scholarly journals Complex genetic admixture histories reconstructed with Approximate Bayesian Computations

2019 ◽  
Author(s):  
Cesar A. Fortes-Lima ◽  
Romain Laurent ◽  
Valentin Thouzeau ◽  
Bruno Toupance ◽  
Paul Verdu
Keyword(s):  
Maximum Likelihood ◽  
Evolutionary Process ◽  
Genetic Admixture ◽  
Human Populations ◽  
Model Parameter ◽  
Parameter Estimations ◽  
Maximum Likelihood Methods ◽  
History Of ◽  
Approximate Bayesian ◽  
Parameter Values

ABSTRACTAdmixture is a fundamental evolutionary process that has influenced genetic patterns in numerous species. Maximum-likelihood approaches based on allele frequencies and linkage-disequilibrium have been extensively used to infer admixture processes from dense genome-wide datasets mostly in human populations. Nevertheless, complex admixture histories, beyond one or two pulses of admixture, remain methodologically challenging to reconstruct, especially when large datasets are unavailable. We develop an Approximate Bayesian Computations (ABC) framework to reconstruct complex admixture histories from independent genetic markers. We built the software package MetHis to simulate independent SNPs in a two-way admixed population for scenarios with multiple admixture pulses, or monotonically decreasing or increasing admixture at each generation; drawing model-parameter values from prior distributions set by the user. For each simulated dataset, we calculate 24 summary statistics describing genetic diversity and moments of individual admixture fraction. We coupled MetHis with existing ABC algorithms and investigate the admixture history of an African American and a Barbadian population. Results show that Random-Forest ABC scenario-choice, followed by Neural-Network ABC posterior parameter estimation, can distinguish most complex admixture scenarios and provide accurate model-parameter estimations. For both admixed populations, we find that monotonically decreasing contributions over time, from the European and African sources, explain the observed data more accurately than multiple admixture pulses. Furthermore, we find contrasted trajectories of introgression decay from the European and African sources between the two admixed populations. This approach will allow for reconstructing detailed admixture histories in numerous populations and species, particularly when maximum-likelihood methods are intractable.

scholarly journals Inferring linguistic transmission between generations at the scale of individuals

2018 ◽  
Author(s):  
Valentin Thouzeau ◽  
Antonin Affholder ◽  
Philippe Mennecier ◽  
Paul Verdu ◽  
Frédéric Austerlitz
Keyword(s):  
Linguistic Diversity ◽  
Simulated Data ◽  
Human Populations ◽  
Linguistic Data ◽  
Demographic Models ◽  
History Of ◽  
Best Fitting ◽  
Approximate Bayesian ◽  
Individual Scale ◽  
The Individual

AbstractHistorical linguistics highly benefited from recent methodological advances inspired by phylogenetics. Nevertheless, no currently available method uses contemporaneous within-population linguistic diversity to reconstruct the history of human populations. Here, we develop an approach inspired from population genetics to perform historical linguistic inferences from linguistic data sampled at the individual scale, within a population. We built four demographic models of linguistic transmission at this scale, each model differing by the number of teachers involved during the language acquisition, and the relative roles of these teachers. We then compared the simulated data obtained with these models with real contemporaneous linguistic data sampled in Tajik speakers in Central Asia, an area known for its high within-population linguistic diversity, using approximate Bayesian computation methods. With these statistical methods, we were able to select the models that best explained the data, and inferred the best-fitting parameters under these selected models, demonstrating the feasibility of using contemporaneous within-population linguistic diversity to infer historical features of human cultural evolution.

scholarly journals Helicobacter pylori’s historical journey through Siberia and the Americas

2021 ◽  
Vol 118 (25) ◽  
pp. e2015523118
Author(s):  
Yoshan Moodley ◽  
Andrea Brunelli ◽  
Silvia Ghirotto ◽  
Andrey Klyubin ◽  
Ayas S. Maady ◽  
...  
Keyword(s):  
Native Americans ◽  
Ethnically Diverse ◽  
Northern Eurasia ◽  
Human Populations ◽  
Bering Strait ◽  
Demographic Bottleneck ◽  
History Of ◽  
Low Levels ◽  
Approximate Bayesian ◽  
H Pylori

The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.

Archaic Lineages in the History of Modern Humans

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 799-808 ◽  
Author(s):  
Damian Labuda ◽  
Ewa Ziętkiewicz ◽  
Vania Yotova
Keyword(s):  
Homo Sapiens ◽  
Large Fraction ◽  
Principal Component ◽  
Distinct Group ◽  
Dystrophin Gene ◽  
Modern Human ◽  
Genetic Admixture ◽  
Human Populations ◽  
History Of ◽  
Sub Saharan

Abstract An important question in the ongoing debate on the origin of Homo sapiens is whether modern human populations issued from a single lineage or whether several, independently evolving lineages contributed to their genetic makeup. We analyzed haplotypes composed of 35 polymorphisms from a segment of the dystrophin gene. We find that the bulk of a worldwide sample of 868 chromosomes represents haplotypes shared by different continental groups. The remaining chromosomes carry haplotypes specific for the continents or for local populations. The haplotypes specific for non-Africans can be derived from the most frequent ones through simple recombination or a mutation. In contrast, chromosomes specific for sub-Saharan Africans represent a distinct group, as shown by principal component analysis, maximum likelihood tree, structural comparison, and summary statistics. We propose that African chromosomes descend from at least two lineages that have been evolving separately for a period of time. One of them underwent range expansion colonizing different continents, including Africa, where it mixed with another, local lineage represented today by a large fraction of African-specific haplotypes. Genetic admixture involving archaic lineages appears therefore to have occurred within Africa rather than outside this continent, explaining greater diversity of sub-Saharan populations observed in a variety of genetic systems.

