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.

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.

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.

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.

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.

Pliocene bats (Chiroptera) from Kanapoi, Turkana Basin, Kenya.

Fossil bats from the Pliocene of Africa are extremely rare, especially in East Africa where meager records have been reported only from two localities in the Omo River Basin Shungura Formation and from a scattering of localities in the Afar Depression, both in Ethiopia. Here we report on a diverse assemblage of bats from Kanapoi in the Turkana Basin that date to approximately 4.19 million years ago. The Kanapoi bat community consists of four different species of fruit bats including a new genus and two new species as well as five species of echolocating bats, the most common of which are two new species of the molossid genus Mops. Additionally, among the echolocating bats, a new species of the emballonurid Saccolaimus is documented at Kanapoi along with an additional Saccolaimus species and a potentially new species of the nycterid Nycteris. Compared to other East African Pliocene bat assemblages, the Kanapoi bat community is unique in preserving molossids and curiously lacks any evidence of cave dwelling bats like rhinolophids or hipposiderids, which are both common at other East African sites. The bats making up the Kanapoi community all typically roost in trees, with some preferring deeper forests and larger trees (molossids), while the others (pteropodids, nycterids and emballonurids) roost in trees near open areas. Living fruit bats that are related to Kanapoi species typically forage for fruits along the margins of forests and in open savannah. The echolocating forms from Kanapoi consist of groups that aerially hawk for insects in open areas between patches of forest and along water courses. The habitats preferred by living relatives of the Kanapoi bats are in agreement with those constructed for Kanapoi based on other lines of evidence.

Diets of mammalian fossil fauna from Kanapoi, northwestern Kenya.

Carbon isotope ratios of mammalian teeth from the Kanapoi site in northern Kenya are interpreted in the context of C3 and C4 derived resources to investigate the paleoecology of Australopithecus anamensis. δ13C values of large mammals, when compared at the taxon level, show an ecosystem that is strongly biased towards mixed feeders and browsers. However, sufficient C4 resources were present such that some C4 dominated grazers were also present in the large mammal fauna. Analyses of micromammals shows that their diets were C3 dominated or C3-C4 mixed. Carbon isotope studies of primates shows that the major primate tribes-Colobini, Papioini, Hominini-all made some use of C4 resources in their respective diets; the Hominini had a higher fraction of C3 diet resources than the other primate tribes represented in the fossil record.

Rodents and other terrestrial small mammals from Kanapoi, north-western Kenya.

Excavations at Kanapoi in north-western Kenya have yielded the most numerically abundant and taxonomically diverse early Pliocene (4.19 Ma) terrestrial small mammal assemblage known from Kenya. A minimum of 15 species are reported, including soricids, sengis, leporids, and rodents: all taxa are referable to extant genera, with the exception of the murine rodent, Saidomys. The majority of the terrestrial small mammals are derived from a bone bed at Nzube's Mandible Site, closely associated with the holotype mandible of Australopithecus anamensis. A smaller number were surface-collected or obtained from screening at several other sites, including the Bat Site. Most small mammals from Nzube's Mandible Site and the Bat Site likely represent prey accumulated as regurgitated pellets from owls, in particular barn owls or giant eagle owls. The small mammal fauna is dominated by the spiny mouse, Acomys: the next most commonly recovered taxa are the multimammate mouse, Mastomys, and the African gerbil, Gerbilliscus. Comparisons of the Kanapoi fauna to other eastern African late Miocene-Pliocene (and one Pleistocene) faunas at the generic level suggest the greatest similarity is to Lemudong'o, Kenya, and Omo B and Aramis, Ethiopia. Further similarities with other localities such as Laetoli, Tanzania, and Hadar, Ethiopia, suggest the existence of a corridor for dispersal along the East African Rift Valley between Ethiopia, Kenya, and Tanzania in the early Pliocene. Further comparisons of the relative abundances of individuals in different families (or subfamilies) emphasize the distinctiveness of the Kanapoi small mammal fauna. The Kanapoi fauna is likely derived from a heterogeneous but relatively arid environment.

A diminutive Pliocene guenon from Kanapoi, West Turkana, Kenya.

