scholarly journals Genomic landscape of human diversity across Madagascar

2017 ◽  
Vol 114 (32) ◽  
pp. E6498-E6506 ◽  
Author(s):  
Denis Pierron ◽  
Margit Heiske ◽  
Harilanto Razafindrazaka ◽  
Ignace Rakoto ◽  
Nelly Rabetokotany ◽  
...  
Keyword(s):  
Genomic Diversity ◽  
Eastern Africa ◽  
Human Populations ◽  
Human Diversity ◽  
Genetic Traits ◽  
Paternal Contribution ◽  
Genome Wide ◽  
Genomic Landscape ◽  
Genome Wide Data ◽  
Admixed Population

Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.

scholarly journals The genomic landscape of contemporary western Remote Oceanians

2022 ◽  
Author(s):  
Lara R. Arauna ◽  
Jacob Bergstedt ◽  
Jeremy Choin ◽  
Javier Mendoza-Revilla ◽  
Christine Harmant ◽  
...  
Keyword(s):  
East Asian ◽  
Genomic Diversity ◽  
Sociocultural Factors ◽  
Genome Wide ◽  
Genomic Landscape ◽  
Population Turnover ◽  
Genome Wide Data ◽  
History Of ◽  
Source Populations ◽  
Sociocultural Processes

The Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands around 3,200 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet, there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity. Here, we report genome-wide data for 1,433 contemporary ni-Vanuatu from 29 different islands, including 287 couples. We find that ni-Vanuatu derive their East Asian- and Papuan-related ancestry from the same source populations and descend from relatively synchronous admixture events that occurred around 1,700-2,300 years ago, indicating a peopling history common to all the archipelago. However, our analyses reveal that the Papuan population turnover was geographically uneven, and that the genetic contribution of Papuan-related peoples was male-biased. Furthermore, we detect Polynesian ancestry arriving around 600-1,000 years ago to South Vanuatu, and map its distribution to both Polynesian- and non-Polynesian-speaking islands. Lastly, we provide evidence for a tendency of spouses to carry similar genetic ancestry, when accounting for relatedness avoidance. The signal is not driven by strong genetic effects of specific loci or trait-associated variants, suggesting that it results instead from social assortative mating. Altogether, our findings provide insight into both the genetic history of ni-Vanuatu populations and how sociocultural processes have shaped the diversity of their genomes.

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 CCR5Δ32 in Brazil: Impacts of a European Genetic Variant on a Highly Admixed Population

2021 ◽  
Vol 12 ◽  
Author(s):  
Bruna Kulmann-Leal ◽  
Joel Henrique Ellwanger ◽  
José Artur Bogo Chies
Keyword(s):  
Allele Frequency ◽  
Genetic Variant ◽  
Population Level ◽  
Brazilian Population ◽  
Human Populations ◽  
Ccr5 Expression ◽  
Genetic Traits ◽  
Genetic Components ◽  
Base Pair Deletion ◽  
Admixed Population

The genetic background of Brazilians encompasses Amerindian, African, and European components as a result of the colonization of an already Amerindian inhabited region by Europeans, associated to a massive influx of Africans. Other migratory flows introduced into the Brazilian population genetic components from Asia and the Middle East. Currently, Brazil has a highly admixed population and, therefore, the study of genetic factors in the context of health or disease in Brazil is a challenging and remarkably interesting subject. This phenomenon is exemplified by the genetic variant CCR5Δ32, a 32 base-pair deletion in the CCR5 gene. CCR5Δ32 originated in Europe, but the time of origin as well as the selective pressures that allowed the maintenance of this variant and the establishment of its current frequencies in the different human populations is still a field of debates. Due to its origin, the CCR5Δ32 allele frequency is high in European-derived populations (~10%) and low in Asian and African native human populations. In Brazil, the CCR5Δ32 allele frequency is intermediate (4-6%) and varies on the Brazilian States, depending on the migratory history of each region. CCR5 is a protein that regulates the activity of several immune cells, also acting as the main HIV-1 co-receptor. The CCR5 expression is influenced by CCR5Δ32 genotypes. No CCR5 expression is observed in CCR5Δ32 homozygous individuals. Thus, the CCR5Δ32 has particular effects on different diseases. At the population level, the effect that CCR5Δ32 has on European populations may be different than that observed in highly admixed populations. Besides less evident due to its low frequency in admixed groups, the effect of the CCR5Δ32 variant may be affected by other genetic traits. Understanding the effects of CCR5Δ32 on Brazilians is essential to predict the potential use of pharmacological CCR5 modulators in Brazil. Therefore, this study reviews the impacts of the CCR5Δ32 on the Brazilian population, considering infectious diseases, inflammatory conditions, and cancer. Finally, this article provides a general discussion concerning the impacts of a European-derived variant, the CCR5Δ32, on a highly admixed population.

scholarly journals Genome-wide data implicate terminal fusion automixis in king cobra facultative parthenogenesis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daren C. Card ◽  
Freek J. Vonk ◽  
Sterrin Smalbrugge ◽  
Nicholas R. Casewell ◽  
Wolfgang Wüster ◽  
...  
Keyword(s):  
Genomic Diversity ◽  
Evolutionary Significance ◽  
Suspected Case ◽  
Squamate Reptiles ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Facultative Parthenogenesis ◽  
Elasmobranch Fishes ◽  
Ophiophagus Hannah ◽  
King Cobra

