clusters in terms of continental European clusters, which is to be published separately. In the plot on the right, you see the British clusters (columns) and their continental European sources (rows). The authors observe that clusters that are widely represented in Britain are likely to be older, while those that are missing in some populations are likely to be younger, because they didn't have the chance to spread across Britain. For example, a couple of Norwegian clusters are strongly represented in the Orkney islands, and these are likely to reflect Viking colonization.

The authors draw conclusions on several historical episodes of British history. The big one is the extent of Anglo-Saxon ancestry:

After the Saxon migrations, the language, place names, cereal crops and pottery styles all changed from that of the existing (Romano-British) population to those of the Saxon migrants. There has been ongoing historical and archaeological controversy about the extent to which the Saxons replaced the existing Romano-British populations. Earlier genetic analyses, based on limited samples and specific loci, gave conflicting results. With genome-wide data we can resolve this debate. Two separate analyses (ancestry profiles and GLOBETROTTER) show clear evidence in modern England of the Saxon migration, but each limits the proportion of Saxon ancestry, clearly excluding the possibility of long-term Saxon replacement. We estimate the proportion of Saxon ancestry in Cent./S England as very likely to be under 50%, and most likely in the range of 10–40%.

Two other details are the lack of Danish Viking ancestry in England:

In particular, we see no clear genetic evidence of the Danish Viking occupation and control of a large part of England, either in separate UK clusters in that region, or in estimated ancestry profiles, suggesting a relatively limited input of DNA from the Danish Vikings and subsequent mixing with nearby regions, and clear evidence for only a minority Norse contribution (about 25%) to the current Orkney population.

And, the absence of a unified pre-Saxon "Celtic" population. What seems to unify "Celts" is lower levels/absence of the Saxon influence, rather than belonging to a homogeneous "Celtic" population:

We saw no evidence of a general ‘Celtic’ population in non-Saxon parts of the UK. Instead there were many distinct genetic clusters in these regions, some amongst the most different in our study, in the sense of being most separated in the hierarchical clustering tree in Fig. 1. Further, the ancestry profile of Cornwall (perhaps expected to resemble other Celtic clusters) is quite different from that of the Welsh clusters, and much closer to that of Devon, and Cent./S England. However, the data do suggest that the Welsh clusters represent populations that are more similar to the early post-Ice-Age settlers of Britain than those from elsewhere in the UK.

Unfortunately, the authors have decided not to make their data publicly available. This is very unfortunate, and will keep this research out of the hands of many people who would be interested in it and who would be interested in analyzing this data. I can already guess the disappointment of people of British ancestry from around the world who have a genealogical interest in tracing their British ancestors to particular areas of the UK. Apparently, the data is deposited in the EGA archive, access requires red tape, and is apparently limited to institutional researchers. Thus, this data, perhaps the richest genetic survey of any country to date, will not be fully utilized to further science.

Nature 519, 309–314 (19 March 2015) doi:10.1038/nature14230

The fine-scale genetic structure of the British population

Stephen Leslie et al.

Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom. This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to southeastern England from Anglo-Saxon migrations to be under half, and identify the regions not carrying genetic material from these migrations. We suggest significant pre-Roman but post-Mesolithic movement into southeastern England from continental Europe, and show that in non-Saxon parts of the United Kingdom, there exist genetically differentiated subgroups rather than a general ‘Celtic’ population.

Link

Genetic pacification of Western Europeans (?)

Evolutionary Psychology www.epjournal.net – 2015. 13(1): 230-243

Western Europe, State Formation, and Genetic Pacification

Peter Frost, Henry C. Harpending

Through its monopoly on violence, the State tends to pacify social relations. Such pacification proceeded slowly in Western Europe between the 5th and 11th centuries, being hindered by the rudimentary nature of law enforcement, the belief in a man’s right to settle personal disputes as he saw fit, and the Church’s opposition to the death penalty. These hindrances began to dissolve in the 11th century with a consensus by Church and State that the wicked should be punished so that the good may live in peace. Courts imposed the death penalty more and more often and, by the late Middle Ages, were condemning to death between 0.5 and 1.0% of all men of each generation, with perhaps just as many offenders dying at the scene of the crime or in prison while awaiting trial. Meanwhile, the homicide rate plummeted from the 14th century to the 20th. The pool of violent men dried up until most murders occurred under conditions of jealousy, intoxication, or extreme stress. The decline in personal violence is usually attributed to harsher punishment and the longer-term effects of cultural conditioning. It may also be, however, that this new cultural environment selected against propensities for violence.

Link (pdf)

DNA of 17th century African slaves frome the Caribbean

PNAS doi: 10.1073/pnas.1421784112

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

Hannes Schroeder, María C. Ávila-Arcos et al.

Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.

Link

Sveti Ivan relics Middle Eastern, mid-1st century AD

Irrespective of one's religious beliefs, a genome from the mid-1st century AD would be interesting. I am personally in favor of the scientific study of saints' relics.

