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Probability Models for DNA Sequence Evolution

ISBN-10: 0387781684
ISBN-13: 9780387781686
Edition: 2nd 2008
Authors: Richard Durrett
List price: $169.00 Buy it from $37.54
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Description: As a starting point the authors address the question, what underlying forces are responsible for the observed patterns of variability, given a collection of DNA sequences? To answer this question they introduce & analyze a number of probability  More...

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Book details

List price: $169.00
Edition: 2nd
Copyright year: 2008
Publisher: Springer
Publication date: 8/12/2008
Binding: Hardcover
Pages: 431
Size: 6.25" wide x 9.00" long x 1.00" tall
Weight: 1.584
Language: English

As a starting point the authors address the question, what underlying forces are responsible for the observed patterns of variability, given a collection of DNA sequences? To answer this question they introduce & analyze a number of probability models.

Preface
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 [theta]
Hypothesis testing overview
Difference statistics
Tajima's D
Fu and Li's D
Fay and Wu's H
Conditioning on S[subscript n]
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 [rho]
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 F[subscript ST]
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

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