(II A) Origin of Present-Day Europeans (and Especially Britons)

choi

, from Harvard Professor Reich's Viewpoints.

======================
In (I) Origin of Present-Day Europeans (and Especially Britons) -- dated Jan 22, 2022 -- I wrote: "Genome-wide data have revealed high proportions of Steppe-related ancestry in Beaker Complex-associated individuals from Germany and the Czech Republic, showing that they derived from mixtures of populations from the Steppe and the preceding Neolithic [Anatolian] farmers of Europe." Early on I had Iranian farmers, but returned to changed to the correct Anatolian farmers.

==================================
(2) This is a summary of the book:
David Reich, Who We Are and How We Got Here; Ancient DNAand the new science of the human past. Pantheon Boos (Penguin and Random House LLC), 2018.

Note:
• The book spent little time on East Asians because there was not much data at the time of publication: Chap 8 The Genomic Origins of East Asians, pp 187-206. Dr Reich conceded it. Therefore I will skip it.

The book also has a chapter for South Asia: Chap 6 The Collision That Formed India. I am interested in Sanskrit-speaking people, not the natives already there.
• I am not interested in Neanderthals or Denisovans, in part due to not sufficient numbers of reports on DNA.

(a1) Chap 4 Humanity's Ghosts, pp 77-98.

pp 94-96 (consecutive paragraphs; footnotes omitted): "Working with [Ron] Pinhasi[, a Canadian whose lab was built in 2017, at Vienna, Austria], we obtained ancient DNA from forty-four ancient Near Easterners across much of the geographic cradle of farming. The results revealed that around ten thousand years ago, at the time that farming was beginning to spread, the population structure of West Eurasia was far from the genetic monoculture we observe today. The farmers of the western mountains of Iran, who may have been the first to domesticate goats, were genetically directly derived from the hunter-gathers who preceded them [in the area]. Similarly, the first farmers of present-day Israel and Jordan [read: farmers 10,000 years ago at present-day Israel and Jordan] were descended largely descended from Natufian hunter-gatherers who preceded them. But these two populations were also very genetically very different from each other. We and another research group found that the degree of genetic differentiation between the first farmers of the western part of the Near East (the Fertile Crescent, including Anatolia and the Levant) and the first farmers of eastern part (Iran) was about as great as the differentiation between Europeans and East Asians today. In the Near East, the expansion of farming was accomplished not just by the movement of people, as happened [millennia latter, twice] in Europe, but also by the spread of common ideas across genetically very different groups.

"The high differentiation of human populations in the Near East ten thousands years ago was a specific instance of a broader pattern across the vast region of West Eurasia, documented by Iosif Lazaridis [in Reich's lab], who led the analysis. Analyzing our data, he found that about ten thousand years ago there were at least four major populations om West Eurasia -- the farmers of the Fertile Crescent, the farmers of of Iran, the hunter-gatherers of central and western Europe, and the hunter-gatherers of eastern Europe. All these populations differed from one another as much as Europeans differ from East Asians today. Scholars in trying to create ancestry-based racial classifications, had they
lived ten thousand years ago, would have categorized these groups as 'races,' even though none of these groups survives in unmixed form today.

"Spurred by the revolutionary technology of plant and animal domestication, which could support much higher population density than hunting and gathering, the farmers of Near East began migrating and mixing with their neighbors. But instead of one group displacing all the others and pushing them to extinction, as had occurred in some of the previous spreads of hunter-gatherers in Europe, in the Near East all the expanding groups contributed to later populations. The farmers in present-day Turkey expanded into Europe/ The farmers in present-day Israel and Jordan expanded into East Africa, and their genetic legacy is greatest in present-day Ethiopia. Farmers related to those in present-day Iran expanded into India as well as the steppe north of the Black and Caspian seas. They mixed with local populations there and established new economies based on herding that allowed the agricultural revolution to spread into parts of the world inhospitable to domesticated crops [that was then; in present-day Ukraine and even Russia can produce bumper crops]. The different food-producing populations also mixed with one another, a process that was accelerated by technological developments in the Bronze Age after around five thousand years ago. This means the high genetic substructure that had previously characterized West Eurasia collapsed into the present-day very low level of genetic differentiation by the Bronze Age. * * *

"The fusion of these highly different populations into today's West Eurasians is vividly evident in what might be considered the classic northern European look: blue eyes, light skin, and blond hair. Analysis of ancient DNA data shows that western European hunter-gatherers around eight thousand years ago had blue eyes but dark skin and dark hair, a combination that is rare today. The first farmers of Europe [descendants of Anatolia farmers] mostly had light skin but dark hair and brown eyes -- thus light skin in Europe largely owes its origins to migrating farmers. The earliest known sample of the classic European blond hair mutation is in an Ancient North Eurasian from the Lake Baikal region of eastern Siberia from seventeen thousand years ago. The hundreds of millions of copies of this mutation in central and western Europe today likely derive from a massive migration into the region of people bearing Ancient North Eurasian ancestry, an event that is related 0ie, talked about] in the next chapter.


