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Thread: The peopling of the last Green Sahara revealed by high-coverage resequencing of trans

  1. #21
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    Quote Originally Posted by NiloSaharan View Post
    Here's some quotes I had in mind...
    "From a morphosyntactic point of view, Nilo-Saharan language groups spoken in an area ranging from northern Ethiopia and Eritrea across north-central Sudan and extending into Chad and Nigeria share typological features with Afroasiatic languages in Ethiopia. These include a basic constituent order whereby the verb occurs in final position, an extensive case marking system, verbal compounding (e.g., with 'say' or other types of light verbs, such as 'put' or 'do'), as well as the use of converbs as dependent verb forms in complex sentences, although not all properties are necessarily present in all groups. These common typological features to some extent may be due to areal diffusion as a result of long-term cultural contacts and corresponding patterns of multilingualism between speech communities in these areas."
    This is an illustration of why I am no fan of theories of relationships among languages based on linguistic typology.

    The list of morphosyntactic features reads like a basic outline of Japanese grammar. Of course, Japanese is spoken in a territory that is geographically greatly removed from the Nile Valley or the Sahara, but is one really much more justified in postulating "long-term cultural contacts and corresponding patterns of multilingualism between speech communities in these areas" because of their geographical proximity to one another than one would be in postulating a relationship between these speech communities and speakers of Japanese on the basis of the same linguistic evidence?

  2. #22
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    Quote Originally Posted by ADW_1981 View Post
    I guess you're suggesting the R-V88 guys moved from modern day "Sicily" to modern day "Tunisia" around 5000 BC?
    Yes, that's my stance based on the evidence we have so far, although it would be necessary to examine north african V88 to see where it fits in the phylogenetic tree.

  3. #23
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    Thanks to all of you who helped to tell a story that needs to be told. The challenge of knowing what happens to a place in time.
    Holocene Epoch: The Age of Man

    By Mary Bagley, LiveScience Contributor | March 27, 2013 12:26pm ET

    The Holocene Epoch is the current period of geologic time. Another term that is sometimes used is the Anthropocene Epoch because its primary characteristic is the global changes caused by human activity. This term can be misleading, though; modern humans were already well established long before the epoch began. The Holocene Epoch began 12,000 to 11,500 years ago at the close of the Paleolithic Ice Age and continues through today.

    The background story sets the place for the events that followed.

    As Earth entered a warming trend, the glaciers of the late Paleolithic retreated. Tundra gave way to the forest. As the climate changed, the very large mammals that had adapted to extreme colds, like mammoth and wooly rhinoceros, became extinct. Humans, once dependent on these “mega mammals” for much of their food, switched to a smaller game and increased their gathering of plant materials to supplement their diet.
    Out of the heat and caught in an icebox.

    Evidence indicates that about 10,800 years ago, the climate underwent a sharp cold turn lasting for several years. The glaciers did not return, but the game and plant materials would have been scarce. As temperatures began to rebound, human population began to increase and we began inventing the processes that would change the planet forever.

    Talking about Africa always challenges the pictures with the realities of this massive continent.

  4. #24
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    Yfull has now added all BAM samples from this paper

    Sample Reference List (Table 1):

