January 1, 2017

Chad's Eurasian genetic input similar to that in Ethiopia

Quickies

Marc Haber et al. Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations. AJHG 2016. Open accessLINK [doi:10.1016/j.ajhg.2016.10.012]

Summary

Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.

Worth a read no doubt but careful, careful, careful with their chronological guesstimates. Their starting point is the assumption (once and again demonstrated all kinds of WRONG) of:

Eurasians and Africans diverged around 60,000–80,000 ya and subsequently had different patterns of population-size changes: in particular, compared with Africans, the Eurasian population experienced a sharp decrease in size ∼60,000 ya.

So add around 65-70% (x1.7) to all dates, else you are bound to fall in the pit of molecular-clock-o-logical self-complacent pseudoscience. So where it reads c. 6-7 Ka for the first migration (R1b-related), it should be 10,000 years ago (which is the actual dating of Afroasiatic expansion by most accounts, with origin not exactly in "Eurasia" but rather in or near Sudan, where those Eurasian lineages, R1b and J1, had since long before most likely), and when they say 3 Ka ago, it's probably 5000 years ago, within the context of Neolithic inflows possibly: 3000 years ago was already well into Ancient Egypt and peoples just did not cross it without proper paperwork anymore, actually 3000 years ago is the Bronze Age collapse and Egypt, Lower Egypt specifically, fell to Africans, to Libyans and other Berbers known as Meshwesh (Amazigh, probably from modern Tunisia) to be precise.

Dr. Haber: time to update your clock, it just doesn't work, and you are confusing people to no avail.

13 comments:

  1. Hello

    Nice read, I always wondered about the east African case.so now chad is similar to it, anyway, I want to confirm one thing , when said "Egypt, Lower Egypt specifically, fell to Africans, to Libyans and other Berbers known as Meshwesh (Amazigh, probably from modern Tunisia) to be precise."

    do you mean by African , E -v22 , E-v12 people?

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    1. I think I was talking about R1b-V88, which is what the paper is about.

      I'm assuming Egypt as stepping stone because it's the most natural path to Sudan but it might also have arrived via the Red Sea, I guess.

      This would have happened, in my model, after the Afroasiatic expansion northwards, which I associate with Mesolithic or late Upper Paleolithic flows well documented archaeologically from Sudan to the North (and Northwest and, via Egypt, to Palestine). This Afroasiatic (and possibly also Nubian/Eastern Sudanic) flow northwards of the Mesolithic is clearly associated to E1b-M78 particularly, which clearly follows that route in its branching pattern on the map, and has been recently detected as very dominant in Natufian samples (Palestinian Mesolithic).

      So we have first that Northwards expansion process in the Mesolithic and later some important backflow from Neolithic West Asia, which would have carried R1b to Sudan and from there westward to the Lake Chad area.

      That's my interpretation but feel free to polish, expand, develop, correct as need be, always according to whatever facts research puts at our disposal.

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  2. So what are the sound evidences for r-v88 having origins in near east or southern Europe.

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    1. I wouldn't use the word "sound" but there is evidence or at least strong indications.

      First of all CT > F > IJK > K > K2 > P > P1 > R > R1 > R1b all happened in Asia, I'd dare say that in the southern regions or near the Indian Ocean arch of this continent. This is sorta obvious but just in case, so we begin with R1b most likely coalescing in West Asia, I hope we can agree with that much.

      Then consider the data discussed at the update here: http://leherensuge.blogspot.com/2010/01/african-r1b-is-distinct-single.html

      "... it is most interesting that, while the new R1b1a (V88) is most frequent in Central Africa (and secondarily North Africa, specially among Siwa Berbers, Egypt), two out of four basal sublineages are exclusively found in Southern Europe."

      I must warn that I was considering R1b-V88* as a single basal branch, if it can be shown that it is made up of various basal branches, then things would change. The question is that there is a strong basal diversity in the European Mediterranean, notably in Sardinia-Corsica (M18) and mainland Italy (V35).

      And later, chewing on the previous, I wrote this: http://leherensuge.blogspot.com/2010/01/r1b1-origin-italy-or-west-asia.html

      Quoting myself now:

      "... the region where R1b1-P25 has highest basal diversity (by haplogroups) are Italy and West Asia. Both regions have R1b1a, R1b1b and some other R1b1* (3/1173=0.25% in Italy and 1/328=0.3% in West Asia)".

      ...

      "The Italian R1b1* seems to belong (by haplotype) to two different subclades, what makes Italy provisionally a good candidate for the origin of R1b1. However notice that the Italian sample is much larger than the West Asian one, almost in direct proportion to the number of R1b1* individuals found.

      "Italy (incl. Corsica and Sardinia) also has high R1b1a diversity (by subhaplogroups: 2/4 basal sublineages, but lacks R1b1a*). This would suggest that the origin of R1b1a actually lays towards Africa, where basal diversity seems somewhat higher".

      So my (soft) theory then was (haven't revised it in all these years) that R1b-P25 ("R1b1" in the nomenclature of the time) originated in the Italy-Levant arch and that R1b-V88 ("R1b1a") may have originated closer to Africa, i.e. in the Levant (I'm excluding Tunisia-Italy sea crossings because archaeology and in general genetics do not support them until much later times).

