search this blog

Thursday, November 9, 2017

Descendants of Greeks in the medieval Himalayas?


Below is an abstract from the upcoming Human Evolution 2017 conference (Cambridge, UK, November 20-22). It'll be interesting to see when the paper comes out how Harney, Patterson et al. uncovered the Greek affinities of some of these individuals; uniparental markers, rare alleles? The accompanying pic is from Wikipedia.

The skeletons of Roopkund Lake: Genomic insights into the mysterious identity of ancient Himalayan travelers

Eadaoin Harney, Niraj Rai, Nick Patterson, Kumarasamy Thangaraj, David Reich

The high-altitude lake of Roopkund, situated over 5000 meters above sea level in the Himalayas, remains frozen for almost 11 months out of the year. When it melts, it reveals the skeletons of several hundred ancient individuals, thought to have died during a massive hail storm during the 8th century, A.D. There has been a great deal of speculation about the possible identity of these individuals, but their origins remain enigmatic. We present genome-wide ancient DNA from 17 individuals from the site of Roopkund. We report that these individuals cluster genetically into two distinct groups-consistent with observed morphological variation. Using population genetic analyses, we determine that one group appears to be composed of individuals with broadly South Asian ancestry, characterized by diffuse clustering along the Indian Cline. The second group appears to be of West Eurasian related ancestry, showing affinities with both Greek and Levantine populations.


85 comments:

Nirjhar007 said...

We will have to see the Hg's .

Anthro Survey said...

Given the timeframe, it's doubtful any resembled continental Greeks or hailed from there in the first place. Thinking they were Byzantine Anatolians, probably Anatolia_BA/Chl or Turkish_Trabzon-like at the time.

Nestorian Christians is another fitting possibility.

epoch2013 said...

Remnants of Greco-Bactrians, maybe? From around the Hindu Kush?

epoch2013 said...

On second thought, if the samples show no Indian ancestry at all that would require that area to have no admixture for centuries after the demise of these kingdoms.

Maybe a diplomatic party we simply are unaware of?

Jaydeep said...

It is difficult to understand how those pilgrims would have Greek and Lebanese affinities. Why not with Central Asian or Iranian affinities ? Unless these people were foreign refugees from the Mediterranean having converted to Hinduism and come for a pilgrimage. But such a situation looks quite extraordinary.

Salden said...

There's a paper on South Asia's population history there.

Philippe said...

This paper: https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-017-0936-9

Palacista said...

Descendents of Graeco-Bactrians as above or legionary prisoners of the Sassanids I would imagine.

Joshua Lipson said...

Western Jews?

Salden said...

Oh, so it is. Well, plenty of other ones there are new. Like the Central Mexico and 2nd Canaanite papers.

rozenfag said...

At last, something from Belarus: Human aDNA diversity from Eastern European territory

Alena Kushniarevich1,2, Lehti Saag3, Kristiina Tambets1, Maxim Charniauski4, Mikalai Pamazanau4, Alexei Avlasovich4, Andrei Voitehowich4, Anu Solnik1, Tuuli Reisberg1, Jüri Parik3, Oleg Davydenko2, Mait Metspalu1

1Estonian Biocentre, Tartu, Estonia; 2Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus; 3University of Tartu, Dep. of Evolutionary Biology; 4Institute of History of the National Academy of Sciences of Belarus, Minsk, Belarus

In our project, we focus on dynamics of human population structure in Eastern Europe during the last four thousand years. We have extracted DNA from 14 teeth representing two temporal layers of today's Belarus territory. One sample belongs to the Bronze Age Corded Ware culture, whereas 13 are from Middle Age (11-13 cc AD) Slavic and Baltic ethnic contexts. Paired-end libraries for all samples were sequenced with Illumina NextSeq500 with the average genome coverage of ~0.3x. Variant calling was done using ANGSD (doHaploCall command) using the list of SNPs from the aDNA data set in Lazaridis et al., 2016. For the initial investigation of the newly generated aDNA sequences we have performed PCA, projecting aDNA samples on the PC, calculated from the modern human variation from Central-East Europe. We also have determined mtDNA haplogroups for all our samples using mtDNA-Server and haplogrep online tools.
To tackle the questions of genetic continuity/discontinuity and the possible reasons thereof (e.g. signals of recent selection) in East Europe during the time period of our interest, we are going to apply allele frequency-based analyses (PCA, ADMIXTURE, f3-statisctics etc) to our low-coverage genomes, available samples from Medieval Central-Eastern Europe and of Bronze Age samples from West Eurasia, as well as today's populations. For the genomes of high coverage, we are planning to run haplotype-based analyses.

Joshua Lipson said...

The genetic origin and heritage of Bronze Age Canaanites

"The Megiddo samples showed high similarity to older Levant BA samples, as well as to a later Iron Age (IA, ≈3 KYA) sample that we sequenced from Abel Beth Maacah in Northern Israel. The genomes of modern native
Levantine populations trace ≈60% of their ancestry to IA Canaanites, ≈10% to Eastern Africa, and theremaining to less well characterized sources, possibly related to Iran. The genomes of Ashkenazi Jews can be modeled as ≈55% BA Canaanites and ≈45% Neolithic Central Europeans, and those of Iraqi Jews as ≈70% BA Canaanites and ≈30% Neolithic Iranians."

Not sure what to make of this modeling of contemporary populations (perhaps more useful in understanding the composition of Levantine Arab populations than Diaspora Jewish populations)—but would not have guessed that Iraqi Jews would be modeled as "more Canaanite" than Palestinians or Ashkenazim. Wonder how Syrian or other Sephardim would shake out.

Labayu said...

@Joshua Lipson

but would not have guessed that Iraqi Jews would be modeled as "more Canaanite" than Palestinians or Ashkenazim.

The Ashkenazi diaspora started with very few Jewish women. That was not the case with Iraqi Jews. Palestinians likely had a fair amount of inward gene-flow from other Muslim populations, whereas Iraqi Jews were endogamous. If they occasionally married Jews from other regions, that wouldn't have made them much less Canaanite in ancestry.

Matt said...

Besides the new twists in the mysterious tale of the "Roopkund deads", following caught my eye:

Big, but innocuous, line for those of us with a strong focus on Holocene dispersals and present day structure:

Uncovering the prehistory of East Asia through ancient nuclear DNA (pS27)

"Recent sampling within 8,000 years from China allows us to start addressing the diversity in China leading up to present-day East Asians."

Early results? I'm still betting there will be structure with a fair amount of different ENA groups in East Asia until recently when they start to merge... The rest of the abstract is interesting as well, just not clear if they're talking about fundamentally new results from the Tianyuan paper this year, or a different way of talking about them.

Human evolution during the last 500,000 years

The dispersal pattern of Homo sapiens from Africa is also being re-evaluated, with growing evidence for at least two radiations – a major one at about 60 ka, and at least one more before 80 ka, which penetrated southern Asia and parts of Sunda. The earlier one(s) seem to have occurred without extirpation of the other contemporaneous human lineages, but within about 20,000 years of the later dispersal, they appear to have become physically extinct.

This is a pretty divisive paragraph. Was there an early wave of H Sapiens which didn't have a competitive edge over archaics like Neanderthals, and was then totally replaced like archaics were...? I don't know if anyone will truly believe it unless we manage to actually sample HS in Eurasia skeletons at this kind of 80k time depth...

Genomics of Middle Neolithic farmers at the fringe of of Europe

We note affinities between the British Isles and Iberia, confirming previous reports. Moreover, we note some indications of interactions between Middle Neolithic Farmers of the British Isles and Scandinavia.

Looks like a big paper on MN farmers from England, Ireland, Scotland, Wales and Scandinavia. Cool, though with what we know, of limited relevance to present day people.

Matt said...

More

On the evolution of lactase persistence in humans

This trait is indeed thought to be an adaptation to the domestication of dairying animals and the subsequent consumption of their milk (the cultural-historical hypothesis). The validity of this hypothesis has however often been questioned, as the frequency of lactase persistence (LP) imperfectly mirrors milk consumption. Indeed, some hunter-gatherers are known to have intermediate LP frequencies while some herders present low LP frequencies. Furthermore, populations from Northern Europe exhibit very high LP frequencies despite a moderate level of pastoralism, which led to the development of alternative explanations such as the calcium assimilation hypothesis.

Together with evidence for an apparently earliest LP allele in a Mesolithic HG context in Mathieson, makes me go hmm, odd as it is to explain *why* HG groups would have LP (esp. completely pre-herding).

