archaics   31

Caught in the act | West Hunter
The fossil record is sparse. Let me try to explain that. We have at most a few hundred Neanderthal skeletons, most in pretty poor shape. How many Neanderthals ever lived? I think their population varied in size quite a bit – lowest during glacial maxima, probably highest in interglacials. Their degree of genetic diversity suggests an effective population size of ~1000, but that would be dominated by the low points (harmonic average). So let’s say 50,000 on average, over their whole range (Europe, central Asia, the Levant, perhaps more). Say they were around for 300,000 years, with a generation time of 30 years – 10,000 generations, for a total of five hundred million Neanderthals over all time. So one in a million Neanderthals ends up in a museum: one every 20 generations. Low time resolution!

So if anatomically modern humans rapidly wiped out Neanderthals, we probably couldn’t tell. In much the same way, you don’t expect to find the remains of many dinosaurs killed by the Cretaceous meteor impact (at most one millionth of one generation, right?), or of Columbian mammoths killed by a wave of Amerindian hunters. Sometimes invaders leave a bigger footprint: a bunch of cities burning down with no rebuilding tells you something. But even when you know that population A completely replaced population B, it can be hard to prove that just how it happened. After all, population A could have all committed suicide just before B showed up. Stranger things have happened – but not often.
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september 2017 by nhaliday
Genetic Architectures | West Hunter
Dairy cattle eventually graduate to McDonalds, so there is some interest in the genetics of beef production in dairy breeds. There is course more interest in the genetics of beef production in beef breeds of cattle.

Usually you don’t find a single allele that makes a lot of difference, but in some beef breeds, there are myostatin mutations that result in a ridiculous-looking, ‘double-muscled’ beast. Homozygosity for myostatin mutations causes difficulties in birth, so it takes really strong selection for beef production to make a myostatin null common. I don’t think you ever see this in dairy breeds.

But, as it turns out, there is a deletion that is pretty common in some dairy breeds that significantly increases milk production while killing homozygotes before birth.

Breeds under weaker selection for single traits, your typical cow of the past, probably have neither.

The point is that the genetic architecture of a quantitative trait does not have to be the same in different populations of the same species. For example, I have the impression that height is not as highly polygenic in Pygmies as it is most other human populations. There’s a particular region on chromosome 3 that seems to influence height- you don’t see such a concentration in Europeans.
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august 2017 by nhaliday
Ethiopian altitude adaptations | West Hunter
I said a while ago that the altitude adaptations in Tibet were too damn good, more effective than those seen in Andean Amerindians, and so must have originated in a population that lived at high altitude for a long time.  This seems to be the case.

The same must be true of Ethiopia. Their altitude adaptations also work well. There is a genetic component in Ethiopia that seems to correspond to the original hunter-gatherers, and the altitude alleles must have originated in that population, not the later components that look like East Africans or Levantines.

In both cases, there’s a fair chance that the ultimate origin could be some archaic group.

https://westhunt.wordpress.com/2014/02/27/ethiopian-adaptations/#comment-22644
You know, I don’t think that is the problem.

I’ve paid attention to the Falasha story for a long time. I think it’s funny as hell.

...

The Falasha are (best guess based on recent genetic studies) locals who converted to an old-fashioned, non-rabbinic Judaism. Genetically pretty much like other highland Ethiopians, definitely so in mtDNA.
On the other hand, the non-African component is probably similar to what we see in the Levant today, as with other Ethiopian highlanders speaking Semitic languages.
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august 2017 by nhaliday
Information Processing: Genetic variation in Han Chinese population
Largest component of genetic variation is a N-S cline (phenotypic N-S gradient discussed here). Variance accounted for by second (E-W) PC vector is much smaller and the Han population is fairly homogeneous in genetic terms: ...while we revealed East-to-West structure among the Han Chinese, the signal is relatively weak and very little structure is discernible beyond the second PC (p.24).

