Alfredo Prieto

Evolution, Systematics, and Phylogeography of Pleistocene Horses in the New World: A Molecular Perspective

The rich fossil record of horses has made them a classic example of evolutionary processes. However, while the overall picture of equid evolution is well known, the details are surprisingly poorly understood, especially for the later Pliocene and Pleistocene, c. 3 million to 0.01 million years (Ma) ago, and nowhere more so than in the Americas. There is no consensus on the number of equid species or even the number of lineages that existed in these continents. Likewise, the origin of the endemic South American genus Hippidion is unresolved, as is the phylogenetic position of the “stilt-legged” horses of North America. Using ancient DNA sequences, we show that, in contrast to current models based on morphology and a recent genetic study, Hippidion was phylogenetically close to the caballine (true) horses, with origins considerably more recent than the currently accepted date of c. 10 Ma. Furthermore, we show that stilt-legged horses, commonly regarded as Old World migrants related to the hemionid asses of Asia, were in fact an endemic North American lineage. Finally, our data suggest that there were fewer horse species in late Pleistocene North America than have been named on morphological grounds. Both caballine and stilt-legged lineages may each have comprised a single, wide-ranging species.

Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes

Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

EVALUACIÓN DE LA MODALIDAD CULTURAL FELL 1 EN MAGALLANES

Se presenta una evaluacion de la modalidad cultural Fell 1 de Magallanes y sus relaciones extrarregionales. Se revisa la historia de la investigacion sobre el tema, los diferentes aspectos que le dan identidad a esta modalidad cultural, su rango cronologico y su relacion con el paisaje del Pleistoceno Final y de la transicion Pleistoceno-Holoceno. Finalmente, se analizan los principales problemas de interpretacion de los contextos Fell 1 y se proyectan algunas lineas de accion para orientar la investigacion futura en relacion al tema

Hunter-gatherers, biogeographic barriers and the development of human settlement in Tierra del Fuego

Tierra del Fuego represents the southernmost limit of human settlement in the Americas. While people may have started to arrive there around 10 500 BP, when it was still connected to the mainland, the main wave of occupation occurred 5000 years later, by which time it had become an island. The co-existence in the area of maritime hunter-gatherers (in canoes) with previous terrestrial occupants pre-echoes the culturally distinctive groups encountered by the first European visitors in the sixteenth century. The study also provides a striking example of interaction across challenging natural barriers.

Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids

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 reveals that 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.

New evidence of the sabertooth cat Smilodon (Carnivora: Machairodontinae) in the late Pleistocene of southern Chilean Patagonia

Surpatagonia es particularmente rica en mamiferos finiplesitocenos, particularmente camelidos, equidos y xenartros. Los carnivoros, por su parte, se encuentran representados en menor numero en el registro paleontologico. Dentro de estos, el genero Smilodon, es de particular interes debido a que su presencia en la region no ha sido convincentemente demostrada. En este trabajo presentamos evidencia dental que permite confirmar la presencia de Smilodon populator (Lund) en la region. Esta evidencia corresponde al registro mas sureno de este taxon y al paso final en la colonizacion de America del Sur despues del Gran Intercambio Biotico Americano. Un fechado radiocarbonico directo AMS indica que los restos de Patagonia del Sur corresponden a los registros mas tardios para este genero en el subcontinente.

The southernmost bear: Pararctotherium (Carnivora, Ursidae, Tremarctinae) in the latest Pleistocene of southern Patagonia, Chile

FRANCISCO J. PREVOSTI1, LEOPOLDO H. SOIBELZON2, ALFREDO PRIETO3, MANUEL SAN ROMAN4, and FLAVIA MORELLO3, 1Facultad de Ciencias Naturales y Museo (U.N.L.P.), cc 223, 1900 La Plata, Buenos Aires, Argentina, protocyon@hotmail.com; 2CONICET, Departamento Cientı́fico Paleontologı́a de Vertebrados, Museo de La Plata, Paseo del Bosque, 1900 La Plata, Buenos Aires, Argentina; 3Centro de Estudios del Hombre Austral, Instituto de la Patagonia, UMAG Casilla 113-D, Punta Arenas, Chile; 4Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica Chilena, Casilla 113-D, Punta Arenas, Chile

Considerations on the Paper “Morphological Convergence in Hippidion and Equus (Amerhippus) South American Equids Elucidated by Ancient DNAAnalysis’’, by Ludovic Orlando, Véra Eisenmann, Frédéric Reynier, PaulSondaar, Catherine Hänni

The paper on South American horse DNA is very interesting but the conclusions are very surprising. In our opinion, the results need a more exhaustive review and new analyses to be done because the material used in the study belongs to the genus Hippidion and not to the subgenus Equus (Amerhippus). Orlando et al. 2003 conclude that the samples belong to Equus (Amerhippus) and not to Hippidion based on the following.

Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America

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 short-faced 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.

PRESENCIA DE RHEIDAE EN TIERRA DEL FUEGO DURANTE LA TRANSICIÓN PLEISTOCENO-HOLOCENO. IMPLICANCIAS BIOGEOGRÁFICAS Y PALEOECOLÓGICAS

*** ABSTRACT Preliminary information related with a taxon-date of 9.960 ± 50 years BP for Rheidae will be introduced in this paper. This date was obtained on a Rheidae first phalanx from the Tres Arroyos 1 site, north of Tierra del Fuego, Chile. Biogeographical, palaeoecological and archaeological implications are discussed.