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Author Durrett, Richard
Title Probability Models for DNA Sequence Evolution
Imprint New York, NY : Springer, 2008
©2008
book jacket
Edition 2nd ed
Descript 1 online resource (441 pages)
text txt rdacontent
computer c rdamedia
online resource cr rdacarrier
Series Probability and Its Applications Ser
Probability and Its Applications Ser
Note Intro -- Preface -- Contents -- Basic Models -- ATGCs of life -- Wright-Fisher model -- The coalescent -- Shape of the genealogical tree -- Infinite alleles model -- Hoppe's urn, Ewens' sampling formula -- Chinese restaurants and sufficient statistics -- Branching process viewpoint -- Infinite sites model -- Segregating sites -- Nucleotide diversity -- Pairwise differences -- Folded site frequency spectrum -- Moran model -- Fixation probability and time -- Site frequency spectrum mean -- Estimation and Hypothesis Testing -- Site frequency spectrum covariance -- Estimates of -- Hypothesis testing overview -- Difference statistics -- Tajima's D -- Fu and Li's D -- Fay and Wu's H -- Conditioning on Sn -- The HKA test -- McDonald-Kreitman test -- Recombination -- Two loci -- Sample of size 2 -- Sample of size n -- m loci -- Samples of size 2 -- Samples of size n -- Pairwise differences -- Linkage disequilibrium -- Ancestral recombination graph -- Simulation -- Two approximate algorithms -- Counting recombinations -- Estimating recombination rates -- Equations for the two-locus sampling distribution -- Simulation methods -- Composite likelihood estimation of -- Haplotypes and hot spots -- Population Complications -- Large family sizes -- Population growth -- Exponential growth -- Sudden population expansion -- Founding effects and bottlenecks -- Effective population size -- Matrix migration models -- Strobeck's theorem -- Fast migration limit -- Symmetric island model -- Identity by descent -- Mean and variance of coalescence times -- Effective population sizes -- Large n limit -- Fixation indices -- Stepping Stone Model -- d = 1, Exact results -- d = 1 and 2, Fourier methods -- d = 2, Coalescence times -- Random walk results -- Samples of size 2 -- Fixation indices FST -- d = 2, Genealogies -- Simulation results -- d = 1, Continuous models
d = 2, Continuous models -- Natural Selection -- Directional selection -- Fixation probability -- Time to fixation -- Three phases of the fixation process -- Ancestral selection graph -- Balancing selection -- Background selection -- Muller's ratchet -- Evolutionary advantages of recombination -- Sex, epistasis, and Kondrashov -- Hitchhiking -- Better approximations -- Recurrent sweeps -- Nucleotide diversity -- Genealogies -- Segregating sites -- Diffusion Processes -- Infinitesimal mean and variance -- Examples of diffusions -- Transition probabilities -- Hitting probabilities -- Stationary measures -- Occupation times -- Green's functions -- Examples -- Conditioned processes -- Boundary behavior -- Site frequency spectrum -- Poisson random field model -- Fluctuating selection -- Multidimensional Diffusions -- K allele model -- Fixation probabilities and time -- Stationary distributions -- Recombination -- A clever change of variables -- Time-dependent behavior -- Equilibrium when there is mutation -- Hill-Robertson interference -- Gene duplication -- Watterson's double recessive null model -- Subfunctionalization -- Genome Rearrangement -- Inversions -- Breakpoint graph -- Hurdles -- When is parsimony reliable? -- Phase transition -- Bayesian approach -- Nadeau and Taylor's analysis -- Genomic distance -- Graph distance -- Bayesian estimation -- Midpoint problem -- Genome duplication -- Yeast -- Maize -- Arabidopsis thaliana -- References -- Index
This book presents mathematical techniques for understanding sequence evolution. The theory is developed in close connection with data from more than 60 experimental studies that illustrate the use of these results
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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2020. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
Link Print version: Durrett, Richard Probability Models for DNA Sequence Evolution New York, NY : Springer,c2008 9780387781686
Subject Evolutionary genetics -- Statistical methods.;Nucleotide sequence -- Statistical methods.;Probabilities.;Variation (Biology) -- Statistical methods
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