scholarly journals Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference

2015 ◽  
Author(s):  
Xumin Ni ◽  
Xiong Yang ◽  
Wei Guo ◽  
Kai Yuan ◽  
Ying Zhou ◽  
...  
Keyword(s):  
African Americans ◽  
General Model ◽  
South Asians ◽  
Demographic History ◽  
Length Distribution ◽  
Theoretical Models ◽  
Population History ◽  
Asian Populations ◽  
Special Cases ◽  
Admixed Population

As a chromosome is sliced into pieces by recombination after entering an admixed population, ancestral tracks of chromosomes are shortened with the pasting of generations. The length distribution of ancestral tracks reflects information of recombination and thus can be used to infer the histories of admixed populations. Previous studies have shown that inference based on ancestral tracks is powerful in recovering the histories of admixed populations. However, population histories are always complex, and previous studies only deduced the length distribution of ancestral tracks under very simple admixture models. The deduction of length distribution of ancestral tracks under a more general model will greatly elevate the power in inferring population histories. Here we first deduced the length distribution of ancestral tracks under a general model in an admixed population, and proposed general principles in parameter estimation and model selection with the length distribution. Next, we focused on studying the length distribution of ancestral tracks and its applications under three typical admixture models, which were all special cases of our general model. Extensive simulations showed that the length distribution of ancestral tracks was well predicted by our theoretical models. We further developed a new method based on the length distribution of ancestral tracks and good performance was observed when it was applied in inferring population histories under the three typical models. Notably, our method was insensitive to demographic history, sample size and threshold to discard short tracks. Finally, we applied our method in African Americans and Mexicans from the HapMap dataset, and several South Asian populations from the Human Genome Diversity Project dataset. The results showed that the histories of African Americans and Mexicans matched the historical records well, and the population admixture history of South Asians was very complex and could be traced back to around 100 generations ago.

scholarly journals Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Xumin Ni ◽  
Xiong Yang ◽  
Wei Guo ◽  
Kai Yuan ◽  
Ying Zhou ◽  
...  
Keyword(s):  
South Asian ◽  
General Model ◽  
Demographic History ◽  
Length Distribution ◽  
Population History ◽  
Population Admixture ◽  
Hapmap Project ◽  
Genome Diversity ◽  
Asian Populations ◽  
Special Cases

Abstract The length of ancestral tracks decays with the passing of generations which can be used to infer population admixture histories. Previous studies have shown the power in recovering the histories of admixed populations via the length distributions of ancestral tracks even under simple models. We believe that the deduction of length distributions under a general model will greatly elevate the power. Here we first deduced the length distributions under a general model and proposed general principles in parameter estimation and model selection with the deduced length distributions. Next, we focused on studying the length distributions and its applications under three typical special cases. Extensive simulations showed that the length distributions of ancestral tracks were well predicted by our theoretical framework. We further developed a new method, AdmixInfer, based on the length distributions and good performance was observed when it was applied to infer population histories under the three typical models. Notably, our method was insensitive to demographic history, sample size and threshold to discard short tracks. Finally, good performance was also observed when applied to some real datasets of African Americans, Mexicans and South Asian populations from the HapMap project and the Human Genome Diversity Project.

scholarly journals An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1429-1437
Author(s):  
Oliver G Pybus ◽  
Andrew Rambaut ◽  
Paul H Harvey
Keyword(s):  
Maximum Likelihood ◽  
Sequence Data ◽  
Demographic History ◽  
Population History ◽  
Maximum Likelihood Estimates ◽  
Viral Population ◽  
True Parameter ◽  
Subtype B ◽  
Exponential Growth Model ◽  
Parameter Values

