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PubMed2000

Grazing optimization, nutrient cycling, and spatial heterogeneity of plant-herbivore interactions: should a palatable plant evolve?

Can the evolution of plant defense lead to an optimal primary production? In a general theoretical model, Loreau (1995) and de Mazancourt et al. (1998, 1999) have shown that herbivory could increase primary production up to a moderate rate of grazing intensity through recycling of a limiting nutrient, provided several conditions are fulfilled. In the present paper, we assume: (1) grazing intensity is controlled by plants through their level of palatability; and (2) plant fitness is determined by its productivity. We explore the conditions under which such an optimal production may be reached through natural selection. We model two competing plant types that differ only in palatability and are distributed in a patchy landscape determined by the plant-herbivore interaction. Patch size is determined by herbivore behavior: herbivores recycle nutrient homogeneously within patches, but recycle nutrient proportionally to consumption between patches. The model shows that a strategy of intermediate palatability can be adaptive in response to a small herbivore that lives on and recycles nutrient around one or a few individual plants. For moderately small herbivores, plant palatability may evolve towards one of two local convergent strategies, depending on the initial conditions. For medium- to large-sized herbivores, the nonpalatable strategy is always selected. We discuss the functional and evolutionary implications of these results, and suggest that the traditional dichotomy describing antagonistic and mutualistic interactions may be misleading.

Adaptation, Physiological↗
PubMed2002

Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat.

The classic wheat evolutionary history is one of adaptive radiation of the diploid Triticum/Aegilops species (A, S, D), genome convergence and divergence of the tetraploid (Triticum turgidum AABB, and Triticum timopheevii AAGG) and hexaploid (Triticum aestivum, AABBDD) species. We analyzed Acc-1 (plastid acetyl-CoA carboxylase) and Pgk-1 (plastid 3-phosphoglycerate kinase) genes to determine phylogenetic relationships among Triticum and Aegilops species of the wheat lineage and to establish the timeline of wheat evolution based on gene sequence comparisons. Triticum urartu was confirmed as the A genome donor of tetraploid and hexaploid wheat. The A genome of polyploid wheat diverged from T. urartu less than half a million years ago (MYA), indicating a relatively recent origin of polyploid wheat. The D genome sequences of T. aestivum and Aegilops tauschii are identical, confirming that T. aestivum arose from hybridization of T. turgidum and Ae. tauschii only 8,000 years ago. The diploid Triticum and Aegilops progenitors of the A, B, D, G, and S genomes all radiated 2.5-4.5 MYA. Our data suggest that the Acc-1 and Pgk-1 loci have different histories in different lineages, indicating genome mosaicity and significant intraspecific differentiation. Some loci of the S genome of Aegilops speltoides and the G genome of T. timophevii are closely related, suggesting the same origin of some parts of their genomes. None of the Aegilops genomes analyzed is a close relative of the B genome, so the diploid progenitor of the B genome remains unknown.

Acetyl-CoA Carboxylase↗
PubMedDate not supplied

Plastids and protein targeting.

Plastids with two bounding membranes--as exemplified by red algae, green algae, plants, and glaucophytes--derive from primary endosymbiosis; a process involving engulfment and retention of a cyanobacterium by a phagotrophic eukaryote. Plastids with more than two bounding membranes (such as those of euglenoids, dinoflagellates, heterokonts, haptopytes, apicomplexa, cryptomonads, and chlorarachniophytes) probably arose by secondary endosymbiosis, in which a eukaryotic alga (itself the product of primary endosymbiosis) was engulfed and retained by a phagotroph. Secondary endosymbiosis transfers photosynthetic capacity into heterotrophic lineages, has apparently occurred numerous times, and has created several major eukaryotic lineages comprising upwards of 42,600 species. Plastids acquired by secondary endosymbiosis are sometimes referred to as "second-hand." Establishment of secondary endosymbioses has involved transfer of genes from the endosymbiont nucleus to the secondary host nucleus. Limited gene transfer could initially have served to stabilise the endosymbioses, but it is clear that the transfer process has been extensive, leading in many cases to the complete disappearance of the endosymbiont nucleus. One consequence of these gene transfers is that gene products required in the plastid must be targeted into the organelle across multiple membranes: at least three for stromal proteins in euglenoids and dinoflagellates, and across five membranes in the case of thylakoid lumen proteins in plastids with four bounding membranes. Evolution of such targeting mechanisms was obviously a key step in the successful establishment of each different secondary endosymbiosis. Analysis of targeted proteins in the various organisms now suggests that a similar system is used by each group. However, rather than interpreting this similarity as evidence of an homologous origin, I believe that targeting has evolved convergently by combining and recycling existing protein trafficking mechanisms already existing in the endosymbiont and host. Indeed, by analyzing the multiple motifs in targeting sequences of some genes it is possible to infer that they originated in the plastid genome, transferred from there into the primary host nucleus, and subsequently moved into the secondary host nucleus. Thus, each step of the targeting process in "second-hand" plastids recapitulates the gene's previous intracellular transfers.

