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PubMed2005

Epigenetic changes and repositioning determine the evolutionary fate of duplicated genes.

Consideration of epigenetic silencing, perhaps by DNA methylation, led to an epigenetic complementation (EC) model for evolution by gene duplication (Rodin and Riggs (2003) J. Mol. Evol., 56, 718-729). This and subsequent work on genome-wide analyses of gene duplicates in several eukaryotic species pointed to a fundamental link between localization in the genome, epigenetic regulation of expression, and the evolutionary fate of new redundant gene copies, which can be either non- or neo-functionalization. Our main message in this report is that repositioning of a new duplicate to an ectopic site epigenetically alters its expression pattern, and concomitantly the rate and direction of mutations. Furthermore, comparison of syntenic vs. non-syntenic pairs of gene duplicates of different age unambiguously indicates that repositioning saves redundant gene duplicates from pseudogenization and hastens their evolution towards a new development-time and tissue-specific pattern of function.

Animals↗

PubMed2004

Changes in physical activity and psychosocial determinants of physical activity in children and adolescents treated for obesity.

The purpose of this study was to describe changes in physical activity and determinants in youngsters treated for obesity. Self-reported physical activity and determinants were assessed at start, during and after an intervention in 24 obese patients (mean age 13.5+/-2.1 years). Participation in activities of moderate to high intensity increased during treatment, but 6-months after treatment this decreased again to pre-treatment levels. Participation in activities of low intensity and television watching decreased during treatment and increased following treatment. Very little change was found in perceived benefits, barriers or self-efficacy scores. Modelling of siblings decreased after treatment, whereas there was no evolution in modelling of parents. Social support by family members increased during treatment, but decreased following treatment. We can conclude that the intervention was successful in activating obese youngsters to move at the desirable exercise intensity and frequency; however, maintenance of the exercise habit after treatment was not successful.

Adolescent↗

PubMed1992

A stochastic evolutionary model of molecular sequences.

A stochastic evolutionary model of molecular sequences is proposed. The basic forces in evolution are supposed to be mutation and selection. The concept is somewhat similar to Kauffman-Levin's concept of adaptive walks and corresponding analytical expressions have been developed. The selective force is divided into two parts: a slowly-varying part and a rapidly-changing fluctuation. The latter influences the distribution of sequences and results in an equation of motion along the flow line. The former plays a more important role in the emergence of evolutionary order. It is demonstrated that the asymmetry of selective forces would lead to a definite order of the system.

Animals↗

PubMed1997

Fragmented and scrambled mitochondrial ribosomal RNA coding regions among green algae: a model for their origin and evolution.

Mitochondrial ribosomal RNA coding regions in the only three green algal taxa investigated to date are fundamentally different in that they are continuous in Prototheca wickerhamii, but highly fragmented and scrambled in Chlamydomonas reinhardtii and Chlamydomonas eugametos. To gain more insight into the mode of evolution of fragmented and scrambled mitochondrial ribosomal RNA (rRNA) genes within the green algal group, this work (1) provides additional information on fragmentation patterns of mitochondrial small- and large-subunit (SSU and LSU) rRNAs that strongly supports the concept of a gradual increase in the extent of discontinuity of mitochondrial rRNAs among chlorophycean green algae and (2) reports the first example of fragmented and scrambled mitochondrial LSU rRNA coding regions in a green algal taxon outside the Chlamydomonas group. The present study (1) suggests that the scrambling of the mitochondrial rRNA coding regions may have occurred early in the evolution of fragmented and scrambled mitochondrial rRNA genes within the chlorophycean green algal group, most likely in parallel with the fragmentation events, (2) proposes recombination as a possible mechanism involved in the evolution of these mitochondrial rRNA genes, and (3) presents a hypothetical pathway for converting continuous mitochondrial rRNA genes into the highly fragmented and scrambled rRNA coding regions of Chlamydomonas through a series of recombinatorial events between short repeated sequences.

Animals↗

PubMed2005

Identification of functional transcription factor binding sites using closely related Saccharomyces species.

Comparative genomics provides a rapid means of identifying functional DNA elements by their sequence conservation between species. Transcription factor binding sites (TFBSs) may constitute a significant fraction of these conserved sequences, but the annotation of specific TFBSs is complicated by the fact that these short, degenerate sequences may frequently be conserved by chance rather than functional constraint. To identify intergenic sequences that function as TFBSs, we calculated the probability of binding site conservation between Saccharomyces cerevisiae and its two closest relatives under a neutral model of evolution. We found that this probability is <5% for 134 of 163 transcription factor binding motifs, implying that we can reliably annotate binding sites for the majority of these transcription factors by conservation alone. Although our annotation relies on a number of assumptions, mutations in five of five conserved Ume6 binding sites and three of four conserved Ndt80 binding sites show Ume6- and Ndt80-dependent effects on gene expression. We also found that three of five unconserved Ndt80 binding sites show Ndt80-dependent effects on gene expression. Together these data imply that although sequence conservation can be reliably used to predict functional TFBSs, unconserved sequences might also make a significant contribution to a species' biology.

