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Tuesday, June 2, 2020

Perhaps a hint of things to come


It's still a mystery how the Hittites and other Anatolian speakers ended up in the Near East. However, the leading theory is that their ancestors migrated from the steppes of Eastern Europe to western Anatolia via the Balkans sometime during the Copper Age.

Consider the qpAdm mixture models below, made possible thanks to some of the ancient samples published recently along with Skourtanioti et al. 2020. The key ancients are described in a text file available here.

TUR_Barcin_C
AZE_Caucasus_lowlands_LN 0.471±0.094
RUS_Vonyuchka_En 0.148±0.040
TUR_Barcin_N 0.381±0.069
chisq 12.874
tail prob 0.116261
Full output

TUR_Barcin_C
RUS_Vonyuchka_En 0.107±0.029
TUR_Buyukkaya_EC 0.893±0.029
chisq 12.107
tail prob 0.207331
Full output

I'd say it's quite clear now that TUR_Barcin_C harbors minor ancestry from the Pontic-Caspian (PC) steppe. The reason this isn't widely accepted yet is because demonstrating it convincingly hasn't been possible without a proximate Anatolian ancestry source for TUR_Barcin_C, precisely like TUR_Buyukkaya_EC.

Admittedly, though, the statistical fits in my models aren't all that great. I suspect the problem lies with RUS_Vonyuchka_En, which is likely to be a rather poor stand in for the people who brought steppe ancestry, and possibly early Anatolian speech, to western Anatolia.

So let's see what happens when I try a more proximate reference for the steppe ancestry in TUR_Barcin_C. How about Yamnaya_BGR, an individual of mixed Balkan and steppe origin from what is now Bulgaria?

TUR_Barcin_C
AZE_Caucasus_lowlands_LN 0.518±0.075
TUR_Barcin_N 0.203±0.056
Yamnaya_BGR 0.279±0.067
chisq 10.602
tail prob 0.225269
Full output

TUR_Barcin_C
TUR_Buyukkaya_EC 0.749±0.058
Yamnaya_BGR 0.251±0.058
chisq 9.687
tail prob 0.376414
Full output

That's a little better. Unfortunately, the problem now is that the models are anachronistic, because TUR_Barcin_C is about a thousand years older than Yamnaya_BGR. Clearly, we need more Copper Age samples from the western edge of the PC steppe, the eastern Balkans, and especially northwestern Anatolia.

The Principal Component Analysis (PCA) below effectively illustrates why my qpAdm models work. It was produced with Global25 data using the Vahaduo PCA tools freely available here. Note that TUR_Barcin_C is shifted away from the essentially perfect cline formed by AZE_Caucasus_lowlands_LN, TUR_Barcin_N and TUR_Buyukkaya_EC towards samples from ancient Eastern Europe, including Yamnaya_BGR.


See also...

Steppe invaders in the Bronze Age Balkans

234 comments:

1 – 200 of 234   Newer›   Newest»
Davidski said...

Looks like Kale at AG just beat me to it...

https://anthrogenica.com/showthread.php?20471-Genomic-History-of-Neolithic-to-Bronze-Age-Anatolia-N-Levant-and-S-Caucasus-2020&p=672102&viewfull=1#post672102

But it's good to see corroboration for my results from a different method.

rozenblatt said...

So, you think that this steppe influx went around western coast of Black sea, as opposed to Eastern route?

Davidski said...

Yep, and to be clear, this really is a hint of things to come. I was just being cute when I said "perhaps".

Samuel Andrews said...

@rozenblatt,

Yeah, the idea four years ago was Barcin_Chl's Steppe ancestry could be from the Caucasus from a population like Armenia Chl (who had signifcant Steppe ancestry).

But, after Wang 2018 got more ancient DNA from the Caucasus we see most pops there did not have Steppe ancestry. And now that this 2020 paper got lots of DNA from Anatolia, we see other pops in Anatolia had Caucasus/Iran ancestry but no Steppe ancestry.

.....Conclusion Barcin_Chl's 10% Steppe ancestry is from Southeast Europe.

gamerz_J said...

@Samuel Andrews

It seems to me that north-western Anatolia was quite separated from the rest of Anatolia, as it has more connections with Europe such as the one described here (among older ones) and seems to be also more related to CHG than Iran_N.

Quite interesting, I was wondering what made Barcin_C so different, Steppe ancestry seems to be it.

Targamos the Based, son of Kavkasos son of CHG son of said...

@Sam
The idea was pretty stupid to begin with because doing a simple model will reveal that Areni prefers Progress much more than any Yamna group, on top of that Barcin is on the opposite end of Anatolia from Areni. Areni picks 26.2 Progress(54 Tepecik,12 GanjDareh,7CHG,0PPNB or other steppe) with a distance of 2.5 with G25 coords.

Samuel Andrews said...

@Targamos, Yeah it was always just special pleading that we took too seriously.

CrM said...

@Davidski

What if you include Areni in the model?
There's a particular outlier in Areni, it packs some Eneolithic Anatolian ancestry (like TUR_Camlibel_Tarlasi_LC) while others prefer Aze_LN.
Barcin_C holds a preference to that Areni outlier.

https://i.imgur.com/GNWBVh3.png

Davidski said...

@CrM

Yeah, Barcin_C can be modeled with the Areni_C samples, especially a couple of them. But this is probably a fluke due to overlapping components from the steppe and Anatolia.

You're likely to see why in the near future when more samples are released.

zardos said...

Like I said in the past, they need samples from Cernavoda and related steppe influenced cultures from the Balkans from the end phase of TCC, as well as Troy, and not just a single one, because it might be a diverse population, but a wide range of samples. There they will find the Proto-Anatolians with significant steppe influence most likely and it will be very interesting for the whole Steppe-Balkan interactions in the earliest phase. By following their trail to Troy and North Western Anatolia, you have the whole movement responsible.

JuanRivera said...

TUR_Ikiztepe_LC:IKI002 (really more of an outlier) and TUR_Kumtepe_N_low_res (who is actually of Chalcolithic age) also have steppe ancestry. Of note is that Vahaduo prefers Chalcolithic/EBA Anatolian ancestry, and when one includes that and samples from Southeastern Europe then ARM_Areni_C doesn't appear in the result. It may be a different thing in the G25.

JuanRivera said...

On the genotypes of ancient Caribbeans mentioned in the past thread:

https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/Fernandes_Sirak2020_Caribbean_0.zip

Davidski said...

I've added the following Caribbean samples to the G25 datasheets.

https://drive.google.com/file/d/14Rdt9Yb5BKfnc9xSDn5uMR5Fi1xWxARc/view?usp=sharing

Same links as always...

https://eurogenes.blogspot.com/2019/07/getting-most-out-of-global25_12.html

epoch said...

Good candidate for change:

https://www.researchgate.net/publication/250139310_The_Late_Chalcolithic_Settlement_of_Barcin_Hoyuk/link/55264c1a0cf24b822b407c0c/download

"The earliest levels encountered so far at the site are Late Neolithic, dating to the
mid to late seventh millennium. Excavations reveal that there was a hiatus in occupation, thereafter, spanning more than two millennia. Settlement on the mound resumed in the Late Chalcolithic period, probably during a relatively short period at the beginning of the fourth millennium BC.
"

Synome said...

The question I have is, if this is the shape of things to come (and I look forward to it), when and how quickly will this lead to a change in approach to the IE question from some of the leading aDNA research teams who so far have spent a great deal of time contesting the previously leading theory of Anatolian and IE origins in the steppe and early migration through the Balkans?

Romulus said...

There was never any migration of Yamnaya or Yamnaya related or derived people into Bronze Age Anatolia. Bronze Age Anatolians did however have abundant contact with Neolithic and EBA Balkans who had EHG ancestry dating to the Mesolithic, and Steppe ancestry as evidenced in the Varna and Tripolye samples.

Davidski said...

@Romulus

Bullshit.

Wait and see.

Archi said...

@Romulus
"There was never any migration of Yamnaya or Yamnaya related or derived people into Bronze Age Anatolia."

Migration from the Northern Black Sea coast to Middle Bronze Age Anatolia is clearly documented archaeologically. A change in lifestyle can be clearly seen there.

Romulus said...

No it is migration out of Anatolia , opposite direction. You can see it in the Mycenean Greek paper. They had a rise in Iranian Neolithic ancestry most related to Ancient Armenians.

FACT - migration of a CHG rich population out of Anatolia ,mixing with EEFs forming Minoans, amd contributing 90-95% to Mycenean

FICTION - Bronze Age migration from Balkans into Anatolia, proven by Krause and the direct conclusion of the paper.

Romulus said...

Also FACT - Phocacian Greeks from 1000 years after Myceneans are identical to Myceneans autosmally and share exclusively Y HG J2a1

No migration from the steppe is involved in Hittites or Myceneans. They are direct desendants of PIE.

Davidski said...

@Romulus

Mycenaeans can't be 90-95% Minoan because they have around 20% European LNBA ancestry, while Minoans have none.

You can read about that here...

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

Romulus said...

As per the paper - They have a minimum 4% to a maximum of 12% possibly Steppe related ancestry which is a poorer model relative to using Armenia.

A totally trivial amount indicative of nothing. 4%-12% Steppe is at best 2%-6% EHG. Iron Gates HGs just north of this had way more EHG and R1b, Varna man had 10% EHG and the Varna outlier was loaded.

No evidence of migration. Minoans are ancestral to Myceneans. Hittites lack the trace amounts of Balkan HG that made it into Myceneans.

Samuel Andrews said...

@Romolus,

Myceneans and Minoans had Kura-Araxes-like Near East admix. Steppe people had NONE of this.

Steppe people's Near East admix comes from PALEOLITHIC HUNTER GATHERERS. It is so old to be linked in any way to Indo European languages.

Davidski said...

@Romulus

You're referring to the distal models from the paper, which aren't realistic.

Obviously, no one really believes that steppe people or Baikal HGs migrated to Greece.

People from north of Greece migrated to Greece, and Mycenaeans have substantial ancestry from these people.

The Armenian angle is bullshit. It was always bullshit.

Samuel Andrews said...

@Romulus,

If Myceneans got their Steppe admix from near East, why don't Minoans have Steppe admix if they have the same kind of Near East admix?

The answer to that question is obviously, Myceneans' Steppe admix is not from the NEar East.

Romulus said...

I listen to the researchers and authors of these papers and accept their conclusions, which are the most intelligent and unbiased interpretation of these facts.

Archi said...

@Romulus
"FICTION - Bronze Age migration from Balkans into Anatolia, proven by Krause and the direct conclusion of the paper."

That's a lie. Stop lying. The Middle Bronze Age Hittite period migrations were not considered there at all.

"No it is migration out of Anatolia , opposite direction."

You have no understanding what this is about, you know nothing.

" Also FACT - Phocacian Greeks from 1000 years after Myceneans are identical to Myceneans autosmally and share exclusively Y HG J2a1"

It's a lie. No such fact, don't make it up.

"Minoans are ancestral to Myceneans."

This is bullshit. Mycenaeans are a lot of nationalities, Mycenae is like Americans, they're as ethnically diverse, no Achaeans (i.e. Greek) have been tested.

"Hittites lack the trace amounts of Balkan HG that made it into Myceneans."

It's a lie. Not a single Hittite has been tested.

"I listen to the researchers and authors of these papers and accept their conclusions, which are the most intelligent and unbiased interpretation of these facts."

You're all perverted and twisted, writing a complete lie.


Romulus said...

@Archi

https://twitter.com/iosif_lazaridis/status/1106262781895077889?lang=en

Archi said...

@Romulus

Learn to read: "probably", it is not fact. Empúries is in Spain and Phocaea is in Asia Minor, not Greece.

Davidski said...

@Romulus

Those Greek samples from Iberia have steppe and Europe LNBA ancestry, just like Mycenaeans do.

I've got a challenge for you. E-mail Iosif Lazaridis and ask him these questions:

- do Mycenaeans have significant ancestry from north of Greece, including the steppe?

- do the Iberian Greeks prove that Mycenaeans are basically like Minoans?

- is there really any direct evidence that Mycenaeans have ancestry from Armenia?

Let us know what he said.

Archi said...

@Davidski @Romulus

Lazaridis has only one question to ask: when will the Achaeans, namely the Achaeans, and the Dorians be tested? And not in a single instance.

Bronze Mycenaen Greece Grave Circle B, Mycenae [Z59] 1500 BC U5a1/U5a1a


@Romulus

She noble Cretan of the Mycenaean period has steppe ancestors.

Mayuresh Madhav Kelkar said...

"I've got a challenge for you. E-mail Iosif Lazaridis and ask him these questions:"

Do it yourself.

Davidski said...

@Mayuresh Madhav Kelkar

But I already know the answers to those questions.

Carlos Aramayo said...

@Davidski,

I want to let you know, regarding Indo-Iranian past, that recently appeared a new chronology for Sintashta culture, instead of the long lasted view that it began around 2100 BCE, now Dr. Alicia Ventresca Miller, Robert Spengler, and their team regards Sintashta began around 2400 BCE and finished around 1800 BCE. Apparently, it is based on calibrated C14 new datings, as Ventresca Miller et al. (2020 b) comment:

"...Middle Bronze Age (2400-1900 cal BCE) people, often referred to as the Sintashta, constructed nucleated settlements, with population estimates ranging from 200 to 700 individuals..." (page 6).

