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PubMed1996

Congruence of fatty acid methyl ester profiles and morphological characters of arbuscular mycorrhizal fungi in Gigasporaceae.

Arbuscular mycorrhizal (AM) fungi (Order Glomales, Class Zygomycetes) are a diverse group of soil fungi that form mutualistic associations with the roots of most species of higher plants. Despite intensive study over the past 25 years, the phylogenetic relationships among AM fungi, and thus many details of evolution of the symbiosis, remain unclear. Cladistic analysis was performed on fatty acid methyl ester (FAME) profiles of 15 species in Gigaspora and Scutellospora (family Gigasporaceae) by using a restricted maximum likelihood approach of continuous character data. Results were compared to a parsimony analysis of spore morphological characters of the same species. Only one tree was generated from each character set. Morphological and developmental data suggest that species with the simplest spore types are ancestral whereas those with complicated inner wall structures are derived. Spores of those species having a complex wall structure pass through stages of development identical to the mature stages of simpler spores, suggesting a pattern of classical Haeckelian recapitulation in evolution of spore characters. Analysis of FAME profiles supported this hypothesis when Glomus leptotichum was used as the outgroup. However, when Glomus etunicatum was chosen as the outgroup, the polarity of the entire tree was reversed. Our results suggest that FAME profiles contain useful information and provide independent criteria for generating phylogenetic hypotheses in AM fungi. The maximum likelihood approach to analyzing FAME profiles also may prove useful for many other groups of organisms in which profiles are empirically shown to be stable and heritable.

Journal Article↗
PubMed1998

The Weyl character formula, the half-spin representations, and equal rank subgroups.

Let B be a reductive Lie subalgebra of a semi-simple Lie algebra F of the same rank both over the complex numbers. To each finite dimensional irreducible representation Vlambda of F we assign a multiplet of irreducible representations of B with m elements in each multiplet, where m is the index of the Weyl group of B in the Weyl group of F. We obtain a generalization of the Weyl character formula; our formula gives the character of Vlambda as a quotient whose numerator is an alternating sum of the characters in the multiplet associated to Vlambda and whose denominator is an alternating sum of the characters of the multiplet associated to the trivial representation of F.

Journal Article↗
PubMed2000

Ecological character displacement in Plethodon: biomechanical differences found from a geometric morphometric study.

Ecological character displacement describes a pattern where morphological differences between sympatric species are enhanced through interspecific competition. Although widely considered a pervasive force in evolutionary ecology, few clear-cut examples have been documented. Here we report a case of ecological character displacement between two salamander species, Plethodon cinereus and Plethodon hoffmani. Morphology was quantified by using linear measurements and landmark-based geometric morphometric methods for specimens from allopatric and sympatric populations from two geographic transects in south-central Pennsylvania, and stomach contents were assayed to quantify food resource use. Morphological variation was also assessed in 13 additional allopatric populations. In both transects, we found significant morphological differentiation between sympatric populations that was associated with a reduction in prey consumption in sympatry and a segregation of prey according to prey size. No trophic morphological or resource use differences were found between allopatric populations, and comparisons of sympatric populations with randomly paired allopatric populations revealed that the observed sympatric morphological differentiation was greater than expected by chance. The major trophic anatomical differences between sympatric populations relates to functional and biomechanical differences in jaw closure: sympatric P. hoffmani have a faster closing jaw, whereas sympatric P. cinereus have a slower, stronger jaw. Because salamanders immobilize prey of different sizes in different ways, and because the observed sympatric biomechanical differences in jaw closure are associated with the differences in prey consumption, the observed character displacement has a functional ecological correlate, and we can link changes in form with changes in function in this apparent example of character displacement.

Analysis of Variance↗
PubMed1998

Incongruence between morphological and mitochondrial-DNA characters suggests hybrid origins of parthenogenetic weevil lineages (Genus aramigus).