AbstractFacultative parthenogenesis (FP) is widespread in the animal kingdom. In vertebrates it was first described in poultry nearly 70 years ago, and since then reports involving other taxa have increased considerably. In the last two decades, numerous reports of FP have emerged in elasmobranch fishes and squamate reptiles (lizards and snakes), including documentation in wild populations of both clades. When considered in concert with recent evidence of reproductive competence, the accumulating data suggest that the significance of FP in vertebrate evolution has been largely underestimated. Several fundamental questions regarding developmental mechanisms, nonetheless, remain unanswered. Specifically, what is the type of automixis that underlies the production of progeny and how does this impact the genomic diversity of the resulting parthenogens? Here, we addressed these questions through the application of next-generation sequencing to investigate a suspected case of parthenogenesis in a king cobra (Ophiophagus hannah). Our results provide the first evidence of FP in this species, and provide novel evidence that rejects gametic duplication and supports terminal fusion as a mechanism underlying parthenogenesis in snakes. Moreover, we precisely estimated heterozygosity in parthenogenetic offspring and found appreciable retained genetic diversity that suggests that FP in vertebrates has underappreciated evolutionary significance.

scholarly journals FST and the Triangle Inequality for Biallelic Markers

2019 ◽  
Author(s):  
Ilana M. Arbisser ◽  
Noah A. Rosenberg
Keyword(s):  
Triangle Inequality ◽  
Distance Measure ◽  
Allele Frequencies ◽  
Pairwise Distance ◽  
Human Populations ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Point Condition ◽  
Frequency Vectors ◽  
Theoretical Results

AbstractThe population differentiation statistic FST, introduced by Sewall Wright, is often treated as a pairwise distance measure between populations. As was known to Wright, however, FST is not a true metric because allele frequencies exist for which it does not satisfy the triangle inequality. We prove that a stronger result holds: for biallelic markers whose allele frequencies differ across three populations, FST never satisfies the triangle inequality. We study the deviation from the triangle inequality as a function of the allele frequencies of three populations, identifying frequency vectors at which the deviation is maximal. We also examine the implications of the failure of the triangle inequality for the four-point condition for groups of four populations. Next, we examine the extent to which FST fails to satisfy the triangle inequality in genome-wide data from human populations, finding that some loci have frequencies that produce deviations near the maximum. We discuss the consequences of the theoretical results for various types of data analysis, including multidimensional scaling and inference of neighbor-joining trees from pairwise FST matrices.

scholarly journals Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions

2015 ◽  
Author(s):  
Ying Zhou ◽  
Kai Yuan ◽  
Yaoliang Yu ◽  
Xumin Ni ◽  
Pengtao Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Exponential Functions ◽  
Dynamic Changes ◽  
Multiple Wave ◽  
Flow Parameters ◽  
Genome Wide ◽  
Complex Population ◽  
Genome Wide Data ◽  
Admixed Population ◽  
Source Populations

Admixture-introduced linkage disequilibrium (LD) has recently been introduced into the inference of the histories of complex admixtures. However, the influence of ancestral source populations on the LD pattern in admixed populations is not properly taken into consideration by currently available methods, which affects the estimation of several gene flow parameters from empirical data. We first illustrated the dynamic changes of LD in admixed populations and mathematically formulated the LD under a generalized admixture model with finite population size. We next developed a new method, MALDmef, by fitting LD with multiple exponential functions for inferring and dating multiple-wave admixtures. MALDmef takes into account the effects of source populations which substantially affect modeling LD in admixed population, which renders it capable of efficiently detecting and dating multiple-wave admixture events. The performance of MALDmef was evaluated by simulation and it was shown to be more accurate than MALDER, a state-of-the-art method that was recently developed for similar purposes, under various admixture models. We further applied MALDmef to analyzing genome-wide data from the Human Genome Diversity Project (HGDP) and the HapMap Project. Interestingly, we were able to identify more than one admixture events in several populations, which have yet to be reported. For example, two major admixture events were identified in the Xinjiang Uyghur, occurring around 27???30 generations ago and 182???195 generations ago, respectively. In an African population (MKK), three recent major admixtures occurring 13???16, 50???67, and 107???139 generations ago were detected. Our method is a considerable improvement over other current methods and further facilitates the inference of the histories of complex population admixtures.

scholarly journals Signatures of long-term balancing selection in human genomes

2017 ◽  
Author(s):  
Bárbara Domingues Bitarello ◽  
Cesare de Filippo ◽  
João Carlos Teixeira ◽  
Joshua M. Schmidt ◽  
Philip Kleinert ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Theoretical Perspective ◽  
Human Populations ◽  
Protein Coding ◽  
Human Genomes ◽  
Genome Wide ◽  
Higher Power ◽  
Genome Wide Data ◽  
Immune Related Genes

AbstractBalancing selection maintains advantageous diversity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe the Non-Central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: about 0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (p < 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap about 8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.

scholarly journals Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 358 ◽  
Author(s):  
Olga Dolgova ◽  
Oscar Lao
Keyword(s):  
Demographic History ◽  
Modern Human ◽  
Human Populations ◽  
Human Genomes ◽  
Fitness Consequences ◽  
Genome Wide ◽  
Anatomically Modern Humans ◽  
Genome Wide Data ◽  
History Of ◽  
Health And Disease

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

scholarly journals Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

2018 ◽  
Author(s):  
Olga Dolgova ◽  
Oscar Lao
Keyword(s):  
Demographic History ◽  
Modern Human ◽  
Human Populations ◽  
Human Genomes ◽  
Fitness Consequences ◽  
Genome Wide ◽  
Anatomically Modern Humans ◽  
Genome Wide Data ◽  
History Of ◽  
Health And Disease

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH introgressed with archaic hominins once they left the African continent. Current out of African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

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