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PubMed1993

A model for the evolution of networks of genes.

An organism persists through the activity of structural genes, which is co-ordinated by clusters of coupled regulatory genes. During evolution, changes of coupling within a cluster can increase the reliability with which its structural genes perform a task. To study the evolution of coupling, we have simulated and analyzed a stochastic model for a simple problem. The assumptions of the model are these: A network of regulatory genes co-ordinates the synthesis of four structural proteins, which associate in distinct heterodimers that form a heterotetramer. Mutation in cis-regulatory regions produces transitions among 64 types of network. In a population, each network reproduces in proportion to its fitness, which depends on its probability (reliability) of synthesizing the tetramer. Fitness-dependent attrition keeps the size of the population constant. Regulatory genes occur in a sequence of levels; each level is associated with a different family of transcription factors. The following results emerge: Because different messengers within a family can give networks with the same connectivity, the 64 types of networks cluster into eight equivalence classes. During evolution with a low mutation rate, high-fitness classes can be approached through various paths on a fitness landscape. With a higher mutation rate, networks remain more uniformly distributed among the 64 types, and lower-fitness networks remain preponderant. An initially homogeneous population becomes more heterogeneous through mutation, but selection according to fitness later reduces its diversity. During this process the dispersion of the population over the possible networks increases, then decreases as the population approaches a unique steady state.

Animals↗
PubMed2000

Time evolution of the Partridge-Barton model.

The time evolution of the Partridge-Barton model in the presence of the pleiotropic constraint and deleterious somatic mutations is exactly solved for arbitrary fecundity in the context of a matricial formalism. Analytical expressions for the time dependence of the mean survival probabilities are derived. Using the fact that the asymptotic behavior for large time t is controlled by the largest matrix eigenvalue, we obtain the steady state values for the mean survival probabilities and the Malthusian growth exponent. The mean age of the population exhibits a t-1 power law decayment. Some Monte Carlo simulations were also performed and they corroborated our theoretical results.

Biological Evolution↗
PubMed1998

A model for the evolution of reproductive skew without reproductive suppression

Reproductive skew is a measure of the way breeding is distributed among the members of an animal society or group. Up to now, explanations of patterns of skew have been limited to one particular model, which assumes that a single dominant has full control over the distribution of subordinate reproduction. If this control is incomplete or absent, however, unsanctioned breeding by subordinate females will increase the total number of young produced. Here I present a new model for the evolution of skew that considers the effect of brood size on the inclusive fitness of dominants and subordinates. By augmenting brood size, a subordinate female reduces the per capita fitness of a dominant's offspring, so the net benefits of producing young are lower for related subordinates. I consider the stable level of skew when both dominant and subordinate attempt to maximize their inclusive fitness under two conditions: (1) when the dominant is unable to anticipate that a subordinate will add to her brood; and (2) the dominant does anticipate subordinate reproduction and can respond by adjusting her own brood size. In the first case, the model predicts that reproductive skew will increase with relatedness between breeders, because related subordinates are selected to add fewer young to the dominant's brood. In the second case, the dominant's optimal response to the presence of a second breeder exaggerates the relationship between relatedness and skew: dominants should produce more young when breeding with related compared with unrelated subordinates. Copyright 1998 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1992

Cloning of the HSP70 gene from Halobacterium marismortui: relatedness of archaebacterial HSP70 to its eubacterial homologs and a model for the evolution of the HSP70 gene.