Population structure of Medieval Estonia

"We use ancient DNA sample from the archaeologial collections of University of Tartu and Tallinn University, covering the time period from 11 to 15 cc AD. The beginning of Christianity at 13 cc AD in the region was a period of vast social, economical and cultural changes, which presumably changed the structure of local population considerably.

We successfully extracted DNA from the archaeological material (teeth) of 41 individuals, who have been uncovered from both rural and town cemeteries of Estonia. While the individuals buried in rural cemeteries are considered as the representatives of local Estonian population, those of big towns can be often associated with the new wave of people who arrived, mostly from West Europe, together with the Christianity, via the economical, cultural and political networks."


Question of whether the West European (German? Dutch? Swedish?) "new wave" was at all important to ancestry of present day people in Estonian at all.

Papers on Latin America remind me of these cool posters from ASHG which I saw on twitter, with really clear distinct clines for different Latin American populations, from ancestry from different Native American groups: https://imgur.com/a/IkEjF

Matt said...

@rozenfag: For the initial investigation of the newly generated aDNA sequences we have performed PCA, projecting aDNA samples (from Belarus) on the PC, calculated from the modern human variation from Central-East Europe.

Oddly timely given the last few Eurogenes posts, and in a way, perhaps a confirmation of the methodology...

@Josh: I wouldn't think of that necessarily as clearly showing "more Canaanite" - this may be a function of the restriction of their models, at least as presented in briefly in the abstract.

If you model Iraqi Jews as BA Canaanite+Iran Neolithic, then that's the absolute most basal Iran_N related population you can use to model Iraqi_Jews. That is, the Iran_N related with the absolute least Levant_N ancestry. If you used BA Canaanite+Iran_Chalcolithic, of course the BA Canaanite ancestry would likely go down somewhat.

Similar issues obtain if you model the present day Levant with IA Canaanite+East Africa - present East Africans themselves have substantial Levant_N and Arabian related ancestry...

Likewise probably not realistic to model Ashkenazis as BA Canaanite+LBK, as opposed to using more proximate populations in time and space, like ancient South Italians of the Roman period, who would likely already have had a bit of CHG and Yamnaya related ancestry.

The full paper, where space permits, will likely have a variety more models than the abstract, since I imagine Carmi will want to explore these questions more fully.

Anthro Survey said...

@Matt

I've modeled Ashkenazi Jews before using Samaritans, Italian_Tuscan and either German or the more western Slav_Czech obtaining some good fits.

This is simplistic, but , imo, largely mirrors their formative migratory history. Italian_Tuscan(from southern Tuscany) should be a good proxy for Roman-age Lazio/CENTRAL Italy and, in all likelihood, early Roman southern Italy before it experienced a Syrian influx. Jews are documented to have passed through and stayed in the cities of Northern Tuscany and Po Valley, as well, but that shouldn't result in dramatic modeling differences.

Italian_South already has plenty of (roman-age?) Levantine-related ancestry so it can confound things and the populations formative to European Jews didn't really hang out in Campania, iirc, even though it was a hotspot for Levantine arrivals.

Samuel Andrews said...

Abstract, The genetic origin and heritage of Bronze Age Canaanites
"Ashkenazi Jews can be modeled as ≈55% BA Canaanites and ≈45% Neolithic Central Europeans"

No way in heck are Ashkenazi a Hebrew-EEF mix. Unless the authors are referring to Late Neolithic Bell Beaker there's no way this statement is true. Ashkenazi have about 15% Steppe ancestry, something they could have only gotten from post-Neolithic Europeans.

Using, D-stats, I'd always get 50% northern European, 50% Levante for Ashkenazi. But apparently some people with knowledge in the subject say Ashkenazi's European ancestry is mostly from southern Europe not the European lands they currently live in.

Anthro Survey said...

"We note affinities between the British Isles and Iberia, confirming previous reports. Moreover, we note some indications of interactions between Middle Neolithic Farmers of the British Isles and Scandinavia."

A lot of those phenotype forum goers are going to be misled by this statement and take it as confirmation of an Iberian origin of "muh Atlantid Brits". I can see it coming.

Never mind that EEFs in Britain were practically replaced by a Beaker-like wave(hence limited relevance as Matt said), the Iberian affinity was owed to comparable resurgence of WHG ancestry and shared ancestry from similar EEF streams independently colonizing both places.

Samuel Andrews said...

"Genomics of Middle Neolithic farmers at the fringe of of Europe"

This should be really interesting. Funnel Beaker might have contributed a lot to both Northern Bell Beaker (Isles Celts-90% North Beaker) and Norse and all German speakers. I suspect lineages like U5b2a1a1, K1a4a1a2, and H1c descend from Funnel Beaker.

Synome said...

Regarding the west Eurasians found at Roopkund: Like Joshua Lipson, I'm tempted to speculate that these may have been Radhanite Jewish traders, on their way through the Silk Road.

Nothing in the release suggests enough to say anything with confidence. Just a guess based on proximity to possible trade routes and documented Levantine related traders at that time period. I don't suppose there are any other archaeological clues laying around in association? Would be helpful.

aniasi said...

This seems odd. The last study on this matter, if I remember correctly, stated that the party was made up of Chitpavan Brahmins. The study is about 10 years old, but a random Greek group here in Roopkund sounds as ridiculous as claims of Greek ancestry in Indians because they found Ydna H2-APT in Greece.

They better have this well lined up.

Ryan said...

Wouldn't a PCA be enough to find the affinities of these travelers?

And maybe they are Radhanite Jews or Nestorian Christians? What reason would anyone have to be up in these mountains though - are there important passes or monasteries? Any important products that would attract foreigners? It seems odd for anyone to just be hanging out in the middle of nowhere in such an unforgiving environment, let alone for people recently arrived from further west?

@Joshua - "Wonder how Syrian or other Sephardim would shake out."

IIRC from Behar, Syrian and Sephardic Jews form a common population to the exclusion of Jewish groups from outside the borders of the Roman Empire, and Ashkenazim are ~70% Sephardic Jews ~30% Europeans of various origins. Sephardim looked to be about ~70-80% descended from a population more or less indistinguishable from Samaritans, Druze and some Lebanese and Jordanians. So that probably lines up with your numbers pretty well.

Rob said...

@ Matt

It's curious you think that 40 million Europeans are of 'limited relevance'. ;)

Matt said...

@Rob, which 40 million is that then?

Anthro Survey said...

@Rob

EEFs of the British Isles and Scandinavia are indeed of rather limited relevance to contemporary populations there.

Thats's because they are essentially and reliably 90% "Europe_MLBA(continental influx) + 10% local EEF after circa 1800BC or so. It's not like in Iberia or western Padania where local EEFs seem to have contributed roughly 40% ancestrally.

Chalcolithic Central European EEFs bear more ancestral importance to present-day Brits and Swedes than do Stonehenge builders.

Salden said...

The news that Iraqi Jews are the closest to the Canaanites (and by extension, the Hebrews) is of no surprise. Other Jewish groups have been intermarrying with non-Near Eastern populations while Palestinians have repeateely been shown to have Arabian and SSA ancestry (courtesy of the slave trade and Egypt). The notion that Palestinians have a special claim to Israel is rooted in Arab Nationalism and/or Islamic Terrorism which is peddled by Western apologists.

Rob said...

@ Anthro
That's not what I'm referring to. I understand the basics of autosomal data findings, but thanks all the same

Joshua Lipson said...

@Salden

The proximity of Iraqi Jews to Mesopotamian and highland West Asian populations has seemed to many to suggest a large share of Assyrian-like ancestry among Iraqi Jews. The truth is that there's a lot of variation between individuals in the Arabic-speaking Iraqi Jewish population—and that Aramaic-speaking "Kurdish" Jews, Caucasian Jews, and Persian Jews are even more West Asian-shifted, and thus probably less "Canaanite".

Also, your political fanaticism re: the Palestinians is showing. I agree, they are not unadmixed Canaanites/Israelites. But deal with it: much to most of their ancestry is indigenous; same goes for most major Diaspora Jewish populations, ironically. That doesn't necessitate one political opinion or another.

Joshua Lipson said...

Regarding Nestorians: their contemporary Assyrian-identified descendants could not be mistaken genetically for Greek-to-Lebanese. Byzantine Cilicians or Syrians could be; so could Western Jews without the additional Central/Eastern admix that characterizes Ashkenazim.

