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Thread: New High-Coverage Northeast African genomes

  1. #1
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    New High-Coverage Northeast African genomes

    Abstract:

    Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.
    So the headcount is:

    44 Sudanese Arabs, 27 Beja, 41 Nubians, 52 Eastern Sudanic speakers (xNubians), 22 Saharan speakers, 14 Copts, 16 Nubas and 5 Hausas.

    Some figures:

     




    And the samples are available here.
    Last edited by Awale; 08-25-2017 at 08:29 PM.
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    However, these old admixture events into the Beni Amer could be driven by admixture from the Cushitic-speaking populations of the Horn of Africa, which themselves have received 30–50% non-African ancestry about 100 generations ago, or 3kya.
    I wonder if this 3kya nonsense will stop when the Skoglund paper with that ~3000 year old Tanzanian pastoralist is released.
    Last edited by blackflash16; 08-26-2017 at 03:18 AM.

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    Quote Originally Posted by blackflash16 View Post
    I wonder if this 3kya nonsense will stop when the Skoglund paper with that ~3000 year old Tanzanian pastoralist is released.
    Yes, I think it'll dawn on them when they see a 3kya old ancient genome south of the Horn with probably the same old West-Eurasian admixture as Somalis. Maybe then they'll realize that their ~3kya signal is probably just them picking up on admixture from the Proto-Ethiosemitic speaking community.
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    Good study, I'll give it a more thorough read when I get the time, but I'll try to address the main points in it for now. The Figure 2 graph is particularly interesting, it seems to imply that Nilotes have remained relatively unmixed with Eurasian populations, indicating strong genetic isolation of Nilotes.

    Also something that I found that was very interesting, was the map that showed the amount of Nilotic and Eurasian admixture and admixture dates in investigated populations. The map doesn't make it very clear, but the S7 table has a breakdown of the relevant dates of admixture for each population sampled http://journals.plos.org/plosgenetic...n.1006976.s035

    Most interesting thing to me, is that all the populations sampled seem to have at least one admixture event, sometimes 2. The 700 year figure for Nubians seems to be an average based on the admixture dates of the Mahas, Danagla, Halfawieen, Gaalien & other Nubian tribes. Some of them like the Gaalien have quite recent admixture dates, at approx 17 generations ago or 425 years ago. Others like the Mahas have admixture dates of 58 generations ago, which is approximately 1450 years ago I believe.

    The Beja groups are similarly interesting, the Beni Amer have 2 admixture events, one that occurs at 107 generations ago or 2675 years ago, long before any arab or muslim migration, & another admix event that occurs 34 generations ago, or 850 years ago which is probably in relation to arab/muslim migrations

    This could be due to admixture from Cushitic groups residing in the Horn at the time, as the date of admixture is very similar to Somali dates of Eurasian admix.

    Another interesting piece of data in regards to the admixture dates, is that the only 2 groups who the software doesn't pick up an admix date between the Nilotic/East African & Eurasian admix is Dinka & Copts. I'm still trying to puzzle out the full implications of this particular piece of data, but I've wanted someone to test admix dates in Copts for a while & the fact that the software couldn't pick up a date for either Dinka or Copts have interesting implications, about the genetic history of either group.

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    Quote Originally Posted by nee4speed111 View Post
    Good study, I'll give it a more thorough read when I get the time, but I'll try to address the main points in it for now. The Figure 2 graph is particularly interesting, it seems to imply that Nilotes have remained relatively unmixed with Eurasian populations, indicating strong genetic isolation of Nilotes.

    Also something that I found that was very interesting, was the map that showed the amount of Nilotic and Eurasian admixture and admixture dates in investigated populations. The map doesn't make it very clear, but the S7 table has a breakdown of the relevant dates of admixture for each population sampled http://journals.plos.org/plosgenetic...n.1006976.s035

    Most interesting thing to me, is that all the populations sampled seem to have at least one admixture event, sometimes 2. The 700 year figure for Nubians seems to be an average based on the admixture dates of the Mahas, Danagla, Halfawieen, Gaalien & other Nubian tribes. Some of them like the Gaalien have quite recent admixture dates, at approx 17 generations ago or 425 years ago. Others like the Mahas have admixture dates of 58 generations ago, which is approximately 1450 years ago I believe.

    The Beja groups are similarly interesting, the Beni Amer have 2 admixture events, one that occurs at 107 generations ago or 2675 years ago, long before any arab or muslim migration, & another admix event that occurs 34 generations ago, or 850 years ago which is probably in relation to arab/muslim migrations

    This could be due to admixture from Cushitic groups residing in the Horn at the time, as the date of admixture is very similar to Somali dates of Eurasian admix.

