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PubMed2002

Gene family phylogenetics: tracing protein evolution on trees.

How have proteins taken on the remarkable diversity of biochemical and physiological functions necessary to create and maintain complex organisms? The majority of proteins are organized hierarchically into families and superfamilies, reflecting an ancient and continuing process of gene duplication and divergence. The techniques of molecular phylogenetics, developed to recover the nested hierarchy of taxa from character information in their gene sequences, can also reconstruct the evolutionary relationships among genes and provide a conceptual foundation for comparative evolutionary analysis of proteins and their functions. In this review, I outline the application of phylogenetic approaches to issues in gene family studies, beginning with the inference of phylogeny and the assessment of the two types of homology by which genes in a family can be related: orthology (common descent from a cladogenetic event) and paralogy (common descent from a gene duplication event). I show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of exon shuffling, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious sequence data being generated by molecular biology and genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.

Animals↗
PubMed2007

Song discrimination learning in zebra finches induces highly divergent responses to novel songs.

Perceptual biases can shape the evolution of signal form. Understanding the origin and direction of such biases is therefore crucial for understanding signal evolution. Many animals learn about species-specific signals. Discrimination learning using simple stimuli varying in one dimension (e.g. amplitude, wavelength) can result in perceptual biases with preferences for specific novel stimuli, depending on the stimulus dimensions. We examine how this translates to discrimination learning involving complex communication signals; birdsongs. Zebra finches (Taeniopygia guttata) were trained to discriminate between two artificial songs, using a Go/No-Go procedure. The training songs in experiment 1 differed in the number of repeats of a particular element. The songs in experiment 2 differed in the position of an odd element in a series of repeated elements. We examined generalization patterns by presenting novel songs with more or fewer repeated elements (experiment 1), or with the odd element earlier or later in the repeated element sequence (experiment 2). Control birds were trained with only one song. The generalization curves obtained from (i) control birds, (ii) experimental birds in experiment 1, and (iii) experimental birds in experiment 2 showed large and systematic differences from each other. Birds in experiment 1, but not 2, responded more strongly to specific novel songs than to training songs, showing 'peak shift'. The outcome indicates that learning about communication signals may give rise to perceptual biases that may drive signal evolution.

Acoustic Stimulation↗
PubMed1999

Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?

The Parabasala are a primitive group of protists divided into two classes: the trichomonads and the hypermastigids. Until recently, phylogeny and taxonomy of parabasalids were mainly based on the comparative analysis of morphological characters primarily linked to the development of their cytoskeleton. Recent use of molecular markers, such as small subunit (SSU) rRNA has led to now insights into the systematics of the Parabasala and other groups of prolists. An updated phylogeny based on SSU rRNA is provided and compared to that inferred from ultrastructural data. The SSU rRNA phylogeny contradicts the dogma equating simple characters with pumitive characters. Hypermastigids, possessing a hyperdeveloped cytoskeleton, exhibit the most basal emergence in the parabasalid lineage. Other observations emerge from the SSU rRNA analysis, such as the secondary loss of some cytoskeleton structures in all representatives of the Monocercomonadidae, the existence of secondarily free living taxa (reversibility of parasitism) and the evidence against the co-evolution of the endobiotic parabasalids and their animal hosts. According to phylogenies based on SSU rRNA, all the trichomonad families are not monophyletic groups, putting into question the validity of current taxonomic assignments. The precise branching order of some taxa remains unclear, but this issue can possibly be addressed by the molecular analysis of additional parabasalids. The goal of such additional analyses would be to propose, in a near future, a revision of the taxonomy of this group of protists that takes into account both molecular and morphological data.

Animals↗
PubMed1999

Srivastavanema cynocephali n. sp. (Nematoda, Trichostrongylina, Heligmosomoidea), a parasite of a dermopteran from Indonesia.