An expanded matrix of morphological characters for the genus Aramigus (Coleoptera: Curculionidae), which includes numerous polyploid parthenogenetic lineages, was compared and combined with a published matrix of mitochondrial DNA (mtDNA) characters. The matrix of morphological characters provides little resolution of the A. tessellatus and A. uruguayensis species complexes but does resolve previously unresolved relationships among other morphologically defined species (A. globoculus + A. intermedius, A. curtulus + A. planioculus). The morphological and mtDNA characters are significantly incongruent (0.435 < or = IM < or = 0.463; IMF = 0.0735), according to the tests of Farris et al. (P = 0.010) and Templeton (P < 0.005), probably because of hybrid origins of polyploid parthenogenetic lineages. For the few sexual lineages included in both matrices, morphology and mtDNA provide congruent estimates of phylogeny. In spite of recent injunctions against combining data sets that are incongruent because of differing histories, the results of the combined analyses were used to select one of the most-parsimonious mtDNA trees as the best estimate of maternal-lineage genealogy and to reconstruct the evolution of parthenogenesis under the assumption that transitions from sexuality to parthenogenesis are irreversible. Where cytogenetically justified, as in weevils, the irreversibility assumption is useful for producing conservative estimates of the age of parthenogenetic lineages in spite of potential sampling bias against sexuals.

Animals↗
PubMed1999

More characters or more taxa for a robust phylogeny--case study from the coffee family (Rubiaceae).

Using different data sets mainly from the plant family Rubiaceae, but in parts also from the Apocynaceae, Asteraceae, Lardizabalaceae, Saxifragaceae, and Solanaceae, we have investigated the effect of number of characters, number of taxa, and kind of data on bootstrap values within phylogenetic trees. The percentage of supported nodes within a tree is positively correlated with the number of characters, and negatively correlated with the number of taxa. The morphological analyses are based on few characters and weakly supported trees are expected. The percentage of supported nodes is also dependent on the kind of data analyzed. In analyses of Rubiaceae based on the same number of characters, RFLP data give trees with higher percentage of supported nodes than rbcL and morphological data. We also discuss the support values for particular nodes at the familial and subfamilial levels. Two new data sets of ndhF and rbcL sequences of Rubiaceae are analyzed and together with earlier studies of the family we can conclude that the monophyly of the Rubiaceae is supported and within the family there are three well supported, but not easily characterized, large subfamilies, Rubioideae, Cinchonoideae s.s. and Ixoroideae s.l. There are also a few genera (Luculia and Coptosapelta) unclassified to subfamily.

Coffee↗
PubMed1975

[Studies on the additive character of amino-acid absorption data obtained from pigs. 2. Studies using regression technic].

The first communication in this series (MEIER et al. 1973) reported the results of studies on the additive character of amino acid absorption data from pigs which were based on the use of the classics technique. In order to verify these results the studies were repeated, partly with the same components using regression techniques. The present studies on the additive character of amino acid absorption data showed that the additive character of these data can also be established in pigs. Moreover, the results of these investigations indicated that studies on the additive character of amino acid absorption values may be carried out by using the classical method. In performing studies of this kind attention should be paid to the fact that the rations tested should be such as to meet or nearly meet the maintenance needs of the animals.

Amino Acids↗
PubMed1999

Hemisphere differences in accessing lexical knowledge of Chinese characters.

The lateralisation of lexical knowledge of Chinese characters is investigated in this study. Three experiments were conducted in which stimuli were presented unilaterally to a visual field for recognition tests. The orthographic similarity of two alternative items for choice in Experiment 1 was manipulated, and the results showed an LVF advantage effect for legal characters in the visually similar condition and a more prominent LVF than RVF character-superiority effect. The phonological similarity of two alternative items for choice was manipulated in Experiment 2. The results showed a prominent RVF advantage effect and a significant phonological similarity effect in the RVF. In Experiment 3, the semantic similarity was manipulated, and the semantic similarity effect was observed in the RVF. These results suggest hemisphere asymmetries in accessing lexical knowledge of Chinese characters.

Journal Article↗
PubMed2003

Fast and simple character classes and bounded gaps pattern matching, with applications to protein searching.

