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PubMed2006

Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.

BACKGROUND: The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. RESULTS: The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. CONCLUSION: Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.

Computational Biology↗
PubMed2006

Response diversity of Arabidopsis thaliana ecotypes in elevated [CO2] in the field.

Free Air [CO(2)] Enrichment (FACE) allows for plant growth under fully open-air conditions of elevated [CO(2)] at concentrations expected to be reached by mid-century. We used Arabidopsis thaliana ecotypes Col-0, Cvi-0, and WS to analyze changes in gene expression and metabolite profiles of plants grown in "SoyFACE" (http://www.soyface.uiuc.edu/), a system of open-air rings within which [CO(2)] is elevated to approximately 550 ppm. Data from multiple rings, comparing plants in ambient air and elevated [CO(2)], were analyzed by mixed model ANOVA, linear discriminant analysis (LDA) and data-mining tools. In elevated [CO(2)], decreases in the expression of genes related to chloroplast functions characterized all lines but individual members of distinct multi-gene families were regulated differently between lines. Also, different strategies distinguished the lines with respect to the regulation of genes related to carbohydrate biosynthesis and partitioning, N-allocation and amino acid metabolism, cell wall biosynthesis, and hormone responses, irrespective of the plants' developmental status. Metabolite results paralleled reactions seen at the level of transcript expression. Evolutionary adaptation of species to their habitat and intrinsic genetic plasticity seem to determine the nature of responses to elevated [CO(2)]. Irrespective of their underlying genetic diversity, and evolutionary adaptation to different habitats, a small number of common, predominantly stress-responsive, signature transcripts appear to characterize responses of the Arabidopsis ecotypes in FACE.

Analysis of Variance↗
PubMed1982

Altered genetic code in Paramecium mitochondria: possible evolutionary trends.

The sequence and presumptive structure of a tRNA trp gene from Paramecium tetraaurelia are given. The gene is located 1,500 bp downstream from the 13S rRNA gene, in about the middle of the genome. Paramecium tRNA trp has a completely normal TpsiC loop and stem, however its anticodon (UCA) constitutes an alteration in the "universal" genetic code, similar to those seen in fungal and mammalian mitochondria. Most features of Paramecium tRNA trp resemble other mitochondrial counterparts; however, its sequence is more homologous to the "unaltered" tRNA trp (anticodon CCA) from E. coli. Paramecium mitochondria may resemble a primitive stage of organelle evolution.

Base Sequence↗
PubMed2002

Physical and genetic characterization reveals a pseudogene, an evolutionary junction, and unstable loci in distal Xq28.

A large portion of human Xq28 has been completely characterized but the interval between G6PD and Xqter has remained poorly understood. Because of a lack of stable, high-density clone coverage in this region, we constructed a 1.6-Mb bacterial and P1 artificial chromosome (BAC and PAC, respectively) contig to expedite mapping, structural and evolutionary analysis, and sequencing. The contig helped to reposition previously mismapped genes and to characterize the XAP135 pseudogene near the int22h-2 repeat. BAC clones containing the distal int22h repeats also demonstrated spontaneous rearrangements and sparse coverage, which suggested that they were unstable. Because the int22h repeats are involved in genetic diseases, we examined them in great apes to see if they have always been unstable. Differences in copy number among the apes, due to duplications and deletions, indicated that they have been unstable throughout their evolution. Taking another approach toward understanding the genomic nature of distal Xq28, we examined the homologous mouse region and found an evolutionary junction near the distal int22h loci that separated the human distal Xq28 region into two segments on the mouse X chromosome. Finally, haplotype analysis showed that a segment within Xq28 has resisted excessive interchromosomal exchange through great ape evolution, potentially accounting for the linkage disequilibrium recently reported in this region. Collectively, these data highlight some interesting features of the genomic sequence in Xq28 and will be useful for positional cloning efforts, mouse mutagenesis studies, and further evolutionary analyses.

Animals↗
PubMed1985

[The nature of genetic recombination].

