Character Mapping Research Articles

Rigidity in the Invariant Theory of Compact Lie Groups

A compact Lie group G and a faithful complex representation V determine the Sato-Tate measure μG,V on C, defined as the direct image of Haar measure with respect to the character map g 7→ tr(g|V ). We give a necessary and sufficient condition for a Sato-Tate measure to be an isolated point in the set of all Sato-Tate measures, regarded as a subset of the space of distributions on C. In particular we prove that if G is connected and semisimple and V is irreducible, then μG,V is an isolated point.

Evolution of the aquatic habit in Ludwigia (Onagraceae): Morpho-anatomical adaptive strategies in the Neotropics

Ludwigia displays a great variety of life forms adapted to aquatic habitats ranging from humid to water saturated. Morpho-anatomical characters were used to characterize and discriminate among selected Neotropical species of Ludwigia in terms of their root and shoot adaptations. A partial molecular phylogenetic hypothesis was reconstructed using the nrDNA ITS and cpDNA rpl32–trnLUAG regions for Neotropical species. ITS accessions of North temperate species were also included to provide a framework for the placement of our sampled taxa. Mapping of morpho-anatomical characters was performed on the resulting phylogenetic tree. We were able to separate the species in three groups according to their morpho-anatomical adaptations to aquatic habitats. Our results strengthen the support for at least two separate origins for the strictly aquatic habit in Neotropical representatives, in line with previous taxonomic classifications. We also suggest that these species experienced convergence of characters, but also diversified into various life forms adequate to live strictly in aquatic environments. We would like to highlight the great value of Ludwigia as a model system for the study of the evolution of characters that respond to pressures imposed by aquatic ecosystems within the dicotyledons, as well as within aquatic plants in general.

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.

BackgroundPorifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards.ResultsThe Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/.ConclusionsBy standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.

Perturbative Corrections to Kähler Moduli Spaces

We propose a general formula for perturbative-in-alpha' corrections to the Kahler potential on the quantum Kahler moduli space of Calabi-Yau n-folds, for any n, in their asymptotic large volume regime. The knowledge of such perturbative corrections provides an important ingredient needed to analyze the full structure of this Kahler potential, including nonperturbative corrections such as the Gromov-Witten invariants of the Calabi-Yau n-folds. We argue that the perturbative corrections take a universal form, and we find that this form is encapsulated in a specific additive characteristic class of the Calabi-Yau n-fold which we call the log Gamma class, and which arises naturally in a generalization of Mukai's modified Chern character map. Our proposal is inspired heavily by the recent observation of an equality between the partition function of certain supersymmetric, two-dimensional gauge theories on a two-sphere, and the aforementioned Kahler potential. We further strengthen our proposal by comparing our findings on the quantum Kahler moduli space to the complex structure moduli space of the corresponding mirror Calabi-Yau geometry.

A phylogenetic re-analysis of groupers with applications for ciguatera fish poisoning.

BackgroundCiguatera fish poisoning (CFP) is a significant public health problem due to dinoflagellates. It is responsible for one of the highest reported incidence of seafood-borne illness and Groupers are commonly reported as a source of CFP due to their position in the food chain. With the role of recent climate change on harmful algal blooms, CFP cases might become more frequent and more geographically widespread. Since there is no appropriate treatment for CFP, the most efficient solution is to regulate fish consumption. Such a strategy can only work if the fish sold are correctly identified, and it has been repeatedly shown that misidentifications and species substitutions occur in fish markets.MethodsWe provide here both a DNA-barcoding reference for groupers, and a new phylogenetic reconstruction based on five genes and a comprehensive taxonomical sampling. We analyse the correlation between geographic range of species and their susceptibility to ciguatera accumulation, and the co-occurrence of ciguatoxins in closely related species, using both character mapping and statistical methods.ResultsMisidentifications were encountered in public databases, precluding accurate species identifications. Epinephelinae now includes only twelve genera (vs. 15 previously). Comparisons with the ciguatera incidences show that in some genera most species are ciguateric, but statistical tests display only a moderate correlation with the phylogeny. Atlantic species were rarely contaminated, with ciguatera occurrences being restricted to the South Pacific.ConclusionsThe recent changes in classification based on the reanalyses of the relationships within Epinephelidae have an impact on the interpretation of the ciguatera distribution in the genera. In this context and to improve the monitoring of fish trade and safety, we need to obtain extensive data on contamination at the species level. Accurate species identifications through DNA barcoding are thus an essential tool in controlling CFP since meal remnants in CFP cases can be easily identified with molecular tools.

