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 ecology of Australopithecus anamensis in the early Pliocene of Kanapoi, Kenya.

Australopithecus anamensis is a pivotal species in human evolution. It is likely to be the direct ancestor of Australopithecus afarensis and the species that may have given rise to the Homo and Paranthropus lineages. It had a suite of adaptations for habitual bipedalism and a diet that differed from that of earlier hominin species. Under what environmental and ecological conditions did this suite of adaptations arise? The early Pliocene site of Kanapoi in the Lake Turkana Basin of Kenya has the largest sample of A. anamensis in eastern Africa and a rich record of fossil vertebrates. Most Kanapoi fossils are chronologically well constrained by radiometrically dated tephras between the ages of 4.2 and 4.1 million years ago. Sedimentological, isotopic, and faunal data indicate that the environments of Kanapoi during the early Pliocene had a complex range of vegetation types that included closed woodlands, shrubs, and grasslands near a river (for most of the sequence) or lake. These were dynamic landscapes that could shift rapidly from fluvial to lacustrine conditions, and then back. Australopithecus anamensis shared its environments with at least 10 species of very large herbivores, which undoubtedly played a major role in modifying the landscape by opening wooded areas and providing pathways for bipedal hominins. Hominins may have competed for terrestrial resources with abundant suids (Nyanzachoerus and Notochoerus) and for arboreal resources with monkeys (Parapapio being the most common cercopithecid). Kanapoi had a formidable group of predators that included a very abundant species of hyena (Parahyaena howelli), two sabre-tooth felids (Dinofelis and Homotherium), a giant otter (Enhydriodon cf. dikikae), and three species of crocodiles. Various measures of abundance indicate that A. anamensis was an important component of the Kanapoi early Pliocene ecosystems, and that its key adaptations allowed this species to thrive in complex and dynamic landscapes.

Dietary changes of large herbivores in the Turkana Basin, Kenya from 4 to 1 Ma.

A large stable isotope dataset from East and Central Africa from ca. 30 regional collection sites that range from forest to grassland shows that most extant East and Central African large herbivore taxa have diets dominated by C4 grazing or C3 browsing. Comparison with the fossil record shows that faunal assemblages from ca. 4.1-2.35 Ma in the Turkana Basin had a greater diversity of C3-C4 mixed feeding taxa than is presently found in modern East and Central African environments. In contrast, the period from 2.35 to 1.0 Ma had more C4-grazing taxa, especially nonruminant C4-grazing taxa, than are found in modern environments in East and Central Africa. Many nonbovid C4 grazers became extinct in Africa, notably the suid Notochoerus, the hipparion equid Eurygnathohippus, the giraffid Sivatherium, and the elephantid Elephas. Other important nonruminant C4-grazing taxa switched to browsing, including suids in the lineage Kolpochoerus-Hylochoerus and the elephant Loxodonta. Many modern herbivore taxa in Africa have diets that differ significantly from their fossil relatives. Elephants and tragelaphin bovids are two groups often used for paleoecological insight, yet their fossil diets were very different from their modern closest relatives; therefore, their taxonomic presence in a fossil assemblage does not indicate they had a similar ecological function in the past as they do at present. Overall, we find ecological assemblages of C3-browsing, C3-C4-mixed feeding, and C4-grazing taxa in the Turkana Basin fossil record that are different from any modern ecosystem in East or Central Africa.

Early Pleistocene third metacarpal from Kenya and the evolution of modern human-like hand morphology.

Despite discoveries of relatively complete hands from two early hominin species (Ardipithecus ramidus and Australopithecus sediba) and partial hands from another (Australopithecus afarensis), fundamental questions remain about the evolution of human-like hand anatomy and function. These questions are driven by the paucity of hand fossils in the hominin fossil record between 800,000 and 1.8 My old, a time interval well documented for the emergence and subsequent proliferation of Acheulian technology (shaped bifacial stone tools). Modern and Middle to Late Pleistocene humans share a suite of derived features in the thumb, wrist, and radial carpometacarpal joints that is noticeably absent in early hominins. Here we show that one of the most distinctive features of this suite in the Middle Pleistocene to recent human hand, the third metacarpal styloid process, was present ∼1.42 Mya in an East African hominin from Kaitio, West Turkana, Kenya. This fossil thus provides the earliest unambiguous evidence for the evolution of a key shared derived characteristic of modern human and Neandertal hand morphology and suggests that the distinctive complex of radial carpometacarpal joint features in the human hand arose early in the evolution of the genus Homo and probably in Homo erectus sensu lato.

Diet of Theropithecus from 4 to 1 Ma in Kenya.

Theropithecus was a common large-bodied primate that co-occurred with hominins in many Plio-Pleistocene deposits in East and South Africa. Stable isotope analyses of tooth enamel from T. brumpti (4.0-2.5 Ma) and T. oswaldi (2.0-1.0 Ma) in Kenya show that the earliest Theropithecus at 4 Ma had a diet dominated by C4 resources. Progressively, this genus increased the proportion of C4-derived resources in its diet and by 1.0 Ma, had a diet that was nearly 100% C4-derived. It is likely that this diet was comprised of grasses or sedges; stable isotopes cannot, by themselves, give an indication of the relative importance of leaves, seeds, or underground storage organs to the diet of this primate. Theropithecus throughout the 4- to 1-Ma time range has a diet that is more C4-based than contemporaneous hominins of the genera Australopithecus, Kenyanthropus, and Homo; however, Theropithecus and Paranthropus have similar proportions of C4-based resources in their respective diets.

