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Results for “Parallel evolution”

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PubMed1994

Neural network for control of rearrangeable Clos networks.

Rapid evolution in the field of communication networks requires high speed switching technologies. This involves a high degree of parallelism in switching control and routing performed at the hardware level. The multistage crossbar networks have always been attractive to switch designers. In this paper a neural network approach to controlling a three-stage Clos network in real time is proposed. This controller provides optimal routing of communication traffic requests on a call-by-call basis by rearranging existing connections, with a minimum length of rearrangement sequence so that a new blocked call request can be accommodated. The proposed neural network controller uses Paull's rearrangement algorithm, along with the special (least used) switch selection rule in order to minimize the length of rearrangement sequences. The functional behavior of our model is verified by simulations and it is shown that the convergence time required for finding an optimal solution is constant, regardless of the switching network size. The performance is evaluated for random traffic with various traffic loads. Simulation results show that applying the least used switch selection rule increases the efficiency in switch rearrangements, reducing the network convergence time. The implementation aspects are also discussed to show the feasibility of the proposed approach.

Algorithms↗

PubMed2002

Polyamine participation in the maturation of glycoprotein fucosylation, but not sialylation, in rat small intestine.

The aim of this study was to determine the role of polyamines in the diet-related maturation of the intestinal glycoprotein glycosylation during postnatal development in the rat. The activity of alpha-2,6-sialyltransferase and the sialylated forms of glycoproteins in the intestinal brush-border membranes were found to decrease considerably after weaning, in parallel with the intestinal level of putrescine. By contrast, the activity of alpha-1,2-fucosyltransferases, the mRNA levels for two alpha-1,2-fucosyltransferase genes, FTA and FTB, and the fucosylated forms of glycoproteins all increased after weaning, in parallel with the levels of spermidine and spermine. These results suggest a possible role of polyamines in the evolution of glycosylation. The treatment of suckling rats with spermidine or spermine reproduced the high intestinal levels of these polyamines corresponding to those normally found after weaning. After these treatments, a rise in the activity of the alpha-1,2-fucosyltransferase was observed, associated with a fall in alpha-L-fucosidase activity. The alpha-1,2-fucosyltransferase FTB gene was found to be regulated at the transcriptional level, but not by its inhibitor, fuctinin. The result of these variations was the precocious appearance of several alpha-1,2-fucoproteins, which are normally found in brush-border membranes after weaning. The treatment of suckling rats with putrescine, which induced only a transitory rise in intestinal putrescine, had a similar but weaker effect on the fucosylation process than spermidine or spermine, and treatment with ornithine was ineffective. alpha-2,6-Sialylation was not affected by any of the treatments. Spermidine and spermine turned out to be more effective than putrescine for intestinal glycoprotein fucosylation, but did not affect their sialylation. Spermidine and spermine, whose intestinal levels where found to increase at weaning time, may have been partly responsible for the natural evolution of the intestinal glycoprotein fucosylation that occurred during this period.

Amine Oxidase (Copper-Containing)↗

PubMed2004

Determination of the molecular orientation of poly(propylene terephthalate) fibers using polarized Raman spectroscopy: a comparison of methods.

For the first time, four different methods to determine the degree of molecular orientation from polarized Raman spectroscopy measurements are compared. The great influence of molecular orientation on the properties of polymers has driven the development of multiple experimental techniques and procedures. This study is based on the C(1)-C(4) ring stretching vibration of poly(propylene terephthalate) (PPT) at 1614 cm(-1). It is shown that simply ratioing the band intensity obtained with the polarization parallel and perpendicular to the unique axis of the sample provides a good qualitative method to observe the evolution of orientation in a series of similar samples. To quantitatively compare the degree of orientation one needs to utilize a more complex method yielding the second- and fourth-order parameters of the orientation distribution function (P(2) and P(4), respectively). To date, most studies have been based on the assumption of a cylindrically symmetric polarizibility tensor. It is shown that this assumption is highly questionable although this method has been used fairly successfully in the past. This method results in orientation parameters that are clearly different from those obtained with the two more complex procedures. The most complex method, both theoretically and experimentally, requires the most measurements per sample. Major problems have occurred when trying to calculate the desired parameters, in particular for samples with high birefringence. These problems are related to experimental complexities occurring for measurements when the samples are tilted with respect to the polarization direction of the incident light. These measurements are replaced by a simple determination of depolarization ratio in the third method. This method assumes that the depolarization ratio is independent of changes in molecular orientation and structure. It was found that this assumption is not correct. Thus, the most complex method is the method of choice to quantitatively determine the second- and fourth-order parameters of the orientation distribution function, unless one has knowledge of the depolarization ratio of each sample being studied. That knowledge permits the use of an experimentally simpler method to obtain the desired parameters.

