The Late Middle Pleistocene mammalian fauna of Oumm Qatafa Cave, Judean Desert: taxonomy, taphonomy and palaeoenvironment.

The Middle Pleistocene archaeological record of the southern Levant has proven key to understanding human evolution and intercontinental faunal biogeography. Knowledge of archaeological sites of that period in the southern Levant is biased, with most Middle Pleistocene localities in the Mediterranean areas in the north, despite the mosaic of environments that mark the entire region. A key Middle Pleistocene location in the Judean Desert - on the eastern margin of the Mediterranean zone - is the site of Oumm Qatafa, excavated in the early 1900s, which yielded a faunal collection spanning an estimated time period of 600-200 kya. Here, we present a revised taxonomy of the macromammalian fauna from the site, discuss the palaeoenvironmental implications of this assemblage, and relate the finds to other Pleistocene sites from the Levant. These data enable a more precise palaeoenvironmental reconstruction which attests to an open landscape, but with the addition of a mesic Mediterranean component close by. In addition, detailed taphonomic observations on butchery marks and Fourier transform infrared spectroscopy analysis of burnt bone link the fauna for the first time to anthropogenic activities in the cave.

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.

The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.

First hominine remains from a ~1.0 million year old bone bed at Cornelia-Uitzoek, Free State Province, South Africa.

We report here on evidence of early Homo around 1.0 Ma (millions of years ago) in the central plains of southern Africa. The human material, a first upper molar, was discovered during the systematic excavation of a densely-packed bone bed in the basal part of the sedimentary sequence at the Cornelia-Uitzoek fossil vertebrate locality. We dated this sequence by palaeomagnetism and correlated the bone bed to the Jaramillo subchron, between 1.07 and 0.99 Ma. This makes the specimen the oldest southern African hominine remains outside the dolomitic karst landscapes of northern South Africa. Cornelia-Uitzoek is the type locality of the Cornelian Land Mammal Age. The fauna contains an archaic component, reflecting previous biogeographic links with East Africa, and a derived component, suggesting incipient southern endemism. The bone bed is considered to be the result of the bone collecting behaviour of a large predator, possibly spotted hyaenas. Acheulian artefacts are found in small numbers within the bone bed among the fossil vertebrates, reflecting the penecontemporaneous presence of people in the immediate vicinity of the occurrence. The hominine tooth was recovered from the central, deeper part of the bone bed. In size, it clusters with southern African early Homo and it is also morphologically similar. We propose that the early Homo specimen forms part of an archaic component in the fauna, in parallel with the other archaic faunal elements at Uitzoek. This supports an emergent pattern of archaic survivors in the southern landscape at this time, but also demonstrates the presence of early Homo in the central plains of southern Africa, beyond the dolomitic karst areas.

Lower Paleolithic hominin ecology at the fringe of the desert: Faunal remains from Bizat Ruhama and Nahal Hesi, Northern Negev, Israel.

The Southern Levant is a pivotal area for the study of hominin paleoecology during the Lower Paleolithic, because of its location on the out-of-Africa dispersal route and its significant ecological diversity. Important information has been gained by archaeofaunal studies, which usually reveal that exploitation of diverse Mediterranean environments with woodlands, marshes and lake margins, represents a dominant subsistence strategy for Lower Paleolithic hominins. Here, we present new taxonomic and taphonomic data from two sites in the southern coastal plain of the Southern Levant, at the fringe of the Negev Desert: Bizat Ruhama (Early Pleistocene) and Nahal Hesi (Middle Pleistocene). The sites preserve anthropogenic faunas, with the former signaling a marrow-exploitation strategy, perhaps related to scavenging from carnivore kills, and the latter showing evidence for primary access to fleshed ungulate carcasses. The species composition of these Northern Negev sites is unique for the Levantine Lower Paleolithic in that these sites lack typical woodland and riparian species, probably indicating an open, relatively uniform environment with patchy water sources and trees, much like this semiarid region today. Bizat Ruhama and Nahal Hesi are among the only Levantine Lower Paleolithic faunas associated with such a setting, thereby widening the known spectrum of environments exploited by hominins in the region. It is suggested that the two sites, coupled with the nearby Late Pleistocene evidence, reflect a largely stable semiarid environment on the northwestern fringe of the Negev Desert throughout much of the Pleistocene.

Sussemionus, a new subgenus of Equus (Perissodactyla, Mammalia).

The new subgenus of Equus, Sussemionus, is defined by peculiar dental characters so far unknown, or exceptional in late Pleistocene and extant Equus; it was in consequence assumed to be restricted to the early and middle Pleistocene. During that period, it was highly successful, ranging from North America to Ethiopia, and included dry-adapted (E. granatensis-like) and more humid-adapted (E. coliemensis-like) species. Recent molecular and osteological analyses concurred to prove its survival until ca 45 KYBP in Khakassia, southwest Siberia, Russia.

