Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA ( mtDNA ) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions. In this method, excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites are all taken into account. Application of this method to human and chimpanzee data suggested that the transition / transversion ratio for the entire control region was - 15 and nearly the same for the two species. The 95% confidence interval of the age of the common ancestral mtDNA was estimated to be 80,000-480,000 years in humans and 0.57-2.72 Myr in common chimpanzees.

/pdf/estimation-of-the-number-of-nucleotide-substitutions-in-the-1ssma80f9s.pdf

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.

The main purpose of this article is to present several new statistical tests of neutrality of mutations against a class of alternative models, under which DNA polymorphisms tend to exhibit excesses of rare alleles or young mutations. Another purpose is to study the powers of existing and newly developed tests and to examine the detailed pattern of polymorphisms under population growth, genetic hitchhiking and background selection. It is found that the polymorphic patterns in a DNA sample under logistic population growth and genetic hitchhiking are very similar and that one of the newly developed tests, Fs, is considerably more powerful than existing tests for rejecting the hypothesis of neutrality of mutations. Background selection gives rise to quite different polymorphic patterns than does logistic population growth or genetic hitchhiking, although all of them show excesses of rare alleles or young mutations. We show that Fu and Li's tests are among the most powerful tests against background selection. Implications of these results are discussed.

/pdf/statistical-tests-of-neutrality-of-mutations-against-27cu9aj4pv.pdf

Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection.

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

/pdf/relaxed-phylogenetics-and-dating-with-confidence-5ez5tgzy1b.pdf

Relaxed Phylogenetics and Dating with Confidence

This book is an introduction to probability theory covering laws of large numbers, central limit theorems, random walks, martingales, Markov chains, ergodic theorems, and Brownian motion. It is a comprehensive treatment concentrating on the results that are the most useful for applications. Its philosophy is that the best way to learn probability is to see it in action, so there are 200 examples and 450 problems.

Probability: Theory and Examples

* Measure Theory-Basic Notions * Measure Theory-Key Results * Processes, Distributions, and Independence * Random Sequences, Series, and Averages * Characteristic Functions and Classical Limit Theorems * Conditioning and Disintegration * Martingales and Optional Times * Markov Processes and Discrete-Time Chains * Random Walks and Renewal Theory * Stationary Processes and Ergodic Theory * Special Notions of Symmetry and Invariance * Poisson and Pure Jump-Type Markov Processes * Gaussian Processes and Brownian Motion * Skorohod Embedding and Invariance Principles * Independent Increments and Infinite Divisibility * Convergence of Random Processes, Measures, and Sets * Stochastic Integrals and Quadratic Variation * Continuous Martingales and Brownian Motion * Feller Processes and Semigroups * Ergodic Properties of Markov Processes * Stochastic Differential Equations and Martingale Problems * Local Time, Excursions, and Additive Functionals * One-Dimensional SDEs and Diffusions * Connections with PDEs and Potential Theory * Predictability, Compensation, and Excessive Functions * Semimartingales and General Stochastic Integration * Large Deviations * Appendix 1: Advanced Measure Theory * Appendix 2: Some Special Spaces * Historical and Bibliographical Notes * Bibliography * Indices

http://cyber.sibsutis.ru:82/Monarev/docs/nauka/PROBABILITY/Kallenberg%20O.%20Foundations%20of%20Modern%20Probability%20(Springer,1997)(ISBN%200387949577)(535s).pdf

Foundations of modern probability

This paper is concerned with models for the genetic variation of a sample of gametes from a large population. The need for consistency between different sample sizes limits the mathematical possibilities to what are here called ‘partition structures Distinctive among them is the structure described by the Ewens sampling formula, which is shown to enjoy a characteristic property of non-interference between the different alleles. This characterization explains the robustness of the Ewens formula when neither selection nor recurrent mutation is significant, although different structures arise from selective and ‘charge-state’ models

Random partitions in population genetics

One of the central problems in the theory of queues has been the study of the singleserver queue with various assumptions about the probabilistic nature of the input and service processes. In particular, the queue GI1//1 (in the notation of Kendall (1953)) has been studied by Lindley (1952), and a complete formal solution, under mild analytic conditions, for the equilibrium waiting-time distribution, has been obtained by Smith (1953). This solution is not, however, easy to evaluate except for very special distributions of interarrival and service times. The present paper is concerned with the mean and variance of the waiting time, which are quantities of some practical importance. Inequalities are derived for these moments, both in equilibrium and non-equilibrium conditions. Thus we consider a queueing system in which customers C0, C1, ... arrive and are attended to by a single server in the order of their arrival. The customer Cn waits in the queue for a time Wn, and is then served in a further time 8nWe denote by tn the time elapsing between the arrivals of successive customers Cn, Cn+?, and write n-i UnSntn Un E Ur. (1) r=O

https://www.jstor.org/stable/info/2333966

Some inequalities for the queue GI/G/1

I. Probability Spaces.- 1. Introduction to ?.- 2. What is a probability space? Motivation.- 3. Definition of a probability space.- 4. Construction of a probability from a distribution function.- 5. Additional exercises*.- II. Integration.- 1. Integration on a probability space.- 2. Lebesgue measure on ? and Lebesgue integration.- 3. The Riemann integral and the Lebesgue integral.- 4. Probability density functions.- 5. Infinite series again.- 6. Differentiation under the integral sign.- 7. Signed measures and the Radon-Nikodym theorem*.- 8. Signed measures on ? and functions of bounded variation*.- 9. Additional exercises*.- III. Independence and Product Measures.- 1. Random vectors and Borel sets in ?n.- 2. Independence.- 3. Product measures.- 4. Infinite products.- 5. Some remarks on Markov chains*.- 6. Additional exercises*.- IV. Convergence of Random Variables and Measurable Functions.- 1. Norms for random variables and measurable functions.- 2. Continuous functions and Lp*.- 3. Pointwise convergence and convergence in measure or probability.- 4. Kolmogorov's inequality and the strong law of large numbers.- 5. Uniform integrability and truncation*.- 6. Differentiation: the Hardy-Littlewood maximal function*.- 7. Additional exercises*.- V. Conditional Expectation and an Introduction to Martingales.- 1. Conditional expectation and Hilbert space.- 2. Conditional expectation.- 3. Sufficient statistics*.- 4. Martingales.- 5. An introduction to martingale convergence.- 6. The three-series theorem and the Doob decomposition.- 7. The martingale convergence theorem.- VI. An Introduction to Weak Convergence.- 1. Motivation: empirical distributions.- 2. Weak convergence of probabilities: equivalent formulations.- 3. Weak convergence of random variables.- 4. Empirical distributions again: the Glivenko-Cantelli theorem.- 5. The characteristic function.- 6. Uniqueness and inversion of the characteristic function.- 7. The central limit theorem.- 8. Additional exercises*.- 9. Appendix*.

J. F. C. Kingman

Papers

Random partitions in population genetics

Some inequalities for the queue GI/G/1

Introduction to measure and probability

The single server queue

The imbedding problem for finite Markov chains