Ancient DNA and deep population structure in sub-Saharan African foragers

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa(1-4). Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations(3,5). Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch. DNA analysis of 6 individuals from eastern and south-central Africa spanning the past approximately 18,000 years, and of 28 previously published ancient individuals, provides genetic evidence supporting hypotheses of increasing regionalization at the end of the Pleistocene.info:eu-repo/semantics/publishedVersio

Middle and Later Stone Age chronology of Kisese II rockshelter (UNESCO World Heritage Kondoa Rock-Art Sites), Tanzania

The archaeology of East Africa during the last ~65,000 years plays a central role in debates about the origins and dispersal of modern humans, Homo sapiens. Despite the historical importance of the region to these discussions, reliable chronologies for the nature, tempo, and timing of human behavioral changes seen among Middle Stone Age (MSA) and Later Stone Age (LSA) archaeological assemblages are sparse. The Kisese II rockshelter in the Kondoa region of Tanzania, originally excavated in 1956, preserves a ≥ 6-m-thick archaeological succession that spans the MSA/LSA transition, with lithic artifacts such as Levallois and bladelet cores and backed microliths, the recurrent use of red ochre, and >5,000 ostrich eggshell beads and bead fragments. Twenty-nine radiocarbon dates on ostrich eggshell carbonate make Kisese II one of the most robust chronological sequences for understanding archaeological change over the last ~47,000 years in East Africa. In particular, ostrich eggshell beads and backed microliths appear by 46–42 ka cal BP and occur throughout overlying Late Pleistocene and Holocene strata. Changes in lithic technology suggest an MSA/LSA transition that began 39–34.3 ka, with typical LSA technologies in place by the Last Glacial Maximum. The timing of these changes demonstrates the time-transgressive nature of behavioral innovations often linked to the origins of modern humans, even within a single region of Africa

Middle and Later Stone Age chronology of Kisese II rockshelter (UNESCO World Heritage Kondoa Rock-Art Sites), Tanzania

The archaeology of East Africa during the last ~65,000 years plays a central role in debates about the origins and dispersal of modern humans, Homo sapiens. Despite the historical importance of the region to these discussions, reliable chronologies for the nature, tempo, and timing of human behavioral changes seen among Middle Stone Age (MSA) and Later Stone Age (LSA) archaeological assemblages are sparse. The Kisese II rockshelter in the Kondoa region of Tanzania, originally excavated in 1956, preserves a ≥ 6-m-thick archaeological succession that spans the MSA/LSA transition, with lithic artifacts such as Levallois and bladelet cores and backed microliths, the recurrent use of red ochre, and >5,000 ostrich eggshell beads and bead fragments. Twenty-nine radiocarbon dates on ostrich eggshell carbonate make Kisese II one of the most robust chronological sequences for understanding archaeological change over the last ~47,000 years in East Africa. In particular, ostrich eggshell beads and backed microliths appear by 46–42 ka cal BP and occur throughout overlying Late Pleistocene and Holocene strata. Changes in lithic technology suggest an MSA/LSA transition that began 39–34.3 ka, with typical LSA technologies in place by the Last Glacial Maximum. The timing of these changes demonstrates the time-transgressive nature of behavioral innovations often linked to the origins of modern humans, even within a single region of Africa

The Thorny Issue of African Porcupines: a New Mandible of Hystrix makapanensis from Olduvai Gorge (Tanzania) and Rediagnosis of the Species

Several porcupine taxa are reported from the middle Miocene to the early Holocene in the Old World. Among these, five species of the subfamily Hystricinae occurred in Africa approximately in the last 6 Ma: the extinct Hystrix makapanensis, Hystrix leakeyi, and Xenohystrix crassidens and the still living Hystrix africaeaustralis and Hystrix cristata. The large-sized H. makapanensis is reported from numerous sites in East and South Africa between the early Pliocene and Early Pleistocene. In this paper, we describe a new mandible of H. makapanensis from the world-renowned Tanzanian paleontological and archeological site of Olduvai Gorge (HWK West; lowermost Bed II; ca. 1.8–1.7 Ma). The discovery of the new mandible triggered a comprehensive review of the entire African record of H. makapanensis. In particular, we describe or re-analyze the samples from South Africa (Makapansgat Limeworks, Gondolin, Kromdraai, Swartkrans, and Sterkfontein), Tanzania (Olduvai and Laetoli), Ethiopia (Omo Shungura and Hadar), and Kenya (Chemeron), enriching the quantity of specimens confidently referable to this species and above all improving the information on its craniodental anatomy. On this basis, we: (1) propose an emended diagnosis of H. makapanensis; (2) point out the morphological and biometric differences between H. makapanensis and other African Hystricinae (also in terms of body mass); and (3) broaden the knowledge on the geographical and chronological distribution of this extinct species

Kisese II in East African context.

<p>(A) Schematic map of East Africa and archaeological sites discussed in text, (B) boulders that form Kisese II below the Irangi Hills as seen in 2015, with arrow pointing to site, (C) view over the Masaai Steppe from Kisese II in 1956, (D) the 1956 Inskeep excavations in progress, (E) view of the shelter in 2015 with retaining wall, and (F) North excavation wall during the 1956 excavation; white labels record spit (level), with spit XX is the base of the excavation at the time the photograph was taken. Spit I (59 cm) and spit II (21 cm) are thicker than the remainder, which are each ~15-cm-thick. 1956 photographs by R. Inskeep (published with permission of J. Charlson, executor of the Inskeep estate), 2015 photographs by C. Tryon.</p

Age-depth relationship of ¹⁴C-dated samples.

<p>Calibrated radiocarbon dates are plotted by depth (estimated as midpoint of excavation spit). Blue dashed-line boxes indicate portions of the stratigraphic sequence with no dated specimens. Yellow bars indicate temporal spans with no measured radiocarbon dates. Dates calibrated using OxCal v.4.2 software [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192029#pone.0192029.ref065" target="_blank">65</a>] and a combined IntCal13/SHCal13 calibration curve [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192029#pone.0192029.ref066" target="_blank">66</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192029#pone.0192029.ref067" target="_blank">67</a>]. The insert shows the youngest dates from Spits I-II.</p

Radiocarbon (¹⁴C) dates from Kisese II.

<p>Radiocarbon (¹⁴C) dates from Kisese II.</p