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PubMed2001

Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference.

Convergence in nucleotide composition (CNC) in unrelated lineages is a factor potentially affecting the performance of most phylogeny reconstruction methods. Such convergence has deleterious effects because unrelated lineages show similarities due to similar nucleotide compositions and not shared histories. While some methods (such as the LogDet/paralinear distance measure) avoid this pitfall, the amount of convergence in nucleotide composition necessary to deceive other phylogenetic methods has never been quantified. We examined analytically the relationship between convergence in nucleotide composition and the consistency of parsimony as a phylogenetic estimator for four taxa. Our results show that rather extreme amounts of convergence are necessary before parsimony begins to prefer the incorrect tree. Ancillary observations are that (for unweighted Fitch parsimony) transition/transversion bias contributes to the impact of CNC and, for a given amount of CNC and fixed branch lengths, data sets exhibiting substantial site-to-site rate heterogeneity present fewer difficulties than data sets in which rates are homogeneous. We conclude by reexamining a data set originally used to illustrate the problems caused by CNC. Using simulations, we show that in this case the convergence in nucleotide composition alone is insufficient to cause any commonly used methods to fail, and accounting for other evolutionary factors (such as site-to-site rate heterogeneity) can give a correct inference without accounting for CNC.

Animals↗

PubMed2006

How sensitive is a nose?

Odor sensitivity may not be due to odor-receptor (OR) binding but rather may be due to emergent properties of transduction pathways and the anatomical convergence of olfactory neurons. A recent study suggests that odor-OR interactions are brief and infrequently activate heterotrimeric GTP-binding proteins (G proteins); in contrast, visual receptors have long-lasting activation states and activate many G proteins. These differences may reflect strategies that evolved to accommodate very different signals, and the mechanisms described might be applicable for receptors across phyla. However, whereas visual receptors (rhodopsin) appeared before protostome-deuterostome separation, ORs may be independently derived in different phyla. Alternatively, phylum-distinct ORs may share common ancestry but be influenced by diversifying selection. Phylum-distinct ORs may imply phylum-specific OR mechanisms, whereas common ancestry may imply common mechanisms. Nonetheless, most animals detect a similar repertoire of olfactory signals, and OR mechanisms may be convergent on those signals independent of receptor relatedness. Thus, recent insights into the molecular characteristics of odor perception in frogs may well be relevant to such processes as how mosquitoes detect host odors for a malaria-transmitting blood meal.

Animals↗

PubMed2026

An ancient alpharetrovirus lineage in bats: Evolutionary insights and possible roles in reproduction.

Alpharetroviruses are an important group of pathogens known to cause leukemias and tumors, and were historically considered to be restricted to avian hosts. The identification of alpharetrovirus-like envelopes in bat genomes has hinted at a potentially wider host range, although their relations to modern alpharetroviruses and distribution remains unclear. Through a paleovirological screening of 818 vertebrate genomes we identified CHIRalphaEnv, a lineage that belongs firmly within alpharetroviruses, and emerged from a cross-class transmission from saurian hosts. We determine that CHIRalphaEnv envelope genes have been co-opted across bats on eight separate occasions between 43.8 and 18.9 million years ago and are preserved in most bat genomes screened. CHIRalphaEnv elements encode full-length envelope proteins and have been maintained under purifying selection, demonstrating multiple instances of exaptation by their bat hosts and a likely ubiquitous function. We observe high expression levels of CHIRalphaEnv envelopes in endometrium tissue from Carollia perspicillata, suggesting an involvement in reproductive function. We find CHIRalphaEnv sequence relatives in multiple mammalian clades (Afrotherians, rodents and bats), expanding the host range and extending origins of alpharetroviruses beyond 43 million years. We also propose the first mammalian co-opted Endogenous retrovirus (ERV) derived from an Alpharetrovirus envelope and explore the convergent functional recruitment of CHIRalphaEnv in hemochorial placentation in bats, elephant shrews and spiny mice. These findings highlight alpharetroviruses as a previously underappreciated source of functional exaptation in mammals.

