Stable association between strains of Mycobacterium tuberculosis and their human host populations.

Mycobacterium tuberculosis is an important human pathogen in virtually every part of the world. Here we investigate whether distinct strains of M. tuberculosis infect different human populations and whether associations between host and pathogen populations are stable despite global traffic and the convergence of diverse strains of the pathogen in cosmopolitan urban centers.

The effect of genetic conflict on genomic imprinting and modification of expression at a sex-linked locus.

We examine how genomic imprinting may have evolved at an X-linked locus, using six diallelic models of selection in which one allele is imprintable and the other is not. Selection pressures are generated by genetic conflict between mothers and their offspring. The various models describe cases of maternal and paternal inactivation, in which females may be monogamous or bigamous.

Gender differences in child survival in contemporary rural China: a county study.

Using data from a survey of deaths of children less than 5 years old conducted in 1997 in a county in Shaanxi Province, China, this paper examines gender differences in child survival in contemporary rural China. First, excess female child mortality in the county in 1994-96 is described, followed by an analysis of the mechanisms whereby the excess mortality takes place, and the underlying social, economic and cultural factors behind it. Excess female child mortality in this county is probably caused primarily by discrimination against girls in curative health care rather than in preventive health care or food and nutrition.

The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time.

We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9x10-4 per 25 years, with a standard deviation across loci of 5.7x10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci.

Cultural niche construction and the evolution of small family size.

A model of cultural niche construction with two culturally transmitted traits is examined. The frequency of individuals with a certain general predisposition, which is transmitted vertically, plays a role as the cultural background, or the cultural niche, of the population. The cultural background determines the rate of oblique, relative to vertical, transmission of another cultural trait that affects fertility of individuals.

Rates of DNA duplication and mitochondrial DNA insertion in the human genome.

The hundreds of mitochondrial pseudogenes in the human nuclear genome sequence (numts) constitute an excellent system for studying and dating DNA duplications and insertions. These pseudogenes are associated with many complete mitochondrial genome sequences and through those with a good fossil record. By comparing individual numts with primate and other mammalian mitochondrial genome sequences, we estimate that these numts arose continuously over the last 58 million years.

Evolution of disassortative and assortative mating preferences based on imprinting.

A two-locus haploid model of sexual selection is investigated to explore evolution of disassortative and assortative mating preferences based on imprinting. In this model, individuals imprint on a genetically transmitted trait during early ontogeny and choosy females later use those parental images as a criterion of mate choice. It is assumed that the presence or absence of the female preference is determined by a genetic locus.

Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools.

In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.

Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci.

Genome duplications may have played a role in the early stages of vertebrate evolution, near the time of divergence of the lamprey lineage. Additional genome duplication, specifically in ray-finned fish, may have occurred before the divergence of the teleosts. The common carp (Cyprinus carpio) has been considered tetraploid because of its chromosome number (2n = 100) and its high DNA content.

Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers.

We study data on variation in 52 worldwide populations at 377 autosomal short tandem repeat loci, to infer a demographic history of human populations. Variation at di-, tri-, and tetranucleotide repeat loci is distributed differently, although each class of markers exhibits a decrease of within-population genetic variation in the following order: sub-Saharan Africa, Eurasia, East Asia, Oceania, and America. There is a similar decrease in the frequency of private alleles.

The application of molecular genetic approaches to the study of human evolution.

The past decade of advances in molecular genetic technology has heralded a new era for all evolutionary studies, but especially the science of human evolution. Data on various kinds of DNA variation in human populations have rapidly accumulated. There is increasing recognition of the importance of this variation for medicine and developmental biology and for understanding the history of our species.

Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster.

Regions of extensive linkage disequilibrium (LD) appear to be a common feature of the human genome. However, the mechanisms that maintain these regions are unknown. In an effort to understand whether gene density contributes to LD, we determined the degree of promoter sequence variation in a large tandem-arrayed gene family, the human protocadherin alpha cluster, on chromosome 5.

Genetic structure of human populations.

We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations.

Carving the cognitive niche: optimal learning strategies in homogeneous and heterogeneous environments.

A model learning system is constructed, in which an organism samples behaviors from a behavioral repertoire in response to a stimulus and selects the behavior with the highest payoff. The stimulus and most rewarding behavior may be kept in the organism's long-term memory and reused if the stimulus is encountered again. The value of the memory depends on the reliability of the stimulus, that is, how the corresponding payoffs of behaviors change over time.

Runaway sexual selection with paternal transmission of the male trait and gene-culture determination of the female preference.

Sexual selection is modeled with a male viability-reducing trait and a female mating preference for that trait both of which are culturally transmitted. Both the male trait and the female preference are transmitted only between same-sex individuals, so that non-random association between the trait and the preference, which would give rise to a Fisherian runaway process, cannot arise. Inclusion of an autosomal gene that confers a female predisposition to acquire a certain preference is shown to allow the coevolution of the male trait and the female preference by a Fisherian process.

Evolutionary genetic models of the ovarian time bomb hypothesis for the evolution of genomic imprinting.

At a small number of loci in eutherian mammals, only one of the two copies of a gene is expressed; the other is silenced. Such loci are said to be "imprinted," with some having the maternally inherited allele inactivated and others showing paternal inactivation. Several hypotheses have been proposed to explain how such a genetic system could evolve in the face of the selective advantages of diploidy.

Coevolution of pathogens and cultural practices: a new look at behavioral heterogeneity in epidemics.

The effect of heterogeneity within populations on the spread of infectious diseases has been a recent focus of research. Such heterogeneity may be, for example, spatial, temporal or behavioral in form. Generally, models that include population subdivision have assumed that individuals are permanently assigned to given behavioral states represented by the subpopulations.

Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors.

One of the central aims of ecology is to identify mechanisms that maintain biodiversity. Numerous theoretical models have shown that competing species can coexist if ecological processes such as dispersal, movement, and interaction occur over small spatial scales. In particular, this may be the case for non-transitive communities, that is, those without strict competitive hierarchies.

Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition.

This article proposes a method of estimating the time to the most recent common ancestor (TMRCA) of a sample of DNA sequences. The method is based on the molecular clock hypothesis, but avoids assumptions about population structure. Simulations show that in a wide range of situations, the point estimate has small bias and the confidence interval has at least the nominal coverage probability.

Evolutionary rate in the protein interaction network.

High-throughput screens have begun to reveal the protein interaction network that underpins most cellular functions in the yeast Saccharomyces cerevisiae. How the organization of this network affects the evolution of the proteins that compose it is a fundamental question in molecular evolution. We show that the connectivity of well-conserved proteins in the network is negatively correlated with their rate of evolution.

ON THE EVOLUTION OF PHENOTYPIC PLASTICITY IN A SPATIALLY HETEROGENEOUS ENVIRONMENT.

A genetic model for the dynamics of a quantitative trait is analyzed in terms of gene frequencies, linkage disequilibria, and environmental effects on the trait. In a randomly mating population, at each generation progeny move to niches where they are subject to weak Gaussian selection on the trait, with different fitness levels in the different niches. Initially, the variability of the trait is due to additive loci with heterozygous homeostasis.