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PubMed2006

Comparative polytene chromosome maps of D. montana and D. virilis.

Chromosomal inversion polymorphism was characterized in Finnish Drosophila montana populations. A total of 14 polymorphic inversions were observed in Finnish D. montana of which nine had not been described before. The number of polymorphic inversions in each chromosome was not significantly different from that expected, assuming equal chance of occurrence in the euchromatic genome. There was, however, no correlation between the number of polymorphic inversions and that of fixed inversions in each chromosome. Therefore, a simple neutral model does not explain the evolutionary dynamics of inversions. Furthermore, in contrast to results obtained by others, no significant correlation was found between the two transposable elements (TEs) Penelope and Ulysses and inversion breakpoints in D. montana. This result suggests that these TEs were not involved in the creation of the polymorphic inversions seen in D. montana. A comparative analysis of D. montana and Drosophila virilis polytene chromosomes 4 and 5 was performed with D. virilis bacteriophage P1 clones, thus completing the comparative studies of the two species.

Animals↗
PubMed2005

Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations.

Triticeae species (including wheat, barley and rye) have huge and complex genomes due to polyploidization and a high content of transposable elements (TEs). TEs are known to play a major role in the structure and evolutionary dynamics of Triticeae genomes. During the last 5 years, substantial stretches of contiguous genomic sequence from various species of Triticeae have been generated, making it necessary to update and standardize TE annotations and nomenclature. In this study we propose standard procedures for these tasks, based on structure, nucleic acid and protein sequence homologies. We report statistical analyses of TE composition and distribution in large blocks of genomic sequences from wheat and barley. Altogether, 3.8 Mb of wheat sequence available in the databases was analyzed or re-analyzed, and compared with 1.3 Mb of re-annotated genomic sequences from barley. The wheat sequences were relatively gene-rich (one gene per 23.9 kb), although wheat gene-derived sequences represented only 7.8% (159 elements) of the total, while the remainder mainly comprised coding sequences found in TEs (54.7%, 751 elements). Class I elements [mainly long terminal repeat (LTR) retrotransposons] accounted for the major proportion of TEs, in terms of sequence length as well as element number (83.6% and 498, respectively). In addition, we show that the gene-rich sequences of wheat genome A seem to have a higher TE content than those of genomes B and D, or of barley gene-rich sequences. Moreover, among the various TE groups, MITEs were most often associated with genes: 43.1% of MITEs fell into this category. Finally, the TRIM and copia elements were shown to be the most active TEs in the wheat genome. The implications of these results for the evolution of diploid and polyploid wheat species are discussed.

DNA Transposable Elements↗
PubMed2001

Representational difference analysis reveals genomic differences between Q. robur and Q. suber: implications for the study of genome evolution in the genus Quercus.

Very similar genome sizes, similar karyotypes and heterochromatin organisation, and identical number/position of ribosomal loci characterise the common oak (Q. robur) and the cork oak (Q. suber), two distantly related oak species. Representational Difference Analysis (RDA) was used to subtract the genome of Q. suber from the genome of Q. robur in order to search for genome differentiation. A library of 400 clones (bearing RDA fragments) representing genome differences between the two species was obtained. Seven Q. robur-specific DNA sequences were analysed with respect to their molecular and chromosome organisation. All belong to the dispersed repetitive component of the genome, as revealed by Southern hybridisation and in situ hybridisation. They are present in the Q. robur genome in between 100 and 700 copies, and are distributed along the length of almost all chromosomes. A search for homologies between RDA fragments and sequences in Genbank revealed similarities of all RDA fragments with known retrotransposons. The RDA fragments were also tested for their presence/absence in the genomes of six additional oak species belonging to different phylogenetic groups, in order to examine the evolutionary dynamics of these DNA sequences.

Base Sequence↗
PubMed2000

Evidence for two distinct subgroups of alfalfa mosaic virus (AMV) from france and italy and their relationships with other AMV strains Brief report.

