Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil

A pilot study of mitochondrial genomic ancestry in admixed Brazilian patients with type 1 diabetes

Interactions between multiple genes and environmental factors could be related to the pathogenesis of type 1 diabetes (T1D). The Brazilian population results from different historical miscegenation events, resulting in a highly diverse genetic pool. This study aimed to analyze the mtDNA of patients with T1D and to investigate whether there is a relationship between maternal ancestry, self-reported color and the presence of T1D. The mtDNA control region of 204 patients with T1D residing in three geographic regions of Brazil was sequenced following the International Society for Forensic Genetics (ISFG) recommendations. We obtained a frequency of Native American matrilineal origin (43.6%), African origin (38.2%), and European origin (18.1%). For self-declared color, 42.6% of the patients with diabetes reported that they were White, 50.9% were Brown, and 5.4% were Black. Finally, when we compared the self-declaration data with maternal ancestral origin, we found that for the self-declared White group, there was a greater percentage of haplogroups of Native American origin (50.6%); for the self-declared Black group, there was a greater percentage of African haplogroups (90.9%); and for the Brown group, there was a similar percentage of Native American and African haplogroups (42.3% and 45.2%, respectively). The Brazilian population with diabetic has a maternal heritage of more than 80% Native American and African origin, corroborating the country's colonization history.

Long-distance dispersal of the beach strawberry, Fragaria chiloensis, from North America to Chile and Hawaii

BACKGROUND AND AIMS

The beach strawberry, Fragaria chiloensis, is found in a narrow coastal band from the Aleutian Islands to central California and then jumps thousands of kilometres all the way to Hawaii and Chile. As it probably had a North American origin, it must have been introduced to the other locations by long-distance dispersal. The aim of this study was to determine which agent carried the beach strawberry to its Pacific and South American locations.

METHODS

A deductive framework was constructed to separate between the possible modes of long-distance dispersal involving animals, wind and ocean currents. Bird migration was subsequently identified as the most likely scenario, and then the routes, habitats, feeding preferences and flight distances of all the shorebird species were evaluated to determine the most likely carrier.

KEY RESULTS

Six species migrate between North America and Chile and feed on the beaches and rocky shores where F. chiloensis grows naturally: Black-bellied Plovers, Greater Yellowlegs, Ruddy Turnstones, Sanderlings, Whimbrels and Willets. Of these, only two eat fruit and migrate in long continuous flight: Ruddy Turnstones and Whimbrels. Two species travel between North America and Hawaii, eat fruit and forage on the beaches and rocky shores where F. chiloensis grows naturally: Pacific Golden-plovers and Ruddy Turnstones. Ruddy Turnstones eat far less fruit than Pacific Golden-plovers and Whimbrels, making them less likely to have introduced the beach strawberry to either location.

CONCLUSIONS

We provide evidence that F. chiloesis seeds were probably dispersed to Hawaii by Pacific Golden-plovers and to Chile by Whimbrels.

Demographic history and selection at HLA loci in Native Americans

The American continent was the last to be occupied by modern humans, and native populations bear the marks of recent expansions, bottlenecks, natural selection, and population substructure. Here we investigate how this demographic history has shaped genetic variation at the strongly selected HLA loci. In order to disentangle the relative contributions of selection and demography process, we assembled a dataset with genome-wide microsatellites and HLA-A, -B, -C, and -DRB1 typing data for a set of 424 Native American individuals. We find that demographic history explains a sizeable fraction of HLA variation, both within and among populations. A striking feature of HLA variation in the Americas is the existence of alleles which are present in the continent but either absent or very rare elsewhere in the world. We show that this feature is consistent with demographic history (i.e., the combination of changes in population size associated with bottlenecks and subsequent population expansions). However, signatures of selection at HLA loci are still visible, with significant evidence selection at deeper timescales for most loci and populations, as well as population differentiation at HLA loci exceeding that seen at neutral markers.

Human migration and the spread of malaria parasites to the New World

We examined the mitogenomes of a large global collection of human malaria parasites to explore how and when Plasmodium falciparum and P. vivax entered the Americas. We found evidence of a significant contribution of African and South Asian lineages to present-day New World malaria parasites with additional P. vivax lineages appearing to originate from Melanesia that were putatively carried by the Australasian peoples who contributed genes to Native Americans. Importantly, mitochondrial lineages of the P. vivax-like species P. simium are shared by platyrrhine monkeys and humans in the Atlantic Forest ecosystem, but not across the Amazon, which most likely resulted from one or a few recent human-to-monkey transfers. While enslaved Africans were likely the main carriers of P. falciparum mitochondrial lineages into the Americas after the conquest, additional parasites carried by Australasian peoples in pre-Columbian times may have contributed to the extensive diversity of extant local populations of P. vivax.