Neandertal ancestry does not vary significantly across provinces, consistent with admixture prior to the dispersal of modern Han Chinese.

http://infoproc.blogspot.com/2014/01/china-1793.html
My fellow officers informed me, that while the negotiation was going on, the ships were constantly crowded with all kinds of refreshments, and that when they were first boarded by the Chinese they received every attention from them that could be shown; and that the presents received by the different officers belonging to the embassy, were of immense value. That the natives of this part of China were of different complexions and manners from those in and near Canton; their colour being nearly white; and in their manners were much more free and candid; and that they were of a larger stature, and more athletic than the southern Chinese—they were much more sociable, and not so particular respecting their women being seen by the men. And were even fond of receiving the officers into their houses, when on shore, provided it could be done without the knowledge of the mandarins.

http://infoproc.blogspot.com/2014/06/large-scale-psychological-differences.html
The study below discusses a psychological/cognitive/personality gradient between N and S China, possibly driven by a history of wheat vs rice cultivation.

https://en.wikipedia.org/wiki/Northern_and_southern_China
http://shanghaiist.com/2015/07/01/average-heights-men-women.php
https://www.quora.com/Why-are-Northern-Chinese-people-generally-taller-than-Southern-Chinese

https://gnxp.nofe.me/2017/08/01/the-great-genetic-map-of-china/
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july 2017 by nhaliday
The story of modern human origins just got more complicated
https://www.gnxp.com/WordPress/2017/06/06/a-reticulation-pulse-expansion-of-modern-human-genetic-variation/
https://www.gnxp.com/WordPress/2017/06/11/the-search-for-eden-opens-up-new-vistas/
https://www.gnxp.com/WordPress/2017/08/26/northeast-africa/

https://www.gnxp.com/WordPress/2018/01/25/out-of-africa-to-out-of-eden-well-perhaps-not-yet/
https://www.gnxp.com/WordPress/2018/01/28/none-dare-call-it-multiregionalism/

The slow death of Out of Africa: http://dienekes.blogspot.com/2018/04/the-slow-death-of-out-of-africa.html
The significance of the discovery of modern humans in Arabia >85kya is that it provides a second spot (other than Israel) were modern humans existed outside Africa long before the alleged 60kya blitz out of the continent. We now have modern humans outside Africa in roughly two locations (Israel and Arabia), and three time slices (~175-85kya) in Misliya, Shkul/Qafzeh, and Al Wusta-1. It is no longer tenable to claim that these modern humans "died out" to make way for the alleged 60kya OoA event.
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june 2017 by nhaliday
Call Him George | West Hunter
I hear that Rasmus Nielsen (speaking at SMBE 2014) has evidence that Tibetans picked up some of their altitude adaptation (EPAS1) from Denisovans.

Who could have imagined that?

https://westhunt.wordpress.com/2012/02/17/islands-in-the-sky/
There are three major high-altitude regions inhabited by humans: highland Ethiopia, Tibet, and the Andean altiplano. In each of these three cases, the locals have adapted in various ways to high altitude – physiological adaptations, as well as cultural. To make it even clearer, those physiological changes are, to a large extent, a consequence of natural selection, rather than individual acclimatization.

https://westhunt.wordpress.com/2013/05/16/tibet/
The Tibetans deal with high altitude much more effectively than the Amerindians of the Altiplano. You have to think that they’ve lived there longer, been exposed to those selective pressures longer – and that’s quite feasible. Anatomically modern humans have been in Asia much longer than in the Americas, and it’s even possible that they picked up some adaptive altitude-adaptation genes from archaic humans that had been there for hundreds of thousands of years.

There’s another interesting point: the hunter-gatherers of Tibet appear to account for a lot of Tibetan ancestry, probably most of it, rather than than being almost entirely replaced by a wave of neolithic agriculturalists, which is the more common pattern. They had a trump card – altitude adaptation. A story like that which has left Bolivia mostly Amerindian.

Modern Eugenics: https://westhunt.wordpress.com/2013/11/13/modern-eugenics/
Recent work in genetics has made it clear that Tibetans, Andean Indians, and Ethiopians adapted independently to high-altitude living. It’s also clear that the Tibetan adaptations are more effective those in Andean Indians. Infant survival is better in Tibet, where babies average about half a pound heavier, and the suite of Tibetan adaptations doesn’t seem to fail with increasing age, while a significant fraction of Andean Indians develop chronic mountain sickness in later life. The Andean pattern look something like an exaggerated acclimatization response, while the Tibetan pattern is more like that seen in mammalian species have lived at high altitude for a long time.

...

The obvious solution to these apparently permanent problems in Bolivia and Peru is a dose of Tibetan genes. Since Tibetan alleles are more effective, they must confer higher fitness, and so their frequencies should gradually increase with time. This doesn’t mean that Bolivians would turn Tibetan overall – the change would only happen in those genes for which the Tibetan version was more efficient. It wouldn’t take all that high a dose: in fact, if you’re not in a hurry, just a few tens of Tibetans could transmit enough copies of the key alleles to do the job, although admittedly you’d have to wait a few thousand years to complete the process.

