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PubMed1981

[Molineinae parasites of mammals].

A revision of Molineinae parasitic in mammals is proposed with the following taxonomic changes: 1) Removal of the genera Ortleppstrongylus Durette-Desset, 1970, from a Bathyergidae of South Africa and Moguranema Yamaguti, 1941, from a Talpidae insectivore of Japan. Both genera are placed in Trichostrongylidae-Cooperiinae for the first, Trichostrongylidae-Haemonchinae for the second. 2) Division of the genus Molineus into two groups separated principally by the arrangement of the bursal rays. a) Molineus sensu stricto, parasitic in Carnivores throughout the world and in South american monkeys; with rays 2 and 3 grouped together and parallel, and with rays 4 equidistant between the 3 and 5. b) Brygoonema n. gen., Hugotnema, n. gen., Nochtia (Nochtia) Travassos and Vogelsang, 1929, and Nochtia (Tenrecola) n. sub. gen., parasitic in Tenrecoidea insectivores of Madagascar and Africa, and Erinacoidea insectivores and lemurs of Africa, with rays 2 and 3 diverging and the papilla of the ray 4 closer to the 3 than the 5. 3) Resurrection of the genus Shattuckius Sandground, 1938 parasitic in Solenodon of Hispaniola. 4) Synonymy of Hooperstrongylus Lie Kian Joe et Ow Yang, 1963 with Pithecostrongylus Lubimov, 1930. The species Molineus vogelianus De Muro, 1933 and M. teocchii Quentin, 1970, parasitic in lemurs are placed in Pithecostrongylus. Hypotheses on the evolution of the Molineinae of mammals are presented, based primarily on the evolution of the bursa. From the basic pattern observed in Molineinae of amphibians and reptiles (rays 2-3 grouped, ray 4 with common base with the 5-6, rays 5-6 grouped), evolution has followed two principal lines: 1) Displacement of the papilla of the ray 4 towards the anterior and disappearance of the common base with the 5-6. 2) Extremities of rays 2-3 and 5-6 converging forming two separate pincer-like formations. Following these and other secondary characters, an evolutionary hierarchy is proposed for the 13 genera. The parasites of Tenrecoidea of Madagascar are apparently of central importance in this evolution. A list of genera and species is given.

Animals↗
PubMed2003

Extinction and re-evolution of similar adaptive types (ecomorphs) in Cenozoic North American ungulates and carnivores reflect van der Hammen's cycles.

Numerous patterns in periodicity (e.g., climate, extinction, and sedimentary cycles) and evolutionary change (e.g., chronofaunas and coordinated stasis) have been described based on aspects of the geologic record. Recently, convergent occurrences of faunal types or "repeating faunas" have received attention, but a highly specific, iterative pattern was first reported over 40 years ago. In the late 1950s, van der Hammen described climatic/floral cycles on the order of six million years based on a succession of A, B, and C pollen community types in South America. These A-B-C cycles are also seen in the replacement pattern of particular carnivore and ungulate adaptive types in Cenozoic North America as reported by Martin in the 1980s. For example, in the last 36 million years, there were four iterations of a sabertooth cat ecomorph independently evolving, dominating the niche through an A-B-C cycle, and then going extinct. Here we show further support for the existence of these cycles in the dominance turnover in hippo and dog ecomorphs in the North American Cenozoic. Shared patterns of extinction and re-evolution of adaptive types among plants and mammals across two continents suggest a global mechanism, which appears to be climatic change. Iterative climatic cycles of various scales may form a predictive framework for understanding fundamental patterns in the geologic record, such as radiations, extinction, rates of change, convergence, and sedimentary cycles.

Acclimatization↗
PubMed2005

Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses.

The human papillomaviruses (HPVs) have long been thought to follow a monophyletic pattern of evolution with little if any evidence for recombination between genomes. On the basis of this model, both oncogenicity and tissue tropism appear to have evolved once. Still, no systematic statistical analyses have shown whether monophyly is the rule across all HPV open reading frames (ORFs). We conducted a taxonomic analysis of 59 mucosal/genital HPVs using whole-genome and sliding-window similarity measures; maximum-parsimony, neighbor-joining, and Bayesian phylogenetic analyses; and localized incongruence length difference (LILD) analyses. The algorithm for the LILD analyses localized incongruence by calculating the tree length differences between constrained and unconstrained nodes in a total-evidence tree across all HPV ORFs. The process allows statistical evaluation of every ORF/node pair in the total-evidence tree. The most significant incongruence was observed at the putative high-risk (i.e., cancer-associated) node, the common oncogenic ancestor for alpha HPV species 9 (e.g., HPV type 16 [HPV16]), 11, 7 (e.g., HPV18), 5, and 6. Although these groups share early-gene homology, including high degrees of similarity among E6 and E7, groups 9 and 11 diverge from groups 7, 5, and 6 with respect to L2 and L1. The HPV species groups primarily associated with cervical and anogenital cancers appear to follow two distinct evolutionary paths, one conferred by the early genes and another by the late genes. The incongruence in the genital HPV phylogeny could have occurred from an early recombination event, an ecological niche change, and/or asymmetric genome convergence driven by intense selection. These data indicate that the phylogeny of the oncogenic HPVs is complex and that their evolution may not be monophyletic across all genes.

