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PubMed1996

Application of morphological trends of evolution to phylogenetic interpretation of chemotaxonomic data.

Data on the membranotropic action of triterpene glycosides from sea cucumbers (Holothurioidea, Echinodermata) are used as a model for studying the evolution of biochemical adaptations. Conceptions such as the theory of modes of organogenesis, and the theory of phylembryogeneses developed by the Russian school of evolutionary morphology, and other morphological trends of evolutionary transformations of anatomical structures are applicable to the phylogenetic interpretation of chemotaxonomic data. The processes of ontogenesis and biosynthesis of secondary metabolites are compared within the framework of the theory of phylembryogeneses. The deep inner similarity of these processes are shown. Concurrence of the modes of phyembryogenesis noted by Severtsov and the principles of micromolecular evolution noted by Gottlieb and Harborne are also shown. The biological significance of presence or absence of substances, (or some features of these substances) for the whole organism that produced them is the main criterion we propose as an approach for polarization of a biochemical phylogenetic series. The application of methods of comparative anatomy to the molecular level for purposes of investigation on evolution of biomolecules and their functions could be called "chemical morphology".

Adaptation, Physiological↗

PubMed1997

The evolution of cooperation in a lattice-structured population.

The evolution of cooperation among unrelated individuals is studied in a lattice-structured habitat, where individuals interact locally only with their neighbors. The initial population includes Tit-for-Tat (abbreviated as TFT, indicating a cooperative strategy) and All Defect (AD, a selfish strategy) distributed randomly over the lattice points. Each individual plays the iterated Prisoner's Dilemma game with its nearest neighbors, and its total pay-off determines its instantaneous mortality. After the death of an individual, the site is replaced immediately by a copy of a randomly chosen neighbor. Mathematical analyses based on mean-field approximation, pair approximation, and computer simulation are applied. Models on one and two-dimensional regular square lattices are examined and compared with the complete mixing model. Results are: (1) In the one-dimensional model, TFT players come to form tight clusters. As the probability of iteration w increases, TFTs become more likely to spread. The condition for TFT to increase is predicted accurately by pair approximation but not by mean-field approximation. (2) If w is sufficiently large, TFT can invade and spread in an AD population, which is impossible in the complete mixing model where AD is always ESS. This is also confirmed by the invasion probability analysis. (3) The two-dimensional lattice model behaves somewhat in between the one-dimensional model and the complete mixing model. (4) The spatial structure modifies the condition for the evolution of cooperation in two different ways: it facilitates the evolution of cooperation due to spontaneously formed positive correlation between neighbors, but it also inhibits cooperation because of the advantage of being spiteful by killing neighbors and then replacing them.

Animals↗

PubMed1997

Consciousness and biological evolution.

It has been suggested that if the preservation and development of consciousness in the biological evolution is a result of natural selection, it is plausible that consciousness not only has been influenced by neural processes, but has had a survival value itself; and it could only have had this, if it had also been efficacious. This argument for mind-brain interaction is examined, both as the argument has been developed by William James and Karl Popper and as it has been discussed by C.D. Broad. The problem of identifying mental phenomena with certain neural phenomena is also addressed. The main conclusion of the analysis is that an explanation of the evolution of consciousness in Darwinian terms of natural selection does not rule out that consciousness may have evolved as a mere causally inert effect of the evolution of the nervous system, or that mental phenomena are identical with certain neural phenomena. However, the interactionistic theory still seems, more plausible and more fruitful for other reasons brought up in the discussion.

Biological Evolution↗

PubMed1998

Ecological mechanisms of evolution by natural selection: causal processes generating density-and-frequency dependent fitness.