Note: Quotation 3 states "a process that was accelerated by technological developments in the Bronze Age after around five thousand years ago."
(i) "The term has fallen into disuse in the English language[citation needed] and has been replaced by the term Middle East."  en.wikipedia.org for "Near East."
(ii) At first I thought that this "after" is not a preposition but an adverb. See
after (adv): "at a later or future time; afterwards  <Duke Frederick died soon after>"
https://www.lexico.com/definition/after
(iii) However, this pattern appeared several times in the 2018 book, and I soon concluded that Dr Reich meant something happened AFTER 5,000 years ago, not before.
(iv) Europeans and East Asians may look different. But both groups – indeed, the entire humanity – are Homo Sapiens, the same species. The truth is there is not much difference. In fact, humans and monkeys, even mice, share genes that are very identical at amino acid level. That explains why pig heart or kidney might work in humans indefinitely (once pig organs are humanized in terms of histocompatibility genes). Scientists do not know mouse genome dictates production of mouse, both the size and different in appearance. I wish to offer the perspectives. Again. The genetic differentiation (or difference) that quotation 2 talked about is SNPs.
(v) "The earliest known sample of the classic European blond hair mutation is in an Ancient North Eurasian from the Lake Baikal region of eastern Siberia from seventeen thousand years ago."
(A) Hanel A and Carlberg C, Skin Colour and Vitamin D: An Update. Experimental Dermatology, 29: 864 (July 3, 2020; review)
https://onlinelibrary.wiley.com/doi/10.1111/exd.14142

Quote:

"In this review, we challenge [but do not end once and for all] the hypothesis of skin lightening due to vitamin D by summarizing recent archeogenomic data on changes of skin, hair and eye colour in European populations within the past 10 000 years.

Please both view Figure 1 and read text underneath it.

"Although large genome-wide association studies highlighted skin colour as a highly polygenic trait, evidence for selection of pigmentation variants in present-day Europeans was found only for a limited number of large-effect variants, the top two of which turned out to be the loci of the genes SLC24A5 and SLC45A2. * * * The SNP rs1426654 within the SLC24A5 gene has the single largest effect on skin lightening of all gene variants identified to date.

"The Anatolian farmers had rather short body stature and predominantly brown eyes, which explains the key anthropomorphic traits of today's southern Europeans, in contrast to Yamnayas, who had a high body stature and settled preferentially in northern Europe. Moreover, these steppe pastoralists brought the horse, the wheel and Indo-European languages. Interestingly, ancient North Eurasian [ANE] derived populations, such as eastern hunter-gatherers and Yamnayas, carried the blond hair allele rs12821256 of the KITLG gene to Europe. Its first evidence was described in an 18 000 years old ancient North Eurasian west of Lake Baikal. * * *