DNA Viruses↗
PubMed2005

Parallel genotypic adaptation: when evolution repeats itself.

Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together.

Adaptation, Biological↗
PubMed1994

Symmetry, beauty and evolution.

Humans and certain other species find symmetrical patterns more attractive than asymmetrical ones. These preferences may appear in response to biological signals, or in situations where there is no obvious signalling context, such as exploratory behaviour and human aesthetic response to pattern. It has been proposed that preferences for symmetry have evolved in animals because the degree of symmetry in signals indicates the signaller's quality. By contrast, we show here that symmetry preferences may arise as a by-product of the need to recognize objects irrespective of their position and orientation in the visual field. The existence of sensory biases for symmetry may have been exploited independently by natural selection acting on biological signals and by human artistic innovation. This may account for the observed convergence on symmetrical forms in nature and decorative art.

Animals↗
PubMed1999

Reelin expression during embryonic brain development in lacertilian lizards.

The expression of reelin mRNA and protein was studied during embryonic brain development in the lacertilian lizards L. viridis and L. galloti, by using radioactive in situ hybridization and immunohistochemistry. At all stages studied, high reelin expression was consistently found in the olfactory bulb, in the lateral cortex, and in neurons of the marginal zone and subplate of medial and dorsal cortical sectors. In the dorsal ventricular ridge (DVR), reelin expression was confined to deeply located, large cells which were more abundant in the caudal than the rostral part of the DVR. In the diencephalon, the ventral lateral geniculate complex and the perirotundal were strongly positive, whereas other nuclei were mostly negative. High reelin signal was associated with some layers in the tectum, with the torus semicircularis, cerebellar granule cell layers, and the ventral horn of the spinal cord. A more moderate signal was detected in the septal nuclei, striatum, retina, habenular nuclei, preoptic and periventricular hypothalamic components, and in reticular nuclei of the mid- and hindbrain. The medial and dorsal cortical plate and Purkinje cells were reelin-negative but expressed disabled-1 (Dab1) mRNA. When they are compared with reelin expression during mammalian brain development, our data reveal an evolutionarily conserved canvas of reelin expression, as well as significant differences, particularly in developing cortical fields. The developing lizard cortex differs from that of turtles, birds, crocodiles, and mammals in that it displays heavy reelin expression not only in neurons of the marginal zone that might be homologous to mammalian Cajal-Retzius cells, but also in subplate neurons. This difference in the pattern of reelin expression suggests that the elaborate radial organization of the lacertilian cortical plate, somewhat reminiscent of its mammalian counterpart, results from evolutionary convergence. Our data lend support to the hypothesis that the reelin signaling pathway played a significant role during cortical evolution.

Animals↗
PubMed1981

Comparative scanning electron microscopic investigations of the sensory epithelia in the teleost sacculus and lagena.

Scanning electron microscopic studies were conducted on the sensory epithelia of the auditory portions of the ears in teleost species representing wide taxonomic diversity. A number of the features of the ears investigated resembled features found in other teleost species, although some major exceptions to earlier patterns were found, particularly in the saccular sensory epithelium. The saccular maculae of all but one species contained basically similar ciliary bundles on the sensory hair cells while there was some significant variation on the lagenar maculae. Hair cell orientation patterns on the sacculus contained four orientation groups in all of the species, other than the mormyrid, Gnathonemus, which only had two groups. Lagenar maculae had two orientation groups, and the orientation patterns were similar to one another. The most divergent form of lagenar macula was found in gnathonemus. These data, combined with data from earlier investigations, provide a broad overview of the surface features of the ear in teleost fishes. Most significantly, it now appears that there are at least five different saccular hair cell orientation patterns among teleost fishes, and all of these patterns are found spread through many major teleost taxa. While there is some similarity in ear structures among some groups of closely related species, such as the Elopomorpha and the Gadiformes, it is becoming more apparent that there is extensive convergence in a number of features of he teleost ear that most likely reflect similar selective pressures during the evolution of the ear. The nature of these selective pressures, however, are not well understood.

Acoustic Maculae↗
PubMed2006

Predominance of clonal reproduction, but recombinant origins of new genotypes in the free-floating aquatic bladderwort Utricularia australis f. tenuicaulis (Lentibulariaceae).

