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

Intermittent Preventive Treatment for Malaria in Papua New Guinean Infants Exposed to Plasmodium falciparum and P. vivax: A Randomized Controlled Trial

A three-arm randomized trial conducted among infants in Papua New Guinea estimates the preventive effect against malaria episodes of intermittent preventive treatment, in an area where children are exposed to both falciparum and vivax malaria

Systematic Ancient DNA Species Identification Fails to Find Late Holocene Domesticated Cattle in Southern Africa

Establishing robust temporal control of the arrival of domesticated stock and the associated husbandry skills and lifeways in Southern Africa remains frustrated by the osteological similarities between domestic stock and wild endemic fauna. We report the results of a systematic ancient DNA survey of appropriately sized bovid remains from Later Stone Age deposits in four South African archaeological sites. We show that none of the tested remains originated in domesticated cattle. The precise date of arrival of domestic cattle in the region awaits further study, although we also report new radiocarbon determinations which further refine the local chronology

Walking backwards into the future: the need for a holistic evolutionary approach in Pacific health research

Context: The Pacific region has had a complex human history. It has been subject to multiple major human dispersal and colonisation events, including some of the earliest Out-of-Africa migrations, the so-called Austronesian expansion of people out of Island Southeast Asia, and the more recent arrival of Europeans. Despite models of island isolation, evidence suggests significant levels of interconnectedness that vary in direction and frequency over time. The Pacific Ocean covers a vast area and its islands provide an array of different physical environments with variable pathogen loads and subsistence opportunities. These diverse environments likely caused Pacific peoples to adapt (both genetically and culturally) in unique ways. Differences in genetic background, in combination with adaptation, likely affect their susceptibility to non-communicable diseases. Objectives: Here we provide an overview of some of the key issues in the natural and human history of the Pacific region which are likely to impact human health. We argue that understanding the evolutionary and cultural history of Pacific peoples is essential for the generation of testable hypotheses surrounding potential causes of elevated disease susceptibility among Pacific peoples

Maternal Relationships among Ancient and Modern Southern African Sheep: Newly Discovered Mitochondrial Haplogroups

We investigated the genetic diversity and historic relationships among southern African sheep as well as the relationships between them and sheep outside the continent by sourcing both archaeological and modern sheep samples. Archaeological sheep samples derived from the site Die Kelders 1, near Cape Town, date to approximately 1500 years ago. The modern samples were taken as ear snips from Damara, Namaqua Afrikaner, and Ronderib Afrikaner sheep on a farm in Prieska in the Northern Cape. Illumina sequencing libraries were constructed for both ancient and modern specimens. Ancient specimens were enriched for the mitochondrial genome using an in-solution hybridization protocol and modern specimens were subjected to shotgun sequencing. Sequences were mapped to the Ovis aries reference genome, assigned to haplogroups and subhaplogroups, and used to calculate a phylogenetic tree using previously published, geographically dispersed mitochondrial genome sheep sequences. Genetic diversity statistics show that southern African sheep have lower diversity than sheep in other regions. Phylogenetic analysis reveals that many modern southern African sheep are likely descended from prehistoric indigenous sheep populations and not from sheep imported from Europe during the historic period

Revisiting the Kalahari debate in the highlands: ancient DNA provides new faunal identifications at Sehonghong, Lesotho

<p>Large numbers of domestic stock have been reported among the faunal remains recovered from archaeological sites with predominantly forager-associated material culture in the highlands of Lesotho. These remains, in conjunction with the presence of artefacts of apparent agropastoralist origin, have led to the suggestion that either a process of neolithisation saw the adoption of livestock-keeping by traditionally foraging peoples, or that extensive contact and trade occurred between foraging groups in the mountains and distant agropastoralist communities. We present here ancient DNA evidence that the frequency of domestic stock in the faunal assemblages has been significantly overestimated and that, as a consequence, the nature of the relationships between highland foragers and agropastoralists has been misconstrued.</p

Origins of Polynesian Pigs Revealed by Mitochondrial Whole Genome Ancient DNA

Domestic pigs (Sus scrofa) were first transported to Polynesia through a series of long-distance voyages ultimately linked to the Neolithic expansion of Austronesian-speaking people out of Asia. The descendants of the founding pigs belong to a rare mtDNA group referred to as the &ldquo;Pacific Clade&rdquo; that may have originated in peninsular or island Southeast Asia. We report the first whole genome mtDNA from domestic pigs from any of the remote islands of the Pacific. In this brief report, we describe the close link we discovered between ancient mtDNA from archaeological specimens from across Polynesia and from that of modern pigs in northern peninsular Southeast Asia, specifically southern China&rsquo;s Yunnan Province. More complete mtDNA coverage in commensal animals is necessary to improve our picture of the settlement of Polynesia (ca. 2800&ndash;700 years before the present) and specify the route, or routes, that pigs took from northern peninsular Southeast Asia

A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa

International audienceWhile Phoenician culture and trade networks had a significant impact onWestern civilizations, we know little about the Phoenicians themselves. In 1994, a Punic burial crypt was discovered on Byrsa Hill, near the entry to the National Museum of Carthage in Tunisia. Inside this crypt were the remains of a young man along with a range of burial goods, all dating to the late 6th century BCE. Here we describe the complete mitochondrial genome recovered from the Young Man of Byrsa and identify that he carried a rare European haplogroup, likely linking his maternal ancestry to Phoenician influenced locations somewhere on the North Mediterranean coast, the islands of the Mediterranean or the Iberian Peninsula. This resultnot only provides the first direct ancient DNA evidence of a Phoenician individual but the earliest evidence of a European mitochondrial haplogroup, U5b2c1, in North Africa

Floristic homogenization of South Pacific islands commenced with human arrival

The increasing similarity of plant species composition among distinct areas is leading to the homogenization of ecosystems globally. Human actions such as ecosystem modification, the introduction of non-native plant species and the extinction or extirpation of endemic and native plant species are considered the main drivers of this trend. However, little is known about when floristic homogenization began or about pre-human patterns of floristic similarity. Here we investigate vegetation trends during the past 5,000 years across the tropical, sub-tropical and warm temperate South Pacific using fossil pollen records from 15 sites on 13 islands within the biogeographical realm of Oceania. The site comparisons show that floristic homogenization has increased over the past 5,000 years. Pairwise Bray–Curtis similarity results also show that when two islands were settled by people in a given time interval, their floristic similarity is greater than when one or neither of the islands were settled. Importantly, higher elevation sites, which are less likely to have experienced human impacts, tended to show less floristic homogenization. While biotic homogenization is often referred to as a contemporary issue, we have identified a much earlier trend, likely driven by human colonization of the islands and subsequent impacts