Srivastavanema cynocephali n. sp., a parasite of Cynocephalus variegatus (Dermoptera) from Indonesia, is described. This species is closely related to S. yapi Durette-Desset & Lim Boo Liat, 1975, in the characters of the synlophe at the mid-body and in the shape of the caudal bursa, but it is distinguished by the pattern of the synlophe in the posterior part of the body, very long, thin rays 2 and 3, a less developed genital cone, the absence of a membrane between left and right rays 6, and longer spicules. Its morphology is slightly less specialised than the four previously known species of the genus, which are all parasites of petauristines. The genus Srivastavanema (Singh, 1962) has a systematic position between the Heligmonellinae and the Brevistriatinae. Therefore, it may be a parasite of the Dermoptera which could have secondarily evolved within the Petauristinae. The Dermoptera may have played an important role in the evolution of the Heligmonellinae.

Animals↗
PubMed2003

Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference.

Vertebrates originated in the lower Cambrian. Their diversification and morphological innovations have been attributed to large-scale gene or genome duplications at the origin of the group. These duplications are predicted to have occurred in two rounds, the "2R" hypothesis, or they may have occurred in one genome duplication plus many segmental duplications, although these hypotheses are disputed. Under such models, most genes that are duplicated in all vertebrates should have originated during the same period. Previous work has shown that indeed duplications started after the speciation between vertebrates and the closest invertebrate, amphioxus, but have not set a clear ending. Consideration of chordate phylogeny immediately shows the key position of cartilaginous vertebrates (Chondrichthyes) to answer this question. Did gene duplications occur as frequently during the 45 Myr between the cartilaginous/bony vertebrate split and the fish/tetrapode split as in the previous approximately 100 Myr? Although the time interval is relatively short, it is crucial to understanding the events at the origin of vertebrates. By a systematic appraisal of gene phylogenies, we show that significantly more duplications occurred before than after the cartilaginous/bony vertebrate split. Our results support rounds of gene or genome duplications during a limited period of early vertebrate evolution and allow a better characterization of these events.

Animals↗
PubMed2001

Improving continuing medical education for surgical techniques: applying the lessons learned in the first decade of minimal access surgery.

OBJECTIVE: To examine the first decade of experience with minimal access surgery, with particular attention to issues of training surgeons already in practice, and to provide a set of recommendations to improve technical training for surgeons in practice. SUMMARY BACKGROUND DATA: Concerns about the adequacy of training in new techniques for practicing surgeons began almost immediately after the introduction of laparoscopic cholecystectomy. The concern was restated throughout the following decade with seemingly little progress in addressing it. METHODS: A preliminary search of the medical literature revealed no systematic review of continuing medical education for technical skills. The search was broadened to include educational, medical, and psychological databases in four general areas: surgical training curricula, continuing medical education, learning curve, and general motor skills theory. RESULTS: The introduction and the evolution of minimal access surgery have helped to focus attention on technical skills training. The experience in the first decade has provided evidence that surgical skills training shares many characteristics with general motor skills training, thus suggesting several ways of improving continuing medical education in technical skills. CONCLUSIONS: The educational effectiveness of the short-course type of continuing medical education currently offered for training in new surgical techniques should be established, or this type of training should be abandoned. At present, short courses offer a means of introducing technical innovation, and so recommendations for improving the educational effectiveness of the short-course format are offered. These recommendations are followed by suggestions for research.

Clinical Competence↗
PubMed1992

The origins of delusion.

Although delusion remains one of the basic problems in psychopathology, attempts to understand its pathogenesis have been dominated by unsubstantiated speculation. Previous psychodynamic formulations have recently given way to increasing interest in measurement, and testing of models derived from cognitive psychology. However, the formation, elaboration, and persistence of delusional beliefs may be an expression of the convergence of numerous causal influences, each exerting an effect at a different stage in the evolution of the belief. This review takes a structured overview of the literature, placing the numerous part theories and scant experimental findings within a general model of delusional development. It argues for a return to systematic research on symptoms rather than complex diagnostic formulations to facilitate better understanding of the development of delusional disorders and stimulate further interest in therapeutic intervention.

Delusions↗
PubMed1995

Diagnosis and treatment of acromegaly.

