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Genome wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar

ABSTRACT: Linguistic and cultural evidence suggests that Madagascar was the final point of two major dispersals of Austronesian and Bantu speaking populations. Today, Mikea are described as the last known Malagasy population reported to be still practising a hunter-gatherer life-style. It is unclear, however, whether Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their life-style that separates them from the other contemporary populations of South Madagascar. In order to address these questions we have performed a genome wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo and 24 Temoro individuals together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family we observe that only one third of their genetic ancestry is related to the populations of Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive to for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life by through cultural reversion.

ORGANISM(S): Homo sapiens

PROVIDER: GSE53445 | GEO | 2013/12/19

SECONDARY ACCESSION(S): PRJNA232031

REPOSITORIES: GEO

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Genome wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar

Project description:Linguistic and cultural evidence suggests that Madagascar was the final point of two major dispersals of Austronesian and Bantu speaking populations. Today, Mikea are described as the last known Malagasy population reported to be still practising a hunter-gatherer life-style. It is unclear, however, whether Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their life-style that separates them from the other contemporary populations of South Madagascar. In order to address these questions we have performed a genome wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo and 24 Temoro individuals together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family we observe that only one third of their genetic ancestry is related to the populations of Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive to for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life by through cultural reversion. 69 samples were analysed with the Illumina platform OmniExpress BeadChips and are described herein.

2013-12-19 | E-GEOD-53445 | biostudies-arrayexpress

Genetic variation in four highland populations in the context of broader genetic diversity in Daghestan.

Project description:Daghestan, with its exceptional combination of linguistic, geographic, and cultural diversity, presents an excellent natural laboratory for tracking the influence of demographic processes on patterns of genetic variation. This study was designed to investigate the co-evolution of genes and languages, comparing and contrasting patterns of linguistic, genetic and geographic variation among Daghestani populations.

2020-01-04 | GSE93106 | GEO

KT2440_Rhizosphere_Adaptation

Project description:A genome-wide analysis of gene expression of the root-colonizing bacterium Pseudomonas putida KT2440 in the rhizosphere of corn (Zea mays var. Girona). To identify reliable rhizosphere differentially expressed genes by this bacterium, populations of P. putida KT2440 previously exposed to a rhizospheric life style for seven days in the rhizosphere of corn were compared with populations previously exposed to a rhizospheric life style for a long period of 138 days.

2014-01-01 | E-MEXP-3804 | biostudies-arrayexpress

A Genome-Wide Search for Greek and Jewish Admixture in the Kashmiri Population

Project description:The Kashmiri population is an ethno-linguistic group that resides in the Kashmir Valley in northern India. A longstanding hypothesis is that this population derives ancestry from Jewish and/or Greek sources. There is historical and archaeological evidence of ancient Greek presence in India and Kashmir. Further, some historical accounts suggest ancient Hebrew ancestry as well. To date, it has not been determined whether signatures of Greek or Jewish admixture can be detected in the Kashmiri population. Using genome-wide genotyping and admixture detection methods, we determined there are no significant or substantial signs of Greek or Jewish admixture in modern-day Kashmiris. The ancestry of Kashmiri Tibetans was also determined, which showed signs of admixture with populations from northern India and west Eurasia. These results contribute to our understanding of the existing population structure in northern India and its surrounding geographical areas.

2016-08-16 | GSE85594 | GEO

Natural selection has contributed to functional immune response differences between human hunter-gatherers and agriculturalists

Project description:The shift from a hunter-gatherer (HG) to an agricultural (AG) mode of subsistence is believed to have been associated with profound changes in the burden and diversity of pathogens across human populations. Yet, the extent to which the advent of agriculture impacted the evolution of the human immune system remains unknown. Here we present a comparative study of variation in the transcriptional responses of peripheral blood mononuclear cells (PBMCs) to bacterial and viral stimuli between the Batwa, a rainforest hunter-gatherer, and the Bakiga, an agriculturalist population from Central Africa. We observed increased divergence between hunter-gatherers and farmers in the transcriptional response to viruses compared to that for bacterial stimuli. We demonstrate that a significant fraction of these transcriptional differences are under genetic control, and we show that positive natural selection has helped to shape population differences in immune regulation. Unexpectedly, we found stronger signatures of recent natural selection in the rainforest hunter-gatherers, which argues against the popularized notion that shifts in pathogen exposure due to the advent of agriculture imposed radically heightened selective pressures in agriculturalist populations.

