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The Haxo and Blinks electrode. A mathematical model.

Fick's diffusion equations have been solved for the Haxo and Blinks electrochemical determination of photosynthetic O(2) evolution. The model shows the method to be quantitative in the case of a "long" chamber measuring constant rates of O(2) evolution. Transients are amplitude distorted by an amount depending on the space distribution of the O(2) sources. A correction equation applied to the raw data permits the recovery of the original signal.

Diffusion↗

Evolution of aphasia in the first year post-onset.

Evolution of aphasia was studied in the first year of recovery in 43 patients sustaining left hemisphere strokes with language impairment. Observations were made daily during acute hospitalization and subsequently at approximately one, two, three, four-to-six and seven-to-twelve month intervals post-stroke. Aphasias were classified according to standard criteria. A significantly larger percentage of the sample (59%) exhibited evolution of aphasia than in previous studies. This was attributed to earlier and more intensive patient observations in this investigation. Most changes occurred within the first two weeks of recovery. Two patterns of evolution were clearly present in the sample, one being early rapid change and the other a more gradual evolution. An expansion and integration of Gloning and Quatember's (1964) model of evolution is proposed on the basis of combined results from several studies. Also, the influence of aging, evolution of aphasia and the emergence of dementia post-stroke are discussed.

Adult↗

Evolution by the birth-and-death process in multigene families of the vertebrate immune system.

Concerted evolution is often invoked to explain the diversity and evolution of the multigene families of major histocompatibility complex (MHC) genes and immunoglobulin (Ig) genes. However, this hypothesis has been controversial because the member genes of these families from the same species are not necessarily more closely related to one another than to the genes from different species. To resolve this controversy, we conducted phylogenetic analyses of several multigene families of the MHC and Ig systems. The results show that the evolutionary pattern of these families is quite different from that of concerted evolution but is in agreement with the birth-and-death model of evolution in which new genes are created by repeated gene duplication and some duplicate genes are maintained in the genome for a long time but others are deleted or become nonfunctional by deleterious mutations. We found little evidence that interlocus gene conversion plays an important role in the evolution of MHC and Ig multigene families.

Animals↗

Mutualism, parasitism and competition in the evolution of coviruses.

Coviruses are viruses with the property that their genetic information is divided up among two or more different viral particles. I model the evolution of coviruses using information on both viral virulence and the interactions between viruses and molecules that parasitize them: satellite viruses, satellite RNAs and defective interfering viruses. The model ultimately, and inevitably contains within it single-species dynamics as well as mutualistic, parasitic, cooperative and competitive relationships. The model shows that coexistence between coviruses and the self-sufficient viruses that spawned them is unlikely, in the sense that the quantitative conditions for coexistence are not easy to satisfy I also describe an abrupt transition from mutualistic two-species to single-species dynamics, showing a new sense in which questions such as 'Is a lichen one species or two?' can be given a definite answer.

Animals↗

MtArt: a new model of amino acid replacement for Arthropoda.

A statistical approach was applied to select those models that best fit each individual mitochondrial (mt) protein at different taxonomic levels of metazoans. The existing mitochondrial replacement matrices, MtREV and MtMam, were found to be the best-fit models for the mt-proteins of vertebrates, with the exception of Nd6, at different taxonomic levels. Remarkably, existing mitochondrial matrices generally failed to best-fit invertebrate mt-proteins. In an attempt to better model the evolution of invertebrate mt-proteins, a new replacement matrix, named MtArt, was constructed based on arthropod mt-proteomes. The new model was found to best fit almost all analyzed invertebrate mt-protein data sets. The observed pattern of model fit across the different data sets indicates that no single replacement matrix is able to describe the general evolutionary properties of mt-proteins but rather that taxonomical biases and/or the existence of different mt-genetic codes have great influence on which model is selected.

Amino Acid Sequence↗

Absorbent Markov chains as a model for the study of the evolution of proteins.

The formalism of absorbent Markov chains, previously developed by Kemeny & Snell (1960) is used as a model for the study of the evolution of proteins. Within the limits of statistical analysis used, the amino acid substitution frequencies of McLachlan (1972) are explained by the numerical values derived from the model used. In addition, the amino acid composition of proteins is partially explained and the relative mutability of amino acids receives a new interpretation in the light of the above mentioned stochastic model. The results show that some basic aspect of protein evolution can be predicted by a stochastic model and therefore a significant component of protein evolution is driven by a random element.

Amino Acid Sequence↗

No BLUE among phylogenetic estimators.