    Code:
     ID	Former IDa	Haplogroup	Country	Population	Age	Reference
    
    S101		A00-L1086	Cameroon	General population	Modern	present study
    S102		A0-V148	Cameroon	General population	Modern	present study
    S103		A0-V148	Algeria	Mozabite Berbers	Modern	present study
    S104	S07	A1-M31	Mali	General population	Modern	present study
    S105	S08	A2-PN3	Angola	!Kung	Modern	present study
    S106	S75	A2-PN3	Cameroon	General population	Modern	present study
    S107	S73	A3-M28	Eritrea	Nara	Modern	present study
    S108		A3-M51	Angola	!Kung	Modern	present study
    S109		A3-M51	Angola	!Kung	Modern	present study
    S110	S10	A3-M13*	Italy	Sardinians	Modern	present study
    S111		A3-M13/V3	Ethiopia	Ethiopian Jews	Modern	present study
    S112		A3-M13/V3	Ethiopia	Ethiopian Jews	Modern	present study
    S113		A3-M13/V3	Ethiopia	Ethiopian Jews	Modern	present study
    S114		A3-M13/V3	Ethiopia	Ethiopian Jews	Modern	present study
    S115		A3-M13/V3	Ethiopia	Ethiopian Jews	Modern	present study
    S116		A3-M13/V3	Ethiopia	Ethiopian Jews	Modern	present study
    S118		A3-M13/V317	Ethiopia	Amhara	Modern	present study
    S119		A3-M13/V317	Ethiopia	Oromo	Modern	present study
    S120		A3-M13*	Kenya	Maasai	Modern	present study
    S121		A3-M13*	Kenya	Maasai	Modern	present study
    S122		A3-M13*	Cameroon	Fulbe	Modern	present study
    S123		A3-M13/V67	Nigeria	Hausa	Modern	present study
    S124		A3-M13*	Chad	Shuwa arabs	Modern	present study
    S125		A3-M13*	Chad	Ngambai	Modern	present study
    S126	S77	A3-M13*	Chad	Massa	Modern	present study
    S127		A3-M13*	Benin	General population	Modern	present study
    S128		A3-M13*	Morocco	Souss Berbers	Modern	present study
    S129	S76	A3-M13*	Egypt	Northern Egyptians	Modern	present study
    S130		B-M236	Chad	Gor	Modern	present study
    S131	S14	B-M236/M146	Burkina Faso	General population	Modern	present study
    S132		B-M150/M109	Cameroon	Moundang	Modern	present study
    S133		B-M150/M109	Chad	Toupouri	Modern	present study
    S134	S74	B-M112	Cameroon	General population	Modern	present study
    S135		E-V44	Ethiopia	Amhara	Modern	present study
    S136		E-V257* (xM81)	Chad	Massa	Modern	present study
    S137		E-M78/V259	Cameroon	Daba	Modern	present study
    S138		E-M78/V259	Cameroon	Guidar	Modern	present study
    S139		E-M78/V12*	Cameroon	Mandara	Modern	present study
    S140		E-M78/V32	Cameroon	Moundang	Modern	present study
    S141		E-M78/V32	Chad	Massa	Modern	present study
    S142		E-M78/V32	Chad	Goulaye	Modern	present study
    S143		E-M78/V32	Chad	Goulaye	Modern	present study
    S144		E-M78/V32	Chad	Madjingay	Modern	present study
    S145		E-M78/V32	Chad	Goulaye	Modern	present study
    S146		E-M78/V12*	Egypt	General population	Modern	present study
    S147		E-M78/V12*	Egypt	General population	Modern	present study
    S148		E-M78/V12*	Morocco	Moroccan Jews	Modern	present study
    S149	S25	E-M78/V65	Libya	Libian Jews	Modern	present study
