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Results for “evolutionary scale model”

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PubMed2002

Predicting the occurrence of genetic adaptation to dioxinlike compounds in populations of the estuarine fish Fundulus heteroclitus.

A population of the nonmigratory estuarine fish species Fundulus heteroclitus (mummichog) indigenous to a polychlorinated biphenyl (PCB)-contaminated Superfund site (New Bedford Harbor, MA, USA) demonstrated an inherited tolerance to local, dioxinlike contaminants (DLCs). These findings suggest that DLCs have acted as selective agents, allowing the survival of only the most tolerant individuals, forming DLC-adapted populations. We hypothesized that DLC-tolerant mummichog populations would reside where local conditions are toxic to sensitive individuals, and that toxic environmental conditions could be predicted based on responses of sensitive early life stages to laboratory exposures of DLCs. As a measure of DLC tolerance, progeny of field-collected fish were tested in the laboratory with a dioxinlike PCB congener, 3,3',4,4',5-pentachlorobiphenyl (PCB 126). Mummichog populations were collected from sites with sediment PCB concentrations predicted to range from nontoxic to toxic. Consistent with predictions, tolerant populations were indigenous to sites with elevated sediment PCB concentrations. Also, as predicted, DLC-tolerant populations were resident to sites far less contaminated than the Superfund site. These results suggest that exposures to persistent, bioaccumulative, and toxic contaminants may produce evolutionary effects on a geographic scale larger than previously envisioned. This study presents an approach and describes a model system that may improve understanding of the scale of occurrence for these potentially irreversible ecological effects.

Adaptation, Physiological↗
PubMed2004

Emergence of community structure in terrestrial mammal-dominated ecosystems.

We present a paper that combines empirical and theoretical research about the trophic organization of biological communities. Some regularities are observed in the analysis of the relationship between the trophic structure (how the species are distributed among a set of feeding groups) of a number of African large mammal communities and the type of ecosystem. Different types of ecosystems are characterized by specific patterns in the trophic structure of the mammal community. In order to explain the origin of these patterns, we propose a model defining the underlying dynamic of mammal-dominated ecosystems. The main aim of this study is to show that it is possible to obtain a dynamic explanation of those patterns. The model is shown to spontaneously define different types of structures in community organization, related to those observed. We propose a model that could help to explain the correlation between different environmental factors and the abundance or diversity of herbivores, and which establishes a general mechanism that makes it possible to understand how some rules constrain the assembly of the communities. In addition, the proposed model leads us to see how biological communities can operate in an integrated way, which allows for the acceptance of their changes on large time-scales as evolutionary. In summary, we suggest that communities are unitary structures with coherent properties that result from the self-organizing dynamic of the whole system.

Animals↗
PubMed2006

Separation of time scales, fixation probabilities and convergence to evolutionary stable states under isolation by distance.

To a first order of approximation, selection is frequency independent in a wide range of family structured models and in populations following an island model of dispersal, provided the number of families or demes is large and the population is haploid or diploid but allelic effects on phenotype are semidominant. This result underlies the way the evolutionary stability of traits is computed in games with continuous strategy sets. In this paper similar results are derived under isolation by distance. The first-order effect on expected change in allele frequency is given in terms of a measure of local genetic diversity, and of measures of genetic structure which are almost independent of allele frequency in the total population when the number of demes is large. Hence, when the number of demes increases the response to selection becomes of constant sign. This result holds because the relevant neutral measures of population structure converge to equilibrium at a rate faster than the rate of allele frequency changes in the total population. In the same conditions and in the absence of demographic fluctuations, the results also provide a simple way to compute the fixation probability of mutants affecting various ecological traits, such as sex ratio, dispersal, life-history, or cooperation, under isolation by distance. This result is illustrated and tested against simulations for mutants affecting the dispersal probability under a stepping-stone model.

Ecology↗
PubMed2004

A test of multiple hypotheses for the species richness gradient of South American owls.