Heat shock induces the synthesis of a set of proteins in Halobacterium marismortui whose molecular sizes correspond to the known major heat shock proteins. By using the polymerase chain reaction and degenerate oligonucleotide primers for conserved regions of the 70-kDa heat shock protein (HSP70) family, we have successfully cloned and sequenced a gene fragment containing the entire coding sequence for HSP70 from H. marismortui. HSP70 from H. marismortui shows between 44 and 47% amino acid identity with various eukaryotic HSP70s and between 51 and 58% identity with its eubacterial and archaebacterial homologs. On the basis of a comparison of all available HSP70 sequences, we have identified a number of unique sequence signatures in this protein family that provide a clear distinction between eukaryotic organisms and prokaryotic organisms (archaebacteria and eubacteria). The archaebacterial (viz., H. marismortui and Methanosarcina mazei) HSP70s have been found to contain all of the signature sequences characteristic of eubacteria (particularly the gram-positive bacteria), which suggests a close evolutionary relationship between these groups. In addition, detailed analyses of HSP70 sequences that we have carried out have revealed a number of additional novel features of the HSP70 protein family. These include (i) the presence of an insertion of about 25 to 27 amino acids in the N-terminal quadrants of all known eukaryotic and prokaryotic HSP70s except those from archaebacteria and the gram-positive group of bacteria, (ii) significant sequence similarity in HSP70 regions comprising its first and second quadrants from organisms lacking the above insertion, (iii) highly significant similarity between a protein, MreB, of Escherichia coli and the N-terminal half of HSP70s, (iv) significant sequence similarity between the N-terminal quadrant of HSP70 (from gram-positive bacteria and archaebacteria) and the m-type thioredoxin of plant chloroplasts. To account for these and other observations, a model for the evolution of HSP70 proteins involving gene duplication is proposed. The model proposes that HSP70 from archaebacteria (H. marismortui and M. mazei) and the gram-positive group of bacteria constitutes the ancestral form of the protein and that all other HSP70s (viz., other eubacteria as well as eukaryotes) containing the insert have evolved from this ancient protein.

Amino Acid Sequence↗
PubMed1991

Genetic variation in the Heterodoxus octoseriatus group (Phthiraptera): a test of Price's model of parasite evolution.

Most of the genetic variation in the H. octoseriatus group is present as fixed gene differences between species which have been described on morphological criteria. Based on allozymes, the taxonomic status of some species was challenged. There was insufficient evidence, however, to demonstrate that these were not 'good' biological species. Overall, the limited intraspecific variation was present as fixed gene differences among lice from different hosts and from different colonies of hosts; heterozygotes were rare. Two predictions derived from Price's model of parasite evolution were met: populations of lice were genetically homogeneous and, where genetic markers were present, we found substantial genetic variation among populations. These data contrast with those for endoparasitic helminths, where, in general, the amount of genetic variation is similar to that of free-living invertebrates.

Animals↗
PubMed1982

[Modelling of spatial evolution and dynamics of a population of healthy then rabies infected foxes].

The authors describe the main feature of a computer model which helps to simulate the evolution of a rabies epi-enzootic in foxes. They show first the goals and interests of the study, then the originality of used methodology. Their results deal successively with dynamic evolution of a healthy population of foxes, then with this same population infected with rabies and, at last, spatial and temporal evolution of the enzootics. Simulated results are discussed by comparison with those observed in the field.

Animals↗
PubMed1982

Functional morphology of beta cells in the area centralis of the cat's retina: a model for the evolution of central retinal specializations.

The dendritic morphology of beta cells in and around the area centralis of the retinae of normally pigmented and Siamese cats is described. Individual central beta cells in the Siamese cat do not differ morphologically from central beta cells in normally pigmented cats, and in both groups of animals, there is a clear morphological continuity between central and peripheral beta cells. On the basis of systematic patterns of beta cell dendritic orientation, ther area centralis of the normal cat can be divided into a central region, approximately 200 micrometers in diameter, and a pericentral region, approximately 1,400 micrometers in diameter. In the central region, nearly all beta cells have a single large primary dendrite which descends perpendicular to the plane of inner plexiform layer, and gives rise to a dendritic tree which is vertically aligned with the cell's soma. In the pericentral region, the single primary dendrite of most cells descends obliquely through the inner plexiform layer and gives rise to a dendritic tree which is displaced laterally from the position of the soma. For most of the cells the trajectory of the dendrite is systematically related to the location of the cell relative to the area centralis such that the somas are displaced away from its center, presumably in order to minimize the thickness of the ganglion cell layer in the high acuity region. Many beta cells outside the pericentral region also have oriented single primary dendrites, but their orientation seems fairly random with respect to the location of the area centralis. In the Siamese area centralis, this systematic pattern of beta cell dendritic orientation is markedly reduced, suggesting that the pattern is under genetic control. On the basis of these observations, a model for the evolution of the area centralis and fovea is presented which involves selection for systematic for systematic patterns of dendritic orientation in regions of high ganglion cell density.

Animals↗
PubMed1996

A model for the evolution of the plastid sec apparatus inferred from secY gene phylogeny.