The nucleotide sequence of the putative coat protein open reading frame of seven previously uncharacterized AMV strains from Italy and France was determined and aligned with comparable sequences of other AMV strains (425 L, 425 M, YSMV, S, VRU, 15/64 and Da). The data set of AMV sequences was used to determine phylogenetic relationships by both a stochastic (stationary Markov model) and a deterministic method (maximum-parsimony) of analysis. The topology of the trees obtained with the two methods was essentially the same showing that all AMV strains clustered in two monophyletic groups. Close clustering of Italian strains in subgroup I and of French strains in subgroup II seems to suggests the effect of geographic distinctiveness of evolutionary dynamics of these AMV strains. This separation did not correlate with differences in host range or symptoms (necrotic or non necrotic) induced in tomato but rather it reflected variations in the amino acid sequence of their CP, which might be related to structural properties of virus particles. A simple and rapid procedure based on the reverse transcriptase-polymerase chain reaction (RT-PCR) followed by ezymatic digestion (RFLP) was developed to identify and classify AMV isolates into the two subgroups. The method applied to a number of other AMV isolates from Italy and France supported their division in two distinct subgroups. This RT-PCR RFLP method may be useful way to investigate the dynamics of AMV populations in nature.

Alfalfa mosaic virus↗
PubMedDate not supplied

Non-concerted evolution of the RET76 satellite DNA family in Reticulitermes taxa (Insecta, Isoptera).

The evolutionary dynamics of satellite DNA is most often studied in canonical mating systems, where bisexuality and panmixis are the rule. In eusocial termites, the limited number of reproducers starting a new colony and the maintenance of the colony through few neotenics act as bottle-necks both in space and time. No data on repetitive DNA are available for Isoptera and for their peculiar reproductive strategy. Here we present the first satellite DNA family isolated in European Reticulitermes. RET76 is a G+C rich satellite embodying two sub-families with a 76 bp monomer. RET76 sequences are highly variable (sequence homology is lower than 80% within sub-families and lower than 68% in the entire family) and this variability is equally distributed among the eight analysed taxa, thus depicting a pattern of non-concerted evolution. The absence of variant fixation--together with the strict monomer length conservation--may be explained at the molecular level as due to functional constraints acting on these sequences, and/or at the organismic level by considering the involvement of eusociality in preventing or greatly reducing variant fixation, somehow mimicking an unisexual strategy.

Animals↗
PubMed1984

A fast method of comparing protein structures.

Comparative studies on protein structures form an integral part of protein crystallography. Here, a fast method of comparing protein structures is presented. Protein structures are represented as a set of secondary structural elements. The method also provides information regarding preferred packing arrangements and evolutionary dynamics of secondary structural elements. This information is not easily obtained from previous methods. In contrast to those methods, the present one can be used only for proteins with some secondary structure. The method is illustrated with globin folds, cytochromes and dehydrogenases as examples.

Animals↗
PubMed1983

The contagion mechanism for the origin of sex.

The origin of sex is one of the least understood aspects of the evolution of sex. Recently it has been proposed that sex arose as a result of a contagious genetic element which acted so as to foster its own transmission. Two continuous-time deterministic models of this mechanism are analysed. The first model lacks population regulation. With this assumption, sex is always established in the population, predominating if the sexual form is viable. The second model includes population regulation, giving rise to evolutionary dynamics in which sex need not be established in the population. In addition, with the second model, when the sexual form is viable, it need not fix. Thus, the contagion mechanism can give rise to sex, but need not do so.

Biological Evolution↗
PubMed1987

The role of recombination and selection in the modifier theory of sex-ratio distortion.