    S150		E-M78/V65	Egypt	Egyptian Berbers from Siwa	Modern	present study
    S151		E-M78/V65	Egypt	Egyptian Berbers from Siwa	Modern	present study
    S152		E-M78/V65	Morocco	Moroccan Arabs	Modern	present study
    S153		E-M78/V65	Morocco	Moroccan Arabs	Modern	present study
    S154		E-M78/V32	Ethiopia	Amhara	Modern	present study
    S155		E-M78/V32	Eritrea/Ethiopia	Tigrai	Modern	present study
    S156		E-M78/V32	Ethiopia	Ethiopian Jews	Modern	present study
    S157		E-M78/V32	Kenya	Borana	Modern	present study
    S158		E-M78/V32	Kenya	Luhya	Modern	present study
    S159		E-M78/V32	Kenya	Maasai	Modern	present study
    S160		E-V68/V2009	Cameroon	Fulbe	Modern	present study
    S161		E-V68/V2009	Morocco	Souss Berbers	Modern	present study
    S162		E-M78/V22	Eritrea	Saho	Modern	present study
    S163		E-M2*	Egypt	Egyptians from Baharia	Modern	present study
    S164		E-M2*	Egypt	Egyptians from Baharia	Modern	present study
    S165		E-M2*	Egypt	Egyptian Berbers from Siwa	Modern	present study
    S166		E-M2*	Egypt	Egyptian Berbers from Siwa	Modern	present study
    S167		E-M2*	Morocco	Ouarzazate Berbers	Modern	present study
    S168		E-M2*	Morocco	Ouarzazate Berbers	Modern	present study
    S169		E-M2*	Morocco	Asni Berbers	Modern	present study
    S170		E-M2*	Morocco	Bouhria Berbers	Modern	present study
    S171		E-M2*	Burkina Faso	General population	Modern	present study
    S173		E-M2*	Senegal	Mandenka	Modern	present study
    S175		E-M2*	Cameroon	Ngambai	Modern	present study
    S176		E-M2*	Cameroon	Fali	Modern	present study
    S177		E-M2*	Niger	Songhai	Modern	present study
    S178	S38	C-V20	Italy	General population	Modern	present study
    S179		C-M8	Japan	General population	Modern	present study
    S181		J-M172	Turkey	Sephardic Turkish	Modern	present study
    S182		J-M267/P58	Chad	Gor	Modern	present study
    S183		R-V88*	Benin	General population	Modern	present study
    S184		R-V88*	Benin	General population	Modern	present study
    S185		R-V88*	Cameroon	Ouldeme	Modern	present study
    S186		R-V88/V69	Cameroon	Moundang	Modern	present study
    S187		R-V88/V69	Cameroon	Fulbe	Modern	present study
    S188		R-V88/V69	Cameroon	Toupouri	Modern	present study
    S189		R-V88/V69	Chad	Toupouri	Modern	present study
    S190		R-V88*	Chad	Madjingay	Modern	present study
    S191		R-V88/V69	Chad	Toupouri	Modern	present study
    S192		R-V88*	Chad	Toupouri	Modern	present study
    S193		R-V88*	Chad	Moundang	Modern	present study
    S194		R-V88*	Chad	Massa	Modern	present study
    S195		R-V88/V8	Chad	Gor	Modern	present study
    S196		R-V88*	Cameroon	Ewondo	Modern	present study
    S197		R-V88*	Bulgaria	Sephardic Bulgarians	Modern	present study
    S198		R-V88*	Algeria	Mozabite Berbers	Modern	present study
    S200		R-V88*	Morocco	Ouarzazate Berbers	Modern	present study
    S201		R-V88*	Egypt	General population	Modern	present study