Please see the paper published on 2 June 2020 at:

https://tinyurl.com/ybwv29du

Davidski said...

@Carlos

Thanks, interesting.

However, I was always under the impression that Sintashta started during the Middle Bronze Age.

https://eurogenes.blogspot.com/2018/04/the-mystery-of-sintashta-people.html

So I guess I was ahead of the curve on the issue. lol

gamerz_J said...

https://twitter.com/iosif_lazaridis/status/1106269566836060166

Given that Sicilians have North African ancestry etc, it is interesting that they plot so close to Mycenaeans.

Modern-day mainland Greeks have substantially more Steppe ancestry than the Mycenaean samples yet they are also very close to ancient Mycenaeans.

I am wondering if Dorians/Achaean were basically Mycenaeans genetically (common source populations) with more Steppe ancestry but not sure.

Copper Axe said...

@Carlos Amayo

Is there any evidence that it was Sintashta associated sites which should be dated to 2400 bc, rather than those just being late Abashevo sites?

Davidski said...

Abashevo in western Siberia?

Samuel Andrews said...

@gamerz_J,

The higher Steppe in modern Greeks compared to ancient Greeks is due to heavy Slavic admixture.

epoch said...

@Romulus

"FICTION - Bronze Age migration from Balkans into Anatolia, proven by Krause and the direct conclusion of the paper."

Let me quote the paper itself:

"However, Mycenaeans can also be modelled as a mixture of Minoans and Bronze Age steppe populations (Table 1 and Supplementary Information section 2), suggesting that,
alternatively, ‘eastern’ ancestry arrived in both Crete and mainland
Greece, followed by about 13–18% admixture with a ‘northern’ steppe
population in mainland Greece only. Such a scenario is also plausible:
first, it provides a genetic correlate for the distribution of shared toponyms
in Crete, mainland Greece, and Anatolia discovered in ref. 21;
second, it postulates a single migration from the east; third, it proposes
some gene flow from geographically contiguous areas to the north
where steppe ancestry was present since at least the mid-third millennium
bc (refs 6, 9).
"

Copper Axe said...

@Davidski

Abashevo culture extended to the Urals, even slightly east of it if I'm not mistaken. Which is the region they are talking about here. I don't see a mention of new datings of the sites ofthe Sintashta culture.

"Middle Bronze Age (2400–1800 cal BCE) people, often referred
to as the Sintashta, constructed nucleated settlements, with
population estimates ranging from 200 to 700 individuals
(Gening et al., 1992; Grigor’yev, 2000; Anthony, 2007; Kohl, 2007;
Koryakova and Epimakhov, 2007; Hanks, 2009)"

They did say they only saw clear evidence of aggregation occuring after 2200 bc, which coincides with the settlements such as Arkaim and Sintashta.

gamerz_J said...

@Samuel Andrews

Only Slavic admixture? Nothing came to Greece from the north between Mycenaean and Slavic migration?

That would make modern-day Greeks quite Slavic actually, and I am not sure they are to that extent.

Archi said...

@Copper Axe said...
"Abashevo culture extended to the Urals, even slightly east of it if I'm not mistaken."

You're mistaken.

"Middle Bronze Age (2400–1800 cal BCE) people, often referred
to as the Sintashta"

Here they talk about the Middle Bronze Age and the range inside it, not about Sintashta chronology, and the word Sintashta is used as the most frequent word for these people (but not only Sintashta did so). And it's not a new chronology, it's an old chronology, just the dates of the epochs in the Steppe are not like those in the Middle East.

Davidski said...

@Copper Axe

Abashevo culture extended to the Urals, even slightly east of it if I'm not mistaken.

You're mistaken.

Matt said...

@gamerzj, I think that the groups who came to Greece post Mycenaean era (and probably mainly not until post-classical era Greece) were a mix of

a) pops from Southeast-Central Europe who probably had more steppe ancestry than Mycenaean but lacked much of the "Baltic-BA HG"/"Baltic-BA drift" that Baltic BA had

b) BA Anatolia like populations.

Modern day Greeks certainly seem more intermediate Anatolia BA and Southern Slavs than Mycenaean and Baltic BA.

This is consistent with the migrations coming from largely immediately North and East of Greece, and the merging of this area into one big Hellenistic / Roman / Byzantine civilization that was Greek speaking, which happened from the first millenniums BC to AD.

Matt said...

Oh, btw I don't think any "Dorian Invasion" mattered because no indication of such in Greek colonists out in Spain, but I think the Hellenisation of Anatolia and other migrations which really existed did actually matter.

Matt said...

Off topic - https://www.biorxiv.org/content/10.1101/2020.06.03.131995v1.full.pdf+html

Salkhit skullcap from Mongolia. 34kya.

Has West Eurasian ancestry which East Asians lack.

Suggests East Asians at this time not evolving as far North as Mongolia, adding to what we knew from Yana at Siberia at 31kya that not evolving in far NE Siberia.

Adds weight to East Asians probably evolving in South / Southwest China until less than 25kya?

Davidski said...

@gamerz_J, Matt & Samuel

Expect some significant substructures in the Bronze Age Greek world, mostly along the Mycenaean > Crete Armenoi cline.

So not all of the extra steppe admix in Greeks today is from Slavs, or even the Iron Age and Hellenistic periods.

gamerz_J said...

@Matt
Re China:
My guess is also southwest China probably reaching all the way to the Himalayan lowlands and at times perhaps Central China too.

Re Anatolia_BA and Greece:
Does Anatolia_BA have extra Iran_N and Levant_N ancestry? If so then I am not sure that it is that prevalent in Greece because not all Greeks (see Vahaduo for example) score these components.
Furthermore, there is also the massive wave of refugees from Asia Minor to Greece after the 1920s that I expect introduced more 'eastern/Anatolia_BA' components to Greece that many Greeks from rural areas in particular might not have. I am not sure how extensive the mixing with Asia Minor Greeks has been since then.

@Davidski
Thanks, yes something like that is going on probably.

gamerz_J said...

@Matt
"Oh, btw I don't think any "Dorian Invasion" mattered because no indication of such in Greek colonists out in Spain, but I think the Hellenisation of Anatolia and other migrations which really existed did actually matter."

Sorry missed that. Depends from where the colonists to Spain were from, how old etc. It might not have been an invasion but there are certainly northern influences in archaeology and linguistics.

Out of curiosity whic other migrations are you referring to?

Matt said...

@gamerzj, Greek colony at Empuries 500BCE. Some of those have differences from Mycenaean samples, but not really in direction of "more steppe ancestry" exactly (PCA the Empuries2 set and you can see). Pretty similar to Mycenaean.

Thinking less of specific "invasions of the people X " pulse migrations, but more slow longer scale movement of individual migrants/families etc into the Greek speaking world from north; Thracians, Dacians, Illyrians, Scythians, Celts and such. Some could've happened through classical era as well.

I don't really know how much IranN / LevantN related ancestry AnatoliaBA have, and some analyses of that could be confounded (e.g. some new TellKurdu samples here have positions on G25 that are seem not well explained as combos of Barcin+Levant+IranN+CHg). Only know that in some PCA AnatoliaBA form base of SEastern Europe Cline better than Mycenaean, and vahaduo seems to like fitting present day Greeks with it, plus it's plausible since Anatolia became Greek (so unlikely to be only one way migration there). I'll have a look at the data later when on my computer.

Copper Axe said...

@Davidski

@Archi

I stand corrected, it seems that the eastern limits of the Abashevo is the southern Ural region, sort of around the mountains. That does overlap with Sintashta but it isn't east of the Urals, but rather within the region.

Copper Axe said...

On the topic of Greeks, are we any closer to finding the ancestral steppe cultures of them? Is it a steppe_mbla mixed late Catacomb culture? Perhaps the Babyno?

Simon_W said...

@gamerz_J

"I am wondering if Dorians/Achaean were basically Mycenaeans genetically (common source populations) with more Steppe ancestry but not sure."

I wouldn't believe everything Archi writes. The Mycenaeans were the early Greeks, they were the Achaeans. From them at least the Ionians, the Aeolians and the Arcadians are derived. According to the traditional migration theory, only the Dorians and the Northwestern Greeks migrated to Greece later, at the BA/IA transition.

@Archi

"Mycenaeans are a lot of nationalities, Mycenae is like Americans, they're as ethnically diverse, no Achaeans (i.e. Greek) have been tested."

That's not the mainstream view. The scholarly consensus is the opposite: The Mycenaeans were Greeks, period. And it's very far from proven that there were any non-Greek peoples living there at the same time. And do you know why? Because there are plenty of Linear B inscriptions from 16 (!) different locations on the Peloponnese, in Middle Greece and on Crete. The only language of Linear B inscriptions is an archaic Greek. And what evidence is there for other languages? Absolutely nothing. Except of course Minoan on Crete and Lemnian on Lemnos. But nothing from mainland Greece. So if you claim otherwise, prove it!

Granted, there may have been Italic mercenaries in Bronze Age Greece, but these were small troops at best, not demographically relevant. And at the northern fringe of Greece, where the Mycenaean culture didn't spread to, there may have been other peoples.

The Mycenaean DNA samples that we have are from the western Peloponnese, the eastern Peloponnese, from Attica near Athens and from Armenoi on Crete. I find it an outrageaous claim of you that at all these places not a single Greek should have lived. Sounds like crazy bullshit, considering that Linear B (archaic Greek) inscriptions have been found (among other places) in Eleusis near Athens, in Olympia on the western Peloponnese, and in Armenoi on Crete. And not a single inscription attesting the presence of other peoples has been found there. (Except the Minoan language on Crete, the language of the natives.)

Rob said...

Understanding modern Mainland Greeks is less about dorians and more about late Byzantine processes
That’s because whatever structure was there in the Bronze & Iron Age was compacted to certain coastal towns (mostly in the Aegean littoral) which show continuity between late Roman and medieval byzantine periods
Much of the hinterland was lost, & colonised by slavs
After all that; the gradual Byzantine reconquista entailed brining in Greek speakers from Sicily , Anatolia & other places from their shrinking empire

gamerz_J said...

@Matt

I also don't have the data handy but will look later. That's interesting but I am just wondering from where in Greece the colonists were from.

What you say about Anatolia_BA is interesting too, and indeed "... in some PCA AnatoliaBA form base of SEastern Europe Cline better than Mycenaean, " but could that also not be due to similar components?

"plus it's plausible since Anatolia became Greek (so unlikely to be only one way migration there). "

It's of course unlikely that only one migration was from there, but we do not know 100% if that migration affected everyone in Greece, at least not equally perhaps.

Even today, there is structure between the islands and the mainland and it seems even between the islands themselves. Though, that is likely due to later events.

gamerz_J said...

@Simon_W

"The Mycenaeans were the early Greeks, they were the Achaeans. From them at least the Ionians, the Aeolians and the Arcadians are derived. According to the traditional migration theory, only the Dorians and the Northwestern Greeks migrated to Greece later, at the BA/IA transition."

I don't exactly disagree here, that's why I only mentioned the Achaeans and Dorians, as Ionians and Arcadians etc were most likely Mycenaean-derived.

And yes, that is the tradional theory though seems to have fallen out of favor in archaeology but then again some other theories I have recently read/heard having been proposed for ancient Greece (such as an Egyptian influence on the Minoans) are even more unlikely.

Archi said...

@Simon_W

"That's not the mainstream view. The scholarly consensus is the opposite: The Mycenaeans were Greeks, period."

What I wrote was a fact in science, it's not mainstream, it's just a fact of no alternative. It is well known from the Mycenaean Archaeology, moreover, that the real Greeks were a minority written by Herodotus, that the Greeks are made up of many non-Greek tribes that in time Herodotus kept their own languages. Scientists have come to the fact that the Mycenaean authority spoke Greek, but not that they have common ancestry.

Archi said...

@@Simon_W

"I find it an outrageaous claim of you that at all these places not a single Greek should have lived. Sounds like crazy bullshit, considering that Linear B (archaic Greek) inscriptions have been found (among other places) in Eleusis near Athens, in Olympia on the western Peloponnese, and in Armenoi on Crete."

This statement is outrageous, you haven't even read the paper.It practically says that on the east coast some fishermen slaves were tested, they definitely weren't Achaeans, they were local tribes that had nothing to do with Achaeans. On the western coast a woman from the royal Minoan tribe of Pylos was tested, it is known for sure that this tribe was not Achaean, it was a tribe associated with Crete. They all had a steppe component, but not in large numbers.And only the Cretan woman was of mixed Aegean origin. In general, this research is outrageous, for him specially selected those Mycenaeans who were not of Achaean origin, to hang us noodles on our ears and show that the Mycenaeans do not have a steppe component. They missed with she Cretan.

EastPole said...

@Davidski
“Expect some significant substructures in the Bronze Age Greek world, mostly along the Mycenaean > Crete Armenoi cline.

So not all of the extra steppe admix in Greeks today is from Slavs, or even the Iron Age and Hellenistic periods.”