The problem of fast exact and approximate searching for a pattern that contains classes of characters and bounded size gaps (CBG) in a text has a wide range of applications, among which a very important one is protein pattern matching (for instance, one PROSITE protein site is associated with the CBG [RK] - x(2,3) - [DE] - x(2,3) - Y, where the brackets match any of the letters inside, and x(2,3) a gap of length between 2 and 3). Currently, the only way to search for a CBG in a text is to convert it into a full regular expression (RE). However, a RE is more sophisticated than a CBG, and searching for it with a RE pattern matching algorithm complicates the search and makes it slow. This is the reason why we design in this article two new practical CBG matching algorithms that are much simpler and faster than all the RE search techniques. The first one looks exactly once at each text character. The second one does not need to consider all the text characters, and hence it is usually faster than the first one, but in bad cases may have to read the same text character more than once. We then propose a criterion based on the form of the CBG to choose a priori the fastest between both. We also show how to search permitting a few mistakes in the occurrences. We performed many practical experiments using the PROSITE database, and all of them show that our algorithms are the fastest in virtually all cases.

Algorithms↗
PubMed1989

Pleiotropic stabilizing selection limits the number of polymorphic loci to at most the number of characters.

We demonstrate that, in a model incorporating weak Gaussian stabilizing selection on n additively determined characters, at most n loci are polymorphic at a stable equilibrium. The number of characters is defined to be the number of independent components in the Gaussian selection scheme. We also assume linkage equilibrium, and that either the number of loci is large enough that the phenotypic distribution in the population can be approximated as multivariate Gaussian or that selection is weak enough that the mean fitness of the population can be approximated using only the mean and the variance of the characters in the population. Our results appear to rule out antagonistic pleiotropy without epistasis as a major force in maintaining additive genetic variation in a uniform environment. However, they are consistent with the maintenance of variability by genotype-environment interaction if a trait in different environments corresponds to different characters and the number of different environments exceeds the number of polymorphic loci that affect the trait.

Algorithms↗
PubMed1991

The genetic basis of a species-specific character in the Drosophila virilis species group.

The genetic basis of the species-specific dorsal abdominal stripe of Drosophila novamexicana was examined. The dorsal stripe is present in D. novamexicana and absent in all other members of the Drosophila virilis species group. Interspecific crosses between D. novamexicana and genetically marked D. virilis revealed that all four of the autosomes (except the tiny dot chromosome, which was not marked) and the sex chromosomes (the X and Y chromosome effects could not be disentangled) showed a significant effect on the width of the dorsal stripe. All the autosomes act approximately additively; only minor interactions were detected among them. No significant maternal effects were found. This means that a minimum of five loci are involved in the character difference between the two species, and this is the maximum number that this technique could discern. These results suggest that, based on the number of factors involved in the character difference, the inheritance of this character should be considered polygenic, but because chromosome 2 (the largest chromosome in the species) contributed over half of the variance toward the character difference, it is best to consider the inheritance oligogenic based on effect. The implications of these findings are discussed in light of the importance of macromutation in speciation and the sex chromosome theory of speciation.

Analysis of Variance↗
PubMed1999

The genetic analysis of age-dependent traits: modeling the character process.

The extension of classical quantitative genetics to deal with function-valued characters (also called infinite-dimensional characters) such as growth curves, mortality curves, and reaction norms, was begun by Kirkpatrick and co-workers. In this theory, the analogs of variance components for single traits are covariance functions for function-valued traits. In the approach presented here, we employ a variety of parametric models for covariance functions that have a number of desirable properties: the functions (1) are positive definite, (2) can be estimated using procedures like those currently used for single traits, (3) have a small number of parameters, and (4) allow simple hypotheses to be easily tested. The methods are illustrated using data from a large experiment that examined the effects of spontaneous mutations on age-specific mortality rates in Drosophila melanogaster. Our methods are shown to work better than a standard multivariate analysis, which assumes the character value at each age is a distinct character. Advantages over existing methods that model covariance functions as a series of orthogonal polynomials are discussed.