Animals↗
PubMed1990

Gene conversion, linkage, and the evolution of repeated genes dispersed among multiple chromosomes.

The evolution of the probabilities of genetic identity within and between the loci of a multigene family dispersed among multiple chromosomes is investigated. Unbiased gene conversion, equal crossing over, random genetic drift, and mutation to new alleles are incorporated. Generations are discrete and nonoverlapping; the diploid, monoecious population mates at random. The linkage map is arbitrary, but the same for every chromosome; the dependence of the probabilities of identity on the location on each chromosome is formulated exactly. The greatest of the rates of gene conversion, random drift, and mutation is epsilon much less than 1. Under the assumption of loose linkage (i.e., all the crossover rates greatly exceed epsilon, though they may still be much less than 1/2), explicit approximations are obtained for the equilibrium values of the probabilities of identity and of the linkage of disequilibria. The probabilities of identity are of order one [i.e., O(1)] and do not depend on location; the linkage disequilibria are of O(epsilon) and, within each chromosome, depend on location through the crossover rates. It is demonstrated also that the ultimate rate and pattern of convergence to equilibrium are close to that of a much simpler, location-independent model. If intrachromosomal conversion is absent, the above results hold even without the assumption of loose linkage. In all cases, the relative errors are of O(epsilon). Even if the conversion rate between genes on nonhomologous chromosomes is considerably less than between genes on the same chromosome or homologous chromosomes, the probabilities of identity between the former genes are still almost as high as those between the latter, and the rate of convergence is still not much less than with equal conversion rates. If the crossover rates are much less than 1/2, then most of the linkage disequilibrium is due to intrachromosomal conversion. If linkage is loose, the reduction of the linkage disequilibria to O(epsilon) requires only O(-ln epsilon) generations.

Alleles↗
PubMed1992

A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly.

The evolutionary relationships of the various orders of placental mammals remain an issue of uncertainty and controversy. Molecular studies of mammalian phylogeny at the DNA level that include more than just a few orders are still relatively meager. Here we report results on mammalian phylogeny deduced from the coding sequence of the single-copy nuclear gene for the interphotoreceptor retinoid binding protein (IRBP). Analysis of 13 species representing eight eutherian orders and one marsupial yielded results that falsify the hypothesis that megachiropteran bats are "flying primates," only convergently resembling microchiropteran bats. Instead, in agreement with more traditional views, as well as those from other recent molecular studies, the results strongly support a monophyletic Chiroptera (micro- and megabats grouped together). The IRBP results also offer some rare molecular support for the Glires concept, in which rodents and lagomorphs form a superordinal grouping. Also in congruence with other recent molecular evidence, IRBP sequences do not support the view of a superorder Archonta that includes Chiroptera along with Dermoptera (flying lemur), Scandentia (tree shrew), and Primates. IRBP was not however, without its shortcomings as a molecular phylogenetic system: high levels of homoplasy, evident in the marsupial outgroup, did not allow us to properly root the tree, and several of the higher level eutherian clades were only weakly supported (e.g., a Carnivora/Chiroptera clade and an Artiodactyla/Carnivora/Chiroptera clade). We suggest that these shortcomings may be diminished as the phylogenetic density of the data set is increased.

Amino Acid Sequence↗
PubMed2002

A Jurassic mammal from South America.