Algorithms↗

PubMed1978

Cell surface antigens containing beta2-microglobulin as the common subunit.

beta2-Microglobulin, which was first discovered in various biological fluids, has been shown to be the common subunit of the human HLA-A,B,C antigens. In the mouse beta2-microglobulin is associated with H-2K, D and L antigens and with TL and Qa-2 antigens, beta2-microglobulin and the heavy HLA antigen chains are similar in structure to the immunoglobulins and it is suggested that the two types of molecules have had an interrelated evolution. Data are also presented which suggest that the structural similarity between transplantation antigens and immunoglobulins may be paralleled by a functional similarity as well.

Animals↗

PubMed1998

Matrix metalloproteinases: structures, evolution, and diversification.

A comprehensive sequence alignment of 64 members of the family of matrix metalloproteinases (MMPs) for the entire sequences, and subsequently the catalytic and the hemopexin-like domains, have been performed. The 64 MMPs were selected from plants, invertebrates, and vertebrates. The analyses disclosed that as many as 23 distinct subfamilies of these proteins are known to exist. Information from the sequence alignments was correlated with structures, both crystallographic as well as computational, of the catalytic domains for the 23 representative members of the MMP family. A survey of the metal binding sites and two loops containing variable sequences of amino acids, which are important for substrate interactions, are discussed. The collective data support the proposal that the assembly of the domains into multidomain enzymes was likely to be an early evolutionary event. This was followed by diversification, perhaps in parallel among the MMPs, in a subsequent evolutionary time scale. Analysis indicates that a retrograde structure simplification may have accounted for the evolution of MMPs with simple domain constituents, such as matrilysin, from the larger and more elaborate enzymes.

Amino Acid Sequence↗

PubMedDate not supplied

The father(to)child affiliative bond: convergent evolution with the canid analogue.

Primate homologues, especially from the African great apes, can usually be successfully utilized to form comparisons with the human condition. However, the man(to)child pair-bond is not paralleled by any terrestrial primate nor even many mammals. Hence, knowledge of primate behavior would not be predictive of the pan-human social father. It is suggested that female choices of mating partners shifted in the direction of a canid analogue in that men's motivations to share resources with the female and to exhibit paternalistic behaviors were positively selected. Accordingly, it is argued that, for humans, convergent evolution occurred which trended toward the canid template. Consequently, it would be predicted that, compared to other terrestrial primates, the neuro-hormonal basis for the mother-child affiliative bond would be similar, but the basis for man(to)child affiliative bond would be dissimilar.

Adult↗

PubMedDate not supplied

Study of serial lymphocyte subsets in multiple sclerosis: their possible role in the evaluation of disease progression.

We followed-up 30 patients with definite multiple sclerosis (MS) for one year recording monthly: clinical evolution, neurological examination and T-lymphocyte subsets in peripheral blood recognized by monoclonal antibodies. Although clinical relapses could not be strictly associated with lymphocyte abnormalities in all cases, the parallel clinical-immunological survey permitted to correlate significantly the type of clinical course (chronic-progressive, relapsing, stable) with a correspondent immunological pattern (steadily high, transiently high, steadily normal CD4/CD8 ratios respectively). Our results suggest a possible role of serial lymphocyte subsets analysis in defining evolution of MS.

Adult↗

PubMedDate not supplied

Evolutionary basis of parallelism in North American scincid lizards.

