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Angoliga
03-10-2022, 02:47 AM
Hunter-gatherer genomes reveal diverse demographic trajectories during the rise of farming in Eastern Africa (Published: March 09, 2022)

ShyamalikaGopalan, Richard E.W.Berl, Justin W.Myrick, Zachary H.Garfield, Austin W.Reynolds, Barnabas K.Bafens, GillianBelbin, MiraMastoras, ColeWilliams, MichelleDaya, Akmel N.Negash, Marcus W.Feldman, Barry S.Hewlett, Brenna M.Henn

(doi: paper link (https://www.cell.com/current-biology/fulltext/S0960-9822(22)00314-1?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com %2Fretrieve%2Fpii%2FS0960982222003141%3Fshowall%3D true))



Highlights

• The Chabu people are related to ancient Southwest Ethiopian hunter-gatherers (HGs)
• Like other African HGs, Chabu population size has declined over the past 1,400 years
• However, other populations with Ethiopian HG ancestry have not experienced declines
• This heterogeneity may stem from variable HG responses to encroaching farmers


Summary

The fate of hunting and gathering populations following the rise of agriculture and pastoralism remains a topic of debate in the study of human prehistory. Studies of ancient and modern genomes have found that autochthonous groups were largely replaced by expanding farmer populations with varying levels of gene flow, a characterization that is influenced by the almost universal focus on the European Neolithic.1, 2, 3, 4, 5 We sought to understand the demographic impact of an ongoing cultural transition to farming in Southwest Ethiopia, one of the last regions in Africa to experience such shifts.6 Importantly, Southwest Ethiopia is home to several of the world’s remaining hunter-gatherer groups, including the Chabu people, who are currently transitioning away from their traditional mode of subsistence.7 We generated genome-wide data from the Chabu and four neighboring populations, the Majang, Shekkacho, Bench, and Sheko, to characterize their genetic ancestry and estimate their effective population sizes over the last 60 generations. We show that the Chabu are a distinct population closely related to ancient people who occupied Southwest Ethiopia >4,500 years ago. Furthermore, the Chabu are undergoing a severe population bottleneck, which began approximately 1,400 years ago. By analyzing eleven Eastern African populations, we find evidence for divergent demographic trajectories among hunter-gatherer-descendant groups. Our results illustrate that although foragers respond to encroaching agriculture and pastoralism with multiple strategies, including cultural adoption of agropastoralism, gene flow, and economic specialization, they often face population decline.

Results

... In order to test hypotheses pertaining to the impact of foraging-to-farming transitions, we estimated genetic ancestry, relative genetic isolation, and the timing and magnitude of demographic fluctuations in Eastern African populations. Our investigation focuses on the Chabu (their preferred ethnonym,7,8 but also referred to in the literature as the “Sabue,” “Sabu,” and “Shabo”9, 10, 11), a group of transitioning hunter-gatherers (HGs) who inhabit the Southwestern Ethiopian highland forests that straddle the borders between the Oromia Regional State, Gambella Regional State, and the Southern Nations, Nationalities, and Peoples’ Region (SNNPR).7 We generated genome-wide data from the Chabu (n = 83) and neighboring Majang, Shekkacho, Bench, and Sheko groups (n = 49, 45, 48, 50) at 1.7 million single nucleotide polymorphisms (SNPs). We combined this dataset with published genotypes from additional groups from across Eastern, Central, and Western Africa, as well as the Near East (Table S1). Importantly, we also include genomic data from Bayira, a 4,500-year-old individual found in Mota Cave in the nearby Gamo Highlands who lived well before any evidence of agriculture or pastoralism in the region,12,13 as well as additional ancient genomes from Eastern Africa, the Levant, and Anatolia.


