Disruption of trait-environment relationships in African megafauna occurred in the middle Pleistocene

Mammalian megafauna have been critical to the functioning of Earth's biosphere for millions of years. However, since the Plio-Pleistocene, their biodiversity has declined concurrently with dramatic environmental change and hominin evolution. While these biodiversity declines are well-documented, their implications for the ecological function of megafaunal communities remain uncertain. Here, we adapt ecometric methods to evaluate whether the functional link between communities of herbivorous, eastern African megafauna and their environments (i.e., functional trait-environment relationships) was disrupted as biodiversity losses occurred over the past 7.4 Ma. Herbivore taxonomic and functional diversity began to decline during the Pliocene as open grassland habitats emerged, persisted, and expanded. In the mid-Pleistocene, grassland expansion intensified, and climates became more variable and arid. It was then that phylogenetic diversity declined, and the trait-environment relationships of herbivore communities shifted significantly. Our results divulge the varying implications of different losses in megafaunal biodiversity. Only the losses that occurred since the mid-Pleistocene were coincident with a disturbance to community ecological function. Prior diversity losses, conversely, occurred as the megafaunal species and trait pool narrowed towards those adapted to grassland environments.

Oldest evidence of abundant C4 grasses and habitat heterogeneity in eastern Africa

The assembly of Africa's iconic C₄ grassland ecosystems is central to evolutionary interpretations of many mammal lineages, including hominins. C₄ grasses are thought to have become ecologically dominant in Africa only after 10 million years ago (Ma). However, paleobotanical records older than 10 Ma are sparse, limiting assessment of the timing and nature of C₄ biomass expansion. This study uses a multiproxy design to document vegetation structure from nine Early Miocene mammal site complexes across eastern Africa. Results demonstrate that between ~21 and 16 Ma, C₄ grasses were locally abundant, contributing to heterogeneous habitats ranging from forests to wooded grasslands. These data push back the oldest evidence of C₄ grass-dominated habitats in Africa-and globally-by more than 10 million years, calling for revised paleoecological interpretations of mammalian evolution.

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.

Giant dwarf crocodiles from the Miocene of Kenya and crocodylid faunal dynamics in the late Cenozoic of East Africa

We describe two new osteolaemine crocodylids from the Early and early Middle Miocene of Kenya: Kinyang mabokoensis tax. nov. (Maboko, 15 Ma) and Kinyang tchernovi tax. nov. (Karungu and Loperot, 18 Ma). Additional material referable to Kinyang is known from Chianda and Moruorot. The skull was broad and dorsoventrally deep, and the genus can be diagnosed based on the combined presence of a partial overbite, a subdivided fossa for the lateral collateral ligament on the surangular, and a maxilla with no more than 13 alveoli. Phylogenetic analyses based on morphological and combined morphological and molecular data support a referral of Kinyang to Osteolaeminae, and morphological data alone put the new taxon at the base of Euthecodontini. Some Kinyang maxillae preserve blind pits on the medial caviconchal recess wall. Kinyang co‐occurs with the osteolaemine Brochuchus at some localities, and together, they reinforce the phylogenetic disparity between early Neogene osteolaemine‐dominated faunas and faunas dominated by crocodylines beginning in the Late Miocene in the Kenya Rift. The causes of this turnover remain unclear, though changes in prevailing vegetation resulting from tectonic and climatic drivers may provide a partial explanation.

Ancient proteins provide evidence of dairy consumption in eastern Africa

Consuming the milk of other species is a unique adaptation of Homo sapiens, with implications for health, birth spacing and evolution. Key questions nonetheless remain regarding the origins of dairying and its relationship to the genetically-determined ability to drink milk into adulthood through lactase persistence (LP). As a major centre of LP diversity, Africa is of significant interest to the evolution of dairying. Here we report proteomic evidence for milk consumption in ancient Africa. Using liquid chromatography tandem mass spectrometry (LC-MS/MS) we identify dairy proteins in human dental calculus from northeastern Africa, directly demonstrating milk consumption at least six millennia ago. Our findings indicate that pastoralist groups were drinking milk as soon as herding spread into eastern Africa, at a time when the genetic adaptation for milk digestion was absent or rare. Our study links LP status in specific ancient individuals with direct evidence for their consumption of dairy products.

