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PubMed2004

Polymorphisms within a polymorphism: SNPs in and around a polymorphic Alu insertion in intron 44 of the human dystrophin gene.

A polymorphic Yb-type Alu insertion on Xp21.3 shows a genotypic gradient across worldwide populations. We used single strand conformational polymorphism (SSCP), denaturing high-pressure liquid chromatography (DHPLC), and sequencing to characterize the level of polymorphism within this region. Two novel polymorphic sites were found within the Alu insertion itself, and a further seven novel polymorphic sites in the 2-kb flanking region. Our results showed that while DHPLC was more sensitive than SSCP, the limitations of DHPLC included the lack of ability to distinguish between multiple alleles or safely identify mutations on a polymorphic background. We believe that this is the first report of polymorphic single nucleotide polymorphisms (SNPs) within a polymorphic Alu distribution and that together they promise to provide a useful marker for human population and evolutionary genetics.

Africa South of the Sahara↗
PubMedDate not supplied

An isoenzyme study of naturally occurring clones of Trypanosoma cruzi isolated from both sides of the West Andes highland.

Seventy-two stocks of Trypanosoma cruzi isolated from both sides of the West Andes highland (Bolivia, Chile and Peru) were analysed by isoenzyme electrophoresis at 12 loci. The data, which were interpreted in terms of population and evolutionary genetics, corroborated the hypothesis of T. cruzi clonal population structure previously proposed, and indicated extensive genetic variability within the taxon T. cruzi. Fifteen different clones (or zymodemes) were identified, which could be grouped into 3 different clusters. Several clones from 2 of these clusters were isolated both in Chile and Bolivia, suggesting a significant circulation of invertebrate and/or vertebrate hosts of T. cruzi between these 2 countries. Low clonal variability in Peru suggested the occurrence of a 'founder effect' in this country. The potential usefulness of a cladistic approach in epidemiology is discussed.

Animals↗
PubMed1989

Maps of linkage and synteny homologies between mouse and man.

The recent introduction of biochemical and molecular methods for characterizing and mapping genes has dramatically increased the number of homologous genes that have been mapped in more than one species. This review assesses the status of the map of genes whose chromosomal locations have been determined in both mouse and man, evaluates progress towards saturated maps, and illustrates the manner in which this information is now being used in fields as diverse as medical and evolutionary genetics.

Animals↗
PubMed2004

Resisting insects: shifting strategies in chemical control.

Throughout the 20th century, scientists developed a variety of chemical compounds to kill insects and other menaces of agriculture and public health. Yet, in many cases, the target insects outmaneuvered the scientists by developing resistance to insecticides--in much the same way as some bacteria can tolerate antibiotics. Insecticide resistance research has involved scientists from a range of disciplines and a variety of institutional contexts that have often guided research strategy. For example, entomologists working at agricultural stations and universities concentrated on insect physiology and evolutionary genetics, while industrial chemists continued the development of novel compounds capable of killing resistant pests. Collaboration between the two groups beginning in the 1940s did not provide a solution to the resistance, but did lead to a strategic shift from pest control to pest management that continues to the present.

Animals↗
PubMed2005

Molecular heterogeneity in Yersinia enterocolitica and 'Y. enterocolitica-like' species--Implications for epidemiology, typing and taxonomy.

Yersinia enterocolitica is an extremely heterogeneous species. Serotyping and biotyping have been used extensively, in the past, to study its heterogeneity and epidemiology. Application of methods like ribotyping, pulsed-field gel electrophoresis and a host of other genomic techniques have further revealed molecular heterogeneity in this species. Furthermore, these methods may be used effectively to supplement serotyping and biotyping schema for studying epidemiology of Y. enterocolitica. This is evident from the ability of some of these methods to subtype strains belonging to serogroups O:3, O:9 and O:8 - which are most commonly encountered in human Yersiniosis. Multilocus enzyme electrophoresis and nucleotide sequencing have reiterated the taxonomic relationships of this organism. However there is paucity of information about the molecular heterogeneity of 'Y. enterocolitica-like' species, which need to be addressed in the future. Also, newer techniques such as amplified fragment length polymorphism, VNTR-based typing and multilocus sequence typing should be applied to further understand epidemiology, population structure and evolutionary genetics of Y. enterocolitica and 'Y. enterocolitica-like' species.

Bacterial Typing Techniques↗
PubMed2004

Rapid turnover and species-specificity of vomeronasal pheromone receptor genes in mice and rats.

Pheromones are used by individuals of the same species to elicit behavioral or physiological changes, and they are perceived primarily by the vomeronasal organ (VNO) in terrestrial vertebrates. VNO pheromone receptors are encoded by the V1r and V2r gene superfamilies in mammals. A comparison of the V1r and V2r repertoires between closely related species can provide significant insights into the evolutionary genetic mechanisms responsible for species-specific pheromone communications. A total of 137 putatively functional V1r genes of 12 families were previously identified from the mouse genome. We report the identification of 95 putatively functional V1r genes from the draft rat genome sequence. These genes map primarily to four blocks in two chromosomes. The rat V1r genes can be phylogenetically grouped into 10 families, which are shared with mouse, and 2 new families, which are rat-specific. Even in many shared families, gene numbers differ between the two species, apparently due to frequent gene duplication and pseudogenization after the separation of the two species. Molecular dating suggests that most of the rat V1r families emerged before or during the radiation of mammalian orders, but many duplications within families occurred as recently as in the past 10 million years (MY). Our results show that the evolution of the V1r repertoire is characterized by exceptionally fast gene turnover via gains and losses of individual genes, suggesting rapid and substantial changes in pheromone communication between species.