Acromegaly is a clinical syndrome that most typically is the manifestation of adenomatous hyperplasia of growth hormone-secreting cells in the pituitary gland. Although the primary process is benign, many disfiguring and potentially serious complications can develop. Because of the slow evolution of signs and symptoms, acromegaly can be a diagnostic challenge. Furthermore, many common diseases, such as hypertension, diabetes mellitus and hyperlipidemia, occur secondary to acromegaly but may initially be treated as isolated primary processes. Systematic evaluation should be performed if acromegaly is suspected. The diagnosis is based on clinical observation, hormonal assays and selective radiologic imaging. Acromegaly is most often treated surgically, but radiotherapy and drug therapy can be effective alternatives.

Acromegaly↗
PubMed2001

Conditions enabling the evolution of inter-agent signaling in an artificial world.

In the research described here we extend past computational investigations of animal signaling by studying an artificial world in which a population of initially noncommunicating agents evolves to communicate about food sources and predators. Signaling in this world can be either beneficial (e.g., warning of nearby predators) or costly (e.g., attracting predators or competing agents). Our goals were twofold: to examine systematically environmental conditions under which grounded signaling does or does not evolve, and to determine how variations in assumptions made about the evolutionary process influence the outcome. Among other things, we found that agents warning of nearby predators were a common occurrence whenever predators had a significant impact on survival and signaling could interfere with predator success. The setting most likely to lead to food signaling was found to be difficult-to-locate food sources that each have relatively large amounts of food. Deviations from the selection methods typically used in traditional genetic algorithms were also found to have a substantial impact on whether communication evolved. For example, constraining parent selection and child placement to physically neighboring areas facilitated evolution of signaling in general, whereas basing parent selection upon survival alone rather than survival plus fitness measured as success in food acquisition was more conducive to the emergence of predator alarm signals. We examine the mechanisms underlying these and other results, relate them to existing experimental data about animal signaling, and discuss their implications for artificial life research involving evolution of communication.

Animals↗
PubMed1990

Molecular evolution of class A beta-lactamases: phylogeny and patterns of sequence conservation.

We present a multiple alignment of the amino acid sequences of eight class A beta-lactamases and utilized it to propose a phylogeny, based on the nucleotide sequences of their corresponding genes. We have also used the alignment, together with the alpha-carbon co-ordinates of the Staphylococcus aureus protein, to search systematically for neighbouring residues that share the same pattern of conservation among the different members of the protein family. The distribution of invariant residues and of groups of residues with co-ordinate changes map, predominantly, at the region of the active site and at interfaces between structural elements, respectively. We have also contrasted the distribution of conserved residues with the positions which are known to differ in mutants and variants of class A beta-lactamases.

Amino Acid Sequence↗
PubMed2005

Cytogenetic repartition of chicken CR1 sequences evidenced by PRINS in Galliformes and some other birds.

Chicken repeat 1 (CR1) belongs to the non-long repeat class of retrotransposons. Nearly 100000 repeats interspersed in the chicken genome are subdivided into at least six distinct subfamilies, each 300 bp long and all sharing substantial sequence similarity. CR1-like elements were found in genomes from invertebrates to mammals, suggesting their importance for genome structure and/or function. Moreover, numerous data support the hypothesis of their implication in regulation of gene expression. So, the chromosomal distribution of these CR1 sequences in vertebrates is of great interest to improve our knowledge about the genome structure, function and evolution. A comparison of the cytogenetic distribution of CR1 sequences was performed by PRINS using consensus chicken primers on the chromosomes of chicken and species of several bird orders: Galliformes, Anseriformes, Passeriformes and Falconiformes. The study revealed that CR1 repeats are spread over nearly all chicken chromosomes with a higher density on the macrochromosomes and in particular with hot spots on subtelomeric regions of chromosome 1, 2, 3q, 4q, 5q. Their distribution on the macrochromosomes forms a kind of banding pattern, which was not systematically matched with R- or G-banding. This banding pattern appears to be conserved on the chromosomes of the Galliformes studied, irrespective of their karyotypes, rearranged or not. CR1 primers also show similar signals on the chromosomes of birds phylogenetically more distant (Anseriformes, Passeriformes and Falconiformes). This fact confirms the importance of these sequences at the large scale of bird evolution and in the chromosomal structure. The location of CR1 sequences, and in particular of the hot spots, mainly within the richest CG areas are in conformity with the data on an epigenetic role of these highly conserved sequences.

