adna   43

Who We Are | West Hunter
I’m going to review David Reich’s new book, Who We Are and How We Got Here. Extensively: in a sense I’ve already been doing this for a long time. Probably there will be a podcast. The GoFundMe link is here. You can also send money via Paypal (Use the donate button), or bitcoins to 1Jv4cu1wETM5Xs9unjKbDbCrRF2mrjWXr5. In-kind donations, such as orichalcum or mithril, are always appreciated.

This is the book about the application of ancient DNA to prehistory and history.

height difference between northern and southern europeans: https://westhunt.wordpress.com/2018/03/29/who-we-are-1/
mixing, genocide of males, etc.: https://westhunt.wordpress.com/2018/03/29/who-we-are-2-purity-of-essence/
rapid change in polygenic traits (appearance by Kevin Mitchell and funny jab at Brad Delong ("regmonkey")): https://westhunt.wordpress.com/2018/03/30/rapid-change-in-polygenic-traits/
schiz, bipolar, and IQ: https://westhunt.wordpress.com/2018/03/30/rapid-change-in-polygenic-traits/#comment-105605
Dan Graur being dumb: https://westhunt.wordpress.com/2018/04/02/the-usual-suspects/
prediction of neanderthal mixture and why: https://westhunt.wordpress.com/2018/04/03/who-we-are-3-neanderthals/
New Guineans tried to use Denisovan admixture to avoid UN sanctions (by "not being human"): https://westhunt.wordpress.com/2018/04/04/who-we-are-4-denisovans/
also some commentary on decline of Out-of-Africa, including:
"Homo Naledi, a small-brained homonin identified from recently discovered fossils in South Africa, appears to have hung around way later that you’d expect (up to 200,000 years ago, maybe later) than would be the case if modern humans had occupied that area back then. To be blunt, we would have eaten them."

Live Not By Lies: https://westhunt.wordpress.com/2018/04/08/live-not-by-lies/
Next he slams people that suspect that upcoming genetic genetic analysis will, in most cases, confirm traditional stereotypes about race – the way the world actually looks.

The people Reich dumps on are saying perfectly reasonable things. He criticizes Henry Harpending for saying that he’d never seen an African with a hobby. Of course, Henry had actually spent time in Africa, and that’s what he’d seen. The implication is that people in Malthusian farming societies – which Africa was not – were selected to want to work, even where there was no immediate necessity to do so. Thus hobbies, something like a gerbil running in an exercise wheel.

He criticized Nicholas Wade, for saying that different races have different dispositions. Wade’s book wasn’t very good, but of course personality varies by race: Darwin certainly thought so. You can see differences at birth. Cover a baby’s nose with a cloth: Chinese and Navajo babies quietly breathe through their mouth, European and African babies fuss and fight.

Then he attacks Watson, for asking when Reich was going to look at Jewish genetics – the kind that has led to greater-than-average intelligence. Watson was undoubtedly trying to get a rise out of Reich, but it’s a perfectly reasonable question. Ashkenazi Jews are smarter than the average bear and everybody knows it. Selection is the only possible explanation, and the conditions in the Middle ages – white-collar job specialization and a high degree of endogamy, were just what the doctor ordered.

Watson’s a prick, but he’s a great prick, and what he said was correct. Henry was a prince among men, and Nick Wade is a decent guy as well. Reich is totally out of line here: he’s being a dick.

Now Reich may be trying to burnish his anti-racist credentials, which surely need some renewal after having pointing out that race as colloquially used is pretty reasonable, there’s no reason pops can’t be different, people that said otherwise ( like Lewontin, Gould, Montagu, etc. ) were lying, Aryans conquered Europe and India, while we’re tied to the train tracks with scary genetic results coming straight at us. I don’t care: he’s being a weasel, slandering the dead and abusing the obnoxious old genius who laid the foundations of his field. Reich will also get old someday: perhaps he too will someday lose track of all the nonsense he’s supposed to say, or just stop caring. Maybe he already has… I’m pretty sure that Reich does not like lying – which is why he wrote this section of the book (not at all logically necessary for his exposition of the ancient DNA work) but the required complex juggling of lies and truth required to get past the demented gatekeepers of our society may not be his forte. It has been said that if it was discovered that someone in the business was secretly an android, David Reich would be the prime suspect. No Talleyrand he.

https://westhunt.wordpress.com/2018/04/12/who-we-are-6-the-americas/
The population that accounts for the vast majority of Native American ancestry, which we will call Amerinds, came into existence somewhere in northern Asia. It was formed from a mix of Ancient North Eurasians and a population related to the Han Chinese – about 40% ANE and 60% proto-Chinese. Is looks as if most of the paternal ancestry was from the ANE, while almost all of the maternal ancestry was from the proto-Han. [Aryan-Transpacific ?!?] This formation story – ANE boys, East-end girls – is similar to the formation story for the Indo-Europeans.