Logically, the easiest way to do this would be to encourage some young Tibetan men to immigrate to the Andes. Clearly, men can be more effective at this than women. We could pay them to donate to the local sperm banks. We could subsidize the process, _giving cash rewards to the mothers of part-Tibetan kids, a la the Howard Foundation_ [lmao]. We could give our heros Corvettes. Considering the general level of discontent in Tibet, it might not be too hard to recruit young men for this kind of work.

The project would take longer than the usual NIH time horizon, so probably the best approach is to find some wealthy sponsor. You could get a sure-fire version of this program going, one big enough to make ultimate success a racing certainty, for under a million bucks. The backer would never see the end result, but so what? When we build, let us think that we build forever.

https://westhunt.wordpress.com/2014/08/07/powerful-stuff/
I was thinking again about that Denisovan allele of EPAS1 that plays a big role in Tibetan altitude adaptation. Considering modern humans, it has only been found in Tibetans (high frequency) and in the Chinese (couple of percent). The preferred model in the paper is that it entered the common ancestors of Tibetans and Han, rising to high frequency among the Tibetans because of its advantage. I doubt this: the authors are clinging to a claim of a recent split in a previous publication of theirs – but the idea that the modern Tibetans are a fusion of a Han-like population with a long-established group of Tibetan hunter-gatherers seems more likely to me. So the few copies of the high-altitude EPAS1 allele among the Chinese are probably a result of recent gene flow, possibly from the Tibetan empire (618-841) that controlled parts of China, or from ethnic Tibetans identifying as Chinese.

This allele has some pretty powerful effects on the hypoxia response, which is there for a reason. The usual evolutionary rule is that change is bad: even though the Denisovan allele confers a big advantage at high altitude, the odds are that it is disadvantageous at low altitude. This would explain why it is rare in China and apparently unknown in Japan. This would also explain why it never made it to the Andes – even though there might have been a copy or two in the long-ago East Asian ancestors of the Amerindians, who have a bit of Denisovan admixture admixture (at least, I think they do – interesting if that isn’t the case) , it would most likely have been lost in Beringia. Along the same lines, altitude adaptations probably never managed to travel from Ethiopia to Tibet, which is why they have different approaches to altitude adaptation today.

It is therefore no surprise that this EPAS1 allele does not exist in Melanesians, even though they have 25 times as much Denisovan ancestry as mainland East Asians.

https://westhunt.wordpress.com/2016/12/11/tibetan-mastiff/
The Tibetan Mastiff can take high altitude better than generic dogs, or so breedists would like you to think. Some of the genetics changes are similar to those seen in human Tibetans – regulatory changes in EPAS1, for example. Domesticated dogs haven’t lived in Tibet all that long – but wolves have. The Tibetan Mastiff picked up some of those useful variants from local wolves, even though the amount of admixture wasn’t large. Adaptive introgression, just as Tibetans seem to have acquired their high-altitude version of EPAS1 from Denisovans.

Andean Indians didn’t have any archaic humans around to steal adaptations from. They have had to develop their own altitude adaptations (in a relatively short time), and they aren’t as effective as the Tibetan adaptations.

Naturally you are now worrying about sad Inca puppies – did they suffer from hypoxia? There are canids in South America, like the maned wolf and the bush dog, but they are probably too divergent to be able to hybridize with dogs. The chromosomes are different, so pre-Columbian dogs probably couldn’t acquire their alleles. Moreover, the dogs of the Amerindians seem to have done poorly in competition with Eurasian dogs: I know of only a few breeds [the Carolina Dog, for example] that are known to have significant pre-Columbian ancestry. Perhaps Amerindian dogs were also scythed down by Eurasian diseases.
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may 2017 by nhaliday
Homo sapiens - Wikipedia
The time frame for the evolution of the genus Homo out of the chimpanzee–human last common ancestor is roughly 10 to 2 million years ago, that of H. sapiens out of Homo erectus roughly 1.8 to 0.2 million years ago.