Multivariate analysis is a branch of statistics that successfully exploits the powerful tools of linear algebra to obtain a fairly comprehensive theory of estimation. The purpose of this paper is to explore to what extent a linear theory of estimation can be developed in the context of coalescent models used in the analysis of DNA polymorphism. We consider a large class of coalescent models, of which the neutral infinite sites model is one example. In the process, we discover several limitations of linear estimators that are quite distinct from those in the classical theory. In particular, we prove that there does not exist a uniformly BLUE (best linear unbiased estimator) for the scaled mutation parameter, under the assumptions of the neutral model of evolution. In fact, we show that no linear estimator performs uniformly better than the Watterson (1975) method based on the total number of segregating sites. For certain coalescent models, the segregating-sites estimator is actually optimal.The general conclusion is the following. If genealogical information is useful for estimating the rate of evolution, then there is no optimal linear method. If there is an optimal linear method, then no information other than the total number of segregating sites is needed.

Base Sequence↗

Thoughts on the cerebellum as a model for cerebral cortical development and evolution.

This chapter explores the prospect of using the cerebellar cortex as a model for the development and evolution of the cerebral neocortex. At first, this would seem a nearly fruitless task given the readily apparent structural and functional differences between the two cortices. Cerebellum and cerebrum perform different associative tasks, the cellular 'circuit diagram' of the two structures is different, even the developmental sequences that give rise to the two structures differ markedly. Yet there are similarities between the structures at the conceptual level that are difficult to ignore. Both structures have a relatively simple modular circuitry and achieve their complexity by an increase in either the size or number of the modules. Both have massive commisures connecting the left and right halves of the structure. For the cortex this commisure is the obvious corpus callosum; the cerebellar commisure is made up of parallel fibres of the granule cells that pass freely across the midline. As they are thin and unmyelinated, the number of these crossing fibres may well exceed the number of the callosal axons by a significant amount. By far the most obvious similarity between cortex and cerebellum, however, is that they are both topologically sheet-like in structure. They are broad and wide in the two-dimensional plane of the pial membrane with a relatively modest thickness in the radial dimension. The question for this chapter then is whether these similarities, in particular the sheet-like organization are coincidental or indicative of larger themes that play deeper roles in the development and function of these two seemingly disparate brain regions.

Animals↗

Competitive interactions between parasitoid larvae and the evolution of gregarious development.

We report experiments using two closely related species of alysiine braconids directed at understanding how gregarious development evolved in one subfamily of parasitoid wasps. Theoretical models predict that once siblicide between parasitoid wasps has evolved, it can only be lost under stringent conditions, making the transition from solitary to gregarious development exiguous. Phylogenetic studies indicate, however, that gregariousness has independently arisen on numerous occasions. New theoretical models have demonstrated that if gregarious development involves reductions in larval mobility, rather than a lack of fighting ability (as in the older models), the evolution of gregariousness is much more likely. We tested the predictions of the older tolerance models (gregariousness based on non-fighting larval phenotypes) and the reduced mobility models (gregariousness based on non-searching larval phenotypes) by observing larval movement and the outcome of interspecific competition between Aphaereta genevensis (solitary) and A. pallipes (gregarious) under multiparasitism. Differences in larval mobility matched the prediction of the reduced mobility model of gregarious development, with the solitary A. genevensis having larvae that are much more mobile. The proportion of hosts producing the solitary species significantly declined after subsequent exposure to females of the gregarious species. This contradicts the prediction of the older models (fighting vs non-fighting phenotypes), under which any competitive interactions between solitary and gregarious larvae will result in a highly asymmetrical outcome, as the solitary species should be competitively superior. The observed outcome of interspecific competition offers evidence, with respect to this subfamily, in favour of the new models (searching vs non-searching phenotypes).

Animals↗

Why do paralogs persist? Molecular evolution of CYCLOIDEA and related floral symmetry genes in Antirrhineae (Veronicaceae).

CYCLOIDEA (CYC) and DICHOTOMA (DICH) are paralogous genes that determine adaxial (dorsal) flower identity in the bilaterally symmetric flowers of Antirrhinum majus (snapdragon). We show here that the duplication leading to the existence of both CYC and DICH in Antirrhinum occurred before the radiation of the Antirrhineae (the tribe to which snapdragon belongs). We find no additional gene duplications within Antirrhineae. Using explicit codon-based models of evolution in a likelihood framework, we show that patterns of molecular evolution after the duplication that gave rise to CYC and DICH are consistent with purifying selection acting at both loci, despite their known functional redundancy in snapdragon. However, for specific gene regions, purifying selection is significantly relaxed across DICH lineages, relative to CYC lineages. In addition, we find evidence for relaxed purifying selection along the lineage leading to snapdragon in one of two putative functional domains of DICH. A model of selection accounting for the persistence of paralogous genes in the absence of diversifying selection is presented. This model takes into account differences in the degree of purifying selection acting at the two loci and is consistent with subfunctionalization models of paralogous gene evolution.