Here is my old drawing showing Crete_Armenoi close to Greek_Thessaloniki:


https://i.postimg.cc/4N3P2GSD/screenshot-258.png

Greek_Thessaloniki is the most Slavic region of Greece. This closeness may explain many Slavic borrowings in ancient Greek. Or maybe Crete_Armenoi was Hyperborean-Slavic priestess Herodotus wrote about, but he wrote about Delos.

Archi said...

@ EastPole

There's no need to anachronistically fantasize about some Slavs there, you have to look at the known facts.

The famous Achaean.
Bronze Mycenaen Greece Grave Circle B, Mycenae [Z59] 1500 BC U5a1/U5a1a

Achaean by mother.
Bronze Mycenaean period / Late Minoan Greece Armenoi, Crete [Armenoi 503 / I9123] 1370-1340 BC F U5a1

Davidski said...

@Matt

OT, but I need to ask, how do you now rate the performance of the UK government in battling Covid-19?

Back in March you seemed to be quite optimistic about the path that they had chosen for the country.

https://eurogenes.blogspot.com/2020/03/novel-coronavirussars-cov-2-open-thread.html

Btw, currently the UK has the highest official Covid-19 death toll in Europe, and things are likely to get worse as restrictions are eased, because as far as I know, the population is nowhere near "herd immunity".

Matt said...

@Davidski, earlier action would've been better, and was too late, so I think that was pretty bad. I think they underestimated how quickly it would ever hyperconnected London and then fan out from there.

Regarding what happened, unfortunately I think they focused too much on lockdown, not on protecting old folks in care, so that led to many deaths. Most of the models of apocalyptic overwhelming of healthcare systems absent lockdown didn't happen in Sweden, but seem to have led to not getting a handle on care home problems. Earlier social distancing and sheltering of elderly probably should've happened. The change of strategy to focus on lockdown and protecting scarce resources probably killed loads of old people. It probably made things worse. There's probably have been fewer dead if they'd stuck to the original focus to shelter the elderly while allowing younger people to continue life while socially distancing, for longer.

I think there's a lot more commonality in outcome with neighbouring countries, per capita, than often stated. I don't know if death totals will get worse or mostly fall off.


I'd say they underestimated how quickly it would enter and then everything got worse from there, then the misguided slogan of effectively "lockdown, protect the NHS" caused the elder care deaths.

gamerz_J said...

Unrelated post but you guys maybe be interested in this, in case it has not been posted earlier (I missed a portion of the last thread)

"Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph" Martiniano et al, 2020
https://www.biorxiv.org/content/10.1101/782755v2

Mr. J said...

"Herd Immunity" has certainly failed in Sweden.

Vladimir said...

https://www.biorxiv.org/content/10.1101/2020.06.03.131995v1

Off topic. It turns out that K2b went through Southeast Asia, where a lot of denisovian DNA was collected, and K2a went through India to Siberia, so Ust-Ishim does not have denisovian DNA?

Archi said...

@Vladimir

Ust-Ishim has a lot of Denisovan impurity, https://vol-vlad.livejournal.com/1105.html. You get confused in research of southern and northern (real) Denisovans, don't forget that Denisovans lived in Altai.

Vladimir said...

@Archie
“ Using data from ~1.7 million SNPs where
Neandertal and/or Denisovan genomes differ from present-day African genomes, we detect 18
segments of Denisovan ancestry longer than 0.2 cM in the Salkhit genome (Fig. 3, Table S18, Fig.
S16 and S27) and 20 such segments in the Tianyuan genome (Table S18, Fig. S17 and S27). We
detect about a third as many segments of Denisovan DNA in the genomes of the ancient Siberians
Yana 1 and Yana 2, and Mal’ta 1 (Table S18, Fig. S18-20 and S27), consistent with that they carry
lower proportions of East Asian ancestry. In contrast, no Denisovan ancestry is detected in the
genome of the ~45,000-year-old Siberian individual from Ust’Ishim in West Siberia, nor in any
European individual older than 20,000 years (Table S18, Fig. S21-24 and S27).”

Vladimir said...

“The overlap of Denisovan DNA segments (Fig. 4, Table S19 Fig. S28-30) is in agreement with this and suggests that the ancestralpopulation ofthe Tianyuan and the Salkhit individuals that mixed with Denisovans contributed ancestry topopulations in large parts of Asia today.The lack of any significant overlap withAboriginal Australian and Papuans suggests that these Oceanian populations received most of their Denisovan ancestry from a different source.”

It turns out that only the Papuans of Oceania interbred with the" southern " denisovans

Archi said...

@Vladimir

Read carrefully
"we detect segments of Denisovan ancestry longer than 0.2 cM"

"In conclusion, we show that the 34,000-year-old Salkhit individual carried more West Eurasian ancestry than the 40,000-year-old Tianyuan individual, indicating that after the major West/East Eurasians split, gene flow from West Eurasia to East Asia occurred prior to 34,000 years ago, perhaps mediated by populations related to the Siberian Yana individuals. We also show that these early East Asians carried segments of Denisovan DNA that come from admixture events that also contributed Denisovan DNA to populations across mainland Asia today but not to Papuans and Aboriginal Australians."

old europe said...

@archi

what do you think is the source population of west eurasian and which is the relationship between Aurignacian, gravettian and Malta/ Afontonova Gora

Matt said...

Quick few PCA focused on Turkey, Balkans, Levant, Caucasus - https://imgur.com/a/qS91vjj

I don't want to get on whether the thread topic is the right model or not (I simply can't tell), but there's a good bit of diversity in the TUR samples in terms of where they sit on what seems like Levant vs Barcin affinities (though really perhaps Tell_Kurdu_EC doesn't sit exactly between either but is different).

Minoans kind of seem to "point" towards away from Greece_N towards the more "northern" set of Turkish samples, like Barcin_C / Ikiztepe. So perhaps whatever Anatolian source they have is related those populations specifically.

Matt said...

On the off-topic Salkhit thing again, one other note I kind of thought of to add (fairly banal observation really) is, that her being admixed between a West Eurasian source related to Yana (or Yana's West Eurasian ancestry) and an East Eurasian source helps make things make more sense.

Before Salkhit, we had this pattern where is seemed like Yana and "ANE" populations generally had some East Eurasian ancestry, but East Eurasian populations living at fairly high latitudes around Mongolia and North China, represented by Tianyuan and modern people, had no West Eurasian admixture.

That didn't really make much sense, as there was no real reason why admixture should be one sided.

Salkhit makes that make more sense; she shows West Eurasian early ANE admixture, so the pattern is probably instead that admixture *was* two-way... but the early NE Eurasian populations like her were simply replaced or heavily diluted by populations later in history, probably coming from the south (and who form most of the ancestry of present day East Asians), where they wouldn't have been in contact with early ANE populations. That makes more sense than these weird one-way admixture models.

gamerz_J said...

@Matt

I think it's the CHG-like ancestry that makes them point to the north. It's probably closer to the one these populations had.

"Salkhit makes that make more sense; she shows West Eurasian early ANE admixture, so the pattern is probably instead that admixture *was* two-way... but the early NE Eurasian populations like her were simply replaced or heavily diluted by populations"

It seems major replacement took place, if not complete one.

Interestingly it also means that Tianyuan is not the main East Asian ancestor since they are about equally related with Salkhit to modern-day East Eurasians.

Not to mention that the ENA ancestry in ANE possibly dates before 33kya.

Davidski said...

@Matt

How did the lockdown cause the spike in elder deaths?

We had a lockdown here too, which was very tight in much of the country, and that didn't happen. So was there something specific about the lockdown in the UK that caused more of the elderly to die?

Davidski said...

@Vladimir

Off topic. It turns out that K2b went through Southeast Asia, where a lot of denisovian DNA was collected, and K2a went through India to Siberia, so Ust-Ishim does not have denisovian DNA?

WTF are you talking about? Where is this in the preprint?

This is what the abstract says...

Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

Matt said...

@davidski, they probably should have done more to take elderly people out of homes and into hospitals, which would've prevented spread in hospitals. I guess the lockdown is not to blame for this, but I think the lockdown was part and parcel with worrying too much that voluntary social distancing (and handwashing) wouldnt be enough and that healthcare would get overwhelmed, leading to lots of excess hospital places which were empty, and coronavirus spreading among old people left in homes. And took focus away from that. I mainly think the big pivot in policy to the worst case scenario is responsible for that.

A said...

R1a and steppe ancestry (via Armenia MLBA) in a sample from Tel Megiddo in Israel, dated 1600-1500 BC.

https://anthrogenica.com/showthread.php?20507-Thread-for-the-Israel-Megiddo-outliers

possible Hyksos?

Davidski said...

@Matt

Isn't it much more reasonable to assume, based on comparative data from several countries, that the healthcare system wasn't overwhelmed because of the lockdown, and that the spike in the elder deaths was just the result of bad policies and practices in care homes?

Davidski said...

@A

R1a and steppe ancestry (via Armenia MLBA) in a sample from Tel Megiddo in Israel, dated 1600-1500 BC.

Via Armenia MLBA? Sounds like bullshit.

Davidski said...

Ever heard of the Mitanni? They made it all the way to Megiddo.

AWood said...

@All

The world let China control the stock of personal protective equipment among many other things. It should be a lesson learned for most nations. I tried getting N95 masks way back in mid-January before the spread and I could not, at least not affordably or timely.

Rob said...

@ Davidski
As you know; I disagree with the total lockdown approach
It had a negative impact on health (other services were cancelled unecesarily; to the detriment of the public) and economics (jobs & lives were ruined)
Instead of blindly following St Jacinda of NZ; Australia should have taken a pragmatic, flexible approach

@ Mr J

“ Herd Immunity" has certainly failed in Sweden.”

Failed how ? It’s not like Sweden has high rates of spreading infection

AWood said...

@Romulus

You might want to back down now. Obviously Davidski has some information you, and the rest or most of us are not privy to.

A said...

@Davidski

the R1a is from one of the Megiddo outliers, described in the following:

"The two outliers from Megiddo (three including the sibling pair) provide additional evidence for the timing and origin of gene flow into the region. ... The reason these individuals are distinct from the rest is that their Caucasus- or Zagros-related genetic component is much higher, reflecting ongoing gene flow into the region from the northeast. The Neolithic Levant component is 22%–27% in I2200, and 9%–26% in I10100. These individuals are unlikely to be first generation migrants, as strontium isotope analysis on the two outlier siblings (I2189 and I2200) suggests that they were raised locally. This implies that the Megiddo outliers might be descendants of people who arrived in recent generations. Direct support for this hypothesis comes from the fact that in sensitive qpAdm modeling (including closely related sets of outgroups), the only working northeast source population for these two individuals is the contemporaneous Armenia_MLBA..."

(The Genomic History of the Bronze Age Southern Levant)
https://www.cell.com/cell/fulltext/S0092-8674(20)30487-6#secsectitle0190

Archi said...

@A "he only working northeast source population for these two individuals is the contemporaneous Armenia_MLBA..."

There's a working model from two other non-working models: Armenia_EBA and Armenia_ChL. The other options are not considered at all. I must say that the vast majority of the members of Armenia_MLBA were later Megiddo.

A said...

@Archi

I think you mean Iran_Chl

"...whereas the earlier Iran_ChL and Armenia_EBA do not fit. The addition of Iran_ChL to the set of outgroups does not change this result or cause model failure. Finally, no other Levantine group shows a similar admixture pattern. This shows that some level of gene flow into the Levant took place during the later phases of the Bronze Age and suggests that the source of this gene flow was the Caucasus."

Archi said...

@A

Yes.

"suggests that the source of this gene flow was the Caucasus."

This assumption is not based on anything. It is limited by the fact that they did not check anything, and as you can see, the earlier Outlaier had distinct Sintashta roots, yet very little time passed between Sintashta and Mitanni, Mitanni had to move quickly. Data from the Alalakh suggest that they moved through Central Asia, but have not yet had time to mix so that the Central Asian component mixed evenly in the population, it takes a significant number of generations.

Davidski said...

@Rob

Failed how? It’s not like Sweden has high rates of spreading infection.

That's the problem. Sweden has low rates of infection (and thus is nowhere near herd immunity) but one of the highest death rates per capita in the world.

And in regards to Australia and NZ, the drama is now pretty much over thanks to the lockdowns if the borders remain closed, or at least are tightly monitored, but watch the shit storm continue overseas, and especially in the US and UK.

A said...

@Archi

"as you can see, the earlier Outlaier had distinct Sintashta roots"

Back in 2019 Davidski wrote:

"A couple of months ago I suggested that populations associated with the Early to Middle Bronze Age (EMBA) Catacomb culture were the vector for the spread of steppe ancestry into what is now Armenia during the MLBA. After taking a closer look at the Lchashen Metsamor samples, I now think that the peoples of the Sintashta and related cultures were also important in this process."

http://eurogenes.blogspot.com/2019/04/early-chariot-drivers-of-transcaucasia.html

Davidski said...

There's no R1a in Armenia and surrounds from this time, which means that it was absent or very rare in Armenia during this period.

On the other hand, R1a was very common in Central Asia during the Bronze Age, and there's direct evidence now of the presence of people from Central Asia in the Bronze Age Levant, thanks to the paper that you quoted.

An early Mitanni?

A said...