The Jurassic period is an important stage in early mammalian evolution, as it saw the first diversification of this group, leading to the stem lineages of monotremes and modern therian mammals. However, the fossil record of Jurassic mammals is extremely poor, particularly in the southern continents. Jurassic mammals from Gondwanaland are so far only known from Tanzania and Madagascar, and from trackway evidence from Argentina. Here we report a Jurassic mammal represented by a dentary, which is the first, to our knowledge, from South America. The tiny fossil from the Middle to Late Jurassic of Patagonia is a representative of the recently termed Australosphenida, a group of mammals from Gondwanaland that evolved tribosphenic molars convergently to the Northern Hemisphere Tribosphenida, and probably gave rise to the monotremes. Together with other mammalian evidence from the Southern Hemisphere, the discovery of this new mammal indicates that the Australosphenida had diversified and were widespread in Gondwanaland well before the end of the Jurassic, and that mammalian faunas from the Southern Hemisphere already showed a marked distinction from their northern counterparts by the Middle to Late Jurassic.

Animals↗
PubMed1983

The embryonic development of the cortical plate in reptiles: a comparative study in Emys orbicularis and Lacerta agilis.

From the earliest stage of its ontogenesis, the mammalian cerebral cortex displays a remarkable cytoarchitectonic organization, with its neurons oriented radially within the cortical plate (CP). It is not known whether this radial organization of cortical neurons is characteristic of every cerebral cortex or whether it reflects a progressive phylogenetic acquisition. In order to study this question, the embryonic development of the cortex has been examined in reptiles, where it is the most primitive. Two species, Emys orbicularis and Lacerta agilis, representative of the two principal reptilian orders (chelonians and squamates), have been studied with histological methods. Golgi impregnation, and electron microscopy. Very similar patterns of cell proliferation, migration, maturation, and synaptogenesis have been observed. However, important species differences are present in the cellular organization of the cortical plate. Whereas in Emys the structure of the cortical plate is rudimentary, in Lacerta it appears well developed and quite reminiscent of its mammalian counterpart. Preliminary comparisons with embryological preparations of Sphenodon and Crocodilus niloticus show that the organization of the cortical plate displays significant variations among the different reptilian groups. The present results suggest that the radial organization of cortical neurons is not an all or nothing phenomenon but has been acquired independently and is thus a case of homoplasy, probably due to convergence (Northcutt, 81). Several possible implications of these findings are discussed and a working hypothesis based on the role of radial glial cells in the formation of cytoarchitectonic patterns (Rakic, '80) is presented.

Animals↗
PubMed2002

Niche-related learning in laboratory paradigms: the case of maze behavior in Norway rats.

The general hypothesis underlying this paper is that behavior in traditional paradigms of laboratory learning is based on niche-related mechanisms. The specific hypothesis is that the behavior of Norway rats in laboratory mazes is based on niche-related mechanisms related to trail following and navigating. I evaluate seven types of evidence for this hypothesis: (a) resemblance of maze behavior to behavior in unconstrained settings; (b) importance of experimenter tuning of apparatus and procedures; (c) overdetermination of laboratory behavior; (d) reverse-engineering of niche-related mechanisms from laboratory data; (e) prediction of laboratory results from ecological data; (f) contribution of specific relative to general mechanisms; and (g) phylogenetic conservation and ecologically-based convergence and divergence of maze mechanisms. I conclude there is strong evidence for the hypothesis that behavior of rats in laboratory mazes is based on niche-related mechanisms. I suggest that a niche-related approach to laboratory learning paradigms has conceptual generality and the potential to facilitate connections with the study of neurophysiology, genetics, and evolution.

Animals↗
PubMed1994

Solution structure and dynamics of ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy.