The biological evolutionary axiom proposed earlier by the author states that in the absence of genetic recombination the evolution of organic forms would be impossible. In the present paper the literature data are considered, illustrating the role of genetic recombination in evolution. It is urged that a tendency towards an increasing complexity of biological organization results from periodical recombinational combining of the diverged genes as well as the whole genomes of different origin. The alternative mechanism implying the production of duplications from the identical gene copies or whole genomes is considered to be unlikely. According to the biological evolutionary axiom, the origin of life is connected with the appearance of a mode of reparation of crystalline type aggregates--the precursors of DNA by means of exchanges among their constituents. A hypothesis is proposed that in the process of recombination a certain distribution of the 6-amino bases (adenine, cytosine) along the DNA molecule is settled, with respect to the 6-carbonyl bases (guanine, thymine). It is proposed that the relative distribution of the bases mentioned influences electrostatic stability of the DNA molecule as a crystalline associate.

Animals↗
PubMed2005

Use of AFLP markers in surveys of arthropod diversity.

Arthropods comprise the most diverse group of animals on earth and as such have been the subject of considerable evolutionary research. For example, much of our understanding of the genetic basis of evolutionary change is derived from the insect genus Drosophila, one of the most well-studied organisms in biology. Arthropods are also of tremendous economic importance as both providers and chief destroyers of food for human consumption. Thus, the genetic diversity of arthropods is of interest from both a pure research perspective and for practical economic reasons. The amplified fragment length polymorphism (AFLP) method of genetic analysis, developed in the early and mid-1990s (Vos et al., 1995; Zabeau, 1992; Zabeau and Vos, 1993), offers a relatively new method for assessing genetic diversity and has been increasingly applied in studies of arthropods. Originally coined selective restriction fragment amplification (SRFA) (Zabeau and Vos, 1993), the method was renamed (Vos et al., 1995) presumably to reflect its similarity to restriction fragment length polymorphism (RFLP). Since then, AFLPs have become a popular tool in both population genetics to estimate population parameters such as heterozygosity, F-statistics, migration rates, and genetic distances, as well as phylogenetics, to infer relationships among closely related taxa. In arthropods, AFLPs have been used to assess genetic variation both within and between species in various taxa including crustaceans, chelicerates, and insects, often yielding novel insights. In this chapter, we briefly describe the AFLP method and its strengths and limitations. We then discuss the use of AFLPs in surveys of arthropod diversity, highlighting the specific questions addressed using AFLPs. Finally, a section on experimental design and methods, based on research in our laboratory, is provided.

Animals↗
PubMed2003

In silico identification of putative regulatory sequence elements in the 5'-untranslated region of genes that are expressed during male gametogenesis.

During pollen development, transcription of a large number of genes results in the appearance of distinct sets of transcripts. Similar mRNA sets are present in pollen of both mono- and dicotyledonous plant species, which indicates an evolutionary conservation of genetic programs that determine pollen gene expression. In pollen, regulation of gene expression occurs at the transcriptional and posttranscriptional level. The 5'-untranslated region (UTR) of several pollen transcripts has been shown to be important for regulation of pollen gene expression. The important regulatory role of 5'-UTR sequences and the evolutionary conservation of genetic programs in pollen led to the hypothesis that the 5'-UTRs of pollen-expressed genes share regulatory sequence elements. In an attempt to identify these pollen 5'-UTR elements, a statistical analysis was performed using 5'-UTR sequences of pollen- and sporophytic-expressed genes. The analysis revealed the presence of several pollen-specific 5'-UTR sequence elements. Assembly of the pollen 5'-UTR elements led to the identification of various consensus sequences, including those that previously have been demonstrated to play a role in the regulation of pollen gene expression. Several pollen 5'-UTR elements were found to be preferentially associated to genes from dicots, wet-type stigma plants, or plants containing bicellular pollen. Moreover, three sequence elements exhibited a preferential association to the 5'-UTR of pollen-expressed genes from Arabidopsis and Brassica napus. Functional implications of these observations are discussed.