Stable isotope-based diet reconstructions of Turkana Basin hominins.

Hominin fossil evidence in the Turkana Basin in Kenya from ca. 4.1 to 1.4 Ma samples two archaic early hominin genera and records some of the early evolutionary history of Paranthropus and Homo. Stable carbon isotopes in fossil tooth enamel are used to estimate the fraction of diet derived from C3 or C4 resources in these hominin taxa. The earliest hominin species in the Turkana Basin, Australopithecus anamensis, derived nearly all of its diet from C3 resources. Subsequently, by ca. 3.3 Ma, the later Kenyanthropus platyops had a very wide dietary range--from virtually a purely C3 resource-based diet to one dominated by C4 resources. By ca. 2 Ma, hominins in the Turkana Basin had split into two distinct groups: specimens attributable to the genus Homo provide evidence for a diet with a ca. 65/35 ratio of C3- to C4-based resources, whereas P. boisei had a higher fraction of C4-based diet (ca. 25/75 ratio). Homo sp. increased the fraction of C4-based resources in the diet through ca. 1.5 Ma, whereas P. boisei maintained its high dependency on C4-derived resources.

Diet of Paranthropus boisei in the early Pleistocene of East Africa.

The East African hominin Paranthropus boisei was characterized by a suite of craniodental features that have been widely interpreted as adaptations to a diet that consisted of hard objects that required powerful peak masticatory loads. These morphological adaptations represent the culmination of an evolutionary trend that began in earlier taxa such as Australopithecus afarensis, and presumably facilitated utilization of open habitats in the Plio-Pleistocene. Here, we use stable isotopes to show that P. boisei had a diet that was dominated by C(4) biomass such as grasses or sedges. Its diet included more C(4) biomass than any other hominin studied to date, including its congener Paranthropus robustus from South Africa. These results, coupled with recent evidence from dental microwear, may indicate that the remarkable craniodental morphology of this taxon represents an adaptation for processing large quantities of low-quality vegetation rather than hard objects.

First record of a parapithecid primate from the Oligocene of Kenya.

Recent excavations in northwestern Kenya have recovered a vertebrate fauna of late early or early late Oligocene age. Among the mammal remains, a fragmentary lower jaw and an isolated upper molar have been attributed to a small primate, Lokonepithecus manai gen. et sp. nov. Lokonepithecus is a primitive member of the Parapithecidae and possibly most closely related to Apidium from the Fayum. The new primate from Kenya is the youngest parapithecid known and its occurrence in the Oligocene of Kenya suggests that sub-Saharan Africa probably played a major role in the evolutionary history of several groups of mammals.

Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar's aye-aye.

In 1967 G.G. Simpson described three partial mandibles from early Miocene deposits in Kenya that he interpreted as belonging to a new strepsirrhine primate, Propotto. This interpretation was quickly challenged, with the assertion that Propotto was not a primate, but rather a pteropodid fruit bat. The latter interpretation has not been questioned for almost half a century. Here we re-evaluate the affinities of Propotto, drawing upon diverse lines of evidence to establish that this strange mammal is a strepsirrhine primate as originally suggested by Simpson. Moreover, our phylogenetic analyses support the recognition of Propotto, together with late Eocene Plesiopithecus from Egypt, as African stem chiromyiform lemurs that are exclusively related to the extant aye-aye (Daubentonia) from Madagascar. Our results challenge the long-held view that all lemurs are descended from a single ancient colonization of Madagascar, and present an intriguing alternative scenario in which two lemur lineages dispersed from Africa to Madagascar independently, possibly during the later Cenozoic.

Hippos stem from the longest sequence of terrestrial cetartiodactyl evolution in Africa.

According to molecular data, hippopotamuses and cetaceans form a clade excluding other extant cetartiodactyls. Despite a wealth of spectacular specimens documenting cetacean evolution, this relationship remains poorly substantiated by the fossil record. Indeed, the evolutionary path leading from the hippo-cetacean ancestor to Hippopotamidae is plagued by missing fossil data and phylogenetic uncertainties. Only an origination within the extinct anthracotheres is compatible with molecular results, substantial filling of phyletic gaps and recent discoveries of early Miocene hippopotamids. Yet, the anthracothere stock that gave rise to Hippopotamidae has not been identified. Consequently, recent phylogenetic accounts do not properly integrate the anthracotheriid hypothesis, and relate Hippopotamidae to a stretched ghost lineage and/or close to Suina. Here we describe a new anthracothere from Lokone (Kenya) that unambiguously roots the Hippopotamidae into a well-identified group of bothriodontines, the first large mammals to invade Africa. The hippos are deeply anchored into the African Paleogene.