scholarly journals Technical Note: Approximate Bayesian Computation to improve long-return flood estimates using historical data

2018 ◽  
Author(s):  
Adam Griffin ◽  
Luke Shaw ◽  
Elizabeth Stewart
Keyword(s):  
Maximum Likelihood ◽  
Approximate Bayesian Computation ◽  
Historical Data ◽  
Flood Frequency ◽  
Flood Frequency Analysis ◽  
Bayesian Computation ◽  
Likelihood Methods ◽  
True Parameter ◽  
Maximum Likelihood Methods ◽  
Approximate Bayesian

Abstract. For the Generalised Logistic distribution as used in UK flood frequency analysis, one standard approach for parameter estimation is through maximum likelihood methods. However, there can be problems with convergence to final estimates in cases where the true parameter values are extreme. This paper applies Approximate Bayesian Computation (ABC), a likelihood-free approach popularised in statistical genetics, which generates candidate parameters and compares data simulated from those candidates to the observed data. Candidates whose data have summary statistics (Partial Probability Weighted Moments, PPWM) sufficiently close to those of the observed data are accepted as draws from the posterior distribution. The ABC-PPWM approach is applied to new historical data points to estimate the flood frequency distribution for the River Severn at the Welsh Bridge in Shrewsbury, UK to improve the estimates of magnitudes of flood events with return period longer than the length of systematic records. Level data are derived from historical sources, and discharge estimates are obtained using data from upstream discharge gauging stations. When used in the ABC-PPWM approach, the results are at least as effective as the maximum likelihood methods, showing similar point estimates, and similar levels of variance. The estimates for the shape parameter for the GLO show some discrepancies, but this is known to be the most challenging to estimate given the availability of only censored historical data. Unlike maximum likelihood methods, for which the estimate may not be obtainable, the ABC-PPWM approach is always successful.

Indirect methods for monitoring and modeling gene flow in natural plant populations.

2021 ◽  
pp. 26-38
Author(s):  
María Eugenia Barrandeguy ◽  
María Victoria García
Keyword(s):  
Molecular Markers ◽  
Gene Flow ◽  
Population Genetic ◽  
Molecular Ecology ◽  
Evolutionary Process ◽  
Genetic Admixture ◽  
Indirect Methods ◽  
Genetic Studies ◽  
Approximate Bayesian ◽  
Sequencing Platforms

Abstract Gene flow is a micro-evolutionary process that maintains the allelic exchange among local populations, increasing population genetic diversity. Because of the immobility of plants, pollen plays a major role in connecting extant populations while seeds are necessary to establish and maintain populations of plants. Despite the widespread use of next-generation sequencing platforms, co-dominant molecular markers, such as microsatellites, are still useful and informative tools in molecular ecology and conservation genetic studies. These markers are currently the most frequently used tools for population genetic studies in plants. These molecular markers reveal information for gene flow estimation by indirect methods and also for comparing the role of gene flow by pollen versus gene flow by seeds in the determination of population genetic structures. Approximate Bayesian computation methods are often used to determine the most probable model of genetic admixture among populations.

scholarly journals The Genetic Structure and East-West Population Admixture in Northwest China Inferred From Genome-Wide Array Genotyping

2021 ◽  
Vol 12 ◽  
Author(s):  
Bin Ma ◽  
Jinwen Chen ◽  
Xiaomin Yang ◽  
Jingya Bai ◽  
Siwei Ouyang ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Northwest China ◽  
Population History ◽  
Genetic Admixture ◽  
Human Populations ◽  
Supporting Evidence ◽  
Chinese Populations ◽  
Genome Wide ◽  
History Of ◽  
East And West

Northwest China is a contacting region for East and West Eurasia and an important center for investigating the migration and admixture history of human populations. However, the comprehensive genetic structure and admixture history of the Altaic speaking populations and Hui group in Northwest China were still not fully characterized due to insufficient sampling and the lack of genome-wide data. Thus, We genotyped genome-wide SNPs for 140 individuals from five Chinese Mongolic, Turkic speaking groups including Dongxiang, Bonan, Yugur, and Salar, as well as the Hui group. Analysis based on allele-sharing and haplotype-sharing were used to elucidate the population history of Northwest Chinese populations, including PCA, ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave/qpAdm and ALDER, fineSTRUCTURE and GLOBETROTTER. We observed Dongxiang, Bonan, Yugur, Salar, and Hui people were admixed populations deriving ancestry from both East and West Eurasians, with the proportions of West Eurasian related contributions ranging from 9 to 15%. The genetic admixture was probably driven by male-biased migration- showing a higher frequency of West Eurasian related Y chromosomal lineages than that of mtDNA detected in Northwest China. ALDER-based admixture and haplotype-based GLOBETROTTER showed this observed West Eurasian admixture signal was introduced into East Eurasia approximately 700 ∼1,000 years ago. Generally, our findings provided supporting evidence that the flourish transcontinental communication between East and West Eurasia played a vital role in the genetic formation of northwest Chinese populations.

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