Robust Demographic Inference from Genomic and SNP Data
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R Nielsen, 2007, Recent and ongoing selection in the human genome, Nat Rev Genet, 8, 857, 10.1038/nrg2187
JL Kelley, 2006, Genomic signatures of positive selection in humans and the limits of outlier approaches, Genome Res, 16, 980, 10.1101/gr.5157306
R Nielsen, 2005, Genomic scans for selective sweeps using SNP data, Genome Res, 15, 1566, 10.1101/gr.4252305
MA Beaumont, 1996, Evaluating loci for use in the genetic analysis of population structure, Proceedings of the Royal Society London B, 263, 1619, 10.1098/rspb.1996.0237
AR Boyko, 2008, Assessing the evolutionary impact of amino acid mutations in the human genome, PLoS Genet, 4, e1000083, 10.1371/journal.pgen.1000083
MK Kuhner, 2000, Usefulness of Single Nucleotide Polymorphism Data for Estimating Population Parameters, Genetics, 156, 439, 10.1093/genetics/156.1.439
P Beerli, 2001, Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach, Proceedings of the National Academy of Sciences USA, 98, 4563, 10.1073/pnas.081068098
J Hey, 2007, Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics, Proc Natl Acad Sci U S A, 104, 2785, 10.1073/pnas.0611164104
J Hey, 2010, Isolation with migration models for more than two populations, Mol Biol Evol, 27, 905, 10.1093/molbev/msp296
C Becquet, 2007, A new approach to estimate parameters of speciation models with application to apes, Genome Res, 17, 1505, 10.1101/gr.6409707
L Naduvilezhath, 2011, Jaatha: a fast composite-likelihood approach to estimate demographic parameters, Mol Ecol, 20, 2709, 10.1111/j.1365-294X.2011.05131.x
C Leuenberger, 2010, Bayesian computation and model selection without likelihoods, Genetics, 184, 243, 10.1534/genetics.109.109058
D Wegmann, 2009, Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood, Genetics, 182, 1207, 10.1534/genetics.109.102509
MA Beaumont, 2009, Adaptive approximate Bayesian computation, Biometrika, 96, 983, 10.1093/biomet/asp052
L Excoffier, 2005, Bayesian Analysis of an Admixture Model With Mutations and Arbitrarily Linked Markers, Genetics, 169, 1727, 10.1534/genetics.104.036236
MA Beaumont, 2002, Approximate Bayesian computation in population genetics, Genetics, 162, 2025, 10.1093/genetics/162.4.2025
R Nielsen, 2000, Estimation of population parameters and recombination rates from single nucleotide polymorphisms, Genetics, 154, 931, 10.1093/genetics/154.2.931
H Chen, 2012, The joint allele frequency spectrum of multiple populations: a coalescent theory approach, Theor Popul Biol, 81, 179, 10.1016/j.tpb.2011.11.004
GT Marth, 2004, The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations, Genetics, 166, 351, 10.1534/genetics.166.1.351
AM Adams, 2004, Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms, Genetics, 168, 1699, 10.1534/genetics.104.030171
RN Gutenkunst, 2009, Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data, PLoS genetics, 5, e1000695, 10.1371/journal.pgen.1000695
D Garrigan, 2009, Composite likelihood estimation of demographic parameters, BMC genetics, 10, 72, 10.1186/1471-2156-10-72
S Lukic, 2011, Non-equilibrium allele frequency spectra via spectral methods, Theoretical population biology, 79, 203, 10.1016/j.tpb.2011.02.003
S Lukic, 2012, Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion, Genetics, 192, 619, 10.1534/genetics.112.141846
H Li, 2011, Inference of human population history from individual whole-genome sequences, Nature, 475, 493, 10.1038/nature10231
I Gronau, 2011, Bayesian inference of ancient human demography from individual genome sequences, Nat Genet, 43, 1031, 10.1038/ng.937
S Myers, 2008, Can one learn history from the allelic spectrum?, Theoretical population biology, 73, 342, 10.1016/j.tpb.2008.01.001
S Gravel, 2011, Demographic history and rare allele sharing among human populations, Proc Natl Acad Sci U S A, 108, 11983, 10.1073/pnas.1019276108
JA Tennessen, 2012, Evolution and functional impact of rare coding variation from deep sequencing of human exomes, Science, 337, 64, 10.1126/science.1219240
V Sousa, 2013, Understanding the origin of species with genome-scale data: modelling gene flow, Nat Rev Genet, 14, 404, 10.1038/nrg3446