Steven said...

Why couldn't the Levantine/Greek samples be from the Arab conquests of the region? It fits better with the time frame we are talking about.

Joshua Lipson said...

Levantine people (who might've been slightly Greek-shifted relative to modern Levantine Arabs) had not been Arabized or Islamized in any significant numbers by this date. Hard to imagine Aramaic-speaking Christian subjects of the Abbasids participating in far-flung Arab conquests.

Anthro Survey said...

@Rob
Sorry bro. Thought that's what you were referring to.

@Salden and Joshua
Non-Muslim minorities in the fertile crescent should all be good proxies for pre-Islamic populations. That's because Muslims picked up some Arabian, Khorasani and, in later times, SSA ancestry. Apart from a few cases, though, it shouldn't be overstated.

So, actually, Christian Palestinians are very much indigenous unlike the Ashkenazim and local Muslims(who got a chunk of Bedouin and even documented NA infusion in the last 4 centuries).

Salden, don't want to get political, but "Islam" is irrelevant to the topic you brought up because early anti-Zionist resistance was spearheaded by Christians who continue to be disproportionately involved. Antun Saadeh and Michel Aflaq---pivotal pioneers in all this---were Christians.

Arab nationalism started out as just pan-Levantinism but grew into a broader anti-colonialist pan-Arabism, so it shouldn't surprise is that Christians played such a huge role. Btw, nationalists were never really buddies with Islamists bolstered by Wahhabi Saudi Arabia(and in turn, Uncle Sam) . Only talk radio and people tied to neocon think tanks like Robert Spencer spread disinformation to the contrary.

Salafists/Wahabists don't generally care about Israel. If anything, they bring joy to right-wing sectors in Israel and their allies abroad, neither of whom desire a strong, stable and secular power in the Levant(other than Israel).

Anthro Survey said...

@Josh

If they clustered in a modernGreek-to-Lebanese spectrum, they were most likely Western Anatolian Byzantine Greeks. Modern Turks there are still quite indigenous, but the pull from Yamnaya and ENA in their Turkic ancestral bundle makes them cluster w/modern Iranians(iirc).

Salden said...

The Old Testament claims Abraham was of Mespotamian descent. And while you could disregard this as mythmaking, there have been investigations:

http://blogs.discovermagazine.com/gnxp/2011/01/the-assyrians-and-jews-3000-years-of-common-history/

The last paper on Canaanites also had the sample have more of an affinity with modern Assyrians than Palestinians. Considering what we now know, I would say the Israelites and Canaanites were both formed from more or less the same stock (that is, migrants from the Mespotamia region or close to it who also intermarried with local Levantines).

>Also, your political fanaticism re: the Palestinians is showing. I agree, they are not unadmixed Canaanites/Israelites. But deal with it: much to most of their ancestry is indigenous; same goes for most major Diaspora Jewish populations, ironically. That doesn't necessitate one political opinion or another.

Didn't say they didn't,

Samuel Andrews said...

Anyone notice, Yemanite Jews are amongst the closest relatives of Bronze age Levanties, ancient Egyptians, and the Middle Eastern gladiator from Roman Britain? Maybe that's because ancient Jews fell under the same Levantie/NE African cluster.

Salden said...

Yemenite Jews overall are descended from converts. Not the Israelites.

ak2014b said...

@Matt
"Together with evidence for an apparently earliest LP allele in a Mesolithic HG context in Mathieson, makes me go hmm, odd as it is to explain *why* HG groups would have LP (esp. completely pre-herding)."


Are you alluding to Iboussieres-25? Although a possible case of LP, the paper added a caution about it on p. 53 of the Supplementary Materials for The Genomic History Of Southeastern Europe pre-print, Mathieson et al 2017,

"Lactase persistence
The approximately 12,000 year old WHG individual Iboussieres-25 appears to carry the derived allele at the SNP rs4988235 that is strongly associated with lactase persistence in present-day Northern Europeans10. Four reads at this SNP all carry the derived allele, although we caution that this is a C>T SNP in a non-UDG treated sample and so might be affected by deamination, and two reads at neighboring SNPs do not support the persistence haplotype, at least in a homozygous state (Supplementary Figure S2.3). The observation of this allele, long before domestication and dairying, would be surprising, but might be consistent with observation of lactase persistence in early Neolithic populations in Iberia and Sweden11,12–observations that were themselves surprising based on the absence of persistence in large samples of Anatolian Neolithic and LBK individuals2,13. One possibility is that the allele was widely distributed at low frequencies before being strongly selected in the Bronze Age, perhaps due to the spread of dairying."



Broushaki et al 2015 likewise added a qualification, especially for sample WC1, for the unexpected results of 3 of their 5 Neolithic Iran samples being apparently derived for LP associated alleles. Supplementary Materials,

"We did, however, observe derived lactase persistence associated alleles in 3 of the 5 individuals: WC1 is heterozygous at rs4988235 (C/T(13910)) and AH1 and AH4 display derived alleles at rs182549. Because this is an unexpected result, we examined these positions in greater detail using samtools tview. Analysis of the specific read groups from which these reads derived along with their base quality and mapping scores did not show signs of contamination. However, the small number of derived reads present at each LCT site, particularly the ratio of derived/ancestral reads (1:10) in WC1, leads us to suspect they may be erroneous."

WC1 is dated 7,455-7,082 cal. BCE, and "the 14C radiocarbon datings for AH2 and AH4 are 8,205-7,756 cal. BCE and 8,204-7,755 cal. BCE, respectively".


In June 2015, Mathieson wrote about earlier studies' findings of LP. Mathieson provided several reasons for why these samples, which I remember as being of later dates, may not have been actually instances of LP,

"There are earlier reports of the LP allele in the Iberian Neolithic (Plantinga et al., 2012) and even earlier Middle Neolithic Sweden (Malmström et al., 2010). I’m mildly skeptical of these results because 1) They only estimate contamination from mtDNA, rather than the autosomes 2) rs4988235 is a C->T SNP where T is the derived allele, so aDNA damage could be an issue."


I'm not sure if that makes the Bell Beaker individual from the Mathieson et al 2015 paper the earliest sample which was confidently LP. Or are Iboussieres-25, and WC1 or at least AH1 and AH4, all plausibly derived for LP associated alleles?

ak2014b said...

@Salden
"The Old Testament claims Abraham was of Mespotamian descent."

"The Bible Unearthed: Archaeology's New Vision of Ancient Isreal and the Origin of Sacred Texts" is a book by the archaeologist Professor Israel Finkelstein‎ (Tel Aviv University) and one Neil Asher Silberman.

"Amazon.com Review
The Bible Unearthed is a balanced, thoughtful, bold reconsideration of the historical period that produced the Hebrew Bible. The headline news in this book is easy to pick out: there is no evidence for the existence of Abraham, or any of the Patriarchs; ditto for Moses and the Exodus; and the same goes for the whole period of Judges and the united monarchy of David and Solomon. In fact, the authors argue that it is impossible to say much of anything about ancient Israel until the seventh century B.C., around the time of the reign of King Josiah. In that period, "the narrative of the Bible was uniquely suited to further the religious reform and territorial ambitions of Judah." Yet the authors deny that their arguments should be construed as compromising the Bible's power. Only in the 18th century--"when the Hebrew Bible began to be dissected and studied in isolation from its powerful function in community life"--did readers begin to view the Bible as a source of empirically verifiable history. For most of its life, the Bible has been what Finkelstein and Silberman reveal it once more to be: an eloquent expression of "the deeply rooted sense of shared origins, experiences, and destiny that every human community needs in order to survive," written in such a way as to encompass "the men, women, and children, the rich, the poor, and the destitute of an entire community." --Michael Joseph Gross"


Some, or many or all, ancient Jews may turn out to have had Mesopotamian ancestry or admixture. However, there's no need to bring up fairy tales in order to make the suggestion. Getting aDNA from Mesopotamia can answer such questions.

Whether there's Mesopotamian ancestry or not, it's clear that Jews are local to or significantly local to the Levant/Middle East, and this has only been further confirmed by recent aDNA studies.

Matt said...

@Anthro Survery: Thats's because they are essentially and reliably 90% "Europe_MLBA(continental influx) + 10% local EEF after circa 1800BC or so.