The current theory of natural selection explains that adaptive evolution occurs because genotypes with greater survival or reproductive tendencies, due to their particular biological properties, tend to increase in frequency over the lesser ones in a common environment; therefore, the former will eventually replace the latter. In nature, such a selection process most often occurs in a local population which is nested in a community involving local ecological dynamics which are not clearly articulated in the explanatory scheme of the theory. This paper seeks to explicate such an ecological process giving rise to the evolution of a local population with a particular focus on dynamic effects of an increase in the number of invasive, new types on the fate of old ones. Arguments using the ecological-mechanistic model, representing negative interactions among alternative types of organisms, suggest major ecological mechanisms by which the new replace the old; a selective increase in the number of one type leads to a decrease in the equilibrial abundance of a limiting resource, an increase in the density of conspecifics, and/or an increase in the density of predators, which would in turn lower the per capita reproductive rate, or raise the morality rate of another and make it extinct. Thus, replacement due to selection is associated with such dynamic shifts in equilibria occurring in a local community. The analysis of three (a resource, a prey and a predator) and four species (those plus a top predator) models suggests that evolutionary processes cannot be predicted without reference to the web structure of the community, that some fitness components causing a selective increase in a particular type can have, in some cases, nothing to do with factors causing selective decreases in alternatives, and that evolution of some traits can occur without resource competition.

Animals↗

PubMed1998

Mafia behaviour and the evolution of facultative virulence.

Some organisms enforce "maladaptive" behaviours on others of the same or different species by imposing costs in the absence of compliance. Such enforcement is used by the enforcer to obtain benefits in the possession of the enforced individual. This mechanism is known as mafia behaviour in humans, but may be widespread in parasite-host relationships in nature, from the cellular level to societies. In this paper we describe the evolution of such mafia mechanisms, and we propose a fuzzy logic model where the mafia mechanism is based on enforcement of hosts by exponentially increasing the cost of resistance to the parasite. The benefits of host resistance can be counteracted by parasite virulence, or even a decrease in response to an increment in its resistance. This parasite response to the host defence increment can be used for the parasite to teach the host that it is better to pay part of its benefits than increase its extremely costly defence. This model differs from others because it takes into account the evolution of host defence related to the evolution of parasite virulence (host-parasite coevolution) and points out an optimum in host defence related to the facultative virulence of the parasite. We provide several potential examples of facultative virulence depending on the antiparasite responses of hosts, and we suggest that this kind of mafia behaviour may be a widespread mechanism in biological processes at a number of different levels.

Animals↗

PubMed1999

Good parent and good genes models of handicap evolution.

We previously studied a good genes handicap model in which male quality was heritable and improved offspring viability. We extend our analysis to species in which males provide direct benefits (e.g. parental care, better resources, the absence of contagious diseases). Male quality now affects female fitness by increasing female reproductive success. For this good parent handicap to work, the male signal must have condition-dependent expression. The equilibrium strength of female preference is controlled by the product of signal transmission efficiency, phenotypic variance of male quality and the effectiveness of male quality in improving female reproductive success. The equilibrium resulting from the good parent handicap has exactly the same form as with the good genes handicap. This allows us to compare the relative importance of these two forces in the evolution of female preferences. The handicap models (both good genes and good parent) also show cyclic evolution, as happens with the pure Fisherian model. However, we predict that the handicap process is often strong enough to lead to a stable equilibrium. This leads to the conclusion that cyclic evolution is less likely to occur for handicap than Fisherian traits.

Animals↗

PubMed2000

Modeling DNA mutation and recombination for directed evolution experiments.

Directed evolution experiments rely on the cyclical application of mutagenesis, screening and amplification in a test tube. They have led to the creation of novel proteins for a wide range of applications. However, directed evolution currently requires an uncertain, typically large, number of labor intensive and expensive experimental cycles before proteins with improved function are identified. This paper introduces predictive models for quantifying the outcome of the experiments aiding in the setup of directed evolution for maximizing the chances of obtaining DNA sequences encoding enzymes with improved activities. Two methods of DNA manipulation are analysed: error-prone PCR and DNA recombination. Error-prone PCR is a DNA replication process that intentionally introduces copying errors by imposing mutagenic reaction conditions. The proposed model calculates the probability of producing a specific nucleotide sequence after a number of PCR cycles. DNA recombination methods rely on the mixing and concatenation of genetic material from a number of parent sequences. This paper focuses on modeling a specific DNA recombination protocol, DNA shuffling. Three aspects of the DNA shuffling procedure are modeled: the fragment size distribution after random fragmentation by DNase I, the assembly of DNA fragments, and the probability of assembling specific sequences or combinations of mutations. Results obtained with the proposed models compare favorably with experimental data.

Animals↗

PubMed2000

Information processing in multigame environments modeling the evolution of sex via punctuated equilibria.

