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YHap: software for probabilistic assignment of Y haplogroups from population re-sequencing data  [PDF]
Fan Zhang,Ruoyan Chen,Dongbing Liu,Xiaotian Yao,Guoqing Li,Yabin Jin,Chang Yu,Yingrui Li,Lachlan Coin
Quantitative Biology , 2013,
Abstract: Y haplogroup analyses are an important component of genealogical reconstruction, population genetic analyses, medical genetics and forensics. These fields are increasingly moving towards use of low-coverage, high throughput sequencing. However, there is as yet no software available for using sequence data to assign Y haplogroup groups probabilistically, such that the posterior probability of assignment fully reflects the information present in the data, and borrows information across all samples sequenced from a population. YHap addresses this problem.
Bounds on coverage probabilities of the empirical likelihood ratio confidence regions  [PDF]
Min Tsao
Mathematics , 2004, DOI: 10.1214/009053604000000337
Abstract: This paper studies the least upper bounds on coverage probabilities of the empirical likelihood ratio confidence regions based on estimating equations. The implications of the bounds on empirical likelihood inference are also discussed.
On the Coverage Bound Problem of Empirical Likelihood Methods For Time Series  [PDF]
Xianyang Zhang,Xiaofeng Shao
Statistics , 2014,
Abstract: The upper bounds on the coverage probabilities of the confidence regions based on blockwise empirical likelihood [Kitamura (1997)] and nonstandard expansive empirical likelihood [Nordman et al. (2013)] methods for time series data are investigated via studying the probability for the violation of the convex hull constraint. The large sample bounds are derived on the basis of the pivotal limit of the blockwise empirical log-likelihood ratio obtained under the fixed-b asymptotics, which has been recently shown to provide a more accurate approximation to the finite sample distribution than the conventional chi-square approximation. Our theoretical and numerical findings suggest that both the finite sample and large sample upper bounds for coverage probabilities are strictly less than one and the blockwise empirical likelihood confidence region can exhibit serious undercoverage when (i) the dimension of moment conditions is moderate or large; (ii) the time series dependence is positively strong; or (iii) the block size is large relative to sample size. A similar finite sample coverage problem occurs for the nonstandard expansive empirical likelihood. To alleviate the coverage bound problem, we propose to penalize both empirical likelihood methods by relaxing the convex hull constraint. Numerical simulations and data illustration demonstrate the effectiveness of our proposed remedies in terms of delivering confidence sets with more accurate coverage.
Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment
Bao-Zhu Yang, Hongyu Zhao, Henry R Kranzler, Joel Gelernter
BMC Genetics , 2005, DOI: 10.1186/1471-2156-6-50
Abstract: In EAs, the assignment accuracy by LBM exceeded 99% using the most efficient marker FY, and reached perfect assignment accuracy using the 10 most efficient markers excluding FY. In AAs, the assignment accuracy reached 96.4% using FY, and >95% when using at least the 9 most efficient markers. The comparison of the observed and reference allele frequencies (which were derived from previous publications and public databases) shows that allele frequencies observed in EAs matched the reference group more accurately than allele frequencies observed in AAs. As a result, the LBM performed better in EAs than AAs, as might be expected given the dependence of LBMs on prior knowledge of allele frequencies. Performance was not dependent on sample size.The performance of the LBM depends on the efficiency and number of markers, and depends greatly on how representative the available reference allele frequencies are for those of the population being assigned. This method is of value when the parental population is known and relevant allele frequencies are available.Population stratification is a crucial issue in conducting genetic association studies, in particular, for case-control study designs, such that if it is not accounted for study results could be invalid – either false positive or false negative [1]. Methods to address the issue have been proposed [2-17]. Before using these methods, an informative set of markers is necessary; this is known as a set of ancestry informative markers (AIMs). In this study, we implemented a likelihood based method (LBM), as an alternative to popular Bayesian methods such as that implemented in STRUCTURE [3,13], and used it to evaluate the informativeness of a selected marker panel and to assess potential for stratification in a sample of European Americans (EAs) and African Americans (AAs) that are known to be admixed.Likelihood-based methods (LBMs) provide a framework for assignment of individuals to specific populations based on observed all
Likelihood ratio intervals with Bayesian treatment of uncertainties: coverage, power and combined experiments  [PDF]
Jan Conrad,Fredrik Tegenfeldt
Physics , 2005,
Abstract: In this note we present studies of coverage and power for confidence intervals for a Poisson process with known background calculated using the Likelihood ratio (aka Feldman & Cousins) ordering with Bayesian treatment of uncertainties in nuisance parameters. We consider both the variant where the Bayesian integration is done in both the numerator and the denominator and the modification where the integration is done only in the numerator whereas in the denominator the likelihood is taken at the maximum likelihood estimate of the parameters. Furthermore we discuss how measurements can be combined in this framework and give an illustration with limits on the branching ratio of a rare B-meson decay recently presented by CDF/D0. A set of C++ classes has been developed which can be used to calculate confidence intervals for single or combining multiple experiments using the above algorithms and considering a variety of parameterizations to describe the uncertainties.