Even in that instance, and even leaving aside Anglo-Saxon migrations, there's plausibly later migration from other populations in Western Europe post MLBA Europe who were similar. So the contribution of the British Middle Neolithic (stonehenge builders) may be less than this for present day people. (10% would be cool, but if that's not how it was, not how it was!).

Regarding your earlier comment: Never mind that EEFs in Britain were practically replaced by a Beaker-like wave(hence limited relevance as Matt said), the Iberian affinity was owed to comparable resurgence of WHG ancestry and shared ancestry from similar EEF streams independently colonizing both places.

It's interesting how there is some degree of extra genetic affinity between West Europe compared to what would be expected based on longitude alone, and compared to Central, and there was then in the MN, but the processes are different - Iberia->British MN via colonisation via Spain->France->Britain, vs likely a Central European Bell Beaker wave into Iberia - Central->Britain and Iberia with varying degrees of replacement, then ongoing admixtures in Central from other diverged BA people. Shows how geography generally constrains to recreate geographical relatedness in one way or another, over the long term...

@ak2014b. Fair. I'm not sure about estimation from the haplotype actually (is this a long haplotype with a deep association with the SNP or is the association due to recent selection?), but understand that it would be difficult to be confident from reads on the SNP alone from Iboussieres-25 with damage issues.

epoch2013 said...

@Matt

"Question of whether the West European (German? Dutch? Swedish?) "new wave" was at all important to ancestry of present day people in Estonian at all."

Tallin was a Hanseatic city (Called Reval in the German period). Part of it was part of the principalities of the German Livonian Order, another part was Danish. There are (used to be) Estonian Swedes.


https://en.wikipedia.org/wiki/Estonian_Swedes
https://en.wikipedia.org/wiki/Estonia#Danish_Estonia.2C_Terra_Mariana_and_the_Middle_Ages

Sounds like enough to leave a legacy.

ak2014b said...

@aniasi said...
"This seems odd. The last study on this matter, if I remember correctly, stated that the party was made up of Chitpavan Brahmins."

Whereas I thought I read here or at anthrogenica that the skeletons were likely composed of West Asians (Iranians) and South Asian individuals. In trying to locate where I came across that, I find every previous study abstract on these skeletons looks to have drawn different conclusions.

The only reference I can find for your suggestion "Chitpavan Brahmins" and Roopkund skeletons is from Nov 2004 news about a study
Finally, Lalji Singh's DNA tests at Hyderabad's Centre for Cellular and Molecular Biology would also suggest an identity of this mystery "family" that died so cataclysmically. His findings support Walimbe's idea that they were relatives, since the DNA matched. He also discovered that some samples showed genetic mutations specific only to Maharashtra's Kokanastha, or Chitpavan, Brahmins.

1. David's Wikipedia link mentions Iran:

Geneticists, Niraj Rai along with Manvendra Singh at the Center for Cellular and Molecular Biology at Hyderabad, conducted DNA tests on a hundred samples from the lake and compared them to the current Indian population. Results indicated that 70 percent of them had an affinity with Iran, while the remaining belonged to the local population. It is hypothesized that the Iran group took the help of local porters to seek new land for settlement.[1][7] Later studies placed the time of mass death around the 9th century CE (1,200 years old).[8]

2. Anthrogenica, June 2015
Ninth ISABS Conference on Forensic and Anthropologic Genetics (22-26 June 2015) Abstract number: ABS-422-ISABS-2015

THE ANCIENT DNA STUDY OF A NORTH INDIAN HIMALAYAN POPULATION
N. Rai, G. Chaubey, L. Singh, K. Thangaraj

The high-altitude (5029 meters) Roopkund lake is situated in the Himalayan Mountains within the Northern Indian state of Uttaranchal. Here, 70 years ago, several hundred human skeletons were found, in the lake itself and in its vicinity. This discovery was puzzling as the reasons for which so many people would have travelled and found their end there remained elusive. This is the first study to address the origin of these individuals through genetic and biological analysis of the 82 skeletal remains. Using amelogenin marker, it was found that the majority of the individuals were males. In the same time, AMS dating of the bones revealed that the individuals had lived in the 8th century AD. To address the ancestry of this population, DNA was extracted from the bones of 80 individuals and the complete mitochondrial genome of each of them was sequenced; furthermore, for 25 of them, 200,000 autosomal markers were also genotyped. The comparative genetic analysis, which includes modern day data from both 700 individuals living in the vicinity of the Roopkund site and 22,000 individuals from across India, suggests that the 8th century Roopkund population comprised two groups of genetically distinct individuals. The majority showed genetic affinity with present day European and Middle Eastern populations, while the others displayed common haplogroups with the Austro-Asiatic population of the North Indian Himalayas.

ak2014b said...

3. Then, Anthrogenica, Aug 2015 refers to a poster by "Niraj Rai, Lalji Singh & K Thangaraj",

Archeogenetics of Roopkund deads
http://yim.indiabioscience.org/poster/67

The high-altitude (5029 meters) Roopkund lake is situated in the Himalayan mountains within the Northern Indian state of Uttaranchal. Here, 70 years ago, several hundred human skeletons were found, in the lake itself and in its vicinity. This discovery was puzzling as the reasons for which so many people would have travelled and found their end there remained elusive. This is the first study to address the origin of these individuals through genetic and biological analysis of the skeletal remains. Using amelogenin marker; it was found that the majority of the individuals were males. In the same time, AMS dating of the bones revealed that the individuals had lived in the 8th century AD. To address the ancestry of this population, DNA was extracted from the bones of 80 individuals and the complete mitochondrial genome of each of them was sequenced; furthermore, for 25 of them, 200,000 autosomal markers were also genotyped. The comparative genetic analysis, which includes modern day data from both 700 individuals living in the vicinity of the Roopkund site and 22,000 individuals from across India, suggests that the 8th century Roopkund population comprised two groups of genetically distinct individuals. The majority showed genetic affinity with present day European and Middle Eastern populations, while the others displayed common haplogroups with the Austro-Asiatic population of the North Indian Himalayas. Finally, genetic continuity was observed in the area, with the present day inhabitants of the Indian Himalayas showing genetic closeness to the ancient Roopkund population. To conclude, this is the first ancient DNA study of a North Indian population; we find evidence of admixture between a putative Indo-Aryan migrating population and an older Austro-Asiatic population in India.


A comment by David at http://eurogenes.blogspot.com/2015/11/the-khvalynsk-men.html refers to the missing page http://eurogenes.blogspot.com.au/2015/08/archeogenetics-of-roopkund-skeletons.html which may have referred to the above abstract.

ak2014b said...

4. Matt's comment from May 2016 referred to the following from ESHG 2016 abstracts,

Title: P18.009 - Ancient DNA study of a mysterious lake of Himalaya.
Keywords: Ancient DNA; Mysterious Lake; Himalayan Mountains
Authors: N. Rai1, G. Chaubey2, L. Singh1, K. Thangaraj1;
1Centre for Cellular and Molecular Biology, Hyderabad, India, 2Estonian Biocentre, Tartu, Estonia.

Abstract: The high-altitude (5029 meters) Roopkund lake is situated in the Himalayan Mountains within the Northern Indian state of Uttaranchal. Here, 70 years ago, several hundred human skeletons were found, in the lake itself and in its vicinity. This discovery was puzzling as the reasons for which so many people would have travelled and found their end there remained elusive. This is the first study to address the origin of these individuals through genetic and biological analysis of the 82 skeletal remains. Using amelogenin marker, it was found that the majority of the individuals were males. In the same time, AMS dating of the bones revealed that the individuals had lived in the 8th century AD. To address the ancestry of this population, DNA was extracted from the bones of 80 individuals and the complete mitochondrial genome of each of them was sequenced; furthermore, for 25 of them, 200,000 autosomal markers were also genotyped. The comparative genetic analysis, which includes modern day data from both 700 individuals living in the vicinity of the Roopkund site and 22,000 individuals from across India, suggests that the 8th century Roopkund population comprised two groups of genetically distinct individuals. The majority showed genetic affinity with present day contemporary higher caste group and also middle eastern populations, while the others displayed common haplogroups with the Austro-Asiatic population of the North Indian Himalayas.


The affinity for the Middle Eastern and the South Asian samples at Roopkund appear already established. But the conclusions about the specific affinity of the remaining skeletons are all quite different.

I wonder whether the Roopkund study would benefit from waiting until publication of the Harvard's paper that will contain Swat results, assuming Swat may have the earliest Indo-European arrivals in South or South Central Asia as generally anticipated. Then those Roopkund skeletons variously described as European or Iranian or high caste can be compared to the early steppe settlers in Swat and not just with Greeks, to see if more proximate sources can be found or whether they're indeed specifically Greek-like.

ak2014b said...