5' Untranslated Regions↗
PubMed2005

The importance of immune gene variability (MHC) in evolutionary ecology and conservation.

Genetic studies have typically inferred the effects of human impact by documenting patterns of genetic differentiation and levels of genetic diversity among potentially isolated populations using selective neutral markers such as mitochondrial control region sequences, microsatellites or single nucleotide polymorphism (SNPs). However, evolutionary relevant and adaptive processes within and between populations can only be reflected by coding genes. In vertebrates, growing evidence suggests that genetic diversity is particularly important at the level of the major histocompatibility complex (MHC). MHC variants influence many important biological traits, including immune recognition, susceptibility to infectious and autoimmune diseases, individual odours, mating preferences, kin recognition, cooperation and pregnancy outcome. These diverse functions and characteristics place genes of the MHC among the best candidates for studies of mechanisms and significance of molecular adaptation in vertebrates. MHC variability is believed to be maintained by pathogen-driven selection, mediated either through heterozygote advantage or frequency-dependent selection. Up to now, most of our knowledge has derived from studies in humans or from model organisms under experimental, laboratory conditions. Empirical support for selective mechanisms in free-ranging animal populations in their natural environment is rare. In this review, I first introduce general information about the structure and function of MHC genes, as well as current hypotheses and concepts concerning the role of selection in the maintenance of MHC polymorphism. The evolutionary forces acting on the genetic diversity in coding and non-coding markers are compared. Then, I summarise empirical support for the functional importance of MHC variability in parasite resistance with emphasis on the evidence derived from free-ranging animal populations investigated in their natural habitat. Finally, I discuss the importance of adaptive genetic variability with respect to human impact and conservation, and implications for future studies.

Journal Article↗
PubMed2006

Genetic conflicts during meiosis and the evolutionary origins of centromere complexity.

Centromeric DNA evolves rapidly, ranging in size and complexity over several orders of magnitude. Traditional attempts at studying centromeres have left unexplained the causes underlying this complexity and rapid evolution. Instead of directly studying centromeric DNA sequence, our approach has been to study the proteins that epigenetically determine centromere identity. We have discovered that centromeric histones (CenH3s) have evolved under positive selection in multiple lineages, suggesting an involvement in recurrent genetic conflict. Our hypothesis is that 'centromere-drive' is the source of this conflict. Under this model, centromeres compete via microtubule attachments for preferential transmission in female meioses occurring in animals and plants. Since only one of four meiotic products will become the egg, this competition confers a selfish advantage to chromosomes that can make more microtubule attachments, resulting in runaway expansions of centromeric satellites. While beneficial to the 'driving' chromosome, these expansions can have deleterious effects on the fitness of an organism and of the species. CenH3s as well as other heterochromatin proteins have evolved under positive selection to suppress the deleterious consequences of 'centromere-drive' by restoring meiotic parity.

Animals↗
PubMed2026

The paradoxical extinction: Exploring signatures of assortative mating as a possible mechanism that maintains canonical Red Wolf genetic ancestry in the American Gulf Coast canids.

Admixed genomes, particularly those with an evolutionary history of genetic exchange with an endangered or extinct species, are valued for innovative and unconventional conservation actions. Here, we show the substantial conservation value that the admixed canids of the Gulf Coast have as they retain high amounts of contemporary Red Wolf ancestry and unique genetic variation of past Red Wolf lineages (e.g. ghost ancestry). We analyzed 54,439 loci genotyped across the genome of 413 North American canids and investigated the role that assortative mating with respect to ancestry proportions played in the retention of endangered genetic variation. We report high correlations of inter-chromosomal ancestry proportions that varied with geographic location along Texas and Louisiana Gulf Coast populations, with the stronger signatures reported in the latter. We found that models of assortative mating promoted greater ancestry variance compared with random mating leading to increased efficiency of selection for Red Wolf and ghost alleles. Despite the Red Wolf being extinct in the wild, original, and ghost genomic variation persists in Gulf Coast admixed canids. We suggest two conservation strategies that value and preserve this unique and endangered genomic variation through designed breeding programs. Ultimately the incorporation of this ghost genetic variation would be valuable to boost the genetic viability of the ex situ Red Wolf breeding program, create in situ redundancy, and avoid extinction for this endemic American wolf species.