Aging↗
PubMed2002

Functional mapping of quantitative trait loci underlying the character process: a theoretical framework.

Unlike a character measured at a finite set of landmark points, function-valued traits are those that change as a function of some independent and continuous variable. These traits, also called infinite-dimensional characters, can be described as the character process and include a number of biologically, economically, or biomedically important features, such as growth trajectories, allometric scalings, and norms of reaction. Here we present a new statistical infrastructure for mapping quantitative trait loci (QTL) underlying the character process. This strategy, termed functional mapping, integrates mathematical relationships of different traits or variables within the genetic mapping framework. Logistic mapping proposed in this article can be viewed as an example of functional mapping. Logistic mapping is based on a universal biological law that for each and every living organism growth over time follows an exponential growth curve (e.g., logistic or S-shaped). A maximum-likelihood approach based on a logistic-mixture model, implemented with the EM algorithm, is developed to provide the estimates of QTL positions, QTL effects, and other model parameters responsible for growth trajectories. Logistic mapping displays a tremendous potential to increase the power of QTL detection, the precision of parameter estimation, and the resolution of QTL localization due to the small number of parameters to be estimated, the pleiotropic effect of a QTL on growth, and/or residual correlations of growth at different ages. More importantly, logistic mapping allows for testing numerous biologically important hypotheses concerning the genetic basis of quantitative variation, thus gaining an insight into the critical role of development in shaping plant and animal evolution and domestication. The power of logistic mapping is demonstrated by an example of a forest tree, in which one QTL affecting stem growth processes is detected on a linkage group using our method, whereas it cannot be detected using current methods. The advantages of functional mapping are also discussed.

Chromosome Mapping↗
PubMed1973

Biometrical genetics with one or two loci: the inheritance of physiological characters in mice.

Maximum likelihood methods have been used to compare the fit of twenty different genetic models to experimental data on fourteen characters, each measured on two parental strains, F(1) hybrids and both backcrosses. Although variation in all characters was continuous, differentiation between the various models was meaningful, the mean likelihood ratio between the best and worst models for each character being greater than 10(4). Models with only one or two loci were adequate to account for the observed genetic variation in eleven of the fourteen characters. These results indicate that even in species without special genetic advantages, it may be possible to identify individually some of the genes responsible for naturally-occurring variation within the range of normality.

Animals↗
PubMed2006

Orthographic neighborhood effects in reading Chinese two-character words.

The present study investigates the effects of neighborhood size and neighborhood frequency in reading Chinese two-character words. The neighborhood size of a word is defined as the summation of neighbors sharing the first constituent (neighborhood size 1) and the second constituent (neighborhood size 2) characters. The first experiment found two opposite neighborhood size effects in lexical decision of high-frequency and low-frequency words. The regression analysis showed that neighborhood size 1 influenced word reading more than the neighborhood size 2. The second experiment confirmed this finding and showed that reading words with higher frequency neighbors took a longer time and elicited greater N400 and LPC than those without higher frequency neighbors. These findings indicate that, when reading Chinese two-character words, all words sharing the first constituent character are activated in the early stage of word recognition and the existence of high-frequency words among neighbors leads to greater competition in the stage of semantic integration and response selection.

Adult↗
PubMed1999

Zinc tolerance and hyperaccumulation are genetically independent characters.

The hyperaccumulation of metals by a rare class of plants is a fascinating and little understood phenomenon. No genetic analysis has been possible since no intraspecific variation is known for this character. Here, we report on crosses between the zinc-hyperaccumulating and -tolerant species Arabidopsis halleri and the non-hyperaccumulating, non-tolerant species Arabidopsis petraea. The F2 segregates for both characters and it appears that the two characters are genetically independent. The data for tolerance are consistent with a single major gene for this character (although the number of genes for hyperaccumulation cannot be determined), and is probably not very large.

Arabidopsis↗
PubMed2004

Online recognition of Chinese characters: the state-of-the-art.