Amino Acid Motifs↗

PubMed2002

Rapid movement of a Heliconius hybrid zone: evidence for phase III of Wright's shifting balance theory?

It has been proposed that a moving hybrid zone can be a mechanism for the spread of adaptive traits in phase III of Wright's shifting balance model of evolution. Here I present an example of a moving hybrid zone in warningly colored Heliconius butterflies, a system which is considered to be a possible case of shifting balance evolution. Having moved approximately 47 km in 17 years, the hybrid zone shift has led to the H. erato hydara color pattern rapidly displacing the adjacent H. erato petiverana pattern. The movement is potentially due to dominance drive augmenting a slight selective advantage of H. erato hydara over H. erato petiverana, which is largely consistent with theoretical conditions favoring the success of phase III.

Animals↗

PubMed2004

The galactic habitable zone and the age distribution of complex life in the Milky Way.

We modeled the evolution of the Milky Way Galaxy to trace the distribution in space and time of four prerequisites for complex life: the presence of a host star, enough heavy elements to form terrestrial planets, sufficient time for biological evolution, and an environment free of life-extinguishing supernovae. We identified the Galactic habitable zone (GHZ) as an annular region between 7 and 9 kiloparsecs from the Galactic center that widens with time and is composed of stars that formed between 8 and 4 billion years ago. This GHZ yields an age distribution for the complex life that may inhabit our Galaxy. We found that 75% of the stars in the GHZ are older than the Sun.

Astronomical Phenomena↗

PubMed1996

Effects of orbit progression on the radiation exposures from solar proton fluxes in low Earth orbit under geomagnetic storm conditions.

The present study examines the effects of orbit progression on the exposures within a Space Station Freedom module in a 51.6-degree inclined orbit at 450 km. The storm evolution is modeled after the November 1960 event, and the solar proton flux evolution is taken from the August 1972 solar proton event. The effects of a strong magnetic shock, such as was observed during the October 1989 event, is also modeled. The statistics on hourly average storm fields for the last forty years reveal that the largest geomagnetic storms approach a Dst value of -500 nanotesla at the storm peak. Similarly, one of the largest satellite-measured proton flux (> 10 MeV) for space exposures is the event of August 1972. The effects of orbit progression (advance of the line of nodes) is examined for the above conditions to study the variation of exposures under differing times of occurrence of the solar proton peak intensity, attainment of geomagnetic storm maximum, and the location of the line of nodes of the last geomagnetically protected orbit. The impact of the inherent inhomogeneity of the space station module is examined as a limiting factor on exposure with regard to the need of additional parasitic shielding.

Algorithms↗

PubMed1996

Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters.

A fundamental problem in reconstructing the evolutionary history of a set of species is to infer the topology of the evolutionary tree that relates those species. A statistical method for estimating such a topology from character data is called consistent if, given data from more and more characters, the method is sure to converge to the true topology. A number of popular methods are based on modeling the evolution of each character as a Markov process along the evolutionary tree. The standard models further assume that each character has in fact evolved according to the same Markov process. This homogeneity assumption is unrealistic; for example, different types of characters are known to experience substitutions at different rates. Certain distance and maximum likelihood methods for topology estimation have been shown to be consistent under the homogeneity assumption. Here we give examples showing that these methods can fail to be consistent when the homogeneity assumption is relaxed. The examples are very simple, requiring only four taxa, binary characters, and characters that evolve at two different rates.

Animals↗

PubMed2000

High DNA sequence variability at the alpha 1 Na/K-ATPase locus of Artemia franciscana (brine shrimp): polymorphism in a gene for salt-resistance in a salt-resistant organism.