So was there something wrong with your 2019 analysis, because 'Sintashta and related cultures' appear to be R1a.

Archi said...

@A

"the Early to Middle Bronze Age (EMBA) Catacomb culture"

The Catacomb culture is simply the Middle Bronze Age. Catacomb culture could have influenced Sumer and Armenia of Middle Bronze Age, but to Mitanni and Megiddo it could not have had anything to do with, too big a time gap, it disappeared before MLBA.

Davidski said...

@A

Take a look at the Bronze Age/Iron Age Swat Valley samples. Those people have significant Sintashta-related admix, but very little R1a. In fact, they have about as much R1a as I2a.

The same thing may have happened in other areas, including the southern Caucasus.

So the fact that R1a is missing from ancient Armenia, and that the Mitanni are attested in Megiddo, suggests that it arrived in the Levant from Central Asia.

Samuel Andrews said...

@Davidski,

My uneducated opinon is your country Australia was not hit by Covid-19 thanks to luck not lockdown. Same reason, most parts of the world weren't hit hard by Covid-19.

Western Europe & USA were hit hard because of economic ties to China. China>Western Europe> USA.

Davidski said...

@Samuel

Australia's biggest trading partner and one of its biggest sources of tourism revenue is China.

Covid-19 has been controlled in Australia because of the following reasons:

- quickly closing the border to people from China, and then also Iran, Italy, USA, and everyone else

- an early, effective nationwide lockdown to stop community spread of the virus

- very high community compliance with lockdown and social distancing rules and guidelines

- emergency economic measures, including widespread welfare support, to make sure that most people accepted these rules and guidelines.


Of course, the fact that Australia is a huge, sparsely populated island nation probably made things easier, but there are many countries in Europe, some more populous than Australia, that have done a better job of controlling Covid-19 than the US and UK.

So I think the poor performance of the US and UK governments and societies in dealing with this crisis can't be explained away as bad luck. There are very good, specific reasons for it.

JuanRivera said...

Seems that Copper Age Western Anatolia would have steppe ancestry as a norm (as we have both TUR_Barcin_C and TUR_Kumtepe_N_low_res). Northern Anatolia is a bit iffy, as we have TUR_Ikiztepe_LC:IKI002, but then nothing else with steppe admixture. Partly relevant to the Anatolian question, what happened to the steppe-admixed GRC_C sample?

Copper Axe said...

@Davidski is there any chance some of the Sintashta/Srubnaya-like ancestry you see in Armenia is from late catacomb peoples who by then had Neolithic European ancestry and/or mixed in with Proto-Indo-Iranians making them resemble steppe_mbla?

Davidski said...

I doubt it, because the post-Catacomb Kubano-Tersk people in the North Caucasus were basically identical to the Catacomb population.

Sintashta-related groups must've made it to Transcaucasia, but the Central Asian route and even the Balkan route are more plausible than the Caucasus one.

Matt said...

@Sam, my view is that as far as I can tell, most OECD countries did no better or worse at preventing introductions from China directly. The US perhaps slightly better than most at preventing this from early travel ban, and CDC response apparently otherwise initially good.

But once there was local community spread in Italy, from China (despite travel ban), perhaps because of bad luck in superspreading events there, only the developed countries that ignored the WHO and then acted very early in Europe (Norway or Denmark I think, for example), or had fairly very weak trade and transport links with Italy were then OK. Unfortunately, Italy was the 'domino' that fell and the dominoes 'near' Italy got hit hard. Where a country sits in the world travel network mattered quite a bit.

The US had a problem in New York because of that same strong travel link with Italy and extremely dense/fast conditions for spread in New York, even though highly effective in stopping virus in Washington earlier, and highly effective at stopping introductions from China directly (considering the scale of US, there is apparently not much evidence for the large scale infections being driven by anything other than the strain from Italy). I've seen some studies of R0 estimates for New York that put it at above 4 (each person infected more than 4 other people); due to unique features of city it spread very fast. Then from there mostly to the rest of the US.

Similarly UK, introduced to London from Italy then ramps up very quickly due to densest city in Western Europe (Netherlands and Belgium, other very dense areas hit pretty hard too, Belgium highest national rate in Europe). The preparation for what happens when there is spread within Europe was weak, and lots of Western countries should probably have raised barriers, taken the hit to tourism, distanced from each other and restricted free movement earlier. I don't know if UKs policy was particularly bad compared to OECD but it frankly needed to be better than just "not particularly bad" given the higher vulnerability of London to infection from its density and globalization level.

Davidski said...

@Matt

Following on from my comment above, can you expand a little more on your theory that the spike in deaths among the elderly in UK care homes was actually the result of the lockdown designed specifically to prevent a spike in deaths, considering that...

- Sweden did not implement a lockdown and its death rate among care home residents is among the highest, if not highest, per capita in the world

- Australia did implement a lockdown and its death rate among care home residents is among the lowest per capita in the world.


Or would you like to back out of this ridiculous theory, which would be the sensible thing to do.

Matt said...

New York locked down and had a similar thing with carehomes. Spain too. I'm not going to discuss any further, but I don't think you can reduce the argument this way. I certainly think in UK, looking at how policy evolved and what the media were pressing the government to take more action on, the shift of policy to conserving hospital resources and locking down probably led to the UK's specific bad outcome there, and probably the same happened in New York, and any further countries are too far out and have too different and unique circumstances for me to discuss.

Davidski said...

@Matt

I certainly think in UK, looking at how policy evolved and what the media were pressing the government to take more action on, the shift of policy to conserving hospital resources and locking down probably led to the UK's specific bad outcome there, and probably the same happened in New York, and any further countries are too far out and have too different and unique circumstances for me to discuss.

Bullshit. The lockdowns in the UK, New York and Spain came too late to be really effective.

But the outcomes would've been far worse if not for the lockdowns. We might soon see when the second wave hits the UK without it being able to call on another lockdown, because it can't afford it.

I'll check back with you in another couple of months about this.

Palacista said...

The death rate in care homes in the UK is down to two connected factors, discharging infected elderly patients from hospitals back to the care homes without testing and the use of bank staff and contract staff who move between care homes and furthermore were not supplied with adequate PPE.

Vladimir said...

The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.24079
All PWC people turned out to be I2a.

how paleogenetics reconciles evolutionists and migrationists. In this case, it is obvious the evolutionary improvement of the same population going back to the Arensburg culture and passing through many cultures and reaching PWC.

Matt said...

@Davidski, pretty "robust" response there! There are definitely some analyses out there that suggest that the voluntary social distancing recommendations had already kicked in and the compulsory orders didn't really help much - e.g. here - https://www.dailymail.co.uk/news/article-8391141/Did-UKs-coronavirus-crisis-peak-lockdown.html, where the author believes the recommendations cut rates by 50% before lockdown contributed little beyond that (the same article suggests that the Norwegian government basically stated the same thing). It's a discussion that will run on.

Those recommendations should have been earlier, but I think that's more to do with perilously underestimating the spread in Italy, them from Italy into London and then speed of spread in the dense megacity when it got established (problems faced across the dense Southern England / Benelux area), and not shutting down travel from Italy. A mistake for sure and the government and UK science can be blamed for not pushing our distancing guidance and support earlier.

I don't think the UK is less likely to lockdown again or to be able to afford to do so, compared to other nations, in the event it becomes viewed that we're moving to a second peak. There's probably about 20% immunity in London now from prior infection, or more if there's this "dark matter" immunity of some kind, and much more use of WFH, masks, etc that will slow any re-emergence. We will see.

@Palacista, right; I think there's a direct cause of some of that releasing back (or not even taking) and stockpiling PPE for the NHS and the "doomsday" scenarios of overwhelmed healthcare systems that also provided the impetus for lockdown. Some may not agree but that's how it looked on the ground. Didn't do as much to help the people in need as could because of phantom ideas about needing to "protect the NHS" and conserve resources for younger people.

Davidski said...

@Matt

Palacista addressed the issue of why the Covid-19 death rate in UK care homes is so high in a single sentence.

But you've now reduced yourself to making things up just to try and keep the comedy rolling.

Nearly half of England's doctors forced to find their own PPE, data shows

There were no stockpiles of PPE in UK hospitals or anywhere else that could have been redistributed to care homes.

Vladimir said...

My version of the "oddities" of the Hittites: A small number of steppe component, the lack of a steppe haplogroup R. I think it was like this. The population of the culture of pearly ringed pottery, bearing the chg component, penetrated along the Western slope of the Caucasus into the North Caucasus steppes in the area of approximately 5000 BC. Y its haplogroups were typically Transcaucasian (J1, J2, L, V1636, E). It reached the mouth of the don, where it met the local population R1b or R1a. The fact that these were different tribes is clearly seen in the monuments of the Lower don. There are monuments of the autochthonous population of the Lower don of the type Rakyshechny Yar and there are monuments of an obviously alien North Caucasian tribe of the type Razdorskoe. These tribes apparently exchanged women, but did not mix. Therefore, they kept their male haplogroups, but autosomally transferred some of their components to each other. The North Caucasian tribe along The black sea coast went West first becoming the Novodanilovka culture then the Suvorovo culture then the Chernavoda culture then the Ezero culture and then moved across the Bosphorus to Anatolia, where it became the Hittites. In turn, the local population of the lower don, already with the chg component, is further known as the Sredniy Stog culture, the Middle don and other Eneolithic cultures of the steppe. It is in this way that some Caucasian elements were included in the future Indo-European languages, and the language of this Caucasian group acquired some elements of the future Indo-European language, which later became the Hittite language. Perhaps as a result of this contact, R1b-M269 broke up into R1b-L23 and R1b-PF7562. The first group remained in the steppe, and the second left with this Caucasian group and also became the Hittites. Since contacts between the don group and the Caucasian group were limited only to marital exchanges, they did not mix much. At the same time, the Caucasian group brought increased content of its CHG to the Balkans and further to the whole of southern Europe. Taking all this into account, we will not be able to detect the Hittites of Anatolia either by single-marker Y haplogroups, since they are Caucasian, or by the autosomal component, since it is minimal.

JuanRivera said...

The MLBA Anatolians (minus the outlier) model as having admixture from TUR_Barcin_C and TUR_Ikiztepe_LC:IKI002 (who I dubbed TUR_Ikiztepe_LC_o in the model because of the steppe admixture she has that is absent in the other Ikiztepe samples). That means that they have Steppe ancestry too. The admixtures are already present in EBA Anatolia but they increase in MLBA Anatolia.

Matt said...

Yeah, there were, there were distribution problems. Anyway, bowing out of this one; I'm more OK to deal with your often belittling and bullying attitude towards others on ancient dna, because you're the sole guy doing what you do, so you kind of have a position of power there. But for Covid19, there's no reason to.

vAsiSTha said...

from a basic PCA plot, i agree Barcin_C and Areni_C do harbour some progress_en related ancestry. but apart from these, south levant mlba, turkey_alalakh_mlba, arslan tepe (chalc & eba), aze_lowlands_en & C etc harbor almost nil progress_en.
So the impact overall seems minimal.

Romulus said...

@Vladimir

Looks like Gotland was a northern analog of Sardinia where instead of Neolithic farmer, HG DNA persisted quite late.

Ric Hern said...

I think a population without discipline is the biggest problem regarding the spread of Covid. I think it is basically hopeless here by us in a Country that can not afford a strict lockdown for more than a month. It is now spreading at more than 3000 per day and I think this is a gross underestimate of the real situation...Looks like herd immunity will eventual be the turning point here by us because so many are stupid or just don't care or both.

Ric Hern said...

If I remember correctly there was a study who found a Paleolithic migration route through a certain Valley in Mongolia. This migration was from North towards the South into Northern China. I think this was the Migration of some K2 and P towards Southeast Asia around 49 000 years ago...Significantly earlier than Yana and even Ust Ishim...

Davidski said...

@Matt

You're the one who just claimed that the lockdown in the UK was the main cause of the high death rate there.

No one who has at least half a brain and is objectively looking at the issue and studying the data would ever believe you or back up your crackpot theory.

Archi said...

@Vladimir
"My version of the "oddities" of the Hittites: A small number of steppe component, the lack of a steppe haplogroup R. ..."

Don't be ridiculous. What's the Hittites' lack of steppe component? Where have you seen the Hittites tested? No Hittites have ever been tested at all. You can't rant about what nobody knows at all.

Further fantasies about archaeological cultures are ridiculous.

Rob said...

@ Ric
Which study was that ?
So far the earliest evidence is ~ 45 kyBp for south Siberia and & 40 for Mongolia & China

Rob said...

@ Davidski

“ the drama is now pretty much over thanks to the lockdowns if the borders remain closed, ”

Well that’s what made the difference - international border closure
All the local measures were superfluous & detrimental
Nor did I appreciate the usual media mind-control tactics and scaremongering . I was disappointed to see doctors & nurses serving as
Useful idiots for the narrative, too

Davidski said...

@Rob

The border closures wouldn't have achieved anything by themselves because Covid-19 was already being transmitted locally in Australia by that stage.

The border closures ensured that no more infections were introduced, which helped, but the virus was controlled thanks to widespread testing, isolating cases, and social distancing.

Rob said...