The equilibrium configurations for a two-locus multialle model of sex-linked meiotic drive are studied with regard to the recombination fraction:limit cycles can occur in the case of small recombination while stable equilibrium points associated with linkage equilibrium can exist for an intermediate range of recombination values depending on the equilibrium sex ratio, linkage disequilibrium at nearby equilibrium points taking turn with loser linkage. The evolutionary dynamics in two-locus sex-ratio distortion systems is enlightened: while equilibria with a sex ratio closer to 1/2 are more likely to be stable with respect to perturbations on the frequencies of sex-ratio distorters that are represented at equilibrium, such equilibria are also more vulnerable to the invasion of mutant distorters when there is some degree of linkage with the sex-determining locus. For X-linked multimodifier systems of sex-ratio distortion, differential fertilities and viabilities are incorporated and a maximum principle is suggested.

Animals↗
PubMed1991

Coevolution of self-fertilization and inbreeding depression. I. Mutation-selection balance at one and two loci.

Simple theories for the evolution of breeding systems suggest that the fate of an allele that modifies the rate of self-fertilization hinges only on the degree to which selfing reduces opportunities for outcrossing ("pollen discounting") and the extent of inbreeding depression. These theories predict that outcrossing evolves whenever deleterious mutations have a more severe effect in combination than expected from their individual effects. We study the evolutionary dynamics of a modifier of the rate of self-fertilization in populations subject to complete pollen discounting and recurrent mutations which impair viability at a single locus in diploids and at two loci in haploids. Our analysis indicates that genetic associations arising immediately upon the introduction of a rare modifier allele generate substantial quantitative and qualitative departures from expectation. Higher rates of segregation under selfing in our one-locus diploid model generate positive associations between enhancers of selfing and wild-type viability alleles, which in turn favor the evolution of selfing under a wider range of conditions than expected. Greater opportunities for recombination under outcrossing in our two-locus haploid model generate positive associations between enhancers of outcrossing and wild-type viability alleles. These associations favor the evolution of outcrossing under a wider range of conditions, and introduce the possibility of stable mixed mating systems involving both selfing and outcrossing. Our explicit analysis of genetic associations between loci affecting viability and the rate of self-fertilization indicates that modifiers that enhance the production of offspring with very high (and very low) viability by promoting segregation or recombination develop positive associations with high viability. This advantage of producing extremes can compensate for an initial disadvantage in offspring number.

Alleles↗
PubMed1991

Coevolution of self-fertilization and inbreeding depression. II. Symmetric overdominance in viability.

We describe the evolutionary dynamics of a modifier of selfing coevolving with a locus subject to symmetric overdominance in viability under general levels of reduction in pollination success as a consequence of self-fertilization (pollen discounting). Simple models of the evolution of breeding systems that represent inbreeding depression as a constant parameter do not admit the possibility of stable mixed mating systems involving both inbreeding and random mating. Contrary to this expectation, we find that coevolution between a modifier of selfing and a single overdominant locus situated anywhere in the genome can generate evolutionarily attracting mixed mating systems. Two forms of association between the modifier locus and the viability locus promote the evolution of outcrossing. The favored heterozygous genotype at the viability locus develops positive associations with modifier alleles that enhance outcrossing and with the heterozygous genotype at the modifier locus. Associations between outcrossing and high viability evolve immediately upon the introduction of a rare modifier allele, even in the absence of linkage.

Alleles↗
PubMed1982

Stochastic information processing biological systems.

We propose a simple, biochemically-based model for stochastic information processing in brain, genetic, and, consequently, evolutionary modelling. The essential features of reaction-diffusion processes are realized by intrinsically stochastic probabilistic automata (Shannon and Weaver, 1948; see also Ashby, 1958, von Neumann, 1966; Burks, 1970; Paz, 1971) whose definition extends that of classical automata. (Classical automata are deterministic; earlier work on probabilistic automata focused on error correction and at least approximating deterministic behavior.) We call these probabilistic automata biochemical to emphasize the role of intrinsically stochastic process in biological information processing. Our model yields descriptions of gradualism (Conrad, 1974), learning, and apparent inefficiencies in the brain, and partially resolves the near impossibility of simultaneous point mutations (Conrad, 1972, 1978) in genetics. The genetic model implies an evolutionary dynamics of punctuated equilibria (Gould and Eldredge, 1977).