    Another interesting piece of data in regards to the admixture dates, is that the only 2 groups who the software doesn't pick up an admix date between the Nilotic/East African & Eurasian admix is Dinka & Copts. I'm still trying to puzzle out the full implications of this particular piece of data, but I've wanted someone to test admix dates in Copts for a while & the fact that the software couldn't pick up a date for either Dinka or Copts have interesting implications, about the genetic history of either group.
    Note that they tested admix dates with LD-based methods which are easily confused by drift of endogamous groups. ALDER fails to find admixture dates for Kalash. That said, Dinka do not look very drifted and likely just don't have European or Near Eastern ancestry.

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    At K=4 it looks like Nuer, Dinka, and Anuak are the three Nilotic populations completely lacking in the CEU/European component (Shilluk looks like it just barely has some trace amounts). They all have a solid chunk of the orange Yoruba component though. Has West African ancestry been corroborated in any of these groups before? And Yoruba has an even bigger chunk of the dark blue Nilotic-esque component, which is pretty interesting.
    Last edited by TuaMan; 08-27-2017 at 02:02 PM.

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    Quote Originally Posted by nee4speed111 View Post
    The Beja groups are similarly interesting, the Beni Amer have 2 admixture events, one that occurs at 107 generations ago or 2675 years ago, long before any arab or muslim migration ... This could be due to admixture from Cushitic groups residing in the Horn at the time, as the date of admixture is very similar to Somali dates of Eurasian admix.
    I half wonder if it's actually tied to the Proto-Ethiopiansemitic speaking community as well given the timing. It's not impossible for them to have been influenced by it as well. Lately I've been wondering if all of the later West-Eurasian admixture in the Horn is actually tied to that and that there isn't one specific to Agaws and the like who might just have less of this admixture because they didn't fully language-shift and mix that much with fully Ethiosemitized Horn-Africans. Hopefully, nMonte might help get to the bottom of this if and when we can get all these samples in the global 10 PCA and perhaps also a more regional one like this one. Then we might be able see if there's a pulse of something more Copt-like before the Yemenite Jew-like stuff.

    Quote Originally Posted by TuaMan View Post
    Has West African ancestry been corroborated in any of these groups before?
    Yes, that's been known for a long time now. The usual Dinka samples out there before these having, on average, a bit less of such admixture than the usual Ethiopian-Anuaks and Sudanese samples is probably why they work better as a proxy for Somalis' African ancestry, in fact:

     
    [1] "distance%=0.6546 / distance=0.006546"

    Somali

    Dinka 54.6
    Natufian 42.6
    MA1 2.3
    Mota 0.4

    --

    [1] "distance%=0.95 / distance=0.0095"

    Somali

    Ethiopian_Anuak 53.05
    Natufian 45.30
    Ari-Blacksmith 0.70
    MA1 0.60
    Mota 0.35

    --

    [1] "distance%=1.0303 / distance=0.010303"

    Somali

    Sudanese 53.5
    Natufian 45.8
    MA1 0.8
    Last edited by Awale; 08-27-2017 at 05:35 PM.
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    Quote Originally Posted by Awale View Post
    Yes, that's been known for a long time now. The usual Dinka samples out there before these having, on average, a bit less of such admixture than the usual Ethiopian-Anuaks and Sudanese samples is probably why they work better as a proxy for Somalis' African ancestry, in fact:
    Interesting. Uniparentally, I know Nilo-Saharan types are dominated by y-DNA A and B and I believe maternally are predominantly L3. So do they get their West-African ancestry from their maternal side (I believe they also have some L2 mtDNA, correct me if I'm wrong).

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    Some of my observations:

    • Based on ADMIXTURE, the Nuba and the Nuer look to be the "purest" Nilotes. I wonder how they would behave as a proxy for Somali's African ancestry
    • The Great Lakes Bantu groups seem to have significant Somali-like and Anuak-like admixture
    • The Beja (Beni Amer) have a small Omotic-like signal at K=10, similar to Somalis, but it disappears at later Ks
    • Most of the Sudanese Arabs have less of a West African-like admixture signal than Horn Africans(?), minus a few outliers
    • At K=18 the Yoruba have a small Kordofan/Darfurian component that makes sense linguistically
    • At K=16 and 18 there is a Sudanese centered component that simply does not exist in Nilo-Saharans proper, and maximizes in the Danagla
    • If you look closely, there is tiny tan-colored component that I'd guess is something hunter-gather-esque in the Ari Cultivators, Anuak, Great Lakes and South Sudanese groups
    Last edited by pgbk87; 08-27-2017 at 09:30 PM.

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    I'd love to see puntDNAL work with this data for a new admix calc . Hopefully there'll be something of value for him with these new samples and components.