Uncertain environments are properly described by probability distributions which, as usual, can be collapsed or conditioned into distributions with reduced uncertainty through the processing of environmental information. Organisms which force this collapse gain evolutionary advantage by being able to employ strategies in a known environment rather than in a merely probable one. The accrued benefit gained from processing information can be precisely quantified by comparing benefits returned using distributions prior to, and after collapse, and these often large and immediate benefits can amply justify the evolutionary cost of information processing systems. More importantly, the evolution of information processing systems must necessarily occur in a predictable evolutionary sequence from less complex to more complex. Practical applications include modeling the evolution of sex modeled here as a sequence from asexual reproduction, to single gene exchange, to gene packet exchange, to same species packet exchange, and finally to sexual reproduction, sexual selection, Red Queen contests and so on. Modeling this sequence requires extensions to game theory originally designed to model a single game, to allow the simultaneous operation of many games. This extension is called a multigame environment. The dynamical evolution of the development sequence shows punctuated equilibria.

Animals↗

PubMed2000

On selection mechanisms during initial evolution and on the possible role of ionic balance.

Initial evolution at the molecular level can proceed through mechanisms that enhance either the generation or the survival of certain molecules. Phenomena related to ionic balance can be the basis for both generative and survival selection mechanisms that may have driven the initial evolution of macromolecules. An important advantage of mechanisms based on ionic balance phenomena is that they can conceivably generate spatial and temporal inhomogeneities in semi-enclosed spaces within cavities of porous materials and/or membranes. Under certain circumstances, such inhomogeneities are required for initial evolution to proceed.

Animals↗

PubMed2001

Integrative study on chromosome evolution of mammals, ants and wasps based on the minimum interaction theory.

There is well-known evidence that in many eukaryotes, different species have different karyotypes (e.g. n=1-47 in ants and n=3-51 in mammals). Alternative (fusion and fission) hypotheses have been proposed to interpret this chromosomal diversity. Although the former has long been accepted, accumulating molecular genetics evidence seems to support the latter. We investigated this problem from a stochastic viewpoint using the Monte Carlo simulation method under the minimum interaction theory. We found that the results of simulations consistently interpreted the chromosomal diversity observed in mammals, ants and wasps, and concluded that chromosome evolution tends to evolve as a whole toward increasing chromosome numbers by centric fission. Accordingly, our results support the fission hypothesis. We discussed the process of chromosome evolution based on the latest theory of the molecular structure of chromosomes, and reconfirmed that the fission burst is the prime motive force in long-term chromosome evolution, and is effective in minimizing the genetic risks due to deleterious reciprocal translocations and in increasing the potential of genetic divergence. Centric fusion plays a biological role in eliminating heterochromatin (C-bands), but is only a local reverse flow in contrast to the previously held views.

Animals↗

PubMed2001

Cooperative boundary populations: the evolution of cooperation on mortality risk gradients.

Cooperative or altruistic behavior is known to be vulnerable to destructive exploitation in the absence of spatial segregation and perceptual discrimination on the part of cooperators. In this study, a non-standard, agent-based, spatially explicit model of the evolution of cooperation shows that spatial gradients of increasing individual mortality risk can allow cooperative subpopulations to persist among players randomly matched for one-shot Prisoner's Dilemma. Further, the dynamically stable cooperator population formed on the gradient at the boundary of the survivable non-cooperative range provides ideal conditions for the evolution of discriminating strategies such as tit-for-tat. It is suggested that such gradients may commonly exist at the boundaries of the ranges of existing populations, providing a new basic mechanism for the evolution of cooperation.

Animals↗

PubMed2002

Evolution of mutualism between globeflowers and their pollinating flies.