Animals↗
PubMed1996

Evolving cooperation: strategies as hierarchies of rules.

To better understand the evolutionary dynamics of cooperative strategies and their behavioral components in populations subjected to individual selection, a new classifier-system model (EvA) was developed. In EvA, strategies are encoded as algorithms composed of a fixed number of rules relating behavior remembered from the recent past to the present action to be taken. Each algorithm is the genotype of an individual within the population, and these individuals play the Iterated Prisoner's Dilemma game against each other to determine their relative contributions to the next generation. The rules are hierarchical, with more specific rules, when they apply, overriding more general rules. Maximal mutual cooperation was obtained when interaction sequences for each pair of individuals playing the game were long, when only the immediately preceeding plays in the game were remembered, and when the algorithms consisted of an intermediate number of rules (20-40). Under other conditions, mutual cooperation was reduced--even becoming less frequent than would be expected if behavior were completely random, with very few rules per algorithm. The algorithms that evolved could sometimes be recognized as Tit-For-Tat, Simpleton, or other well-known strategies; but when memory of several previous events was invoked by algorithms based on a substantial number of rules, the resulting strategies were considerably more complex. This approach shows considerable promise for providing a much deeper understanding of how cooperation may evolve in nature. Moreover, classifier-system models could prove to be broadly useful for addressing many optimization questions in biology.

Algorithms↗
PubMed1996

Evolving continuous behaviors in the Iterated Prisoner's Dilemma.

Evolutionary programming experiments are conducted on a variant of the Iterated Prisoner's Dilemma. Rather than assume each player having two alternative moves in the stage-game, cooperate or defect, a continuum of possible moves are available. Players' strategies are represented by feed-forward perceptrons with a single hidden layer. The population size and the number of nodes in the hidden layer are varied across a series of experiments. The results of the simulations indicate a minimum amount of complexity is required in a player's strategy in order for cooperation to evolve. Moreover, under the evolutionary dynamics of the simulation, cooperation does not appear to be a stable outcome.

Communication↗
PubMed1993

Evolution of genetic redundancy for advanced players.

An ever expanding database on the sequence organization and repetition of genic and non-genic components of nuclear and organelle genomes reveals that the vast majority of sequences are subject to one or other mechanism of DNA turnover (gene conversion, unequal crossing over, slippage, retrotransposition, transposition and others). Detailed studies, using novel methods of experimental detection and analytical procedures, show that such mechanisms can operate one on top of another and that wide variations in their unit lengths, biases, polarities and rates create bizarre and complex patterns of genetic redundancy. The ability of these mechanisms to operate both within and between chromosomes implies that realistic models of the evolutionary dynamics of redundancy, and of the potential interaction with natural selection in a sexual species, need to consider the diffusion of variant repeats across multiple chromosome lineages, in a population context. Recently, important advances in both experimental and analytical approaches have been made along these lines. There is increasing awareness that genetic redundancy and turnover induces a molecular co-evolution between functionally interacting genetic systems in order to maintain essential functions.

Animals↗
PubMed2004

Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis.

Candidate attenuators were identified that regulate operons responsible for biosynthesis of branched amino acids, histidine, threonine, tryptophan, and phenylalanine in gamma- and alpha-proteobacteria, and in some cases in low-GC Gram-positive bacteria, Thermotogales and Bacteroidetes/Chlorobi. This allowed us not only to describe the evolutionary dynamics of regulation by attenuation of transcription, but also to annotate a number of hypothetical genes. In particular, orthologs of ygeA of Escherichia coli were assigned the branched chain amino acid racemase function. Three new families of histidine transporters were predicted, orthologs of yuiF and yvsH of Bacillus subtilis, and lysQ of Lactococcus lactis. In Pasteurellales, the single bifunctional aspartate kinase/homoserine dehydrogenase gene thrA was predicted to be regulated not only by threonine and isoleucine, as in E. coli, but also by methionine. In alpha-proteobacteria, the single acetolactate synthase operon ilvIH was predicted to be regulated by branched amino acids-dependent attenuators. Histidine biosynthetic operons his were predicted to be regulated by histidine-dependent attenuators in Bacillus cereus and Clostridium difficile, and by histidine T-boxes in L. lactis and Streptococcus mutans.