https://westhunt.wordpress.com/2018/04/18/who-we-are-7-africa/
In some ways, on some questions, learning more from genetics has left us less certain. At this point we really don’t know where anatomically humans originated. Greater genetic variety in sub-Saharan African has been traditionally considered a sign that AMH originated there, but it possible that we originated elsewhere, perhaps in North Africa or the Middle East, and gained extra genetic variation when we moved into sub-Saharan Africa and mixed with various archaic groups that already existed. One consideration is that finding recent archaic admixture in a population may well be a sign that modern humans didn’t arise in that region ( like language substrates) – which makes South Africa and West Africa look less likely. The long-continued existence of homo naledi in South Africa suggests that modern humans may not have been there for all that long – if we had co-existed with homo naledi, they probably wouldn’t lasted long. The oldest known skull that is (probably) AMh was recently found in Morocco, while modern humans remains, already known from about 100,000 years ago in Israel, have recently been found in northern Saudi Arabia.

While work by Nick Patterson suggests that modern humans were formed by a fusion between two long-isolated populations, a bit less than half a million years ago.

So: genomics had made recent history Africa pretty clear. Bantu agriculuralists expanded and replaced hunter-gatherers, farmers and herders from the Middle East settled North Africa, Egypt and northeaat Africa, while Nilotic herdsmen expanded south from the Sudan. There are traces of earlier patterns and peoples, but today, only traces. As for questions back further in time, such as the origins of modern humans – we thought we knew, and now we know we don’t. But that’s progress.

https://westhunt.wordpress.com/2018/04/18/reichs-journey/
David Reich’s professional path must have shaped his perspective on the social sciences. Look at the record. He starts his professional career examining the role of genetics in the elevated prostate cancer risk seen in African-American men. Various social-science fruitcakes oppose him even looking at the question of ancestry ( African vs European). But they were wrong: certain African-origin alleles explain the increased risk. Anthropologists (and human geneticists) were sure (based on nothing) that modern humans hadn’t interbred with Neanderthals – but of course that happened. Anthropologists and archaeologists knew that Gustaf Kossina couldn’t have been right when he said that widespread material culture corresponded to widespread ethnic groups, and that migration was the primary explanation for changes in the archaeological record – but he was right. They knew that the Indo-European languages just couldn’t have been imposed by fire and sword – but Reich’s work proved them wrong. Lots of people – the usual suspects plus Hindu nationalists – were sure that the AIT ( Aryan Invasion Theory) was wrong, but it looks pretty good today.

Some sociologists believed that caste in India was somehow imposed or significantly intensified by the British – but it turns out that most jatis have been almost perfectly endogamous for two thousand years or more…

It may be that Reich doesn’t take these guys too seriously anymore. Why should he?

varnas, jatis, aryan invastion theory: https://westhunt.wordpress.com/2018/04/22/who-we-are-8-india/

europe and EEF+WHG+ANE: https://westhunt.wordpress.com/2018/05/01/who-we-are-9-europe/

https://www.nationalreview.com/2018/03/book-review-david-reich-human-genes-reveal-history/
The massive mixture events that occurred in the recent past to give rise to Europeans and South Asians, to name just two groups, were likely “male mediated.” That’s another way of saying that men on the move took local women as brides or concubines. In the New World there are many examples of this, whether it be among African Americans, where most European ancestry seems to come through men, or in Latin America, where conquistadores famously took local women as paramours. Both of these examples are disquieting, and hint at the deep structural roots of patriarchal inequality and social subjugation that form the backdrop for the emergence of many modern peoples.
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march 2018 by nhaliday
The Science of Roman History: Biology, Climate, and the Future of the Past (Hardcover and eBook) | Princeton University Press
Forthcoming April 2018

How the latest cutting-edge science offers a fuller picture of life in Rome and antiquity
This groundbreaking book provides the first comprehensive look at how the latest advances in the sciences are transforming our understanding of ancient Roman history. Walter Scheidel brings together leading historians, anthropologists, and geneticists at the cutting edge of their fields, who explore novel types of evidence that enable us to reconstruct the realities of life in the Roman world.