This study uses a phylogenetic framework to explore the causes of parallelism in two North American scincid lizard assemblages: the skiltonianus and fasciatus species groups of the genus Plestiodon. Each group consists of several closely related species with conserved neonate morphology; features that distinguish species become accentuated during ontogeny, and these differences often resemble different endpoints along a developmental continuum. This continuum is believed to be an expression of the ancestral ontogeny, and has led to the hypothesis that evolutionary change in development has generated much of the observed morphological diversity. However, progress on understanding these mechanisms is limited by a lack of well-supported phylogenetic data for the fasciatus group, and for Plestiodon in general. Recent phylogenetic studies on the skiltonianus group have revealed previously undetected cases of parallelism, and raise the possibility that similar cases have yet to be discovered in the fasciatus group. Here, I estimate a phylogeny to test the monophyly of the fasciatus group and infer its relationship with other North American Plestiodon using 2537 bp from six mtDNA genes. I use the phylogeny to reconstruct the mode (graduated vs. punctuated) and direction of body size evolution, to map the evolution of two predominant color morphs, and to test whether size and color pattern evolve concertedly. The results show that the morphotypes of the traditional fasciatus group constitute good species, but that the species group is rendered paraphyletic by several geographically overlapping species that deviate from the fasciatus-like ontogeny. Body size evolution has occurred gradually and bi-directionally, and shifts to large body size have been consistently associated with the loss of the striped color pattern during ontogeny. I show that parallelism, a lack of rigorous phylogenetic analysis, and a reliance on shared ontogenetic features for predicting phylogenetic relatedness, has misled the traditional systematics of these lizards, but that general ideas concerning the role of development in their morphological evolution remain supported. I close by proposing that the processes influencing repeated phyletic patterns in the skiltonianus and fasciatus groups represent adherence to an ancestral ground state, and discuss the importance of using phylogenies for the initial characterization of evolutionary changes in development.

Animals↗

PubMed2003

Hox genes and the crustacean body plan.

The Crustacea present a variety of body plans not encountered in any other class or phylum of the Metazoa. Here we review our current knowledge on the complement and expression of the Hox genes in Crustacea, addressing questions related to the evolution of body architecture. Specifically, we discuss the molecular mechanisms underlying the homeotic transformation of legs into feeding appendages, which occurred in parallel in several branches of the crustacean evolutionary tree. A second issue that can be approached by the comparative study of Hox genes and their expression in the Crustacea bears on the homology of the abdomen. We discuss whether the so-called "abdominal" tagma of the crustaceans is homologous to the abdomen of insects. In addition, the homology of the abdomen between malacostracan and non-malacostracan crustaceans has also been questioned. We also address the question of the molecular developmental basis of the apparent lack of an abdomen in barnacles. We discuss these issues in relation to the problem of constraint versus adaptation in evolution.

Animals↗

PubMed2000

Rapid and parallel chromosomal number reductions in muntjac deer inferred from mitochondrial DNA phylogeny.

Muntjac deer (Muntiacinae, Cervidae) are of great interest in evolutionary studies because of their dramatic chromosome variations and recent discoveries of several new species. In this paper, we analyze the evolution of karyotypes of muntjac deer in the context of a phylogeny which is based on 1,844-bp mitochondrial DNA sequences of seven generally recognized species in the muntjac subfamily. The phylogenetic results support the hypothesis that karyotypic evolution in muntjac deer has proceeded via reduction in diploid number. However, the reduction in number is not always linear, i.e., not strictly following the order: 46-->14/13-->8/9-->6/7. For example, Muntiacus muntjak (2n = 6/7) shares a common ancestor with Muntiacus feae (2n = 13/14), which indicates that its karyotype was derived in parallel with M. feae's from an ancestral karyotype of 2n >/= 13/14. The newly discovered giant muntjac (Muntiacus vuquangensis) may represent another parallel reduction lineage from the ancestral 2n = 46 karyotype. Our phylogenetic results indicate that the giant muntjac is relatively closer to Muntiacus reevesi than to other muntjacs and may be placed in the genus Muntiacus Analyses of sequence divergence reveal that the rate of change in chromosome number in muntjac deer is one of the fastest in vertebrates. Within the muntjac subfamily, the fastest evolutionary rate is found in the Fea's lineage, in which two species with different karyotypes diverged in around 0.5 Myr.

Animals↗

PubMed2004

Morphological evolution in sea urchin development: hybrids provide insights into the pace of evolution.

Hybridisations between related species with divergent ontogenies can provide insights into the bases for evolutionary change in development. One example of such hybridisations involves sea urchin species that exhibit either standard larval (pluteal) stages or those that develop directly from embryo to adult without an intervening feeding larval stage. In such crosses, pluteal features were found to be restored in fertilisations of the eggs of some direct developing sea urchins (Heliocidaris erythrogramma) with the sperm of closely (Heliocidaris tuberculata) and distantly (Pseudoboletia maculata) related species with feeding larvae. Such results can be argued to support the punctuated equilibrium model-conservation in pluteal regulatory systems and a comparatively rapid switch to direct development in evolution.1,2 Generation of hybrids between distantly related direct developers may, however, indicate evolutionary convergence. The 'rescue' of pluteal features by paternal genomes may require maternal factors from H. erythrogramma because the larva of this species has pluteal features. In contrast, pluteal features were not restored in hybridisations with the eggs of Holopneustes purpurescens, which lacks pluteal features. How much of pluteal development can be lost before it cannot be rescued in such crosses? The answer awaits hybridisations among indirect and direct developing sea urchins differing in developmental phenotype, in parallel with investigations of the genetic programs involved.

