Polygenic models for the evolution of human skin color differences.
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Biological Evolution↗
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A model for the evolution of high frequencies of males in an androdioecious plant based on a cross-compatibility advantage of males.
Lloyd's (1975) and Charlesworth & Charlesworth's (1978) phenotypic selection models for the maintenance of androdioecy predict that males (female-sterile individuals) must have an advantage in fertility (K) of at least two in order to invade a hermaphroditic population, and that their equilibrium frequency (x(eq)=(K - 2)/2(K - 1)) is always less than 0.5. In this paper, we develop a model in which male fertility is frequency-dependent, a situation not investigated in the previous models, to explore the conditions under which a high frequency of males (i.e. more than 50%) could be maintained at equilibrium. We demonstrate that a gametophytic self-incompatibility (GSI) locus linked to a nuclear sex determination locus can favour rare alleles through male function, by causing frequency-dependent selection. Thus, the spread of a female-sterility allele in a hermaphroditic population may be induced. In contrast with the previous models, our model can explain male frequencies greater than 50% in a functionally androdioecious species, as long as there is (i) dominance of female-sterility at the sex locus, and (ii) a few alleles at the self-incompatibility locus, even if the advantage in fertility of male phenotype is lower than two.
Biological Evolution↗
[Mathematical model for an evolutive and hierarchical living system, based on the theory of categories].
The notion of an evolutive hierarchical system proposed here retains the following characteristics of some natural systems, like living organisms: they have an internal organization consisting of more or less complex components with interrelations; they maintain their organization in time although their components are changing; they may be studied at several complexity levels (e.g., molecular, cellular, ...). The idea is to model the state of the system at a given instant by a category, the state transition by a functor, a complex object by the (direct) limit of a pattern of linked objects (its own organization). The emergence of new properties for a complex object is measured, and a development process is described.
Animals↗
Evolving hardware as model of enzyme evolution.
Organism growth and survival is based on thousands of enzymes organized in networks. The motivation to understand how a large number of enzymes evolved so fast inside cells may be relevant to explaining the origin and maintenance of life on Earth. This paper presents electronic circuits called 'electronic enzymes' that model the catalytic function performed by biological enzymes. Electronic enzymes are the hardware realization of enzymes defined as molecular automata with a finite number of internal conformational states and a set of Boolean operators modelling the active groups of the active site. One of the main features of electronic enzymes is the possibility of evolution finding the proper active site by means of a genetic algorithm yielding a metabolic ring or k-cycle that bears a resemblance to Krebs (k=7) or Calvin (k=4) cycles present in organisms. The simulations are consistent with those results obtained in vitro evolving enzymes based on polymerase chain reaction (PCR) as well as with the general view that suggests the main role of recombination during enzyme evolution. The proposed methodology shows how molecular automata with evolvable features that model enzymes or other processing molecules provide an experimental framework for simulation of the principles governing metabolic pathways evolution and self-organization.
Algorithms↗
Genetic definition of a protein-splicing domain: functional mini-inteins support structure predictions and a model for intein evolution.
Inteins are protein-splicing elements, most of which contain conserved sequence blocks that define a family of homing endonucleases. Like group I introns that encode such endonucleases, inteins are mobile genetic elements. Recent crystallography and computer modeling studies suggest that inteins consist of two structural domains that correspond to the endonuclease and the protein-splicing elements. To determine whether the bipartite structure of inteins is mirrored by the functional independence of the protein-splicing domain, the entire endonuclease component was deleted from the Mycobacterium tuberculosis recA intein. Guided by computer modeling studies, and taking advantage of genetic systems designed to monitor intein function, the 440-aa Mtu recA intein was reduced to a functional mini-intein of 137 aa. The accuracy of splicing of several mini-inteins was verified. This work not only substantiates structure predictions for intein function but also supports the hypothesis that, like group I introns, mobile inteins arose by an endonuclease gene invading a sequence encoding a small, functional splicing element.
Amino Acid Sequence↗
The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution.