Plastids possess a bacteria-like sec apparatus that is involved in protein import into the thylakoid lumen. We have analyzed one of the genes essential for this process, secY. A secY gene from the unicellular red alga Cyanidium caldarium was found to be transcriptionally active, demonstrating for the first time that secY is functional in a plastid. Unlike the situation seen in bacteria the C. caldarium gene is transcribed monocistronically, despite the fact that it is part of a large ribosomal gene cluster that resembles bacterial spc operons. A molecular phylogeny is presented for 8 plastid-encoded secY genes, four of which have not been published yet. In this analysis plastid secY genes fall into two classes. One of these, comprising of genes from multicellular red algae and Cryptophyta, clusters in a neighbour-joining tree with a cyanobacterial counterpart. Separated from the aforesaid are secY genes from Chromophyta, Glaucocystophyta and a unicellular red alga. All plastid and cyanobacterial sequences are located on the same branch, separated from bacterial homologues. We postulate that the two classes of secY genes are paralogous, i.e. their gene products are involved in different protein translocation processes. Based on this assumption a model for the evolution of the plastid sec apparatus is presented.

Cloning, Molecular↗
PubMed2001

Models of sequence evolution for DNA sequences containing gaps.

Most evolutionary tree estimation methods for DNA sequences ignore or inefficiently use the phylogenetic information contained within shared patterns of gaps. This is largely due to the computational difficulties in implementing models for insertions and deletions. A simple way to incorporate this information is to treat a gap as a fifth character (with the four nucleotides being the other four) and to incorporate it within a Markov model of nucleotide substitution. This idea has been dismissed in the past, since it treats a multiple-site insertion or deletion as a sequence of independent events rather than a single event. While this is true, we have found that under many circumstances it is better to incorporate gap information inadequately than to ignore it, at least for topology estimation. We propose an extension to a class of nucleotide substitution models to incorporate the gap character and show that, for data sets (both real and simulated) with short and medium gaps, these models do lead to effective use of the information contained within insertions and deletions. We also implement an ad hoc method in which the likelihood at columns containing multiple-site gaps is downweighted in order to avoid giving them undue influence. The precision of the estimated tree, assessed using Markov chain Monte Carlo techniques to find the posterior distribution over tree space, improves under these five-state models compared with standard methods which effectively ignore gaps.

Algorithms↗
PubMed2001

A model of the evolution of the unusual sex chromosome system of Microtus oregoni.

In the creeping vole, Microtus oregoni, females are X0 and males are XY. In the female germ line, mitotic nondisjunction ensures that the products of meiosis all carry the X chromosome. Similarly, mitotic nondisjunction in the male germ line leads to the production of 0 and Y sperm. We propose that the present situation in M. oregoni has evolved by invasion of a normal XX/XY system by a mutant X chromosome, X', with a complete transmission advantage in X'X females, and a complete transmission disadvantage in X'Y males. X' is at best initially nearly neutral, but can gain a transmission advantage if it reaches a high enough frequency. This is due to the production of X0 females in matings between XX females and X'Y males; low fertility and embryo loss of such females reduce the fitness of the X chromosome in females, relative to that of X'. Under some conditions, however, the enhanced reproductive value of males, caused by the production of inviable Y0 embryos in X0 x X'Y matings, can outweigh any advantage to X'. Inbreeding also reduces any advantage to X'.

Animals↗
PubMed2001

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.

Phylogenetic inference from amino acid sequence data uses mainly empirical models of amino acid replacement and is therefore dependent on those models. Two of the more widely used models, the Dayhoff and JTT models, are estimated using similar methods that can utilize large numbers of sequences from many unrelated protein families but are somewhat unsatisfactory because they rely on assumptions that may lead to systematic error and discard a large amount of the information within the sequences. The alternative method of maximum-likelihood estimation may utilize the information in the sequence data more efficiently and suffers from no systematic error, but it has previously been applicable to relatively few sequences related by a single phylogenetic tree. Here, we combine the best attributes of these two methods using an approximate maximum-likelihood method. We implemented this approach to estimate a new model of amino acid replacement from a database of globular protein sequences comprising 3,905 amino acid sequences split into 182 protein families. While the new model has an overall structure similar to those of other commonly used models, there are significant differences. The new model outperforms the Dayhoff and JTT models with respect to maximum-likelihood values for a large majority of the protein families in our database. This suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates. Potentially, this matrix, and the methods used to generate it, may also be useful in other areas of research, such as biological sequence database searching, sequence alignment, and protein structure prediction, for which an accurate description of amino acid replacement is required.

