Entwined African and Asian genetic roots of medieval peoples of the Swahili coast.

The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people1,2. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast3. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia4. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.

A nonanalog Pliocene ungulate community at Laetoli with implications for the paleoecology of Australopithecus afarensis.

The dietary guild structure of ungulate communities is a useful paleoecological tool for understanding the context of hominin paleobiology and evolution. Ungulates are well represented in the fossil record, and their dietary preferences reflect those of major habitat types. However, paleoecology relies on modern ecological patterns as analogs for recreating ecologies of the past. It has previously been suggested that for much of the Pliocene, no such modern analogs exist for the herbivore communities associated with hominins in eastern Africa. This study aims to determine whether the ungulate community associated with A. afarensis at the Pliocene site of Laetoli, Tanzania, shares similarities with extant communities or whether it lacks a modern analog. Our multiproxy approach using mesowear, hypsodonty, and stable carbon isotopes of tooth enamel to infer the diets of ungulates in the Upper Laetolil Beds shows that this community is dominated by browsers and mixed feeders and has a very low prevalence of grazers and frugivores. This dietary guild composition distinguishes the Upper Laetolil Beds from modern African communities and suggests either that the Upper Laetolil Beds had a unique vegetation structure which was able to support a higher diversity of browsing ungulates than that exists in African ecosystems today or that it retained an ungulate community that was resilient to environmental change. The Upper Laetolil Beds ungulate community is also unique relative to other mid-Pliocene communities in eastern Africa, some of which are similar to extant communities, while others, such as Laetoli, lack modern counterparts. This suggests that A. afarensis was a eurytopic species that inhabited a variety of ecosystems, including those with and without modern analogs. The co-occurrence of both analog and nonanalog communities in the Pliocene suggests that the transformation toward ungulate communities of modern aspect occurred asynchronously in eastern Africa.

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 Africa1-4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. 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.

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. Supplementary Information: The online version contains supplementary material available at 10.1007/s10914-021-09588-z.

Human burials at the Kisese II rockshelter, Tanzania.

OBJECTIVES: The Late Pleistocene and early Holocene in eastern Africa are associated with complex evolutionary and demographic processes that contributed to the population variability observed in the region today. However, there are relatively few human skeletal remains from this time period. Here we describe six individuals from the Kisese II rockshelter in Tanzania that were excavated in 1956, present a radiocarbon date for one of the individuals, and compare craniodental morphological diversity among eastern African populations. MATERIALS AND METHODS: This study used standard biometric analyses to assess the age, sex, and stature of the Kisese II individuals. Eastern African craniodental morphological variation was assessed using measures of dental size and a subset of Howells' cranial measurements for the Kisese II individuals as well as early Holocene, early pastoralist, Pastoral Neolithic, and modern African individuals. RESULTS: Our results suggest a minimum of six individuals from the Kisese II collections with two adults and four juveniles. While the dating for most of the burials is uncertain, one individual is directly radiocarbon dated to ~7.1 ka indicating that at least one burial is early Holocene in age. Craniodental metric comparisons indicate that the Kisese II individuals extend the amount of human morphological diversity among Holocene eastern Africans. CONCLUSIONS: Our findings contribute to a growing body of evidence that Late Pleistocene and early Holocene eastern Africans exhibited relatively high amounts of morphological diversity. However, the Kisese II individuals suggest morphological similarity at localized sites potentially supporting increased regionalization during the early Holocene.

Eyasi Plateau Paleontological Expedition, Laetoli, Tanzania, fossil specimen database 1998-2005.