Riemann–Roch for equivariant K-theory

We show that for a linear algebraic group G acting on a smooth quasi-projective scheme X over a field, there is a Chern character map KiG(X)⊗R(G)R(G)ˆ→chXGCHG⁎(X,i)⊗S(G)S(G)ˆ with rational coefficients, which is an isomorphism. This establishes the equivariant version of the Riemann–Roch isomorphism between the higher algebraic K-theory and the higher Chow groups of smooth quasi-projective schemes.

WE-G-16A-01: Evolution of Radiation Treatment Planning

WE-G-16A-01: Evolution of Radiation Treatment Planning

Phylogenetic Analysis Reveals Multiple Cases of Morphological Parallelism and Taxonomic Polyphyly in <I>Lomatium</I> (Apiaceae)

Abstract The genera Lomatium and Cymopterus, along with many others, form a group that has been referred to previously as the perennial endemic Apiaceae subfamily Apioideae of western North America. This group of ecologically important and widespread species has been the target of numerous systematic studies, but the evolutionary relationships among these species remain elusive. Here we show that this confusion is due to high levels of morphological parallelism and homoplasy in the characters that have traditionally been used to define them, a result that is concordant with previous studies of the group. We explore patterns of evolution in traditionally important morphological characters using Bayesian stochastic character mapping on a phylogeny constructed from novel nrDNA and cpDNA sequence data for 96 specific and infraspecific taxa of the estimated 200 species in the group. We consider the implications of these results for taxonomic classification, the evolution of morphologies, and the utility of the...

MrEnt: an editor for publication‐quality phylogenetic tree illustrations

We developed MrEnt, a Windows-based, user-friendly software that allows the production of complex, high-resolution, publication-quality phylogenetic trees in few steps, directly from the analysis output. The program recognizes the standard Nexus tree format and the annotated tree files produced by BEAST and MrBayes. MrEnt combines in a single software a large suite of tree manipulation functions (e.g. handling of multiple trees, tree rotation, character mapping, node collapsing, compression of large clades, handling of time scale and error bars for chronograms) with drawing tools typical of standard graphic editors, including handling of graphic elements and images. The tree illustration can be printed or exported in several standard formats suitable for journal publication, PowerPoint presentation or Web publication.

Relating divergence in polychaete musculature to different burrowing behaviors: A study using opheliidae (Annelida)

Divergent morphologies among related species are often correlated with distinct behaviors and habitat uses. Considerable morphological and behavioral differences are found between two major clades within the polychaete family Opheliidae. For instance, Thoracophelia mucronata burrows by peristalsis, whereas Armandia brevis exhibits undulatory burrowing. We investigate the anatomical differences that allow for these distinct burrowing behaviors, then interpret these differences in an evolutionary context using broader phylogenetic (DNA-based) and morphological analyses of Opheliidae and taxa, such as Scalibregmatidae and Polygordiidae. Histological three-dimensional-reconstruction of A. brevis reveals bilateral longitudinal muscle bands as the prominent musculature of the body. Circular muscles are absent; instead oblique muscles act with unilateral contraction of longitudinal muscles to bend the body during undulation. The angle of helical fibers in the cuticle is consistent with the fibers supporting turgidity of the body rather than resisting radial expansion from longitudinal muscle contraction. Circular muscles are present in the anterior of T. mucronata, and they branch away from the body wall to form oblique muscles. Helical fibers in the cuticle are more axially oriented than those in undulatory burrowers, facilitating radial expansion during peristalsis. A transition in musculature accompanies the change in external morphology from the thorax to the abdomen, which has oblique muscles similar to A. brevis. Muscles in the muscular septum, which extends posteriorly to form the injector organ, act in synchrony with the body wall musculature during peristalsis: they contract to push fluid anteriorly and expand the head region following a direct peristaltic wave of the body wall muscles. The septum of A. brevis is much thinner and is presumably used for eversion of a nonmuscular pharynx. Mapping of morphological characters onto the molecular-based phylogeny shows close links between musculature and behavior, but less correlation with habitat.

Character mapping and cladogram comparison versus the requirement of total evidence: does it matter for polychaete systematics?

