DNA and pacific commensal models : applications, construction, limitations, and future prospects

Components of the Pacific transported landscape have been used as proxies to trace the prehistoric movement of humans across the Pacific for almost two decades. Analyses of archaeological remains and DNA sequences of plants, animals, and microorganisms moved by or with humans have contributed to understanding prehistoric migration, trade, exchange, and sometimes revealed the geographic origins of particular plants and animals. This paper presents the basic elements of a DNA-based commensal model and discusses the phylogenetic and population genetic approaches these models employ. A clear delineation of the underlying assumptions of these models and the background information required to construct them have yet to appear in the literature. This not only provides a framework with which to construct a commensal model but also highlights gaps in current knowledge. The ways in which commensal models have enriched archaeological reconstructions will be highlighted, as will their current limitations. With these limitations in mind, options will be outlined for augmenting commensal models through the application of established techniques and new technologies in order to provide the best tools for reconstructing ancient human mobility and behavior in the Pacific and beyond

Investigating the global dispersal of chickens in prehistory using ancient mitochondrial dna signatures

Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testingExcavations in Fais by MI were made possible by a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science. DB gratefully acknowledges support from the Marsden Fund, and the Allan Wilson Centre for Molecular Ecology and Evolution. During the course of this research AS was supported by a Postgraduate Scholarship from the University of Auckland and a Fellowship from the Allan Wilson Centre for Molecular Ecology and Evolutio

Geographic population structure analysis of worldwide human populations infers their biogeographical origins

The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000–130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS’s accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing

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

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

Ancient mitogenomes of Lapita pigs confirm continuity of the Pacific Clade in Remote Oceania

The movement of Lapita peoples into western Remote Oceania ∼ 3000 BP, and subsequent dispersal into Polynesia, is one of the most extensive migration events in human history. While the origins of these settlers and their commensal animals in the west are generally well understood, questions remain about their dispersal into eastern Remote Oceania, and post-settlement interactions. The pig, Sus scrofa, is one of the commensal animals carried across Remote Oceania, and previous genetic studies identified a single lineage, the “Pacific Clade”, linking Pacific pigs to Island and Peninsular Southeast Asia. Here, we present 16 complete mitogenomes (>99 % coverage) and 8 partial mitogenomes (>80 % coverage) from eleven Remote Oceanic archaeological sites, spanning the Lapita period to the historic period. Phylogenetic analyses show a continuous pig population in Remote Oceania from their first introduction ∼ 3000 BP. Furthermore, sustained pig mitochondrial diversity is detected in western Remote Oceania from the Lapita period until today. In comparison, very limited diversity is found in eastern Remote Oceania, suggesting a bottleneck associated with human expansion into East Polynesia. The contrasting genetic signatures between west and east suggest that little to no pig movement occurred between these regions following the initial settlement of Polynesia. Comparison of the newly generated sequences to previously published ancient pig mitogenomes reveals the first ancient Pacific Clade pig in China, extending their range geographically to mainland East Asia, and temporally to 7000–6000 BP. Overall, this study contributes to a more nuanced understanding of Remote Oceania’s settlement and pig husbandry

Community partnerships are fundamental to ethical ancient DNA research

The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article “Ethics of DNA research on human remains: five globally applicable guidelines” published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of “scientific” and “community” concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines’ authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on “ethical” grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research.Community partnerships should guide aDNA research Open data, publication, and Indigenous Data Sovereignty The risks of not consulting Conclusion

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

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