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Literature DB >> 22441586

FTEC: a coalescent simulator for modeling faster than exponential growth.

Mark Reppell¹, Michael Boehnke, Sebastian Zöllner.

Abstract

SUMMARY: Recent genetic studies as well as recorded history point to massive growth in human population sizes during the recent past. To model and understand this growth accurately we introduce FTEC, an easy-to-use coalescent simulation program capable of simulating haplotype samples drawn from a population that has undergone faster than exponential growth. Samples drawn from a population that has undergone faster than exponential growth show an excess of very rare variation and more rapid LD decay when compared with samples drawn from a population that has maintained a constant size over time. AVAILABILITY: Source code for FTEC is freely available for download from the University of Michigan Center for Statistical Genetics Wiki at http://genome.sph.umich.edu/wiki/FTEC

Entities: Species

Mesh：

Year: 2012 PMID： 22441586 PMCID： PMC3338023 DOI： 10.1093/bioinformatics/bts135

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

8 in total

1. Generating samples under a Wright-Fisher neutral model of genetic variation.

Authors: Richard R Hudson
Journal: Bioinformatics Date: 2002-02 Impact factor: 6.937

2. A high-resolution recombination map of the human genome.

Authors: Augustine Kong; Daniel F Gudbjartsson; Jesus Sainz; Gudrun M Jonsdottir; Sigurjon A Gudjonsson; Bjorgvin Richardsson; Sigrun Sigurdardottir; John Barnard; Bjorn Hallbeck; Gisli Masson; Adam Shlien; Stefan T Palsson; Michael L Frigge; Thorgeir E Thorgeirsson; Jeffrey R Gulcher; Kari Stefansson
Journal: Nat Genet Date: 2002-06-10 Impact factor: 38.330

3. Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms.

Authors: Alison M Adams; Richard R Hudson
Journal: Genetics Date: 2004-11 Impact factor: 4.562

4. Simultaneous inference of selection and population growth from patterns of variation in the human genome.

Authors: Scott H Williamson; Ryan Hernandez; Adi Fledel-Alon; Lan Zhu; Rasmus Nielsen; Carlos D Bustamante
Journal: Proc Natl Acad Sci U S A Date: 2005-05-19 Impact factor: 11.205

Review 5. Coalescents and genealogical structure under neutrality.

Authors: P Donnelly; S Tavaré
Journal: Annu Rev Genet Date: 1995 Impact factor: 16.830

6. The effect of change in population size on DNA polymorphism.

Authors: F Tajima
Journal: Genetics Date: 1989-11 Impact factor: 4.562

7. A map of human genome variation from population-scale sequencing.

Authors: Gonçalo R Abecasis; David Altshuler; Adam Auton; Lisa D Brooks; Richard M Durbin; Richard A Gibbs; Matt E Hurles; Gil A McVean
Journal: Nature Date: 2010-10-28 Impact factor: 49.962

8. Deep resequencing reveals excess rare recent variants consistent with explosive population growth.

Authors: Alex Coventry; Lara M Bull-Otterson; Xiaoming Liu; Andrew G Clark; Taylor J Maxwell; Jacy Crosby; James E Hixson; Thomas J Rea; Donna M Muzny; Lora R Lewis; David A Wheeler; Aniko Sabo; Christine Lusk; Kenneth G Weiss; Humeira Akbar; Andrew Cree; Alicia C Hawes; Irene Newsham; Robin T Varghese; Donna Villasana; Shannon Gross; Vandita Joshi; Jireh Santibanez; Margaret Morgan; Kyle Chang; Walker Hale Iv; Alan R Templeton; Eric Boerwinkle; Richard Gibbs; Charles F Sing
Journal: Nat Commun Date: 2010-11-30 Impact factor: 14.919

8 in total

1. An efficient resampling method for calibrating single and gene-based rare variant association analysis in case-control studies.

Authors: Seunggeun Lee; Christian Fuchsberger; Sehee Kim; Laura Scott
Journal: Biostatistics Date: 2015-09-11 Impact factor: 5.899

8. Inference of Super-exponential Human Population Growth via Efficient Computation of the Site Frequency Spectrum for Generalized Models.

Authors: Feng Gao; Alon Keinan
Journal: Genetics Date: 2015-10-08 Impact factor: 4.562

8 in total

FTEC: a coalescent simulator for modeling faster than exponential growth.

1. Generating samples under a Wright-Fisher neutral model of genetic variation.

2. A high-resolution recombination map of the human genome.

3. Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms.

4. Simultaneous inference of selection and population growth from patterns of variation in the human genome.

Review 5. Coalescents and genealogical structure under neutrality.

6. The effect of change in population size on DNA polymorphism.

7. A map of human genome variation from population-scale sequencing.

8. Deep resequencing reveals excess rare recent variants consistent with explosive population growth.

1. An efficient resampling method for calibrating single and gene-based rare variant association analysis in case-control studies.

2. The impact of accelerating faster than exponential population growth on genetic variation.

3. Analysis of rare variant population structure in Europeans explains differential stratification of gene-based tests.

4. Theory and applications of a deterministic approximation to the coalescent model.

5. An efficient algorithm for generating the internal branches of a Kingman coalescent.

6. DESCARTES' RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA.

Review 7. Explosive genetic evidence for explosive human population growth.

8. Inference of Super-exponential Human Population Growth via Efficient Computation of the Site Frequency Spectrum for Generalized Models.