Animals↗
PubMed2005

The evolutionary dynamics of plant duplicate genes.

Given the prevalence of duplicate genes and genomes in plant species, the study of their evolutionary dynamics has been a focus of study in plant evolutionary genetics over the past two decades. The past few years have been a particularly exciting time because recent theoretical and experimental investigations have led to a rethinking of the classic paradigm of duplicate gene evolution. By combining recent advances in genomic analysis with a new conceptual framework, researchers are determining the contributions of single-gene and whole-genome duplications to the diversification of plant species. This research provides insights into the roles that gene and genome duplications play in plant evolution.

Evolution, Molecular↗
PubMed2004

Capturing the adaptive mutation in yeast.

An accurate view of adaptive mutations is essential to evolutionary genetics, but their rarity makes them difficult to study. This can be partially overcome using the many tools of yeast genetics and the ability to study very large populations over many generations. Adaptation to laboratory environments has occurred primarily by chromosomal rearrangements, often involving retrotransposons and apparently selected for their effects on gene regulation. Estimated rates of adaptive mutation are on the order of 1 in 10(11) cell divisions. There remains great potential for the genomic study of variation within yeast species to contribute to our understanding of adaptive mutation.

Adaptation, Biological↗
PubMed2006

Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme.

The introduction and wide use of antibacterial drugs has resulted in the emergence of resistant organisms. DfrB dihydrofolate reductase (DHFR) is a bacterial enzyme that is uniquely associated with mobile gene cassettes within integrons, and confers resistance to the drug trimethoprim. This enzyme has intrigued microbiologists since it was discovered more than thirty years ago because of its simple structure, enzymatic inefficiency and its virtual insensitivity to trimethoprim. Here, for the first time, a comprehensive discussion of genetic, evolutionary, structural and functional studies of this enzyme is presented together. This information supports the ideas that DfrB DHFR is a poorly adapted catalyst and has recently been recruited to perform a novel enzymatic activity in response to selective pressure.

Amino Acid Sequence↗
PubMed2002

Microsatellite analysis of Toxoplasma gondii shows considerable polymorphism structured into two main clonal groups.

Previous studies on Toxoplasma gondii population structure, based essentially on multilocus restriction fragment length polymorphism analysis or on multilocus enzyme electrophoresis, indicated that T. gondii comprises three clonal lineages. These studies showed a weak polymorphism of the markers (2-4 alleles by locus). In this study, we used eight microsatellite markers to type 84 independent isolates from humans and animals. Two microsatellite markers were present in the introns of two genes, one coding for beta-tubulin and the other for myosin A, and six were found in expressed sequence tags. With 3-16 alleles detected, these markers can be considered as the most discriminating multilocus single-copy markers available for typing T. gondii isolates. This high discriminatory power of microsatellites made it possible to detect mixed infections and epidemiologically related isolates. Evolutionary genetic analyses of diversity show that the T. gondii population structure consists of only two clonal lineages that can be equated to discrete typing units, but there is some evidence of occasional genetic exchange that could explain why one of these discrete typing units is less clearly individualised than the other.

Animals↗
PubMed1997

What restricts the activity of mariner-like transposable elements.

A number of mechanisms have recently been described that might be important in restricting the level of activity of mariner-like transposable elements (MLEs) in natural populations. These mechanisms include overproduction inhibition, in which increasing the dose of transposase decreases net activity. Another mechanism is mediated by certain missense mutations, in which a mutant transposase protein impairs the activity of the wild-type transposase in heterozygous mutant/nonmutant genotypes. A further mechanism is the potential for transposase titration by defective elements that retain transposase binding activity. The issue of regulation is not only of theoretical importance in understanding the molecular and evolutionary genetics of MLEs, but also of practical significance in learning how best to use MLEs in the germline transformation of insect pests and disease vectors.

Animals↗
PubMed2001

Theory and speciation.

The study of speciation has become one of the most active areas of evolutionary biology, and substantial progress has been made in documenting and understanding phenomena ranging from sympatric speciation and reinforcement to the evolutionary genetics of postzygotic isolation. This progress has been driven largely by empirical results, and most useful theoretical work has concentrated on making sense of empirical patterns. Given the complexity of speciation, mathematical theory is subordinate to verbal theory and generalizations about data. Nevertheless, mathematical theory can provide a useful classification of verbal theories; can help determine the biological plausibility of verbal theories; can determine whether alternative mechanisms of speciation are consistent with empirical patterns; and can occasionally provide predictions that go beyond empirical generalizations. We discuss recent examples of progress in each of these areas.

Journal Article↗
PubMed1983

[Establishment of a DNA bank of human origin].