Animals↗
PubMed2005

PIRLs: a novel class of plant intracellular leucine-rich repeat proteins.

Leucine-rich repeat (LRR) proteins feature tandem leucine-rich motifs that form a protein-protein interaction domain. Plants contain diverse classes of LRR proteins, many of which take part in signal transduction. We have identified a novel family of nine Arabidopsis LRR proteins that, based on predicted intracellular location and LRR motif consensus sequence, are related to Ras-binding LRR proteins found in signaling complexes in animals and yeast. This new class has been named plant intracellular Ras group-related LRR proteins (PIRLs). We have characterized PIRL cDNAs, rigorously defined gene and protein annotations, investigated gene family evolution and surveyed mRNA expression. While LRR regions suggested a relationship to Ras group LRR proteins, outside of their LRR domains PIRLs differed from Ras group proteins, exhibiting N- and C-terminal regions containing low complexity stretches and clusters of charged amino acids. PIRL genes grouped into three subfamilies based on sequence relationships and gene structures. Related gene pairs and dispersed chromosomal locations suggested family expansion by ancestral genomic or segmental duplications. Expression surveys revealed that all PIRL mRNAs are actively transcribed, with three expressed differentially in leaves, roots or flowers. These results define PIRLs as a distinct, plant-specific class of intracellular LRR proteins that probably mediate protein interactions, possibly in the context of signal transduction. T-DNA knock-out mutants have been isolated as a starting point for systematic functional analysis of this intriguing family.

Amino Acid Sequence↗
PubMed2000

Perception of female reproductive state from vocal cues in a mammal species.

While acoustic signalling by males is known to affect male-male competition, mate attraction and the timing of ovulation, the extent to which sexual selection has shaped the evolution of female acoustic signals is poorly understood. Among mammals, experimental evidence indicates that females attract mating partners by using olfactory and visual signals to advertise their reproductive state. Whether or not males ascertain female reproductive state from vocal signals has, however, never been systematically tested. In this study, we use playbacks of recorded vocalizations to demonstrate that male Barbary macaques, Macaca sylvanus, can discriminate between female copulation calls given at different stages of the oestrous cycle, responding more strongly to those given around the time when conception is most likely to occur. Acoustic analysis suggests that the mean dominant frequency of call units and a number of temporal parameters could provide males with the information necessary to discern the proximity of ovulation in this way Our results provide the first experimental evidence that the calls of female mammals may contain information on reproductive state, which males can perceive and use in such a way as to increase their reproductive success.

Animals↗
PubMed2001

On the dispersion index of a Markovian molecular clock.

The number of nucleotide substitutions accumulated in a gene or in a lineage is an important random variable in the study of molecular evolution. Of particular interest is the ratio of the variance to the mean of that random variable, often known as the dispersion index. Because nucleotide substitution is most commonly modeled by a continuous-time four-state Markov chain, this paper provides a systematic method of computing the dispersion indices exhibited by a continuous-time four-state Markov chain. Using this method along with computer algebra and Monte Carlo simulation, this paper offers partially proven conjectures that were supported by thorough computer experiments. It is believed that the Tamura model, the equal-input model and the Takahata-Kimura model always exhibit dispersion indices less than 2. It is also believed that a general four-state model can be chosen to exhibit a dispersion index of any desired magnitude, although the chance of a randomly chosen such model exhibiting a dispersion index greater than 2 is as small as about 2%. Relevance of these findings to the neutral theory is discussed.

Computer Simulation↗
PubMed1999

The geography of fundholding in southwest England: implications for the evolution of primary care groups.

