Genealogical trees, coalescent theory and the analysis of genetic polymorphisms.

The coalescent process is a powerful modeling tool for population ge- netics. The allelic states of all homologous gene copies in a population are determined by the genealogical and mutational history of these copies. The coalescent approach is…

Coalescent theory provides the foundation for molecular population genetics and genomics. It is the conceptual framework for studies of DNA sequence variation within species, and is the source of essential tools for making inferences about mutation,…

In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to exactly…

Repetitions within a given genealogical tree provide some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point transformations. In…

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…

A coalescent theory for a sample of DNA sequences from a partially selfing diploid population and an algorithm for simulating such samples are developed in this article. Approximate formulas are given for the expectation and the variance of the…

This paper presents a critique of expected utility theory as a descriptive model of decision making under risk, and develops an alternative model, called prospect theory. Choices among risky prospects exhibit several pervasive effects that are…

The rooting of intraspecific gene or haplotype trees has proven to be difficult using the traditional techniques of rooting species trees such as outgroups. As an alternative, we apply neutral coalescent theory to the problems of determining the…

The positive results on the association between a genetic polymorphism and a specific complex disease in population-based association studies (e.g. case-control) are rarely replicated in independent studies. Furthermore, the design of these studies…

A computer program was used to test Wong's coevolution theory of the genetic code. The codon correlations between the codons of biosynthetically related amino acids in the universal genetic code and in randomly generated genetic codes were compared.…