Animals↗
PubMed1994

The evolutionary ecology of Daphnia.

In order to generate genetic markers from both nuclear and mitochondrial DNA, we used three PCR-based techniques (RAPD, mtDNA-RFLPs, and sequencing of an amplified mtDNA fragment) to illuminate various aspects of the population genetics of large-lake Daphnia species. Estimations of genetic diversity at different taxonomic levels integrated with ecological data revealed insights into the genetic components of the evolutionary process of interspecific hybridization in these Daphnia species, which had previously been documented with allozyme markers. Our new molecular data suggest the occurrence of recent hybridization and backcrossing events, and allow the identification of the maternal species of hybrid clones.

Animals↗
PubMed2005

Human immunodeficiency virus type 1 genetic diversity in the nervous system: evolutionary epiphenomenon or disease determinant?

Over the past decade there has been a revolution in the understanding and care of human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS)-associated disease. Much of this progress stems from a broader recognition of the importance of differences in viral types, including receptor preference(s), replication properties, and reservoirs, as contributing factors to immunosuppresion and disease progression. In contrast, there is limited conceptualizatin of viral diversity and turnover in the brain and circulation in relation to neurocognitive impairments. Herein, the authors review current concepts regarding viral molecular diversity and phenotypes together with features of HIV-1 neuroinvasion, neurotropism, neurovirulence and neurosusceptiblity. Viral genetic and antigenic diversity is reduced within the brain compared to blood or other systemic organs within individuals. Conversely, viral molecular heterogeneity is greater in patients with HIV-associated dementia compared to nondemented patients, depending on the viral gene examined. Individual viral proteins exert multiple neuropathogenic effects, although the neurological consequences of different viral polymorphisms remain uncertain. Nonetheless, host genetic polymorphisms clearly influence neurological disease outcomes and likely dictate both acquired and innate immune responses, which in turn shape viral evolution within the host. Emerging issues include widespread antiretroviral therapy resistance and increasing awareness of viral superinfections together with viral recombination, all of which are likely to impact on both HIV genetic variation and neuropathogenesis. With the persisting prevalence of HIV-induced neurocognitive disabilities, despite marked improvements in managing immunosuppression, it remains imperative to fully define and understand the mechanisms by which viral dynamics and diversity contribute to neurological disease, permitting the development of new therapeutic strategies.

AIDS Dementia Complex↗
PubMed2004

The evolution of molecular genetic pathways and networks.

There is growing interest in the evolutionary dynamics of molecular genetic pathways and networks, and the extent to which the molecular evolution of a gene depends on its position within a pathway or network, as well as over-all network topology. Investigations on the relationships between network organization, topological architecture and evolutionary dynamics provide intriguing hints as to how networks evolve. Recent studies also suggest that genetic pathway and network structures may influence the action of evolutionary forces, and may play a role in maintaining phenotypic robustness in organisms.

Animals↗
PubMed1995

Moving up the hierarchy: a hypothesis on the evolution of a genetic sex determination pathway.

A hypothesis on the evolutionary origin of the genetic pathway of sex determination in the nematode Caenorhabditis elegans is presented here. It is suggested that the pathway arose in steps, driven by frequency-dependent selection for the minority sex at each step, and involving the sequential acquisition of dominant negative, neomorphic genetic switches, each one reversing the action of the previous one. A central implication is that the genetic pathway evolved in reverse order from the final step in the hierarchy up to the first. The possible applicability of the model to the other well-characterized sex determination pathway, that of Drosophila melanogaster, and to sex determination in mammals, is discussed, along with some potential implications for pathway evolution in general. Finally, the specific molecular and population genetic questions that the model raises are described and some tests are proposed.