Many mechanisms have been proposed to explain broad scale spatial patterns in species richness. In this paper, we evaluate five explanations for geographic gradients in species richness, using South American owls as a model. We compared the explanatory power of contemporary climate, landcover diversity, spatial climatic heterogeneity, evolutionary history, and area. An important aspect of our analyses is that very different hypotheses, such as history and area, can be quantified at the same observation scale and, consequently can be incorporated into a single analytical framework. Both area effects and owl phylogenetic history were poorly associated with richness, whereas contemporary climate, climatic heterogeneity at the mesoscale and landcover diversity explained ca. 53% of the variation in species richness. We conclude that both climate and environmental heterogeneity should be retained as plausible explanations for the diversity gradient. Turnover rates and scaling effects, on the other hand, although perhaps useful for detecting faunal changes and beta diversity at local and regional scales, are not strong explanations for the owl diversity gradient.

Animals↗
PubMed1998

A molecular evolutionary framework for the phylum Nematoda.

Nematodes are important: parasitic nematodes threaten the health of plants, animals and humans on a global scale; interstitial nematodes pervade sediment and soil ecosystems in overwhelming numbers; and Caenorhabditis elegans is a favourite experimental model system. A lack of clearly homologous characters and the absence of an informative fossil record have prevented us from deriving a consistent evolutionary framework for the phylum. Here we present a phylogenetic analysis, using 53 small subunit ribosomal DNA sequences from a wide range of nematodes. With this analysis, we can compare animal-parasitic, plant-parasitic and free-living taxa using a common measurement. Our results indicate that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision. We identify five major clades within the phylum, all of which include parasitic species. We suggest that animal parasitism arose independently at least four times, and plant parasitism three times. We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species.

Animals↗
PubMed2006

Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences.

Major advances in large-scale yeast two-hybrid screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all species studied have a degree distribution of protein-protein binding that is approximately scale-free (varies as a power law) even though their evolutionary divergence times differ by billions of years. The universal power law shows only the surface of the rich information harbored by these high-throughput data. We develop a detailed mathematical model of the protein-protein interaction network based on association free energy, the biochemical quantity that determines protein-protein interaction strength. This model reproduces the degree distribution of all of the large-scale yeast two-hybrid data sets available and allows us to extract the distribution of free energy, the likelihood that a pair of proteins of a given species will bind. We find that across-species interactomes have significant differences that reflect the strengths of the protein-protein interaction. Our results identify a global evolutionary shift: more evolved organisms have weaker binary protein-protein binding. This result is consistent with the evolution of increased protein unfoldedness and challenges the dogma that only specific protein-protein interactions can be biologically functional.

Animals↗
PubMed2004

Medaka genomics: a bridge between mutant phenotype and gene function.

Recent advances in medaka genetics have proven that the medakafish is an excellent model system for developmental and evolutionary biology studies and that it can complement similar studies in zebrafish. Large-scale mutagenesis projects are now being conducted by several groups in Japan and are delivering a vastly expanded pool of medaka mutant stocks. This growing availability of genomic resources will greatly accelerate progress in moving from mutant phenotypes to the elucidation of gene function. This phenotype-driven approach can be expected to lead to the identification and characterization of novel genes and pathways in vertebrate genomes. This review discusses the current state of medaka genomic resources, the state of medaka gene mapping and medaka genome sequencing projects.

Animals↗
PubMed1998

Big trees from little genomes: mitochondrial gene order as a phylogenetic tool.

Gene arrangement comparisons are a powerful tool for phylogenetic studies, especially those focused on ancient relationships. Recent reports using metazoan mitochondrial genomes address evolutionary relationships as well as rates and mechanisms of rearrangement. Mitochondrial systems serve as a model for larger-scale comparisons of whole organismal genomes and a stimulus for developing methods for reconstructing the patterns of rearrangement.

Animals↗
PubMed2026

Seasonal fluctuations in fitness result in severe reductions in effective population size.

Genetic evidence for fluctuating selection has begun to accumulate for different species over the past few decades, especially for the Drosophila genus where studies have reported hundreds of loci undergoing putatively adaptive oscillations across successive seasons. However, most theoretical and simulation studies of fluctuating selection have relied on abstract or weakly parameterized models, making it difficult to assess their relevance for natural populations. In this study, we simulate multilocus seasonally fluctuating selection acting on standing genetic variation under a recently developed model and examine its effect on the variance effective population size (Ne) at a genome-wide scale. By recapitulating genomic, demographic, and evolutionary parameters from natural Drosophila populations in our simulations, we were able to reproduce allele frequency oscillations reported in recent studies and show that these lead to ∼50% genome-wide reductions in Ne. We also demonstrate that Ne reductions are well predicted by the maximum frequency amplitude among all adaptively fluctuating loci, and that the frequency amplitudes are largely determined by the number of adaptively fluctuating loci and the strength of their epistatic interactions. Our results demonstrate that fluctuating selection can substantially reduce effective population size and underscore the importance of temporally variable selection in shaping genome-wide patterns of variation beyond classical models.