Using postcode-ED linkage to calculate patient-weighted deprivation indices for 330 general practices in southwest England, this study examines whether the populations served by fundholding and non-fundholding practices varied with respect to socio-economic status. Little evidence is found of systematic socio-economic bias in the uptake of fundholding. However, a distinct spatial pattern to the distribution of fundholding is revealed in this article, urban practices having adopted the scheme more readily than their rural and mixed rural/urban counterparts. As practice-level fundholding is replaced by commissioning at the locality level, such geographical variation is likely to be expressed in the way in which primary care groups evolve.

Catchment Area, Health↗
PubMed1987

[Original adaptive characters of intestinal Digenea of Sarpa salpa (Teleostei, Sparidae) and their interpretation in terms of evolution].

In the family Sparidae, the genus Sarpa is distinguished by a few characteristics: monospecificity, vegetarian diet and wide geographical distribution. The helminth fauna of Sarpa salpa is also very original. Indeed, the digenean parasites of this Teleostean fish are essentially classified into two families restricted to this fish. In the present paper, the author redescribes Mesometra orbicularis, M. brachycoelia, Centroderma spinosissima, Elstia stossichianum, Wardula capitellata (family Mesometridae) together with Robphildollfusium fractum (family Robphildollfusidae). Various original and yet unknown features are pointed out. Among these unusual structures, several correspond to adaptive characteristics favouring the settlement of the Digenean on the peculiar digestive gut wall of this herbivorous fish. Indeed, the intestinal mucous membrane of Sarpa salpa exhibits very few villi giving it an unusual smooth aspect. Therefore, the Mesometridae which always have just a single sucker (monostomatous) have selected a new kind of compensatory adhesive structure. Sometimes, the anterior end of the body becomes a sucker due to the particular distribution of the muscle strings; in other examples, the whole body becomes a sucker and its edges become considerably thinner to improve the tightness of the adhesive system. Other original anatomical features have been selected to allow survival in a medium rich in plant detritus. So, in the oral sucker crests ornemented by numerous sclerous denticles seem to act as a microfilter for the intestinal chyme in which plant fibres predominate. The original pharynx seems to act as a suction-force pump. The excretory system, which is of a reticular type, penetrates the whole parenchyma and this could be a response to huge intestinal fermentations. The Digenea of Sarpa salpa are not interpreted by the author as true parasites but as endocommensal symbionts. These inquiline species are not immunogenic, or at least only slightly so, since they do not feed upon the host itself but upon its intestinal chyme. In most cases this results in a high parasite density (post larvae and adults) together with a cohabitation of the various species along the various intestinal segments. Coexistence of several species, systematically very close, evidently raises the question of their reproductive isolation. The author proposes an answer founded upon data of allopatric speciation.

Adaptation, Physiological↗
PubMed2004

Pack-MULE transposable elements mediate gene evolution in plants.

Mutator-like transposable elements (MULEs) are found in many eukaryotic genomes and are especially prevalent in higher plants. In maize, rice and Arabidopsis a few MULEs were shown to carry fragments of cellular genes. These chimaeric elements are called Pack-MULEs in this study. The abundance of MULEs in rice and the availability of most of the genome sequence permitted a systematic analysis of the prevalence and nature of Pack-MULEs in an entire genome. Here we report that there are over 3,000 Pack-MULEs in rice containing fragments derived from more than 1,000 cellular genes. Pack-MULEs frequently contain fragments from multiple chromosomal loci that are fused to form new open reading frames, some of which are expressed as chimaeric transcripts. About 5% of the Pack-MULEs are represented in collections of complementary DNA. Functional analysis of amino acid sequences and proteomic data indicate that some captured gene fragments might be functional. Comparison of the cellular genes and Pack-MULE counterparts indicates that fragments of genomic DNA have been captured, rearranged and amplified over millions of years. Given the abundance of Pack-MULEs in rice and the widespread occurrence of MULEs in all characterized plant genomes, gene fragment acquisition by Pack-MULEs might represent an important new mechanism for the evolution of genes in higher plants.

Base Sequence↗