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 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions

2016 ◽  
Author(s):  
Ying Zhou ◽  
Kai Yuan ◽  
Yaoliang Yu ◽  
Xumin Ni ◽  
Pengtao Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Simulated Data ◽  
Population Admixture ◽  
Multiple Wave ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Complex Population ◽  
Important Challenge ◽  
Source Populations ◽  
Admixture Linkage Disequilibrium

AbstractTo infer the histories of population admixture, one important challenge with methods based on the admixture linkage disequilibrium (ALD) is to get rid of the effect of source LD (SLD) which is directly inherited from source populations. In previous methods, only the decay curve of weighted LD between pairs of sites whose genetic distance were larger than a certain starting distance was fitted by single or multiple exponential functions, for the inference of recent single- or multiple-wave of admixture. However, the effect of SLD has not been well defined and no tool has been developed to estimate the effect of SLD on weighted LD decay. In this study, we defined the SLD in the formularized weighted LD statistic under the two-way admixture model, and proposed polynomial spectrum (p-spectrum) to study the weighted SLD and weighted LD. We also found reference populations could be used to reduce the SLD in weighted LD statistic. We further developed a method, iMAAPs, to infer Multiple-wave Admixture by fitting ALD using Polynomial spectrum. We evaluated the performance of iMAAPs under various admixture models in simulated data and applied iMAAPs into analysis of genome-wide single nucleotide polymorphism data from the Human Genome Diversity Project (HGDP) and the HapMap Project. We showed that iMAAPs is a considerable improvement over other current methods and further facilitates the inference of the histories of complex population admixtures.

scholarly journals Killer whale genomes reveal a complex history of recurrent admixture and vicariance

2019 ◽  
Author(s):  
Andrew D. Foote ◽  
Michael D. Martin ◽  
Marie Louis ◽  
George Pacheco ◽  
Kelly M. Robertson ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Killer Whale ◽  
Natural Populations ◽  
Major Axis ◽  
Glacial Cycle ◽  
Genome Wide ◽  
Complex Population ◽  
Genome Wide Data ◽  
History Of ◽  
Global Population

AbstractReconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species’ range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium

2009 ◽  
Vol 33 (3) ◽  
pp. 266-274 ◽  
Author(s):  
Anders Albrechtsen ◽  
Thorfinn Sand Korneliussen ◽  
Ida Moltke ◽  
Thomas van Overseem Hansen ◽  
Finn Cilius Nielsen ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genome Wide ◽  
Genome Wide Data

scholarly journals The genetic legacy of continental scale admixture in Indian Austroasiatic speakers

2018 ◽  
Author(s):  
Kai Tätte ◽  
Luca Pagani ◽  
Ajai K. Pathak ◽  
Sulev Kõks ◽  
Binh Ho Duy ◽  
...  
Keyword(s):  
South Asians ◽  
Asian Population ◽  
South Asian Population ◽  
Southeast Asians ◽  
Continental Scale ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Different Populations ◽  
Source Populations ◽  
Austroasiatic Languages

AbstractSurrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000 – 3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.78/0.22 are Lao people from Laos and Dravidian speakers from Kerala in India, while the South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data.

scholarly journals Exploiting Linkage Disequilibrium for Ultrahigh-Dimensional Genome-Wide Data with an Integrated Statistical Approach

Genetics ◽  
2015 ◽  
Vol 202 (2) ◽  
pp. 411-426 ◽  
Author(s):  
Michelle Carlsen ◽  
Guifang Fu ◽  
Shaun Bushman ◽  
Christopher Corcoran
Keyword(s):  
Linkage Disequilibrium ◽  
Statistical Approach ◽  
Genome Wide ◽  
Genome Wide Data

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 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.

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