The human genome is divided into isochores, large stretches (>>300 kb) of genomic DNA with more or less consistent GC content. Mutational/neutralist and selectionist models have been put forward to explain their existence. A major criticism of the mutational models is that they cannot account for the higher GC content at fourfold-redundant silent sites within exons (GC4) than in flanking introns (GCi). Indeed, it has been asserted that it is hard to envisage a mutational bias explanation, as it is difficult to see how repair enzymes might act differently in exons and their flanking introns. However, this rejection, we note, ignores the effects of transposable elements (TEs), which are a major component of introns and tend to cause them to have a GC content different from (usually lower than) that dictated by point mutational processes alone. As TEs tend not to insert at the extremities of introns, this model predicts that GC content at the extremities of introns should be more like that at GC4 than are the intronic interiors. This we show to be true. The model also correctly predicts that small introns should have a composition more like that at GC4 than large introns. We conclude that the logic of the previous rejection of neutralist models is unsafe.
Base Composition↗
General kin selection models for genetic evolution of sib altruism in diploid and haplodiploid species.
A population genetic approach is presented for general analysis and comparison of kin selection models of sib and half-sib altruism. Nine models are described, each assuming a particular mode of inheritance, number of female inseminations, and Mendelian dominance of the altruist gene. In each model, the selective effects of altruism are described in terms of two general fitness functions, A(beta) and S(beta), giving respectively the expected fitness of an altruist and a nonaltruist as a function of the fraction of altruists beta in a given sibship. For each model, exact conditions are reported for stability at altruist and nonaltruist fixation. Under the Table 3 axions, the stability conditions may then be partially ordered on the basis of implications holding between pairs of conditions. The partial orderings are compared with predictions of the kin selection theory of Hamilton.
Biological Evolution↗
The domain model for eukaryotic DNA organization. 2: A molecular basis for constraints on development and evolution.
A model for eukaryotic DNA organization has been proposed in which DNA regulatory processes depend on multiple site-specific DNA-nuclear matrix interactions throughout a DNA domain. In this model gene regulation depends on combinations of a few control factors in a cell to activate cell type-specific genes. This model suggests simple molecular mechanisms for organismal development which can account for sequential activation of appropriate groups of genes throughout development and for specific constraints on developmental pathways. Additionally, these suggested developmental pathways are consistent with mechanisms of evolution in which gradualism and punctuated equilibrium are not exclusive of one another and are interrelated mechanisms of evolution that are both induced by specific chromosomal mutations.
Animals↗
Models of molecular evolution and phylogeny.
Phylogenetic reconstruction is a fast-growing field that is enriched by different statistical approaches and by findings and applications in a broad range of biological areas. Fundamental to these are the mathematical models used to describe the patterns of DNA base substitution and amino acid replacement. These may become some of the basic models for comparative genome research. We discuss these models, including the analysis of observed DNA base and amino acid mutation patterns, the concept of site heterogeneity, and the incorporation of structural biology data, all of which have become particularly important in recent years. We also describe the use of such models in phylogenetic reconstruction and statistical methods for the comparison of different models.
Amino Acid Substitution↗
Animal models for the evolution of thrombotic disease.
Naturally occurring hemorrhagic and thrombotic diseases of animals closely parallel their human counterparts. While such models may be particularly useful in studying the pathogenesis of human disease, it is usually more realistic to depend upon experimentally induced disease models. The species selected for use is therefore of major importance in providing meaningful extrapolation to humans, as are the experimental design and type of procedure (in vitro, ex vivo, in vivo). Regardless of the test system used when in vitro procedures are employed, these must be translated eventually to the in vivo situation. Information about the normal aging process of different species is important here and should influence selection of the species and test system. The ideal situation may not be feasible or pertain because of cost, availability, size, and investigator familiarity, or lack thereof, with the most suitable species or model.
Animals↗
Modelling the isotopic evolution of the Earth.