Animals↗

PubMed2007

Hormones and body size evolution in papionin primates.

This study examines the evolution of size differences among papionin primates by measuring hormones that regulate size growth during ontogeny and influence ultimate adult size (insulin-like growth factor-I (IGF-I), insulin-like growth factor binding protein-3 (IGFBP-3), growth hormone binding protein (GHBP), dehydroepiandrosterone sulfate (DHEAS), testosterone, estradiol). The analyses assess longstanding ideas about circulating hormone levels and body size. Importantly, because the consensus papionin molecular phylogeny implies at least two episodes of size increase, this study offers opportunities to determine whether or not similar hormone profiles regulate this apparent evolutionary convergence (i.e., do larger-bodied papionins have higher levels of growth-related hormones than smaller-bodied papionins?). Five hundred and sixty serum samples (from 161 individuals) from 11 papionin species were analyzed using a two-level approach to address this issue. One used mixed longitudinal samples from two papionin species to test whether, during growth, large- and small-bodied species have higher and lower hormone levels, respectively. The second compared multiple papionin species to assess whether or not hormone levels covary with size in adult animals. Result show that size and hormone levels do not covary consistently across papionins, either during growth or in adulthood. Specifically, some smaller-bodied papionin species have higher absolute hormone levels than larger-bodied species. Differences in some hormone levels appear to track phylogeny more closely than body size. In contrast to studies based on single species, we demonstrate that, while the hormones analyzed affect growth, absolute circulating hormone levels either during growth or adulthood may be decoupled from interspecific differences in body size.

Age Factors↗

PubMed1996

Structure and organization of the human metaxin gene (MTX) and pseudogene.

Metaxin encodes a mitochondrial protein and is an essential nuclear gene in mice. The cDNA sequence and genomic organization of the human metaxin gene (MTX) have now been determined. MTX is 6 kb and consists of eight protein-encoding exons. The gene is contiguous to thrombospondin 3 (THBS3) and to the pseudogene for glucocerebrosidase (psGBA), but it transcribed in a direction opposite to the latter two genes. Thus, MTX and THBS3 share a common promoter region and are transcribed convergently, whereas MTX and psGBA are transcribed convergently and have closed apposed polyadenylation sites. Human metaxin contains 317 amino acids and is 91.5% identical to mouse metaxin. Metaxin is rich in leucine (14.2%) and in basic (12.9%) and acidic (12.0%) amino acids. The predicted protein lacks an amino-terminal signal sequence and N-glycosylation sites, but contains a putative transmembrane domain near its carboxy terminus. A DNA duplication has led to a direct repeat and the evolution of a pseudogene for GBA. A pseudogene for metaxin (psMTX) is also located within the 16 kb of DNA separating GBA from psGBA. The psMTX sequence is nearly identical to the 3' part of exon 2 through exon 8 of MTX, and both the intronic and the 3'-flanking sequences are highly conserved. Thus, there is a 278 amino acid open reading frame that is 97.8% identical to metaxin. However, psMTX lacks the first intron and promoter present in MTX, and at least in liver, the pseudogene is not expressed.

Amino Acid Sequence↗

PubMed2005

A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome.

Most reported examples of change in vertebrate mitochondrial (mt) gene order could be explained by a tandem duplication followed by random loss of redundant genes (tandem duplication-random loss [TDRL] model). Under this model of evolution, independent loss of genes arising from a single duplication in an ancestral species are predicted, and remnant pseudogenes expected, intermediate states that may remain in rearranged genomes. However, evidence for this is rare and largely scattered across vertebrate lineages. Here, we report new derived mt gene orders in the vertebrate "WANCY" region of four closely related caecilian amphibians. The novel arrangements found in this genomic region (one of them is convergent with the derived arrangement of marsupials), presence of pseudogenes, and positions of intergenic spacers fully satisfy predictions from the TDRL model. Our results, together with comparative data for the available vertebrate complete mt genomes, provide further evidence that the WANCY genomic region is a hotspot for gene order rearrangements and support the view that TDRL is the dominant mechanism of gene order rearrangement in vertebrate mt genomes. Convergent gene rearrangements are not unlikely in hotspots of gene order rearrangement by TDRL.