• The "rs" stands for "Reference SNP cluster ID."
• sodium/potassium/calcium exchanger 5
https://en.wikipedia.org/wiki/So ... calcium_exchanger_5
("Sodium/potassium/calcium exchanger 5 (NCKX5), also known as solute carrier family 24 member 5 (SLC24A5), is a protein that in humans is encoded by the SLC24A5 gene * * * The NCKX5 protein is a member of the potassium-dependent sodium/calcium exchanger family")
• The name of a protein is typed as usual, whereas that of a gene, italic.
• membrane-associated transporter protein
https://en.wikipedia.org/wiki/Me ... transporter_protein
(MATP, also known as solute carrier family 45 member 2 (SLC45A2) )
• OCA2
https://en.wikipedia.org/wiki/OCA2
("is a protein that in humans is encoded by the oculocutaneous albinism II (OCA2) gene. * * * The exact function of protein P is unknown")
(B) Guenther CA (first author) * * * Kingsley D(avid)M (last author, of Stanford), A Molecular Basis for Classic Blond Hair Color in Europeans. Nature Genetics, 46: 748 (July 2014)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704868/
("KITLG encodes a secreted ligand for the receptor tyrosine kinase, KIT * * * Null mutations affecting Kitlg or Kit [in contrast to human where both proteins and genes are all upper case, mouse counterparts have the first letter capitalized but not the remaining letters] are lethal in mice * * * A non-coding SNP (rs12821256) located in a large intergenic region over 350 kb upstream of the KITLG transcription start site is significantly associated with blond hair color * * * The blond[-]associated A to G [G causes blondness] substitution at this position is prevalent in northern European populations but virtually absent in Africa and Asia")
• The presence of G reduces but does not eliminate lymphoid enhancer-binding factor (LEF) transcription factor's binding to this site -- and reducing transcription of KITLG. Kingsley's paper quantified the extent of reduction:
In vitro (human keratinocyte cell culture) and in vivo (mouse), the A to G change decreases KITLG expression by 22 and 21%, respectively -- a small but consistent reduction in activity.
• The KIT gene in humans was found to be similar in DNA sequence to that of a virus that infects and causes a sarcoma (a kind of cancer) in cats -- hence so named (kit, which is not an acronym).
(C) Is Hair Color Determined by Genetics?  Medline Plus, undated
https://medlineplus.gov/genetics/understanding/traits/haircolor/
("The best-studied hair-color gene in humans is called MC1R. This gene provides instructions for making a protein called the melanocortin 1 receptor, which is involved in the pathway that produces melanin. The melanocortin 1 receptor controls which type of melanin is produced by melanocytes. When the receptor is turned on (activated), it triggers a series of chemical reactions inside melanocytes that stimulate these cells to make eumelanin. If the receptor is not activated or is blocked, melanocytes make pheomelanin instead of eumelanin")
• melanocortin 1 receptor
https://en.wikipedia.org/wiki/Melanocortin_1_receptor
(acronym: MC1R; "binds to a class of pituitary peptide hormones known as the melanocortins, which include adrenocorticotropic hormone (ACTH) and the different forms of melanocyte-stimulating hormone (MSH). * * * MC1R is one of the key proteins involved in regulating mammalian skin and hair color. It is located on the plasma membrane of specialized cells known as melanocytes")
(D) So, how do you reconcile that at least two proteins (MC1R and KITLG) are implicated in blondness. Well, I do not, and will await future publications to clear things up. But see
Blonde on Blonder. 23andMe, Feb 3, 2015
https://blog.23andme.com/health-traits/blonde-on-blonder/
("23andMe scientists looking at the biology behind hair color found three genetic variants already known to be strongly associated with having golden locks among 23andMe customers with Northern European ancestry. The three variants are on or near the genes HERC2, KITLG and SLC24A4. * * * And these three genetic variants by no means account for all the genetic factors that influence hair color. But at least for people with Northern European ancestry they explain a lot. * * * While blond hair is most common in people of Northern European ancestry, it is also found in people without European ancestry. But the biology behind blond hair in those populations is different. For example, between five to ten percent of Solomon Islanders have blond hair that is caused by a single variant in the TYRP1 gene")
• At the bottom of this Web page are rs12821256 (around KITLG gene), rs1667394 (HERC2) and rs12896399 (SLC24A4).
• Kenny EE et al (Stanford Univ), Melanesians Blond Hair Is Caused by an Amino Acid Change in TYRP1. Science, 336: 554 (2012).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3481182/
(introduction: "Here, we focus on understanding the genetic basis of blond hair in the Solomon Islands, a population that breaks from the general trend of darker skin and hair pigmentation near the equator where there is higher UVR [ultraviolet radiation]. Strikingly, while individuals from the Solomon Islands and other locations in Oceania near the equator have both the darkest skin pigmentation outside of Africa, they also have the highest prevalence of blond hair (5–10%) outside of Europe" / result shows that DNA base change T --> C leads to change in amino acid from arginine to cysteine at amino acid position 93 of the protein tyrosinase-related protein 1 (TYRP1) )
• Melanocyte-specific (found only in melanocytes), TYRP1 belongs to the tyrosinase family.
(E) What about East Asians, some of whom are as white as Europeans and Americans? Well, no research is done. In fact, why some genes cause white skins -- all those mentioned so far -- are all unknown.

choi

(a2) The first three quotations (all observations are correct even today) are based on
Lazaridis I (first author) * * * Reich D (last author), Genomic Insights into the Origin of Farming in the Ancient Near East. Nature, 536: 419 (Aug 25, 2016).
https://www.nature.com/articles/nature19310
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003663/

Please read the entire Abstract carefully, as every word in it is supported by data presented: "We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE [pay attention to the time frame, as it is critical], from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