Algorithms↗
PubMed2002

Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model.

The evolution of cis-regulatory elements (or enhancers) appears to proceed at dramatically different rates in different taxa. Vertebrate enhancers are often very highly conserved in their sequences, and relative positions, across distantly related taxa. In contrast, functionally equivalent enhancers in closely related Drosophila species can differ greatly in their sequences and spatial organization. We present a population-genetic model to explain this difference. The model examines the dynamics of fixation of pairs of individually deleterious, but compensating, mutations. As expected, small populations are predicted to have a high rate of evolution, and the rate decreases with increasing population size. In contrast to previous models, however, this model predicts that the rate of evolution by pairs of compensatory mutations increases dramatically for population sizes above several thousand individuals, to the point of greatly exceeding the neutral rate. Application of this model predicts that species with moderate population sizes will have relatively conserved enhancers, whereas species with larger populations will be expected to evolve their enhancers at much higher rates. We propose that the different degree of conservation seen in vertebrate and Drosophila enhancers may be explained solely by differences in their population sizes and generation times.

Animals↗
PubMed1984

Genetic and strategic models for the evolution of mating systems.

Male and female fitnesses in the Shaw-Mohler equation are partitioned into components which putatively determine mating systems. The resultant genetic models provide criteria for evolutionary stable population states and yield strategic models based on maximization principles and fitness sets.

Alleles↗
PubMed2002

Carbon isotopes as a tool to evaluate the origin and fate of vinyl chloride: laboratory experiments and modeling of isotope evolution.

Accumulation of vinyl chloride (VC) is often a main concern at sites contaminated with chlorinated ethenes and ethanes due to its high toxicity. Since there can be several possible sources of VC and ethene at such sites, assessing the origin and fate of VC can be complicated. Aim of this study was to evaluate carbon isotope fractionation associated with various anaerobic processes that lead to the production of VC and ethene in view of using isotopes to evaluate the origin and fate of these compounds in groundwater. Microcosms were constructed using sediments and groundwater from a contaminated site and amended with potential precursors for VC and ethene production. In the microcosms with dichloroethene isomers, sequential reductive dechlorination was observed, and isotopic enrichmentfactors of -19.9 +/- 1.5 per thousand for cis-1,2-dichloroethene, -30.3 +/- 1.9 per thousand for trans-1,2-dichloroethene, and -7.3 +/- 0.4 per thousand for 1,1-dichloroethene were obtained. In microcosms with chlorinated ethanes, 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA) were predominantly transformed by dichloroelimination to ethene and VC, respectively, and enrichmentfactors of -32.1 +/- 1.1 per thousand for 1,2OCA and -2.0 +/- 0.2 per thousand for 1,1,2-TCA were observed. Except for 1,1,2-TCA, a strong 13C enrichment in each of the potential precursor of VC was observed, which opens the possibility to trace the origin of VC based on the isotope ratio of potential precursors. Furthermore, it was possible to model the isotope evolution of VC present as substrate or intermediate product as a function of time. The study demonstrates that carbon isotope ratios can potentially be used for qualitative and possibly quantitative evaluation of the origin and fate of VC at sites with complex contaminant mixtures.

Carbon Isotopes↗
PubMed1988

A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution.

A model for eukaryotic chromatin organization is presented in which the basic structural and functional unit is the DNA domain. This simple model predicts that both chromosome replication and cell type-specific control of gene expression depend on a combination of stable and dynamic DNA-nuclear matrix interactions. The model suggests that in eukaryotes, DNA regulatory processes are controlled mainly by the intranuclear compartmentalization of the specific DNA sequences, and that control of gene expression involves multiple steps of specific DNA-nuclear matrix interactions. Predictions of the model are tested using available biochemical, molecular and cell biological data. In addition, the domain model is discussed as a simple molecular mechanism to explain cell differentiation in multi-cellular organisms and to explain the evolution of eukaryotic genomes consisting mainly of repetitive sequences and "junk" DNA.

Animals↗