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Thread: Male-biased migration from East Africa introduced pastoralism into southern Africa

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    Male-biased migration from East Africa introduced pastoralism into southern Africa

    Mario Vicente, Imke Lankheet, Thembi Russell, Nina Hollfelder, Vinet Coetzee, Himla Soodyall, Michael De Jongh & Carina M. Schlebusch
    (Paper Published: 07 December 2021)


    Abstract
    Background
    Hunter-gatherer lifestyles dominated the southern African landscape up to ~ 2000 years ago, when herding and farming groups started to arrive in the area. First, herding and livestock, likely of East African origin, appeared in southern Africa, preceding the arrival of the large-scale Bantu-speaking agro-pastoralist expansion that introduced West African-related genetic ancestry into the area. Present-day Khoekhoe-speaking Namaqua (or Nama in short) pastoralists show high proportions of East African admixture, linking the East African ancestry with Khoekhoe herders. Most other historical Khoekhoe populations have, however, disappeared over the last few centuries and their contribution to the genetic structure of present-day populations is not well understood. In our study, we analyzed genome-wide autosomal and full mitochondrial data from a population who trace their ancestry to the Khoekhoe-speaking Hessequa herders from the southern Cape region of what is now South Africa.

    Results
    We generated genome-wide data from 162 individuals and mitochondrial DNA data of a subset of 87 individuals, sampled in the Western Cape Province, South Africa, where the Hessequa population once lived. Using available comparative data from Khoe-speaking and related groups, we aligned genetic date estimates and admixture proportions to the archaeological proposed dates and routes for the arrival of the East African pastoralists in southern Africa. We identified several Afro-Asiatic-speaking pastoralist groups from Ethiopia and Tanzania who share high affinities with the East African ancestry present in southern Africa. We also found that the East African pastoralist expansion was heavily male-biased, akin to a pastoralist migration previously observed on the genetic level in ancient Europe, by which Pontic-Caspian Steppe pastoralist groups represented by the Yamnaya culture spread across the Eurasian continent during the late Neolithic/Bronze Age.

    Conclusion
    We propose that pastoralism in southern Africa arrived through male-biased migration of an East African Afro-Asiatic-related group(s) who introduced new subsistence and livestock practices to local southern African hunter-gatherers. Our results add to the understanding of historical human migration and mobility in Africa, connected to the spread of food-producing and livestock practices.




    Fig.1)






    Fig.2)





    Fig S2 - ADMIXTURE K10:
     


    Fig S5 - qpGraph tree:
     


    Table S6 - Summary results for the mitochondrial haplogroup assignment for the 87 sub-sampled Hessequa-descendants. Average sequence coverage is also provided:

    Code:
    ID	Sampling Place	Major clade	mtDNA haplogroup	Haplogrep Score	Ancestry assigned*	mtDNA coverage (X)
    HSQ090	Suurbraak	B4b	B4b1a2	0.8695	Asian	218
    HSQ018	Riversdale	B5b	B5b1c	0.9226	Asian	364
    HSQ082	Slangriver	E1a	E1a1a1	1.0432	Asian	256
    HSQ142	Swellendam	H	H	0.9865	European	256
    HSQ145	Swellendam	J1c	J1c1a	0.9908	European	275
    HSQ022	Riversdale	L0a	L0a2a2a1	0.9065	Bantu-speaker	75
    HSQ094	Suurbraak	L0a	L0a2a2a1	0.8171	Bantu-speaker	58
    HSQ123	Stomsvlei	L0a	L0a1b1a	0.8859	Bantu-speaker	66
    HSQ126	Stomsvlei	L0a	L0a2a2a1	0.9679	Bantu-speaker	118
    HSQ143	Swellendam	L0a	L0a2a2a1	0.868	Bantu-speaker	108
    HSQ003	Melkhoutfontein	L0d	L0d1b2b1b1	0.9728	Khoe-San	466
    HSQ005	Melkhoutfontein	L0d	L0d1b2b1b1	0.9853	Khoe-San	693
    HSQ008	Melkhoutfontein	L0d	L0d2b1a	1.0923	Khoe-San	334
    HSQ011	Melkhoutfontein	L0d	L0d2a1	0.9818	Khoe-San	246
    HSQ012	Melkhoutfontein	L0d	L0d1a1a1	0.9206	Khoe-San	577
    HSQ013	Melkhoutfontein	L0d	L0d1a1a1	0.893	Khoe-San	109
    HSQ014	Melkhoutfontein	L0d	L0d1b2b1b1	0.9022	Khoe-San	86
    HSQ016	Melkhoutfontein	L0d	L0d1b2b1b1	0.9126	Khoe-San	54
    HSQ017	Riversdale	L0d	L0d1b2b1b	0.746	Khoe-San	36
    HSQ019	Riversdale	L0d	L0d2a1a	0.9746	Khoe-San	190
    HSQ024	Riversdale	L0d	L0d2a1a	1.0109	Khoe-San	517
    HSQ025	Riversdale	L0d	L0d1b2b1b1	0.9907	Khoe-San	225
    HSQ026	Riversdale	L0d	L0d1b2b2b1	0.8992	Khoe-San	127
    HSQ027	Riversdale	L0d	L0d1a1a	0.9478	Khoe-San	275
    HSQ036	Riversdale	L0d	L0d1b2b2b1	0.9775	Khoe-San	308
    HSQ038	Riversdale	L0d	L0d1b2b1b1	0.9579	Khoe-San	301
    HSQ042	Riversdale	L0d	L0d2a1a	0.9752	Khoe-San	521
    HSQ048	Heidelberg	L0d	L0d1b2b1b1	0.971	Khoe-San	284
    HSQ050	Heidelberg	L0d	L0d1b2b1b1	0.8295	Khoe-San	91
    HSQ052	Heidelberg	L0d	L0d1b2b2b1	0.9687	Khoe-San	416
    HSQ053	Heidelberg	L0d	L0d2a1a2	0.8522	Khoe-San	201
    HSQ055	Heidelberg	L0d	L0d2a1a	0.9578	Khoe-San	339
    HSQ056	Heidelberg	L0d	L0d1b2b1b1	0.9933	Khoe-San	606
    HSQ058	Heidelberg	L0d	L0d2a1a	0.9087	Khoe-San	121
    HSQ059	Heidelberg	L0d	L0d2a1a	0.9512	Khoe-San	157
    HSQ060	Heidelberg	L0d	L0d2a1a	0.9947	Khoe-San	608
    HSQ076	Slangriver	L0d	L0d2c1a1	0.9255	Khoe-San	143
    HSQ079	Slangriver	L0d	L0d2b1a	0.9417	Khoe-San	519
    HSQ081	Slangriver	L0d	L0d2c1a	0.9794	Khoe-San	797
    HSQ083	Slangriver	L0d	L0d2a1a	0.9452	Khoe-San	152
    HSQ087	Slangriver	L0d	L0d1b2b2b1	0.9687	Khoe-San	489
    HSQ088	Suurbraak	L0d	L0d1b2b1b1	0.9818	Khoe-San	280
    HSQ089	Suurbraak	L0d	L0d1a1a	0.9532	Khoe-San	267