The Anthrogenica link for number 3 repeated the one for 2, should be this.

Ryan said...

@Salden - "Other Jewish groups have been intermarrying with non-Near Eastern populations"

Right.

"while Palestinians have repeateely been shown to have Arabian and SSA ancestry (courtesy of the slave trade and Egypt). The notion that Palestinians have a special claim to Israel is rooted in Arab Nationalism and/or Islamic Terrorism which is peddled by Western apologists."

The hell are you smoking? Just because Palestinians did their own mixing with Bedouins doesn't invalidate their deeper ancestry in region. Jesus.

Salden said...

Ashkenazi Jews certainly have much Israelite ancestry, but that doesn't make it an issue to say that they aren't the closest to the Biblical inhabitants of Israel. Palestinians are from reliable evidence overall no more connected to the Hebrews than the AJs are today.

Joshua Lipson said...

@Salden. Truth is, we don't know. If I had to guess, I'd put Palestinian Christians, Samaritans, Syrian Jews at the top.

Samuel Andrews said...

@Salden,
"Yemenite Jews overall are descended from converts. Not the Israelites."

I doubt that because Yemanite Arabs have too much African ancestry to be big contributors to Yemanite Jews.

Richard Holtman said...

Thanks David for this. I'll look over it. Its just not in my field of expertise so I can't really have a good response but I still like your effort.

Joshua Lipson said...

Samuel Andrews: I think your reads on Jewish population genetics are a bit naive. Likely that West African (and additional East African) admixture reached Yemen after the formation of the Jewish community there (6th century CE, probably). Yemenite Jews have much more East African admixture than any other Jewish populations, particularly reflected in their mtDNA. They tend to cluster with Bedouins as ‘the purest Arabians’, and show no particular genetic connection to any other historically Arabic-speaking Jews.

Ryan said...

@Salden - "Ashkenazi Jews certainly have much Israelite ancestry, but that doesn't make it an issue to say that they aren't the closest to the Biblical inhabitants of Israel. Palestinians are from reliable evidence overall no more connected to the Hebrews than the AJs are today."

Ah fair enough. I'd just point out that not all of the inhabitants of ancient Israel were Jews though, and that not all of Palestine is contained within ancient Israel either, but yah. Probably similar levels of continuity - my guess would be Palestinian continuity would be closer to that of Sephardic Jews rather than Ashkenazim but I don't think we have firm numbers on that anyways.

Simon_W said...

Two drop my two cents here on these Palestinian/Jewish issues: The question about who's more indigenous really shouldn't matter for modern politics. Otherwise non-Native Americans should be very concerned, for example. The ethical guideline ought to be utilitarian, i.e. the sum of individul well-being has to be maximised. Hence neither further colonisation nor a backlash of ethnic cleansing are desirable. (Yeah I know, politics are not welcome here, so I won't say anything more on this.)

Samuel Andrews said...

@Lipson,
"Samuel Andrews: I think your reads on Jewish population genetics are a bit naive."

How am I being naive? Yemanite Jews are the closest match for ancient Cannites. How is it naive to then suggest that's because Yemanite Jews have lots of ancestry from ancient Jews who were likely genetically similar to Caanites?

"Likely that West African (and additional East African) admixture reached Yemen after the formation of the Jewish community there (6th century CE, probably)."

Even excluding the African admixture, Yemanite Jews are still significantly different from Arab Yemenites.

"They tend to cluster with Bedouins as ‘the purest Arabians’."

Ancient Canaanites and Egyptians were also quite similar to Bedouin. IMO, Yemanite Jews have pseudo Bedouin affinities caused by preserving what was once a common genetic makeup in the Middle East.

Arkaim said...

@Descendants of Greeks in the medieval Himalayas?
So, I bet on people related to the Kushunda/Kharia and Jews/ancient Byzantines? It might have been a trade route who went wrong and they got lost, who knows.

@Matt
Uncovering the prehistory of East Asia through ancient nuclear DNA
Human evolution during the last 500,000 years
Good papers

@The genetic origin and heritage of Bronze Age Canaanites
Ashkenazi Jews are absolutely NOT ~55% Canaanite and ~45% EEF. This may be the start of politicizing these studies, which have been the most neutral as possible until now.
Ashkenazi Jews are probably British_Roman_Outlier + Italian or Greek/Balkans.

The closest population to Ancient Canaanites/Levantines in general are Iraqi/Iranian/Georgian Jews or the Druze, or the Armenians, or the Assyrians.
But even then, these people are more shifted to the Caucasus.

Samuel Andrews said...

@Arkaim,
"Ashkenazi Jews are probably British_Roman_Outlier + Italian or Greek/Balkans."

Formal stats and PCA place Ashkenazi in roughly the same position as Sicilian and South Italian which can also be explained as halfway between northern Europe and the Levant.

I don't have any strong convictions about the issue but I do tend to think Ashkenazi have a decent amount of northern European ancestry. If all their European ancestry were from Italy or Greece then they'd be overwhelmingly of non-Hebrew origin, something I doubt.

Phenotypically, I can definitely see northern European looks in Ashkenazi. For example, DNA has confirmed Ashkenazi have as high levels of red hair as Germans. Where do you think they got that from? Definitely not Greece or Italy or the ancient Hebrews.

Arkaim said...

@Samuel Andrews
They have too little European Hunter Gatherer admixture for that compared to their Bedouin.
About red hair, the Udmurt have it, the Pashtu have it, the Uyghur have it, the Iranians have it.
Phenotypes are dependent on very few genes and you know that.
Look at this Burusho girl - one might have said she's from Europe, maybe from Belarus.
http://1.bp.blogspot.com/-o156IdeQmRA/VBv_SymOyOI/AAAAAAAA3CY/Zf9UFxlhgQE/s1600/Hunza.png

Ashkenazi Jews seldom have Northern European facial features, they have Mediterranean structure.

Salden said...

>Ancient Canaanites and Egyptians were also quite similar to Bedouin.

The last Canaanite sample had a significantly stronger affinity to Assyrians than Arabians.

Salden said...

Light hair and eyes for Eurasian to North African populations orginate from from the Middle East to Central Asia. It's not at all a surprise for isolated and/or endogamous populations to have them.

Davidski said...

@All

Richard Holtman is now banned.

http://eurogenes.blogspot.com.au/2017/09/banned-commentators-list.html

epoch2013 said...

@Matt

"Human evolution during the last 500,000 years



This is a pretty divisive paragraph. Was there an early wave of H Sapiens which didn't have a competitive edge over archaics like Neanderthals, and was then totally replaced like archaics were...? I don't know if anyone will truly believe it unless we manage to actually sample HS in Eurasia skeletons at this kind of 80k time depth...
"

Ofer Bar-Yoseph considers it true: https://www.youtube.com/watch?v=Pmjl9izlMkM

Labayu said...

@Samuel Andrews

Phenotypically, I can definitely see northern European looks in Ashkenazi. For example, DNA has confirmed Ashkenazi have as high levels of red hair as Germans. Where do you think they got that from? Definitely not Greece or Italy or the ancient Hebrews.

Red hair is pretty common in Samaritans as well. They've been endogamous for ~2,500 years and never left the region of historical Israel. I also wouldn't discount founder effect and/or selection playing a role in the increased frequency.

Ric Hern said...

@ Samuel Andrews

Maybe from the Galatians ?

Open Genomes said...

Regarding Southern European admixture among Ashkenazi Jews, I would like to repost a comment previously made in a different post about the migrations of Jews to and through Italy:

As far as Ashkenazi Southern European admixture goes, aren't the "East Sicilians" and "South Italians" a better fit than the Tuscans?

There are Jewish Medieval traditions that indicate that male prisoners from the First Jewish War were settled in the towns of Calabria, Apulia, Naples, and Rome. Archaeological evidence from Jewish catacombs and inscriptions also indicates this to be the case.

While the Northern Lombards expelled the Jews from the Kingdom of the Lombards in 680 and again in 755, upon converting to Catholicism, and the Byzantines expelled the Jews from their domains in 712, the Arian Lombard Duchy Benevento had a treaty with the Byzantine Catepanate of Italy which basically demilitarized the Byzantine towns of Southern Italy while leaving the Lombard Duchy in control of the interior.