Plant/seed-eater pollinators mutualisms involve a plant pollinated by an insect whose larvae develop by eating a fraction of host-plant seeds. The outcome of the interaction therefore depends on the number of ovules fertilized by adult visits and the number of seeds destroyed by larvae. Among the very few cases of such mutualisms reported so far is the globeflower-globeflower flies mutualism, which is unique in that it involves several congeneric fly species (Chiastocheta genus) coexisting within a single host-plant species, Trollius europaeus. These species exhibit contrasted oviposition behaviors resulting in a more or less beneficial outcome for the plant. We designed an adaptive dynamics model to investigate how morphological traits of globeflower could affect the evolution of oviposition in its pollinating flies. Three fly traits (flower age at oviposition, clutch size and the level of avoidance of already parasitized flowers) and one plant trait (closed or open corolla) were examined. Whatever the shape of the flower, evolutionary branching occurs between early and late ovipositing flies, driven by strong competition among larvae within a fruit. Once this branching occurred, the closed shape of the corolla is likely to offer a better protection to eggs of early but not of late ovipositing flies. The difference in egg survival results in higher competition among early larvae and thus selects for decreased clutch size in early flies. This can be seen as a first step in the evolution of a mutualistic behavior. The prediction of our model fits field observations of fly behavior, giving theoretical support to the hypothesis of fly sympatric speciation within its host plant. Moreover, flower closed globe shape can be positively selected in globeflowers as it results in a reduction of parasitism strength. This last evolution therefore leads to a stable mutualism between globeflowers and globeflower flies.

Animals↗

PubMed1996

The evolution of human populations: a molecular perspective.

Human evolution exhibits repeated speciations and conspicuous morphological change: from Australopithecus to Homo habilis, H. erectus, and H. sapiens; and from their hominoid ancestor to orangutans, gorillas, chimpanzees, and humans. Theories of founder-event speciation propose that speciation often occurs as a consequence of population bottlenecks, down to one or very few individual pairs. Proponents of punctuated equilibrium claim in addition that founder-event speciation results in rapid morphological change. The major histocompatibility complex (MHC) consists of several very polymorphic gene loci. The genealogy of 19 human alleles of the DQB1 locus coalesces more than 30 million years ago, before the divergence of apes and Old World monkeys. Many human alleles are more closely related to pongid and cercopithecoid alleles than to other human alleles. Using the theory of gene coalescence, we estimate that these polymorphisms require human populations of the order of N = 100,000 individuals for the last several million years. This conclusion is confirmed by computer simulations showing the rate of decay of the polymorphisms over time. Computer simulations indicate, in addition, that in human evolution no bottlenecks have occurred with fewer than several thousand individuals. We evaluate studies of mtDNA, Y-chromosome, and microsatellite autosomal polymorphisms and conclude that they are consistent with the MHC result that no narrow population bottlenecks have occurred in human evolution. The available molecular information favors a recent African origin of modern humans, who spread out of Africa approximately 100,000 to 200,000 years ago.

Africa↗

PubMed1997

Molecular systematics of Middle American cichlid fishes and the evolution of trophic-types in 'Cichlasoma (Amphilophus)' and 'C. (Thorichthys)'.

The majority of Middle American cichlids are placed in the informal assemblage 'Cichlasoma.' The group is divided into eight sections which appear to be based primarily on trophic morphology. Although several members of 'Cichlasoma' have been used in ecomorphological, behavioral, and biogeographic studies, no phylogenetic hypotheses for the group exist. In an attempt to develop a better understanding of the phylogenetic relationships of 'cichlasomine' cichlids, we examined the evolution of the trophic specialization, substratum-sifting, in two sections, 'Cichlasoma (Thorichthys)' and 'C. (Amphilophus),' to determine whether the trait reflects common ancestry. We sequenced the complete mitochondrial cytochrome b gene for 19 cichlids representing six sections of 'Cichlasoma,' and representatives of other Neotropical Cichlidae. Additional cichlid, and noncichlid outgroup sequences were included for a total of 22 taxa. The molecular phylogeny supports the recognition of the section 'C. (Thoricthys)' as a natural group, and we place those cichlids in the genus Thorichthys. The phylogeny also depicts 'C. (Amphilophus)' as paraphyletic, with substratum-sifters and generalized predators forming separate nonsister clades. We recommend that the substratum-sifting clade of the section 'C. (Amphilophus)' be placed in the resurrected genus Astatheros. The generalized predator clade of 'C. (Amphilophus)' contains only two species, 'C. (A.) citrinellum' and 'C. (A.) labiatum,' which we place in the genus Amphilophus. The phylogenetic hypotheses generated indicate that the substratum-sifting genera Thorichthys and Amphilophus do not share a common ancestor. Reconstruction of the evolution of substratum-sifting is equivocal, requiring either the independent evolution of the trait on two separate occasions or its presence in a more inclusive clade and subsequent loss in nonsubstratum sifting species.