Conclusion: "By analysing genome-wide ancient DNA data from ancient individuals from the Levant, Anatolia, the southern Caucasus and Iran, we have provided a first glimpse of the demographic structure of the human populations that transitioned to farming. We reject the hypothesis that the spread of agriculture in the Near East [the conclusion is correct with respect to 'Near East,' but not to Europe (two different locations, though sitting side by side); the fact of the matter is peoples/farmers in Near East/Middle East stay put (to create Assyria and Babylonia, to name a couple), whereas farmers in Anatolia migrated to populate Europe] was achieved by the dispersal of a single farming population displacing the hunter-gatherers they encountered. Instead, the spread of ideas and farming technology moved faster than the spread of people, as we can determine from the fact that the population structure of the Near East was maintained throughout the transition to agriculture. * * *

Note:
(i) Iosif LAZARIDIS: Sheds light on the Genetic History of Europeans. Ellines.com, undated
https://www.ellines.com/en/achie ... story-of-europeans/
("He was born in Kavala, Greece, in 1976. In 1999 he graduated from the School of Electrical and Computer Engineering of the National Technical University of Athens (NTUA). He earned his master’s degree (2002) and received his Ph.D. (2006) in Information and Computer Science from the University of California-Irvine")

Hence he probably does not do bench work; Others (the workhorses) did, and Dr Lazaridis became the first first author. On the other hand, a postdoctoral fellow in Professor Reich's lab does work no different than a technician: grinding bones and extracting DNA whose sequencing is done by machines. Bones are generous gifts of various museums. Sometimes, I reflect on Dr Reich's contribution to science: It is there, but another scientist with data on ancient DNA (which is available to the public, once a paper is published) may well contribute the same.  
(ii) Natufian culture
https://en.wikipedia.org/wiki/Natufian_culture
(section 2 Discovery: British archaeologist Dorothy Garrod "suggested the name 'the Natufian culture,' after Wadi an-Natuf that ran close to Shuqba" cave near the town of Shuqba in West Bank close to Israeli border)
(A) English dictionary:
* wadi (n; etymology: Arabic): "valley"
https://en.wiktionary.org/wiki/wadi
(B) I am clueless about what "an" and "Natuf" mean, and can not find information online (probably searching in Arabic will fare better).
(iii) Actually the term "Basal Eurasian" was coined and posited by David Reich with little description other than it was a hypothetical ghost population that he imagined existed but did not know when, where or how present-day Asians (not much ancient DNA reported) are related to present-day Europeans in a phylogenetic tree. See Figure 2 in
Lazaridis I et al, Ancient Human Genomes Suggest Three Ancestral Populations for Present-Day Europeans. Nature, 513: 409 (Sept 18, 2014)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574/
(Fig 2's caption said, "Present-day samples [populations] are colored in blue [ovals], ancient in red, and reconstructed [read: hypothetical] ancestral populations in green."
• The acronyms used in Fig 2 were first described in Abstract: ANE = Ancient North Eurasians; WHG = West European Hunter-Gatherers; EEF = Early European Farmers [from Anatolia].
• YET, do not trip over by this term, because Reich himself, after using it twice (in 2014 and 2016 Nature papers), stops using it. And only four other research papers have used the term simce. Most importantly this 2014 Nature paper is all wrong.
• One of the four papers mentioned in the preceding sentence is interesting, though:
Almarri MA et al (from Wellcome Sanger Institute, in Cambridge, England), The Genomic History of the Middle East. Cell, 184: 4612 (Sept 2, 2021)
https://www.cell.com/cell/fulltext/S0092-8674(21)00839-4
("We found that the closest source of African ancestry for most populations in our dataset is Bantu Speakers from Kenya, in addition to contributions from Nilo-Saharan speakers from Ethiopia. We estimate that African admixture in the Middle East occurred within the last 2,000 years, with most populations showing signals of admixture around 500–1,000 years ago (Figure S1 [Supplemental 1]; Table S1), in agreement with previous studies (Hellenthal et al, 2014) * * * Lazaridis et al, 2016 proposed that a basal Eurasian population, with low-to-no Neanderthal ancestry, had contributed different proportions to ancient and modern Eurasians, reaching ∼50% in Neolithic Iranians and Natufians. Since Arabians have an excess of Natufian-like ancestry compared to elsewhere in the Middle East, we found they also carry an excess of basal Eurasian ancestry that will reduce their Neanderthal ancestry. In addition, most modern Middle Easterners carry African ancestry from recent admixture")

No need to read the rest of this paper. No wonder Americans do not consider Middle Easterners white.
(A) phylogenesis (n; etymology)
https://www.lexico.com/en/definition/phylogenesis