X Yi, 2010, Sequencing of 50 human exomes reveals adaptation to high altitude, Science, 329, 75, 10.1126/science.1190371
R Nielsen, 2012, SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data, PloS one, 7, e37558, 10.1371/journal.pone.0037558
RM Durbin, 2010, A map of human genome variation from population-scale sequencing, Nature, 467, 1061, 10.1038/nature09534
JE Crawford, 2012, Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data, Front Genet, 3, 66, 10.3389/fgene.2012.00066
R Nielsen, 2011, Genotype and SNP calling from next-generation sequencing data, Nat Rev Genet, 12, 443, 10.1038/nrg2986
M Lynch, 2009, Estimation of allele frequencies from high-coverage genome-sequencing projects, Genetics, 182, 295, 10.1534/genetics.109.100479
SY Kim, 2011, Estimation of allele frequency and association mapping using next-generation sequencing data, BMC Bioinformatics, 12, 231, 10.1186/1471-2105-12-231
PL Johnson, 2006, Inference of population genetic parameters in metagenomics: a clean look at messy data, Genome Res, 16, 1320, 10.1101/gr.5431206
A Wollstein, 2010, Demographic history of Oceania inferred from genome-wide data, Current biology : CB, 20, 1983, 10.1016/j.cub.2010.10.040
A Albrechtsen, 2010, Ascertainment biases in SNP chips affect measures of population divergence, Mol Biol Evol, 27, 2534, 10.1093/molbev/msq148
AG Clark, 2005, Ascertainment bias in studies of human genome-wide polymorphism, Genome Res, 15, 1496, 10.1101/gr.4107905
N Patterson, 2012, Ancient admixture in human history, Genetics, 192, 1065, 10.1534/genetics.112.145037
Lu Y, Patterson N, Zhan Y, Mallick S, Reich D (2011) Technical design document for a SNP array that is optimized for population genetics. Available: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="ftp://ftp.cephb.fr/hgdp_supp10/8_12_2011_Technical_Array_Design_Document.pdf" xlink:type="simple">ftp://ftp.cephb.fr/hgdp_supp10/8_12_2011_Technical_Array_Design_Document.pdf</ext-link>
R Nielsen, 2004, Reconstituting the Frequency Spectrum of Ascertained Single-Nucleotide Polymorphism Data, Genetics, 168, 2373, 10.1534/genetics.104.031039
JK Pickrell, 2012, The genetic prehistory of southern Africa, Nature communications, 3, 1143, 10.1038/ncomms2140
J Wakeley, 1997, Estimating ancestral population parameters, Genetics, 145, 847, 10.1093/genetics/145.3.847
L Excoffier, 2004, Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model, Mol Ecol, 13, 853, 10.1046/j.1365-294X.2003.02004.x
NJ Fagundes, 2007, Statistical evaluation of alternative models of human evolution, Proc Natl Acad Sci U S A, 104, 17614, 10.1073/pnas.0708280104
F Zakharia, 2009, Characterizing the admixed African ancestry of African Americans, Genome Biol, 10, R141, 10.1186/gb-2009-10-12-r141
P Sjodin, 2012, Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period, Mol Biol Evol, 29, 1851, 10.1093/molbev/mss061
BM Henn, 2011, Hunter-gatherer genomic diversity suggests a southern African origin for modern humans, Proc Natl Acad Sci U S A, 108, 5154, 10.1073/pnas.1017511108
H Akaike, 1974, New Look at Statistical-Model Identification, Ieee Transactions on Automatic Control, Ac19, 716, 10.1109/TAC.1974.1100705
KR Veeramah, 2012, An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data, Molecular biology and evolution, 29, 617, 10.1093/molbev/msr212
MF Hammer, 2011, Genetic evidence for archaic admixture in Africa, Proc Natl Acad Sci U S A, 108, 15123, 10.1073/pnas.1109300108
CM Schlebusch, 2012, Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History, Science, 338, 374, 10.1126/science.1227721
GJ Dimmendaal, 2008, Language Ecology and Linguistic Diversity on the African Continent, Language and Linguistics Compass, 840, 10.1111/j.1749-818X.2008.00085.x
C Ehret, 2001, Bantu expansions: Re-envisioning a central problem of early African history, International Journal of African Historical Studies, 34, 5, 10.2307/3097285
D Reich, 2010, Genetic history of an archaic hominin group from Denisova Cave in Siberia, Nature, 468, 1053, 10.1038/nature09710
M Meyer, 2012, A high-coverage genome sequence from an archaic Denisovan individual, Science, 338, 222, 10.1126/science.1224344
