Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “convergent evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,279 records · Page 71Linked to original sources
PubMed1999

A compact gene cluster in Drosophila: the unrelated Cs gene is compressed between duplicated amd and Ddc.

Cs, a gene with unknown function, and amd and Ddc, which encode decarboxylases, are among the most closely spaced genes in D. melanogaster. Untranslated 3' ends of the convergently transcribed genes Cs and Ddc are known to overlap by 88bp. A number of questions arise about the organization of this tightly-packed gene region and about the evolution and function of the Cs gene. We have now investigated this three-gene cluster in Scaptodrosophila lebanonensis (which diverged from D. melanogaster 60-65 MYA), as well as in D. melanogaster and D. simulans. Gene order and direction of transcription is the same in all three species. The Cs gene codes, in Scaptodrosophila, for a polypeptide of 544 amino acids; in D. melanogaster, it consists of 504 amino acids, which is twice as long as previously suggested, which makes the gene density even more spectacular. The Cs sequences exhibit higher number of non-synonymous substitutions between species, higher ratios of non-synonymous to synonymous substitutions, and lower codon usage bias than other genes, suggesting that Cs is less functionally constrained than the other genes. This is consistent with the failure of inducing phenotypic mutations in D. melanogaster. The function of Cs remains to be identified, but a high degree of similarity indicates that it is homologous to genes coding for a corticosteroid-binding protein in yeast and a polyamine oxidase in maize.

Amino Acid Sequence↗
PubMed1995

Species limits in Rhizobium populations that nodulate the common bean (Phaseolus vulgaris).

Evolutionary genetic relationships among 146 bean-nodulating Rhizobium strains, including 94 field isolates from three localities in Colombia and 36 strains from Mexico, were examined by multilocus enzyme electrophoresis and restriction fragment length polymorphism analysis of a PCR-amplified 260-bp segment of the 16S rRNA gene. Seventy-five electrophoretic types (ETs), corresponding to multilocus enzyme genotypes, were identified, including a genotypically diverse group of 18 ETs in Colombia that is strongly differentiated from the ETs of R. etli, which occur in Mexico, Colombia, and Brazil. Most strains of the distinctive Colombian ETs carried the same 16S rRNA allele as did strains of R. etli, but, surprisingly, 17 isolates of two of these ETs had the allele that is characteristic of R. leguminosarum, and strains of two other divergent groups of ETs were also polymorphic for the two alleles. No fully satisfactory explanation for the occurrence of the R. leguminosarum 16S rRNA allele in three distantly related groups of strains is available, but horizontal transfer and recombination of the gene, in whole or in part, would seem to be more plausible than convergence in nucleotide sequence.

Alleles↗
PubMed1995

Expert systems for third-party reimbursement: planting seeds for accuracy.

Predictably, the genesis of most business expert systems development is not related to one particular issue, but to a series of business issues that converge to form the basis for system design as either enhancements or overhauls. Rarely, if ever, is there a conclusion to the system's enhancement process, but rather, an ongoing evolution of the system as dictated by a multitude of both internal and external forces. The focal point of these processes must be to benefit our customers and the markets we serve.

Computer Communication Networks↗
PubMed1999

Evolution of stepping-stone dispersal rates.

We present a general model of the evolution of dispersal in a population with any distribution of dispersal distance. We use this model to analyse evolutionarily stable (ES) dispersal rates for the classical island model of dispersal and for three different stepping-stone models. Using general techniques to compute relatedness coefficients in the different dispersal models which we consider, we find that the distribution of dispersal distance may affect the ES dispersal rate when the cost of dispersal is low. In this case the ES dispersal rate increases with the number of demes that can be reached by one dispersal event. However, for increasing cost the ES dispersal rate converges to a value independent of the distribution of dispersal distance. These results are in contrast to previous analyses of similar models. The effects of the size (number of demes) and shape (ratio between the width and the length) of the population on the evolution of dispersal are also studied. We find that larger and more elongated populations lead generally to higher ES dispersal rates. However, both of these effects can only be observed for extreme parameter values (i.e. for very small and very elongated populations). The direct fitness method and the analytical techniques used here to compute relatedness coefficients provide an efficient way to analyse ES strategies in subdivided populations.

Animals↗
PubMed2002

Limits of a multi-patch SIS epidemic model.