Graphical Abstract
https://i.imgur.com/joEfRLM.png



Fig 1) Global ancestry proportions of individuals inferred from unsupervised clustering of genotype data

https://i.imgur.com/7irnNVq.png

(A) Each color corresponds to one of the K = 7 hypothesized genetic components, and each vertical bar represents one individual genome (Bayira bar is plotted five times wider to aid visualization).
Population labels include linguistic codes in brackets: Afro-Asiatic (AA), Niger-Congo (NC), Nilo-Saharan (NS), and linguistic isolates (I).
Within Afro-Asiatic speakers, we further differentiate between Chadic (Ch), Cushitic (Cu), Egyptian (E), Omotic (O), and Semitic (S) speakers.
(B–F) The geographic distributions for 5 of these ancestry components, with the intensity of the color corresponding to the mean population proportion of the respective ancestry.
Each component is labeled below the map. (G) The effective migration surface, inferred from the rate of decay of genetic similarity across geographic space.
Cool colors correspond to effective migration corridors, while warm colors correspond to effective migration barriers.



Fig 2) Population structure and F3 outgroup estimates for modern and ancient individuals

https://i.imgur.com/q3Y5rJi.png
(A) A principal component analysis (PCA) of genotype data from modern populations from Eastern Africa and the Near East, with ancient DNA samples superimposed, for PC1 and PC2. Bayira falls close to the Chabu cluster, which anchors the second PC.
(B ) As in (A), but for PC1 and PC3. Here, the Chabu lie near other modern and ancient hunter-gatherers.
(C–E) F3 outgroup tests for X, listed in each row, for shared drift with (C) ancient Bayira or (D) the Chabu relative to the Yoruba. (E) The Anuak, a Nilo-Saharan-speaking Ethiopian group have higher F3 outgroup statistics with the Majang and Gumuz than with the Dinka or Shilluk, despite having a high proportion of NS ancestry (Figure 1A). Overall, the F3 outgroup statistic indicates that, among extant populations, Bayira is most closely related to the Aari Blacksmiths, Aari Cultivators, Bench, and Sheko, followed by the Chabu; conversely, the Chabu carry the most shared drift with their Majang neighbors, followed by Bayira. The whiskers represent standard errors on the F3 estimates.

Fig 3) Distributions of the total amount of the genome in runs of homozygosity (RoH) in Southwest Ethiopian populations
https://i.imgur.com/oJMTnZG.png
RoH are represented by colored violins for (A) all RoH segments and (B) separate RoH size classes. The white point represents the median value of the distribution, and the black rectangle represents values between the lower and upper quartiles. The thin black “whiskers” extend to data points that lie within 1.5 times the interquantile range below or above the lower and upper quantiles, respectively. The Chabu and Aari Blacksmiths showed significantly elevated total RoH in only the longest class suggesting that these populations’ genomic signatures of isolation and demographic decline are a result of relatively recent events. See also Figure S3.

Fig 4) Divergent demographic trajectories for Eastern African populations over the past 2,000 years
https://i.imgur.com/PsVLuZO.png
Historical effective population sizes (Ne), from 4 to 60 generations ago, were inferred from distributions of identical-by-descent segments >4 cM among pairs of individuals. Shown from the upper left are the Chabu, the Majang and Gumuz, the Aari populations, the Bench and Sheko, the Shekkacho and Wolyata, and the Hadza and Sandawe hunter-gatherers of Tanzania. The number of samples and number of IBD segments used for each population are indicated by "n" and "nseg," respectively. Filled circles represent the estimated Ne at a given generation. Colored ribbons indicate bootstrapped 95% confidence intervals around these estimates. Note that the y axis scale changes across panels and is on a log scale for the Shekkacho/Wolyata panel.




Supplemental info:



Fig S1) Global Ancestry Proportions of Individuals for K=2 to K=12, Related to Figure 1 and STAR Methods
https://i.imgur.com/PvowYl7.png
Fig S2) Visualization of Effective Migration Rate Estimates Over Geographic and Linguistic Features, Related to Figure 1 and STAR Methods
https://i.imgur.com/X7d3gzK.png

Michalis Moriopoulos
03-10-2022, 03:11 AM
I wonder if we'll get a shot at looking at these. It says they will be updated on dbGaP under accession "phs001123.v2.p2"

I don't see them there yet, but maybe they will indeed be public. I hope so. These are very unusual and enviable genomes.

drobbah
03-10-2022, 07:49 PM
I wonder if the AA ancestry in these Omotics speakers is of Cushitic origin or possibly pre-Cushitic

beyoku
03-16-2022, 02:06 PM
Both?