The Eyasi Plateau Paleontological Expedition (EPPE) Laetoli specimen database contains 13716 records of plant and animal fossils (ca. 28248 specimens) collected by EPPE field teams working at Laetoli, Tanzania between 1998 and 2005. This dataset is a digital version of the original hard-copy specimen catalog, and it documents the discovery, stratigraphic provenience and taxonomic diversity of Plio-Pleistocene fauna and flora in northern Tanzania between 4.4 Ma and >200 ka. Laetoli is renowned for the discovery of important hominin fossils, including the lectotype for Australopithecus afarensis, one of our early hominin ancestors, the first record of Paranthropus aethiopicus outside Kenya-Ethiopia, and an early record of our own species Homo sapiens. This database is one of the few publicly available palaeoanthropological fossil datasets and serves as an example for expanding open access to primary fossil occurrence data in palaeoanthropology. The taxonomic identifications appearing in this dataset are the original field identifications and are provisional. Any taxonomic analysis employing this dataset should refer to updated taxonomic identifications published by specialists.

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.

How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.

A new fossil cercopithecid tibia from Laetoli and its implications for positional behavior and paleoecology.

Detailed analyses and comparisons of postcranial specimens of Plio-Pleistocene cercopithecids provide an opportunity to examine the recent evolutionary history and locomotor diversity in Old World monkeys. Studies examining the positional behavior and substrate preferences of fossil cercopithecids are also important for reconstructing the paleoenvironments of Plio-Pleistocene hominin sites. Here we describe a new fossil cercopithecid tibia (EP 1100/12) from the Australopithecus afarensis-bearing Upper Laetolil Beds (∼3.7 Ma) of Laetoli in northern Tanzania. The fossil tibia is attributed to cf. Rhinocolobus sp., which is the most common colobine at Laetoli. In addition to qualitative comparisons, the tibial shape of EP 1100/12 was compared to that of 190 extant cercopithecids using three-dimensional landmarks. Discriminant function analyses of the shape data were used to assess taxonomic affinity and shape variation relating to positional behavior. EP 1100/12 clustered with extant colobines, particularly the large-bodied genera Nasalis and Rhinopithecus. Comparisons reveal that EP 1100/12 belongs to a large-bodied monkey that engaged in arboreal pronograde quadrupedalism. These findings add further support to previous inferences that woodland and forest environments dominated the paleoenvironment of the Upper Laetolil Beds, which supported the diverse community of cercopithecids at Laetoli. The inferred paleoecology and the presence of large-bodied arboreally-adapted monkeys at Laetoli show that A. afarensis had access to a range of diverse habitats, including woodlands and forests. This supports the possibility that A. afarensis, with its potential range of positional capabilities, was able to utilize arboreal settings for food acquisition and refuge from predators.

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.

Protein sequences bound to mineral surfaces persist into deep time.

Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C).

Reconstructed Homo habilis type OH 7 suggests deep-rooted species diversity in early Homo.

Besides Homo erectus (sensu lato), the eastern African fossil record of early Homo has been interpreted as representing either a single variable species, Homo habilis, or two species. In the latter case, however, there is no consensus over the respective groupings, and which of the two includes OH 7, the 1.8-million-year-old H. habilis holotype. This partial skull and hand from Olduvai Gorge remains pivotal to evaluating the early evolution of the Homo lineage, and by priority names one or other of the two taxa. However, the distorted preservation of the diagnostically important OH 7 mandible has hindered attempts to compare this specimen with other fossils. Here we present a virtual reconstruction of the OH 7 mandible, and compare it to other early Homo fossils. The reconstructed mandible is remarkably primitive, with a long and narrow dental arcade more similar to Australopithecus afarensis than to the derived parabolic arcades of Homo sapiens or H. erectus. We find that this shape variability is not consistent with a single species of early Homo. Importantly, the jaw morphology of OH 7 is incompatible with fossils assigned to Homo rudolfensis and with the A.L. 666-1 Homo maxilla. The latter is morphologically more derived than OH 7 but 500,000 years older, suggesting that the H. habilis lineage originated before 2.3 million years ago, thus marking deep-rooted species diversity in the genus Homo. We also reconstructed the parietal bones of OH 7 and estimated its endocranial volume. At between 729 and 824 ml it is larger than any previously published value, and emphasizes the near-complete overlap in brain size among species of early Homo. Our results clarify the H. habilis hypodigm, but raise questions about its phylogenetic relationships. Differences between species of early Homo appear to be characterized more by gnathic diversity than by differences in brain size, which was highly variable within all taxa.