Genetic Ancestry of Rapanui before and after European Contact

The origins and lifeways of the inhabitants of Rapa Nui (Easter Island), a remote island in the southeast Pacific Ocean, have been debated for generations. Archaeological evidence substantiates the widely accepted view that the island was first settled by people of Polynesian origin, as late as 1200 CE [1-4]. What remains controversial, however, is the nature of events in the island's population history prior to the first historic contact with Europeans in 1722 CE. Purported contact between Rapa Nui and South America is particularly contentious, and recent studies have reported genetic evidence for Native American admixture in present-day indigenous inhabitants of Rapa Nui [5-8]. Statistical modeling has suggested that this genetic contribution might have occurred prior to European contact [6]. Here we directly test the hypothesis that the Native American admixture of the current Rapa Nui population predates the arrival of Europeans with a paleogenomic analysis of five individual samples excavated from Ahu Nau Nau, Anakena, dating to pre- and post-European contact, respectively. Complete mitochondrial genomes and low-coverage autosomal genomes show that the analyzed individuals fall within the genetic diversity of present-day and ancient Polynesians, and we can reject the hypothesis that any of these individuals had substantial Native American ancestry. Our data thus suggest that the Native American ancestry in contemporary Easter Islanders was not present on the island prior to European contact and may thus be due to events in more recent history.

Ancestry of Amerindians and its Impact in Anthropology, Transplantation, HLA Pharmacogenomics and Epidemiology by HLA Study in Wiwa Colombian Population

Background:

HLA autosomic genes are unique because they conform the most polymorphic human system. Importance of this system is recognized in Medicine for Transplantation, Epidemiology (HLA and disease linkage), Pharmacogenomics (HLA linked to drug side effects) and for defining the origin of populations in both male and female lineages.

Objectives:

Studying HLA profile of a isolated Amerindian group from North Colombia (Wiwa) in order to draw conclusions about its Preventive Medicine, the genetic relationship with Worldwide populations and America peopling, since this last issue is hotly debated.

Methodology:

A total of 14,660 HLA chromosomes were included. Peripheral blood was obtained from volunteer blood donors belonging to Wiwa (also named Arsario) ethnic group. HLA-A, -B, -C, -DRB1 and -DQB1 genes were analyzed by standard methods. Wiwa Amerindians relationships with others were calculated by using Arlequin, Dispan and Vista software computer packages.

Results:

Extended HLA, -A, -B, -C, -DRB1 and -DQB1 haplotypes have been studied for the first time in this population. Classical Amerindian haplotypes have been found and also new Wiwa (Arsario) Amerindian haplotypes. New haplotypes are A*68:01 - B*15:01 - C*03:03 - DRB1*14:02 - DQB1*03:02, A*11:01 - B*07:02 - C*07:02 - DRB1*15:03 - DQB1*06:02 and A*68:01 - B*15:01 - C*03:04 - DRB1*14:02 - DQB1*03:01.

Conclusion:

They have been reached after exhaustive comparisons of Wiwa with other Amerindians and Worldwide populations by using genetic distances, Neighbor Joining trees, correspondence analysis and specific group of alleles which are common and frequent in both Amerindians and Pacific Islanders. They are: 1) The Americas First Inhabitants have been probably come through Bering Strait and also through Pacific (from Austronesia and Asia) and Atlantic (from Europe) routes. A bidirectional gene flow is not discarded. 2) Genetic HLA Amerindian profile is separated from that of other Worldwide populations. 3) Amerindians geographical proximity groups’ relatedness is not concordant with HLA genetic relatedness, neither with language. This may be explained by a substantial population decrease that occurred after Europeans invaded America in 1492 and carried new pathogens and epidemics. 4) Our results are also useful for Wiwa and other Amerindians future preventive medicine (HLA linked diseases), HLA pharmacogenomics and transplantation regional programs.