    Relating to Nubians, I found the dating within these confidence intervals relevant to the decline of the Kingdom of MeroŽ (1st-4th century AD):

    *If the LD-decay estimates have any merit, could these Eurasian introgression dates for the Danagla and Mahas reflect the turning point of the Nobatae, Blemmyes, and later Aksumites conquering Nubia?

     
    The roughly 56 generation estimate (56x30=~1680ybp) happens to fall within this time period:

    "Assuming that the Nubian population is a mixture of an incoming Eurasian (TSI is used as a proxy) group and a resident group that is genetically similar to the current day Nilotes (Nuer is used as a proxy), first contact is dated using patterns of LD-decay [34] to roughly 56 generations ago for the Danagla (54.45 +/- 10.34, Z = 5.26437) and the Mahas (58.35 +/- 12.2, Z = 4.78402); the Halfawieen have received Eurasian admixture later, around 19 generations ago (19.31 +/- 3.81, Z = 5.05949, S7 Table, Fig 3C). Assuming a generation time of 30 years, the admixture dates for Danagla and Mahas predate the Arab expansion in the 7th century, and may suggest that the migrations and admixture predate Islamic conquest. However, the confidence intervals overlap with the 7th century, and these admixture estimates largely coincide with the Arab expansion into the northeast of Sudan. It is known from historic sources that Arabic groups encountered the Nubians first in the 7th century, and were held back from advancing further into the Sahel until the fall of Dongola in 1315/1316AD [36] and the collapse of the Kingdom of Makuria. This is consistent with the later date for the admixture into Halfawieen and the Arabic populations of Sudan. Previous studies [37, 38] have found a similar pattern for populations of Maghreb, where admixture times coincide with the time of the historically documented Arab conquest."

    This would agree with the Sudanes YDNA from ancient remains:

    "Accordingly, through limited on number of aDNA samples, there is enough data to suggest and to tally with the historical evidence of the dominance by Nilotic elements during the early state formation in the Nile Valley, and as the states thrived there was a dominance by other elements particularly Nuba/Nubians. In Y-chromosome terms this mean in simplest terms introgression of the YAP insertion (haplogroups E and D), and Eurasian Haplogroups which are defined by F-M89 against a background of haplogroup A-M13. The data analysis of the extant Y-chromosomes suggests that the bulk of genetic diversity appears to be a consequence of recent migrations and demographic events" (Hisham, 2009).


    Brief summary of the decline of MeroŽ (1st-4th century):

    "..the Kingdom of Meroe began to fade as a power by the 1st or 2nd century AD, sapped by the war with Roman Egypt, the decline of its traditional industries and the increasingly destructive attacks from the Blemmyes.

    Indeed, at the end of the 2nd century AD, the Nobatae occupied the Nile's west bank in northern Kush. They are believed to have been one of several well-armed bands of horse- and camel-borne warriors who sold their
    vagility to the Meroitic Population for protection; eventually they intermarried and established themselves among the Meroitic people as a military aristocracy.

    ...the old Meroitic kingdom contracted because of the expansion of the powerful Ethiopic Kingdom of Aksum to the east. By AD 350, King Ezana of Axum
    had captured and destroyed Meroe city, ending the kingdom's independent existence, and conquering its territory into modern-day northern Sudan."


    Why no Central Sudanics?

     

    Central Sudanic Linguistic Map

    This paper had me super elated and depressed at the same time. I was hoping to finally see a true reflection of my own admixture through samples from Central-Sudanic speakers but it looks like we've been scapegoated yet again. IMO at least the inclusion of the CS Lugbara speakers with a population size (~1.7 million) comparable to Nubians, and exceeding many on the list, should have been on the sample-collection-radar. So far, the Chadian Bulala are the only CS samples I've ever come across. Despite our geographical distance (<2,000km - Central Chad to NW Uganda), and our supposed period of migration towards the end of the Holocene Wet Phase (~3500-3000), the Bulala still appear as my closest oracle population. As the paper suggests, many of these NE nilotic populations must have stayed "strongly endogamous" - perhaps for several millennia.

    Based on Bulala samples and my own observation with immediate family members, if CS populations (minus pygmy speakers) were included in the paper, I'd assume ~40% of their admixture would be the orange West-African component. The rest would be the blue NE component along with a minor Eurasian affinity (~ <10%) at lower K levels. The closest comparable sample with these fractions are found in one of the Zagawa (perhaps an anomaly from neighbouring CS speakers in Chad?).


    I'm looking forward to learn more from this thread, I'll definitely chime in on more observations of interest -- these were just the first to come to mind.


    *This caught me a little off guard, I think the naming for the nilotic population "Baria" might have been incorrect. This is probably referring to the "Bari" of equatorial Southern-Sudan (~1,000,000 pop.).
    Last edited by Angoliga; 08-28-2017 at 07:37 PM. Reason: additional spoiler added

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