egyptian_eediat
03-19-2022, 04:23 AM
Could the Epipaleolithic Helwan culture outlined here:http://anthrogenica.com/showthread.php?22787-Epipalaeolithic-Helwan-Early-dispersal-between-Egypt-and-East-Africa-(E-CTS10880-) be a source of the pre-cushitic AA ancestry in Omotic speakers?

beyoku
03-21-2022, 07:58 PM
Could the Epipaleolithic Helwan culture outlined here:http://anthrogenica.com/showthread.php?22787-Epipalaeolithic-Helwan-Early-dispersal-between-Egypt-and-East-Africa-(E-CTS10880-) be a source of the pre-cushitic AA ancestry in Omotic speakers?

Maybe not even Pre-Cushitic. It could be actual Cushitic. The dates that they provide agree with the Early Dates of Cushitic in the Horn of Africa Under the African origin hypothesis. It also agrees with the evidence of multiple pulse migration from North to South by humans with a somewhat similar Natufian/Dinka composite of ancestry. In a scenario like this, lineages E-V1515 and E-V68 migrate into the Horn of Africa in distinct migrations separated by 1000's of years. In essence later Cushitic speakers encounter the earlier Cushitic speakers on arrival to the Horn and Rift Valley.

drobbah
03-21-2022, 10:27 PM
Maybe not even Pre-Cushitic. It could be actual Cushitic. The dates that they provide agree with the Early Dates of Cushitic in the Horn of Africa Under the African origin hypothesis. It also agrees with the evidence of multiple pulse migration from North to South by humans with a somewhat similar Natufian/Dinka composite of ancestry. In a scenario like this, lineages E-V1515 and E-V68 migrate into the Horn of Africa in distinct migrations separated by 1000's of years. In essence later Cushitic speakers encounter the earlier Cushitic speakers on arrival to the Horn and Rift Valley.
The problem with this multiple pulse is that according to linguists like Ehret the Cushites enter the Horn as parts of a similar wave as the Agaw-South-East Cushitic node splitting off from North Cushitic (Beja) and arriving in the Northern edges of the Ethiopian Highlands around 5000 BCE, they start heading towards modern Somaliland/Djibouti between 5000 & 3500 BCE.We have the South Cushites who split off from East-South node arriving in Northern Kenya by 3000 BCE by way of the Ethiopian Rift valley.

There seems to be Middle Eastern crops and agricultural practices vocab in both East Cushitic and Northern Agaw Cushitic, words such as an East Cushitic term for barley and ofcourse the use of the plow that pre-existed Ethio-Semitic that both Horner East Cushites and Northern Agaw speakers share that the South Cushites lack.Perhaps there were migrations from the North that diffused such knowledge and perhaps brought an increase in Sudanese-related ancestry via another migration (the E-Z813 in East Cushites is a good candidate from descending from such a migration).

The Cushitic ancestry in Omotic populations could have come from when Highland East Cushitic speakers penetrated the Ethio highlands from modern Somaliland/Eastern Ethiopian lowlands.


https://i.imgur.com/nFbB7q2.png

beyoku
03-22-2022, 07:00 PM
I guess to rephrase what i am saying.....I dont think there would be too much of a difference between these southern migrants. It's similar to the cultural difference between the East African Pastoral Neolithic and the distinct Elmenteitan that were THOUGHT to be genetically distinct but were just some more people with similar type of Ancestry. I think this composite type ancestry typified as "Cushitic" (language affiliated or not) is going to be related to any and all movements from the Red Sea into the HOA, including the oldest ones indicated (https://brill.com/view/journals/jaa/15/1/article-p42_42.xml)via archelogy (http://in-africa.org/wp-content/uploads/2012/12/Robbins-LH-2006-Ethnohist-Turkana-Arch-Hol.pdf).

At the moment i dont see the point of associating these types of migrants with any ancestry other than the dominant one that is in the region now. Whether or not these early migrants were linguistically "Cushitic" is something i cant answer.

pgbk87
04-08-2022, 01:41 AM
I wonder if we'll get a shot at looking at these. It says they will be updated on dbGaP under accession "phs001123.v2.p2"

I don't see them there yet, but maybe they will indeed be public. I hope so. These are very unusual and enviable genomes.

Any update?