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A genetic map of the world – Gene Expression
The above map is from a new preprint on the patterns of genetic variation as a function of geography for humans, Genetic landscapes reveal how human genetic diversity aligns with geography. The authors assemble an incredibly large dataset to generate these figures. The orange zones are “troughs” of gene flow. Basically barriers to gene flow.  It is no great surprise that so many of the barriers correlate with rivers, mountains, and deserts. But the aim of this sort of work seems to be to make precise and quantitative intuitions which are normally expressed verbally.
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december 2017 by nhaliday
Ancient Admixture in Human History
- Patterson, Reich et al., 2012
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean “Iceman.”
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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
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
And your little dog, too! | West Hunter
It sure looks as if we’re talking near-complete replacement – which means that the historical process involved does not look much like a peaceful, diffusion-style range expansion.  Perhaps more like the Death Song of Ragnar Lodbrok, which abounds in phrases like this: “Where the swords were whining while they sundered helmets”

Interestingly, there is a very similar  pattern in canine mtDNA.  Today Europeans dogs fall into four haplotypes: A (70%), B(16%), C (6%), and D(8%).  But back in the day, it seems that the overwhelming majority of dogs (88%)  were type C,  12% were in group A, while B and D have not been detected at all.

The ancestors of today’s Europeans didn’t fool around.
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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
Caste system in India - Wikipedia
A recent series of research papers, by Reich et al. (2009), Metspalu et al. (2011), and Moorjani et al. (2013), make clear that India was peopled by two distinct groups who split genetically ca. 50,000 years ago,[81][82] which they called "Ancestral North Indians" (ANI) and "Ancestral South Indians" (ASI) respectively.[note 1] They found that the ANI genes are close to those of Middle Easterners, Central Asians and Europeans whereas the ASI genes are dissimilar to all other known populations outside India.[note 2][note 3] These two distinct groups, which had split ca. 50,000 years ago, formed the basis for the present population of India.[83]

According to Moorjani et al. these two groups mixed between 4,200 and 1,900 years ago (2200 BCE-100 CE), whereafter a shift to endogamy took place.[84] David Reich stated, "Prior to 4,200 years ago, there were unmixed groups in India. Sometime between 1,900 to 4,200 years ago, profound, pervasive convulsive mixture occurred, affecting every Indo-European and Dravidian group in India without exception.".[85] Following this mixture,

Strong endogamy must have applied since then (average gene flow less than 1 in 30 per generation) to prevent the genetic signatures of founder events from being erased by gene flow. Some historians have argued that "caste" in modern India is an "invention" of colonialism in the sense that it became more rigid under colonial rule. However, our results suggest that many current distinctions among groups are ancient and that strong endogamy must have shaped marriage patterns in India for thousands of years.[81]

Moorjani et al. discerned two waves of admixture in this period, with northern India showing later dates of admixture.[86] GaneshPrasad et al. (2013) studied "12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India." According to this study, southern India was already socially stratified 4,000 to 6,000 years ago, which is best explained by "the emergence of agricultural technology in South Asia." The study concludes that "The social stratification (in Tamil Nadu) was established 4,000 to 6,000 years ago and there was little admixture during the last 3,000 years, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area."[87]

https://en.wikipedia.org/wiki/Wikipedia:Genetic_research_on_the_origins_of_India%27s_population

http://www.nytimes.com/2010/09/11/world/asia/11caste.html
A crucial factor is the collapse of the caste system over the last half century, a factor that undergirds many of the other reasons that the south has prospered — more stable governments, better infrastructure and a geographic position that gives it closer connections to the global economy.

“The breakdown of caste hierarchy has broken the traditional links between caste and profession, and released enormous entrepreneurial energies in the south,” said Ashutosh Varshney, a professor at Brown University who has studied the role of caste in southern India’s development. This breakdown, he said, goes a long way to explaining “why the south has taken such a lead over the north in the last three decades.”

http://www.livemint.com/Opinion/FLn6TiQPArdQZUN9LE2ZsM/The-impact-of-caste-on-economic-mobility-in-India.html
Caste Is Stunting All of India’s Children: http://foreignpolicy.com/2017/09/15/caste-is-stunting-all-of-indias-children/
Fears of impurity continue to steer Indians away from toilets — and towards deadly fecal germs.

https://twitter.com/MWStory/status/895580461879107584
https://archive.is/AsTwB
These Indian govt funded ads to encourage the wealthy but declining Parsi population to reproduce are quite extraordinary

http://marginalrevolution.com/marginalrevolution/2017/12/india-marriage-markets-everything.html
India’s government has expanded a scheme offering payment incentives to Hindus who marry members of the country’s poorest and most oppressed caste, the Dalits.
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june 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
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

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