Fitzhugh, K. 2014. Character mapping and cladogram comparison versus the requirement of total evidence: does it matter for polychaete systematics? Memoirs of Museum Victoria 71: 67–78. The practice of partitioning data for the inferences of phylogenetic hypotheses has become a routine practice in biological systematics. Two popular approaches: (i) mapping ‘morphological’ characters onto ‘molecular’ phylogenies, and (ii) comparing ‘morphological’ and ‘molecular’ phylogenies, are examined in light of what is known as the requirement of total evidence. Inferences of phylogenetic hypotheses, indeed all taxa, occur by a type of non-deductive reasoning known as abduction. The intent of abduction is to offer at least tentative causal accounts that explain character data. The rational acceptance of abductively derived hypotheses is subject to conditions of the requirement of total evidence as a matter of the evidential support for those hypotheses. It is shown that both character mapping and comparisons of cladograms using partitioned datasets are procedures that severely reduce the credibility of phylogenetic hypotheses. This problem is alleviated by acknowledging the formal structure of the why-questions we ask in relation to character data, for which phylogenetic hypotheses serve as answers.

Construction of Molecular Genetic Linkage Map of Sugarbeet

Molecular genetic map is a fundamental tool for genomic research. In this study, a molecular genetic map was constructed using an F2 population consisting of 200 individuals from a cross between sugarbeet JV34-2(the high beet yield and low sugar content line) and sugarbeet 2B023(the low beet yield and high sugar content line) and a total of 561 SRAP primers and 114 SSR primers. Approximately 56 out of 561 and 20 out of 114 primers, respectively, showed polymorphisms. Each of these polymorphic primers produced at least one scorable polymorphic DNA band which was visible enough for detection and scoring. The map consisted of nine linkage groups which included 141(123 SRAP and 18 SSR) markers, and covered 1399.88 cM with an average distance of 9.92 cM. Three markers were still unlinked. All nine linkage groups consisting of 3–26 markers were 15.69–237.21 cM in length. Twenty point five six percent partially segregated markers distributed in the map, were mainly located on Chr.3 linkage groups, and the others were mapped on Chr.1, Chr.2, Chr.8, and Chr.9. This is the first gene map of sugarbeet, constructed by SRAP and SSR markers in China. It will provide the basis for gene mapping of important characters and cloning of excellent gene in sugarbeet.

Handwritten Pattern Recognition Using Kohonen Neural Network Based on Pixel Character

Handwriting is the human way in communicating each other using written media. By the advancement in technology and development of science, there are a lot of changes of technology in terms of communication with computer through handwriting. Therefore, it is needed computer able to receive input in the form of handwriting data and able to recognize the handwriting input. Therefore, this research focuses on handwritten character recognition using Kohonen neural network. The purpose of this research is to find handwriting recognition algorithm which can receive handwriting input and recognize handwritten character directly inputted in computer using Kohonen neural network. This method studies the distribution of a set of patterns without any class information. The basic idea of this technique is understood from how human brain stores images/patterns that have been recognized through eyes, and then able to reveal the images/patterns back. This research has been successful in developing an application to recognize handwritten characters using Kohonen neural network method, and it has been tested. The application is personal computer based and using a canvas as input media. The recognition process consist of 3 stages layer: Input layer, Training Layer and Hidden Layer. The Kohonen neural network method on handwritten character recognition application has good similarity level of character patterns in character mapping process.

Interplay between postcranial morphology and locomotor types in Neotropical sigmodontine rodents

Sigmodontine rats are one of the most diverse components of the Neotropical mammal fauna. They exhibit a wide ecological diversity and a variety of locomotor types that allow them to occupy different environments. To explore the relationship between morphology and locomotor types, we analyzed traits of the postcranial osteology (axial and appendicular skeletons) of 329 specimens belonging to 51 species and 29 genera of sigmodontines exhibiting different locomotor types. In this work, postcranial skeletal characters of these rats are considered in an ecomorphological study for the first time. Statistical analyses showed that of the 34 osteological characters considered, 15 were related to the locomotor types studied, except for ambulatory. However, character mapping showed that climbing and jumping sigmodontines are the only taxa exhibiting clear adaptations in their postcranial osteology, which are highly consistent with the tendencies described in many other mammal taxa. Climbing, digging and swimming rats presented statistically differences in traits associated with their vertebral column and limbs, whereas jumping rats showed modifications associated with all the skeletal regions. Our data suggest that sigmodontine rats retain an all-purpose morphology that allows them to use a variety of habitats. This versatility is particularly important when considering the lack of specialization of sigmodontines for a specific locomotor mode. Another possible interpretation is that our dataset probably did not consider relevant information about these groups and should be increased with other types of characters (e.g. characters from the external morphology, myology, etc.).

