Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Convergence of Probability Measures. By P. Billingsley. Chichester, Sussex, Wiley, 1968. xii, 253 p. 9 1/4“. 117s.

Convergence of Probability Measures

Stable non-Gaussian random processes , by G. Samorodnitsky and M. S. Taqqu. Pp. 632. £49.50. 1994. ISBN 0-412-05171-0 (Chapman and Hall).

(1987). Applied Probability and Queues. Journal of the Operational Research Society: Vol. 38, No. 11, pp. 1095-1096.

https://link.springer.com/content/pdf/10.1057%2Fjors.1987.184.pdf

Applied Probability and Queues

Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from the species phylogeny. This counterintuitive result implies that in combining data on multiple loci, the straightforward procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can be asymptotically guaranteed to produce an incorrect estimate. We conclude with suggestions that can aid in overcoming this new obstacle to accurate genomic inference of species phylogenies.

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Discordance of species trees with their most likely gene trees.

We investigate conditions under which a model with stochastic demography or population structure converges to the coalescent with a linear change in timescale. We argue that this is a necessary condition for the existence of a meaningful effective population size. We find that such a linear timescale change is obtained when demographic fluctuations and coalescence events occur on different timescales. Simple models of population structure and randomly fluctuating population size are used to exemplify the ideas and provide an intuitive feel for the meaning of the conditions.

https://www.genetics.org/content/genetics/169/2/1061.full.pdf

On the meaning and existence of an effective population size

The ratio of divergence at nonsynonymous and synonymous sites, dN/dS, is a widely used measure in evolutionary genetic studies to investigate the extent to which selection modulates gene sequence evolution. Originally tailored to codon sequences of distantly related lineages, dN/dS represents the ratio of fixed nonsynonymous to synonymous differences. The impact of ancestral and lineage-specific polymorphisms on dN/dS, which we here show to be substantial for closely related lineages, is generally neglected in estimation techniques of dN/dS. To address this issue, we formulate a codon model that is firmly anchored in population genetic theory, derive analytical expressions for the dN/dS measure by Poisson random field approximation in a Markovian framework and validate the derivations by simulations. In good agreement, simulations and analytical derivations demonstrate that dN/dS is biased by polymorphisms at short time scales and that it can take substantial time for the expected value to settle at its time limit where only fixed differences are considered. We further show that in any attempt to estimate the dN/dS ratio from empirical data the effect of the intrinsic fluctuations of a ratio of stochastic variables, can even under neutrality yield extreme values of dN/dS at short time scales or in regions of low mutation rate. Taken together, our results have significant implications for the interpretation of dN/dS estimates, the McDonald-Kreitman test and other related statistics, in particular for closely related lineages.

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

It has become common practice to use heavy-tailed distributions in order to describe the variations in time and space of network traffic workloads. The asymptotic behavior of these workloads is complex; different limit processes emerge depending on the specifics of the work arrival structure and the nature of the asymptotic scaling. We focus on two variants of the infinite source Poisson model and provide a coherent and unified presentation of the scaling theory by using integral representations. This allows us to understand physically why the various limit processes arise.

/pdf/convergence-to-fractional-brownian-motion-and-to-the-telecom-456utabz3p.pdf

Convergence to Fractional Brownian Motion and to the Telecom Process: the Integral Representation Approach

We study the genealogical structure of samples from a population for which any given generation is made up of direct descendants from several previous generations. These occur in nature when there are seed banks or egg banks allowing an individual to leave offspring several generations in the future. We show how this temporal structure in the reproduction mechanism causes a decrease in the coalescence rate. We also investigate the effects of age-dependent neutral mutations. Our main result gives weak convergence of the scaled ancestral process, with the usual diffusion scaling, to a coalescent process which is equivalent to a time-changed version of Kingman's coalescent.

/pdf/coalescent-theory-for-seed-bank-models-39oovs7ie2.pdf

Coalescent theory for seed bank models

This thesis, consisting of three papers and a summary, studies topics in the theory of stochastic processes related to long-range dependence. Much recent interest in such probabilistic models has its origin in measurements of Internet traffic data, where typical characteristics of long memory have been observed. As a macroscopic feature, long-range dependence can be mathematically studied using certain scaling limit theorems. Using such limit results, two different scaling regimes for Internet traffic models have been identified earlier. In one of these regimes traffic at large scales can be approximated by long-range dependent Gaussian or stable processes, while in the other regime the rescaled traffic fluctuates according to stable ``memoryless'' processes with independent increments. In Paper I a similar limit result is proved for a third scaling scheme, emerging as an intermediate case of the other two. The limit process here turns out to be a non-Gaussian and non-stable process with long-range dependence.In Paper II we derive a representation for the latter limit process as a stochastic integral of a deterministic function with respect to a certain compensated Poisson random measure. This representation enables us to study some further properties of the process. In particular, we prove that the process at small scales behaves like a Gaussian process with long-range dependence, while at large scales it is close to a stable process with independent increments. Hence, the process can be regarded as a link between these two processes of completely different nature.In Paper III we construct a class of processes locally behaving as Gaussian and globally as stable processes and including the limit process obtained in Paper I. These processes can be chosen to be long-range dependent and are potentially suitable as models in applications with distinct local and global behaviour. They are defined using stochastic integrals with respect to the same compensated Poisson random measure as used in Paper II.

/pdf/convergence-of-scaled-renewal-processes-and-a-packet-arrival-30vp5ka64q.pdf

Ingemar Kaj

Papers

On the meaning and existence of an effective population size

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

Convergence to Fractional Brownian Motion and to the Telecom Process: the Integral Representation Approach

Coalescent theory for seed bank models

Convergence of scaled renewal processes and a packet arrival model