Animals↗
PubMed2005

Ancient DNA.

In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.

DNA↗
PubMed1987

Genetic differentiation of quantitative characters between populations or species. II: Optimal selection in infinite populations.

Using a new and more general genetic model called the discrete-allelic state model and assuming discrete-time process, the evolutionary changes of genetic variation of quantitative characters, controlled by a few loci, within and between populations during the process of genetic differentiation of populations or species, are studied under the effects of mutation and centripetal selection in infinitely large populations. While in a finite population and ignoring selection, the rate of change of additive genetic variance depends on mutation and effective population size, traits under optimal selection in infinitely large populations go through the dynamics of a rather complicated form depending on the relative intensities of selection and mutation. When a population, which has reached steady-state by mutation-selection balance, splits into two, in one of which the same optimum genotype holds but in the other the optimum shifts a few standard deviations away from the original optimum, the corresponding daughter population starts differentiating from its sister population by favouring certain class of mutant alleles and discarding others which were originally favoured. During this process of turn over of genes, both the intra- and inter-populational variances undergo a complicated change, and the ratio of the former to the latter is a non-linear function of time of divergence. This pattern is qualitatively very different from the case when selection is absent. The intra-population distribution of genotypic values, during this transition, is shown to deviate considerably from normality. The presence of linkage seems to retard the accumulation of intra-populational genetic variance. The implications of these results are discussed in comparison with the earlier findings of evolutionary models of quantitative traits.

Alleles↗
PubMed2001

Developmental interactions and the constituents of quantitative variation.

Development is the process by which genotypes are transformed into phenotypes. Consequently, development determines the relationship between allelic and phenotypic variation in a population and, therefore, the patterns of quantitative genetic variation and covariation of traits. Understanding the developmental basis of quantitative traits may lead to insights into the origin and evolution of quantitative genetic variation, the evolutionary fate of populations, and, more generally, the relationship between development and evolution. Herein, we assume a hierarchical, modular structure of trait development and consider how epigenetic interactions among modules during ontogeny affect patterns of phenotypic and genetic variation. We explore two developmental models, one in which the epigenetic interactions between modules result in additive effects on character expression and a second model in which these epigenetic interactions produce nonadditive effects. Using a phenotype landscape approach, we show how changes in the developmental processes underlying phenotypic expression can alter the magnitude and pattern of quantitative genetic variation. Additive epigenetic effects influence genetic variances and covariances, but allow trait means to evolve independently of the genetic variances and covariances, so that phenotypic evolution can proceed without changing the genetic covariance structure that determines future evolutionary response. Nonadditive epigenetic effects, however, can lead to evolution of genetic variances and covariances as the mean phenotype evolves. Our model suggests that an understanding of multivariate evolution can be considerably enriched by knowledge of the mechanistic basis of character development.

Animals↗
PubMed2006

The quantitative genetic basis of polyandry in the parasitoid wasp, Nasonia vitripennis.

Understanding the evolution of female multiple mating (polyandry) is crucial for understanding sexual selection and sexual conflict. Despite this interest, little is known about its genetic basis or whether genetics influences the evolutionary origin or maintenance of polyandry. Here, we explore the quantitative genetic basis of polyandry in the parasitoid wasp Nasonia vitripennis, a species in which female re-mating has been observed to evolve in the laboratory. We performed a quantitative genetic experiment on a recently collected population of wasps. We found low heritabilities of female polyandry (re-mating frequency after 18 h), low heritability of courtship duration and a slightly higher heritability of copulation duration. However, the coefficients of additive genetic variance for these traits were all reasonably large (CV(A)>7.0). We also found considerable dam effects for all traits after controlling for common environment, suggesting either dominance or maternal effects. Our work adds to the evidence that nonadditive genetic effects may influence the evolution of mating behaviour in Nasonia vitripennis, and the evolution of polyandry more generally.

Animals↗