Schematic representation of the emergence of H. sapiens from earlier species of Homo. The horizontal axis represents geographic location; the vertical axis represents time in millions of years ago. Blue areas denote the presence of a certain species at a given time and place.

https://en.wikipedia.org/wiki/Archaic_human_admixture_with_modern_humans
On the basis of linkage disequilibrium patterns, a recent admixture event is likewise confirmed by the data.[7] From the extent of linkage disequilibrium, it was estimated that the last Neanderthal gene flow into early ancestors of Europeans occurred 47,000–65,000 years BP.[7] In conjunction with archaeological and fossil evidence, the gene flow is thought likely to have occurred somewhere in Western Eurasia, possibly the Middle East.[7] Through another approach—using one genome each of a Neanderthal, Eurasian, African, and chimpanzee (outgroup), and dividing it into non-recombining short sequence blocks—to estimate genome-wide maximum-likelihood under different models, an ancient population sub-structure in Africa was firmly ruled out and a Neanderthal admixture event was confirmed.[4]

...

Recent studies show a higher Neanderthal admixture in East Asians than in Europeans,[5][9][10][11][12] which is estimated to be about 20% more introgression into East Asians.[5][9][12] This could possibly be explained by the occurrence of further admixture events in the early ancestors of East Asians after the separation of Europeans and East Asians,[5][9][10][12] dilution of Neanderthal ancestry in Europeans by populations with low Neanderthal ancestry from later migrations,[9][12] or natural selection that may have been relatively lower in East Asians than in Europeans.[11][12] Studies indicate that a reduced efficacy of purifying selection against Neanderthal alleles in East Asians could not account for the greater proportion of Neanderthal ancestry of East Asians, thus favoring more-complex models involving additional pulses of Neanderthal introgression into East Asians.[13][14] It has also been observed that there's a small but significant variation of Neanderthal admixture rates within European populations, but no significant variation within East Asian populations.[5]
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april 2017 by nhaliday
Bloggingheads.tv: Gregory Cochran (The 10,000 Year Explosion) and Razib Khan (Unz Foundation, Gene Expression)
http://bloggingheads.tv/videos/1999
one interesting tidbit: doesn't think Homo sapiens smart enough for agriculture during previous interglacial period
https://westhunt.wordpress.com/2014/06/04/the-time-before/
Although we’re still in an ice age, we are currently in an interglacial period. That’s a good thing, since glacial periods are truly unpleasant – dry, cold, low biological productivity, high variability. Low CO2 concentrations made plants more susceptible to drought. Peter Richerson and Robert Boyd have suggested that the development of agriculture was impossible in glacial periods, due to these factors.

There was an earlier interglacial period that began about 130,000 years ago and ended about 114,000 years ago. It was a bit warmer than the current interglacial (the Holocene).

The most interesting events in the Eemian are those that didn’t happen. In the Holocene, humans developed agriculture, which led to all kinds of interesting trouble. They did it more than once, possibly as many as seven times independently. Back in the Eeemian, nichevo. Neanderthals moved father north as the glaciers melted, AMH moved up into the Middle East, but nobody did much of anything new. Populations likely increased, as habitable area expanded and biological productivity went up, but without any obvious consequences. Anatomically modern humans weren’t yet up to displacing archaic groups like the Neanderthals.

So, it is fair to say that everybody back then, including AMH, lacked capabilities that some later humans had. We could, if we wished, call these new abilities ‘behavioral modernity’.

The Bushmen are the most divergent of all human populations, and probably split off earliest. They are farther from the Bantu (in genetic distance) than the French or Chinese are.

According to some models, this split (between the Bushmen and other populations of sub-Saharan Africa) occurred more than 100,000 years ago. Recent direct measurements of mutations show much lower rates than previously thought, which tends to place such splits even farther back in time.

The question is whether they split off before the development of practical behavioral modernity.

https://westhunt.wordpress.com/2016/04/08/the-long-count/
They are anatomically modern: they have chins, etc. Behaviorally modern? There have been only a few attempts to measure their intelligence: what has been done indicates that they have very low IQs. They definitely talk, tell stories, sing songs: does that imply that they could, given the right environment, have developed the Antikythera mechanism or a clipper ship?

This means that language is older than some had thought, a good deal older. It also means that people with language are quite capable of going a quarter of a million years without generating much technological advance – without developing the ability to push aside archaic humans, for example. Of course, people with Williams syndrome have language, and you can’t send them into the kitchen and rely on them to bring back a fork. Is the sophistication of Bushman language – this means the concepts they can and do convey, not the complexity of the grammar – comparable with that of other populations? I don’t know. As far as I can see, one of the major goals of modern anthropology is to make sure that nobody knows. Or that they know things that aren’t so.

...

