A Land of Plenty? Colonial Diet in Rural New Zealand

Colonial New Zealand was built on the ideal of creating better lives for settlers. Emigrants came looking to escape the shackles of the class-system and poor conditions in Industrial Revolution period Britain. Colonial propaganda claimed that most emigrants achieved their aims, but the lives the colonists actually experienced upon reaching New Zealand remain relatively unexplored from a biosocial perspective. In this paper we present a pilot study of stable isotope results of bone collagen from seven adults interred in the St. John’s Cemetery (SJM), Milton, New Zealand (ca. AD 1860–1900). We interpret the diet at Milton and broadly compare our isotopic results with contemporaneous samples from Britain. We show that, like contemporary Britain, the diet of our studied individuals was focused on C3 crops and terrestrial meat sources. Despite higher ????15N values in contemporary UK populations (which can simplistically be interpreted as indicative of higher meat intake), consideration of different local baselines makes it likely that this New Zealand population had relatively similar levels of meat intake. Interestingly marine resources did not form an important part of the Milton diet, despite the site's proximity to the ocean, hinting at the possible stigmatisation of local resources and the development of a European New Zealand (pākehā) food identity

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 and modern mitogenomes from Central Argentina: New insights into population continuity, temporal depth and migration in South America

The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.This work was supported by Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (PICT 2007-1549, PICT 2012-711 and PICT 2015-3155), Secretaría de Ciencia y Tecnología (Universidad Nacional de Córdoba), Ministerio de Ciencia y Tecnología de la Provincia de Córdoba (PID 2018-79) and Consejo Nacional de Investigaciones Científicas y Técnicas (2015-11220150100953CO). M.P. is a postdoctoral fellow and A.G., R.N., J.M.B.M, C.M.B., M.F. and D.A.D. are research career members of CONICET, Argentina

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

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

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

Neolithic Mitochondrial Haplogroup H Genomes and the Genetic Origins of Europeans

Haplogroup H dominates present-day Western European mitochondrial DNA variability (\u3e40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria

The Impact of Human Conflict on the Genetics of Mastomys natalensis and Lassa Virus in West Africa

Environmental changes have been shown to play an important role in the emergence of new human diseases of zoonotic origin. The contribution of social factors to their spread, especially conflicts followed by mass movement of populations, has not been extensively investigated. Here we reveal the effects of civil war on the phylogeography of a zoonotic emerging infectious disease by concomitantly studying the population structure, evolution and demography of Lassa virus and its natural reservoir, the rodent Mastomys natalensis, in Guinea, West Africa. Analysis of nucleoprotein gene sequences enabled us to reconstruct the evolutionary history of Lassa virus, which appeared 750 to 900 years ago in Nigeria and only recently spread across western Africa (170 years ago). Bayesian demographic inferences revealed that both the host and the virus populations have gone recently through severe genetic bottlenecks. The timing of these events matches civil war-related mass movements of refugees and accompanying environmental degradation. Forest and habitat destruction and human predation of the natural reservoir are likely explanations for the sharp decline observed in the rodent populations, the consequent virus population decline, and the coincident increased incidence of Lassa fever in these regions. Interestingly, we were also able to detect a similar pattern in Nigeria coinciding with the Biafra war. Our findings show that anthropogenic factors may profoundly impact the population genetics of a virus and its reservoir within the context of an emerging infectious disease