Reconstructing Prehistoric African Population Structure
Skoglund P, Thompson JC, Prendergast ME et al.
Publication Details
Comprehensive information about this research publication
Abstract
Summary of the research findings
We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.
Ancient DNA Samples
70 ancient DNA samples referenced in this publication
| Sample ID | Date/Era | Country | Locality | Sex | mtDNA | Y-DNA |
|---|---|---|---|---|---|---|
| I0595 | 1445 BCE | Kenya | Kilifi. Panga ya Saidi | M | L4b2a2 |
E-M293 |
| I0595 | 1445 BCE | Kenya | Kilifi. Panga ya Saidi | M | L4b2a2 |
E-M293 |
| I2966 | 7131 BCE | Malawi | Mzimba District. Hora | M | L0k2 |
B-M6557 |
| I2966 | 7131 BCE | Malawi | Mzimba District. Hora | M | L0k2 |
B-M6557 |
| I2967 | 6222 BCE | Malawi | Mzimba District. Hora | F | L0a2 |
|
| I2967 | 6222 BCE | Malawi | Mzimba District. Hora | F | L0a2 |
|
| I2967 | 6222 BCE | Malawi | Mzimba District. Hora | F | L0a2 |
|
| I2967 | 6222 BCE | Malawi | Mzimba District. Hora | F | L0a2 |
|
| I4468 | 4230 BCE | Malawi | Fingira | M | L0d1c |
B-M6557 |
| I4427 | 4227 BCE | Malawi | Fingira | M | L0d1b2b |
B-M8500 |
| I4421 | 3400 BCE | Malawi | Chencherere | F | L0k2 |
|
| I4422 | 3351 BCE | Malawi | Chencherere | F | L0k1 |
|
| I4426 | 542 BCE | Malawi | Fingira | F | L0f |
|
| I4421 | 3400 BCE | Malawi | Chencherere | F | L0k2 |
|
| I4422 | 3351 BCE | Malawi | Chencherere | F | L0k1 |
|
| I4426 | 542 BCE | Malawi | Fingira | F | L0f |
|
| I2967 | 6222 BCE | Malawi | Mzimba District. Hora | F | L0a2 |
|
| I2966 | 7131 BCE | Malawi | Mzimba District. Hora | M | L0k2 |
BT |
| I4427 | 4227 BCE | Malawi | Fingira | M | L0d1b2b |
B-M8500 |
| I4468 | 4230 BCE | Malawi | Fingira | M | L0d1c |
B-M6557 |
| MAL-015 | 2000 CE | Malawi | Blantyre // Yao | M | |
|
| MAL-032 | 2000 CE | Malawi | Blantyre // Yao | M | |
|
| MAL-043 | 2000 CE | Malawi | Chev // Chichewa | M | |
|
| MAL-025 | 2000 CE | Malawi | Chev // Ngoni | M | |
|
| MAL-026 | 2000 CE | Malawi | Chev // Ngoni | M | |
|
| MAL-124 | 2000 CE | Malawi | Chev Distr // Chichewa | M | |
|
| MAL-019 | 2000 CE | Malawi | Dedza // Chichewa | M | |
|
| MAL-005 | 2000 CE | Malawi | Dedza // Yao | M | |
|
| MAL-045 | 2000 CE | Malawi | Dowa // Chichewa | M | |
|
| MAL-079 | 2000 CE | Malawi | Karonga // Tumbuka | M | |
|
| MAL-099 | 2000 CE | Malawi | Karonga // Tumbuka | M | |
|
| MAL-122 | 2000 CE | Malawi | Lilongwe // Chichewa | M | |
|
| MAL-028 | 2000 CE | Malawi | Lilongwe // Chichewa | M | |
|
| MAL-101 | 2000 CE | Malawi | Machinga // Chichewa | M | |
