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 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 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 Tracing the biogeographical origin of South Asian populations using DNA SatNav

2016 ◽  
Author(s):  
Ranajit Das ◽  
Priyanka Upadhyai
Keyword(s):  
Population Structure ◽  
South Asian ◽  
South India ◽  
Indian Subcontinent ◽  
Population History ◽  
Genetic Admixture ◽  
Indian Populations ◽  
Asian Populations ◽  
South Indian ◽  
North And South

AbstractThe Indian subcontinent includes India, Bangladesh, Pakistan, Nepal, Bhutan, and Sri Lanka that collectively share common anthropological and cultural roots. Given the enigmatic population structure, complex history and genetic heterogeneity of populations from this region, their biogeographical origin and history remain a fascinating question. In this study we carried out an in-depth genetic comparison of the five South Asian populations available in the 1000 Genomes Project, namely Gujarati Indians from Houston, Texas (GIH), Punjabis from Lahore (PJL), Indian Telugus from UK (ITU), Sri Lankan Tamils from UK (STU) and Bengalis from Bangladesh (BEB), tracing their putative biogeographical origin using a DNA SatNav algorithm - Geographical Population Structure (GPS). GPS positioned >70% of GIH and PJL genomes in North India and >80% of ITU and STU samples in South India. All South Asian genomes appeared to be assigned with reasonable accuracy, along trade routes that thrived in the ancient Mauryan Empire, which had played a significant role in unifying the Indian subcontinent and in the process brought the ancient North and South Indian populations in close proximity, promoting admixture between them, ~2300 years before present (YBP). Our findings suggest that the genetic admixture between ancient North and South Indian populations likely first occurred along the Godavari and Krishna river basin in Central-South India. Finally our biogeographical analyses provide critical insights into the population history and sociocultural forces driving migration patterns that may have been instrumental in shaping the population structure of the Indian subcontinent.

scholarly journals Indian genetic heritage in Southeast Asian populations

2021 ◽  
Author(s):  
Piya Changmai ◽  
Kitipong Jaisamut ◽  
Jatupol Kampuansai ◽  
Wibhu Kutanan ◽  
N. Ezgi Altınışık ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Ethnic Groups ◽  
South Asian ◽  
Southeast Asian ◽  
Population History ◽  
Published Data ◽  
Indian Culture ◽  
Asian Populations ◽  
Snp Data ◽  
Mainland Southeast Asia

AbstractThe great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Deeply divergent East Eurasian hunter-gatherers were the first anatomically modern human population known to migrate to the region. Agriculturalists from South China migrated to the region and admixed with the local hunter-gatherers during the Neolithic period. During the Bronze and Iron Ages, the genetic makeup of people in MSEA changed again, indicating an additional influx of populations from South China. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, and this cultural influence is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA, we generated genome-wide SNP data (the HumanOrigins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data from MSEA using the PCA, ADMIXTURE, f3-statistics, qpAdm, and qpGraph methods. We found South Asian low-level admixture in various MSEA populations which are probably descendants of people from the ancient Indian-influenced states, but failed to find a South Asian genetic component in present-day hunter-gatherer groups and relatively isolated groups from highlands in Northern Thailand. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.Author SummaryMainland Southeast Asia is a region with great ethnolinguistic diversity and complex population history. We studied genetic population history of present-day mainland Southeast Asian populations using genome-wide SNP data (the HumanOrigins array). We generated new data for 10 present-day ethnic groups from Thailand, which we further combined with published data from mainland and island Southeast Asians and worldwide populations. We revealed South Asian genetic admixture in various mainland Southeast Asian ethnic groups which are highly influenced by Indian culture, but failed to find it in groups who remained culturally isolated until recently. Our finding suggests that a massive migration of Indian people in the past was responsible for the spread of Indian culture in mainland Southeast Asia. We also found support for a close genetic affinity between Kra-Dai- and Austronesianspeaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.

scholarly journals Inference of Multiple-wave Admixtures by Length Distribution of Ancestral Tracks

2016 ◽  
Author(s):  
Xumin Ni ◽  
Xiong Yang ◽  
Kai Yuan ◽  
Qidi Feng ◽  
Wei Guo ◽  
...  
Keyword(s):  
Expectation Maximization ◽  
Length Distribution ◽  
Specific Model ◽  
Population History ◽  
Ratio Test ◽  
Population Admixture ◽  
Simulation Studies ◽  
Optimal Model ◽  
Real Situation ◽  
Multiple Wave

