Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

Malaspinas, Anna-Sapfo; Lao, Oscar; Schroeder, Hannes; Rasmussen, Morten; Raghavan, Maanasa; Moltke, Ida; Campos, Paula F.; Sagredo, Francisca Santana; Rasmussen, Simon; Gonçalves, Vanessa F.; Albrechtsen, Anders; Allentoft, Morten E.; Johnson, Philip L.; Li, Mingkun; Reis, Silvia; Bernardo, Danilo Vicensotto; DeGiorgio, Michael; Duggan, Ana T.; Bastos, Murilo; Wang, Yong; Stenderup, Jesper; Moreno-Mayar, J. Víctor; Brunak, Søren; Sicheritz-Pontén, Thomas; Hodges, Emily; Hannon, Gregory J.; Orlando, Ludovic; Price, T. Douglas; Jensen, Jeffrey D.; Nielsen, Rasmus; Heinemeier, Jan; Olsen, Jesper; Rodrigues-Carvalho, Cláudia; Lahr, Marta Mirazón; Neves, Walter Alves; Kayser, Manfred; Higham, Thomas; Stoneking, Mark; Pena, Sérgio Danilo Junho; Willerslev, Eske

doi:10.1016/j.cub.2014.09.078

Cited by 75 publications

(55 citation statements)

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“…Furthermore, unrepresented regions such as Siberia and Oceania would allow for the investigation of genetic continuity/discontinuity across northeastern and southeastern Asia to the Americas and the Pacific, respectively. A deeper analysis of Asian, American, and Austronesian bacterial genomes may also help shed light on alternative Pacific routes for the colonization of the Americas, a hypothesis that has been widely debated in the literature (see Gonçalves et al 2013;Malaspinas et al 2014). Figure S1.…”

Section: Outer Membrane Proteinsmentioning

confidence: 99%

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

et al. 2015

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Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipa) and hitherto unknown functional genes.KEYWORDS adaptation; neutral evolution; human pathogens H ELICOBACTER pylori is a Gram-negative bacterium that infects the mucosa of the human stomach. It was first described in the 1980s, when it was initially identified in association with chronic gastritis and later causally linked to serious gastric pathologies such as gastric cancer and ulcers (Marshall and Warren 1984;Suerbaum and Michetti 2002). It infects .80% of humans in developing countries and, although its prevalence is lower in developed countries, nearly 50% of the worldwide human population is infected (Ghose et al. 2005;Salih 2009;Salama et al. 2013).Due to its clinical and evolutionary importance, there has been considerable research on mechanisms of H. pylori transmission, as well as on the population genetics and phylogenetic relationships among global isolates. Thus far, population genetic analyses have mainly focused on seven housekeeping genes (usually referred to as multilocus sequence typing or MLST), with the primary conclusions being that H. pylori strains appear highly structured, and their phylogeographic patterns correlate consistently with that of their human hosts. Given that the H. pylori-humans association is at least 100,000 years old (Moodley et al. 2012), the current population structure of H. pylori may be regarded as mirroring past human expansions and migrations Linz et al. 2007;Breurec et al. 2011) and thus help us shed light on yet unknown dynamics of local demographic processes in human evolution. However, despite the knowledge gained thus far, the long-term global demographic history of H. pylori has never been directly inferred. The long, intimate association of H. pylori with humans suggests a history of bacterial adaptation. Considerable attention has focused on specific genes involved in modulating adaptive immunity of the host (for a review see Yamaoka 2010 andSalama et al. 2013) and on genomic changes occurring during acute and chronic H. pylori infection (Kennemann et al. 2011;Linz et a...