A high-resolution solution structure of the GDP form of a truncated version of the ras p21 protein (residues 1-166) has been determined using NMR spectroscopy. Ras p21 is the product of the human ras protooncogene and a member of a ubiquitous eukaryotic gene family which is highly conserved in evolution. A virtually complete assignment (13C, 15N, and 1H), including stereospecific assignments of 54 C beta methylene protons and 10 C gamma methyl protons of valine residues, was obtained by analysis of three- and four-dimensional (3D and 4D) heteronuclear NMR spectra using a newly developed 3D/4D version of the ANSIG software. A total of 40 converged structures were computed from 3369 experimental restraints consisting of 3,167 nuclear Overhauser effect (NOE) derived distances, 14 phi and 54 chi 1 torsion angle restraints, 109 hydrogen bond distance restraints, and an additional 25 restraints derived from literature data defining interactions between the GDP ligand, the magnesium ion, and the protein. The structure in the region of residues 58-66 (loop L4), and to a lesser degree residues 30-38 (loop L2), is ill-defined. Analysis of the dynamics of the backbone 15N nuclei in the protein showed that residues within the regions 58-66, 107-109, and, to a lesser degree, 30-38 are dynamically mobile on the nanosecond time scale. The root mean square (rms) deviations between the 40 solution structures and the mean atomic coordinates are 0.78 A for the backbone heavy atoms and 1.29 A for all non-hydrogen atoms if all residues (1-166) are included in the analysis. If residues 30-38 and residues 58-66 are excluded from the analysis, the rms deviations are reduced to 0.55 and 1.00 A, respectively. The structure was compared to the most highly refined X-ray crystal structure of ras p21.GDP (1-189) [Milburn, M. V., Tong, L., de Vos, A. M., Brünger, A. T., Yamaizumi, Z., Nishimura, S., & Kim, S.-H. (1990) Science 24, 939-945]. The structures are very similar except in the regions found to be mobile by NMR spectroscopy. In addition, the second alpha-helix (helix-2) has a slightly different orientation. The rms deviation between the average of the solution structures and the X-ray crystal structure is 0.94 A for the backbone heavy atoms if residues 31-37 and residues 59-73 are excluded from the analysis.

Chemical Phenomena↗
PubMed1988

Somatic immunoglobulin sequence divergence and its implications for studies of evolutionary divergence.

The divergence of immunoglobulin genes due to somatic mutation provides a natural example of DNA sequence divergence. This divergence was examined to gain insight into the processes of evolution and the determinants of the variance-to-mean ratio of sequence divergence. Normally, this ratio is found to be larger than expected (1.0 under Poisson assumptions) for the evolutionary divergence or most genes. Although not significantly less than one, all seven groups of immunoglobulin amino acid sequences have ratios smaller than expected, contrary to the evolutionary pattern generally observed. The substitutions in the immunoglobulin genes appear to be highly nonrandom and an excess of parallel changes (the major nonrandom feature of these mutations) is shown to cause smaller ratios. Because convergent or parallel mutations are often observed in the evolutionary divergence of genes, this suggests that forces causing the large observed ratios may actually have to be more powerful than previously expected. Further, since selection is one of the likely causes of parallel mutations, it should be noted that selection could significantly decrease the variance-to-mean ratio. The high frequency of parallel mutations and their resulting effects, as observed in the immunoglobulin genes, suggest that only poor inferences of sequence divergence can be made without actual knowledge of the ancestral sequence.

Amino Acid Sequence↗
PubMed2001

Using artificial evolution and selection to model insect navigation.

BACKGROUND: An animal's behavioral strategies are often constrained by its evolutionary history and the resources available to it. Artificial evolution allows one to manipulate such constraints and explore how they influence evolved strategies. Here we compare the navigational strategies of flying insects with those of artificially evolved "animats" endowed with various motor architectures. Using evolutionary algorithms, we generated artificial neural networks that controlled a virtual animat's navigation within a 2D, simulated world. Like a flying insect, the animat possessed motors that generated thrust and torque, a compass, and visual sensors. Some animats were limited to forward motion, while others could also move sideways. Animats were selected for the precision with which they reached a target specified by a visual landmark. RESULTS: Animats given sideways motors could alter flight direction without changing body orientation and evolved strategies similar to those of flying bees or wasps performing the same task. Both animats and insects first aimed at the landmark. In the last phase, both adopted a fixed body orientation and adjusted their position to keep the landmark at a fixed retinal location. Animats unable to uncouple flight direction and body orientation evolved subtly different strategies and performed less robustly. CONCLUSIONS: This convergence between the navigational strategies of animals and animats suggests that the insect's strategies are primarily an adaptation to the demands of using visual information and compass direction to reach a position in space and that they are not significantly compromised by the insect's evolutionary history.

Animals↗
PubMed2004

Mutation and evolution of microsatellite loci in Neurospora.