We start from a stochastic SIS model for the spread of epidemics among a population partitioned into M sites, each containing N individuals; epidemic spread occurs through within-site ('local') contacts and global contacts. We analyse the limit behaviour of the system as M and N increase to infinity. Two limit procedures are considered, according to the order in which M and N go to infinity; independently of the order, the limiting distribution of infected individuals across sites is a probability measure, whose evolution in time is governed by the weak form of a PDE. Existence and uniqueness of the solutions to this problem is shown. Finally, it is shown that the infected distribution converges, as time goes to infinity, to a Dirac measure at the value x(*), the equilibrium of a single-patch SIS model with contact rate equal to the sum of local and global contacts.

Animals↗
PubMed2001

Stage-dependent changes in the modulation of spinal nociceptive neuronal activity during the course of inflammation.

Spinal and supraspinal controls can tonically or phasically modulate the output of spinal nociceptive neurons. Alterations of these modulatory systems have been described during the acute stage of inflammation. In the present study in the rat, tonic descending controls were assessed during acute (24--48 h) and chronic (3--4 weeks) stages of monoarthritis of the ankle. The electrophysiological properties of spinal convergent neurons with ankle input were compared before and after spinalization. In a parallel series of experiments, spinal convergent neurons were recorded from the normal side in order to assess the propriospinal and supraspinal inhibitory controls triggered by nociceptive stimulation of the inflamed ankle. Tonic descending inhibition of convergent neurons with input from the inflamed ankle was enhanced during the acute stage and then decreased during the chronic stage of monoarthritis. Contralateral-induced inhibitions exhibited a similar temporal evolution. Time-dependent changes in the spinal transmission of nociceptive signals were shown by removing descending modulation in animals with monoarthritis; sensitization of spinal neurons with input from the inflamed ankle was demonstrated during the acute stage of monoarthritis, whereas a crossed transmission between inflamed and normal sides was observed during the chronic stage of the disease. These results show that dynamic and stage-dependent modifications of descending controls tend to dampen the central changes associated with inflammation.

Animals↗
PubMed2003

[Interferon : antiviral mechanisms and viral escape].

15 % of human cancers have virus origin, meaning that viruses are the second cause of cancers after tabagism. The knowledge of antiviral mechanisms is essential for treatment and prevention of infection evolution towards cancers. Interferons (IFNs) are a large family of multifunctional cytokines. They are involved in regulation of cell growth and modulation of immune response. But, all these functions seem to converge toward the most important of them : the antiviral activity. IFN secretion is the first event induced by viral infection, and will act on specific receptors on neighbour cells and prevent their infection by inducing numbers of antiviral genes. Although few of them are well known like the PKR, the 2-5OAS/RNase L pathway and the Mx proteins, many others need extensive studies to understand the wide range of IFN effect. Viruses have evolved to circumvent the IFN antiviral activity, and are able not only to divert the cellular machinery but also to lure the antiviral mechanisms of the host cell. The purpose of this review is to describe the many antiviral pathways and proteins induced by IFNs and to summarize the strategies of viral escape.

Animals↗
PubMed2005

DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.

Understanding relationships between sequence, structure, and evolution is important for functional characterization of proteins. Here, we define a novel DOM-fold as a consensus structure of the domains in DmpA (L-aminopeptidase D-Ala-esterase/amidase), OAT (ornithine acetyltransferase), and MocoBD (molybdenum cofactor-binding domain), and discuss possible evolutionary scenarios of its origin. As shown by a comprehensive structure similarity search, DOM-fold distinguished by a two-layered beta/alpha architecture of a particular topology with unusual crossing loops is unique to those three protein families. DmpA and OAT are evolutionarily related as indicated by their sequence, structural, and functional similarities. Structural similarity between the DmpA/OAT superfamily and the MocoBD domains has not been reported before. Contrary to previous reports, we conclude that functional similarities between DmpA/OAT proteins and N-terminal nucleophile (Ntn) hydrolases are convergent and are unlikely to be inherited from a common ancestor.

Acetyltransferases↗
PubMed2002

A survey of unequal crossover systems and their mathematical properties.