A Auton, 2007, Recombination rate estimation in the presence of hotspots, Genome Research, 17, 1219, 10.1101/gr.6386707
PA Jenkins, 2012, Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae, PloS one, 7, e46947, 10.1371/journal.pone.0046947
R Nielsen, 2009, Darwinian and demographic forces affecting human protein coding genes, Genome Res, 19, 838, 10.1101/gr.088336.108
RD Hernandez, 2007, Context dependence, ancestral misidentification, and spurious signatures of natural selection, Mol Biol Evol, 24, 1792, 10.1093/molbev/msm108
C Varin, 2011, An Overview of Composite Likelihood Methods, Statistica Sinica, 21, 5
MA Beaumont, 2003, Estimation of population growth or decline in genetically monitored populations, Genetics, 164, 1139, 10.1093/genetics/164.3.1139
C Andrieu, 2009, The Pseudo-Marginal Approach for Efficient Monte Carlo Computations, Annals of Statistics, 37, 697, 10.1214/07-AOS574
A Kong, 2012, Rate of de novo mutations and the importance of father's age to disease risk, Nature, 488, 471, 10.1038/nature11396
A Scally, 2012, Revising the human mutation rate: implications for understanding human evolution, Nature reviews Genetics, 13, 745, 10.1038/nrg3295
S Li, 2012, Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation, BMC genetics, 13, 22, 10.1186/1471-2156-13-22
K Csillery, 2010, Approximate Bayesian Computation (ABC) in practice, Trends in ecology & evolution, 25, 410, 10.1016/j.tree.2010.04.001
JS Lopes, 2010, ABC: a useful Bayesian tool for the analysis of population data, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 10, 826, 10.1016/j.meegid.2009.10.010
S Aeschbacher, 2012, A novel approach for choosing summary statistics in approximate Bayesian computation, Genetics, 192, 1027, 10.1534/genetics.112.143164
MA Nunes, 2010, On optimal selection of summary statistics for approximate Bayesian computation, Statistical applications in genetics and molecular biology, 9, Article34, 10.2202/1544-6115.1576
VC Sousa, 2009, Approximate bayesian computation without summary statistics: the case of admixture, Genetics, 181, 1507, 10.1534/genetics.108.098129
P Beerli, 2004, Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations, Mol Ecol, 13, 827, 10.1111/j.1365-294X.2004.02101.x
M Slatkin, 2005, Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations, Mol Ecol, 14, 67, 10.1111/j.1365-294X.2004.02393.x
A Gelman, 1996, Posterior predictive assessment of model fitness via realized discrepancies, Statistica Sinica, 6, 733
Box GEP, Draper NR (1987) Empirical model-building and response surfaces. New York; Chichester etc.: J. Wiley. XIV, 669 pp.
XL Meng, 1993, Maximum likelihood estimation via the ECM algorithm: A general framework, Biometrika, 80, 267, 10.1093/biomet/80.2.267
Brent RP (1973) Algorithms for Minimization without Derivatives. Englewood Cliffs, NJ: Prentice-Hall.
Press WH, Teukolsky SA, Vetterling WT, Flannery BP (2007) Numerical Recipes in C++: The Art of Scientific Computing. Cambridge: Cambridge University Press. 1256 p.
L Excoffier, 2011, fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios, Bioinformatics, 27, 1332, 10.1093/bioinformatics/btr124
R Drmanac, 2010, Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays, Science, 327, 78, 10.1126/science.1181498
B O'Fallon, 2013, Purifying selection causes widespread distortions of genealogical structure on the human×chromosome, Genetics, 194, 485, 10.1534/genetics.113.152074
Karolchik D, Hinrichs AS, Kent WJ (2012) The UCSC Genome Browser. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al] Chapter 1: Unit1 4.
MA Beaumont, 2004, Recent developments in genetic data analysis: what can they tell us about human demographic history?, Heredity, 92, 365, 10.1038/sj.hdy.6800447
J Wakeley, 1999, Nonequilibrium migration in human history, Genetics, 153, 1863, 10.1093/genetics/153.4.1863
JB Johnson, 2004, Model selection in ecology and evolution, Trends in ecology & evolution, 19, 101, 10.1016/j.tree.2003.10.013
L Zhu, 2005, A composite-likelihood approach for detecting directional selection from DNA sequence data, Genetics, 170, 1411, 10.1534/genetics.104.035097