Contributors discuss climate change and its impact on Roman history, and then cover botanical and animal remains, which cast new light on agricultural and dietary practices. They exploit the rich record of human skeletal material--both bones and teeth—which forms a bio-archive that has preserved vital information about health, nutritional status, diet, disease, working conditions, and migration. Complementing this discussion is an in-depth analysis of trends in human body height, a marker of general well-being. This book also assesses the contribution of genetics to our understanding of the past, demonstrating how ancient DNA is used to track infectious diseases, migration, and the spread of livestock and crops, while the DNA of modern populations helps us reconstruct ancient migrations, especially colonization.

Opening a path toward a genuine biohistory of Rome and the wider ancient world, The Science of RomanHistory offers an accessible introduction to the scientific methods being used in this exciting new area of research, as well as an up-to-date survey of recent findings and a tantalizing glimpse of what the future holds.

Walter Scheidel is the Dickason Professor in the Humanities, Professor of Classics and History, and a Kennedy-Grossman Fellow in Human Biology at Stanford University. He is the author or editor of seventeen previous books, including The Great Leveler: Violence and the History of Inequality from the Stone Age to the Twenty-First Century (Princeton).
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november 2017 by nhaliday
It made their brown eyes blue.. | West Hunter
Assuming population continuity, the selective advantage of the alleles they examined must have been very high. In order to see if there had been population continuity, they looked at the mtDNA frequencies of the ancient populations and compared them with mtDNA frequencies of modern populations in the same areas. Since they’re different, but not wildly different, they conclude that there has been population continuity, which was their null assumption.

That null assumption might have been reasonable, if someone had burned every history book ever written, while at the same time suppressing all the ancient DNA evidence.

Since that has not yet happened, I think their assumption is downright embarrassing. People have been moving in and out of this area for all of recorded history (as Razib Khan has also pointed out) : Cimmerians, Scythians, Goths, Khazars, Kievian Rus, the Golden Horde, eventually Russians.

There is no logical reason for geneticists to ignore information outside their field. Ignorance is no excuse. I could say the same for every other discipline. Cross the streams – it would be good.
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august 2017 by nhaliday
The Genomic Health Of Ancient Hominins | bioRxiv
On a broad scale, hereditary disease risks are similar for ancient hominins and modern-day humans, and the GRS percentiles of ancient individuals span the full range of what is observed in present day individuals. In addition, there is evidence that ancient pastoralists may have had healthier genomes than hunter-gatherers and agriculturalists. We also observed a temporal trend whereby genomes from the recent past are more likely to be healthier than genomes from the deep past.

Gwern has interesting take (abstract is misleading): https://twitter.com/gwern/status/871061144152178688

here it is in conclusion (and cf Figure 3A):
The genomic health of ancient individuals appears to have improved over time (Figure 3B). This calls into question the idea that genetic load has been increasing in human populations (Lynch 2016). However, there exists a perplexing pattern: ancient individuals who lived within the last few thousand years have healthier genomes, on average, than present day humans.

http://www.pnas.org/content/early/2017/08/08/1703856114
After controlling for age, BMI, and other variables, knee OA prevalence was 2.1-fold higher (95% confidence interval, 1.5–3.1) in the postindustrial sample than in the early industrial sample. Our results indicate that increases in longevity and BMI are insufficient to explain the approximate doubling of knee OA prevalence that has occurred in the United States since the mid-20th century. Knee OA is thus more preventable than is commonly assumed, but prevention will require research on additional independent risk factors that either arose or have become amplified in the postindustrial era.
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june 2017 by nhaliday
Genetics allows the dead to speak from the grave - The Unz Review
BOOKMARKIt is a running joke of mine on Twitter that the genetics of white people is one of those fertile areas of research that seems to never end. Is it a surprise that the ancient DNA field has first elucidated the nature of this obscure foggy continent, before rich histories of the untold billions of others? It’s funny, and yet these stories, true tales, do I think tell us a great deal about how modern human populations came to be in the last 10,000 years. The lessons of Europe can be generalized. We don’t have the rich stock of ancient DNA from China, the Middle East, or India. At least not enough to do population genomics, which requires larger sample sizes than a few. But, climate permitting, we may.

...