      Do you have anything more elaborate (newer data maybe?) that would make me change my mind?

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    2. PS- Also the Sardinian R1b-V88 is concentrated in the interior (Gallura, rel. Basque gailurra = summit), the area most conservative genetically, where we expect (and do find) greater concentration of Neolithic lineages.

      PS2- Notice however that I do suspect that Basque/Vasconic is related to Nubian languages and that, while I understand that there is strong evidence for Nubian genetic influence in the Levant prior to the Neolithic (later influencing Europe via the Neolithic), I do not fully understand the possible backflow interactions from the Levant to the Nile, which seem to be backed by some genetic elements like R1b (strong also in Sudan).

      The most parsimonious scenario for me would be that R1b migrated to Sudan in the Neolithic (or earlier???) and from there it spread eastward to the Eastern Chadic region, along with Afroasiatic (Chadic) languages.

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    3. PS3- Sadly Sudan's R1b sublineages are not studied yet as far as I know.

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  3. "(Gallura, rel. Basque gailurra = summit)"

    Hausa [West Chadic]: ḳ̣ṓlṓlúwā́ ['summit, top (esp. of a rock)']

    Source: http://starling.rinet.ru/cgi-bin/main.cgi?flags=eygtnnl

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    1. But let's be systematic, please: anecdotal evidence in linguistics mean nothing. Either you make a mass lexical comparison and count all these coincidences methodically or attempt to trace them via etymology/reconstruction, what usually brings you to short words of 1-2 syllables.

      I can do that for Basque "gailur" (-a is just nominative declension) to some extent: the firs syllabe must be gain(-a) (= height, hill), present in words like gaineko (from the heights) and surely related to other Basque words about the upper side of geography being g-something: goi (up, high) and its derivatives gora (up, upwards), goia (the high, that's the origin of Goya's surname), goiko (from the high, present in many names sus as Goikoetxea). So what is "gain"? Originally it must be goian (in/on/at the high, such as in the RIP-equivalent sentence "goian bego": "let him/her be in the high"). Alternatively from goien, which means "highest" (absolutely regular all from goi-).

      So we have gain-lur or goi-lur. And what does lur mean? Lur = land, soil, earth (also Planet Earth by extension, as in most languages). So what is gailur? Highland, literally.

      Now, can you make the same analysis for the coincental Hausa form? I'm sorry to sound so dismissive but truly anecdotal evidence means nothing.

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  4. Thanks for the detailed information. Well for what it's worth 'Kai' means "top" in Hausa and 'ganiya' means "peak".

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    1. Aha, now you got my attention. How is that possible? Are there more "coincidences"? Does this come from the Vasco-Nubian root at Sudan or Palestine I speculated about (with a proper mass lexical comparison) some time ago?

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  5. Basque 'hazi' ("seed"); Hausa 'hatsi' ("grain"). I have many more such examples from Chadic and also Benue Congo languages. The Basque and Sardinian word for "dog" is one of two words for "dog" used by the Teda of northern Chad (Toubou languages, Nilo-Saharan). I'll post some more examples over the weekend.

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  6. "Arrow"
    Basque: 'gezi'

    Proto-EChadic: *kis-
    Meaning: 'bow' 1, 'arrow' 2
    Tumak: kès-ké 1 [Cp]
    Ndam: ʔad̀ū-kēsé 1 [JgD]
    Kwang: kēsé 2 [JgD]
    Migama: kêsè1 [Jg]
    Bidiya: kḕse 1 [JBid]
    Sokoro: sáwìŋ kɛ̀sɛ́ 1 [CLR: 29], kɛsɛ́ 2 [CLR: 3]

    Proto-CChadic: *kis-
    Meaning: 'bow' 1, 'arrow' 2
    Mbara: kèsé 2 [TMba]
    Musgu: kise 1 [LMsg]

    More to follow as time permits.

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    1. Ok, "gezi" is a real word, not very much used since gunpowder became popular but it does exist.

      Why don't you try a mass lexical comparison?, with a pre-existent word list to compare an from which obtain numerical data of coincidences, and, well, why not include Nubian in the equation, and whatever you think interesting, Mande?, some Dogon maybe?, not the first time Dogon comes around but beware: not all Dogon languages are made equal, in fact they seem to belong to two different families altogether!

      There's this guy, Arnaiz-Villena, and his colleague Alonso-García, who have been there already and argue relation between Basque and (some) Dogon, and a bunch of other languages mostly from the Ancient Mediterranena, including ancient Egyptian, Hittite, Sumerian, Hurrian, Ugaritic, Akkadian, Phoenician, Guanche, Elamite, Minoan, Etruscan and what-not. I really don't want to get into that because it really goes against mainstream linguistics which consider most of these languages part of other families (Afroasiatic notably) but maybe he's only talking about some substrate elements, and not challenging the whole classification, IDK. But, in any case, as you are so interested, this is part of his work (in English for your convenience): http://chopo.pntic.mec.es/~biolmol/publicaciones/Usko.pdf

      Now, assuming you're right, how would you explain that "Vasconic" influenced West Africa in such a way? There seems to be only the thinnest possible relations between Europe and West Africa before Portuguese naval imperialism (and all them go through Sudan and Palestine).

      Delete

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