@ Davidski
The intra-community transmission rates were ~ 1%
One needs to consider diminishing marginal utility; and cost/ harm of each additional measure ; which is why I would have preferred a tailored approach
I know Australia got off well; but we need to consider the collateral effects. And that’s a massive back log to the healthcare system due to closures; with peoples treatment put off and their pathology worsening
Essentially; the health care system was ~ 70% idle for 3 Months . That’s a big impact

More generally; what’s going to happen when Job Seeker runs out in a Couple of weeks; and who’s going to burden the costs of the Govt’s “stimulus packages “?

Rob said...

@ Vladimir

Although PWC are southwest shifted compared to SHGs
If anything; aDNA continues to disprove evolutionists & immobilists, in most cases

Davidski said...

@Rob

The growth in infections is exponential, so a 1% transmission rate can become thousands of cases and deaths in a matter of weeks.

There are examples of this from many places, especially the US, where people didn't notice much of a problem until the morgues in NYC started overfilling.

Lockdowns and social distancing measures are though, especially on the economy, but no economy and society can function in the long term when thousands of people are dying and people are scared. Eventually it'll collapse.

Nick A said...

Ric Hern,

I'd argue the migration was the other way. South to North. In all likelihood ydna K2 and P is East Eurasian.

Ryan said...

Could we get a thread on the Salkhit paper? It's pretty interesting if not that surprising.

Nick A said...

Yea that's an interesting paper.

@Davidski,

Do you think the US will experience a second wave due to reopening too early and the protests?

vAsiSTha said...


@rob
"Well that’s what made the difference - international border closure
All the local measures were superfluous & detrimental
Nor did I appreciate the usual media mind-control tactics and scaremongering . I was disappointed to see doctors & nurses serving as
Useful idiots for the narrative, too"

100% agree. covid nowhere to be seen on the media agenda with the american protests on.
anyway, looking at US and sweden stats, the median age of covid deaths is same or slightly higher than life expectancy in those countries, nothing like the spanish flu of 1918.

Rob said...

@ Davidski

NYC and northern Italy are their own entities. Northern Italy is basically a retirement village, and NYC is densely populated, high transit and poor healthcare zone.
As i stated when this all began, I don't think we should be conditioned & scared by media showing us the same picture over & over again from Italy of people with bubbles on their head.
I know all the NSW data first hand, and the affected people were, as expected, over 60, comorbid, etc. There was never going to be an avalnche in Australia. Anyhow, retrospective analyses are always difficult

One doesn;t need to be a conspiracy theorist to question some of the narratives here. The politicians and their mouthpieces are all saying the same thing - Merkle - this is the worst thing since WW2, US Surgeon general - this is our Pearl harbour. Aus politicians - we are in the frontline.. Of what ? This isn't a war. Their metaphors & hyperboles betray them, although it proved highly effective in controlling the sheeple. This was just a testm a piecemeal step.

Davidski said...

@Nick A

Yes, I think the US is in a lot of trouble (and, by extension, so are we).

I don't know what's going to happen there now, because the country is in a very bad shape. But the most plausible scenario is that Americans will try to live with Covid-19 and an economic depression, and in the end, before a vaccine appears, as many as a million of them will die from Covid-19 alone.

The UK is also in a bad position, because it largely squandered its gains from the lockdown and now has to open up to save its economy.

Don't believe Matt when he claims that herd immunity and immunological dark matter will significantly cushion the impact. Hopefully the people in charge over there get a grip and come up with some real solutions immediately.

This might be worth a read...

https://www.theguardian.com/politics/2020/jun/05/uk-experts-call-for-coronavirus-inquiry-to-prevent-deadly-second-wave

Samuel Andrews said...

@Davidski,

Georgia, Flordia, Mississipi, Tennessee, Indiana are amoung the USA states which reopened over a month ago. They have seen no spike in cornavirus.

Some sparsley populated states never had a lockdown.

All cornavirus outbreaks have been in densly populated areas. I think it is ubsurd they have the same lock-down measures for sparsly populated areas. For example, the majority of NEw York State has no serious cornavirus problem but has been locked down alongside New York city.

Nick A said...

The herd immunity argument always sounded like bullshit.

Sadly I think you're right. The US is screwed. We're also filled with idiots in power. One party thinks coronavirus was a hoax and is reopening early. The other party had some sense until social justice got in the way and they became as dumb as the other party.

Davidski said...

@Rob

There are plenty of other places with per capita death rates similar to those in NYC and North Italy, so their situations aren't really all that specific.

The reason you're seeing this as an old man's disease is because the infection rates are still very low, and that's due to lockdowns and social distancing. If infection rates reached 30%, a lot more 20, 30 and 40 year olds would also be dying.

Yeah, Australia's low population density would help in keeping the death rate lower than in most other countries, but many thousands of people would still die, and I just don't see how society could function properly in such a situation.

You'll see this play out in the US very soon, in areas similar to Australia, and then you can judge whether controlling Covid-19 was such a bad thing for Australia.

Davidski said...

@Samuel

Georgia, Flordia, Mississipi, Tennessee, Indiana are amoung the USA states which reopened over a month ago. They have seen no spike in cornavirus.

They haven't really opened up yet, but they'll have to soon, and then we'll see.

Samuel Andrews said...

@Davidski,

I take seriously the research you've done on COVID-19. I don't mean to just dissmiss it. But maybe, we have to just live with COVID-19. I have heard it will now be with us for years, although in less deadly versions.

Davidski said...

@Samuel

I've just done some reading about Covid-19, like the rest of us here.

I believe that a vaccine will be available next year and it's likely that Covid-19 will be stamped out eventually.

jeanlohizun said...

Davidski,

Aside, will you be including the newly releases genomes of Caribbean indigenous individuals into your G25 database?

https://reich.hms.harvard.edu/datasets

"Genotypes of ancient individuals analyzed in Fernandes, Sirak et al. bioRxiv 2020"

It includes both Taino(Ceramic Genomes, late arrival from South America) and Guanahatabeye (Hunter Gatherers in the paper Archaic) who arrived starting in 3000 BC.

jeanlohizun said...

@ Nick A,

"The Constitution’s Article V requires that an amendment be proposed by two-thirds of the House and Senate, or by a constitutional convention called for by two-thirds of the state legislatures. It is up to the states to approve a new amendment, with three-quarters of the states voting to ratifying it."

Currently and for the foreseeable future we have more Republican state assemblies than democrat ones. So the 1st and 2nd amendments are safe for the time being. Fear mongering solves nothing. The idea that the President of the United States has the power to repeal a constitutional amendment reveals a deep misunderstanding of Executive Power, and a belief that the office of Presidency is far more Authoritarian than it is in reality.

Vladimir said...

@Archie. I, of course, will not argue, but I strongly advise you to read the article of a major expert on the cultures of the North Caucasus, Sergey Korenevsky. It's in Russian. I will somehow gather the strength to translate it into English. There is a lot of interesting information on the topic under discussion about the proximity of ceramics and much more between the cultures of pearl-tipped ceramics of the settlements of the North Caucasus (Nalchik burial ground, Svobodnoe, Yaseneva polyna, etc.) and the cultures of Western Georgia ( Dzudzuana, Darkveti), Arslantepe eneolite ceramics, generally Ubaid culture Mesopotamia, as well as with Novodanilovka culture. In General, I would really look at the R1b-V1636. There is a suspicion that we are not fully evaluating the role of this group yet.

ENEOLITHIC SETTLEMENTS IN CISCAUCASUS, YASENEVA POLYANA AND CULTURE OF PIN PEARL CERAMICS IN CISCAUCASUS
https://cyberleninka.ru/article/n/poselenie-eneoliticheskoy-epohi-predkavkazya-yaseneva-polyana-i-kultura-nakolchatoy-zhemchuzhnoy-keramiki-predkavkazya

Ric Hern said...

Here in South-Africa we had about 16 cases in the Least populated province during lockdown stage 5. Now at lockdown stage 3 two months later its numbers are in the 100s...

Al Bundy said...

@Davidski I don't know if anyone mentioned it yet but antibody tests done by Stanford and also in NYC seem to show the virus was in the US earlier than thought and many more people had it making the death rate lower.It's been pretty much harmless for young healthy people.Nursing homes account for a large chunk of the deaths and most, yea it sounds harsh, would have died pretty soon anyways had comorbidity.Hospitals weren't overrun anywhere.I'm skeptical about the lockdowns, especially considering how crushing they were.

Davidski said...

@jeanlohizun

Those samples have been in the G25 datasheets for several days now.

Davidski said...

@Al Bundy

The Stanford results haven't been corroborated by data from places know to be hit hard by Covid-19.

Be careful what you wish for, because you're now likely to see the full force of this thing in your neighborhood, and your hopes that you and your family already had it won't count for shit.

Ric Hern said...

My Mother had SARS. It is not a prity sight. She was in intensive care for months. Yellow jelly like fluid was extracted from her lungs...After recovering she battled with the after effect of the damage to her lungs for 10 years. She couldn't walk more than 20 metres without feeling extremely exhausted...So no I personally do not take Covid-19 lightly.

Al Bundy said...

In Orange County, Ca., it's been very mild and we should be cautious about the reopening that's going on.I'm glad Australia is doing Ok.A vaccine would be great news and eliminate a lot of worry.

Al Bundy said...

@Ric That sucks, I don't take it lightly either but I think it's closer to a really nasty flu than what the mainstream media is saying.

Ric Hern said...

@ Al Bundy

As far as I understand it, it can progress easier into a form of extreme pneumonia than regular flu.

vAsiSTha said...

There's going to be no vaccine for many years to come.
Don't let vaccine cos fool you with feel good prelim results that help to jack up their stock prices

Rob said...

A vaccine on an RNA virus isn’t a good investment
Focus on cancer and childhood diseases

Davidski said...

It's an excellent investment considering the impact that Covid-19 is having.

Also, it would be the first coronavirus vaccine, which might be very important if another, more lethal strain of such a virus passes into humans.

Davidski said...

@Rob

Almost 400,000 people have died from Covid-19 in less than six months. That's surely worse than the Spanish flu considering where we are in the pandemic.

https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

It's likely that hundreds of thousands of other people will die, and not all of these victims will be on their death beds before catching Covid-19.

So if this isn't a good candidate for vaccine research, then OK, let's wait another six months and I'm pretty sure it will be.

Rob said...

Dave
The number of deaths in Aus =102 (undoubtedly over inflated , as any death ‘with CVD’ is labelled as ‘death’ from it)
That’s from 72000 cases
That’s a case fatality of 1%

Paper cuts have a higher mortality rate

Davidski said...

@Rob

But why would Australia have a high death rate considering that it successfully controlled it?

Take a look at the countries which haven't managed to do so, like the USA.

Over 100,000 deaths and counting. Where do you think this will stop if nothing is done?

Ric Hern said...

@ Nick A

Does it make sense that Haplogroup Ks closest relatives (Haplogroups I and J) were found in Europe and the Caucasus but K2 popped up in East Asia ? Ust Ishim was found in the North of Central Asia (Southern Siberia) for a reason...

Rob said...

@ Davidski
Ceteris paribus
Unless one is rich; the quality of healthcare in USA is below par. They’re the most obese nation in earth

Davidski said...

OK, but millions of people around the world will die within the next 12 months because of this, obese or not.

Shouldn't something be done?

Rob said...

I sincerely hope those numbers aren’t that high
But we should
- devote resources to “hotspots”
- protect the at risk: elderly , underlying lung disease
- let the rest of the world return to function

Archi said...

@Vladimir

Pinned Pearl Pottery is originally northern, it is thick-walled, it came from the north, it has nothing to do with Transcaucasian pottery, dyed and thin-walled. It's the Novodanilovskiy type from the north (from Khvalynsk-SredniyStog community), it's not Caucasian. I wouldn't be surprised if pearl pottery belong to Novodanilovskiy type. Nalchik burial site belongs to Khvalynsk culture or Khvalynsk-SredniyStog community.

Previous pottery: quote
"The pinned pearl ornamented pottery of these settlements, as noted above, is only one characteristic decoration technique for the pottery of the group in question. Its area in the Caucasian region is limited. In itself, dishes with pins and protruding bulges-pearls, of course, are known as an element of decoration, from other regions and cultural formations.
Such tableware is characteristic of the cultures of the Pit Gravel Ceramics of the Dnieper River forest-steppe.
It is a vessel with convex ornament of cones, is known from the repeatedly published burial near Novodanilovka village. But whether it is really an analogue of the pinned pearl pottery of the Caucasus is an open question. It is important to note that such tableware is found in the lower layer of the Mikhailovka settlement, though pottery of that layer clearly differs from pre-Caucasian pottery."

So the cause-and-effect relationships and dates you gave are wrong, they contradict the article to which you refer. It is directly written to you there that tribes of different ethnic origin lived in the Pre-Caucasus and that "Pinned Pearl Pottery" has nothing to do with Western Georgia.

George said...


Flattening the case curve was to avoid overloading hospital resources to prevent unnecessary deaths due to lack of care. It was not to stop all exposure and crash economies but to by time for development of better treatment protocols, and possibly a vaccine. We will likely be in an oscillatory environment for a while.