At about the same time the evidence for Neanderthal admixture came out, Luke Jostins posted results which showed that other human lineages were also undergoing encephalization, before their trajectory was cut short. That is, their brains were getting bigger before they went extinct. To me this suggested that the broader Homo lineage was undergoing a process of nearly inevitable change due to a series of evolutionary events very deep in our history, perhaps ancestral on the order of millions of years. Along with the evidence for admixture it made me reconsider my priors. Perhaps some Homo lineage was going to expand outward and do what we did, and perhaps it wasn’t inevitable that it was going to be us. Perhaps the Neanderthal Parallax scenario is not as fantastical as we might think?
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may 2017 by nhaliday
War Before Civilization | West Hunter
When you think of war, you usually think of organized states, or at minimum peoples with moderately sophisticated modes of production, agriculturalists or pastoralists. But hunter-gatherers manage as well. Not just war, but decisive war, the kind that that obliterates the enemy and results in a major geographic expansion. Before the Eskimos, there was a different population living in arctic North America and Greenland, the Dorset culture. Over a fairly short period, between 1000 AD and 1500 AD, the Thule (ancestors of modern Inuit) moved east, replacing the Dorset. It looks as if the Thule didn’t mix much with the previous occupants either: we have an early Dorset genome that looks very Na-dene-like, while the Eskimos are not. The conflict was recent enough to leave legends among the Eskimo: they say the first inhabitants were giants, taller and stronger but easily scared off.

https://westhunt.wordpress.com/2014/08/28/deguello/
There’s a new paper out on the genetic prehistory of the Canadian Arctic. Basically, it says that existing Eskimos replaced a genetically different population less than 700 years ago, and that those earlier Paleo-Eskimos (Dorset culture) represent yet another separate migration from Asia (in addition to the PaleoIndians, the Na-Dene, and the Eskimo). They put this in such a nice way: “the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population.”

Which likely means that the neo-Eskimos killed off the Dorset people. Obviously they weren’t farmers, the usual suspects in replacement, but the new guys had a more sophisticated technology ( and probably greater numbers) , with bows, large skin boats, dog sleds, whale-hunting gear, etc. The neo-Eskimos have certainly done their share of fighting in recent historical times – they went at it hammer-and-tongs with various Amerindian tribes.

This is fairly obvious, so much so that even the New York Times and the Washington Post mentioned extermination by the newcomers as a possible explanation. There is no mention of that possibility in the original research article, but I’m sure that some of the authors were quite aware of it. What they said is probably influenced by the fear that saying anything negative, no matter how true, might cause the Eskimos to refuse cooperation in the future.

This pre-agricultural genocide makes you wonder just how often similar wipeouts may happened in the past. Maybe the Gravettians and Aurignacians weren’t the same people.
west-hunter  scitariat  discussion  sapiens  genetics  gene-flow  migration  history  antiquity  farmers-and-foragers  canada  usa  multi  archaeology  peace-violence  conquest-empire  war  kumbaya-kult  aDNA  traces 
may 2017 by nhaliday
Reconstruction | West Hunter
Since power descended through the male line, you don’t expect to see the same thing happen with autosomal genes. Genghis accounts for about 25% of Mongolia’s Y-chromosomes, but the general ancestry fraction attributable to him must be a lot lower. Still, what if the average Mongol today is 0.5% Genghis? Upon sequencing lots of typical contemporary Mongols, you would notice certain chromosomal segments showing up again and again: not just in one family but in the whole country, and in other parts of inner Asia as well. If you started keeping track of those segments, you would eventually be able to make a partial reconstruction of Genghis’s genome. It would be incomplete, since any given region of the genome might have missed being transmitted to any of his four legitimate sons (Jochi, Chagatai, Ogedei, and Tolui). They certainly didn’t carry his X-chromosome. You might be able to distinguish the autosomal genes of Genghis and his wife Borte by looking at descendants of his by-blows, if you could find them. Still, even if you managed to retrieve 75% of his genome, that’s not enough to make a clone. It would however, allow sure identification if we found his tomb.

And since he’s likely buried in permafrost, his DNA could be in good shape. Then we could clone him (assuming reasonable continuing progress in genetics) and of course some damn fool would. Will.
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april 2017 by nhaliday
The Ionian Mission | West Hunter
I have have had famous people ask me how the Ionian Greeks became so smart (in Classical times, natch). In Classical times, the Greeks – particularly the Ionian Greeks – gave everybody this impression – in everyday experience, and certainly in terms of production of outstanding intellects. Everybody thought so. Nobody said this about the Persians – and nobody said it about the Jews, who never said it about themselves.

It’s an interesting question: perhaps there was some process analogous to that which we have proposed as an explanation for the high intelligence of the Ashkenazi Jews. Or maybe something else happened – a different selective process, or maybe it was all cultural. It’s hard to know – the Greek Dark Ages, the long period of illiteracy after the fall of Mycenaean civilization, is poorly understood, certainly by me.

Suppose that your biological IQ capacity (in favorable conditions) is set by a few hundred or thousand SNPS, and that we have identified those SNPS. With luck, we might find enough skeletons with intact DNA to see if the Ionian Greeks really were smarter than the average bear, and how that changed over time.

