View Full Version : Male-biased migration from East Africa introduced pastoralism into southern Africa

12-07-2021, 06:07 PM
Mario Vicente, Imke Lankheet, Thembi Russell, Nina Hollfelder, Vinet Coetzee, Himla Soodyall, Michael De Jongh & Carina M. Schlebusch
(Paper (https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01193-z)Published: 07 December 2021)

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.

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.

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 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:

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).

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

12-09-2021, 07:58 AM
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.

12-09-2021, 11:46 PM
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.