We previously reported that the Na/K-ATPase alpha 1 subunit coding gene showed signs of being a very polymorphic locus in Artemia franciscana. This species is adapted to highly saline waters, and the Na/K-ATPase alpha 1 isoform presumably plays a key role in this adaptation. Therefore, we were interested in further study of the alpha 1 Na/K-ATPase polymorphisms to examine whether they might be due to an adaptation to salt resistance driven by natural selection. Using coding sequences from 10 genomic clones and 3 cDNAs, we observed that most substitutions are in synonymous positions (88.8%). The 12 nonsynonymous substitutions code for conservative amino acid replacements with an apparent scattered distribution across functional domains of the protein. Interspecific comparison between these sequences and two genomic clones from Artemia parthenogenetica containing 1,122 bp of the alpha 1 Na/K-ATPase locus coding sequence showed independence of the synonymous/nonsynonymous ratio in the comparison within A. franciscana and between A. franciscana and A. parthenogenetica, which fits the neutral model of evolution. Since there were no previous studies on DNA polymorphism for other A. franciscana genes, we also studied variability at the Actin 302 locus for comparison. Both loci were amplified by reverse transcription-polymerase chain reaction, and 20 sequences were obtained for each. This study shows that the amplified region of the alpha 1 Na/K-ATPase gene is 3.5 times as polymorphic as the Actin 302 gene and 2.9 times as heterozygotic. Interestingly, under a model of neutral evolution, the data observed would be expected with a probability of approximately 0.05, suggesting an excess of intraspecific variation of alpha 1 Na/K-ATPase with respect to Actin 302. Restriction fragment length polymorphism studies show similar patterns of polymorphism along the approximately 41-kb span of the alpha 1 Na/K-ATPase locus. Most of the nucleotide differences are linked in a few haplotypes, although recombination events are also inferred from the data. We propose a possible explanation for the high polymorphic levels at the alpha 1 Na/K-ATPase locus which invokes positive selection acting tightly to the locus in transiently isolated or semi-isolated subpopulations.

Actins↗

PubMed2002

Pigment pattern formation in zebrafish: a model for developmental genetics and the evolution of form.

The zebrafish Danio rerio is an emerging model organism for understanding vertebrate development and genetics. One trait of both historical and recent interest is the pattern formed by neural crest-derived pigment cells, or chromatophores, which include black melanophores, yellow xanthophores, and iridescent iridophores. In zebrafish, an embryonic and early larval pigment pattern consists of several stripes of melanophores and iridophores, whereas xanthophores are scattered widely over the flank. During metamorphosis, however, this pattern is transformed into that of the adult, which comprises several dark stripes of melanophores and iridophores that alternate with light stripes of xanthophores and iridophores. In this review, we place zebrafish relative to other model and non-model species; we review what is known about the processes of chromatophore specification, differentiation, and morphogenesis during the development of embryonic and adult pigment patterns, and we address how future studies of zebrafish will likely aid our understanding of human disease and the evolution of form.

Animals↗

PubMed2001

Comparative methods for the analysis of continuous variables: geometric interpretations.

This study is concerned with statistical methods used for the analysis of comparative data (in which observations are not expected to be independent because they are sampled across phylogenetically related species). The phylogenetically independent contrasts (PIC), phylogenetic generalized least-squares (PGLS), and phylogenetic autocorrelation (PA) methods are compared. Although the independent contrasts are not orthogonal, they are independent if the data conform to the Brownian motion model of evolution on which they are based. It is shown that uncentered correlations and regressions through the origin using the PIC method are identical to those obtained using PGLS with an intercept included in the model. The PIC method is a special case of PGLS. Corrected standard errors are given for estimates of the ancestral states based on the PGLS approach. The treatment of trees with hard polytomies is discussed and is shown to be an algorithmic rather than a statistical problem. Some of the relationships among the methods are shown graphically using the multivariate space in which variables are represented as vectors with respect to OTUs used as coordinate axes. The maximum-likelihood estimate of the autoregressive parameter, p, has not been computed correctly in previous studies (an appendix with MATLAB code provides a corrected algorithm). The importance of the eigenvalues and eigenvectors of the connection matrix, W, for the distribution of p is discussed. The PA method is shown to have several problems that limit its usefulness in comparative studies. Although the PA method is a generalized least-squares procedure, it cannot be made equivalent to the PGLS method using a phylogenetic model.

Evolution, Molecular↗

PubMed2005

Theories of adaptation: what they do and don't say.

Theoretical work on adaptation has lagged behind experimental. But two classes of adaptation model have been partly explored. One is phenotypic and the other DNA sequence based. I briefly consider an example of each--Fisher's geometric model and Gillespie's mutational landscape model, respectively--reviewing recent results. Despite their fundamental differences, these models give rise to several strikingly similar results. I consider possible reasons for this congruence. I also emphasize what predictions do and, as important, do not follow from these models.

Adaptation, Biological↗

PubMed1990

Open systems living in a closed biosphere: a new paradox for the Gaia debate.