The Lombard Duchy of Benevento
The Catepanate of Italy

The Arian Lombards, unlike the Orthodox-Catholic Romans/Byzantines, did not have much of a problem with Jews living in their domains. The Jews of Southern Italy in fact helped the Arian Goths resist the [re]conquest of Italy by the Roman Byzantines under Justinian in 526.

"According to tradition, the settlement of the Jews in southern Italy is connected with the captives brought there by Titus after the sack of Jerusalem (Jerahmeel, in Neubauer, "Medieval Jewish Chron." i. 190; Ahimaaz, "Chronicle," ib. ii. 112, line 4; "Jewish Quart. Rev." iv. 623). If there is any truth in this tradition, then together with Naples, Venosa, Otranto, Taranto, and Oria, Bari must at an early date have become a seat of Jewish influence."
(Rome itself should be included in this list, but Rome was almost depopulated during the Lombard Era.)

Jewish Encyclopedia - Bari
Jewish Encyclopedia - Apulia
Jewish Encyclopedia - Otranto

On the other hand, until the start of the Muslim conquest of Sicily, there seems to have been a hiatus in the Jewish presence in Sicily, because the Byzantines exclusively controlled Sicily and were therefore able to entirely exclude the Jews from residing there.

The Kalonymos rabbinical family from Bari apparently was brought north to Mainz after the siege of Bari in 987 by the Holy Roman Emperor Otto III. Apparently the Jews of Bari were key to negotiating the surrender to the Holy Roman Empire rather than the Antisemitic Byzantines who formerly ruled the Catepanate of [Southern] Italy.

Jewish Encyclopedia - Kalonymus

So I think we need to look for the specific source of Ashkenazi Southern European admixture in the territory of the Duchy of Benevento and the Catepanate of Italy, in other words, mainland Southern Italy, rather than Tuscany or Sicily.

Open Genomes said...

I would like to point out another confounding factor in determining the percentages of ancestral components among various Jewish populations:

Both Sephardic Jews have up to 10% of the North African ("Mozabite"-like) component, less so among Ashkenazi Jews, who have about 2%-5%. Historically, the Jews of Alexandria were expelled in 415 with the Christianization of Egypt, and it is thought that at least some of these migrated westward to Roman North Africa, where they mixed with the local Berber population. In particular, the Arian Vandals and Alans who ruled North Africa after 429 were friendly toward the Jews, and very hostile toward the Byzantines and the "Roman-Orthodox Catholic" Church. In 656, the Jews of Iberia were expelled, and many fled as refugees to Byzantine North Africa (not yet conquered by the Muslims until 680).

This resulted in a historically documented conversion of some Berber tribes, and some of these converted Berber groups remained Jews after the Muslim conquest and assimilated to the general Jewish population.

Jewish Encyclopedia - Morocco
Jewish Encyclopedia - Tunis

Berber Jews
Jewish Encyclopedia - Daggatun

In 1149, the Almohades, who had conquered most of Spain and North Africa eastward to Tunisia, ordered the forced conversion of Jews to Islam. During the rule of the Almohades, North Africa (and Muslim Spain) became mostly depopulated of Jews:
Jewish Encyclopedia - Almohades

Roger II of Sicily, as part of his conquests in North Africa and Greece during the Crusades, had his admiral George of Antioch capture and deport the Jews of the cities of Tunisia (and the Peloponnese) and bring them to Sicily, where they were granted privileges in new silk industry. It seems that with the persecution of the Almohades in North Africa that the Jews (and likely the Christians) of North Africa took advantage of the welcoming environment in Sicily and migrated there. (The documented Jewish "Di Masi" of Medieval Sicily were originally "Sijilmasi", from Sijilmasa in Morocco.)

After the expulsion of the Jews from Aragonese Sicily in 1493, Jews successively were expelled from Southern Italy, and ghettoized in Northern Italy, which resulted in a migration first to Prague and then on to the Polish-Lithuanian Commonwealth. These later Ashkenazi Jews would have incorporated any native North African ancestry found among the Jews of Sicily.

In various Eurogenes calculators, Ashkenazi Jews can have between 2%-5% of this North African component. Even more interesting, North Africans consistently show a supposed "Ashkenazi" component in various calculators, including DNA.land. Because these groups have been generally regarded as having entirely separate ancestry, this has caused much confusion, including showing some 100% North Africans of Muslim origin as having "84% Jewish" in the Eurogenes JTest calculator. Because of the Late Neolithic admixture between European Neolithic people and north Africans (resulting in the "KEB" population in the recent Fregel et al. preprint) North African admixture raises the "European Neolithic" percentage both among Jews and Southern Europeans.

Open Genomes said...

Among Ashkenazi Jews, mtDNA haplogroup L2a1l2, Y haplogroups E1a1-M33 and E-M81, and the autosomal Parkinson's disease risk allele LRRK2 G2019S allele are of North African origin.


The History of African Gene Flow into Southern Europeans, Levantines, and Jews - Moorjani et al. (2011)

A striking finding from our study is the consistent detection of 3–5% sub-Saharan African ancestry in the 8 diverse Jewish groups we studied, Ashkenazis (from northern Europe), Sephardis (from Italy, Turkey and Greece), and Mizrahis (from Syria, Iran and Iraq). This pattern has not been detected in previous analyses of mitochondrial DNA and Y chromosome data [7], and although it can be seen when re-examining published results of STRUCTURE-like analyses of autosomal data, it was not highlighted in those studies, or shown to unambiguously reflect sub-Saharan African admixture [15], [38]. We estimate that the average date of the mixture of 72 generations (∼2,000 years assuming 29 years per generation [30]) is older than that in Southern Europeans or other Levantines. The point estimates over all 8 populations are between 1,600–3,400 years ago, but with largely overlapping confidence intervals.

Among Near Eastern Jews, a majority of Syrian Jews are of Spanish (Sephardic) and South Italian Jewish origin, and Sephardic Jews settled throughout the Ottoman Empire, including Romania, Crimea, Egypt, and Ottoman Iraq. Some even settled in Isfahan, the capital of the Sassanian Empire. We should expect to see some European (Iberian and South Italian) and North African ancestry among the Jews of the cities of Iraq as well.

Open Genomes said...

The Carmi et al. Abstract that compares the Bronze Age Canaanites from Megiddo and Iron Age (Israelite?) sample from Abel-Beth-Maacah to modern Jews suffers from the same flaw that as these other studies that attempt to compare modern populations to ancient samples:

A valid comparison requires at least one other contemporary ancient DNA sample to form an outgroup.

As has been pointed out here, it isn't valid to compare Iraqi Jews to Bronze Age Canaanites (pre-Late Bronze Age Collapse), an Early Iron Age Levantine (Israelite? Post-Late Bronze Age Collapse, Sea Peoples) and Early Neolithic Iranians. These are respectively dated to about 1600 BCE, 1000 BCE, and 7500 BCE. We also don't have ancient DNA samples from Mesopotamia, and Mesopotamians would be the documented source for much of the local admixture among Iraqi Jews. (See the contemporary Early Medieval account from the Babylonian Talmud, Tractate Gittin, 70b-74b.)

Arkaim said...

@Salden
We know this isn't true.
WHG had the first Blue eyes, Blonde hair comes from Afontova Gora and light skin was already present in SHG and EHG. Red hair is still fuzzy, but probably associated with R1b.
So not from the Middle East - these phenotypes in the Middle East and Central Asia are remnants of the Indo-European expansions.

@Open Genomes
Thank you for contributing greatly to the topic.

Open Genomes said...

Here are two concrete examples of how such studies ignore direct evidence from ancient DNA:

Here we see sample F38, from Tepe Hasanlu, Iran, East of Lake Urmia c. 850 BCE, which has a tMRCA with the "Ashkenazi" (Spira family) R-Y11410 clade at c. 2300 BCE.
YFull R-Y16852 tree
Sergey Malyshev's R1b-M269 (P312- U106-) Phylogenetic Tree. v 38. May 30, 2017

Regardless of anything else, this is evidence of direct Northern Mesopotamian (Urartean or Assyrian) admixture among the ancestors of Ashkenazi Jews, in a Near Eastnern R-L584 Y clade that dates at least to the time of the 4.2 Kiloyear Event.