High molecular weight DNA extracted from 50 unrelated parisian individuals constitutes a "DNA-thèque" which can be used at the population level. This procedure allows preparation from a variety of tissues such as liver, placenta and leucocytes. The "quality" of the DNA obtained (about 50 Kb, RNA and protein free) and the efficiency of the method (in terms of the yield of DNA obtained) are considered. Blood is the easiest material to obtain and permits the obtaining of a reasonable amount of human and primate DNA, particularly when familial investigation is planned for polymorphism studies. One of the objects of this article is to encourage others to make use of our bank, for studies in population and evolutionary genetics.

Animals↗
PubMed2001

Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms.

With the massive amount of sequence and structural data being produced, new avenues emerge for exploiting the information therein for applications in several fields. Fold distributions can be mapped onto entire genomes to learn about the nature of the protein universe and many of the interactions between proteins can now be predicted solely on the basis of the genomic context of their genes. Furthermore, by utilising the new incoming data on single nucleotide polymorphisms by mapping them onto three-dimensional structures of proteins, problems concerning population, medical and evolutionary genetics can be addressed.

Apolipoproteins E↗
PubMed2003

Genes that determine flower color: the role of regulatory changes in the evolution of phenotypic adaptations.

A central goal of evolutionary genetics is to trace the causal pathway between mutations at particular genes and adaptation at the phenotypic level. The proximate objective is to identify adaptations through the analysis of molecular sequence data from specific candidate genes or their regulatory elements. In this paper, we consider the molecular evolution of floral color in the morning glory genus (Ipomoea) as a model for relating molecular and phenotypic evolution. To begin, flower color variation usually conforms to simple Mendelian transmission, thus facilitating genetic and molecular analyses. Population genetic studies of flower color polymorphisms in the common morning glory (Ipomoea purpurea) have shown that some morphs are subject to complex patterns of selection. Striking differences in floral color and morphology are also associated with speciation in the genus Ipomoea. The molecular bases for these adaptive shifts can be dissected because the biosynthetic pathways that determine floral pigmentation are well understood and many of the genes of flavonoid biosynthesis have been isolated and extensively studied. We present a comparative analysis of the level of gene expression in Ipomoea for several key genes in flavonoid biosynthesis. Specifically we ask: how frequently are adaptive shifts in flower color phenotypes associated with changes in regulation of gene expression versus mutations in structural genes? The results of this study show that most species differences in this crucial phenotype are associated with changes in the regulation of gene expression.

Adaptation, Physiological↗
PubMed2003

Quantitative trait loci for growth trajectories in Populus.

Growth trajectories are a biological process important to plant and animal breeding, and to evolutionary genetic studies. In this article, we report the detection of quantitative trait loci (QTLs) responsible for growth trajectories in poplars that are used as a model system for the study of forest biology. These QTLs were localized on a genetic linkage map of polymorphic markers using a statistical mapping method incorporating growth-curve models. The effects of the QTLs on growth are described as a function of age, so that age-specific changes in QTL effects can be readily projected throughout the entire growth process. The QTLs identified display increased effects on growth when trees age, yet the timing of QTL activation is earlier for stem height than diameter, which is consistent with the ecological viewpoint of canopy competition. The implications of the results for breeding and silviculture are discussed.

Genetic Linkage↗
PubMed2006

Modelling epistatic effects of embryo and endosperm QTL on seed quality traits.

Coordinated expression of embryo and endosperm tissues is required for proper seed development. The coordination among these two tissues is controlled by the interaction between multiple genes expressed in the embryo and endosperm genomes. In this article, we present a statistical model for testing whether quantitative trait loci (QTL) active in different genomes, diploid embryo and triploid endosperm, epistatically affect a trait expressed on the endosperm tissue. The maximum likelihood approach, implemented with the EM algorithm, was derived to provide the maximum likelihood estimates of the locations of embryo- and endosperm-specific QTL and their main effects and epistatic effects. This model was used in a real example for rice in which two QTL, one from the embryo genome and the other from the endosperm genome, exert a significant interaction effect on gel consistency on the endosperm. Our model has successfully detected Waxy, a candidate gene in the embryo genome known to regulate one of the major steps of amylose biosynthesis in the endosperm. This model will have great implications for agricultural and evolutionary genetic research.

Algorithms↗
PubMed1999

Correlated responses to selection on body size in Drosophila melanogaster.

Correlated responses to artificial selection on body size in Drosophila melanogaster were investigated, to determine how the changes in size were produced during development. Selection for increased thorax length was associated with an increase in larval development time, an extended growth period, no change in growth rate, and an increased critical larval weight for pupariation. Selection for reduced thorax length was associated with reduced growth rate, no change in duration of larval development and a reduced critical larval weight for pupariation. In both lines selected for thorax length and lines selected for wing area, total body size changed in the same direction as the artificially selected trait. In large selection lines of both types, the increase in size was achieved almost entirely by an increase in cell number, while in the small lines the decrease in size was achieved predominantly by reduced cell size, and also by a reduction in cell number. The implications of the results for evolutionary-genetic change in body size in nature are discussed.

Animals↗