    S202		R-V88*	Egypt	General population	Modern	present study
    S203	TV18	R-V88*	Egypt	General population	Modern	present study
    S204		R-V88*	Egypt	Northern Egyptians	Modern	present study
    S206		J-M267/P58	Ethiopia	Amhara	Modern	present study
    S207		J-M267* (xP58)	Ethiopia	Oromo	Modern	present study
    S208		J-M267/P58	Algeria	Mozabite Berbers	Modern	present study
    S209		J-M267* (xP58)	Yemen	Yemenites	Modern	present study
    S210		J-M267* (xP58)	Ethiopia	Amhara	Modern	present study
    GS16204		A-M13/V243b	Ethiopia	Ethiopian Jews	Modern	1
    GS35245		E-M2/U174b	Congo	Congo-pygmies	Modern	1
    GS16179		E-V32b	Iran	Iranians	Modern	1
    GS16217		E-M4145b	Israel	Arab-Christian	Modern	1
    GS16206		E-M34b	Israel	Arab-Christian	Modern	1
    GS13741		J1c-PF7256b	Azerbaijan	Azeri	Modern	1
    GS14421		J1a1-B232b	Russia	Tabas-saran	Modern	1
    GS13724		J1a2-B234b	Russia	Lezgin	Modern	1
    GS35126		J1b6-PR6622b	Armenia	Armenian	Modern	1
    GS35125		J1b5-CTS11284b	Armenia	Armenian	Modern	1
    GS14474		J1b4-B235b	Jordan	Jordanian	Modern	1
    GS16136		J1b2-L829b	Israel	Druze	Modern	1
    GS16180		J1b1-B243b	Saudi Arabia	Arabian	Modern	1
    GS35124		J1b3-B382b	Armenia	Armenian	Modern	1
    NA18940		D2-M55b	Japan	 JPT	Modern	2
    NA19239		E1a-P110b	Nigeria	YRI	Modern	2
    NA18504		E1b1a-U174b	Nigeria	YRI	Modern	2
    NA19026		E1b1a-U174b	Kenya	LWK	Modern	2
    NA19834		E1b1a-U174b	USA	ASW	Modern	2
    NA19703		E1b1a-U181b	USA	ASW	Modern	2
    NA18501		E1b1a-U209* (xU290)b	Nigeria	YRI	Modern	2
    NA19020		E1b1a-U209* (xU290)b	Kenya	LWK	Modern	2
    NA19025		E1b1a-U209* (xU290)b	Kenya	LWK	Modern	2
    NA19700		E1b1a-U290* (xU181)b	USA	ASW	Modern	2
    NA20510		E1b1b-V13b	Italy	TSI	Modern	2
    NA21732		E1b1b-V22b	Kenya	MKK	Modern	2
    NA21737		E1b1b-V22b	Kenya	MKK	Modern	2
    NA19670		G-U8b	USA	MXL	Modern	2
    NA06994		I1-M253b	USA	CEU	Modern	2
    NA12891		I1-M253b	USA	CEPH/Utah Pedigree 1463	Modern	2
    NA20511		I1-M253b	Italy	TSI	Modern	2
    NA18558		N-M231b	China	CHB	Modern	2
    NA19735		Q1a-M3b	USA	MXL	Modern	2
    NA20846		R1a-M17b	USA	GIH	Modern	2
    NA20850		R1a-M17b	USA	GIH	Modern	2
    NA10851		R1b1-M529* (xM222)b	USA	CEU	Modern	2
    NA12889		R1b1-P312* (xDF27,U152,M529,L238)b	USA	CEPH/Utah Pedigree 1463	Modern	2
    HG00731		R1b1-U152b	USA	PUR	Modern	2
    NA07357		R1b1-U152b	USA	CEU	Modern	2
    NA19649		R1b1-U152b	USA	MXL	Modern	2
    NA20509		R1b1-U152b	Italy	TSI	Modern	2
    NA20845		R2-M124b	USA	GIH	Modern	2
    Ust'-Ishim		NOc	Siberia	-	45 kya	3
    Bichon		I2ab	Switzerland	-	13.7 kya	4
    Kotias		J2b	Georgia	-	9.7 kya	4
    Loschbour		I2c	Luxembourg	-	8 kya	5
    I requested a few A-M13s a week ago and was delightfully surprised to see all samples added just a few days later -- the folks at Yfull are amazing!
    Given this paper came out early 2018, it's pretty funny no one had thought to request these earlier
    .... .. I have spoken."

