scholarly journals Reconstructed lost Native American populations from Eastern Brazil are shaped by differential Jê/Tupi ancestry

2019 ◽  
Author(s):  
Alex Mas-Sandoval ◽  
Lara R Arauna ◽  
Mateus H Gouveia ◽  
Mauricio L Barreto ◽  
Bernardo L Horta ◽  
...  
Keyword(s):  
Native American ◽  
North East ◽  
Genetic Components ◽  
Genome Wide ◽  
Eastern Brazil ◽  
Show Evidence ◽  
Genome Wide Data ◽  
Sub Saharan ◽  
Brazilian Populations ◽  
American Genetic

Abstract After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African and the Native American. The study of the Native American genetic history is challenged by the availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies and the low proportions of the Native American component in the admixed Brazilian populations (in average 7%). We analysed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North East), Bambui (South East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui and 197 in Pelotas). We compared the reconstructed populations with non-admixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê- speaking ancestry related groups. We also show evidence of a decrease of the diversity of non-admixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.

scholarly journals Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

Science ◽  
2019 ◽  
Vol 365 (6448) ◽  
pp. eaaw6275 ◽  
Author(s):  
Mary E. Prendergast ◽  
Mark Lipson ◽  
Elizabeth A. Sawchuk ◽  
Iñigo Olalde ◽  
Christine A. Ogola ◽  
...  
Keyword(s):  
Iron Age ◽  
Food Production ◽  
Sub Saharan Africa ◽  
Eastern Africa ◽  
Multiphase Model ◽  
Later Stone Age ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Sub Saharan ◽  
Pastoral Neolithic

How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African–related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African–related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.

scholarly journals Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

2020 ◽  
Vol 6 (24) ◽  
pp. eaaz0183 ◽  
Author(s):  
Ke Wang ◽  
Steven Goldstein ◽  
Madeleine Bleasdale ◽  
Bernard Clist ◽  
Koen Bostoen ◽  
...  
Keyword(s):  
Southern Africa ◽  
Sub Saharan Africa ◽  
The Past ◽  
Genome Wide ◽  
Movement Interaction ◽  
Genome Wide Data ◽  
Sub Saharan ◽  
Population Interactions ◽  
Eastern And Southern Africa ◽  
Complex Trajectories

Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.

scholarly journals The genetic prehistory of the Greater Caucasus

2018 ◽  
Author(s):  
Chuan-Chao Wang ◽  
Sabine Reinhold ◽  
Alexey Kalmykov ◽  
Antje Wissgott ◽  
Guido Brandt ◽  
...  
Keyword(s):  
Native American ◽  
Human Movement ◽  
North Caucasus ◽  
Hunter Gatherers ◽  
The Caucasus ◽  
The North ◽  
European Languages ◽  
Snp Data ◽  
Genome Wide ◽  
Show Evidence

AbstractArchaeogenetic studies have described the formation of Eurasian ‘steppe ancestry’ as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4thmillennium BCE that subsequently facilitated the advance of pastoral societies likely linked to the dispersal of Indo-European languages. To address this, we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting that – unlike today – the Caucasus acted as a bridge rather than an insurmountable barrier to human movement. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry.

scholarly journals Inferring adaptive gene-flow in recent African history

2017 ◽  
Author(s):  
George Busby ◽  
Ryan Christ ◽  
Gavin Band ◽  
Ellen Leffler ◽  
Quang Si Le ◽  
...  
Keyword(s):  
Gene Flow ◽  
African Ancestry ◽  
The Gambia ◽  
Sub Saharan Africa ◽  
Histocompatibility Complex ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Multiple Regions ◽  
Novel Method ◽  
Sub Saharan

AbstractGene-flow from an ancestrally differentiated group has been shown to be a powerful source of selectively advantageous variants. To understand whether recent gene-flow may have contributed to adaptation among humans in sub-Saharan Africa, we applied a novel method to identify deviations in ancestry inferred from genome-wide data in 48 populations. Among the signals of ancestry deviation that we find in the Fula, an historically pastoralist ethnic group from the Gambia, are the region that encodes the lactose persistence phenotype, LCT/MCM6, which has the highest proportion of Eurasian ancestry in the genome. The region with the lowest proportion of non-African ancestry is across DARC, which encodes the Duffy null phenotype and is protective for Plasmodium vivax malaria. In the Jola from the Gambia and a Khoesan speaking group from Namibia we find multiple regions with inferred ancestry deviation including the Major Histocompatibility Complex. Our analysis shows the potential for adaptive gene-flow in recent human history.

scholarly journals Paleo-Eskimo genetic legacy across North America

2017 ◽  
Author(s):  
Pavel Flegontov ◽  
N. Ezgi Altinişik ◽  
Piya Changmai ◽  
Nadin Rohland ◽  
Swapan Mallick ◽  
...  
Keyword(s):  
Native American ◽  
North America ◽  
Allele Frequency ◽  
Genetic Relationship ◽  
Rare Allele ◽  
Comprehensive Model ◽  
Haplotype Sharing ◽  
New Methods ◽  
Genome Wide ◽  
Genome Wide Data

AbstractPaleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yupik. The genetic relationship between Paleo-Eskimos and Native American populations remains uncertain. We analyze ancient and present-day genome-wide data from the Americas and Siberia, including new data from Alaskan Iñupiat and West Siberian populations, and the first genome-wide DNA from ancient Aleutian Islanders, ancient northern Athabaskans, and a 4,250-year-old individual of the Chukotkan Ust'-Belaya culture. Employing new methods based on rare allele and haplotype sharing as well as established methods based on allele frequency correlations, we show that Paleo-Eskimo ancestry is widespread among populations who speak Na-Dene and Eskimo-Aleut languages. Using phylogenetic modelling with allele frequency correlations and rare variation, we present a comprehensive model for the complex peopling of North America.

scholarly journals New insights from GWAS on longitudinal and cross-sectional BMI and related phenotypes in admixed children with Native American and European ancestries

2021 ◽  
Author(s):  
Lucas Vicuña ◽  
Esteban Barrientos ◽  
Tomás Norambuena ◽  
Danilo Alvares ◽  
Juan Cristobal Gana ◽  
...  
Keyword(s):  
Native American ◽  
Genetic Architecture ◽  
Association Studies ◽  
Genetic Ancestry ◽  
Immune Gene ◽  
Genome Wide Association Studies ◽  
Cross Sectional ◽  
Adiposity Rebound ◽  
Genome Wide ◽  
American Genetic

AbstractBody-mass index (BMI) is a well-known marker of adiposity across all ages. The genetic architecture of BMI has been thoroughly studied among adults. In contrast, there are a few genome-wide association studies (GWAS) on children. Further, GWAS on children have been performed almost exclusively in Europeans at single ages. We aimed to better understand the genetic architecture of BMI trajectory across ages and how BMI is affected by Native American genetic ancestry. We performed cross-sectional and longitudinal GWAS for BMI-related traits on 904 admixed Chilean children with mostly European and Mapuche Native American genetic ancestry. We focused on BMI and two traits that occur at the minimum of the childhood BMI growth trajectory, namely, age at adiposity rebound (Age-AR) and BMI at adiposity rebound (BMI-AR). We found several variants in the immune gene HLA-DQB3 that are strongly associated with BMI at ages 1.5-2.5 years old, but not at other ages. We also identified a variant in the sex-determining gene DMRT1 significantly associated with Age-AR (P = 9.8 × 10−9). Further, BMI was significantly higher in Mapuche than in European children at all ages between 5.5 and 16.5 years old, but not before. Finally, Age-AR was significantly lower (P = 0.013) by 1.64 years in the Mapuche children compared with Europeans.

scholarly journals Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types

2021 ◽  
Vol 7 (3) ◽  
pp. eabd9036
Author(s):  
Sara Saez-Atienzar ◽  
Sara Bandres-Ciga ◽  
Rebekah G. Langston ◽  
Jonggeol J. Kim ◽  
Shing Wan Choi ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Polygenic Risk Score ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Data Driven Approach ◽  
Single Nucleus ◽  
Lateral Sclerosis

Despite the considerable progress in unraveling the genetic causes of amyotrophic lateral sclerosis (ALS), we do not fully understand the molecular mechanisms underlying the disease. We analyzed genome-wide data involving 78,500 individuals using a polygenic risk score approach to identify the biological pathways and cell types involved in ALS. This data-driven approach identified multiple aspects of the biology underlying the disease that resolved into broader themes, namely, neuron projection morphogenesis, membrane trafficking, and signal transduction mediated by ribonucleotides. We also found that genomic risk in ALS maps consistently to GABAergic interneurons and oligodendrocytes, as confirmed in human single-nucleus RNA-seq data. Using two-sample Mendelian randomization, we nominated six differentially expressed genes (ATG16L2, ACSL5, MAP1LC3A, MAPKAPK3, PLXNB2, and SCFD1) within the significant pathways as relevant to ALS. We conclude that the disparate genetic etiologies of this fatal neurological disease converge on a smaller number of final common pathways and cell types.

scholarly journals Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

2021 ◽  
Vol 7 (13) ◽  
pp. eabe4414
Author(s):  
Guido Alberto Gnecchi-Ruscone ◽  
Elmira Khussainova ◽  
Nurzhibek Kahbatkyzy ◽  
Lyazzat Musralina ◽  
Maria A. Spyrou ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Gene Pools ◽  
Social Rules ◽  
Eurasian Steppe ◽  
Central Asian ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

scholarly journals Genome diversity in Ukraine

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Taras K Oleksyk ◽  
Walter W Wolfsberger ◽  
Alexandra M Weber ◽  
Khrystyna Shchubelka ◽  
Olga T Oleksyk ◽  
...  
Keyword(s):  
Sequence Data ◽  
Copy Number Variations ◽  
Genomic Variation ◽  
High Coverage ◽  
Genome Data ◽  
New Information ◽  
Genome Wide ◽  
Public Data ◽  
Genome Wide Data ◽  
Multiple Samples

Abstract Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

scholarly journals Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Nature ◽  
2021 ◽  
Vol 592 (7853) ◽  
pp. 253-257 ◽  
Author(s):  
Mateja Hajdinjak ◽  
Fabrizio Mafessoni ◽  
Laurits Skov ◽  
Benjamin Vernot ◽  
Alexander Hübner ◽  
...  
Keyword(s):  
Family History ◽  
East Asia ◽  
Late Pleistocene ◽  
Modern Human ◽  
Human Migration ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Genome Wide ◽  
Genome Wide Data

AbstractModern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

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