We present a model of gene duplication by means of unequal crossover (UCO) where the probability of any given pairing between homologous sequences scales as a penalty factor pz < or = 1, with z the number of mismatches due to asymmetric sequence alignment. From this general representation, we derive several limiting case models of UCO, some of which have been treated elsewhere in the literature. One limiting case is random unequal crossover (RUCO), obtained by setting p = 1 (corresponding to equiprobable pairings at each site). Another limiting case scenario (the 'Krueger-Vogel' model) proposes an optimal 'endpoint' alignment which strongly penalizes both overhang and deviations from endpoint matching positions. For both of these scenarios, we make use of the symmetry properties of the transition operator (together with the more general UCO properties of copy number conservation and equal parent-offspring mean copy number) to derive the stationary distribution of gene copy number generated by UCO. For RUCO, the stationary distribution of genotypes is shown to be a negative binomial, or alternatively, a convolution of geometric distributions on 'haplotype' frequencies. A different type of model derived from the general representation only allows recombination without overhang (internal UCO or IntUCO). This process has the special property of converging to a single copy length or a distribution on a pair of copy lengths in the absence of any other evolutionary forces. For UCO systems in general, we also show that selection can readily act on gene copy number in all of the UCO systems we investigate due to the perfect heritability (h 2 = 1) imposed by conservation of copy number. Finally, some preliminary work is presented which suggests that the more general models based on misalignment probabilities seem to also converge to stationary distributions, which are most likely functions of parameter value p.

Animals↗
PubMed1994

Exchanges of short polymorphic DNA segments predating speciation in feline major histocompatibility complex class I genes.

Sequence comparisons of 14 distinct MHC class I cDNA clones isolated from species representing the three major taxonomic lineages of Felidae (domestic cat lineage, ocelot lineage, and pantherine lineage) revealed that feline MHC class I alleles have highly mosaic structures with short polymorphic sequence motifs that are rearranged between alleles of individual MHC loci, between MHC class I genes within cat species, and between homologous MHC loci in different species. The pattern of sequence variation in felids supports the role of the following factors in production and maintenance of MHC variation: (1) gradual spontaneous mutation; (2) selective pressure to conserve certain residues but also to vary in hypervariable regions, notably residues that functionally participate in antigen recognition and presentation; and (3) recombination-mediated gene exchange between alleles and between related genes. The overall amount of genetic variation observed among MHC class I genes in the Felidae family is no greater than the amount of variation within any outbred cat species (i.e., domestic cat, ocelot). The occurrence of equivalent levels of polymorphism plus the simultaneous persistence of the same sequence motifs in divergent feline species suggest that most MHC class I nucleotide site polymorphism predated species divergences. Ancient polymorphisms have been transmitted through the speciation events and modern feline MHC class I alleles were derived by recombinational exchange of polymorphic sequence motifs. Moreover, some of these sequence motifs were found in other mammalian MHC class I genes, such as classical human HLA-B5, nonclassical human HLA-E class I genes, and bovine class I genes. These results raise the prospect of an ancient origin for some motifs, although the possibility of convergence in parallel mammalian radiations cannot be excluded.

Amino Acid Sequence↗
PubMed1979

The molecular heterogeneity and diversity of reptilian keratins.

Reptile keratins produce complex electrophoretic patterns, contain a number of size classes, and contain protein fractions analogous to the fractions found in other keratins. Thus, reptile keratins are similar to the heterogenous keratins of birds and mammals, and quite different from amphibian epidermal keratins. This heterogeneity may be related to the multiple functions performed by the epidermis of these organisms. The chemical diversity of reptile keratins seems to depend on the morphological differences between the tissues in which they occur. This situation is also found among these proteins in mammals and birds suggesting that keratin diversity is related to the morphological and presumably functional differentiation of epidermal tissues. The distribution of the keratin fractions in each tissue contributes to this diversity but the significance of these fractional differences is uncertain. A comparison of the half-cystine and glycine content of vertebrate alpha and ø keratins suggests that the alpha and ø proteins of reptiles may be related to the soft alpha keratins of mammals and amphibians. Mammalian hard keratins probably represent a uniquely derived group of proteins which are unlike the other vertebrate keratins. The presence of a "high sulphur" matrix component in both hard mammalian alpha and reptilian ø keratins may represent some form of molecular convergence which provides these distantly related proteins with similar physical or organizational properties.

Animals↗
PubMed1989

Fixation probabilities for advantageous mutants: a note on multiplication and sampling.

If the average number of gametes produced by the individual is small, as may be the case for haploid organisms, then sampling with and without replacement can lead to considerable differences in the fixation probabilities of mutant alleles. As a function of the population size N, these probabilities converge quickly to the survival probabilities given by branching processes with Poisson or Bernoulli offspring distributions.

Biological Evolution↗
PubMed2004

Molecular systematics and radiation of western North American nymphophiline gastropods.

