An Efficient Computational Approach for Constructing the Allele Frequency Spectrum of Populations with Arbitrary Complex History

The allele frequency spectrum (AFS), or site frequency spectrum, is commonly used to summarize the genomic polymorphism pattern of a sample, which is informative for inferring population history and detecting natural selection. Recently, Chen and Chen (2013) developed a method for analytically deriving the AFS for populations with temporally varying size through the coalescence time-scaling function. However, their approach is only applicable for population history scenarios in which the analytical form of the time-scaling function is tractable. In this paper, we propose a computational approach to extend the method to populations with arbitrary complex history by numerically approximating the time-scaling function. We demonstrate the performance of the approach by constructing the AFS for two population history scenarios: the logistic growth model and the Gompertz growth model, for which the AFS are unavailable with existing approaches.

• Publication year

  2018

• Venue

  bioRxiv

• Publication date

  2018-10-29

• Fields of study

  Biology, Mathematics, Computer Science

• Identifiers
  DOI 10.1101/456335
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Coalescent Theory

  2019cited by this paper
• The use of Gompertz models in growth analyses, and new Gompertz-model approach: An addition to the Unified-Richards family

  2017cited by this paper
• Exploring Population Size Changes Using SNP Frequency Spectra

  2015cited by this paper
• Inferring Very Recent Population Growth Rate from Population-Scale Sequencing Data: Using a Large-Sample Coalescent Estimator.

  2015cited by this paper
• Inference of Super-exponential Human Population Growth via Efficient Computation of the Site Frequency Spectrum for Generalized Models

  2015cited by this paper
• Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data

  2014cited by this paper
• Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth

  2014cited by this paper
• Asymptotic Distributions of Coalescence Times and Ancestral Lineage Numbers for Populations with Temporally Varying Size

  2013influential reference
• Neutral genomic regions refine models of recent rapid human population growth

  2013influential reference
• On the Nature of the Function Expressive of the Law of Human Mortality

  2013cited by this paper
• Robust Demographic Inference from Genomic and SNP Data

  2013cited by this paper
• Intercoalescence Time Distribution of Incomplete Gene Genealogies in Temporally Varying Populations, and Applications in Population Genetic Inference

  2013influential reference
• The joint allele frequency spectrum of multiple populations: a coalescent theory approach.

  2012influential reference
• An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

  2012cited by this paper
• Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

  2012cited by this paper
• Demographic history and rare allele sharing among human populations

  2011cited by this paper
• Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory.

  2011cited by this paper
• Deep resequencing reveals excess rare recent variants consistent with explosive population growth

  2010cited by this paper
• Non-equilibrium allele frequency spectra via spectral methods.

  2010cited by this paper
• Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

  2009cited by this paper
• Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans

  2007cited by this paper
• Non-equilibrium theory of the allele frequency spectrum.

  2006cited by this paper
• Coalescent lineage distributions

  2006cited by this paper
• Genomic scans for selective sweeps using SNP data.

  2005cited by this paper
• Simultaneous inference of selection and population growth from patterns of variation in the human genome

  2005cited by this paper
• The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations

  2004cited by this paper
• A note on distributions of times to coalescence, under time-dependent population size.

  2003influential reference
• New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth.

  2003cited by this paper
• Sampling theory for neutral alleles in a varying environment

  2003cited by this paper
• Sequence variations in the public human genome data reflect a bottlenecked population history

  2002cited by this paper
• DNA sequence variation in a 3.7-kb noncoding sequence 5' of the CYP1A2 gene: implications for human population history and natural selection.

  2002cited by this paper
• The matrix coalescent and an application to human single-nucleotide polymorphisms.

  2002cited by this paper
• Generating samples under a Wright-Fisher neutral model of genetic variation

  2002cited by this paper
• Directional selection and the site-frequency spectrum.

  2001cited by this paper
• The age of a mutation in a general coalescent tree

  1998influential reference
• Convergence Properties of the Nelder-Mead Simplex Method in Low Dimensions

  1998cited by this paper
• Coalescents and genealogical structure under neutrality.

  1995cited by this paper
• Statistical properties of segregating sites.

  1995influential reference
• Sampling theory for neutral alleles in a varying environment.

  1994cited by this paper
• Population genetics of polymorphism and divergence.

  1992cited by this paper
• Numerical Recipes in C: The Art of Scientific Computing (William H. Press, Brian P. Flannery, Saul A. Teukolsky, and William T. Vetterling); Numerical Recipes: Example Book (C) (William T. Vetterling, Saul A. Teukolsky, William H. Press, and Brian P. Flannery)

  1989cited by this paper
• A Gompertzian model of human breast cancer growth.

  1988cited by this paper
• Asymptotic line-of-descent distributions

  1984cited by this paper
• THE COALESCENT

  1980cited by this paper
• Predicting the course of Gompertzian growth

  1976cited by this paper
• Dynamics of Tumour Growth

  1964cited by this paper
• An Introduction to Probability Theory and Its Applications

  1959cited by this paper
• SOLUTION OF A PROCESS OF RANDOM GENETIC DRIFT WITH A CONTINUOUS MODEL.

  1955cited by this paper
• XXIV. On the nature of the function expressive of the law of human mortality, and on a new mode of determining the value of life contingencies. In a letter to Francis Baily, Esq. F. R. S. &c

  year unknowncited by this paper

• No citing papers are available for this paper.