Hominin dental remains from the Pliocene localities at Lomekwi, Kenya (1982-2009)

Increasing evidence for both taxonomic diversity and early stone manufacture during the Pliocene highlights the importance of the hominin fossil record from this epoch in eastern Africa. Here, we describe dental remains from Lomekwi (West Turkana, Kenya), which date from between 3.2 and 3.5 Ma. The sample was collected between 1982 and 2009 and includes five gnathic specimens and a total of 67 teeth (mostly isolated permanent postcanine teeth). Standard linear dimensions indicate that, although the Lomekwi teeth are relatively small, there is broad overlap in size with contemporary Australopithecus afarensis and Australopithecus deyiremeda specimens at most tooth positions. However, some dental characters differentiate this sample from these species, including a relatively large P₄ and M₃ compared with the M₁, a high incidence of well-developed protostylids, and specific accessory molar cuspules. Owing to a lack of well-preserved tooth crowns (and the complete absence of mandibular teeth) in the holotype and paratype of Kenyanthropus platyops, and limited comparable gnathic morphology in the new specimens, it cannot be determined whether these Lomekwi specimens should be attributed to this species. Attribution of these specimens is further complicated by a lack of certainty about position along the tooth row of many of the molar specimens. More comprehensive shape analyses of the external and internal morphology of these specimens, and additional fossil finds, would facilitate the taxonomic attribution of specimens in this taxonomically diverse period of human evolution.

Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.

Introduction to special issue Kanapoi: Paleobiology of a Pliocene site in Kenya

This paper introduces this Special Issue of the Journal of Human Evolution entitled "Kanapoi: Paleobiology of a Pliocene site in Kenya." Kanapoi, West Turkana, Kenya, is part of the Omo-Turkana Basin and is the type site of the earliest known genus of Australopithecus, A. anamensis. Kanapoi preserves among the earliest earliest evidence of Australopithecus in deposits dated between 4.195 to 4.108 million years old. Explored by several teams since the 1960s, the Kanapoi sediments have yielded a rich and abundant fauna, providing important information about the paleoenvironments and the context surrounding the earliest evolution of the genus Australopithecus, as well as about the evolution and biogeography of African Pliocene vertebrate faunas.

Cercopithecid fossils from Kanapoi, West Turkana, Kenya (2007-2015)

Recent fieldwork at Kanapoi has expanded the sample of fossil cercopithecids, facilitating a re-appraisal of their taxonomy. The assemblage now includes at least one species of cercopithecin, two papionins, and two colobines. The guenon Nanopithecus browni is similar in dental size to extant Miopithecus. We tentatively re-affirm the identification of Parapapio cf. ado and confirm the presence of Theropithecus. The colobines include a small form tentatively attributed to Kuseracolobus and a second larger species. The Kanapoi fossils represent the oldest occurrences of guenons in Africa and of the important genus Theropithecus, the most abundant and widespread primate in the Neogene of Africa. In the assemblage, Parapapio cf. ado is the most abundant form, comprising the majority of specimens. All of the other taxa are comparatively rare. Colobines make up a small part of the Kanapoi fossil assemblage compared to most other contemporary sites, including Allia Bay, Kenya, where, like Kanapoi, Australopithecus anamensis has been found. The presence of Theropithecus is consistent with the presence of some relatively open habitat at Kanapoi. While the ecological preferences of the small cercopithecin are unknown, most guenons are associated with relatively wooded habitats, as are most colobines, suggesting the availability of at least some wooded areas.

Comparative isotopic evidence from East Turkana supports a dietary shift within the genus Homo

It has been suggested that a shift in diet is one of the key adaptations that distinguishes the genus Homo from earlier hominins, but recent stable isotopic analyses of fossils attributed to Homo in the Turkana Basin show an increase in the consumption of C₄ resources circa 1.65 million years ago, significantly after the earliest evidence for Homo in the eastern African fossil record. These data are consistent with ingesting more C₄ plants, more animal tissues of C₄ herbivores, or both, but it is also possible that this change reflects factors unrelated to changes in the palaeobiology of the genus Homo. Here we use new and published carbon and oxygen isotopic data (n = 999) taken from large-bodied fossil mammals, and pedogenic carbonates in fossil soils, from East Turkana in northern Kenya to investigate the context of this change in the isotope signal within Homo. By targeting taxa and temporal intervals unrepresented or undersampled in previous analyses, we were able to conduct the first comprehensive analysis of the ecological context of hominin diet at East Turkana during a period crucial for detecting any dietary and related behavioural differences between early Homo (H. habilis and/or H. rudolfensis) and Homo erectus. Our analyses suggest that the genus Homo underwent a dietary shift (as indicated by δ¹³C_ena and δ¹⁸O_ena values) that is (1) unrelated to changes in the East Turkana vegetation community and (2) unlike patterns found in other East Turkana large mammals, including Paranthropus and Theropithecus. These data suggest that within the Turkana Basin a dietary shift occurred well after we see the first evidence of early Homo in the region.

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.