2018-09-27 | GSE120502 | GEO

Peptide Ancestry Informative Markers in Uterine Neoplasms from Women of European, African and Asian Ancestry

Project description:Characterization of ancestry-linked peptide variants in disease-relevant patient tissues represents a foundational step to connect patient ancestry with molecular disease pathogenesis. Nonsynonymous single nucleotide polymorphisms (SNPs) encoding missense substitutions within tryptic peptides exhibiting high allele frequencies in European, African, and East Asian populations, termed peptide ancestry informative markers (pAIMs), were prioritized from 1000 genomes. In silico analysis shows that as few as 20 pAIMs can determine ancestry proportions similarly to >260K SNPs (R2=0.9905). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma (ULM) tissues combined resulted in the quantitation of 62 pAIMs that correlate with self-described race and genotype-confirmed patient ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. These efforts describe a generalized set of markers for proteoancestry assessment that will further support studies investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms.

2022-02-16 | PXD029323 | Pride

TIME-COURSE GENE EXPRESSION OF Metharizium anisopliae GROWING IN PLANT ROOT EXUDATE

Project description:The presence of genetic groups of the entomopathogenic fungus Metarhizium anisopliae in soil is shaped by its adaptability to specific soil and habitat types, and by soil insect populations. Although the entomopathogenic life style of this fungus is well studied, its saprophytic life style has received little consideration. While a set of functionally related genes can be commonly expressed for the adaptability of this fungus to different environments (insect cuticle, insect blood and root exudates), a different subset of genes is also expected for each environment. In order to increase the knowledge of the potential use of M. anisopliae as a rhizosphere competent organism, in this study we evaluated the genetic expression of this fungus while growing on plant root exudates in laboratory conditions during a time course.

2010-12-29 | GSE16848 | GEO

Genotyping of SNP array in individuals with San ancestry in southeastern Africa

Project description:Only a few scattered groups with oral traditions of Khoe-San hunter-gatherer ancestry remain in southeastern Africa. We investigate genomic variation of remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published datasets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu-speakers. Specifically, we found that the Lake Chrissie San are closely related to current southern San groups (i.e. the Karretjie People). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. Samples were genotyped on the Illumina Omni2.5M (HumanOmni25-8v1-2_A1) SNP chip. Results were analyzed using the software GenomeStudio 2011.1 and the data were exported to Plink format, aligned to Human Genome build version 37.

2016-09-21 | E-MTAB-5119 | biostudies-arrayexpress

CentralAfricanCMC_Pemberton

Project description:The CentralAfricanCMC_Pemberton dataset encompasses 153,798 SNPs from the Illumina Cardio-MetaboChip (Voight et al. 2012) genotyped in 406 individuals from 19 Central African Populations from Gabon, Cameroon, Centralafrican Republic and Uganda). Individual phenotypic and cultural information at the individual level for this data set encompass gender, lifestyle (hunter-gatherer or farmer), and, when available, stature phenotype (standing height in cm, sitting-height in cm, and weight in kg). Other cultural, linguistic, and geographical location information about the sampled populations can be found in Pemberton et al. , Human Genetics, 2018 (https://doi.org/10.1007/s00439-018-1902-3).This dataset can only be accessed and used for non-commercial research purposes with a finality complying with the informed consent provided by Central African donors for the study of human evolutionary history only.

| EGAD00010001584 | EGA

The Caucasus as an asymmetric semipermeable barrier to ancient human migrations

Project description:The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture. 204 samples were analysed with the Illumina platform Human610-Quad v 1.0 and are described herein.

2012-04-17 | E-GEOD-37342 | biostudies-arrayexpress

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