While energetically open, the biosphere is appreciably closed from the standpoint of matter exchange. Matter cycling and recycling is hence a necessary and emergent property of the global-scale system known as Gaia. But how can an aggregate of open-system life forms have evolved and persisted for billions of years within a planetary system that is largely closed to matter influx and outflow? The puzzling nature of a closed yet persistent biosphere draws our attention to the course of evolution of fundamental metabolic strategies and matter-capture techniques. It suggests a facet of the Gaia hypothesis, framed in terms of persistence. The oceans, atmosphere, soils and biota constitute a complex system which maintains and adjusts matter cycling and recycling within the constraints of planetary closure such that open-system forms of life can persist. This weaker version of the Gaia hypothesis may be useful because it readily lends itself to at least one form of test. What is the solution to the closed biosphere puzzle, and does it indicate that Gaia merits status as a discrete entity? We suggest several disciplines within the field of biology that might provide tools and perspectives toward reaching a solution. These disciplines include artificial closed ecosystems, prokaryote evolution, the nexus of thermodynamics and evolutionary biology, and hierarchy theory in ecosystem modeling and evolution theory.

Biological Evolution↗

PubMed2004

A metric model of amino acid substitution.

MOTIVATION: We address the question of whether there exists an effective evolutionary model of amino-acid substitution that forms a metric-distance function. There is always a trade-off between speed and sensitivity among competing computational methods of determining sequence homology. A metric model of evolution is a prerequisite for the development of an entire class of fast sequence analysis algorithms that are both scalable, O(log n) and sensitive. RESULTS: We have reworked the mathematics of the point accepted mutation model (PAM) by calculating the expected time between accepted mutations in lieu of calculating log-odds probabilities. The resulting substitution matrix (mPAM) forms a metric. We validate the application of the mPAM evolutionary model for sequence homology by executing sequence queries from a controlled yeast protein homology search benchmark. We compare the accuracy of the results of mPAM and PAM similarity matrices as well as three prior metric models. The experiment shows that mPAM significantly outperforms the other three metrics and sufficiently approaches the sensitivity of PAM250 to make it applicable to the management of protein sequence databases.

Algorithms↗

PubMed2006

GARD: a genetic algorithm for recombination detection.

MOTIVATION: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments. RESULTS: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection. AVAILABILITY: Freely available http://www.datamonkey.org/GARD/

Algorithms↗

PubMedDate not supplied

[Convergent origin of repeats in genes coding for globular proteins. An analysis of the factors determining the presence of inverted and symmetrical repeats].

The factors, determining the presence of inverted and symmetrical repeats in genes coding for globular proteins, have been analysed. An interesting property of genetical code has been revealed in the analysis of symmetrical repeats: the pairs of symmetrical codons corresponded to pairs of amino acids with mostly similar physical-chemical parameters. This property may explain the presence of symmetrical repeats and palindromes only in genes coding for beta-structural proteins-polypeptides, where amino acids with similar physical-chemical properties occupy symmetrical positions. A stochastic model of evolution of polynucleotide sequences has been used for analysis of inverted repeats. The modelling demonstrated that only limiting of sequences (uneven frequencies of used codons) is enough for arising of nonrandom inverted repeats in genes.

Amino Acid Sequence↗

PubMed2003

Evolution of complex flowering strategies: an age- and size-structured integral projection model.

We explore the evolution of delayed age- and size-dependent flowering in the monocarpic perennial Carlina vulgaris, by extending the recently developed integral projection approach to include demographic rates that depend on size and age. The parameterized model has excellent descriptive properties both in terms of the population size and in terms of the distributions of sizes within each age class. In Carlina the probability of flowering depends on both plant size and age. We use the parameterized model to predict this relationship, using the evolutionarily stable strategy (ESS) approach. Despite accurately predicting the mean size of flowering individuals, the model predicts a step-function relationship between the probability of flowering and plant size, which has no age component. When the variance of the flowering-threshold distribution is constrained to the observed value, the ESS flowering function contains an age component, but underpredicts the mean flowering size. An analytical approximation is used to explore the effect of variation in the flowering strategy on the ESS predictions. Elasticity analysis is used to partition the agespecific contributions to the finite rate of increase (lambda) of the survival-growth and fecundity components of the model. We calculate the adaptive landscape that defines the ESS and generate a fitness landscape for invading phenotypes in the presence of the observed flowering strategy. The implications of these results for the patterns of genetic diversity in the flowering strategy and for testing evolutionary models are discussed. Results proving the existence of a dominant eigenvalue and its associated eigenvectors in general size- and age-dependent integral projection models are presented.

Adaptation, Biological↗