Drosophila melanogaster↗
PubMed2026

Seasonal fluctuations in fitness result in severe reductions in effective population size.

Genetic evidence for fluctuating selection has begun to accumulate for different species over the past few decades, especially for the Drosophila genus where studies have reported hundreds of loci undergoing putatively adaptive oscillations across successive seasons. However, most theoretical and simulation studies of fluctuating selection have relied on abstract or weakly parameterized models, making it difficult to assess their relevance for natural populations. In this study, we simulate multilocus seasonally fluctuating selection under a recently developed model and examine its effect on the variance effective population size (Ne ) at a genome-wide scale. By recapitulating genomic, demographic, and evolutionary parameters from natural Drosophila populations in our simulations, we were able to reproduce allele frequency oscillations reported in recent studies and show that these lead to ~50% genome-wide reductions in Ne . We also demonstrate that Ne reductions are well predicted by the maximum frequency amplitude among all adaptively fluctuating loci, and that the frequency amplitudes are largely determined by the number of adaptively fluctuating loci and the strength of their epistatic interactions. Our results demonstrate that fluctuating selection can substantially reduce effective population size and underscore the importance of temporally variable selection in shaping genome-wide patterns of variation beyond classical models.

Drosophila melanogaster↗
PubMed1999

Adaptive walks on time-dependent fitness landscapes.

The idea of adaptive walks on fitness landscapes as a means of studying evolutionary processes on large time scales is extended to fitness landscapes that are slowly changing over time. The influence of ruggedness and of the amount of static fitness contributions is investigated for model landscapes derived from Kauffman's NK landscapes. Depending on the amount of static fitness contributions in the landscape, the evolutionary dynamics can be divided into a percolating and a nonpercolating phase. In the percolating phase, the walker performs a random walk over the regions of the landscape with high fitness.

Biological Evolution↗
PubMed2001

Evolutionary self-organization of cell-free genetic coding.

Genetic encoding provides a generic construction scheme for biomolecular functions. This paper addresses the key problem of coevolution and exploitation of the multiple components necessary to implement a replicable genetic encoding scheme. Extending earlier results on multicomponent replication, the necessity of spatial structure for the evolutionary stabilization of the genetic coding system is established. An individual-based stochastic model of interacting molecules in three-dimensional space is presented that allows the evolution of genetic coding to be analyzed explicitly. A massively parallel configurable computer (NGEN) is used to implement the model, on the time scale of millions of generations, directly in electronic hardware. The spatial correlations between components of the genetic coding system are analyzed and found to be essential for evolutionary stability.

Animals↗
PubMed2005

Fine-scale predictions of distributions of Chagas disease vectors in the state of Guanajuato, Mexico.

One of the most daunting challenges for Chagas disease surveillance and control in Mexico is the lack of community level data on vector distributions. Although many states now have assembled representative domestic triatomine collections, only two triatomine specimens had been collected and reported previously from the state of Guanajuato. Field personnel from the state's Secretaría de Salud conducted health promotion activities in 43 of the 46 counties in the state and received donations of a total of 2,522 triatomine specimens between 1998 and 2002. All specimens were identified, and live insects examined for Trypanosoma cruzi. In an effort to develop fine-scale distributional data for Guanajuato, collection localities were georeferenced and ecological niches were modeled for each species by using evolutionary-computing approaches. Five species were collected: Triatoma mexicana (Herrich-Schaeffer), Triatoma longipennis (Usinger), Triatoma pallidipennis (Stål), Triatoma barberi (Usinger), and Triatoma dimidiata (Latreille) from 201 communities located at elevations of 870-2,200 m. Based on collection success, T. mexicana had the broadest dispersion, although niche mapping indicates that T. barberi represents the greatest risk for transmission of Chagas disease in the state. T. dimidiata was represented in collections by a single adult collected from one village outside the predicted area for all species. For humans, an estimated 3,755,380 individuals are at risk for vector transmission in the state, with an incidence of 3,500 new cases per year; overall seroprevalences of 2.6% indicate that 97,640 individuals are infected with T. cruzi at present, including 29,300 chronic cases.