The patterns of mutation and evolution at 13 microsatellite loci were studied in the filamentous fungal genus Neurospora. First, a detailed investigation was performed on five microsatellite loci by sequencing each microsatellite, together with its nonrepetitive flanking regions, from a set of 147 individuals from eight species of Neurospora. To elucidate the genealogical relationships among microsatellite alleles, repeat number was mapped onto trees constructed from flanking-sequence data. This approach allowed the potentially convergent microsatellite mutations to be placed in the evolutionary context of the less rapidly evolving flanking regions, revealing the complexities of the mutational processes that have generated the allelic diversity conventionally assessed in population genetic studies. In addition to changes in repeat number, frequent substitution mutations within the microsatellites were detected, as were substitutions and insertion/deletions within the flanking regions. By comparing microsatellite and flanking-sequence divergence, clear evidence of interspecific allele length homoplasy and microsatellite mutational saturation was observed, suggesting that these loci are not appropriate for inferring phylogenetic relationships among species. In contrast, little evidence of intraspecific mutational saturation was observed, confirming the utility of these loci for population-level analyses. Frequency distributions of alleles within species were generally consistent with the stepwise mutational model. By comparing variation within species at the microsatellites and the flanking-sequence, estimated microsatellite mutation rates were approximately 2500 times greater than mutation rates of flanking DNA and were consistent with estimates from yeast and fruit flies. A positive relationship between repeat number and variance in repeat number was significant across three genealogical depths, suggesting that longer microsatellite alleles are more mutable than shorter alleles. To test if the observed patterns of microsatellite variation and mutation could be generalized, an additional eight microsatellite loci were characterized and sequenced from a subset of the same Neurospora individuals.

Base Sequence↗
PubMed2003

Bifurcation analysis of an orientational aggregation model.

We consider an integro-differential equation for the evolution of a function f on the circle, describing an orientational aggregation process. In the first part we analyze generic bifurcations of steady-state solutions when a single eigenvalue changes sign. Lyapunov-Schmidt reduction leads to the bifurcation equation which is solved explicitly by formal power series. We prove that these series have positive radius of convergence. Two examples exhibit forward and backward bifurcations, respectively. In the second part we assume that the first and second eigenvalues become positive. Again we use Lyapunov-Schmidt reduction to arrive at the reduced bifurcation system from which we get the bifurcating branches as power series. We calculate the two most important parameters of the reduced system for two examples; one of them has interesting mode interactions which lead to various kinds of time-periodic solutions.

Actin Cytoskeleton↗
PubMed2004

Evolutionarily stable transition rates in a stage-structured model. An application to the analysis of size distributions of badges of social status.

This paper deals with the adaptive dynamics associated to a hierarchical non-linear discrete population model with a general transition matrix. In the model, individuals are categorized into n dominance classes, newborns lie in the subordinate class, and it is considered as evolutionary trait a vector eta of probabilities of transition among classes. For this trait, we obtain the evolutionary singular strategy and prove its neutral evolutionary stability. Finally, we obtain conditions for the invading potential of such a strategy, which is sufficient for the convergence stability of the latter. With the help of the previous results, we provide an explanation for the bimodal distribution of badges of status observed in the Siskin (Carduelis spinus). In the Siskin, as in several bird species, patches of pigmented plumage signal the dominance status of the bearer to opponents, and central to the discussion on the evolution of status signalling is the understanding of which should be the frequency distribution of badge sizes. Though some simple verbal models predicted a bimodal distribution, up to now most species display normal distributions and bimodality has only been described for the Siskin. In this paper, we give conditions leading to one of these two distributions in terms of the survival, fecundity and aggression rates in each dominance class.

Animals↗
PubMed1989

Evolutionary learning and hierarchical Markov systems.

The observation is made that various forms of evolutionary learning systems and classical evolutionary processes can be formally described as hierarchical systems of Markov processes. This leads to a simplification of issues such as convergence criteria and limiting behavior of such systems. The hierarchical structures in question are derived from the notion of rules and meta-rules for moving on graphs studied previously.

Biological Evolution↗
PubMed1995

Convergent designs for electrogenesis and electroreception.

New- and old-world tropical electric fish lack a common electrical ancestor, suggesting that the mechanisms of signal generation and recognition evolved independently in the two groups. Recent research on convergent designs for electrogenesis and electroreception has focused on the structure of electric organs, the neural circuitry controlling the pacemaker driving the electric organ, and the neural circuitry underlying time coding of electric waveforms.

Animals↗
PubMed2006

Comparative neurophysiology: an electric convergence in fish.

Two lineages of fishes convergently evolved electric organs; recent research has shown that they independently took advantage of an extra copy of a sodium channel gene to alter channel kinetics for the electric organ discharge.

Amino Acid Sequence↗