Some have suggested that the key to technological development is higher population: that produces more intellects past a high threshold, sure. I don’t think that’s the main factor. Eskimos have a pretty advanced technology, but there were never very many of them. On the other hand, they have the highest IQ of any existing hunter-gatherer population: that’s got to help. Populations must have gone up the Eemian, the previous interglacial period, but nothing much got invented back then. It would seem that agriculture would have been possible in the Eemian, but as far as we know it didn’t happen. Except for Valusia of course. With AMH going back at least 300,000 years, we have to start thinking about even earlier interglacial peiods, like Mindel-Riss (424-374 k years ago)

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

https://westhunt.wordpress.com/2017/08/28/same-old/
We now know ( from ancient DNA) that Bushmen split off from the rest of humanity (or we from them) at least a quarter of a million years ago. Generally, when you see a complex trait in sister groups, you can conclude that it existed in the common ancestor. Since both Bushmen and (everybody else) have complex language, one can conclude that complex language existed at least a quarter million years ago, in our common ancestor. You should also suspect that unique features of Bushmen language, namely those clicks, are not necessarily superficial: there has been time enough for real, baked-in, biologically rooted language differences to evolve. It also shows that having complex language isn’t enough, in itself, to generate anything very interesting. Cf Williams syndrome. Certainly technological change was very slow back then. Interglacial periods came and went without AMH displacing archaics in Eurasia or developing agriculture.

Next, the ability to generate rapid cultural change, invent lots of stuff, improvise effective bullshit didn’t exist in the common ancestor of extant humanity, since change was very slow back then.

Therefore it is not necessarily the case that every group has it today, or has it to the same extent. Psychic unity of mankind is unlikely. It’s also denied by every measurement ever made, but I guess invoking data, or your lying eyes, would be cheating.

https://westhunt.wordpress.com/2017/08/28/bushmen-palate/
“it has been observed by several researchers that the Khoisan palate ends to lack a prominent alveolar ridge.”

https://westhunt.wordpress.com/2013/02/17/unchanging-essence/
John Shea is a professor of anthropology at Stony Brook, specializing in ancient archaeology. He’s been making the argument that ‘behavioral modernity’ is a flawed concept, which it is. Naturally, he wants to replace it with something even worse. Not only are all existing human populations intellectually equal, as most anthropologists affirm – all are ‘behaviorally modern’ – all past populations of anatomically modern humans were too! The idea that our ancestors circa 150,000 B.C. might not be quite as sharp as people today is just like the now-discredited concept of race. And you know, he’s right. They’re both perfectly natural consequences of neodarwinism.

Behavioral modernity is a silly concept. As he says, it’s a typological concept: hominids are either behaviorally modern or they’re not. Now why would this make sense? Surely people vary in smarts, for example: it’s silly to say that they are either smart or not smart. We can usefully make much finer distinctions. We could think in terms of distributions – we might say that you score in the top quarter of intelligence for your population. We could analyze smarts in terms of thresholds: what is the most complex task that a given individual can perform? What fraction of the population can perform tasks of that complexity or greater? Etc. That would be a more reasonable way of looking at smarts, and this is of course what psychometrics does.

It’s also a group property. If even a few members of a population do something that anthropologists consider a sign of behavioral modernity – like making beads – everyone in that population must be behaviorally modern. By the the same argument, if anyone can reach the top shelf, we are all tall.

The notion of behavioral modernity has two roots. The first is that if you go back far enough, it’s obvious that our distant ancestors were pretty dim. Look at Oldowan tools – they’re not much more than broken rocks. And they stayed that way for a million years – change was inhumanly slow back then. That’s evidence. The second is not. Anthropologists want to say that all living populations are intellectually equal – which is not what the psychometric evidence shows. Or what population differences in brain size suggest. So they conjured up a quality – behavioral modernity – that all living people possess, but that homo erectus did not, rather than talk about quantitative differences.
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april 2017 by nhaliday
Tibetan Plateau Discovery Shows Humans May Be Tougher Than We Thought - Scientific American
The first humans venturing onto the Tibetan Plateau, often called the “roof of the world,” faced one of the most brutal environments our species can endure. At an average elevation of over 4,500 meters, it is a cold and arid place with half the oxygen present at sea level. Science has long held that humans did not set foot in this alien place until 15,000 years ago, as suggested by archaeological evidence of the earliest known settlement on the northeastern fringe of the plateau 3,000 meters above sea level. But now new genetic data indicate this may have occurred much earlier—possibly as far back as the last ice age, 62,000 years ago.
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december 2016 by nhaliday

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