    HSQ095	Suurbraak	L0d	L0d2c1a1	0.9629	Khoe-San	610
    HSQ097	Suurbraak	L0d	L0d1b2b1b1	1.0467	Khoe-San	533
    HSQ098	Suurbraak	L0d	L0d1a1a	0.9872	Khoe-San	756
    HSQ099	Suurbraak	L0d	L0d2a1	0.9246	Khoe-San	146
    HSQ118	Stomsvlei	L0d	L0d1b2b2b1	0.965	Khoe-San	580
    HSQ119	Stomsvlei	L0d	L0d1b2b2b1	0.9893	Khoe-San	911
    HSQ122	Stomsvlei	L0d	L0d1b2b1b1	0.8746	Khoe-San	77
    HSQ124	Stomsvlei	L0d	L0d1b2b2a	1.2806	Khoe-San	147
    HSQ125	Stomsvlei	L0d	L0d1b2b1b1	0.9391	Khoe-San	118
    HSQ127	Stomsvlei	L0d	L0d1b2b1b1	1.0313	Khoe-San	575
    HSQ130	RotterdamFarm	L0d	L0d2a1	0.841	Khoe-San	45
    HSQ131	RotterdamFarm	L0d	L0d1b2b1b1	1.0019	Khoe-San	567
    HSQ135	RotterdamFarm	L0d	L0d2a1a	0.9036	Khoe-San	119
    HSQ136	RotterdamFarm	L0d	L0d1b2b1b1	0.9742	Khoe-San	360
    HSQ137	Swellendam	L0d	L0d1b2b1b1	0.9722	Khoe-San	135
    HSQ138	Swellendam	L0d	L0d1c	0.9646	Khoe-San	602
    HSQ139	Swellendam	L0d	L0d1b2b1b1	0.9578	Khoe-San	452
    HSQ140	Swellendam	L0d	L0d1b	0.6471	Khoe-San	339
    HSQ144	Swellendam	L0d	L0d1a1b	0.9011	Khoe-San	272
    HSQ146	Swellendam	L0d	L0d2a1	0.9627	Khoe-San	257
    HSQ147	Swellendam	L0d	L0d1b2b2b1	0.9365	Khoe-San	301
    HSQ154	Railton	L0d	L0d1b2b1b1	0.8527	Khoe-San	95
    HSQ155	Railton	L0d	L0d1b2b1b1	0.987	Khoe-San	329
    HSQ156	Railton	L0d	L0d2a1a	0.8935	Khoe-San	61
    HSQ157	Railton	L0d	L0d1b2b1b1	0.908	Khoe-San	123
    HSQ158	Railton	L1b	L1b1a15	0.9676	Bantu-speaker	134
    HSQ086	Slangriver	L2a	L2a1a2	1.0072	Bantu-speaker	591
    HSQ120	Stomsvlei	L2a	L2a1a2	0.9083	Bantu-speaker	93
    HSQ121	Stomsvlei	L2a	L2a1a2	1.0119	Bantu-speaker	133
    HSQ148	Railton	L2a	L2a1b1a	0.9878	Bantu-speaker	570
    HSQ001	Melkhoutfontein	L3d	L3d3a1	0.9242	Bantu-speaker	158
    HSQ096	Suurbraak	L3e	L3e1a	1.0158	Bantu-speaker	84
    HSQ134	RotterdamFarm	L3e	L3e3b	0.8497	Bantu-speaker	65
    HSQ153	Railton	L3e	L3e3a	0.9538	Bantu-speaker	260
    HSQ093	Suurbraak	L4b	L4b2a2c	0.9613	East-African	248
    HSQ132	RotterdamFarm	L5a	L5a2	0.9832	East-African	825
    HSQ009	Melkhoutfontein	M2a	M2a1a	1.3414	Asian	45
    HSQ040	Riversdale	M2a	M2a1a	1.0244	Asian	530
    HSQ141	Swellendam	M2a	M2a1a	0.9954	Asian	113
    HSQ080	Slangriver	M2b	M2b1	0.9678	Asian	249
    HSQ162	Railton	M33	M33a2a	0.9095	Asian	62
    HSQ128	RotterdamFarm	M5a	M5a2a	0.932	Asian	120
    HSQ102	Suurbraak	U2a	U2a1a	0.9334	Asian	56
    HSQ054	Heidelberg	U7a	U7a3a	1.1032	Asian	229
    Table S7 - Summary results for the Ychr haplogroup assignment for the 58 male Hessequa-descendants. Haplogroup assigned with SNAPPY (Severson et al. 2018).