Animals↗

PubMed1994

Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution.

The neotropical Heliconius butterflies are famous examples of Müllerian mimicry, due to the diverse array of shared, brightly colored wing patterns that advertise the butterflies' unpalatability. The parallel geographical variation in these patterns within several widespread species has been invoked to support the controversial Pleistocene refugium hypothesis of tropical diversification. However, in no Heliconius species have either evolutionary rates or relationships among geographical races been explicitly examined. I present a phylogenetic hypothesis based on mitochondrial DNA sequences for 14 divergent races of Heliconius erato, which reveals that similar wing patterns have evolved rapidly and convergently within the species. There is a basal split between groups of races from east and west of the Andes, reflecting a vicariant separation at the base of the Pleistocene. Within each of these clades, sequence divergence is very low, and some haplotypes are shared between allopatric races with radically different wing patterns. The topology implies a simultaneous radiation of races in these two areas within the last 200,000 years. Ages for the clades are estimated by comparing sequence divergence to a plot of mitochondrial divergence in several arthropod taxa with independently dated divergence times. This plot is linear and suggests that mitochondrial DNA in arthropods evolves in a clocklike manner, at least initially, when sequence divergence is low.

Animals↗

PubMed2006

Waves of parthenogenesis in the desert: evidence for the parallel loss of sex in a grasshopper and a gecko from Australia.

The rarity of parthenogenesis, reproduction without sex, is a major evolutionary puzzle. To understand why sexual genetic systems are so successful in nature, we must understand why parthenogenesis sometimes evolves and persists. Here we use DNA sequence data to test for similarities in the tempo and mode of the evolution of parthenogenesis in a grasshopper and a lizard from the Australian desert. We find spectacular congruence between genetic and geographic patterns of parthenogenesis in these distantly related organisms. In each species, parthenogenesis evolved twice and appears to have expanded in parallel waves across the desert, suggesting a highly general selective force against sex.

Animals↗

PubMed2005

Evolution of an avirulence gene, AVR1-CO39, concomitant with the evolution and differentiation of Magnaporthe oryzae.

The significance of AVR1-CO39, an avirulence gene of the blast fungus corresponding to Pi-CO39(t) in rice cultivars, during the evolution and differentiation of the blast fungus was evaluated by studying its function and distribution in Pyricularia spp. When the presence or absence of AVR1-CO39 was plotted on a dendrogram constructed from ribosomal DNA sequences, a perfect parallelism was observed between its distribution and the phylogeny of Pyricularia isolates. AVR1-CO39 homologs were exclusively present in one species, Pyricularia oryzae, suggesting that AVR1-CO39 appeared during the early stage of evolution of P. oryzae. Transformation assays showed that all the cloned homologs tested are functional as an avirulence gene, indicating that selection has maintained their function. Nevertheless, Oryza isolates (isolates virulent on Oryza spp.) in P. oryzae were exceptionally noncarriers of AVR1-CO39. All Oryza isolates suffered from one of the two types of known rearrangements at the Avr1-CO39 locus (i.e., G type and J type). These types were congruous to the two major lineages of Oryza isolates from Japan determined by MGR586 and MAGGY. These results indicate that AVR1-CO39 was lost during the early stage of evolution of the Oryza-specific subgroup of P. oryzae. Interestingly, its corresponding resistance gene, Pi-CO39(t), is not widely distributed in Oryza spp.

Evolution, Molecular↗

PubMed2000

Rapid speciation via parallel, directional selection on regulatory genetic pathways.

Regulatory genetic pathways are ubiquitous in organisms and play a central role in the realization of the phenotype during development. We explored the proposition that these pathways can provide a plausible source of the epistatic variation that has been implicated in the evolution of postzygotic reproductive isolation. We modeled gene regulation as a matching function between the product of one locus and the promoter site of the next locus in the pathway, with binding strength determining the amount of product. When the phenotype is subject to parallel selection in a pair of independent populations, we find that the fitnesses of F(1)and F(2)hybrids often drop to very low values as the populations respond in genetically different and incompatible ways. The simulations support the predictions of the analytical models. Hybrid fitness reduction occurs more often as the number of loci in the pathway increases, and as the binding site interactions become more complex. Less hybrid fitness reduction is seen when the populations start with imperfect binding in the pathway. In contrast, when we constructed the phenotype without gene regulation using multiplicative rules, isomorphic to the additive phenotype commonly assumed in evolutionary models, we found no appreciable F(1)fitness reduction and only slight F(2)fitness reduction. The interaction of genetic drift and mutation, even at very high rates, did not reduce hybrid fitness at all on the time-scales we considered. Clearly, the evolution of regulatory genetic pathways can play an important role in speciation, but much more empirical information is needed on the effect of allelic variability in regulatory site interactions before this role is fully understood.