Distribution of East Eurasian Y-Chromosome and Mitochondrial DNA Haplogroups across Eurasia: Insights into the Genetic Ancestry of Bulgarians  [PDF]
Sena Karachanak-Yankova, Desislava Nesheva, Angel S. Galabov, Draga Toncheva
Advances in Anthropology (AA) , 2015, DOI: 10.4236/aa.2015.54019
Abstract: The modern Bulgarian mitochondrial DNA (mtDNA) and Y-chromosome gene pools predominantly consist of Western Eurasian haplogroups. In contrast, the Eastern Eurasian lineages are found at very low frequencies in Bulgarians, being represented only by mtDNA haplogroups C (0.2%), D (0.4%) and Z (0.1%) (Karachanak et al., 2012) and Y-chromosome haplogroups C, N and Q (each 0.5%) (Karachanak et al., 2013). A similar pattern is observed in ancient mtDNA samples of proto-Bulgarian human remains, which belong exclusively to Western Eurasian mtDNA haplogroups (Nesheva et al., 2015). In order to investigate Bulgarian ancestry from the perspective of Eastern Eurasian haplogroups, we have analyzed the distribution of Y-chromosome haplogroups C, N and Q and mtDNA haplogroups C, D and Z across Eurasia. The survey was performed using literature data for more than 15,000 individuals from different Eurasian (sub-) populations for each of these haplogroups. The collected data were used to construct Eurasian frequency maps of the considered haplogroups and to test the significance of their incidence between Bulgarians and Europeans, European neighboring populations of Bulgaria and populations, which according to some historical conceptions could have common ancestry with proto-Bulgarians, namely: Altaian, Caucasus, Siberian and Central Asian populations. The spatial distribution of mtDNA haplogroups C, D and Z and Y-chromosome haplogroups C, N and Q contrasts their high frequency among Altaic populations and their occasional appearance in Bulgarians. Furthermore, the comparison of the occurrence of these haplogroups shows no link between Bulgarians and Altaic and Caucasus populations. Based on the substantial genetic input of proto-Bulgarians to the modern Bulgarian gene pool, the present study confirms the nonexistence of a close Y-chromosomal or mtDNA link between proto-Bulgarians on the one hand and Altaic and Caucasus populations on the other.
Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations
Thijessen Naidoo, Carina M Schlebusch, Heeran Makkan, Pareen Patel, Rajeshree Mahabeer, Johannes C Erasmus, Himla Soodyall
Investigative Genetics , 2010, DOI: 10.1186/2041-2223-1-6
Abstract: Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Y chromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a few Eurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry.The use of these single base extension assays in screening increased haplogroup resolution and sampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeat markers would considerably improve resolution, thus refining the geographic ancestry of individuals.The Y chromosome has demonstrated its utility, for a number of years, in shedding light on human history and identifying population affinities. Given that human genome variation evolves over time due to several factors - among them mutation, genetic drift, migration and selection - the genome has retained some of the record of these historical and evolutionary events. This record is more easily read from the Y chromosome due to the lack of recombination along most of its length and a strict paternal mode of transmission. Consequently, the Y chromosome has become a marker of the male contribution to the shaping of human populations and their histories.A standard nomenclature established by the Y Chromosome Consortium [1] resolved the global pattern of Y chromosome variation into 18 major haplogroups that were classified using capital letters A through to R. This has
Convergence of Y chromosome STR haplotypes from different SNP haplogroups compromises accuracy of haplogroup prediction  [PDF]
Chuan-Chao Wang,Ling-Xiang Wang,Rukesh Shrestha,Shaoqing Wen,Manfei Zhang,Xinzhu Tong,Li Jin,Hui Li
Quantitative Biology , 2013,
Abstract: Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are two kinds of commonly used markers in Y chromosome studies of forensic and population genetics. There has been increasing interest in the cost saving strategy by using the STR haplotypes to predict SNP haplogroups. However, the convergence of Y chromosome STR haplotypes from different haplogroups might compromise the accuracy of haplogroup prediction. Here, we compared the worldwide Y chromosome lineages at both haplogroup level and haplotype level to search for the possible haplotype similarities among haplogroups. The similar haplotypes between haplogroups B and I2, C1 and E1b1b1, C2 and E1b1a1, H1 and J, L and O3a2c1, O1a and N, O3a1c and O3a2b, and M1 and O3a2 have been found, and those similarities reduce the accuracy of prediction.