Amphibians↗

PubMed2000

Search and discovery strategies for biotechnology: the paradigm shift.

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.

Biotechnology↗

PubMed1988

Gene conversion, linkage, and the evolution of multigene families.

The evolution of the probabilities of genetic identity within and between the loci of a multigene family is investigated. Unbiased gene conversion, equal crossing over, random genetic drift, and mutation to new alleles are incorporated. Generations are discrete and nonoverlapping; the diploid, monoecious population mates at random. The linkage map is arbitrary, and the location dependence of the probabilities of identity is formulated exactly. The greatest of the rates of gene conversion, random drift, and mutation is epsilon much less than 1. For interchromosomal conversion, the equilibrium probabilities of identity are within order epsilon [i.e., O(epsilon)] of those in a simple model that has no location dependence and, at equilibrium, no linkage disequilibrium. At equilibrium, the linkage disequilibria are of O(epsilon); they are evaluated explicitly with an error of O(epsilon 2); they may be negative if symmetric heteroduplexes occur. The ultimate rate and pattern of convergence to equilibrium are within O(epsilon 2) and O(epsilon), respectively, of that of the same simple model. If linkage is loose (i.e., all the crossover rates greatly exceed epsilon, though they may still be much less than 1/2), the linkage disequilibria are reduced to O(epsilon) in a time of O(-ln epsilon). If intrachromosomal conversion is incorporated, the same results hold for loose linkage, except that, if the crossover rates are much less than 1/2, then the linkage disequilibria generally exceed those for pure interchromosomal conversion.

Biological Evolution↗

PubMed2005

A phylogenetic analysis of woodpeckers and their allies using 12S, Cyt b, and COI nucleotide sequences (class Aves; order Piciformes).

Although the woodpeckers have long been recognized as a natural, monophyletic taxon, morphological analyses of their intra- and intergeneric relationships have produced conflicting results. To clarify this issue, and as part of a larger study of piciform relationships, nucleotide sequences for the 12S ribosomal RNA (12S; 1123 bp), cytochrome b (Cyt b; 1022 bp), and cytochrome oxidase c subunit 1 (COI; 1512 bp) mitochondrial genes were obtained from 34 piciform species that included 16 of the 23 currently recognized woodpecker genera (subfamily Picinae), three piculets (subfamily Picumninae), a wryneck (subfamily Jynginae), a honeyguide (family Indicatoridae), and three barbets (infraorder Ramphastides). Analyses were conducted on the individual and combined 12S, Cyt b, and COI sequences with maximum parsimony, neighbor-joining, maximum likelihood, and Bayesian algorithms. Based on the strong, congruent support among the different data partitions and models of sequence evolution, a highly resolved consensus of the relationships among woodpeckers and their allies could be formed. The monophyly of Indicatoridae + Picidae (infraorder Picides), Picidae, Picinae + Picumninae, and Picinae was strongly supported in all analyses. However, the tribes Colaptini, Picini, Campephilini, and Campetherini were shown to be paraphyletic as were the genera of Colaptes and Piculus. A revision of the tribal-level classification of woodpeckers is proposed and the importance of plumage convergence among woodpeckers is discussed.

Animals↗

PubMed2005

A study of the utility of convergent characters for phylogeny reconstruction: do ecomorphological characters track evolutionary history in Anolis lizards?

The reconstruction of phylogeny requires homologous similarities across species. Characters that have been shown to evolve quickly or convergently in some species are often considered to be poor phylogenetic markers. Here I evaluate the phylogenetic utility of a set of morphological characters that are correlated with ecology and have been shown to evolve convergently in Anolis lizards in the Greater Antilles. Results of randomization tests suggest that these "ecomorph" characters are adequate phylogenetic markers, both for Anolis in general and for the Greater Antillean species for which ecomorphological convergence was originally documented. Explanations for this result include the presence of ecomorphologically similar species within evolutionary radiations within islands, some monophyly of ecomorphs across islands, and the existence of several species that defy ecomorphological characterization but share phylogenetic similarity in some ecomorph characters.