Evolutionary and Ecological Relationships of Gill Slit Morphology in Extant Sharks

One of the defining characteristics of Elasmobranchii is the external gill slits, through which water is expelled during exhalation. The morphology of the gill slits is presumed to vary among elasmobranchs, between ram and suction ventilators, and between pelagic and benthic species. However, the evolution of gill slit morphology and the relationship to behavior and ecology is not clear. The relative length of each slit, relative distance between adjacent pairs of slits, and number of slits positioned over the pectoral fin were quantified in 289 preserved specimens representing 185 species in 69 genera, 28 families, and 8 orders of sharks. Six character states of relative gill slit length, five character states of relative inter-gill slit spacing, and five gill slit positions over the pectoral fin were identified. Character mapping onto a phylogeny reveals that the basal state for extant Selachii is to possess slits of similar relative length and spacing with no slits over the pectoral fin. Multiple character states in various combinations evolved within the Carcharhiniformes, which is the most speciose extant group. Ontogenetic differences in gill slit morphology were found in the 12 genera in which adult and juvenile data were collected. Slit spacing in juveniles has an equal tendency to become more similar or more different in adults, whereas slit length changes more often from more similar in juveniles to increasingly different in adults. Exploring the relationships among gill slit morphology and ventilation mode in modern sharks reveals character complexes that are common to four body types. Macropelagic types are ram ventilators with a longer first slit length, similar slit spacing in most, and no slits over the pectoral fin. Most littoral types are ram ventilators, with decreasing slit length and spacing and with one slit over the fin. Benthic types are suction ventilators with decreasing slit length and spacing and up to four slits over the fin. Bathic and micropelagic types are suction ventilators with no slits over the fin and most having similar slit length and spacing. Morphological differences in gill slit morphology may correspond to hydrodynamic differences in exhaled water from the slits by habitat.

Chinese-Japanese Machine Translation Exploiting Chinese Characters

The Chinese and Japanese languages share Chinese characters. Since the Chinese characters in Japanese originated from ancient China, many common Chinese characters exist between these two languages. Since Chinese characters contain significant semantic information and common Chinese characters share the same meaning in the two languages, they can be quite useful in Chinese-Japanese machine translation (MT). We therefore propose a method for creating a Chinese character mapping table for Japanese, traditional Chinese, and simplified Chinese, with the aim of constructing a complete resource of common Chinese characters. Furthermore, we point out two main problems in Chinese word segmentation for Chinese-Japanese MT, namely, unknown words and word segmentation granularity, and propose an approach exploiting common Chinese characters to solve these problems. We also propose a statistical method for detecting other semantically equivalent Chinese characters other than the common ones and a method for exploiting shared Chinese characters in phrase alignment. Results of the experiments carried out on a state-of-the-art phrase-based statistical MT system and an example-based MT system show that our proposed approaches can improve MT performance significantly, thereby verifying the effectiveness of shared Chinese characters for Chinese-Japanese MT.

An In-silico Genomic Survey to Annotate Genes Coding for Early Development-Relevant Signaling Molecules in the Pearl Oyster, Pinctada fucata

The pearl oyster Pinctada fucata has great potential as a model system for lophotrochozoan developmental biology research. Pinctada fucata is an important commercial resource, and a significant body of primary research on this species has emphasized its basic aquaculture biology such as larval biology and growth, aquaculture, pearl formation and quality improvement, shell formation, and biomineralization. Recently, a draft genome sequence of this species was published, and many experimental resources are currently being developed, such as bioinformatics tools, embryo and larva manipulation methods, gene knockdown technique, etc. In this paper, we report the results from our genomic survey pertaining to gene families that encode developmental signaling ligands (Fgf, Hedgehog, PDGF/VEGF, TGFβ, and Wnt families). We found most of the representative genes of major signaling pathways involved in axial patterning, as well as copies of the signaling molecule paralogs. Phylogenetic character mapping was used to infer a possible evolutionary scenario of the signaling molecules in the protostomes, and to reconstruct possible copy numbers of signaling molecule-coding genes for the ancestral protostome. Our reconstruction suggests that P. fucata retains the ancestral protostome gene complement, providing further justifications for the use of this taxon as a model organism for developmental genomics research.