The Samaritans are known to have been a population isolate from about 444-338 BCE, when they split from Judaism. Unlike Jews, for religious reasons, the Samaritans did not accept either male or female converts (after 1924, they accepted female Jewish converts). On the autosomal PCA plots Samaritans cluster very closely with Bronze Age Levantines and the 3DRIF-26 Roman York gladiator outlier.

BR2 is an individual from Late Bronze Age Hungary, c. 1105 BCE. He is J-Y17946* (under J2a-M67). He appears to be a typical Bronze Age European, with no traces of extra Near Eastern admixture.

However, one of 4 remaining Samaritan Y lineages appears in J-Y23162 (samples YF10693 and ERR1395574), a subclade of BR2's branch J-Y17946, with a tMRCA with an Englishman and a Swiss at 1600 BCE. The tMRCA with BR2 is at 2700 BCE:

YFull J-Y17946 Tree

While it could be J-Y17946 is Near Eastern in origin, given the presence of Europeans in this clade from the Late Bronze Age onward, it may represent a back-migration from Europe to the Levant before the Hellenistic Era. A good candidate for such a migration is the migration of Sea Peoples from the Aegean during the Late Bronze Age Collapse between 1204-1184 BCE. (That is, unless the Englishman and Swiss are Levantines, for example, Phoenicians, which seems very unlikely.)

If, according to what Josephus and other historical evidence says, we consider the Samaritans to be generally a subset of the Judean population c. 444 BCE (because apparently thousands of Judeans split in a religious schism and joined the Samaritans), then based on the genetic evidence as well as the archaeology and Higher Criticism of the Biblical text, we could say that the Iron Age Levantines - including the Israelites - had Southern European admixture from the Sea Peoples in addition to ancestry from Bronze Age Levantines (Canaanites). There would also be admixture with Mesopotamians during the Babylonian Exile among the Judean returnees during the Achaemenid Era, as well as with any settlers brought to Israel by the Assyrians. (See the cuneiform prism of Sargon II of Assyria which describes this settlement.) Even the Biblical text admits that thousands of slaves and "Temple Servants" of non-Levantine origin as well as the descendants of Judeans returned to form the new Persian colony of Judea.

The above genetic evidence directly contradicts the simplistic model of Jewish ancestral admixture offered by Carmi et al. in their abstract.

Arkaim said...

Open Genomes
You mentioned back migrations and the Sea Peoples.
You might not have seen this yet then, this year of 2017 they managed to link the Luwians (an Indo-European society) to being the Sea Peoples.
They probably were Mycenaean-like with some other admixture from Anatolia, probably with a different level of Indo-European admixture as well, which I can't guess being more or less.

https://www.archaeology.org/news/5975-171010-luwian-inscription-translated

Matt said...

@Arkaim:So not from the Middle East - these phenotypes in the Middle East and Central Asia are remnants of the Indo-European expansions.

Blue eyes probably pre-IE in Anatolia at least, Mathieson et al states frequency of causal OCA2 allele almost identical between Anatolia_N (Barcin) and present day Spain: https://i.imgur.com/JGBLnfg.png

Higher frequency in Central European Neolithic than Central European Bronze Age, or Steppe.

Selection may have changed frequencies.

Unclear how true this is for groups other than Anatolians. Sample size not sufficient, I'd guess.

OCA2 allele may have originated on a WHG background. Not so clear whether WHG from the Balkans or a pre-Basal Eurasian Near East, etc.

Open Genomes said...

Of course, these examples regarding Jewish admixture and the Carmi et al. Bronze Age Canaanite study apply even more so to the Harney, Patterson et al. Medieval Roopkund samples. An affinity with "Greeks and Levantines" (clearly, not the same thing, unless one considers Cypriots) based on modern populations, would not be valid unless as some here pointed out, there were samples from Medieval Byzantines, Nestorians, and even possibly Jewish Radhanites (who were said to have traded between the "Palace of the Roman Emperor" in Mainz and China). BTW, we have no idea of the exact identities of these Radhanites, whether they were Iranian Jews from Rayy Iran (Rhages) or even proto-Ashkenazi / Sephardic Jews of Narbonne, France and Italy (e.g the somewhat later Benjamin of Tudela).

Open Genomes said...

IMHO, unphased D-statistics have reached their limit. A better model is IBD, particularly phased IBD, if possible. Even using IBD, there is always the possibility that the IBD derives from a common ancestor, not the ancient population in question. It seems that the Y-DNA of the Egyptian Saite Era mummies (J2b1-M205 and J1-Z2313) reflects the Middle Bronze Age 14th, 15th, and 16th Dynasty settlement of Bronze Age Canaanites in the Eastern Nile Delta. One of these mummies (J1-Z2313) on the PC plot also seems to have ancestry from a North African Berber-like group, presumably the Ma (Meshwesh) of the 22nd and 23rd Dynasties of Egypt, who mixed with the previous Egyptian elite.

When a study says "Ancient Egyptians from the 25th and 26th Dynasty" or "Early Iron Age Levantines", these Iron Age people cannot be assumed to be identical to their Middle Bronze Age predecessors, or to their Early Bronze Age and Chalcolithic ancestors.

Aside from the issue of unphased samples and DNA damage, many of the ancient samples have rather low coverage, which can produce IBS (false) "shared segments" when at higher resolution these would not be shared. Imagine then what individual SNPs in D-statistics can produce among highly similar populations or in modern people with ancestry from the same general region.

It's time that these aDNA studies of already admixed post-Neolithic populations start using IBD, and that other ancient individuals from important regions that had Early Bronze Age population explosions like the Old Kingdom of Egypt and Early Bronze Age Mesopotamia are tested, so the comparisons of ancient samples are valid. What became of the so-called "Teal People", when actual CHG and Iranian Early Neolithic samples became available? Everything changed. Not testing individuals from important ancient civilizations and population centers makes these studies "obsolete" even before they're published. Is "Iranian Chalcolithic" an imperfect proxy for Early Bronze Age Mesopotamian"?

As see, these conclusions can't be valid without a detailed analysis of the uniparental markers, and particularly the Y-DNA, which can be dated in a way that the mtDNA can't. "1240K" SNPs, which just give a cursory examination of the Y aren't enough. There are good capture arrays for the Y (not the Big Y) that can be used alongside the mtDNA capture arrays that these studies use. Even "looking at Y SNPs we already know about" cannot precisely place many samples, especially those with low coverage. Hopefully the Y chip being developed for the Tianyuan individual can be used for many other studies, as well as they already extracted DNA from the Reich Lab samples.

Y-DNA in particular could answer the question about the origins of the Roopkund so-called "Greek and Levantine" population. It's interesting that neither the Y nor the mtDNA was mentioned in the abstract. Is this supposed to be a "big surprise" upon publication, and if so, what's the point of releasing the abstract before publication?

Again, where is peer review in all of this, and why are these studies passing peer review when their methodologies are flawed?

Labayu said...

@Open Genomes

Iron Age (Israelite?) sample from Abel-Beth-Maacah

The material culture is Canaanite in the 11th-10th centuries BCE.

Here we see sample F38, from Tepe Hasanlu, Iran, East of Lake Urmia c. 850 BCE, which has a tMRCA with the "Ashkenazi" (Spira family) R-Y11410 clade at c. 2300 BCE.
YFull R-Y16852 tree

Sergey Malyshev's R1b-M269 (P312- U106-) Phylogenetic Tree. v 38. May 30, 2017

Regardless of anything else, this is evidence of direct Northern Mesopotamian (Urartean or Assyrian) admixture among the ancestors of Ashkenazi Jews, in a Near Eastnern R-L584 Y clade that dates at least to the time of the 4.2 Kiloyear Event.


Archeologically, it's clear people from the Transcausian Kura–Araxes culture settled in the area of northern Israel c. 2750 BCE. In the late 7th and early 6th centuries BCE, the Neo-Assyrians also settled defeated rebels and enemies from the fringes of their empire in Israel, Judah and Philistia.

Grey said...

@ Samuel Andrews
"Phenotypically, I can definitely see northern European looks in Ashkenazi. For example, DNA has confirmed Ashkenazi have as high levels of red hair as Germans. Where do you think they got that from? Definitely not Greece or Italy or the ancient Hebrews."

my pet theory is red hair is connected to the southern Urals so my answer to that would be trade routes

for example

https://en.wikipedia.org/wiki/Radhanite

(although potentially a lot older than that time period)

the Volga part of that network overlaps the Viking one

https://en.wikipedia.org/wiki/Volga_trade_route

Matt said...