Aquatic plants are a biological group sharing several adaptations to aquatic conditions. The most striking evolutionary convergence in this group is the extensive reliance on clonal reproduction, which largely determines the patterns and process of evolution in aquatic plants. Utricularia australis f. tenuicaulis is a free-floating aquatic bladderwort that reproduces both sexually via seeds and clonally via turions and shoot fragments. Amplified fragment length polymorphism analysis was conducted on 267 ramets collected from 30 populations in Japan. The genotypic diversity within populations was extremely low, regardless of the geographical distribution range: the mean number of genotypes per population (G) was 1.4 and the mean genotypic diversity (D), including monoclonal populations, was 0.17. In contrast to the predominance of a few clones within populations, many of the populations investigated had different genotypes; a large portion of the genetic variation was explained by variation among populations. Character compatibility analysis clearly revealed that somatic mutations did not contribute to the origin of genotypic diversity in this aquatic bladderwort; instead, rare-to-sporadic sexual reproduction probably generated new genotypes. Thus, future studies should examine the role of sexual reproduction in this species from the viewpoint of long-term evolutionary benefits.

Ecosystem↗
PubMed2004

Intramolecular orbital alignments in serine protease/protein inhibitor complexes.

By an analysis of PDB crystal structures, the mean conformations of protein strands bound in serine protease active sites are shown to contain extensively aligned atomic orbitals. The active-serine-bearing segment of each enzyme (subtilisin BPN' and beta-trypsin) also contains such alignments. The participating orbitals are almost identical in each system. All of the alignments converge on the targeted linkage. They suggest that a kind of through-strand polarizability is being optimized by evolution, presumably due to corresponding benefits in proteolysis rate. Such polarizability would help to explain the high values of kcat seen for long oligopeptide substrates. The idea predicts long substrates to be relatively reactive even under non-enzymatic conditions, which in fact they are.

Binding Sites↗
PubMed2006

Physical origins of protein superfamilies.

In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using a standard exact three-dimensional lattice model we evolve sequences starting from random ones and determine the exact native structure after each mutation. Acceptance of mutations is biased to select for stable proteins. We found that certain structures, "wonderfolds", are independently discovered numerous times as native states of stable proteins in many unrelated runs of selection. The strong dependence of lattice fold usage on the structural determinant of designability quantitatively reproduces uneven fold usage in natural proteins. Diversity of sequences that fold into wonderfold structures gives rise to superfamilies, i.e. sets of dissimilar sequences that fold into the same or very similar structures. The present work establishes a model of pre-biotic structure selection, which identifies dominant structural patterns emerging upon optimization of proteins for survival in a hot environment. Convergently discovered pre-biotic initial superfamilies with wonderfold structures could have served as a seed for subsequent biological evolution involving gene duplications and divergence.

Amino Acid Sequence↗
PubMed2001

IR and UV spectroscopic data for polyynes: predictions for long carbon chain compounds in Titan's atmosphere.

A better understanding of the complex organic chemistry occurring in the methane rich atmosphere of Titan can be achieved via the comparison of observations with results obtained by theoretical models. Available observations are still few but their analysis requires the knowledge of a large set of data, namely frequencies and absolute band intensities. Cross sections are also needed to develop the chemical schemes of photochemical models, in particular the schemes leading to the formation of haze particles visible on Titan. Unfortunately, some of these parameters are not well known, especially if one takes into account the extreme physical conditions of the studied object. This lack of data is particularly enhanced for polyynes because these compounds are highly unstable at the usual pressure and temperature conditions of a laboratory and therefore are very difficult to study. We have developed UV and IR studies, coupling experimental and theoretical approaches, in order to extrapolate the parameters available for short polyynes to longer carbon chains. In the mid-UV range, when the length of the chain increases, the absorption system of polyynes is shifted to longer wavelength and its oscillator strength increases linearly. In the IR range, with the increase of the number of carbon bonds, the positions of the CCC and CCH bending modes shift to lower energy, the latest converging rapidly to a fixed value of 620.5 cm-1 for an infinite length polyyne. Implications for detection and evolution of polyynes in Titan's atmosphere are emphasised.

Acetylene↗
PubMed2005

Shadows of culture in psychosis in south India: a methodological exploration and illustration.

Transcultural studies suggest a possible influence of culture on the course and outcome of schizophrenia. However, the notion of culture remains ill-defined in these studies; most often, hypotheses regarding protective factors seem to derive more from stereotyped visions of cultural differences than be empirically based. Explorative studies conducted in south India consider subjective experience as a key mediating variable between culture and course and outcome in schizophrenia. They explore patients and relatives experience and its evolution and aim at identifying the explicit and implicit references to culture throughout the narratives. Ethnographically oriented data collected through an open-ended Turning Point/Period Interview systematically reconstructs the perceived evolution of signs, coping, explanations, reactions and help-seeking from different perspectives. This paper examines the degree of convergence and divergence between narratives collected from a small sample of female schizophrenic patients and one of their relatives. A high degree of convergence at the level of symptoms and differences in their narrative construction are observed.