Alphaproteobacteria↗
PubMed2026

Lineage-specific adaptation and resistance in Candida albicans.

Candida albicans exhibits substantial phenotypic and ecological diversity; however, the exact relationship between its population structure, adaptation to specific niches, and antifungal resistance remains incompletely understood. To investigate these evolutionary dynamics, we analyzed the whole-genome sequences from 591 publicly available isolates, integrating nuclear and mitochondrial phylogenomics with ecological and resistance-associated genomic analyses. Phylogenomic analyses resolved 18 core nuclear clusters together with multiple admixed lineages. Strong cytonuclear concordance was noted in the majority of the central lineages, contrasting with a higher discordance among the admixed groups, consistent with recurrent genetic exchange. The analysis revealed that geographic origin explains a larger fraction of genetic variance than anatomical niche, supporting a predominantly generalist population structure. A notable exception was Cluster N16 (Candida africana), which presented a strict genital origin in our dataset (n = 34). Additionally, although the mitochondrial genome exhibits strong purifying selection, candidate residues under diversifying selection correlated with specific niches (e.g., bloodstream) have been identified. Analysis of five resistance-associated genes (ERG11, UPC2, FKS1, TAC1 and FUR1) revealed that resistance-associated variants were generally rare but exhibited distinct gene-specific patterns. In case of ERG11 and FUR1 they were concentrated in a specific clade (N11, N17, and their admixed Group A) and exhibit gene-dependent zygosity patterns. In summary, the evolution of C. albicans appears to be driven by a predominantly clonal model punctuated by episodic genetic exchange, where both ecological adaptation and antifungal resistance mutations exhibit genomic signatures marked by lineage specificity.

Antifungal resistance↗
PubMed2004

Comparative primate genomics: the year of the chimpanzee.

This is the year of the chimpanzee genome. Chimpanzee chromosome 22 has been sequenced and soon will be followed by the whole genome, and thousands of chimpanzee cDNA sequences are available for comparative analysis. Not only does this genomic information allow us to identify human-specific changes in particular genes that are potentially under selection, but also to understand molecular evolutionary dynamics characterizing the two most closely related mammalian genomes sequenced so far. Studies comparing gene expression in chimpanzees and other closely related primates reveal significant species differences in brain, liver and fibroblasts. New empirical data, in combination with models of speciation, are giving insight into how humans and chimpanzees speciated.

Animals↗
PubMed2004

Phylogenetic and structural analysis of mitochondrial complex I proteins.

Our understanding of the evolutionary process would benefit from a better understanding of protein structural changes during evolution. I report that combining phylogenetic and structural analyses of the mitochondrial protein sequences allow to identify important differences between protostomes and deuterostomes mitochondrial proteins: (1) ND5, and with less intensity, ND1, ND2 and ND4, have significantly lower hydrophobicity in deuterostomes than in proterostomes; (2) the C-terminal half portion of ND5 has lower hydrophobicity than the N-terminal half portion, suggesting the presence of larger extra-membrane hydrophilic loops in deuterostomes with respect to protostomes; (3) substitution matrices generated from different complex I proteins show different patterns of amino acid substitutions, suggesting that mitochondrial proteins have different evolutionary dynamics. I hypothesise that the better performances in phylogenetic inference of ND5 with respect to other mitochondrial proteins may be related to its position inside the complex I.

Amino Acid Substitution↗