Animals↗

PubMed1989

The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction.

Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

Bacteria↗

PubMed2003

Characterizing T-cell receptor gamma-variable gene in Aotus nancymaae owl monkey peripheral blood.

Gammadelta T lymphocytes have a heterodimeric complex formed by the association of gamma and delta chains as receptor. Proliferation of this lymphocyte population has been observed, when infection by several pathogens such as Mycobacterium tuberculosis and Plasmodium spp. occurs. The New World Monkey Aotus nancymaae has become a very good experimental model for the immunological and physiopathological study of these infectious agents. The A. nancymaae gamma-variable region was characterized from peripheral blood samples by using cDNA and genomic DNA polymerase chain reaction amplification, DNA sequencing, and dot-blot hybridization techniques. Seventeen different T-cell receptor gamma-variable (TCRGV) sequences were obtained. These sequences were distributed among TCRGV subsets 1, 2, or 3, according to human subset classification. Although no subset 4 amplification was obtained, this subset was detected by dot-blot hybridization. The presence of these 4 subsets resembles the behavior displayed by 'gammadelta-low species' (humans and mice), where high diversity among these lymphocytes can be observed. Homologies greater than 70% were found with respect to humans. Sequence convergence between human and A. nancymaae subsets 1 and 3 highlights Aotus as a promising model for studying these lymphocyte functions.

Amino Acid Sequence↗

PubMed2000

An axisymmetric boundary integral model for incompressible linear viscoelasticity: application to the micropipette aspiration contact problem.

The micropipette aspiration test has been used extensively in recent years as a means of quantifying cellular mechanics and molecular interactions at the microscopic scale. However, previous studies have generally modeled the cell as an infinite half-space in order to develop an analytical solution for a viscoelastic solid cell. In this study, an axisymmetric boundary integral formulation of the governing equations of incompressible linear viscoelasticity is presented and used to simulate the micropipette aspiration contact problem. The cell is idealized as a homogeneous and isotropic continuum with constitutive equation given by three-parameter (E, tau 1, tau 2) standard linear viscoelasticity. The formulation is used to develop a computational model via a "correspondence principle" in which the solution is written as the sum of a homogeneous (elastic) part and a nonhomogeneous part, which depends only on past values of the solution. Via a time-marching scheme, the solution of the viscoelastic problem is obtained by employing an elastic boundary element method with modified boundary conditions. The accuracy and convergence of the time-marching scheme are verified using an analytical solution. An incremental reformulation of the scheme is presented to facilitate the simulation of micropipette aspiration, a nonlinear contact problem. In contrast to the halfspace model (Sato et al., 1990), this computational model accounts for nonlinearities in the cell response that result from a consideration of geometric factors including the finite cell dimension (radius R), curvature of the cell boundary, evolution of the cell-micropipette contact region, and curvature of the edges of the micropipette (inner radius a, edge curvature radius epsilon). Using 60 quadratic boundary elements, a micropipette aspiration creep test with ramp time t* = 0.1 s and ramp pressure p*/E = 0.8 is simulated for the cases a/R = 0.3, 0.4, 0.5 using mean parameter values for primary chondrocytes. Comparisons to the half-space model indicate that the computational model predicts an aspiration length that is less stiff during the initial ramp response (t = 0-1 s) but more stiff at equilibrium (t = 200 s). Overall, the ramp and equilibrium predictions of aspiration length by the computational model are fairly insensitive to aspect ratio a/R but can differ from the half-space model by up to 20 percent. This computational approach may be readily extended to account for more complex geometries or inhomogeneities in cellular properties.

Biomechanical Phenomena↗

PubMed1989

Stress proteins, arthritis, and autoimmunity.