Although modern guenons are diverse and abundant in Africa, the fossil record of this group is surprisingly sparse. In 2012 the West Turkana Paleo Project team recovered two associated molar teeth of a small primate from the Pliocene site of Kanapoi, West Turkana, Kenya. The teeth are bilophodont and the third molar lacks a hypoconulid, which is diagnostic for Cercopithecini. The teeth are the same size as those of extant Miopithecus, which is thought to be a dwarfed guenon, as well as a partial mandible preserving two worn teeth, previously recovered from Koobi Fora, Kenya, which was also tentatively identified as a guenon possibly allied with Miopithecus. Tooth size and proportions, as well as analysis of relative cusp size and shearing crest development clearly separate the fossil from all known guenons. Based on the Kanapoi material, we erect a new genus and species, Nanopithecus browni gen. et sp. nov. The small size of the specimen suggests either that dwarfing occurred early in the lineage, or at least twice independently, depending on the relationship of the new species with extant Miopithecus. Further, the distinctive habitat and geographic separation from Miopithecus suggests that the origin of small body size is not uniquely linked to the current habitat of Miopithecus, and possibly that relatives of extant Miopithecus were much more widely distributed in the past. This in turn argues caution in using extant biogeography in models of the origins of at least some guenons.

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 δ13Cena and δ18Oena 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.

A systematic revision of Proconsul with the description of a new genus of early Miocene hominoid.

For more than 80 years, Proconsul has held a pivotal position in interpretations of catarrhine evolution and hominoid diversification in East Africa. The majority of what we 'know' about Proconsul, however, derives from abundant younger fossils found at the Kisingiri localities on Rusinga and Mfangano Islands rather than from the smaller samples found at Koru--the locality of the type species, Proconsul africanus--and other Tinderet deposits. One outcome of this is seen in recent attempts to expand the genus "Ugandapithecus" (considered here a junior subjective synonym of Proconsul), wherein much of the Tinderet sample was referred to that genus based primarily on differentiating it from the Kisingiri specimens rather than from the type species, P. africanus. This and other recent taxonomic revisions to Proconsul prompted us to undertake a systematic review of dentognathic specimens attributed to this taxon. Results of our study underscore and extend the substantive distinction of Tinderet and Ugandan Proconsul (i.e., Proconsul sensu stricto) from the Kisingiri fossils, the latter recognized here as a new genus. Specimens of the new genus are readily distinguished from Proconsul sensu stricto by morphology preserved in the P. africanus holotype, but also in I(1)s, lower incisors, upper and lower canines, and especially mandibular characteristics. A number of these differences are more advanced among Kisingiri specimens in the direction of crown hominoids. Proconsul sensu stricto is characterized by a suite of unique features that strongly unite the included species as a clade. There have been decades of contentious debate over the phylogenetic placement of Proconsul (sensu lato), due in part to there being a mixture of primitive and more advanced morphology within the single genus. By recognizing two distinct clades that, in large part, segregate these character states, we believe that better phylogenetic resolution can be achieved.

A 17-My-old whale constrains onset of uplift and climate change in east Africa.

Timing and magnitude of surface uplift are key to understanding the impact of crustal deformation and topographic growth on atmospheric circulation, environmental conditions, and surface processes. Uplift of the East African Plateau is linked to mantle processes, but paleoaltimetry data are too scarce to constrain plateau evolution and subsequent vertical motions associated with rifting. Here, we assess the paleotopographic implications of a beaked whale fossil (Ziphiidae) from the Turkana region of Kenya found 740 km inland from the present-day coastline of the Indian Ocean at an elevation of 620 m. The specimen is ∼ 17 My old and represents the oldest derived beaked whale known, consistent with molecular estimates of the emergence of modern strap-toothed whales (Mesoplodon). The whale traveled from the Indian Ocean inland along an eastward-directed drainage system controlled by the Cretaceous Anza Graben and was stranded slightly above sea level. Surface uplift from near sea level coincides with paleoclimatic change from a humid environment to highly variable and much drier conditions, which altered biotic communities and drove evolution in east Africa, including that of primates.