See page 12 from an older report:
https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf

Plans and protocols have existed for flu outbreaks in the US since 2006. The most recent update for the US is from 2017. Links are near the bottom of the page
https://www.cdc.gov/flu/pandemic-resources/national-strategy/index.html

My source for medical information over the last 4 months has been from a front line physician that treats COVID patients and who also runs a medical education company.
He backs his observations primarily with peer reviewed literature.
https://www.youtube.com/user/MEDCRAMvideos/videos.

For current talleys:
https://www.worldometers.info/coronavirus/

COVID-19 vaccine development pipeline gears up:
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)31252-6/fulltext

Be safe

Davidski said...

Yes, and of course, a couple of weeks after the lockdown started in the UK, the number of hospital admissions and deaths from Covid-19 plateaued and eventually fell.

That's exactly what was expected to happen within the time frame that it did happen, because there's a time lag from infection to hospital admission and death.

So I don't know what Matt is playing at, but I suspect that he's either trolling or he's lost his mind.

un said...

@ Ric Hern
IJ-P124 from Sri Lanka
https://www.familytreedna.com/public/y-dna-haplotree/A

Davidski said...

Modern samples don't prove anything, because you don't know where that lineage was 1000 years ago, let alone 10,000 years ago.

Nick A said...

Wasn't Tianyuan East Eurasian and closer to the ancestor of Y P? He was K2a no while Ust-Ishim was K2b. Also every other clade below K2 is East Eurasian no? Those are the arguments I've heard. I'm not sure either way. I do know that anti science people cry racism if you claim that y P is West Eurasian (or acknowledge Native Americans might be paternally West Eurasian and maternally East Eurasian).

Nick A said...

Not sure what that Sri Lankan sample proves. Sri Lanka has seen plenty of settlement from India (and therefore West Asia, Central Asia and Europe). There's also J2 in Sri Lanka. I guess it evolved in situ from y IJ? What a joke.

jeanlohizun said...

@Davidski.

Thanks for uploading the genomes. An interesting finding is that in this study:

"Genomic insights into the early peopling of the Caribbean"

They find that Cuba was populated by at least three waves of Native People. Per figure-3 Tree-mix model shows an interesting pattern.

Early samples from "Early San Nicolas" dated circa 4900 BP and "CIP 2700 BP, in Figure 3-a (Z-score=|2.988|):

"...branches off the main Native American lineage together with individuals from the California Channel Islands (16) prior to the diversification of Central and South Americans"

On the other hand, later samples such as "GUY002" dated to 2500 BP required South-America related ancestry to make the model fit (Z-score = |2.888|). In fact "GUY002" is modeled as a mixture of 61% "Early San Nicolas" and 39% coming from a branch that goes into a sample called "Brazil 9600 BP".

Finally in the same figure3-c the Taino sample Cuba 500 BP is modeled in the same branches as fellow Taino samples from Puerto Rico 900 BP, St. Lucia 750 BP and Bahamas 800 BP, which branches off from Piapoco. The Z-score is |3.034|.

to be continued...

jeanlohizun said...

...

This is interesting because the other study published by the Reich team:

https://www.biorxiv.org/content/10.1101/2020.06.01.126730v1

Only features a subset of Cuban samples, all from one site (Canímar Abajo (Matanzas Province, Cuba)), with the oldest being:

"Radiocarbon dates from charcoal at the site have provided dates as early as 5590-4622 BP (Cooper 2010; Rodríguez Suárez et al. 2006), while more recently acquired dates from skeletal material indicate that the site spans at least 3000-1250 BP (Rodríguez Suárez et al. 2010; Roksandic et al. 2015). Although more dates are required, especially considering the difficulty of taphonomic interpretation of the site chronology due to disturbance and the reuse of burial space, these dates make Canímar Abajo one of the oldest sites in Cuba, particularly Western Cuba (Cooper 2010; Dumas León 2009; Martínez López et al. 2007, 2009; Rodríguez Suárez et al. 2006). In this study, we include samples from both the older (OC) and the more recent (YC) cemeteries."

What is interesting is that the study finds that:

"A largely homogeneous ceramic-using population most likely originating in northeastern South America and related to present-day Arawak-speaking groups moved throughout the Caribbean at least 1,800 years ago, spreading ancestry that is still detected in parts of the region today. These people eventually almost entirely replaced Archaic-related lineages in Hispaniola but not in northwestern Cuba, where unadmixed Archaic-related ancestry persisted into the last millennium."

BTW, you can throw Puerto Rico into the band of complete replacement. What is interesting is that in the Reich study the treemix model see Figure S22 and Figure S23, has "GreaterAntilles_Archaic" as branching off from a South America branch (Figure S22), and when admixture is allowed (Figure S23), it seems to branch off from the root of all Northern South American samples, but not before Quechua and Aymara branch off.

There appears to be an apparent contradiction between the two papers, as the "Science" paper has the Archaic group in its earliest form as some sort of "North America" group (See Figure-3), but it think the best way to reconcile the two results is that Figure-3b shows that there was a subsequent admixture event that predated the arrival of the Taino(ceramic) groups to the Western Caribbean. Without this fact, and this sample, the position of the "Greater_Antilles_Archaic" is placed in South America.

This is very important because it highlights how a tree-mix model can "erroneously" place groups, if all the information is unknown. Had earlier samples been included in the "Reich" arxiv study, it is very likely that the "GreaterAntilles_Archaic" sample would have branched off much earlier, and that the admixture with South American genomes would have stayed.

What do you all think of that?

jeanlohizun said...

This is from the Reich study Supplementary info:

"A single 1-way model with the Chibchan-speaking Cabécar was found for GreaterAntilles_Archaic, but in this case most of the working 2-way models did not involve Chibchan-related ancestry, and instead modeled GreaterAntilles_Archaic as combinations of present-day populations speaking the Carib, Andean, Tupi, and Arawak languages. The results on the Illumina dataset support this by identifying a valid 1-way model also for the Quechua (Table S14). These results are consistent with the lack of affinity between GreaterAntilles_Archaic and populations from a particular language family (Fig. 3a,b; Supplementary Information section 10; Supplementary Data 8 and 9) and with Treemix results (Fig. 3c), all of which point to an early split position relative to other South and Central American populations."

However Table-13S and Table-14S, show p-values for 1 and 2 way qpAdm models for GreaterAntilles_Archaic are at best 0.07 for a combination of Surui 9.2% and Cabecar 90.8%. One way qpAdm models(Table-14S) have p-values of 0.586 and 0.639, which is insane.

I wonder why the Reich team did not include North America natives? Hopefully they revise their models given the publication of the Science paper and get better fits. I do not think most people will be comfortable with a p-value of 0.07.

jeanlohizun said...

@Samuel Andrews

Florida has had three continuous days of over 1300 cases reported, which is highest new case count since ever. Not sure what the hell you are talking about there not being spikes. See here:

https://experience.arcgis.com/experience/96dd742462124fa0b38ddedb9b25e429

That's only counting resident cases. So time to reconsider your statements.

I live in Florida, and our Governor is not exactly being straightforward with us, there was the scandal of the gal who was fired because she refused to manipulate the data, she was the one that made the dashboard linked above. Also, there are allegations of Coroners being discourage from putting "Covid-19" as a cause of death in certificates. Also, also, we have had a 5 year spike of "Pneumonia" deaths.

I voted for him the 2018 election, which he won by less than 0.4%, not sure if I will vote for him again in 2022, he has shown himself to be a partisan hack, and shown complete disregard for public trust.

Angantyr said...

@Romulus

"Looks like Gotland was a northern analog of Sardinia where instead of Neolithic farmer, HG DNA persisted quite late."

Well, it's perhaps an analogue in the sense that "steppe" DNA reached the island later than nearby areas, but it wasn't unique in the survival of HG DNA, as the PWC co-existed with the Battle Axe Culture in mainland Scandinavia and on other islands in the Baltic sea at the same time as it was the single culture in Gotland. Not to mentioned that the Mesolithic (non-pottery) Slate Culture of Northern Scandinavia persisted far longer than the PWC did.

The conclusion of this PWC paper is mostly of regional interest - it doesn't mean anything in the grand scheme of things as the PWC disappeared completely, also on Gotland, at the onset of the Nordic Late Neolithic, and their genes don't seem to have made a lasting mark anywhere. But it answers a question Swedish archaeologists have the debated for a long time; what those "BAC influenced" burials mean, and perhaps raises another point: If you find an individual buried in a hocker position in a flat earth single grave in coastal Scandinavia, you might not be 100% sure that it's a BAC burial, as the PWC obviously mimicked these burials, and could even put battle axes in them.

vAsiSTha said...

"Florida has had three continuous days of over 1300 cases reported, which is highest new case count since ever. Not sure what the hell you are talking about there not being spikes."

No shit, opening up lockdown is going to cause case spikes. But if the virs is already spreading in community, lockdown doesnt eliminate the virus either. It will keep lingering till the next time economy opens up and then it again spreads.

If the end goal is to only to minimize infections and deaths, without giving a damn about the economy and society, then you better lock everyone down for at least a year and see where it leads you.

Davidski said...

@vAsiSTha

See here...

https://eurogenes.blogspot.com/2020/06/perhaps-hint-of-things-to-come_2.html?showComment=1591443104537#c1958023136662866219

Reto said...

@un
"IJ-P124 from Sri Lanka
https://www.familytreedna.com/public/y-dna-haplotree/A"

Actually, Block Tree and FTDNA public tree considers also transfers such Nat Geno's, single SNP tests, SNP Packs and BigYs, so not just the latter. If you open the branch IJ-P124 in Block Tree, you'll notice that it's not informed a number of private variants for a supposed basal IJ. It looks like there is no BigY associated. In my opinion the odds are the guy is just a J.

Samuel Andrews said...

@jeanlohizun,

They are doing more testing which explains spikes rise in infections. New cases is caused by two variables: Spread of the virus and number tests being done. Rising number of infections doesn't always mean the virus is peaking.

You guys are having under 40 deaths per day. That's low for a state as populous as Flordia.

Your Death rate has not come close to being serious in anyway since you reopened. 10,000s and 10,000s of people have visited Florida since it reopened. No spike.

I understand the reopening is half-way. But, it helps businesses tremendously. It is wrong that other states keep grocery stores open but keep restaurants closed.

jeanlohizun said...

@vAsiSTha

Alright my friend, I'm going to teach you something today about debate. Take it or leave it, either way do not expect another response from me.

@Samuel Andrews said:

"Georgia, Flordia, Mississipi, Tennessee, Indiana are amoung the USA states which reopened over a month ago. They have seen no spike in cornavirus."

To which I replied:

"
Florida has had three continuous days of over 1300 cases reported, which is highest new case count since ever. Not sure what the hell you are talking about there not being spikes. See here:

https://experience.arcgis.com/experience/96dd742462124fa0b38ddedb9b25e429

That's only counting resident cases. So time to reconsider your statements. "

I then expressed my opinion that the governor has been less than straightforward with us Floridians, and there was a controversial firing.

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

What you did, in a very vulgar manner, was engage in a Strawman argument. Why you might ask?

Because I never said anything about whether I agree or disagree with the decision to open the state up. I also did not say that lock down eliminate viruses.

So my question to you:

Why should I be require to defend arguments that I did not make?

Can you refute the evidence base assertion that there has been spikes in Florida, unlike what Samuel Andrews claimed? If not, then I will kindly ask you to remain quiet, instead of launching pathetic logical fallacies my way. I have grown tired of them, which is one of the reasons why I rarely post anymore. I hope you have a good day my friend, and hopefully, you learn something new today.

mirgould said...

The two things that astound me the most with the Covid-19

1: The numbers from East Asia

Less than 1,000 dead in Japan, 250 in South Korea and 7 in Taiwan
My city (New York) has almost 17,000 deaths

2: The incompetence of The WHO and western health experts

After we were told constantly by the media in the US that harsh lockdowns and social distancing were the answer we now have “1,200 health professionals” saying it’s okay to go riot in the streets and others who were criticizing states reopening telling us it’s our moral duty to protest and we are complicit with racism if we stay at home? What happened to the second wave we were warned about? Absolutely insane. It’s just like with the hypocrite Neil Ferguson. His model was laughable garbage code and all the while he was breaking lockdown rules to lay with a married woman. Or like when The WHO told everyone not to wear masks and that masks were only needed for doctors and nurses.

As per CDC’s latest estimates the death rate of Covid-19 is .26 %, (WHO original estimate was 3.4%), this includes the elderly and those with comorbidities (around 85 to 90% of deaths involve comorbities namely, hypertension and diabetes). Seeing as the average age of death for a coronavirus victim is the mid 80s in retrospect it would have been a good idea to take special care with nursing homes. That’s likely why NY’s death toll was so catastrophic since Cuomo was sending infected patients back to the home.

Here’s some some quick thoughts I have, what do you guys think?