Americas↗

PubMed1999

Evolution and molecular characterization of a beta-globin gene from the Australian Echidna Tachyglossus aculeatus (Monotremata).

Coinciding with a period in evolution when monotremes, marsupials, and eutherians diverged from a common ancestor, a proto-beta-globin gene duplicated, producing the progenitors of mammalian embryonic and adult beta-like globin genes. To determine whether monotremes contain orthologues of these genes and to further investigate the evolutionary relationships of monotremes, marsupials, and eutherians, we have determined the complete DNA sequence of an echidna (Tachyglossus aculeatus) beta-like globin gene. Conceptual translation of the gene and sequence comparisons with eutherian and marsupial beta-like globin genes and echidna adult beta-globin indicate that the gene is adult expressed. Phylogenetic analyses do not clearly resolve the branching pattern of mammalian beta-like globin gene lineages and it is therefore uncertain whether monotremes have orthologues of the embryonic beta-like globin genes of marsupials and eutherians. Four models are proposed that provide a framework for interpreting further studies on the evolution of beta-like globin genes in the context of the evolution of monotremes, marsupials, and eutherians.

Amino Acid Sequence↗

PubMed1999

Gene duplications in early metazoan evolution.

Major increases in complexity during animal evolution occurred at the transition from a unicellular protozoan to a multicellular metazoan, the evolution of Bilateria from diploblasts (possibly the Cambrian explosion) and during early vertebrate evolution. A role for gene duplication in the third event has been widely discussed. Here I examine the possible role of gene duplications and domain shuffling in the first two events. There is evidence for a wave of gene duplications and shuffling which may have paved the way for multicellularity; there are also examples of gene duplications that may have facilitated the transition from diploblasts to Bilateria.

Animals↗

PubMed2000

Undermining the Baldwin expediting effect: does phenotypic plasticity accelerate evolution?

The claim that phenotypic plasticity speeds up evolution towards a target phenotype is a recent incarnation of the Baldwin effect. To differentiate this theory from earlier interpretations of Baldwin's ideas, we name it the Baldwin expediting effect. Models that demonstrate this effect assume an extreme fitness scenario which bestows high fitness upon a single optimal phenotype and treats all other phenotypes as equal. In two modeling frameworks, we demonstrate that the effects of plasticity on the rate of evolution are highly dependent on the fitness function and population starting conditions. We argue that phenotypic plasticity does not universally facilitate evolution. Furthermore, in cases where the Baldwin expediting effect occurs, it is not necessarily correlated with increased fitness and therefore is not sufficient to explain the evolutionary success of plasticity.

Biological Evolution↗

PubMed2002

Mutational equilibrium model of genome size evolution.

The paper describes a mutational equilibrium model of genome size evolution. This model is different from both adaptive and junk DNA models of genome size evolution in that it does not assume that genome size is maintained either by positive or stabilizing selection for the optimum genome size (as in adaptive theories) or by purifying selection against too much junk DNA (as in junk DNA theories). Instead the genome size is suggested to evolve until the loss of DNA through more frequent small deletions is equal to the rate of DNA gain through more frequent long insertions. The empirical basis for this theory is the finding of a strong correlation and of a clear power-function relationship between the rate of mutational DNA loss (per bp) through small deletions and genome size in animals. Genome size scales as a negative 1.3 power function of the deletion rate per nucleotide. Such a relationship is not predicted by either adaptive or junk DNA theories. However, if genome size is maintained at equilibrium by the balance of mutational forces, this empirilical relationship can be readily accommodated. Within this framework, this finding would imply that the rate of DNA gain through large insertions scales up a quarter-power function of genome size. On this view, as genome size grows, the rate of growth through large insertions is increasing as a quarter power function of genome size and the rate of DNA loss through small deletions increases linearly, until eventually, at the stable equilibrium genome size value, rates of growth and loss equal each other. The current data also suggest that the long-term variation is genome size in animals is brought about to a significant extent by changes in the intrinsic rates of DNA loss through small deletions. Both the origin of mutational biases and the adaptive consequences of such a mode of evolution of genome size are discussed.

Base Sequence↗