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Section: Outer Membrane Proteinsmentioning

confidence: 99%

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

et al. 2015

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“…The skulls were accessioned in 1890 and direct radiocarbon dates clearly show that these individuals died post-Columbian contact with the New World (AD 1492), and post-Magellan contact (AD 1521) in Oceania (Individual identified as Bot15, OxA-27184, 408 ± 24 BP and AAR-17522, 417 ± 25 BP; and the individual identified as Bot17, AAR-17657, 487 ± 25 BP). Malaspinas et al [103] point out that there is a high probability that these two people died before the traffic in EuroAmerican ships increased in AD 1760, but do not think it Diversity 2017, 9, 37 13 of 21 likely these were people who have traveled on early Western voyages. They suggest that these remains are evidence of possible pre-contact expansion of people out of Polynesia.…”

Section: Ancient Dnamentioning

confidence: 99%

“…Here, we focus on three high-profile cases of new claims that support Jones and Klar's model of Polynesian-American contact: (1) direct evidence for transfer of the domesticated chicken (Gallus gallus) from Polynesia to South America [96][97][98][99][100][101][102]; and, (2) skulls of two Polynesians within collections of human remains attributed to a Native American group in Central-Eastern Brazil (Botocudo) [103]; and, (3) full genomic study of modern Rapa Nui indicating pre-European contact admixture with Native Americans [104].…”

Section: Long-distance Contacts Between Polynesians and Native Americasmentioning

confidence: 99%

“…Major critiques, and the replies to those critiques, center on two issues: the reliability of the radiocarbon date and the question of contamination in the molecular identification of the bones at the Chilean site of El Arenal-1 [98,99,102,103,129]. Others have pointed to alternative models for the evidence at hand [93,100,130].…”

Section: Ancient Dnamentioning

confidence: 99%

“…Recent ancient DNA studies of human skulls in the collections of the National Museum of Brazil (Museu Nacional)/Universidade Federal do Rio de Janeiro (UFRJ), attributed to a Native American group in Eastern-Central Brazil called the Botocudo have been shown to have mtDNA linages (B4a1a1a and B4a1a1) [103] and nuclear DNA typical of Polynesians [131]. The skulls were accessioned in 1890 and direct radiocarbon dates clearly show that these individuals died post-Columbian contact with the New World (AD 1492), and post-Magellan contact (AD 1521) in Oceania (Individual identified as Bot15, OxA-27184, 408 ± 24 BP and AAR-17522, 417 ± 25 BP; and the individual identified as Bot17, AAR-17657, 487 ± 25 BP).…”

Section: Ancient Dnamentioning

confidence: 99%

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Dispersal, Isolation, and Interaction in the Islands of Polynesia: A Critical Review of Archaeological and Genetic Evidence

Horsburgh

McCoy

2017

Diversity

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Integration of archaeology, modern genetics, and ancient DNA holds promise for the reconstruction of the human past. We examine the advances in research on the indigenous peoples of Polynesia to determine: (1) what do archaeological and genetic data (ancient and modern DNA) tell us about the origins of Polynesians; and, (2) what evidence is there for long-distance travel and contacts between Polynesians and indigenous populations of the Americas? We note that the general dispersal pattern of founding human populations in the remote islands of the Pacific and long-distance interaction spheres continue to reflect well-established models. New research suggests that the formation of an Ancestral Polynesia Culture in Western Polynesia may have involved differential patterns of dispersal followed by significant later migrations. It has also been suggested that the pause between the settlement of Western and Eastern Polynesia was centuries longer than currently thought, followed by a remarkably rapid pulse of island colonization. Long-distance travel between islands of the Pacific is currently best documented through the sourcing of artifacts, while the discovery of admixture of Native American DNA within the genome of the people from Easter Island (Rapa Nui) is strong new evidence for sustained contacts between Polynesia and the Americas.

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Migration/gene flow

Raghavan

2018

The International Encyclopedia of Biological Anthropology

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As people move, so do their genes. Migrations cause changes in the spatial distribution of genetic signatures, and mapping these signatures of gene flow over time can shed light on past movements. The evolutionary history of anatomically modern humans (AMH) has witnessed several key dispersals, from the migration out of Africa to the eventual peopling of the rest of the world. Since the initial peopling process, movement of peoples has occurred at numerous time points in prehistory and history, and over short distances as well as on continental and even intercontinental scales. Together, these events have heavily influenced the patterns in genetic diversity that we see today. Massively parallel sequencing coupled to advances in ancient genomics is adding tremendously to the growing literature on known and previously unknown migrations in the past, and how ancient gene flow events have shaped the present‐day human gene pool.

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Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

Cited by 75 publications

References 5 publications

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Dispersal, Isolation, and Interaction in the Islands of Polynesia: A Critical Review of Archaeological and Genetic Evidence

Migration/gene flow

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