Three mitochondrial DNA (mtDNA) markers were used to infer the phylogenetic relationships of the morphologically diverse, species rich, and poorly understood western North American aquatic gastropod genus Pyrgulopsis (Hydrobiidae: Nymphophilinae). Sequences were obtained from 62 of 124 currently recognized species of Pyrgulopsis and representatives of four related genera of North American nymphophilines. Separate and combined analyses of the mtDNA datasets recovered a well supported clade composed of Pyrgulopsis and two other North American nymphophiline genera (Floridobia, Nymphophilus) consistent with the results of a prior study based on a single gene and with anatomical evidence suggesting that these taxa form a monophyletic group. Phylogenetic relationships among lineages of Pyrgulopsis were little resolved in our analyses and provided no obvious basis for splitting this large genus into multiple genera. The little differentiated Mexican genus Nymphophilus was consistently placed within Pyrgulopsis in our trees and is formally synonymized with it herein. Pyrgulopsis was also depicted as paraphyletic with respect to Floridobia in some of our trees while in others the latter was sister to a Nymphophilus + Pyrgulopsis clade. Based on these equivocal results and the morphological and geographical divergence of eastern North American Floridobia relative to Pyrgulopsis, we recommend that the former be maintained as a separate genus. The short, weakly supported branches within Pyrgulopsis and the noncongruence between our molecular phylogenetic hypotheses and geographical groupings of species are attributed to an early rapid diversification of the genus, perhaps triggered by the complex changes in western topography which occurred during the late Tertiary. Our results also indicate that penial morphologies used to define species groups of Pyrgulopsis have been subject to striking convergence throughout the West, suggesting another compelling facet of the radiation of these snails.

Animals↗
PubMed1992

Chromatophore systems in teleosts and cephalopods: a levels oriented analysis of convergent systems.

The neural control of chromatophore display in cephalopod mollusks and teleost fishes is reviewed in the context of convergence of functional-anatomical pathways and mechanisms at several levels of organization. The effector elements or chromatophores are different in origin and design in the two groups of animals. Major functional differences appear to be in the speed of response (greatest in cephalopods) and the magnitude of non-neural control mechanisms (greatest in teleosts). Despite the differences, the elements demonstrate striking overall functional similarity. Elements of different types form highly organized array patterns of similar general complexity. Innervation patterns in cephalopods and teleosts seem comparable, with control being unidirectional (albeit in opposite directions); some elements demonstrate polyaxonal innervation. Motor units in both groups are generally composed of many chromatophores. Packard's concept of 'cronological units' of similar age-classes of chromatophores being innervated by similar age-classes of motor neurons greatly simplifies the understanding of relationships between the static arrays and the physiological units that utilize them to produce chromatic displays. The lower motor control areas for both groups have been grossly identified. Chromatomotor neurons in cephalopods are mostly located in the chromatophore lobes of the subesophageal brain while comparable systems in teleosts are situated in sympathetic chain ganglia (preganglionics) and the rostral spinal cord (postganglionics). Chromatic components are the simplest visually detectable units of color display, e.g. vertical bands and fin spots. They combine to form more complex chromatic patterns, which, in turn, are integrated with components of skin texture, posture and movement to produce display behaviors. Complexity of such systems seems to be of the same order of magnitude in both cephalopods and teleosts. Areas of the CNS related to each of the categorical levels have not been clearly defined. Crude patterning may take place in the basal and, perhaps, peduncle lobes in cephalopods and in the lower and intermediate medulla in teleosts. In both groups, higher level control relates to areas involved in sensorimotor integration and mediation of agonistic, sexual, and, perhaps, other types of behavior: the peduncle and optic lobes in cephalopods and the hypothalamus, tegmentum, otic tectum, torus semicircularis, thalamus and telencephalon in fishes. The systems appear to parallel each other in being organized hierarchically, with similar levels of complexity. Some of the regions may be especially important for regulating color patterns in response to visual input. Overall, chromatomotor control systems in cephalopods and teleosts demonstrate many apparent convergent features. Possible factors responsible for the similarities are discussed.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2003

Evolution of the bacterial community during granules formation in denitrifying reactors followed by molecular, culture-independent techniques.

The microbial community in two acetate-fed denitrifying reactors, inoculated with methanogenic sludge, was monitored by 16S rDNA-based methods (SSCP and FISH). Both reactors converged to similar, stable communities. The predominant organisms belonged to the genera Thauera, Paracoccus and Denitrobacter, detected both by molecular and culture-based methods.

Bacteria↗
PubMed1997

Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence.