The importance of molecular dating analyses for inferring Hawaiian biogeographical history: a case study with bark lice (Psocidae: Ptycta)

AbstractAimThe use of intuitive or explicit biogeographical reconstruction techniques to estimate the timing of species radiations on the Hawaiian Islands, while often incorporating evidence on the timing of island formation, may be misleading if the effects of extinction are overlooked. Using phylogenies of the bark louse genus Ptycta (Psocidae), we compared results from biogeographical character mapping with those from molecular dating analyses. These results were used to evaluate the ‘progression model’, which predicts an oldest‐to‐youngest pattern of island colonization.LocationThe main Hawaiian Islands (Kauai, Oahu, Maui, Lanai, Molokai and Hawaii).MethodsWith a data set including 101 Hawaiian Ptycta specimens and 18 outgroup species, we constructed molecular phylogenies based on sequences of the nuclear gene wingless and mitochondrial genes 12S, 16S and cytochrome c oxidase subunit I (COI). Maximum‐likelihood, maximum‐parsimony and Bayesian phylogenetic analyses were used. We used beast to estimate a time‐calibrated tree under a relaxed clock model.ResultsOur analyses suggested a single colonization event, followed by extensive movement of Ptycta among islands and species radiations within and between islands. This monophyletic radiation is composed of two well‐supported clades that are also supported by two synapomorphic characters of the male genitalia.Main conclusionsVery different biogeographical patterns are inferred by molecular dating versus approaches based on character mapping. Simple biogeographical reconstruction over the molecular phylogeny supports a pattern of youngest‐to‐oldest island colonization, the reverse of that predicted by the ‘progression model’, and implies that this radiation could be as young as the most recent islands of Maui (1.4 Ma) or Hawaii (0.5 Ma). Molecular dating, however, infers a pattern consistent with oldest‐to‐youngest island colonization, and suggests a lineage age of 7.1 Ma. Extinction on the oldest island of Kauai may account for the differences in results between the two analyses.

Molecular phylogeny, biogeography, and host plant shifts in the bee genus Melitta (Hymenoptera: Anthophila)

New molecular studies suggested that the family Melittidae is either a paraphyletic group from which all the other bees are derived, or the sister clade to all other existing bees. Studying the historical biogeography and evolution of each major lineage within this group is a key step to understand the origin and early radiation of bees. Melitta is the largest genus of melittid bees, for which a robust molecular phylogeny and a biogeographic analysis are still lacking. Here, we derive a phylogenetic hypothesis from the sequences of seven independent DNA fragments of mitochondrial and nuclear origin. This phylogenetic hypothesis is then used to infer the evolution of the species range and of the host-plant shifts in Melitta. Our results confirmed the monophyly of Melitta, but did not recover all previously defined clades within the genus. We propose new taxa by splitting the genus in three subgenera (including two new subgenera described in the Appendix: Afromelitta subgen. nov., Plesiomelitta subgen. nov.) and describe two new species: Melitta avontuurensis sp. n. and M. richtersveldensis sp. n. Regarding the evolution of host-plant use, our analysis suggests that all species currently specialized on one plant family originated from an ancestor that was specialized on Fabaceae plants. The inferred biogeographic history for the genus supported an African origin. In concordance with previous studies identifying Africa as the geographic origin for many clades of bees, our data bring new evidence for an African origin of melittid bees.

On the Evolutionary and Biogeographic History of Saxifraga sect. Trachyphyllum (Gaud.) Koch (Saxifragaceae Juss.)

Arctic-alpine plants in the genus Saxifraga L. (Saxifragaceae Juss.) provide an excellent system for investigating the process of diversification in northern regions. Yet, sect. Trachyphyllum (Gaud.) Koch, which is comprised of about 8 to 26 species, has still not been explored by molecular systematists even though taxonomists concur that the section needs to be thoroughly re-examined. Our goals were to use chloroplast trnL-F and nuclear ITS DNA sequence data to circumscribe the section phylogenetically, test models of geographically-based population divergence, and assess the utility of morphological characters in estimating evolutionary relationships. To do so, we sequenced both genetic markers for 19 taxa within the section. The phylogenetic inferences of sect. Trachyphyllum using maximum likelihood and Bayesian analyses showed that the section is polyphyletic, with S. aspera L. and S bryoides L. falling outside the main clade. In addition, the analyses supported several taxonomic re-classifications to prior names. We used two approaches to test biogeographic hypotheses: i) a coalescent approach in Mesquite to test the fit of our reconstructed gene trees to geographically-based models of population divergence and ii) a maximum likelihood inference in Lagrange. These tests uncovered strong support for an origin of the clade in the Southern Rocky Mountains of North America followed by dispersal and divergence episodes across refugia. Finally we adopted a stochastic character mapping approach in SIMMAP to investigate the utility of morphological characters in estimating evolutionary relationships among taxa. We found that few morphological characters were phylogenetically informative and many were misleading. Our molecular analyses provide a foundation for the diversity and evolutionary relationships within sect. Trachyphyllum and hypotheses for better understanding the patterns and processes of divergence in this section, other saxifrages, and plants inhabiting the North Pacific Rim.