Stress proteins have been highly conserved during evolution not only because of their fundamental importance in the response of the cell to stressful assaults, but also because they have critical roles in cellular activation and cell growth, regulation of protein function, protein transport, and protein assembly. Research focusing on the basic cell biology of stress proteins is intense at present, and will surely continue to be for some time to come. Of particular interest to immunologists and rheumatologists is the convergence of data in several fields that suggest that stress proteins in microorganisms that commonly infect humans may be triggers of humoral and cellular autoimmune responses and consequent overt autoimmune disease expression. Thus, stress proteins of M tuberculosis and other bacteria are close homologs of stress proteins in mammals, and may be involved in the pathogenesis of adjuvant-induced arthritis in rats and, possibly, of RA and reactive arthritis in humans. A great deal of work remains to be done in this area, including (a) generation and propagation of specifically reactive T cell clones, (b) molecular delineation of the immune recognition elements and critical epitopes shared by microbial stress proteins and host proteins, (c) definition of the relative contribution of alpha beta and gamma delta TCRs to T cell reactivity to stress proteins, and (d) clarification of the circumstances that enable persistent T cell autoreactivity to stress proteins. The data at hand are sufficiently compelling, however, to suggest that vaccination against T cells that recognize stress proteins may eventually become part of our therapeutic armamentarium to prevent or cure some forms of arthritis.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2005

The effect of salt concentration on DNA conformation transition: a molecular-dynamics study.

We performed three 3-ns molecular dynamics simulations of d(CGCGAATTCGCG)2 using the AMBER 8 package to determine the effect of salt concentration on DNA conformational transitions. All the simulations were started with A-DNA, with different salt concentrations, and converged with B-DNA with similar conformational parameters. However, the dynamic processes of the three MD simulations were very different. We found that the conformation transition was slow in the solution with higher salt concentration. To determine the cause of this retardation, we performed three additional 1.5-ns simulations starting with B-DNA and with the salt concentrations corresponding to the simulations mentioned above. However, astonishingly, there was no delayed conformation evolution found in any of the three simulations. Thus, our simulation conclusion is that higher salt concentrations slows the A --> B conformation transition, but have no effect on the final stable structure. [Figure: see text].

Carbohydrates↗

PubMed1977

Measures of fitness and demographic stability.

The concepts of entropy and reproductive potential of a genotype were introduced in a previous paper [Demetrius, L. (1974) Proc. Natl. Acad. Sci. USA 71, 4645-4647] and an analoge of the fundamental theorem of natural selection was derived. This paper relates to entropy of a population with the rate of convergence of the population to the stable age distribution. I show that (i) at maximal entropy, no oscillatory components exist and the birth sequence is unaffected by perturbations in the stable age distribution; and (ii) at zero entropy, oscillatory components occur and increase as rapidly as the real exponential component in the birth sequence. These results have implications towards (i) the relation between population fitness and adaptedness, (ii) modes of selection and the evolution of reproductive strategies, and (iii) the evolution of senescence.

Aging↗

PubMed2002

Energy spectrum of superfluid turbulence with no normal-fluid component.

The energy of superfluid turbulence without the normal fluid is studied numerically under the vortex filament model. Time evolution of the Taylor-Green vortex is calculated under the full nonlocal Biot-Savart law. It is shown that for k<2pi/l the energy spectrum is very similar to the Kolmogorov's -5/3 law which is the most important statistical property of the conventional turbulence, where k is the wave number of the Fourier component of the velocity field and l is the average intervortex spacing. The vortex length distribution converges to a scaling property reflecting the self-similarity of the tangle.

Journal Article↗

PubMed2006

Gravitational-wave extraction from an inspiraling configuration of merging black holes.

We present new ideas for evolving black holes through a computational grid without excision, which enable accurate and stable evolutions of binary black hole systems with the accurate determination of gravitational waveforms directly from the wave zone region. Rather than excising the black hole interiors, our approach follows the "puncture" treatment of black holes, but utilizing a new gauge condition which allows the black holes to move successfully through the computational domain. We apply these techniques to an inspiraling binary, modeling the radiation generated during the final plunge and ringdown. We demonstrate convergence of the waveforms and good conservation of mass-energy, with just over 3% of the system's mass converted to gravitational radiation.

Journal Article↗