Algorithms↗
PubMed2006

Breeding system variation, genetics and evolution in the Turneraceae.

We review the genetics and evolution of breeding systems in the Turneraceae. Distyly occurs in seven of 10 genera and 81% of species. The remaining species are homostylous. Polyploid evolution has been significant in Turnera. Approximately 60% of species are polyploid ranging from diploid through decaploid. No relationship between breeding system and polyploidy is evident. The genetics of distyly involves a one-locus two-allele system (S and s). Evidence from crosses with homostylous species and mutants is consistent with the possibility that a "Primula-type" supergene underlies distyly but does not prove this to be the case. A polygalacturonase, and an alpha-dioxygenase specific to the transmitting tissue of short-styled plants both exhibit morph-limited expression in concert with predictions from an evolutionary model. The function of the proteins in distyly, if any, is unknown. We have begun constructing a fine-scale genetic map of Turnera. Two genetic markers lie within 0.2 cm of the distyly locus. This should provide a starting point for positional cloning of the distyly locus and reveal the genetic architecture and molecular basis of distyly.

Biological Evolution↗
PubMed1996

Comparative analysis of plant genome architecture.

Many genes are similar in most plants and it is clear that the ordering of genes is highly conserved across wide taxonomic groupings. Repetitive DNA, consisting of sequence motifs between 2 and 10,000 base pairs long, repeated many hundreds or thousands of times in the genome, represents the majority of most plant genomes and defines some of the differences between species. Some sequences are highly conserved in many species, while other sequences show species or even chromosome specificity. Different types of sequences have markedly contrasting genomic distributions; even among tandem repeats, some are sub-terminal, some paracentromeric and others intercalary. The reasons for these different distributions are largely unknown, and mechanisms of homogenization, dispersion and amplifications are the subject of much speculation. Aspects of plant genome architecture-the organization of repetitive and single-copy DNA sequences along the chromosomes, and the positioning of those sequences within the nucleus at interphase-have important consequences for plant genetics. Models of large scale genome organization may be useful in learning the function of different components of the genome, in evolutionary studies and in plant breeding.

Biological Evolution↗
PubMed2005

Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes.

A major component of the plant nuclear genome is constituted by different classes of repetitive DNA sequences. The structural, functional and evolutionary aspects of the satellite repetitive DNA families, and their organization in the chromosomes is reviewed. The tandem satellite DNA sequences exhibit characteristic chromosomal locations, usually at subtelomeric and centromeric regions. The repetitive DNA family(ies) may be widely distributed in a taxonomic family or a genus, or may be specific for a species, genome or even a chromosome. They may acquire large-scale variations in their sequence and copy number over an evolutionary time-scale. These features have formed the basis of extensive utilization of repetitive sequences for taxonomic and phylogenetic studies. Hybrid polyploids have especially proven to be excellent models for studying the evolution of repetitive DNA sequences. Recent studies explicitly show that some repetitive DNA families localized at the telomeres and centromeres have acquired important structural and functional significance. The repetitive elements are under different evolutionary constraints as compared to the genes. Satellite DNA families are thought to arise de novo as a consequence of molecular mechanisms such as unequal crossing over, rolling circle amplification, replication slippage and mutation that constitute "molecular drive".

Centromere↗
PubMed2000

Evolutionary trade-offs at two time-scales: competition versus persistence.

The evolution of many natural systems is complicated due to dynamics at a mixture of time-scales. This is especially true when there is a trade-off between large reproductive rates and long-term persistence; such behaviour is frequently observed in disease models. In this paper, a simple partial differential equation model is formulated which describes the evolutionary dynamics of two disease strains in a metapopulation: one strain is a better short-term competitor; the other has greater persistence. By considering the behaviour of means and higher-order moments, analytical expressions for the evolutionary behaviour are produced in the case when the two strains are phenotypically close.

Biological Evolution↗