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.DNA taxonomy ͉ equid evolution ͉ macroevolution ͉ phylogeny ͉ ancient DNA T he original sequence of horse fossils found in the 1870s by paleontologist Othaniel Charles Marsh, and popularized by Thomas Huxley (1), has been enriched by a large fossil record over the years and has now become one of the most widely known examples of macroevolutionary change (2). The original linear model of gradual modification of fox-sized animals (Hyracothere horses) to the modern forms has been replaced by a more complex tree, showing periods of explosive diversification and branch extinctions over 55 MY (3). The end of the Early Miocene (15-20 MYA) marks a particularly important transition, separating an initial phase of small leafy browsers from a second phase of more diverse animals, exhibiting tremendous body-size plasticity and modifications in tooth morphology (4). This explosive diversification has been accompanied by several stages of geographic extension from North America to the rest of the New and Old Worlds, so that by the end of the Miocene (5 MYA) more than a dozen distinct genera are represented in the fossil record (4) (Astrohippus,

Patagonian megafaunal extinctions reveal synergistic roles of climate change and human impacts.

South America lost around 52 genera of mammals during a worldwide event known as the Late Quaternary Extinction episode. More than 80% of South American mammals weighing > 44 kg succumbed. Analysis of the megafaunal extinction chronology in relation to human arrival and major climate changes have revealed slightly different extinction patterns in different eco‐regions of the continent, highlighting the importance of detailed regional analysis in order to understand how the possible drivers of extinction operated. Here we present an analysis of the megafaunal extinction in the Última Esperanza (UE) area of southwestern Patagonia, Chile. We have compiled a comprehensive chronology of megafaunal extinctions and earliest human occupation between 18–7 cal ka BP, based on radiocarbon dates from published literature. We calculated confidence intervals using the GRIWM method to estimate the times of human arrival and megafaunal local extinctions, and then compared these events to the timing of major climate and vegetation changes, fire frequency increase, and the Reclús volcanic eruption. Our results suggest that a combination of human impacts and climate–vegetation change drove megafaunal extinctions in the UE area, with the balance of factors being taxon specific; the volcanic eruption does not seem to have exacerbated extinctions. Competition between humans and mega‐carnivores seems to be the most plausible cause for the extinction of the mega‐carnivores. Coexistence of humans with extinct horses, extinct camels, and mylodonts for several thousand years rules out a scenario of blitzkrieg overkill of megafauna by humans. The transition of vegetation from cold grasslands to Nothofagus forests corresponds with the disappearance of Hippidion saldiasi and Lama cf. owenii. The later full establishment of Nothofagus forests and an increasing fire frequency coincided with the disappearance of mylodonts. A climate‐driven reduction of open environments plausibly reduced herbivore's populations making them susceptible to local extinction.

The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilise collagen sequence information, both separately and in combination with published mtDNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not 64 Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America. The sloths (Xenarthra, Folivora), nowadays a taxonomically narrow (6 species in 2 genera) component of the fauna of South and Central America 1,2 were once a highly successful clade of placental mammals as measured by higher-level diversity (Fig. 1). Diverging sometime in the Palaeogene from their closest relatives, the anteaters (Vermilingua), folivorans greatly expanded their diversity and range, eventually reaching North America as well as the West Indies 3-8. During the late Cenozoic sloth lineage diversity may have expanded and contracted several times 9. Final collapse occurred in the late Quaternary (end-Pleistocene on the continents, mid

Almost all large carnivorans (Carnivora; > 20 kg) that inhabited South America became extinct around the Late Pleistocene–Early Holocene transition. Two exceptions were species of coyote‐sized Dusicyon, one insular (D.  australis) and one continental (D.  avus). The extinction of the former is a resolved matter, but that of D. avus, found in the Patagonian and Pampean regions, is still poorly understood. Using the Gaussian‐Resampled Inverse‐Weighted McInerny method we present new radiocarbon evidence indicating that its disappearance occurred in very recent times (about 324–496 years cal bp). We found no evidence to support a role for hybridization with domestic dogs in causing the extirpation of this fox. Climatic change may have reduced its distributional range, as has happened with other mammals, although not to the extent of explaining its extinction. Climatic change, however, coupled with increased anthropogenic impacts such as hunting, domestic dogs, and/or other aspects relating to the impact of European colonization in South America's southern cone, were the probable main drivers of the recent extinction of D. avus.

Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hippidion could have diverged from the lineage leading to modern equids before 10 Ma. In contrast, a much later divergence date, with Hippidion nesting within modern equids, was indicated by partial ancient mitochondrial DNA sequences. Here, we characterized eight Hippidion complete mitochondrial genomes at 3.4-386.3-fold coverage using target-enrichment capture and next-generation sequencing. Our dataset revealsthat the two morphospecies sequenced (H. saldiasi and H. principale) formed a monophyletic clade, basal to extant and extinct Equus lineages. This contrasts with previous genetic analyses and supports Hippidion as a distinct genus, in agreement with palaeontological models. We date the Hippidion split from Equus at 5.6-6.5 Ma, suggesting an early divergence in North America prior to the colonization of South America, after the formation of the Panamanian Isthmus 3.5 Ma and the Great American Biotic Interchange.

No abstract

The Tremarctinae are a subfamily of bears endemic to the New World, including two of the largest terrestrial mammalian carnivores that have ever lived: the giant, short-faced bears Arctodus simus from North America and Arctotherium angustidens from South America (greater than or equal to 1000 kg). Arctotherium angustidens became extinct during the Early Pleistocene, whereas Arctodus simus went extinct at the very end of the Pleistocene. The only living tremarctine is the spectacled bear (Tremarctos ornatus), a largely herbivorous bear that is today only found in South America. The relationships among the spectacled bears (Tremarctos), South American short-faced bears (Arctotherium) and North American shortfaced bears (Arctodus) remain uncertain. In this study, we sequenced a mitochondrial genome from an Arctotherium femur preserved in a Chilean cave. Our molecular phylogenetic analyses revealed that the South American short-faced bears were more closely related to the extant South American spectacled bear than to the North American short-faced bears. This result suggests striking convergent evolution of giant forms in the two groups of short-faced bears (Arctodus and Arctotherium), potentially as an adaptation to dominate competition for megafaunal carcasses.