Antirrhinum↗

The inheritance of phenotypes: an adaptation to fluctuating environments.

We discuss simple models for the evolution of rates of spontaneous and induced heritable phenotypic variations in a periodically fluctuating environment with a cycle length between two and 100 generations. For the simplest case, the optimal spontaneous transition rate between two states is approximately 1/n (where n is the cycle length). It is also shown that selection for the optimal transition rate under these conditions is surprisingly strong. When n is small, this means that the heritable variations are produced by non-classical inheritance systems, including non-DNA inheritance systems. Thus, it is predicted that in genes controlling adaptation to such environments, non-classical genetic effects are likely to be observed. We argue that the evolution of spontaneous and induced heritable transitions played an important role in the evolution of ontogenies of both unicellular and multicellular organisms. The existence of a machinery for producing induced heritable phenotypic variations introduces a "Lamarckian" factor into evolution.

Adaptation, Physiological↗

The phylogeny of the subgroups within the melanogaster species group: likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny.

The relationships among the majority of the subgroups in the Drosophila melanogaster species group remain unresolved. We present a 2223basepair dataset for mitochondrial cytochrome oxidase I and cytochrome oxidase II for 43 species (including new data from 11 species), sampled to include the major subgroups. After a brief review of competing hypotheses for the ananassae, montium, suzukii, and takahashii subgroups, we combine the two genes based on a new use of the SH test and present KH and SH likelihood comparisons (Kishino and Hasegawa, 1989. J. Mol. Evol. 29, 170-179; Shimodaira and Hasegawa, 1999) to test the monophyly and placement of these subgroups within the larger species group. Although we find insignificant differences between the two suggested placements for the ananassae subgroup, the ananassae is sister to the rest of the subgroups in the melanogaster species group in every investigation. For the takahashii subgroup, although we cannot reject monophyly, the species are so closely related to the suzukii subgroup for these data that the two subgroups often form one clade. Finally, we present a Bayesian estimate of the phylogeny for both genes combined, utilizing a recently published method that allows for different models of evolution for different sites.

Animals↗

Re-creating the RNA world.

Results from in vitro selection experiments can be used to construct and test models for the evolution of the RNA world. Surprisingly, the success of selected RNAs at binding ligands and catalyzing reactions may make it difficult to determine precisely the lineage of molecular fossils, molecules that are believed to have survived from the RNA world to the present.

Evolution, Molecular↗

Evolutionary route to diploidy and sex.

By using a bit-string model of evolution, we find a successful route to diploidy and sex in simple organisms. Allowing the sexually reproducing diploid individuals to also perform mitosis, as they do in a haploid-diploid cycle, leads to the complete takeover of the population by sexual diploids. This mechanism is so robust that even the accidental conversion and pairing of only two diploids give rise to a sexual population.

Algorithms↗

Fundamental differences between the methods of maximum likelihood and maximum posterior probability in phylogenetics.

Using a four-taxon example under a simple model of evolution, we show that the methods of maximum likelihood and maximum posterior probability (which is a Bayesian method of inference) may not arrive at the same optimal tree topology. Some patterns that are separately uninformative under the maximum likelihood method are separately informative under the Bayesian method. We also show that this difference has impact on the bootstrap frequencies and the posterior probabilities of topologies, which therefore are not necessarily approximately equal. Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434, 1996) stated that bootstrap frequencies can, under certain circumstances, be interpreted as posterior probabilities. This is true only if one includes a non-informative prior distribution of the possible data patterns, and most often the prior distributions are instead specified in terms of topology and branch lengths. [Bayesian inference; maximum likelihood method; Phylogeny; support.].

Bayes Theorem↗

Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network.

UNLABELLED: Serial NetEvolve is a flexible simulation program that generates DNA sequences evolved along a tree or recombinant network. It offers a user-friendly Windows graphical interface and a Windows or Linux simulator with a diverse selection of parameters to control the evolutionary model. Serial NetEvolve is a modification of the Treevolve program with the following additional features: simulation of serially-sampled data, the choice of either a clock-like or a variable rate model of sequence evolution, sampling from the internal nodes and the output of the randomly generated tree or network in our newly proposed NeTwick format. AVAILABILITY: From website http://biorg.cis.fiu.edu/SNE Contacts: giri@cis.fiu.edu SUPPLEMENTARY INFORMATION: Manual and examples available from http://biorg.cis.fiu.edu/SNE.

Algorithms↗