Online handwriting recognition is gaining renewed interest owing to the increase of pen computing applications and new pen input devices. The recognition of Chinese characters is different from western handwriting recognition and poses a special challenge. To provide an overview of the technical status and inspire future research, this paper reviews the advances in online Chinese character recognition (OLCCR), with emphasis on the research works from the 1990s. Compared to the research in the 1980s, the research efforts in the 1990s aimed to further relax the constraints of handwriting, namely, the adherence to standard stroke orders and stroke numbers and the restriction of recognition to isolated characters only. The target of recognition has shifted from regular script to fluent script in order to better meet the requirements of practical applications. The research works are reviewed in terms of pattern representation, character classification, learning/adaptation, and contextual processing. We compare important results and discuss possible directions of future research.

Algorithms↗
PubMed2002

Generalized character process models: estimating the genetic basis of traits that cannot be observed and that change with age or environmental conditions.

The genetic analysis of characters that change as a function of some independent and continuous variable has received increasing attention in the biological and statistical literature. Previous work in this area has focused on the analysis of normally distributed characters that are directly observed. We propose a framework for the development and specification of models for a quantitative genetic analysis of function-valued characters that are not directly observed, such as genetic variation in age-specific mortality rates or complex threshold characters. We employ a hybrid Markov chain Monte Carlo algorithm involving a Monte Carlo EM algorithm coupled with a Markov chain approximation to the likelihood, which is quite robust and provides accurate estimates of the parameters in our models. The methods are investigated using simulated data and are applied to a large data set measuring mortality rates in the fruit fly, Drosophila melanogaster.

Age Factors↗
PubMed2002

Character release following extinction in a Caribbean reef coral species complex.

The Pleistocene extinction of the widespread organ-pipe Montastraea coral had measurable morphological and ecological effects on surviving lineages of the Montastraea "annularis" species complex. Extinction of the organ-pipe Montastraea occurred after more than 500,000 years of dominance in the shallow-water reef habitat of Barbados. Extinction resulted in a morphological shift of the columnar Montastraea lineage from thick to thin columns in modern reef environments. Pleistocene colonies of the columnar morphotype sympatric with organ-pipe Montastraea showed greater column widths than those in allopatry. We subjected our data to a number of criteria for interpreting the morphological shift as character release following lifting of competitive pressure after extinction. The morphological differences do not appear to be due either to chance or to physical properties of the marine environment. Differential local extinction and recolonization of four members of the species complex did not occur on Barbados, so that the species coexisted and appear to have coevolved between more than 600,000 and 82,000 years ago. The morphological shift is related to coral growth form and growth rate, and thus reflects the acquisition of a primary resource in corals--light. Character release occurred at the same oceanic Caribbean island (Barbados) where environments have fluctuated with similar variance throughout the period of coexistence. Not only has competition among living members of the Montastraea "annularis" species complex been convincingly demonstrated, but trends in relative abundance among fossil members of the species complex strongly suggest that a competitive hierarchy was operating during their Pleistocene coexistence on Barbados. We also observed an ecological analogue to character release on another Caribbean island. Curaçao. The distribution and abundance of living columnar M. annularis s.s. and massive M. faveolata from the leeward reef crest in Curaçao is greater now than in the Pleistocene, when organ-pipe Montastraea dominated this shallow-water reef habitat. Extinction of the faster growing, shallow-water organ-pipe Montastraea resulted in higher abundance of the columnar Montastraea lineage in shallow-water habitats, where it shifted its morphology to one adapted to high light levels. The species extinction released surviving lineages from a competitive network that had resulted in lower rank abundance in the Pleistocene community and enhanced abundance of both columnar M. annularis s.s. and M. faveolata in modern communities. Full validation of our interpretation of character release must await experiments that demonstrate whether phenotypic differences between populations have a genetic basis. However, we believe the results of this study point to the important, yet heretofore neglected, role that biological interactions have played in the evolution of closely related reef coral species.

Animals↗