Mitochondrial DNA data indicate an introduction through Mainland Southeast Asia for Australian dingoes and Polynesian domestic dogs

In the late stages of the global dispersal of dogs, dingoes appear in the Australian archaeological record 3500 years BP, and dogs were one of three domesticates brought with the colonization of Polynesia, but the introduction routes to this region remain unknown. This also relates to questions about human history, such as to what extent the Polynesian culture was introduced with the Austronesian expansion from Taiwan or adopted en route, and whether pre-Neolithic Australia was culturally influenced by the surrounding Neolithic world. We investigate these questions by mapping the distribution of the mtDNA founder haplotypes for dingoes (A29) and ancient Polynesian dogs (Arc1 and Arc2) in samples across Southern East Asia (n = 424) and Island Southeast Asia (n = 219). All three haplotypes were found in South China, Mainland Southeast Asia and Indonesia but absent in Taiwan and the Philippines, and the mtDNA diversity among dingoes indicates an introduction to Australia 4600–18 300 years BP. These results suggest that Australian dingoes and Polynesian dogs originate from dogs introduced to Indonesia via Mainland Southeast Asia before the Neolithic, and not from Taiwan together with the Austronesian expansion. This underscores the complex origins of Polynesian culture and the isolation from Neolithic influence of the pre-Neolithic Australian culture

Biological anthropology in the Indo-Pacific Region: New approaches to age-old questions

Biological anthropological research, the study of both modern and past humans, is a burgeoning field in the Indo-Pacific region. It is becoming increasingly apparent that the unique environments of the Indo-Pacific have resulted in an archaeological record that does not necessarily align with those in the northern hemisphere. New, regionally-specific archaeological models are being developed, and biological anthropological research has an important role to play in establishing past human experience within these models. In the Indo-Pacific, research using ancient and modern human tissues is adding insight into global processes of prehistoric settlement and migrations, subsistence change and human biosocial adaptation. This review synthesises current themes in biological anthropology in this region. It highlights the diverse methods and approaches used by biological anthropologists to address globally-relevant archaeological questions. In recent decades a collaborative approach between archaeologists, biological anthropologists and local communities has become the norm in the region. The many positive outcomes of this multi-disciplinary approach are highlighted here through the use of regionally-specific case studies. This review ultimately aims to stimulate further collaborations between archaeologists, biological anthropologists and the communities in the region, and demonstrate how the evidence from Indo-Pacific research may be relevant to global archaeological models

Determinación de la madurez térmica de los carbones de la formación guaduas en el Sinclinal Checua - Lenguazaque

66 páginas : ilustraciones color, figuras, tablas.Se realizó un muestreo de los mantos de carbón en la formación Guaduas, flanco Occidental de la cuenca del sinclinal Checua-Lenguazaque, municipios de Sutatausa, Lenguazaque, Guachetá, Raquira y Samaca; con el fin de calcular el gradiente paleogeotérmico a partir del análisis reflectancia media de la vitrinita. El estudio determinó que los carbones de la zona tienen un rango de reflectancia media de 0.64 a 1.6, clasificándose como carbones desde bituminosos bajos volátiles hasta bituminosos altos volátiles. Para la determinación del gradiente paleogetermico se utilizó la fórmula propuesta por Baker, C & Pawlewicz, M, en la cual el valor de la reflectancia se tiene como variable principal; estableciéndose que para esta cuenta el gradiente geotérmico está en un rango de 520 C/Km hacia el sector de Sutatausa y de 1000C/Km hacia el sector de Samacá; asumiéndose que esta variación en el gradiente se debe al mayor efecto del fallamiento en la zona de Samacá que en Sutatausa.Bibliografía y webgrafía: páginas 64-65PregradoIngeniero Geólog

From cheek swabs to consensus sequences : an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes

Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. Results: Here we present an ‘A to Z’ protocol for obtaining complete human mitochondrial (mtDNA) genomes – from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). Conclusions: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual ‘modules’ can be swapped out to suit available resources

Ancient DNA of guinea pigs (Cavia spp.) indicates a probable new center of domestication and pathways of global distribution