ABSTRACTThe ancestral tracks in admixed genomes are of valuable information for population history inference. A few methods have been developed to infer admixture history based on ancestral tracks. Nonetheless, these methods suffered the same flaw that only population admixture history under some specific models can be inferred. In addition, the inference of history might be biased or even unreliable if the specific model is deviated from the real situation. To address this problem, we firstly proposed a general discrete admixture model to describe the admixture history with multiple ancestral populations and multiple-wave admixtures. We next deduced the length distribution of ancestral tracks under the general discrete admixture model. We further developed a new method, MultiWaver, to explore the multiple-wave admixture histories. Our method could automatically determine an optimal admixture model based on the length distribution of ancestral tracks, and estimate the corresponding parameters under this optimal model. Specifically, we used a likelihood ratio test (LRT) to determine the number of admixture waves, and implemented an expectation??maximization (EM) algorithm to estimate parameters. We used simulation studies to validate the reliability and effectiveness of our method. Finally, good performance was observed when our method was applied to real datasets of African Americans, Mexicans, Uyghurs, and Hazaras.

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.

scholarly journals A systematic review of barriers and enablers to South Asian women’s attendance for asymptomatic screening of breast and cervical cancers in emigrant countries

BMJ Open ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. e020892 ◽  
Author(s):  
Rachel Mary Anderson de Cuevas ◽  
Pooja Saini ◽  
Deborah Roberts ◽  
Kinta Beaver ◽  
Mysore Chandrashekar ◽  
...  
Keyword(s):  
Systematic Review ◽  
South Asian ◽  
Asian Women ◽  
South Asian Women ◽  
Analysis Method ◽  
Asian Populations ◽  
Breast And Cervical Cancer ◽  
Social Structural ◽  
Behavioural Factors ◽  
Screening Attendance

ObjectivesThe aim of this review was to identify the cultural, social, structural and behavioural factors that influence asymptomatic breast and cervical cancer screening attendance in South Asian populations, in order to improve uptake and propose priorities for further research.DesignA systematic review of the literature for inductive, comparative, prospective and intervention studies. We searched the following databases: MEDLINE/In-Process, Web of Science, EMBASE, SCOPUS, CENTRAL, CDSR, CINAHL, PsycINFO and PsycARTICLES from database inception to 23 January 2018. The review included studies on the cultural, social, structural and behavioural factors that influence asymptomatic breast and cervical cancer screening attendance and cervical smear testing (Papanicolaou test) in South Asian populations and those published in the English language. The framework analysis method was used and themes were drawn out following the thematic analysis method.SettingsAsymptomatic breast or cervical screening.ParticipantsSouth Asian women, including Bangladeshi, Indian, Pakistani, Sri Lankan, Bhutanese, Maldivian and Nepali populations.Results51 included studies were published between 1991 and 2018. Sample sizes ranged from 25 to 38 733 and participants had a mean age of 18 to 83 years. Our review showed that South Asian women generally had lower screening rates than host country women. South Asian women had poorer knowledge of cancer and cancer prevention and experienced more barriers to screening. Cultural practices and assumptions influenced understandings of cancer and prevention, emphasising the importance of host country cultures and healthcare systems.ConclusionsHigh-quality research on screening attendance is required using prospective designs, where objectively validated attendance is predicted from cultural understandings, beliefs, norms and practices, thus informing policy on targeting relevant public health messages to the South Asian communities about screening for cancer.PROSPERO registration numberCSD 42015025284.

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 A Validation Study of the Mandibular Canine Index Method of Sexual Assessment Using Two Decedent American Populations

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Samantha Coberly
Keyword(s):  
South Asian ◽  
Biological Anthropology ◽  
Index Method ◽  
Arch Width ◽  
Asian Populations ◽  
Sexual Assessment ◽  
Sex Assessment ◽  
Mandibular Canine ◽  
The Right ◽  
Larger Sample

Rao and colleagues created the Mandibular Canine Index (MCI) as a method of sex assessment. It has primarily been used on living South Asian populations. This study applies the Index to two decedent American populations in hopes that it will applicable to the field of Forensic Anthropology. Forty-five individuals from the C.A. Pound Human Identification Lab and the Wichita State Biological Anthropology Lab with full mandibular dentition were studied. The mesio-distal width of both right and left canines and the canine arch width were taken and the MCI calculated along with the standard MCI. Results show that the MCI is not statistically significant in determining males from females (p=.461 for right and p=.473 for left).  The standard MCI was .242 for the right and .246 for the left. This gave an accuracy of 37% to 44% for males and 44% to 45% for females. The mesio-distal length (p = .002 for right and .001 for left) and canine arch width (p=.019) on their own were statistically significant and can be used in sex assessment if the teeth are present although they should be used with other methods.  Further study should be done with a larger sample size to see if results are consistent.

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