@Sam: I can definitely see northern European looks in Ashkenazi

One thing that may be worth bearing in mind is that the Ashkenazis look to have come from a small founder population, and Xue and Carmi suggest it could be as low as 350 people
(https://www.timesofisrael.com/ashkenazi-jews-descend-from-350-people-study-finds/).

So if those people had an unusual balance of "looks", then their descendants who mostly just recombine their looks may look different to basic expected version of the overall autosomal mix. (Even Brits and Irish / Scandinavians only carry most of red hair variant MC1R alleles at 8-12%, so a founder effect among 300 odd people to get that to a higher level than expected is not too crazy.)

That said, Carmi also estimated 15-23% "Western or Eastern European" ancestry (http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006644).

There is some scattering of IBD shared CM of Ashkenazis with Eastern Europe, in the data Davidski ran - https://i.imgur.com/LqizRmP.png - but very slight.

So I don't think it's off base to have some ongoing ancestry from Eastern Europe.

One thing that does look fairly certain about Ashkenazis is that height seems about 4cm lower than NW Europe - "We found that ADNI individuals with a NW ancestry are on average 4 cm taller than ADNI individuals with a SE or Ashkenazi Jewish ancestry (p = 7.3 × 10−6), consistent with previously observed differences in height across Europe" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171282/) and this is *exactly* what the genetic height score would place AJ - https://i.imgur.com/K9Ywrw5.png (and exactly the same as Sicilians and South_Italian). (Though this is an old cohort with likely many born outside the USA...)

(Not to get weird about this, conscious of the history, etc.)

Rob said...

@ OG , or anyone

Slightly aside, does anyone have any feeling about the history E-V22 in Sephardi ?

Spanked said...

@ak2014b
Finkelstein's a discredited flake. I'm shocked anyone would seriously reference him.

Samuel Andrews said...

Matt, that's a reasonable explanation. I've considered that before.

@Everyone,

As far as I know if you model ashkenazi as a south European-Near Eastern mix they come out overwelmingly European. And keep in mind Greece was probably more "southern/basal" before Slavic admixture.

Also, Sephardic Jews are clearly more Near Eastern than Ashkenazi. Maybe the pull towards Europe comes from North European admixture that Sephardic lack.

Wouldn't Germans not Slavs be the most likely EuroHG rich ancestor? Yiddish is a German dialect.

Salden said...

>Finkelstein's a discredited flake.

You haven't shown that. And it's been established there isn't archaelogical or non-religious textual evidence supporting that there was ever an Exodus.

Labayu said...

The Exodus text itself is also filled with anachronisms. Finkelstein is one of the most widely respected archaeologists working in the Levant. While his low chronology was initially met with signifigant opposition, even his most vocal critics have been forced by the evidence to adjust their views. The only reason I can imagine for having such a vehement objection to citing his work is a dogmatic adherence to Biblical literalism. On the topic of the Exodus, there are no scientific arguments to counter Finkelstein's position, which is the Exodus could not have happened as described in the text. This is a mainstream archeological view. That does not preclude the possibility that the text contains some essence of a historical memory, but even that remains speculative.

Incidentally, if it weren't for Finkelstein, this Carmi et al paper we're discussing wouldn't have happened. For a variety of reasons, it's actually quite difficult to get excavation directors in Israel to provide samples for genetic research, but Finkelstein happens to be one of the directors interested enough in genetics to be willing to deal with the potential hassles.

Chad Rohlfsen said...

@OG,

The North African thing seems legit. I did an admixture run with Berbers and it seemed this was in all Jews. I can try some graphs to see if the same shows up. I was wondering how I also got Berber showing up for myself, then thought of Alexandria too and noticed it in all Jews. I'll try to recreate it.

Grey said...

Labayu
"On the topic of the Exodus, there are no scientific arguments to counter Finkelstein's position, which is the Exodus could not have happened as described in the text. This is a mainstream archeological view. That does not preclude the possibility that the text contains some essence of a historical memory, but even that remains speculative."

based purely on my take of human nature i'd say the Exodus story was based on a real event somewhere and sometime but maybe conflated with a later event like for example some event connected to Assyria, Babylon, Saba (or wherever) getting conflated with the later Hyksos expulsion from Egypt.

Samuel Andrews said...

GailT, the U5 expert, found unpublished 382 mitogenomes from Pamir, including 14 U5 mitogenomes.

http://www.anthrogenica.com/showthread.php?1417-New-U5-sequences&p=310146&viewfull=1#post310146

I've got 25k European low coverage mtDNA samples and 5k mitogenomes (inclu. lots of U5). Yeah, these Indian U5s do undoubtly fit within European U5 diversity or in other words they are from Europe.

U5a1a, U5a1b (popular in Ukraine HGs), U5a1d2 (popular in Comb Ceramic) are all Steppe dead ringers. Without ancient DNA (which shows those lineages emerging and spreading out of eastern Europe), using only modern mtDNA I'd suggest they spread across Europe and Asia very recently from an unknown location somewhere in Europe.

One Pamir had U5b2a1b. U5b2a1 peaks in frequency and diversity in the East Baltic. It has a similar distribution to other forms of U5b2a. Based on modern mtDNA, I think both U5b2a2 and U5b2a1 were involved in LNBA migrations from eastern Europe into western Europe and Scandinavia. 5b2a1a existed in Mesolithic Eastern Europeans (inclu. Ukraine) and so it is totally beleivable some proto Indo Iranians carried U5b2a1 and brought it to India.

The one exception is a U5b2* which GailT suggests arrived in India in the LGM. I polietly dis agree. Modern European mtDNA variation doesn't account for all the mtDNA variation that existed in Europe in the past. What I mean is, many of the mtDNA lineages IE people of largely eastern European origin brought to India disappeared from their homeloand, no longer exist in modern Europe.

I'm sure some of the mHG C in Turkey is basal to mHG C in Siberia but because of other pieaces of evidence we can confidently conclude even that C, with no close matches in Siberia, arrived in Turkey very recently from Siberia.

ak2014b said...

@Arkaim
"WHG had the first Blue eyes"

I can't recall any more the age of the earliest WHG sample that had blue eyes. However, derived alleles for blue eyes look to have been present in Iran Neolithic since quite early on too.

The Iran Neolithic WC1 sample from 7,455-7,082 cal. BCE of Broushaki et al 2016's dataset was heterozygous at rs12913832 (HERC2), so it had a derived allele for blue eyes. It was also heterozygous at most, or possibly all, of the locations of the usual blue eye haplotype, including rs1129038. (The sample may have had blue-eyed ancestry possibly)

The result for sample WC1 may lend weight to Gallego-Llorente et al 2016's imputed genotype results for their Iran Neolithic sample GD13a, a sample dated to 10000-9700 BP. Page 16 of the Supplementary Information goes over the HERC2 results for GD13a, which had some chance of being heterozygous at rs12913832,

"The eye-colour HERC2 variant rs12913832 was assigned almost equal likelihoods of being homozygous for the ancestral allele (A; genotype probability = 0.501) and heterozygous (AG; genotype probability = 0.499). Given this result, and that the ancestral allele was observed (2-fold coverage) in the sample it is very likely that GD13a had at least one copy of the ancestral dominant allele associated with brown eyes."

Blue eyes might not have been exclusive to WHG and could have had a wide spread in distant times. They may have become more common among some populations and remained at low level in others.


@Spanked
"Finkelstein's a discredited flake. I'm shocked anyone would seriously reference him."

As Labayu already observed, only biblical fundamentalists who confuse religious fables with history have an interest in asserting that Finkelstein is supposedly discredited. What shocks persons like you upon seeing anyone citing the impartial findings of professionals like Finkelstein, is that their findings contradict the fairy tales you want to impose on everyone (or everyone gullible) as history.

One Cehtan Vit, another like you who commented here, behaved identically when he thought to discredit evolutionary biology and biologists like Dawkins by citing theologians' nonsense from the preposterous answersingenesis as attempted retort. It's a waste of time explaining things to people like you, as you don't want correction, but want to herd everyone else into believing along with you in things that contravene facts.

Some people wrongly assume religious nutters are comical for their comical beliefs, but I think you're all dangerous.

And there definitely needs to be an embargo on the export of such further dangerous beliefs into Asia, as I can see in it a sinister effort to reduce as many Asians as possible to similar intractable states, to prevent Asia from progressing by stultifying it as a permanent third world, drugged by a new dose of absurd religious fairy tales, ones that have already been disproven.