Guinea pigs (Cavia spp.) have a long association with humans. From as early as 10,000 years ago they were a wild food source. Later, domesticated Cavia porcellus were dispersed well beyond their native range through pre-Columbian exchange networks and, more recently, widely across the globe. Here we present 46 complete mitogenomes of archaeological guinea pigs from sites in Peru, Bolivia, Colombia, the Caribbean, Belgium and the United States to elucidate their evolutionary history, origins and paths of dispersal. Our results indicate an independent centre of domestication of Cavia in the eastern Colombian Highlands. We identify a Peruvian origin for the initial introduction of domesticated guinea pigs (Cavia porcellus) beyond South America into the Caribbean. We also demonstrate that Peru was the probable source of the earliest known guinea pigs transported, as part of the exotic pet trade, to both Europe and the southeastern United States. Finally, we identify a modern reintroduction of guinea pigs to Puerto Rico, where local inhabitants use them for food. This research demonstrates that the natural and cultural history of guinea pigs is more complex than previously known and has implications for other studies regarding regional to global-scale studies of mammal domestication, translocation, and distribution.Fil: Lord, E.. Stockholms Universitet; Suecia. University of Otago; Nueva ZelandaFil: Collins, C.. University of Otago; Nueva ZelandaFil: deFrance, S.. University of Florida; Estados UnidosFil: LeFebvre, M. J.. University of Florida; Estados UnidosFil: Pigière, F.. Universidad de Dublin; IrlandaFil: Eeckhout, P.. Université Libre de Bruxelles; BélgicaFil: Erauw, C.. Université Libre de Bruxelles; BélgicaFil: Fitzpatrick, S. M.. State University of Oregon; Estados UnidosFil: Healy, P. F.. Trent University; CanadáFil: Martínez Polanco, M. F.. Muséum National d'Histoire Naturelle; Francia. Universitat Rovira I Virgili; España. Institut Català de Paleoecologia Humana i Evolució Social; EspañaFil: Garcia, J. L.. Stetson University; Estados UnidosFil: Ramos Roca, E.. Universidad de los Andes. Facultad de Ciencias Sociales. Departamento de Antropología; ColombiaFil: Delgado Burbano, Miguel Eduardo. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Área Antropológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. School of Life Sciences and Human Phenome Institute Fudan University; ChinaFil: Sánchez Urriago, A.. Instituto Colombiano de Antropología e Historia; ColombiaFil: Peña Léon, G. A.. Universidad Nacional de Colombia; ColombiaFil: Toyne, J. M.. University of Florida; Estados UnidosFil: Dahlstedt, A.. Arizona State University; Estados UnidosFil: Moore, K. M.. State University of Pennsylvania; Estados UnidosFil: Laguer Diaz, C.. University of Florida; Estados UnidosFil: Zori, C.. Baylor University; Estados UnidosFil: Matisoo-Smith, E.. University of Otago; Nueva Zeland

Evolutionary relationships and divergence times among the native rats of Australia

Background The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. Results Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades. Conclusions Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats

Characterizing Genetic Diversity of Contemporary Pacific Chickens Using Mitochondrial DNA Analyses

Background\ud Mitochondrial DNA (mtDNA) hypervariable region (HVR) sequences of prehistoric Polynesian chicken samples reflect dispersal of two haplogroups—D and E—by the settlers of the Pacific. The distribution of these chicken haplogroups has been used as an indicator of human movement. Recent analyses suggested similarities between prehistoric Pacific and South American chicken samples, perhaps reflecting prehistoric Polynesian introduction of the chicken into South America. These analyses have been heavily debated. The current distribution of the D and E lineages among contemporary chicken populations in the Western Pacific is unclear, but might ultimately help to inform debates about the movements of humans that carried them.\ud \ud Objectives\ud We sought to characterize contemporary mtDNA diversity among chickens in two of the earliest settled archipelagoes of Remote Oceania, the Marianas and Vanuatu.\ud \ud Methods\ud We generated HVR sequences for 43 chickens from four islands in Vanuatu, and for 5 chickens from Guam in the Marianas.\ud \ud Results\ud Forty samples from Vanuatu and three from Guam were assigned to haplogroup D, supporting this as a Pacific chicken haplogroup that persists in the Western Pacific. Two haplogroup E lineages were observed in Guam and two in Vanuatu. Of the E lineages in Vanuatu, one was identical to prehistoric Vanuatu and Polynesian samples and the other differed by one polymorphism. Contrary to our expectations, we observed few globally distributed domesticate lineages not associated with Pacific chicken dispersal. This might suggest less European introgression of chickens into Vanuatu than expected. If so, the E lineages might represent lineages maintained from ancient Pacific chicken introductions. The Vanuatu sample might thus provide an opportunity to distinguish between maintained ancestral Pacific chicken lineages and replacement by global domesticates through genomic analyses, which could resolve questions of contemporary haplogroup E chicken relationships and inform interpretations of debated sequences from archaeological samples

Complex history of dog (Canis familiaris) origins and translocations in the Pacific revealed by ancient mitogenomes

Archaeological evidence suggests that dogs were introduced to the islands of Oceania via Island Southeast Asia around 3,300 years ago, and reached the eastern islands of Polynesia by the fourteenth century AD. This dispersal is intimately tied to human expansion, but the involvement of dogs in Pacific migrations is not well understood. Our analyses of seven new complete ancient mitogenomes and five partial mtDNA sequences from archaeological dog specimens from Mainland and Island Southeast Asia and the Pacific suggests at least three dog dispersal events into the region, in addition to the introduction of dingoes to Australia. We see an early introduction of dogs to Island Southeast Asia, which does not appear to extend into the islands of Oceania. A shared haplogroup identified between Iron Age Taiwanese dogs, terminal-Lapita and post-Lapita dogs suggests that at least one dog lineage was introduced to Near Oceania by or as the result of interactions with Austronesian language speakers associated with the Lapita Cultural Complex. We did not find any evidence that these dogs were successfully transported beyond New Guinea. Finally, we identify a widespread dog clade found across the Pacific, including the islands of Polynesia, which likely suggests a post-Lapita dog introduction from southern Island Southeast Asia

The GenoChip: A New Tool for Genetic Anthropology

The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and nonmedical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, they were designed for medical genetic studies and contain medically related markers that are inappropriate for global population genetic studies. GenoChip, the Genographic Project’s new genotyping array, was designed to resolve these issues and enable higher resolution research into outstanding questions in genetic anthropology. TheGenoChip includes ancestry informativemarkers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all knownY-chromosome andmtDNAhaplogroups. The chip was carefully vetted to avoid inclusion ofmedically relevant markers. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highestmean FST, attesting to its ability to discern subpopulations. The chip performances are illustrated in a principal component analysis for 14 worldwide populations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of approximately 12,000 Y-chromosomal and approximately 3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPswithout any known health,medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and population genetics