1. We should assess the steps taken by nations like Taiwan and SK to address the virus and send our experts and officials there to learn from them
2. End strict lockdowns, they are unnecessary
3. Promote and if needed enforce the use of masks and gloves, they’re effective
4. Protect and provide special funding to nursing homes as they are the most vulnerable


@jeanlohizun

I’d say Florida is incredibly lucky. They were .4 % from having this man as their Governor

https://www.sun-sentinel.com/news/politics/fl-ne-andrew-gillum-miami-beach-drugs-20200313-3plsrtuvdnhcpglfo34ojrehvu-story.html

https://www.foxnews.com/us/photos-police-body-cam-video-released-of-andrew-gillum-hotel-room-report

Being in a room passed out with two other men (one a known escort), ED medication, meth and vomit everywhere doesn’t exactly inspire confidence in crisis. Reminds me of the fiasco with Katie Hill, some of these young politicians have serious problems

Davidski said...

@Samuel

I know it must be hard to comprehend and accept the trouble that your country is in right now, because it's difficult for me too.

I think the difficulty isn't just the result of how complex the situation is, but also how dangerous and frightening it is, so there's a significant amount of denial involved for everyone.

However, try to step back and access this objectively.

Surely you must understand that Covid-19 isn't going away anytime soon, and that the steps that have been taken in the US to minimize its impact have had limited success.

Also, it's likely that thanks to the protests and riots some cities will experience major infection outbreaks that will require expensive lockdowns that no one can afford, so they're no longer an option.

In parts of New York as much as 25% of the population may have been infected, so if these people have immunity, then that might cushion the impact of the second wave locally, but let's see how that works out.

Much of the rest of the country, except the most sparsely populated parts, are probably screwed until a vaccine is mass produced, maybe later this year or early next year if all goes according to plan.

Bottom line: expect hundreds of thousands of Covid-19 deaths before the year is out, a divided and frightened society, and a stuttering economy.

Rob said...

As Dave said; time will tell. Let’s hope for the best for all
ADNA has shown us how devastating plague pandemics & climate change might have been to our ancestral populations.
Us moderns are able to resist the cycles of nature and make sure that we continue to proliferate , for better or worse

vAsiSTha said...

@davidski
There's going to be no vaccine or effective treatment protocol for a long time.
We just have to protect seniors from this for a year. We are goingto see bigger spikes post july-aug.

Davidski said...

@vAsiSTha

The mass production of one of the vaccine candidates is already starting, so that the vaccine can be distributed even this year if human trials prove successful.

https://www.theguardian.com/business/2020/jun/04/astrazeneca-doubles-capacity-for-potential-covid-19-vaccine-to-2bn-doses

Also, several treatments are being tested and at least one of them is likely to be widely used soon.

https://www.theguardian.com/world/2020/jun/07/breakthrough-close-on-coronavirus-antibody-therapy-reports

It looks like you bring the brain dead touch to just about every debate that you get into. You might want to do something about that.

mirgould said...

The two things that astound me with Covid-19

1: The numbers from East Asia

Less than 1,000 dead in all of Japan, 250 in South Korea and 7 in Taiwan
My city (New York) has almost 17,000 deaths

2: The early incompetence of The WHO and western health experts

After we were told constantly by the media in the US that harsh lockdowns and social distancing were the answer we now have “1,200 health professionals” saying it’s okay to go riot in the streets and others who were criticizing states reopening early telling us it’s our moral duty to protest and we are complicit with racism if we stay at home? What happened to the second wave we were warned about? Absolutely insane. It’s just like with the hypocrite Neil Ferguson. His model was laughable garbage code and all the while he was breaking lockdown rules to do the dirty with a married woman. Or like when The WHO told everyone not to wear masks and they were only needed for doctors and nurses.

As per CDC’s latest estimates, the death rate of Covid-19 is .26 %, (WHO originally claimed 3.4%), this includes the elderly and those with comorbidities (around 85 to 90% of deaths involve comorbidities namely, hypertension and diabetes). Seeing as the average age of death for a coronavirus victim is the mid 80s in retrospect it would have been a good idea to take special care with nursing homes. That’s likely why NY’s death toll was so catastrophic since Cuomo was sending infected patients back to the homes

Here’s some some quick thoughts I have, what do you guys think?

1. Assess the steps taken by nations like Taiwan and SK to address the virus and send our experts and officials there to learn from them
2. End strict lockdowns, they are unnecessary
3. Promote and if needed enforce the use of masks and gloves, they’re effective
4. Protect and provide special funding to nursing homes as they are the most vulnerable

@jeanlohizun

I’d say Florida is incredibly lucky. They were .4 % from having this man as their Governor

https://www.foxnews.com/us/photos-police-body-cam-video-released-of-andrew-gillum-hotel-room-report

Being in a room passed out two other men (one a known escort), ED medication, methamphetamine and vomit everywhere doesn’t exactly inspire confidence in crisis. Reminds me of the fiasco with Katie Hill, some of these young politicians have issues

Davidski said...

@mirgould

The death rate for Covid-19 is around 1% based on all of the data I've seen from around the world.

It increases when hospitals are overwhelmed, and that can happen very quickly because the growth in infections is exponential and hospital recovery time can take weeks.

Anything that the CDC claims is likely to be way off, considering its performance to date.

vAsiSTha said...


"It looks like you bring the brain dead touch to just about every debate that you get into. You might want to do something about that."

Lmao, you're very gullible aren't you.
Hcq- failed trial, remedisivir- failed trial, moderna vaccine - failed

The moderna CEO was selling his stock all the while pumping up the stock with half truths about the vaccine results.

Davidski said...

A wide range of already available treatments are being tested, and almost all will fail because they weren't designed for Covid-19 specifically.

So what's your point?

George said...


Somethings I'm wadding through.

The 2015 thesis is 691 pages:
EXCAVATING WAR:
THE ARCHAEOLOGY OF CONFLICT IN EARLY CHALCOLITHIC
TO EARLY BRONZE III CENTRAL AND SOUTHEASTERN ANATOLIA

The first chapter of this dissertation defines the various terms used in this dissertation, with particular focus on the definition warfare and violence. The previous scholarship in the study of warfare in the ancient Near East is reviewed, as well as a history of the anthropology of warfare. Finally, a study of various theories on the rise of the state in the ancient Near East is put forth, with an overview of the theoretical model utilized.

https://oi.uchicago.edu/sites/oi.uchicago.edu/files/uploads/shared/docs/Research_Archives/Dissertations/Selover%20Dissertation.pdf


Hittite Mortuary Practices by Anton M Axelsson
http://www.diva-portal.org/smash/get/diva2:1111635/FULLTEXT01.pdf


Web search for Erdal_and_Erdal_2012_son_hali_1.pdf not registered at Tiny Link.
Organized violence in Anatolia: A retrospective research on the injuries from the Neolithic to Early Bronze Age.
Erdal YS1, Erdal ÖD1 31 May 2012


jeanlohizun said...

@ Samuel Andrews said

"They are doing more testing which explains spikes rise in infections. New cases is caused by two variables: Spread of the virus and number tests being done. Rising number of infections doesn't always mean the virus is peaking.

You guys are having under 40 deaths per day. That's low for a state as populous as Flordia."

Your first assertion is demonstrably false. Again, take a look a the Florida Dashboard, and hop over to the testing tab. Keep in mind it is a week behind,but still the trends are useful.

https://experience.arcgis.com/experience/96dd742462124fa0b38ddedb9b25e429

In the week ending on 5/17 there were 241,523 tests done, and 4952 positive new cases. On the week ending on 5/24 there were 171,769 tests done, and 5466 positive new cases. Strangely, they have not posted the subsequent week yet, but we know that all of the last 4 days have featured over 1,300 daily new cases.

The deaths usually lagged the spikes in hospital admissions, which themselves lagged the new cases. The average time from testing positive to dying is about 21 days. Also 40 deaths/day is about 14600 deaths/year, and consider that the virus is less active in summer months, due to secondary mode(virus resting active on surfaces) of transmission being heavily reduced and most people being outside.

jeanlohizun said...

@mirgould said:

"I’d say Florida is incredibly lucky. They were .4 % from having this man as their Governor

https://www.foxnews.com/us/photos-police-body-cam-video-released-of-andrew-gillum-hotel-room-report

Being in a room passed out two other men (one a known escort), ED medication, methamphetamine and vomit everywhere doesn’t exactly inspire confidence in crisis. Reminds me of the fiasco with Katie Hill, some of these young politicians have issues"

Yes, I am quite aware of the situation, I am also quite aware that Andrew Gillum claims to have fallen into a depression post election. I will venture out an say I did not vote for him, and voted for deSantis based on policy, Gillum wanted to increase State Business income tax, he was a proponent of Medicare-for-all, and had pretty mainstream big government policies. You are making an assumption though, Gillum will not be running in 2022, and there is always the choice of not voting for either candidate or choosing third party. Not sure, deSantis can afford to be losing Independent voters who voted for him last time.

Mayuresh Madhav Kelkar said...

Link posted by George:

From five years ago.

"As a final note on possible external influences, a major and ongoing debate centering on
central Anatolia concerns the so-called Indo-European issue. This conflict focuses on whether the Indo-European language, and its associated peoples, found in abundance in literature and culture of Middle and Late Bronze Age central Anatolia, in the form of the Hittite, Luwian, and Palaic languages, first entered into Anatolia, or indeed, if they ever 'entered' at all. This debate focuses on such aspects of linguistic origins (e.g. Burney and Lang 1971; Gamkrelidze and Ivanov 1985; Mallory 1989; Renfrew 1987); the origins of agriculture (e.g. Anthony 2007; Bellwood 2005; Zvelebil and Zvelebil 1988) or archaeological evidence (Anthony 2001; Thomas 1992). Despite great efforts, this migration still has not been effectively proven through archaeological means. Therefore, for the purposes of this dissertation, the Indo-European question will be largely silent in the consideration of the effects of warfare on central Anatolia. If indeed an Indo-European population did enter central Anatolia during the Chalcolithic to Early Bronze Age period, they may have had a very large impact on interpersonal violence in the region. As not enough information is known at this time to say more about the subject, it will not be addressed. "

mirgould said...



It’s always best to err on the side of caution with estimates, but in this case I trust the CDC more than those claiming much higher estimates.

Some may find this humorous or scary, but USAtoday fact checked the CDC estimate and called it false simply because it’s an estimate subject to change (Where are the fact checks on all the other estimates?). They cite a scientists who’s reasoning is we should use NYC (AKA the worst managed area) as the sole parameter for the model. What I find humorous though is that the same scientist they source as expressing grievances with the figure as too low, Dr. Carl Bergstrom at University of Washington, is from the very institution that drafted the letter encouraging protests and disregarding any contribution they may have on the spread of the virus. A study proclaiming to show the death rate at 1.3% is, low and behold, from the University of Washington as well and comically cites the disgraced Dr. Neil Furgeson as their first citation.

The same people telling the public to ignore CDC estimates as too low are now saying it’s okay to fill the streets, it’s incredible. This is why I trust the CDC estimate more than the greater estimates being given, many are made in bad faith and appear to be politically motivated. Could the Covid-19 death rate be higher than .26%? Of course. The experts here claiming that it's exceptionally higher have voluntarily thrown away any trust they once had though. Meanwhile just 7 deaths in Taiwan, there are already roadmaps for success out there we can follow regardless of where the death rate might be.

@jeanlohizun
No worries, you have every right to be frustrated with your Governor if you believe he's handling the situation badly. I look at every state with envy as to how we handled the virus here in NY though.

Davidski said...

@mirgould

The US can't learn much from Taiwan, because the sort of community compliance that is routine there doesn't exist in the US, not even during a pandemic.

Also, I have to reiterate that the CDC death rate estimate looks like BS, considering that we already have 400K reported deaths worldwide in less than six months, and the infection rate even in the hardest hit areas usually doesn't approach 15%.

And most cases are still going, which means that a fair few of these people will be added to the death toll eventually.

Samuel Andrews said...

Trump did do a poor job with Cornavirus. And he has also done a poor a job with keeping law and order during the riots. But, I'm still going to vote for him cuz he's much better than Democrats.

He should have brought in the military. It is 100% unacceptable, that in a civilized country angry mobs can get away with mass theft and destruction of property. Then get defended by our country's media and intellectuals who think riots are an acceptable form of political expression.

Democrat states and cities don't protect their citizens from riots. And these won't be the last riots. American business owners in Democrat-run big cities are forced to defend themselves. As if we live in anarchy. These business owners are probably mostly Democrats who don't believe in guns so they're not actually going to defend themselves.

vAsiSTha said...

@davidski

you have been posting links of the astrazeneca/oxford vaccine and how its got a great shot at being THE ONE. The vaccine is called chadox1 or AZD1222.

It failed to prevent infection in vaccinated monkeys as per the preprint, but the company of course sees rays of hope.

https://www.telegraph.co.uk/global-health/science-and-disease/doubts-oxford-vaccine-fails-stop-coronavirus-animal-trials/

"That viral loads in the noses of vaccinated and unvaccinated animals were identical is very significant. If the same happened in humans, vaccination would not stop spread," he said. "I genuinely believe that this finding should warrant an urgent re-appraisal of the ongoing human trials of the ChAdOx1 vaccine."

"One measure of infection is an increased breathing rate as the virus attacks the lungs – three of the vaccinated animals displayed this symptom. On autopsy, the researchers found the virus in the vaccinated monkeys' lungs."

They now have smartly changed the name from chadox1 to AZD1222. In a sane world, the vaccine would have been stopped after the failed animal trial. But we live in an insane and corrupt world, so instead astrazeneca got billions in funding.