|
| MAL-009 | 2000 CE | Malawi | Machinga // Yao | M | |
|
| MAL-197 | 2000 CE | Malawi | Majimba // Chichewa | M | |
|
| MAL-047 | 2000 CE | Malawi | Majimba // Tumbuka | M | |
|
| MAL-112 | 2000 CE | Malawi | Mangochi // Chichewa | M | |
|
| MAL-136 | 2000 CE | Malawi | Mangochi // Yao | M | |
|
| MAL-024 | 2000 CE | Malawi | Mangochi // Yao | M | |
|
| MAL-011 | 2000 CE | Malawi | Mchinga // Chichewa | M | |
|
| MAL-023 | 2000 CE | Malawi | Mchisi // Chichewa | M | |
|
| MAL-074 | 2000 CE | Malawi | Mzimba // Ngoni | M | |
|
| MAL-058 | 2000 CE | Malawi | Mzimba // Tumbuka | M | |
|
| MAL-059 | 2000 CE | Malawi | Mzimba // Tumbuka | M | |
|
| MAL-065 | 2000 CE | Malawi | Mzimba // Tumbuka | M | |
|
| MAL-073 | 2000 CE | Malawi | Mzimba // Tumbuka | M | |
|
| MAL-206 | 2000 CE | Malawi | Mzimba // Tumbuka | M | |
|
| MAL-014 | 2000 CE | Malawi | Nambuma // Chichewa | M | |
|
| MAL-018 | 2000 CE | Malawi | Nkotankhota // Chichewa | M | |
|
| MAL-097 | 2000 CE | Malawi | Nlekata bay // | M | |
|
| MAL-012 | 2000 CE | Malawi | Salima // Chichewa | M | |
|
| MAL-050 | 2000 CE | Malawi | Zomba // Chichewa | M | |
|
| MAL-196 | 2000 CE | Malawi | Zomba // chiyao | M | |
|
| UCT473 | 665 BCE | South Africa | Kasteelberg | F | L0d1a1a |
|
| UCT386 | 88 BCE | South Africa | Faraoskop Rock Shelter | M | L0d1b2b1b |
A-M51 |
| UCT473 | 665 CE | South Africa | Kasteelberg | F | L0d1a1a |
|
| UCT386 | 88 BCE | South Africa | Faraoskop Rock Shelter | M | L0d1b2b1b |
A-M51 |
| KhoesanLeipzigHunter | 403 BCE | South Africa | St. Helena | M | L0d2c1 |
A-M51 |
| I0589 | 586 BCE | Tanzania | Zanzibar. Kuumbi Cave | F | L4b2a2c |
|
| I1048 | 539 BCE | Tanzania | Zanzibar. Pemba Island. Mapangani Cave | F | L0a |
CT-M168 |
| I2298 | 1319 BCE | Tanzania | Zanzibar. Pemba Island. Mapangani Cave | F | L2a1a2 |
|
| I1048 | 539 BCE | Tanzania | Zanzibar. Pemba Island. Mapangani Cave | F | L0a |
CT-M168 |
| I0589 | 586 BCE | Tanzania | Zanzibar. Kuumbi Cave | F | L4b2a2c |
|
| I3726 | 1204 BCE | Tanzania | Luxmanda. UVS40 | F | L2a1 |
|
| I1048 | 539 BCE | Tanzania | Zanzibar. Pemba Island. Mapangani Cave | F | L0a |
CT-M168 |
| I3726 | 1204 BCE | Tanzania | Luxmanda. UVS40 | F | L2a1 |
|
| I1048 | 539 CE | Tanzania | Zanzibar. Pemba Island. Mapangani Cave | F | L0a |
|
| I2298 | 1319 CE | Tanzania | Zanzibar. Pemba Island. Mapangani Cave | F | L2a1a2 |
|
| I0589 | 586 CE | Tanzania | Zanzibar. Kuumbi Cave | F | L4b2a2c |
|
Analysis
Comprehensive review of ancestry and genetic findings
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