We present a flexible multi-reservoir (primitive lower mantle, depleted upper mantle, upper continental crust, lower continental crust and atmosphere) forward-transport model of the Earth, incorporating the Sm-Nd, Rb-Sr, U-Th-Pb-He and K-Ar isotope-decay systematics. Mathematically, the model consists of a series of differential equations, describing the changing abundance of each nuclide in each reservoir, which are solved repeatedly over the history of the Earth. Fluxes between reservoirs are keyed to heat production and further constrained by estimates of present-day fluxes (e.g. subduction, plume flux) and current sizes of reservoirs. Elemental transport is tied to these fluxes through 'enrichment factors', which allow for fractionation between species. A principal goal of the model is to reproduce the Pb-isotope systematics of the depleted upper mantle, which has not been done in earlier models. At present, the depleted upper mantle has low (238)U/(204)Pb (mu) and (232)Th/(238)U (kappa) ratios, but Pb-isotope ratios reflect high time-integrated values of these ratios. These features are reproduced in the model and are a consequence of preferential subduction of U and of radiogenic Pb from the upper continental crust into the depleted upper mantle. At the same time, the model reproduces the observed Sr-, Nd-, Ar- and He-isotope ratios of the atmosphere, continental crust and mantle. We show that both steady-state and time-variant concentrations of incompatible-element concentrations and ratios in the continental crust and upper mantle are possible. Indeed, in some cases, incompatible-element concentrations and ratios increase with time in the depleted mantle. Hence, assumptions of a progressively depleting or steady-state upper mantle are not justified. A ubiquitous feature of this model, as well as other evolutionary models, is early rapid depletion of the upper mantle in highly incompatible elements; hence, a near-chondritic Th/U ratio in the upper mantle throughout the Archean is unlikely. The model also suggests that the optimal value of the bulk silicate Earth's K/U ratio is close to 10000; lower values suggested recently seem unlikely.
Atmosphere↗
Empirical and mechanistic mathematical models of temporal evolution of milk production in ruminants.
In the various sectors of animal science there has been little exploration of the theoretical mathematical aspects of data analysis and modelling. The dominant statistical methods used for the analysis of experimental data are rarely valuable for developing a deeper understanding of the problem. In addition they do not take account of the evolution over time of those variables of major interest to be studied. Only recently have more sophisticated methods of mathematical modelling begun to be used. Nonetheless attention tends to be focused exclusively on empirical models. Mathematical models with greater explanatory power, in particular those which use differential equations, are as yet little used. This work develops a mathematical approach to a problem that is of great interest in animal science: the development over time of milk production in economically important ruminant species.
Animals↗
Some models of neutral evolution, compensatory evolution, and the shifting balance process.
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Animals↗
Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution.
Three patterns of DNA sequence conservation have been identified from five human and rodent genomic sequence comparisons. First, a divergent pattern was observed in the noncoding sequences of the beta-globin and gamma-crystallin gene clusters, and second, a highly conserved pattern was observed in the noncoding regions of the T cell receptor C alpha-C delta, and the alpha- and beta-myosin-heavy-chain genes. A third, mixed pattern has also been found in the immunoglobulin IgH C mu-C delta gene region. These three patterns of genomic evolution pose the fascinating possibility that large portions of the genome evolve at different rates.
Animals↗
A model for the evolution of the proteins. Cytochrome c : mammals, reptiles, insects.
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Amino Acids↗
Computational evolution of a model polymer that folds to a specified target conformation.
A method is described for folding polymers to specific target conformations. The approach uses a fast but approximate dynamics algorithm, coupled with a genetic algorithm that is used to evolve the large number of free parameters needed. The dynamics algorithm uses a state transition matrix approach. At each time step, the distances between pairs of atoms are adjusted by shifting them from Dij to Dij + Sij where Sij is an element of the state transition matrix S. Atom pairs that are attractive have Sij < 0 and pairs that are repulsive have S ij > 0. The atomic movement is carried out by gradient minimizing the molecular mechanics energy of the molecule subject to harmonic distance constraints. The method is applied to a simple test case, a 19 atom 2-D polymer. The paper also show that the S matrices can correctly fold a limited variety of initial conformations that differ from the one used during the evolution phase.
Algorithms↗
Minimal model for genome evolution and growth.
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random mutation but primarily grows by random segmental duplication. That genomes grew mostly by duplication is consistent with the observation that repeat sequences in all genomes are widespread and intragenomic and intergenomic homologous genes are preponderant across all life forms.
DNA, Bacterial↗
A Prisoner's Dilemma model of the evolution of paternal care.
The heavy energetic demands of gestation, lactation and rearing of offspring mean that studies of paternal care in primates usually focus on female reproductive effort. Here it is shown that both male and female reproductive effort must be considered in order to understand how paternal care evolved. This is done using the Prisoner's Dilemma, best known as a model of reciprocal altruism. It is found that the relative cost of reproduction for males and females is crucially important in determining co-operative and competitive strategies. In particular, when male reproductive costs are less than female reproductive costs, males co-operate with females even when females do not reciprocate. This surprising behaviour, termed non-reciprocal altruism, is comparable with male investment in a female and her offspring.
Altruism↗