Davidski said...

@vAsiSTha

I never claimed that the Oxford vaccine was the one, so I'm not sure what you're babbling about.

There are several vaccines being tested and I don't trust your predictions that they'll all be failures.

Your claims that there won't be any effective treatments for Covid-19 are also rather strange, considering it's still early days.

Shut the hell up and wait.

jeanlohizun said...

@Samuel Andrews said:

"Democrat states and cities don't protect their citizens from riots. And these won't be the last riots. American business owners in Democrat-run big cities are forced to defend themselves. As if we live in anarchy. These business owners are probably mostly Democrats who don't believe in guns so they're not actually going to defend themselves. "

A loss is a loss, so what do you make of the 40%+ businesses that went under because of the lockdown, what about the Cares Act, which gave 1.5 Trillion dollars to big businesses, and a measly 250 Billion to small businesses for the PPP? Airlines got 16 Billion each, and these are forgivable loans, meaning they do not have to pay them back if they follow certain conditions. National Debt is at nearly 26 Trillion:

https://www.usdebtclock.org/

A 6 Trillion with a T, dollar increase since 2016.

https://www.usdebtclock.org/2016.html

You are absolutely correct about many Democract run cities being Shitholes, namely because welfare and free benefits only attracts more homeless and more crime, Western European countries ought to learn that lesson. However, ask yourself? When was the last time, Republicans acted like Republicans? It seems as soon as Trump took over, they all forgot about all of their policies. Remember when they use to care about the Debt Ceiling to the point of shutting down the government over it in 2013? I do.

So, why should they take us for granted? I will rather endure 4 years of a centrist kettle like Joe Biden, if it teaches Republicans that they need to govern on fiscally conservative policies, and simply saying we are somehow better than the opposing party is not good enough. Also, they were the very first party to have a government shutdown while controlling both chambers of Congress and they White House. All because little Dictator Mitch McConnell, is too chicken sh...t to get rid of the Filibuster, I guess he is afraid of the Senate actually doing its job.

jeanlohizun said...

@Daviski

Moving away from politics and into genetics, what do you make of the placement in treemix of admixed populations?

To me, it highlights issues with the Reich.et.al group, they seems to be putting the hypothesis before the data. Here is why:

In there was a study which use mitochondrial DNA to conclude that the first inhabitants of the Caribbean must have come from South America. Reich's team, did not include any samples from the US, only one sample from Canada. The Science article, shows that Aboriginal people from the California Channel Islands, specifically the site of San Nicholas dated to 4900 BP, branched off the Tree at the same time as the earliest Cuban Inhabitants, Figure-3a in Nagale.et.al.2020:

https://science.sciencemag.org/content/early/2020/06/03/science.aba8697

They show in Figure-3b that around 2500 ybp there was a subsequent aceramic migration from South America, with the population being ~63% San Nicholas and 37% South American-like. The placement in the tree still puts them branching off before all South and Central American samples. In the Reich study, they are well within the South American samples, in fact branching off after the Aymara and Quechua.

To me it shows, that the placement in the treemix is highly susceptible to the choice of ancient/modern samples (Reich's study used mostly modern samples, Science used ancient ones), and that this is something that could potentially affect other studies.

I'm very frustrated that they did not choose to explore alternative hypotheses, and instead when all Ad Hoc with their populations choices. It seems to reflect the same approach they have taken with the PIE hypothesis and their idea that Iran was the contributor of the CHG-like ancestry to Steppe. Your take?

George said...

To Mayuresh:

Thank you for your posting. The locations mentioned are primarily in SE Anatolia out of what many would consider the main areas for Indo-European migration.

Probably the best one could hope for would be Indo-European symbols and remains with some steppe DNA. Something along the lines of: The importance of archaeology for historical linguistics, part 3. Posted by Victor Mair, 3 June, 2020
https://languagelog.ldc.upenn.edu/nll/?p=47335. He mentions Alaca Höyük.

From the Thesis on SE Anatolia
Table 3.9 Early Bronze II to III
p548 Alaca Höyük 14 Royal Burials and 10 non-Royal; many
weapons from the Royal Tombs.

I would not expect 'armies' but raiding bands that might have brought their language with them as they settled territory. Injuries consistent with these types of raids are reported in the thesis. similar to what was reported in: Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave
https://www.pnas.org/content/early/2019/04/30/1820210116

It would be nice if DNA could be collected from some of these samples

A selection of some table entries hint at this:
Table 3.9 Early Bronze II to III
p549 Elmalı-Karataş Relatively large number of healed injuries on the adultremains, both male and female; mainly ulnar parry fractures and healed and unhealed cranial trauma; two adult males had fatal cranial trauma on the occipital from an axe
p550 Ikiztepe Total of 84 remains with cranial trauma, 18.9% of the
population studied; 43% of the studied male population
showed signs of violent trauma, 17 males died of their
trauma

Table 3:10 Early to Middle Chalcolithic
p 551 Domuztepe Signs of human consumption of the human remains; all
remains were decapitated with evidence of severe blunt
force trauma, though unclear if peri- or post-mortem; the
remains were de-fleshed before being placed in the pit;
outside of the death pit, three more individuals showed
signs of cranial blunt force trauma

Table 3.11 Late Chalcolithic to Early Bronze I
p 556 Titriş Höyük
From the EBII, three individuals had healed cranial
trauma, one a perimortem trauma; From EBIII, most had
cranial trauma, both male and female, likely made by
battle axe blows to the skull, as well as spears and
daggers, on the parietal, occipital and frontal

Table 3.12 Early Bronze II to III
Three adults with sings of healed trauma from rib
fractures and a parry fracture; In unhealed trauma, three
sub-adults and four adults had no signs of trauma, 8 adults
did, both male and female. Four with single trauma, four
with multiple, up to 15 fractures. Cranial fractures on the
frontal, parietal and occipital bones, made with ovular
weapons, likely a macehead, most likely the fatal wounds.
Post-cranial trauma included 2 ulna fractures, 5 rib
fractures, 3 metacarpals, one metatarsal. All from a single
burial context.

vAsiSTha said...

"Your claims that there won't be any effective treatments for Covid-19 are also rather strange, considering it's still early days."
Not never, but not this year. Probability is very low.
This isn't pessimism, it's realism and policy should depend on real probability of medicine/vaccine success.

epoch said...

Recently I have increasingly grown far more optimistic that this epidemic is going to go away pretty soon. There are two very important discoveries which caused that change of view:

1) There appears to be a substantial immunity in the population to SARS_C0V_2 in people who did not have any contact with the virus [0]. In Germany 38% [1] of the population seems to have T-cells that respond to SARS_C0V_2 infection, in Singapore even 50% [2]. It looks like the immunity is caused by a yet unkown coronavirus [3]. Several other coronavisusses that cause mild common colds appear to train the immune system to remember responding *even* after the antibodies disappear. These virusses seem to have a pretty high abundance among children.

2) It starting to look that this epidemic is mainly driven by superspreaders [4]. If correct the large majority of cases will infect less than one other patient on average, whereas some cases may infect hunderds. But this system will only causes an expanding epidemic if it finds enough "fresh meat". If, say, 20% of a population is immune by a previous infection and on top of that 40% of the population is either naturally immune or highly resistant because of point 1 we have herd immunity at a far lower level of seropositiveness than thought. This does not mean that a initial infection spree won't be able to infect a larger part of the population in the initial phase, but it won't be able to do so after a while.

If I am right there will be a second wave but a very small one, easily contained. Countries with notable high prevalence of children in early daycare - Netherlands, Scandinavia, Taiwan, Singapore - will have a smaller second wave.

[0] https://www.cell.com/cell/fulltext/S0092-8674(20)30610-3
[1] https://www.wz.de/panorama/wissenschaft/drosten-hinweis-auf-hintergrundimmunitaet-gegen-neues-coronavirus_aid-50235539
[2] https://www.biorxiv.org/content/10.1101/2020.05.26.115832v1.full.pdf
[3] https://twitter.com/BallouxFrancois/status/1266265088157081601
[4] https://www.bloomberg.com/opinion/articles/2020-05-28/superspreader-events-might-actually-help-control-covid-19

epoch said...

@vAsiSTha

The virus doesn't do much harm in the nasal tissue and nasal tissue isn't very involved in immune responses. It's when the virus sinks into the lungs where it gets the ability to kill. If the Oxford vaccine is able to trigger an IgA respons in the lungs - IgA being antibodies typical of mucous tissue - it will be effective enough.

"One measure of infection is an increased breathing rate as the virus attacks the lungs – three of the vaccinated animals displayed this symptom. On autopsy, the researchers found the virus in the vaccinated monkeys' lungs.

On the upside, none of the vaccinated monkeys displayed pneumonia which suggests that, while not stopping the virus, it may be partially protective.
"

Davidski said...

@jeanlohizun

I'm not in a position to comment because I'm not familiar with the topic.

I would need to take a close look at the data, but I'm not likely to do that anytime soon.

ANI EXCAVATOR said...

Since a number of comments were deleted from the previous comment thread, I'll repost what I wrote in reply to "Nick A" on what ancient and modern DNA tells us about the route Haplogroup P took to Northern Eurasia.

Tianyuan Man from Beijing is K2b, the haplogroup just upstream of PQR and MS. He dates back to 42-39 thousand years ago, which means he lived a very short time after the formation of K2b (estimated to be around 45 thousand years ago) and was completely East Asian in ancestry. His ancestry is the component that distinguishes Northeast Asians from Oceanians and ASI. All analyses of the proto-ANE Yana males (Y-haplogroup P1*), from about 30 thousand years ago, show that ancestry from Tianyuan or Salkhit (closely related to Tianyuan) took part in the formation of of the proto-ANE people.

After Tianyuan, the most basal sample of haplogroup P (P*) in the record now was recovered from a skeleton from the Andaman islands from the 19th century. This person has three of the most important ancestral snps (P284, PF5482 and PF5883/M1197) covered by at least 3 reads each. Two of them are transversion sites which are less affected by ancient DNA damage. This confirms his position as the most basal P found so far. One level down from this guy (P-BY49600, P1*) are 10 other Andamanese samples and some Agta samples, who are a negrito people of the Philippines. One level down again (P1-P337) we find the Yana samples, and another level down (P1-226 -> R*) we find Mal'ta. Of course, the Tianyuan K2b is found at the very top of this tree.

The determination that the most basal P found so far is from an ancient Andamanese sample has been accepted by Yfull: https://www.yfull.com/tree/P/
The individual id:HistAndamanIND [IN-AN] is included as a leaf at the P* level in their tree.

The Andamanese have been separated from outside contact for almost 45 thousand years. Furthermore, if you have only one basal lineage in a population, it might be an extremely random founder effect from a man coming in from outside, but if you have two, the evidence is much stronger that the ancestors of this population carried many basal lineages that had their common ancestor in this group or in related populations.

Furthermore, the proto-ANE population, as well as later ANE, carried Denisovan ancestry, which further confirms admixture from East Asia:

https://www.biorxiv.org/content/10.1101/2020.06.03.131995v1.full.pdf
"Using data from ~1.7 million SNPs where
Neandertal and/or Denisovan genomes differ from present-day African genomes, we detect 18
segments of Denisovan ancestry longer than 0.2 cM in the Salkhit genome (Fig. 3, Table S18, Fig.
S16 and S27) and 20 such segments in the Tianyuan genome (Table S18, Fig. S17 and S27). We
detect about a third as many segments of Denisovan DNA in the genomes of the ancient Siberians
Yana 1 and Yana 2, and Mal’ta 1 (Table S18, Fig. S18-20 and S27), consistent with that they carry
lower proportions of East Asian ancestry. In contrast, no Denisovan ancestry is detected in the
genome of the ~45,000-year-old Siberian individual from Ust’Ishim in West Siberia, nor in any
European individual older than 20,000 years (Table S18, Fig. S21-24 and S27)."

East Asians and West Eurasians had separated for only a short time at 45 thousand years ago, but P might have ended up on the eastern side right after the split, and moved northwards East of the Himalayas. Ust-Ishim and West Eurasians appear to have taken another route to Siberia than East Asians did.

epoch said...

I withdraw my remark that COVID19 can not cause much harm in the nose:

https://twitter.com/DrZoeHyde/status/1269252956345389056

Archi said...

@ANI EXCAVATOR

1. Tianyuan is the closest match to a European Goyet Q116-1. So Tianyuan is as East Asian as the European Goyet Q116-1.

2. Tianyuan contains an admixture of northern Denisovan, not an admixture of southern Denisovans.

"Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians."

Consequently, Tianyuan received it in the Altai-Baikal region, where a huge number of ancient man sites, very recently, we are talking about several generations.

As the latest research on East Asian modern Eastern Asians has shown, they spread from North to South.

Yang M., et al. 2020, Ancient DNA indicates human population shifts and admixture in northern and southern China.


From here it follows that they penetrated through the Hindu Kush to the Altai, from where one wave went to the east, and which became East Asians, and the second wave to the west were the first Europeans - Goyet Q116-1, and Oase1 and Oase2, relatives of Ust'-Ishim.

Andamanians have a haplogroup D, and in general they came from the north, they are very frost-resistant, they walk quite naked in cold weather.

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