The English noun phylum
https://www.lexico.com/en/definition/phylum
shares the same root as phylo-.
(B) basal (phylogenetics)
https://en.wikipedia.org/wiki/Basal_(phylogenetics)
(section 2 Example: illustration (basal angiosperms) )
• clade (n; etymology)
https://www.lexico.com/definition/clade
• Until now I have not learned of the word "basal" in phylogenesis, which, however, is the same in plaint English. The basal clae in phylogenesis is "basal to." but IN PARALLEL TO (rather the spawning), later clade(s). In other words, the common, immediate ancestral group branched out first to create basal clade, and branched out later for other clades, extinct or extant.
• David Reich is a DNA guy, who once (in 2014) borrowed the concept and term "basal" from phylogenesis. He should abide by the established definition and use of that term. Instead, either due to ignorance or stubbornness, Reich meant, by "Basal Eurasian," the ancestral group of all future Europeans and Asians (extinct or extant). See Nature, 513: 409 (Fig 2( cited at the very beginning of Note (iii).
(C) For angiosperm, see flowering plant
https://en.wikipedia.org/wiki/Flowering_plant
, which you see just about every day everywhere. The English prefix angio- is from Ancient Greek noun neuter "angeion" that means vessels: Humans have blood and lymphatic vessels, and angiosperms have xylem (transport water and minerals from root up) and phloem
https://en.wikipedia.org/wiki/Phloem
(illustration; transport sucrose (comprised two molecules of glucose kubjed side by side) down)
(iv) "Between 10,000-9,000 BCE, humans began practicing agriculture in the Near East," specifically Fertile Crescent
https://en.wikipedia.org/wiki/Fertile_Crescent
(take notice of Anatolia and its location)
.
(v) "In order to overcome the obstacle of poor DNA preservation, we took advantage of two methodological developments. First, we sampled from the inner ear region of the petrous bone [first reported in 2014 by Pinhasi, as opposed to molars] that can yield up to ~100 times more endogenous DNA than other skeletal elements. Second, we used in-solution hybridization to enrich extracted DNA for about 1.2 million single nucleotide polymorphism (SNP) targets6,7, making efficient sequencing practical by filtering out microbial and non-informative human DNA."  (footnotes omitted).
Bones are destroyed, by grinding, during the process of DNA collection.

If one presses behind earlobe, midpoint is a cone-shaped mastoid (breast-like, from Ancient Greek noun masculine (yes, masculine) mastós, as opposed to Latin noun feminine mamma – both meaning breast). About 1 inch long right above mastoid, up and behind earlobe is a ridge, which is petrous (meaning stone) part of template bone. "houses in its [petrous] interior, the components of the inner ear." en,wikipedia.org for "petrous part of the temporal bone."
(vi) "The samples include Epipaleolithic Natufian hunter-gatherers from Raqefet Cave in the Levant (12,000-9,800 BCE) * * * and early farmers from Ganj Dareh in the Zagros mountains of western Iran (8,200-7,600 BCE).
(A) Figure 1(a) of the article in (a)(2) displayed the physical locations of the samples used in this article.
(B) Raqefet Cave
https://en.wikipedia.org/wiki/Raqefet_Cave
(map)
(C) Ganj Dareh
https://en.wikipedia.org/wiki/Ganj_Dareh
(Persian: تپه گنج دره)

• Persian (Farci)-English dictionary:
* دره (noun; romanization dare): "valley"
https://en.wiktionary.org/wiki/دره
* گنج (n; romanization ganj; from Middle Persian, from Old Persian): "treasure"
https://en.wiktionary.org/wiki/گنج
* تپه (n; romanization tappe; from Ottoman Turkish tepe): "hill"
https://en.wiktionary.org/wiki/تپه
(D) Persian grammar
https://en.wikipedia.org/wiki/Persian_grammar  
(one of "Indo-European languages. * * * Persian has a standard subject-object-verb (SOV) word order [as in Japanese] * * * Persian nouns and pronouns have no grammatical gender. * * * Adjectives typically follow the nouns they modify")
(E) "Arabic, Hebrew, Farsi [ie, Persian], Urdu, Sindhi and other ancient languages have a common denominator: they are languages written from right to left.": from the Web.  Sanskrit is written left to right.
(F) Zagros Mountains
https://en.wikipedia.org/wiki/Zagros_Mountains
(table: Elevation 4,409 m (14,465 ft) )
(vii) Talking about his results, Reich in this 2016 Nature paper stated, "A population without Neanderthal admixture, basal to other Eurasians, may have plausibly lived in Africa." That is, Basal Eurasians might live in Africa, but this was a pure speculation on his part (for he provided no data or citations, and is not an archeologist. I call this sentence to your attention merely to demonstrate Reich's status of mind.