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

In this book, Andrew Harvey sets out to provide a unified and comprehensive theory of structural time series models. Unlike the traditional ARIMA models, structural time series models consist explicitly of unobserved components, such as trends and seasonals, which have a direct interpretation. As a result the model selection methodology associated with structural models is much closer to econometric methodology. The link with econometrics is made even closer by the natural way in which the models can be extended to include explanatory variables and to cope with multivariate time series. From the technical point of view, state space models and the Kalman filter play a key role in the statistical treatment of structural time series models. The book includes a detailed treatment of the Kalman filter. This technique was originally developed in control engineering, but is becoming increasingly important in fields such as economics and operations research. This book is concerned primarily with modelling economic and social time series, and with addressing the special problems which the treatment of such series poses. The properties of the models and the methodological techniques used to select them are illustrated with various applications. These range from the modellling of trends and cycles in US macroeconomic time series to to an evaluation of the effects of seat belt legislation in the UK.

Forecasting, Structural Time Series Models and the Kalman Filter

Long-distance seed dispersal influences many key aspects of the biology of plants, including spread of invasive species, metapopulation dynamics, and diversity and dynamics in plant communities. However, because long-distance seed dispersal is inherently hard to measure, there are few data sets that characterize the tails of seed dispersal curves. This paper is structured around two lines of argument. First, we argue that long-distance seed dispersal is of critical importance and, hence, that we must collect better data from the tails of seed dispersal curves. To make the case for the importance of long-distance seed dispersal, we review existing data and models of long-distance seed dispersal, focusing on situations in which seeds that travel long distances have a critical impact (colonization of islands, Holocene migrations, response to global change, metapopulation biology). Second, we argue that genetic methods provide a broadly applicable way to monitor long-distance seed dispersal; to place this argument in context, we review genetic estimates of plant migration rates. At present, several promising genetic approaches for estimating long-distance seed dispersal are under active development, including assignment methods, likelihood methods, genealogical methods, and genealogical/demographic methods. We close the paper by discussing important but as yet largely unexplored areas for future research.

Long-distance seed dispersal in plant populations.

One enduring question in evolutionary biology is the extent of archaic admixture in the genomes of present-day populations. In this paper, we present a test for ancient admixture that exploits the asymmetry in the frequencies of the two nonconcordant gene trees in a three-population tree. This test was first applied to detect interbreeding between Neandertals and modern humans. We derive the analytic expectation of a test statistic, called the D statistic, which is sensitive to asymmetry under alternative demographic scenarios. We show that the D statistic is insensitive to some demographic assumptions such as ancestral population sizes and requires only the assumption that the ancestral populations were randomly mating. An important aspect of D statistics is that they can be used to detect archaic admixture even when no archaic sample is available. We explore the effect of sequencing error on the false-positive rate of the test for admixture, and we show how to estimate the proportion of archaic ancestry in the genomes of present-day populations. We also investigate a model of subdivision in ancestral populations that can result in D statistics that indicate recent admixture.

http://www.sfb680.uni-koeln.de/docs/Journal%20Club%20Durand%20et%20al.%20November%202011.pdf

Testing for ancient admixture between closely related populations

To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 × 10−9 base substitutions per site per generation, the majority of which are G:C→A:T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light–induced mutagenesis.

/pdf/the-rate-and-molecular-spectrum-of-spontaneous-mutations-in-ywopsnbxvd.pdf

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

Whether in sexual or asexual organisms, selection among cell lineages during development is an effective way of eliminating deleterious mutations. Using a mathematical analysis, we find that relatively small differences in cell replication rates during development can translate into large differences in the proportion of mutant cells within the adult, especially when development involves a large number of cell divisions. Consequently, intraorganismal selection can substantially reduce the deleterious mutation rate observed among offspring as well as the mutation load within a population, because cells rather than individuals provide the selective "deaths" necessary to stem the tide of deleterious mutations. The reduction in mutation rate among offspring is more pronounced in organisms with plastic development than in those with structured development. It is also more pronounced in asexual organisms that produce multicellular rather than unicellular offspring. By effecting the mutation rate, intraorganismal selection may have broad evolutionary implications; as an example, we consider its influence on the evolution of ploidy levels, finding that cell-lineage selection is more effective in haploids and tends to favor their evolution.

https://www.genetics.org/content/genetics/141/3/1173.full.pdf

Evolutionary consequences of mutation and selection within an individual.

Effective population size in organisms with complex life-histories.

Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae)

/pdf/direct-estimation-of-the-mutation-rate-at-dinucleotide-dmj3eowlig.pdf

Somatic mutations in organisms with complex life histories.

We investigate the effect of purifying selection at multiple sites on both the shape of the genealogy and the distribution of mutations on the tree. We find that the primary effect of purifying selection on a genealogy is to shift the distribution of mutations on the tree, whereas the shape of the tree remains largely unchanged. This result is relevant to the large number of coalescent estimation procedures, which generally assume neutrality for segregating polymorphisms--applying these estimators to evolutionarily constrained sequences could lead to a significant degree of bias. We also estimate the statistical power of several neutrality tests in detecting weak to moderate purifying selection and find that the power is quite good for some parameter combinations. This result contrasts with previous studies, which predicted low statistical power because of the minor effect that weak purifying selection has on the shape of a genealogy. Finally, we investigate the effect of Hill-Robertson interference among linked deleterious mutations on patterns of molecular variation. We find that dependence among selected loci can substantially reduce the efficacy of even fairly strong purifying selection.

/pdf/the-genealogy-of-a-sequence-subject-to-purifying-selection-47tlhy9dhr.pdf

Maria E. Orive

Papers

Evolutionary consequences of mutation and selection within an individual.

Effective population size in organisms with complex life-histories.

Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae)

Somatic mutations in organisms with complex life histories.

The Genealogy of a Sequence Subject to Purifying Selection at Multiple Sites