Animals↗

PubMed2002

Theory and practice of parallel direct optimization.

Our ability to collect and distribute genomic and other biological data is growing at a staggering rate (Pagel, 1999). However, the synthesis of these data into knowledge of evolution is incomplete. Phylogenetic systematics provides a unifying intellectual approach to understanding evolution but presents formidable computational challenges. A fundamental goal of systematics, the generation of evolutionary trees, is typically approached as two distinct NP-complete problems: multiple sequence alignment and phylogenetic tree search. The number of cells in a multiple alignment matrix are exponentially related to sequence length. In addition, the number of evolutionary trees expands combinatorially with respect to the number of organisms or sequences to be examined. Biologically interesting datasets are currently comprised of hundreds of taxa and thousands of nucleotides and morphological characters. This standard will continue to grow with the advent of highly automated sequencing and development of character databases. Three areas of innovation are changing how evolutionary computation can be addressed: (1) novel concepts for determination of sequence homology, (2) heuristics and shortcuts in tree-search algorithms, and (3) parallel computing. In this paper and the online software documentation we describe the basic usage of parallel direct optimization as implemented in the software POY (ftp://ftp.amnh.org/pub/molecular/poy).

Animals↗

PubMed1996

Evolution of photochemically induced focal cerebral ischemia in the rat. Magnetic resonance imaging and histology.

BACKGROUND AND PURPOSE: Magnetic resonance imaging (MRI) is increasingly used to study the pathophysiological evolution of cerebral ischemia in humans and animals. We have investigated photochemically induced (rose bengal) focal cerebral ischemia, a relatively noninvasive, reproducible model for stroke, and compared the evolution of the ischemic response in vivo and postmortem with MRI and histology, respectively. METHODS: MR images weighted for T2, diffusion, and T2* and parallel histological sections stained with cresyl fast violet (CFV) and for glial fibrillary acid protein were obtained from 34 adult male Hooded Lister rats at seven time points (3.75 to 196 hours) after bilateral ischemia induction. From CFV histology, lesion volumes and cell counts were calculated; from diffusion-weighted and T2-weighted images, apparent diffusion coefficients and lesion volumes were determined. RESULTS: Both MRI and histology revealed a well-defined lesion at 3.75 hours after irradiation and a consistent pattern of temporal evolution; lesion apparent diffusion coefficients decreased significantly by 3.75 hours, increased significantly by day 2, and correlated strikingly with the decline in lesion CFV-positive cell numbers. After day 2, astrocytes and connective tissue cells invaded the infarct. Throughout the time course, lesion volumes determined in vivo and postmortem (after shrinkage correction) agreed well. CONCLUSIONS: MRI changes quantitatively reflect histopathology, revealing reproducible primary and secondary damage characteristics noninvasively. These changes essentially replicate those reported for other animal stroke models and clinically, emphasizing the value both of MRI and the photochemically induced focal cerebral ischemia model in stroke research.

Animals↗

PubMed2006

Analysis of ribosomal protein gene structures: implications for intron evolution.

Many spliceosomal introns exist in the eukaryotic nuclear genome. Despite much research, the evolution of spliceosomal introns remains poorly understood. In this paper, we tried to gain insights into intron evolution from a novel perspective by comparing the gene structures of cytoplasmic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs), which are held to be of archaeal and bacterial origin, respectively. We analyzed 25 homologous pairs of CRP and MRP genes that together had a total of 527 intron positions. We found that all 12 of the intron positions shared by CRP and MRP genes resulted from parallel intron gains and none could be considered to be "conserved," i.e., descendants of the same ancestor. This was supported further by the high frequency of proto-splice sites at these shared positions; proto-splice sites are proposed to be sites for intron insertion. Although we could not definitively disprove that spliceosomal introns were already present in the last universal common ancestor, our results lend more support to the idea that introns were gained late. At least, our results show that MRP genes were intronless at the time of endosymbiosis. The parallel intron gains between CRP and MRP genes accounted for 2.3% of total intron positions, which should provide a reliable estimate for future inferences of intron evolution.

Amino Acid Sequence↗