Re-Examining the Out-of-Africa Theory and the Origin of Europeoids (Caucasoids). Part 2. SNPs, Haplogroups and Haplotypes in the Y Chromosome of Chimpanzee and Humans  [PDF]
Anatole A. Klyosov, Igor L. Rozhanskii, Lyudmila E. Ryabchenko
Advances in Anthropology (AA) , 2012, DOI: 10.4236/aa.2012.24022
Abstract: Our consideration of human haplogroups, and our analysis of the dynamics of the Y-chromosome nucleotide flow from primates to humans during the evolution of genus Homo has shown that a common ancestor of the majority of present day human males, both African and non-African, lived approximately 160,000 years ago. The haplogroup of this common ancestor has been identified as the α-haplogroup, which is equivalent or close to haplogroups A1/A1b in the current phylogeny. The archaic lineages (currently summarily designated A0) descend from an ancestor who lived no later than 180,000 years ago, and probably much earlier. The α-haplogroup and the A0 lineages have significantly different nucleotide patterns, and they certainly did not descend one from another. Furthermore, our research points up the areas of mutations in Y-chromosome in H. sapiens, which allows us to use chimpanzee MSY (the male-specific region of the Y-chromosome) as a proxy for genus Homo’s common α-haplogroup ancestor. When we studied slow mutating 16-marker haplotypes, we discovered that chimpanzees and present day humans had a common ancestor 5.5 ± 0.9 million years before the present. It is clear that, when they are compared to loci in other primates, such as gorillas, orangutans, and macaques, many human Y-chromosome loci have been conserved from our common ancestor. Results of our analysis of haplotypes, conserved (ancestral) nucleotides, and SNPs suggest that there is no reason to believe that ancestors of non-Africans (β-haplogroup, i.e. haplogroup BT and its downstream haplogroups) descended from haplogroups A0, A1a, or any other African haplogroup. The data are adequately described by a model which shows that the African lineages and non-African lineages diverged from the α-haplogroup approximately 160,000 years before the present and that the Y-chromosomes of the two groups have evolved independently (in terms of Y-chromosome) since then. We have no indication of where the common ancestor of the α-haplogroup lived; he could just as easily have lived in Europe, in Asia, or in the Middle East, as in (less likely) Africa. We believe that all the presuppositions posited in support of the Out-of-Africa hypothesis fail to hold up under simple scrutiny. This study shows that the Out-of-Africa hypothesis has not been adequately substantiated. The common assertion that “anatomically modern humans came out of Africa some 70,000 years ago” has never been convincingly calculated or determined otherwise; our research suggests that it is incorrect.
Statistical models, likelihood, penalized likelihood and hierarchical likelihood  [PDF]
Daniel Commenges
Mathematics , 2008,
Abstract: We give an overview of statistical models and likelihood, together with two of its variants: penalized and hierarchical likelihood. The Kullback-Leibler divergence is referred to repeatedly, for defining the misspecification risk of a model, for grounding the likelihood and the likelihood crossvalidation which can be used for choosing weights in penalized likelihood. Families of penalized likelihood and sieves estimators are shown to be equivalent. The similarity of these likelihood with a posteriori distributions in a Bayesian approach is considered.
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