More generally, we could see if civilization boosted or decreased IQ, in various situations. This could be a big part of the historical process – civilizations falling because average competence has dropped, science being born because the population is now ready for it…

I think we’ll be ready to try this in a year or two. The biggest problems will be political, since this approach would also predict results in existing populations – although that would probably not be very interesting, since we already know all those results.

The Ancient Greeks Weren’t All Geniuses: http://www.unz.com/akarlin/ancient-greeks-not-geniuses/
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april 2017 by nhaliday
The Vasconic Program | West Hunter
https://westhunt.wordpress.com/2013/10/09/the-old-breed-2/
My question is what local circumstances give the best chance for a substantial dollop of the formerly-common genotypes persisting for a long time – ideally, to the present day. Where do we find the blood of the Old Ones?

https://westhunt.wordpress.com/2014/07/24/washukanni/
Mitanni, controlling northern Syria and southeastern Anatolia, was a major player in the Bronze Age Near East from 1500 BC-1300 BC. They contended and negotiated with the Hittites and the Egyptian New Kingdom.

Most of the population seems to have spoken Hurrian, but there are traces of something very different in their ruling class. We have preserved diplomatic correspondence (cuneiform tablets last!) showing that the rulers of Mitanni swore by Mitra, Varuna, Indra, and Nasatya. There are other hints: names of the ruling class often make sense in Sanskrit. Kikkuli of Mitanni’s horse conditioning manual has some Indo-Aryan words (aika, tera, panza, satta). Etc. The semi-educated guess is that Indo-Aryans, as early charioteers, were hired by Mitanni as mercenaries and eventually grabbed the reins of power. After, of course, making a wrong turn at Albuquerque: North Syria is quite a ways from the known stomping grounds of the Indo-Aryans.

There’s likely an interesting story here, but we are missing almost all of it, because we have never found Washukanni, the Mitanni capital. If we did, we’d probably find lots of cuneiform tablets – as we have other capital cities of that era, such as Boğazköy.

Washukanni was probably somewhere in the Khabur triangle. Which brings me to the present, and possible near future: if we end up occupying that area, it’d be nice if we could manage a little digging on the side. We just need to start embedding archaeologists into the infantry.
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april 2017 by nhaliday
The Birth of Britain | West Hunter
Recent studies considering modern and ancient DNA show that about 25-40% of British ancestry is Anglo-Saxon, with a high in East Anglia and gradual decreasing as you move north and west. While the Britons of Roman times look like the Welsh.

Winston Churchill wrote about this, in The Birth of Britain, the first installment of his history of the English-speaking peoples. He mentions that place names in Sussex suggested total replacement, while the West Saxon legal code made provision for the rights of Welshmen.. But he didn’t know how much replacement had occurred. Still, he said “.. we may cherish the hope that somewhere a maiden’s cry for pity, the appear of beauty in distress, the lustful needs of an invading force,would create some bond between victor and vanquished. Thus the blood would be preserved, thus the rigours of subjugation would fade as generations passed away. The complete obliteration of an entire race is repulsive to the human mind. There should at least have been, in default of pity, a hearing for practical advantage or the natural temptations of sex.”

However, being repulsive doesn’t stop something from happening. This time, it didn’t. Perhaps Churchill’s ghost, or his ghost’s ghost, is pleased by this result.

Bell beakers – or, the birth of Britain: https://westhunt.wordpress.com/2017/05/17/bell-beakers-or-the-birth-of-britain/
It looks as if people in western Germany picked up these ideas – of course we have a radically imperfect idea of what those ideas were – and then settled Britain. Before all this Britain was populated by a kindof-Sardinian population (with some hunter-gatherer mixed in) that had probably came from Spain. Afterwards they were almost indistinguishable from people of that era living in the Netherlands, who had a lot of steppe ancestry. 93% replacement, minimum. Some Anglo-Saxon ancestry was added about 1400 years ago but A. they’re not very different from the Brits B. most British ancestry today still goes back to the Bell Beaker conquest.

https://gnxp.nofe.me/2003/05/27/british-genes/
https://gnxp.nofe.me/2006/07/18/celts-anglo-saxons-part-n/
https://gnxp.nofe.me/2006/07/19/celts-and-anglo-saxons-part-n-1/
https://gnxp.nofe.me/2006/07/23/celts-and-anglo-saxons-part-n-2/
https://gnxp.nofe.me/2006/09/22/blood-of-the-british/
https://gnxp.nofe.me/2007/02/03/blood-of-the-isles/
https://gnxp.nofe.me/2008/03/04/origins-of-the-british/
https://gnxp.nofe.me/2008/04/23/no-anglo-saxon-apartheid/
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march 2017 by nhaliday

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