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  6. #25
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    Great to see some Africans in the African branches previously represented entirely by Arabs.

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  8. #26
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    Quote Originally Posted by NiloSaharan View Post
    Yfull has now added all BAM samples from this paper

    I requested a few A-M13s a week ago and was delightfully surprised to see all samples added just a few days later -- the folks at Yfull are amazing!
    Given this paper came out early 2018, it's pretty funny no one had thought to request these earlier
    Thanks for sharing and for bringing it to their attention! Nice to see some more Africans in the YFull phylogeny. Some interesting results here, looks like the most common Saudi A-M13 lineage shares a recent (<3 ky old) TMRCA with Ethiopian A-M13. Would have been nice if we could also have some more Z830/V1515 samples, but I'll try to be patient for a while longer.

    BTW, for any Africans interested in getting sequenced, Dante Labs have a promotion until Nov 26th offering WGS 30x sequencing for just $199/€169 (free worldwide shipping). They've had some issues with delays in the past, but this is still a great deal.
    Last edited by Lank; 11-21-2018 at 12:24 PM.

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  10. #27
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    Quote Originally Posted by Lank View Post
    BTW, for any Africans interested in getting sequenced, Dante Labs have a promotion until Nov 26th offering WGS 30x sequencing for just $199/€169 (free worldwide shipping). They've had some issues with delays in the past, but this is still a great deal.
    It's not so good with the Y-Chrom though. It misses a lot of info the Big Y covers IIRC.
    Last edited by NetNomad; 11-21-2018 at 04:17 PM.

  11. #28
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    Quote Originally Posted by Megalophias View Post
    Great to see some Africans in the African branches previously represented entirely by Arabs.
    However, most of the E-M35 subclades among Peninsular Arabs do not seem post-Islamic.

    The Arabian Peninsula should be viewed as ''North Africa'' when it comes to human genetics. 23andMe were on to something when they lumped them with Berbers.

  12. #29
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    So far the 6 Cameroonian/Chadian V32 samples are all Y28701*, potentially representing an early split from the Cushitic types, not sure if it's still updating though? The 3 Habesha/Jewish V32 samples are in different branches, as you might expect there is some diversity in the Ethiopian highlands. 2 Kenyan Borana/Maasai are Y15945*, and the last new Kenyan sample, a Luhya, belongs to a subclade shared with 2 other Luhya samples.

    As for J1, 2/3 samples (an Amhara and an Oromo) belong to J1-P56. A tiny sample size, but it does fit with Agamemnon's suggestion that most Ethiopian J1 may be P56. P56 is a fairly old clade that's surprisingly rare across the sea in Arabia. I wouldn't be surprised at this point if modern Arabian J1-P56 represents African back-migration. The last Ethiopian J1 sample, an Amhara, belongs to a small P58 clade that also includes the only Eritrean J1 sample in YFull's tree.

    Quote Originally Posted by NetNomad View Post
    It's not so good with the Y-Chrom though. It misses a lot of info the Big Y covers IIRC.
    I haven't had either test, but I don't think they are directly comparable as the Big Y doesn't sequence the entire Y chromosome. So normal WGS tests actually reveal more novel variants compared to the Big Y. The latter does offer higher coverage, but the Y-DNA coverage offered by 30x WGS tests including Dante Labs doesn't look too shabby either. A poster who did both tests ran some stats comparing the two. Here are some other statistics.

    And of course, the WGS test is a lot cheaper with this offer, and you also get to sequence the rest of your genome at a decent coverage.
    Last edited by Lank; 11-21-2018 at 05:35 PM.

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    Quote Originally Posted by NetNomad View Post
    However, most of the E-M35 subclades among Peninsular Arabs do not seem post-Islamic.
    Of course not, E-M35 is some 24000 years old. Even E-M123 is 11k yo, it's old as balls, possibly even older than Proto-Afroasiatic languages
    Last edited by Ruderico; 11-21-2018 at 05:45 PM.
    YDNA E-Y31991>PF4428>Y134097>Y134104>Y168273>FT17866 (TMRCA ~800AD) - Domingos Rodrigues, b. circa 1690 Hidden Content , Viana do Castelo, Portugal - Stonemason, miller.
    mtDNA H20 - Monica Vieira, b. circa 1700 Hidden Content , Porto, Portugal

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    [1] "distance%=1.6023"

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