The number of distinct functional classes of single-stranded RNAs (ssRNAs) and the number of sequences representing them are substantial and continue to increase. Organizing this data in an evolutionary context is essential, yet traditional comparative sequence analyses require that homologous sites can be identified. This prevents comparative analysis between sequences of different functional classes that share no site-to-site sequence similarity. Analysis within a single evolutionary lineage also limits evolutionary inference because shared ancestry confounds properties of molecular structure and function that are historically contingent with those that are imposed for biophysical reasons. Here, we apply a method of comparative analysis to ssRNAs that is not restricted to homologous sequences, and therefore enables comparison between distantly related or unrelated sequences, minimizing the effects of shared ancestry. This method is based on statistical similarities in nucleotide base composition among different functional classes of ssRNAs. In order to denote base composition unambiguously, we have calculated the fraction G+A and G+U content, in addition to the more commonly used fraction G+C content. These three parameters define RNA composition space, which we have visualized using interactive graphics software. We have examined the distribution of nucleotide composition from 15 distinct functional classes of ssRNAs from organisms spanning the universal phylogenetic tree and artificial ribozymes evolved in vitro. Surprisingly, these distributions are biased consistently in G+A and G+U content, both within and between functional classes, regardless of the more variable G+C content. Additionally, an analysis of the base composition of secondary structural elements indicates that paired and unpaired nucleotides, known to have different evolutionary rates, also have significantly different compositional biases. These universal compositional biases observed among ssRNAs sharing little or no sequence similarity suggest, contrary to current understanding, that base composition biases constitute a convergent adaptation among a wide variety of molecular functions.

Computer Graphics↗
PubMed1998

Sexual selection and the evolution of mechanical sound production in manakins (Aves: Pipridae).

I surveyed and described modulated, non-vocal, mechanical sounds of the lek-breeding Neotropical manakins (Pipridae). Variation among manakin species in mechanical sound production, repertoire size, acoustic structure, associated feather specialization, and mechanical sound production mechanisms were analysed comparatively in the context of a phylogenetic hypothesis for the family. Mechanical sound production has probably evolved five or six times independently and been lost once within the 42 species of manakins. Complex mechanical sound repertoires have also evolved independently several times. Acoustic structure of these sounds indicates that at least four different physical mechanisms of mechanical sound production have evolved: short, broad-frequency spectrum pulses; short, low-frequency pulses; aerodynamic vortices; and harmonic oscillations. All well-known mechanical sounds in manakins are associated with obvious wing movements and sexually dimorphic wing feather specializations. Both primary and secondary wing feather specializations have evolved convergently within the family for the production of short, broad-frequency mechanical sound pulses. Two less well-known manakin clades also have tail feather specializations that may function in mechanical sound production. A concentrated-changes test documented that the dynamic patterns of evolution in mechanical sound production in the polygynous manakins are highly unlikely by chance alone. Intersexual selection for acrobatic display may have created subsequent opportunities for the evolution of novel preferences for incidental non-vocal sounds produced by acrobatic movements. Novel female preferences for these mechanical sounds led to further elaboration of these sounds and to the evolution of complex mechanical sound repertoires in independent lineages of the family. Copyright 1998 The Association for the Study of Animal Behaviour. Copyright 1998 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1982

The contribution of time and local geography to craniofacial variation in Nubia's Batn el Hajar.

While the history of Lower Nubia has traditionally been explained in terms of racial migrations and mixture, recent studies of craniofacial variation have emphasized the biological continuity in Lower Nubia over the past 12,000 years. Carlson and Van Gerven for example have demonstrated a trend among the populations for changes in craniofacial form that are best explained by changing masticatory function and in situ evolution independent of major racial migrations. The purpose of the present research is to extend the analysis of craniofacial variation in Lower Nubia to a culturally and geographically distinctive region to the south known as the Batn el Hajar. Data for Lower Nubia were obtained in the field from 44 Meroitic, 94 X-Group, and 36 Christian crania during the 1964 Colorado Expedition to Nubia. Data from the Batn el Hajar were obtained from 188 crania excavated in 1979 at the Christian site of Kulubnarti which spans the entire Christian era from 550 to 1450+. Analysis of 12 metric variables using discriminant function revealed two sources of variation. The first is temporal and reflects the pattern of facial reduction previously reported for Lower Nubia. The second is geographic and suggests a morphological convergence between the people of Kulubnarti and Lower Nubia during late Christian times. This convergence reflects the southward migration of Lower Nubian Christians following the annexation of Lower Nubia by Islamic Egypt in the middle 15th century.

Biological Evolution↗