Abstract We describe a unified set of methods for the inference of demographic history using genealogies reconstructed from gene sequence data. We introduce the skyline plot, a graphical, nonparametric estimate of demographic history. We discuss both maximum-likelihood parameter estimation and demographic hypothesis testing. Simulations are carried out to investigate the statistical properties of maximum-likelihood estimates of demographic parameters. The simulations reveal that (i) the performance of exponential growth model estimates is determined by a simple function of the true parameter values and (ii) under some conditions, estimates from reconstructed trees perform as well as estimates from perfect trees. We apply our methods to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

scholarly journals Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Fan Jiang ◽  
Ruiyi Lin ◽  
Changyi Xiao ◽  
Tanghui Xie ◽  
Yaoxin Jiang ◽  
...  
Keyword(s):  
Gene Flow ◽  
South Asia ◽  
South Asian ◽  
Demographic History ◽  
Nervous System Development ◽  
Chromosome 1 ◽  
Whole Genome ◽  
Chinese Populations ◽  
Asian Populations ◽  
History Of

Abstract Background The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Results Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). Conclusions Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

scholarly journals Population Dynamics in Pre-Modern China

2013 ◽  
Author(s):  
Zhongwei Zhao
Keyword(s):  
Economic Development ◽  
Population Growth ◽  
Chinese Population ◽  
Environmental Changes ◽  
Demographic History ◽  
Social Institutions ◽  
Population History ◽  
Chinese History ◽  
Population Changes ◽  
The Past

China constituted one of the earliest civilizations in the world. During most of the past two millennia, China was also one of the most advanced economies and the home of around a quarter of the world’s population. By the start of the first millennium, the Chinese population was already about sixty million. In the next two thousand years, China’s population growth and economic development significantly influenced the world’s population changes and history. Partly for these reasons, in the study of population and social history, China’s historical population growth, demographic regimes, marriage patterns, and household formation systems are frequently used as examples in the discussion of population changes, microsocial structure, and their relationships with natural resources and economic development in past times. Population changes were one of the key components of Chinese history. The size and density of the population, the rise and fall of fertility and mortality, and the increase and decrease of population movements were not only related to demographic factors such as age structure. They were also strongly affected by political and economic conditions, social institutions and cultural traditions, and natural and social environments. Therefore, studies of demographic history, those conducted recently in particular, often shed new light on economic, political, social, and environmental changes in the past. This bibliography, through reviewing major works published in Chinese and English, provides an introduction to China’s main historical population data sources, major research questions, and debates in the study of Chinese population history. It also introduces recent advances in Chinese historical demography and important research findings made by these developments.

scholarly journals Contact and Chord Length Distribution Functions of the Poisson-Voronoi Tessellation in High Dimensions

2010 ◽  
Vol 42 (1) ◽  
pp. 48-68 ◽  
Author(s):  
L. Muche
Keyword(s):  
Voronoi Tessellation ◽  
Length Distribution ◽  
Distribution Functions ◽  
Chord Length ◽  
Dimensional Euclidean Space ◽  
Spherical Contact ◽  
Chord Length Distribution ◽  
Special Cases ◽  
Contact Distribution ◽  
Contact Distribution Function

In this paper we present formulae for contact distributions of a Voronoi tessellation generated by a homogeneous Poisson point process in the d-dimensional Euclidean space. Expressions are given for the probability density functions and moments of the linear and spherical contact distributions. They are double and simple integral formulae, which are tractable for numerical evaluation and for large d. The special cases d = 2 and d = 3 are investigated in detail, while, for d = 3, the moments of the spherical contact distribution function are expressed by standard functions. Also, the closely related chord length distribution functions are considered.

scholarly journals OR08-05 Sex and Ethnic Differences in Advanced Lipoprotein Profiles in South Asians, African-Americans, and Caucasians

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Camila Sarcone ◽  
Andin Fosam ◽  
Abdul-Latif Armiyaw ◽  
Shivraj Grewal ◽  
Rashika Bansal ◽  
...  
Keyword(s):  
Insulin Sensitivity ◽  
African Americans ◽  
Ethnic Differences ◽  
Particle Number ◽  
South Asians ◽  
Density Lipoprotein ◽  
Lipoprotein Profile ◽  
Men And Women ◽  
Lipoprotein Particles ◽  
Lipoprotein Profiles