Bulgarian bones could be John the Baptist's, scientists say

So when Bulgarian archeologists announced in 2010 that they had found the bones of John the Baptist, Tom Higham was skeptical.

He got a surprise.

Higham, an Oxford University scientist and an atheist who doesn't believe in "any kind of religion or God or anything like that," was asked to test six small bone fragments found on an island named Sveti Ivan - St. John.

The bones turned out to be from a man who lived in the Middle East at the same time as Jesus, Higham said.

"We got a date that was exactly where it should be, right in the middle of the first century," said Higham, a radiocarbon dating expert.
...

DNA testing by colleagues at the University of Copenhagen suggested that the person was most likely to have been from the Middle East, he said.
"We have a complete genome. It's possible that we could step this a step further and see if there is any similarity," in the genetic material of all the relics.

St. John's father Zechariah belonged to to the Aaronic line of priests. While modern Jewish priests (Cohanim) belong to multiple Y-chromosomal lineages, I think it's a good bet that at least one or a few of these lineages could be traced to Jewish priests of 2,000 years ago (leaving the question of the ultimate Aaronic lineage open). If the remains from Sveti Ivan island match one of these lineages, then this would be a powerful piece of evidence in favor of their attribution to St. John the Baptist.

The plight of the Assyrians

ISIS Onslaught Engulfs Assyrian Christians as Militants Destroy Ancient Art

ISTANBUL — The reports are like something out of a distant era of ancient conquests: entire villages emptied, with hundreds taken prisoner, others kept as slaves; the destruction of irreplaceable works of art; a tax on religious minorities, payable in gold.

A rampage reminiscent of Tamerlane or Genghis Khan, perhaps, but in reality, according to reports by residents, activist groups and the assailants themselves, a description of the modus operandi of the Islamic State’s self-declared caliphate this week. The militants have prosecuted a relentless campaign in Iraq and Syria against what have historically been religiously and ethnically diverse areas with traces of civilizations dating to ancient Mesopotamia.

The latest to face the militants’ onslaught are the Assyrian Christians of northeastern Syria, one of the world’s oldest Christian communities, some speaking a modern version of Aramaic, the language of Jesus.

The New York Times reporter need not have gone to so distant a past to find parallels to the plight of the Assyrians, as this is merely a repeat of what happened only a hundred years ago.

Five people were buried in Amphipolis tomb

Bones found in Magnificent Amphipolis Tomb belong to Five People, Ministry Announced

The Greek Ministry of Culture has announced the long-awaited results of the analysis on the bones found inside the 4th century BC tomb uncovered in Amphipolis in northern Greece, and the news is quite unexpected – the bones belong to not one, but five individuals, pointing to the likelihood that it is a family tomb. 

... 

Person 1: Female, approximately 60 years
Persons 2 and 3: Two men, 35 to 45 years
Person 4: Newborn infant
Person 5: Cremated individual of unknown age and sex  

... 

The scientific team will continue to carry out in-depth studies of the bones, including DNA analysis, to obtain more detailed information about the individuals including their diet, their affinity and place of origin, whether they grew up in Amphipolis or had moved from elsewhere, when they were buried/cremated, and whether the individuals are related to each other.

Y chromosome super-fathers

This is a very exciting paper. Most of these lineages are so young that there are good chances that their founders were figures from history or mythology.

The most interesting one is DC2 which was also found in south Siberian Kurgans, belongs to haplogroup R1a1 and is given an age of 3,284 years by the authors (with some almost impossibly wide confidence intervals). Based on its distribution, and if a Bronze Age date is right, it is difficult to see in it anything other than a patrilineage that was present in Proto-Indo-Iranians.

European Journal of Human Genetics advance online publication 14 January 2015; doi: 10.1038/ejhg.2014.285

Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations

Patricia Balaresque et al.

High-frequency microsatellite haplotypes of the male-specific Y-chromosome can signal past episodes of high reproductive success of particular men and their patrilineal descendants. Previously, two examples of such successful Y-lineages have been described in Asia, both associated with Altaic-speaking pastoral nomadic societies, and putatively linked to dynasties descending, respectively, from Genghis Khan and Giocangga. Here we surveyed a total of 5321 Y-chromosomes from 127 Asian populations, including novel Y-SNP and microsatellite data on 461 Central Asian males, to ask whether additional lineage expansions could be identified. Based on the most frequent eight-microsatellite haplotypes, we objectively defined 11 descent clusters (DCs), each within a specific haplogroup, that represent likely past instances of high male reproductive success, including the two previously identified cases. Analysis of the geographical patterns and ages of these DCs and their associated cultural characteristics showed that the most successful lineages are found both among sedentary agriculturalists and pastoral nomads, and expanded between 2100 BCE and 1100 CE. However, those with recent origins in the historical period are almost exclusively found in Altaic-speaking pastoral nomadic populations, which may reflect a shift in political organisation in pastoralist economies and a greater ease of transmission of Y-chromosomes through time and space facilitated by the use of horses.

Link