Revising the recent evolutionary history of equids using ancient DNA.

The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.

Geographic distribution of an extinct equid (Equus hydruntinus: Mammalia, Equidae) revealed by morphological and genetical analyses of fossils.

Equus hydruntinus inhabited Europe and the Middle East for more than 300 000 years. For a long time, palaeontological data failed to place E. hydruntinus into the equid phylogenetic tree, confronted with the fact that it shares primitive Equus characters with both zebras and asses, and derived characters with asses and hemiones. However, the study of a recently discovered skull points to a relationship with hemiones. Extraction of DNA from ancient samples from Crimea (E. hydruntinus) and Iran (E. cf. hydruntinus) yielded 134-288 bp of the mtDNA control region and 143 bp of the cytochrome b gene. This DNA analysis supports the proximity of E. hydruntinus and Equus hemionus suggested by skull and limb bone analyses, and rejects proximity to either Equus burchelli or the asses suggested by tooth morphology. Dental morphology may thus be of poor taxonomical value if used alone for establishing equid phylogenetic relationships. Furthermore, the small genetic distance between E. cf. hydruntinus of Iran and the classical E. hydruntinus of Crimea suggests that both samples belong to the same species. Accordingly, the geographic range of E. hydruntinus -- until now believed to be restricted to Europe, Israel, and Turkey -- can be extended towards East as far as Iran.

Morphological convergence in Hippidion and Equus (Amerhippus) South American equids elucidated by ancient DNA analysis.

Unusual equids named hippidions inhabited South America for more than 2 MY (million years). Like many other animals they succumbed to the worldwide climatic change that occurred 10 KY (thousand years) ago and completely disappeared during the great late Pleistocene megafaunal extinction. According to fossil records and numerous dental, cranial, and postcranial characters, Hippidion and Equus lineages are known to have diverged prior to 10 MY. Some equid bones from Rio Verde and Ultima Esperanza (Patagonia, Chile) dating back to the late Pleistocene period (8-13 KY) have been identified as Hippidion saldiasi, while a few teeth have been assigned to Equus. Six samples of those remains have been obtained from the Zoological Museum of Amsterdam for ancient DNA analysis to try to place Hippidion in the evolutive tree of Perissodactyla. Two samples of Hippidion and one sample of Equus yielded 241-394 bp of the mtDNA control region and 172-296 bp of the cytochrome b gene. Unexpectedly, all the sequences clustered deep inside the Equus genus, casting doubt on the initial identification of the bones. For paleontologists, one of the striking and classical diagnostic characters of Hippidion is their extremely short and massive metapodials, a probable locomotory adaptation to the Andine steep slopes. However, our DNA analysis reveals that a very Hippidion-like metapod might also have been possessed by another South American equid, i.e., Equus (Amerhippus), an interpretation supported by complementary anatomical observations. This adaptive convergence between members of the two South American equid genera may lead paleontologists to limb bone misidentification.

Geology and palaeontology of the Upper Miocene Toros-Menalla hominid locality, Chad.

All six known specimens of the early hominid Sahelanthropus tchadensis come from Toros-Menalla site 266 (TM 266), a single locality in the Djurab Desert, northern Chad, central Africa. Here we present a preliminary analysis of the palaeontological and palaeoecological context of these finds. The rich fauna from TM 266 includes a significant aquatic component such as fish, crocodiles and amphibious mammals, alongside animals associated with gallery forest and savannah, such as primates, rodents, elephants, equids and bovids. The fauna suggests a biochronological age between 6 and 7 million years. Taken together with the sedimentological evidence, the fauna suggests that S. tchadensis lived close to a lake, but not far from a sandy desert, perhaps the oldest record of desert conditions in the Neogene of northern central Africa.

A new hominid from the Upper Miocene of Chad, Central Africa.

The search for the earliest fossil evidence of the human lineage has been concentrated in East Africa. Here we report the discovery of six hominid specimens from Chad, central Africa, 2,500 km from the East African Rift Valley. The fossils include a nearly complete cranium and fragmentary lower jaws. The associated fauna suggest the fossils are between 6 and 7 million years old. The fossils display a unique mosaic of primitive and derived characters, and constitute a new genus and species of hominid. The distance from the Rift Valley, and the great antiquity of the fossils, suggest that the earliest members of the hominid clade were more widely distributed than has been thought, and that the divergence between the human and chimpanzee lineages was earlier than indicated by most molecular studies.