Adaptation, Psychological↗
PubMed2006

Macroevolution of plant defense strategies.

Theories of plant defense expression are typically based on the concepts of tradeoffs among traits and of phylogenetic conservatism within clades. Here, I review recent developments in phylogenetic approaches to understanding the evolution of plant defense strategies and plant-herbivore coevolutionary interactions. I focus particularly on multivariate defense against insect herbivores, which is the simultaneous deployment of multiple traits, often arranged as convergently evolved defense syndromes. Answering many of the outstanding questions in the biology of plant defense will require generating broad hypotheses that can be explicitly tested by using comparative approaches and interpreting phylogenetic patterns. The comparative approach has wide-spread potential to reinvigorate tests of classic hypotheses about the evolution of interspecific interactions.

Animals↗
PubMed1981

An evaluation of the phylogenetic position of the dinoflagellate Crypthecodinium cohnii based on 5S rRNA characterization.

Partial nucleotide sequences for the 5S and 5.8S rRNAs from the dinoflagellate Crypthecodinium cohnii have been determined, using a rapid chemical sequencing method, for the purpose of studying dinoflagellate phylogeny. The 5S RNA sequence shows the most homology (75%) with the 5S sequences of higher animals and the least homology (less than 60%) with prokaryotic sequences. In addition, it lacks certain residues which are highly conserved in prokaryotic molecules but are generally missing in eukaryotes. These findings suggest a distant relationship between dinoflagellates and the prokaryotes. Using two different sequence alignments and several different methods for selecting an optimum phylogenetic tree for selecting an optimum phylogenetic tree for a collection of 5S sequences including higher plants and animals, fungi, and bacteria in addition to the C. cohnii sequence, the dinoflagellate lineage was joined to the tree at the point of the plant-animal divergence well above the branching point of the fungi. This result is of interest because it implies that the well-documented absence in dinoflagellates of histones and the typical nucleosomal subunit structure of eukaryotic chromatin is the result of secondary loss, and not an indication of an extremely primitive state, as was previously suggested. Computer simulations of 5S RNA evolution have been carried out in order to demonstrate that the above-mentioned phylogenetic placement is not likely to be the result of random sequence convergence. We have also constructed a phylogeny for 5.8S RNA sequences in which plants, animals, fungi and the dinoflagellates are again represented. While the order of branching on this tree is the same as in the 5S tree for the organisms represented, because it lacks prokaryotes, the 5.8S tree cannot be considered a strong independent confirmation of the 5S result. Moreover, 5.8S RNA appears to have experienced very different rates of evolution in different lineages indicating that it may not be the best indicator of evolutionary relationships. We have also considered the existing biological data regarding dinoflagellate evolution in relation to our molecular phylogenetic evidence.

Animals↗
PubMed2003

Parallel functional changes in the digestive RNases of ruminants and colobines by divergent amino acid substitutions.

A morphological or physiological trait may appear multiple times in evolution. At the molecular level, similar protein functions may emerge independently in different lineages. Whether these parallel functional changes are due to parallel amino acid substitutions has been a subject of debate. Here, I address this question using digestive ribonucleases (RNases) of two groups of foregut-fermenting mammals: ruminant artiodactyls and colobine monkeys. The RNase1 gene was duplicated twice in ancestral ruminants at least 40 MYA, and it was also duplicated in the douc langur, an Asian colobine, approximately 4 MYA. After duplication, similar functional changes occurred in the ruminant and monkey enzymes. Interestingly, five amino acid substitutions in ruminant RNases that are known to affect its catalytic activity against double-stranded (ds) RNA did not occur in the monkey enzyme. Rather, a similar functional change in the monkey was caused by a different set of nine substitutions. Site-directed mutagenesis was used to make three of the five ruminant-specific substitutions in the monkey enzyme. Functional assays of these mutants showed that one of the three substitutions has a similar effect in monkeys, the second has a stronger effect, and the third has an opposite effect. These results suggest that (1) an evolutionary problem can have multiple solutions, (2) the same amino acid substitution may have opposite functional effects in homologous proteins, (3) the stochastic processes of mutation and drift play an important role even at functionally important sites, and (4) protein sequences may diverge even when their functions converge.

Amino Acid Sequence↗
PubMed2000

[Aspects and convergences in the evolutionary theory of biological selection and the development of psychosomatic theory].

Psychotherapeutic theories have a lamarcistic trait in interpreting psychogeneous symptoms and signs. In the theory of Ch. Darwin the mechanism of selection plays an important role to interpret evolutionary processes. According to the psychotherapeutic process early infant relation-ships, the relation between description and structure, the six components of the affect and the convergence between non-verbal interaction and motivation are important.

Biological Evolution↗