Dental microwear and Pliocene paleocommunity ecology of bovids, primates, rodents, and suids at Kanapoi

Reconstructions of habitat at sites like Kanapoi are key to understanding the environmental circumstances in which hominins evolved during the early Pliocene. While Australopithecus anamensis shows evidence of terrestrial bipedality traditionally associated with a more open setting, its enamel has low δ¹³C values consistent with consumption of C₃ foods, which predominate in wooded areas of tropical Africa. Habitat proxies, ranging from paleosols and their carbonates to associated herbivore fauna and their carbon isotope ratios, suggest a heterogeneous setting with both grass and woody plant components, though the proportions of each have been difficult to pin down. Here we bring dental microwear texture analysis of herbivorous fauna to bear on the issue. We present texture data for fossil bovids, primates, rodents, and suids (n = 107 individuals in total) from the hominin bearing deposits at Kanapoi, and interpret these in the light of closely related extant mammals with known differences in diet. The Kanapoi bovid results, for example, are similar to those for extant variable grazers or graze-browse intermediate taxa. The Kanapoi suid data vary by taxon, with one similar to the pattern of extant grazers and the other more closely resembling mixed feeders. The Kanapoi primates and rodents are more difficult to associate with a specific environment, though it seems that grass was likely a component in the diets of both. All taxa evince microwear texture patterns consistent with a mosaic of discrete microhabitats or a heterogeneous setting including both tree and grass components.

A pterodactyloid pterosaur from the Upper Cretaceous Lapurr sandstone, West Turkana, Kenya

An isolated pterosaurian caudal cervical (~ postcervical) vertebra was recovered from the Upper Cretaceous Lapurr sandstone ofWest Turkana, northwestern Kenya. The vertebral centrum is short, wide, and dorsoventrally compressed. Although the specimen is lightly built similar to most pterosaurs, it is here referred to Pterodactyloidea and tentatively to the Azhdarchidae in that it lacks pneumatic features on both the centrum and neural arch. This represents one of the few pterosaurs recovered from the entirety of Afro-Arabia, the first pterosaur recovered from the Cretaceous of East Africa, and, significantly, a specimen that was recovered from fluvial deposits rather than the near-shore marine setting typical of most pterosaur discoveries.

Anterior dental evolution in the Australopithecus anamensis-afarensis lineage

Australopithecus anamensis is the earliest known species of the Australopithecus-human clade and is the likely ancestor of Australopithecus afarensis. Investigating possible selective pressures underlying these changes is key to understanding the patterns of selection shaping the origins and early evolution of the Australopithecus-human clade. During the course of the Au. anamensis-afarensis lineage, significant changes appear to occur particularly in the anterior dentition, but also in jaw structure and molar form, suggesting selection for altered diet and/or food processing. Specifically, canine tooth crown height does not change, but maxillary canines and P(3)s become shorter mesiodistally, canine tooth crowns become more symmetrical in profile and P(3)s less unicuspid. Canine roots diminish in size and dimorphism, especially relative to the size of the postcanine teeth. Molar crowns become higher. Tooth rows become more divergent and symphyseal form changes. Dietary change involving anterior dental use is also suggested by less intense anterior tooth wear in Au. afarensis. These dental changes signal selection for altered dietary behaviour and explain some differences in craniofacial form between these taxa. These data identify Au. anamensis not just as a more primitive version of Au. afarensis, but as a dynamic member of an evolving lineage leading to Au. afarensis, and raise intriguing questions about what other evolutionary changes occurred during the early evolution of the Australopithecus-human clade, and what characterized the origins of the group.

Implications of new early Homo fossils from Ileret, east of Lake Turkana, Kenya

Sites in eastern Africa have shed light on the emergence and early evolution of the genus Homo. The best known early hominin species, H. habilis and H. erectus, have often been interpreted as time-successive segments of a single anagenetic evolutionary lineage. The case for this was strengthened by the discovery of small early Pleistocene hominin crania from Dmanisi in Georgia that apparently provide evidence of morphological continuity between the two taxa. Here we describe two new cranial fossils from the Koobi Fora Formation, east of Lake Turkana in Kenya, that have bearing on the relationship between species of early Homo. A partial maxilla assigned to H. habilis reliably demonstrates that this species survived until later than previously recognized, making an anagenetic relationship with H. erectus unlikely. The discovery of a particularly small calvaria of H. erectus indicates that this taxon overlapped in size with H. habilis, and may have shown marked sexual dimorphism. The new fossils confirm the distinctiveness of H. habilis and H. erectus, independently of overall cranial size, and suggest that these two early taxa were living broadly sympatrically in the same lake basin for almost half a million years.