    Code:
    ID	Place	Major Y haplogroup	Specific Y haplogroup	Accuracy Score	Ancestry*
    HSQ033	Riversdale	A1b	A1b1a1	1	Khoe-San
    HSQ050	Heidelberg	A1b	A1b1b2a	0.8	Khoe-San
    HSQ100	Suurbraak	A1b	A1b1b	1	Khoe-San
    HSQ156	Railton	A1b	A1b1b2a	0.8	Khoe-San
    HSQ107	Suurbraak	B2b	B2b	1	Bantu-speaker
    HSQ085	Slangriver	C	C	1	Asian
    HSQ089	Suurbraak	C	C	1	Asian
    HSQ005	Melkhoutfontein	E1b1a1	E1b1a1a1c1a1	0.875	Bantu-speaker
    HSQ049	Heidelberg	E1b1a1	E1b1a1a1c1a1	0.882	Bantu-speaker
    HSQ054	Heidelberg	E1b1a1	E1b1a1a1c1a1	0.882	Bantu-speaker
    HSQ058	Heidelberg	E1b1a1	E1b1a1a1d1	0.867	Bantu-speaker
    HSQ105	Suurbraak	E1b1a1	E1b1a1a1c1a1	0.882	Bantu-speaker
    HSQ120	Stomsvlei	E1b1a1	E1b1a1a1c1a1	0.882	Bantu-speaker
    HSQ138	SwellemdamMuseum 	E1b1a1	E1b1a1a1d1a	0.875	Bantu-speaker
    HSQ145	SwellemdamMuseum 	E1b1a1	E1b1a1a1c1a1	0.882	Bantu-speaker
    HSQ151	Railton	E1b1a1	E1b1a1	0.833	Bantu-speaker
    HSQ017	Riversdale	E1b1b1	E1b1b1b2b	0.9	East-Africa
    HSQ067	Heidelberg	E1b1b1	E1b1b1b2b	0.889	East-Africa
    HSQ086	Slangriver	E1b1b1	E1b1b1b2b	0.889	East-Africa
    HSQ136	RotterdamFarm	E1b1b1	E1b1b1b2b	0.9	East-Africa
    HSQ137	SwellemdamMuseum 	E1b1b1	E1b1b1b2b	0.9	East-Africa
    HSQ011	Melkhoutfontein	E2b	E2b1a	0.889	Bantu-speaker
    HSQ016	Melkhoutfontein	E2b	E2b1a	0.889	Bantu-speaker
    HSQ106	Suurbraak	G2a	G2a2b2a	1	European
    HSQ141	SwellemdamMuseum 	G2a	G2a2b	1	European
    HSQ072	Heidelberg	H	H	1	Asian
    HSQ117	Suurbraak	H	H	1	Asian
    HSQ132	RotterdamFarm	H	H	1	Asian
    HSQ019	Riversdale	I1	I1a2	0.947	European
    HSQ068	Heidelberg	I1	I1a2a1	0.947	European
    HSQ024	Riversdale	I2	I2a2a1c2a2	0.963	European
    HSQ083	Slangriver	I2	I2a2a1c2a	0.962	European
    HSQ140	SwellemdamMuseum 	I2	I2a2a1c2a2	0.963	European
    HSQ028	Riversdale	J2a	J2a1b	1	European
    HSQ045	Heidelberg	J2a	J2a	0.75	European
    HSQ029	Riversdale	O1a	O1a2	0.962	Asian
    HSQ064	Heidelberg	O1a	O1a2	0.962	Asian
    HSQ073	Heidelberg	O1a	O1a2	0.962	Asian
    HSQ131	RotterdamFarm	O1a	O1a	0.958	Asian
    HSQ139	SwellemdamMuseum 	O1a	O1a2	0.962	Asian
    HSQ006	Melkhoutfontein	R1a	R1a1a1b2	0.971	European
    HSQ134	RotterdamFarm	R1a	R1a1a1b2	0.971	European
    HSQ143	SwellemdamMuseum 	R1a	R1a1a1b2	0.971	European
    HSQ144	SwellemdamMuseum 	R1a	R1a1a1b1	0.971	European
    HSQ007	Melkhoutfontein	R1b	R1b1a2a1a2a1a	0.938	European
    HSQ008	Melkhoutfontein	R1b	R1b1a2a1a2a1a	0.938	European
    HSQ021	Riversdale	R1b	R1b1a2a1a	0.964	European
    HSQ023	Riversdale	R1b	R1b1a2a1a1c2b2	0.969	European
    HSQ034	Riversdale	R1b	R1b1a2a1a1c1	0.968	European
    HSQ036	Riversdale	R1b	R1b1a2a1a2a1a	0.938	European
    HSQ066	Heidelberg	R1b	R1b1a2a1a2a1a1	0.939	European
    HSQ075	Slangriver	R1b	R1b1a2a1a1c2b2	0.969	European
    HSQ135	RotterdamFarm	R1b	R1b1a2a1a	0.966	European
    HSQ149	Railton	R1b	R1b1a2a1a	0.966	European
    HSQ162	Railton	R1b	R1b1a2a1a1c2b2	0.969	European
    HSQ027	Riversdale	R2a	R2a1	0.952	Asian
    HSQ104	Suurbraak	R2a	R2a1	0.952	Asian
    HSQ118	Stomsvlei	R2a	R2a	0.95	Asian

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  3. #2
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    Congo Kinshasa United States of America
    Very interesting findings! We need another one on the westward spread of pastoralist into the Great Lakes region.

    I see a couple individuals, one Rwandan and another one Burundian outlier. Their Eurasian is between 25 to 30%. Makes me think they are Tutsis.

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  5. #3
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    Interesting paper, the distribution of the E lineages is similar to the paper on South African Bantu speakers in terms of the E haplogroup percentage. Just that there is lower East African and higher E2b1a. My MTDNA is very rare it seems.

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