Pre-Hispanic Mortuary Practices in Quebrada de Humahuaca (North-Western Argentina): Genetic Relatedness among Individuals Buried in the Same Grave

Almost all pre-Hispanic societies from Quebrada de Humahuaca (north-western Argentina) buried their defuncts in domestic areas, demonstrating the importance of death and its daily presence among the living. Presumably, the collective graves contained related individuals, a hypothesis that can be tested through the study of ancient DNA. This study analyzes autosomal and uniparental genetic markers in individuals from two archaeological sites in Quebrada de Humahuaca occupied during the Late Formative (1450-1050 BP) and Regional Developments I (1050-700 BP) periods. Mitochondrial and Y-chromosome haplotypes were compared in order to establish possible maternal and paternal relatedness. Genotypes for 15 autosomal STRs were used to calculate pairwise relatedness coefficients and pedigree probabilities. High kinship levels among individuals buried in the same graves were found in both sites. Although only two particular cases were analyzed, these results represent an important contribution to the study of mortuary practices in the region by means of ancient DNA.

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

The cranial morphology of the Botocudo Indians, Brazil

The Botocudo Indians were hunter-gatherer groups that occupied the East-Central regions of Brazil decimated during the colonial period in the country. During the 19th century, craniometric studies suggested that the Botocudo resembled more the Paleoamerican population of Lagoa Santa than typical Native Americans groups. These results suggest that the Botocudo Indians might represent a population that retained the biological characteristics of early groups of the continent, remaining largely isolated from groups that gave origin to the modern Native South American variation. Moreover, recently, some of the Botocudo remains have been shown to have mitochondrial and autosomal DNA lineages currently found in Polynesian populations. Here, we explore the morphological affinities of Botocudo skulls within a worldwide context. Distinct multivariate analyses based on 32 craniometric variables show that 1) the two individuals with Polynesian DNA sequences have morphological characteristics that fall within the Polynesian and Botocudo variation, making their assignation as Native American specimens problematic, and 2) there are high morphological affinities between Botocudo, Early Americans, and the Polynesian series of Easter Island, which support the early observations that the Botocudo can be seen as retaining the Paleoamerican morphology, particularly when the neurocranium is considered. Although these results do not elucidate the origin of the Polynesian DNA lineages among the Botocudo, they support the hypothesis that the Botocudo represent a case of late survival of ancient Paleoamerican populations, retaining the morphological characteristics of ancestral Late Pleistocene populations from Asia.

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

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 Tipα) and hitherto unknown functional genes.

Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity

BACKGROUND

Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice.

RESULTS

In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya.

CONCLUSIONS

The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.

Ancient DNA and the human settlement of the Pacific: a review

The Pacific region provides unique opportunities to study human evolution including through analyses of ancient DNA. While some of the earliest studies involving ancient DNA from skeletal remains focused on Pacific samples, in the following 25 years, several factors meant that little aDNA research, particularly research focused on human populations, has emerged. This paper briefly presents the genetic evidence for population origins, reviews what ancient DNA work has been undertaken to address human history and evolution in the Pacific region, and argues that the future is bright but research requires a collaborative approach between academic disciplines but also with local communities.

Insights into the origin of rare haplogroup C3* Y chromosomes in South America from high-density autosomal SNP genotyping

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Revisited the previous discovery of a rare Y haplogroup in two Ecuador populations.

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Hypotheses for the origin of the haplogroup tested with autosomal SNP genotype data.

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We favoured one of the three hypotheses, ‘founder plus drift’.

The colonization of Americas is thought to have occurred 15–20 thousand years ago (Kya), with little or no subsequent migration into South America until the European expansions beginning 0.5 Kya. Recently, however, haplogroup C3* Y chromosomes were discovered in two nearby Native American populations from Ecuador. Since this haplogroup is otherwise nearly absent from the Americas but is common in East Asia, and an archaeological link between Ecuador and Japan is known from 6 Kya, an additional migration 6 Kya was suggested. Here, we have generated high-density autosomal SNP genotypes from the Ecuadorian populations and compared them with genotypes from East Asia and elsewhere to evaluate three hypotheses: a recent migration from Japan, a single pulse of migration from Japan 6 Kya, and no migration after the First Americans. First, using forward-time simulations and an appropriate demographic model, we investigated our power to detect both ancient and recent gene flow at different levels. Second, we analyzed 207,321 single nucleotide polymorphisms from 16 Ecuadorian individuals, comparing them with populations from the HGDP panel using descriptive and formal tests for admixture. Our simulations revealed good power to detect recent admixture, and that ≥5% admixture 6 Kya ago could be detected. However, in the experimental data we saw no evidence of gene flow from Japan to Ecuador. In summary, we can exclude recent migration and probably admixture 6 Kya as the source of the C3* Y chromosomes in Ecuador, and thus suggest that they represent a rare founding lineage lost by drift elsewhere.

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

Understanding the peopling of the Americas remains an important and challenging question. Here, we present (14)C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as 'Botocudos'. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport.

Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans

BACKGROUND

Rapa Nui (Easter Island), located in the easternmost corner of the Polynesian Triangle, is one of the most isolated locations on the planet inhabited by humans. Archaeological and genetic evidence suggests that the island was first colonized by Polynesians around AD 1200, during their eastward expansion. Although it remains contentious whether Polynesians reached South America, suggestive evidence has been brought forward supporting the possibility of Native American contact prior to the European "discovery" of the island in AD 1722.

RESULTS

We generated genome-wide data for 27 Rapanui. We found a mostly Polynesian ancestry among Rapanui and detected genome-wide patterns consistent with Native American and European admixture. By considering the distribution of local ancestry tracts of eight unrelated Rapanui, we found statistical support for Native American admixture dating to AD 1280-1495 and European admixture dating to AD 1850-1895.

CONCLUSIONS

These genetic results can be explained by one or more pre-European trans-Pacific contacts.

Mixtec Mexican Amerindians: an HLA alleles study for America peopling, pharmacogenomics and transplantation

HLA-A, -B and -DRB1 alleles have been studied in a Mixtec Mexican Amerindian population by indirect DNA sequencing. HLA relatedness has been tested by comparing results with other Amerindians and worldwide populations; a total of 15,681 chromosomes have been used. Genetic distances between populations, Neighbour Joining (NJ) dendrograms and correspondence analyses have been carried out. Conclusions are: 1) Our Mixtec sample from Oaxaca Coastal Mexican area shows an HLA profile different to that of Oaxaca Central Mountains area showing that genes and languages do not correlate which is inferred both by plane genetic distances and NJ dendrograms and correspondence analyses. 2) Genetic distances and NJ dendrograms join together Mazatecan Mexican Amerindians with our studied Coastal Mixtec group; it fits with the historical relationship between Mixtec and Mazatecans. 3) A*24:02-B*35:14-DRB1*04:11, A*02:01-B*15:15-DRB1*04:11 and A*68:03-B*39:08-DRB1*08:02 extended HLA haplotypes have been "de novo" found in our Mixtec Coastal sample. 4) Shared HLA alleles are found between our Pacific Coast Mixtec Amerindians and Pacific Islanders. 5) These results are useful for establishing a future area transplantation waiting list, for the study of HLA linked diseases epidemiology and for pharmacogenomics in certain drug therapy.

Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific

The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.

MtDNA ancestry of Rio de Janeiro population, Brazil

Polymorphism studies concerning HVI and HVII regions of mitochondrial DNA (mtDNA) have improved the understanding of the admixture genetic process related to the occupation of the continents by human population groups. We have analyzed the mtDNA lineages of 190 healthy and maternally unrelated individuals born in the metropolitan region of the Rio de Janeiro city, the capital of the State of Rio de Janeiro, southeastern Brazil. The data showing that 57.9, 25.3 and 16.8 % of the matrilineages found in Rio de Janeiro come from African, Amerindian and European population groups. They are, respectively, in close agreement with historical records which indicate that the admixture population of Brazil is the resulting of interethnic asymmetry crosses between individuals from those population groups. The high proportion of African mtDNA lineages in the population of Rio de Janeiro is in accordance with studies related to other Brazilian states.

High-throughput sequencing of a South American Amerindian

The emergence of next-generation sequencing technologies allowed access to the vast amounts of information that are contained in the human genome. This information has contributed to the understanding of individual and population-based variability and improved the understanding of the evolutionary history of different human groups. However, the genome of a representative of the Amerindian populations had not been previously sequenced. Thus, the genome of an individual from a South American tribe was completely sequenced to further the understanding of the genetic variability of Amerindians. A total of 36.8 giga base pairs (Gbp) were sequenced and aligned with the human genome. These Gbp corresponded to 95.92% of the human genome with an estimated miscall rate of 0.0035 per sequenced bp. The data obtained from the alignment were used for SNP (single-nucleotide) and INDEL (insertion-deletion) calling, which resulted in the identification of 502,017 polymorphisms, of which 32,275 were potentially new high-confidence SNPs and 33,795 new INDELs, specific of South Native American populations. The authenticity of the sample as a member of the South Native American populations was confirmed through the analysis of the uniparental (maternal and paternal) lineages. The autosomal comparison distinguished the investigated sample from others continental populations and revealed a close relation to the Eastern Asian populations and Aboriginal Australian. Although, the findings did not discard the classical model of America settlement; it brought new insides to the understanding of the human population history. The present study indicates a remarkable genetic variability in human populations that must still be identified and contributes to the understanding of the genetic variability of South Native American populations and of the human populations history.