Abstract Background: African-Americans (AA) and South Asians (SA) are known to have higher risk for T2D and cardiovascular disease (CVD) compared to Caucasians (CA). Advanced analysis of lipoprotein particles with nuclear magnetic resonance (NMR) spectroscopy can offer insights into CVD risk and lipid metabolism beyond a standard lipid panel. Insulin resistance (IR) is known to be associated with atherogenic lipoprotein profile. Objective: To characterize the lipoprotein profile in AA, CA, and SA men and women. Design: A cross-sectional study of 182 healthy, non-diabetic SA, AA and CA patients was conducted at NIH. Subjects underwent an intravenous glucose tolerance test from which insulin sensitivity (Si) was derived using the Minimal Model. Lipoprotein profiles were measured by NMR with the LP4 deconvolution algorithm, which reports triglyceride-rich lipoprotein particles (TRLPs), high-density lipoprotein particles (HDLPs), and low-density lipoprotein particles (LDLPs). For group comparisons, Si was adjusted for age and fat free mass. Lipoprotein parameters were adjusted for age and body fat %. Results: Fifty-nine non-diabetic SA (33 males, 26 females), 49 AA (26 males, 23 females), and 74 CA (29 males, 45 females) were included in the study. Ethnic differences in Si were observed in men (p=0.002) but not in women (p=0.43). SA men had a significantly lower Si than both AA and CA men (p=0.02). TG concentrations and TRL particle number were significantly higher in CA men and women when compared with AA. TRLP size was not different between the ethnic groups in either sex. LDL particle number and ApoB concentration was significantly higher in SA men and women compared to AA and CA. There were no ethnic or sex differences in LDL size. HDL concentration, HDL particle number, and ApoA-I levels were not different between the groups in both sexes. However, in SA, large HDL particle number and HDL particle size was significantly lower than CA. Cholesteryl ester transfer protein (CETP) activity was significantly higher in SA men, but not women, when compared with AA and CA. Ethnic differences in LDLP and L-HDLP number remained even after adjusting for Si. Conclusions: In SA men and women, the lipoprotein phenotype (higher LDLP and lower L-HDLP) is independent of insulin sensitivity. Increased CETP activity may contribute to the lower large HDL particle number in this group. In AA, TG and TRLP number were lower as previously reported. Further investigation is needed to determine the factors mediating the atherogenic profile in SA.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

Diabetes in South Asians

2011 ◽  
pp. 1799-1803
Author(s):  
A. Ramachandran ◽  
C. Snehalatha
Keyword(s):  
South Asian ◽  
Indian Subcontinent ◽  
South Asians ◽  
Stress Factors ◽  
Rapid Urbanization ◽  
Asian Populations ◽  
Adults And Children ◽  
Diabetic Population

Developing countries, mainly in the Indian subcontinent and China, contribute nearly 80% to the rising global diabetic population. Conservative estimates, based on population growth, ageing of population, and rate of urbanization in Asia, show that India and China will remain the top two countries with the highest number of people with diabetes by 2025: 71 and 38 million, respectively. Two other South Asian countries, Pakistan and Bangladesh, also are in the top ten list. The South Asian populations of Bangladesh, Bhutan, India, the Maldives, Nepal, Pakistan, and Sri Lanka are racially heterogeneous, but all have high risk for diabetes and cardiovascular diseases. Type 1 diabetes is relatively less common, and nearly 95% of all diabetic cases in these regions are type 2 diabetes. The steady rise in the prevalence of diabetes seen in last three decades coincides with rapid urbanization and industrialization, and associated sociological and political changes, occurring in these countries (1). Among the populations, physical activity has reduced significantly, intake of energy-dense food has increased, and mental and physical stress factors associated with urban living have also increased. A tilt in the energy balance towards conservation and fat deposition has contributed to the alarming increase in the rate of obesity, both in adults and children.

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