Frequency-Dependent Selection Predicts Patterns of Radiations and Biodiversity

Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking pre-existing niches, whereas constant rates have been attributed to non-adaptive processes such as sexual selection and mutation. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the temporal trend in the speciation rate can also be explained by frequency-dependent selection. We construct a frequency-dependent and DNA sequence-based model of speciation. We compare our model to empirical diversity patterns observed for cichlid fish and Darwin's finches, two classic systems for which speciation rates and richness data exist. Negative frequency-dependent selection predicts well both the declining speciation rate found in cichlid fish and explains their species richness. For groups like the Darwin's finches, in which speciation rates are constant and diversity is lower, speciation rate is better explained by a model without frequency-dependent selection. Our analysis shows that differences in diversity may be driven by incipient species abundance with frequency-dependent selection. Our results demonstrate that genetic-distance-based speciation and frequency-dependent selection are sufficient to explain the high diversity observed in natural systems and, importantly, predict decay through time in speciation rate in the absence of pre-existing niches.

A chrysophyte-based quantitative reconstruction of winter severity from varved lake sediments in NE Poland during the past millennium and its relationship to natural climate variability

Chrysophyte cysts are recognized as powerful proxies of cold-season temperatures. In this paper we use the relationship between chrysophyte assemblages and the number of days below 4 °C (DB4 °C) in the epilimnion of a lake in northern Poland to develop a transfer function and to reconstruct winter severity in Poland for the last millennium. DB4 °C is a climate variable related to the length of the winter. Multivariate ordination techniques were used to study the distribution of chrysophytes from sediment traps of 37 low-land lakes distributed along a variety of environmental and climatic gradients in northern Poland. Of all the environmental variables measured, stepwise variable selection and individual Redundancy analyses (RDA) identified DB4 °C as the most important variable for chrysophytes, explaining a portion of variance independent of variables related to water chemistry (conductivity, chlorides, K, sulfates), which were also important. A quantitative transfer function was created to estimate DB4 °C from sedimentary assemblages using partial least square regression (PLS). The two-component model (PLS-2) had a coefficient of determination of View the MathML sourceRcross2 = 0.58, with root mean squared error of prediction (RMSEP, based on leave-one-out) of 3.41 days. The resulting transfer function was applied to an annually-varved sediment core from Lake Żabińskie, providing a new sub-decadal quantitative reconstruction of DB4 °C with high chronological accuracy for the period AD 1000–2010. During Medieval Times (AD 1180–1440) winters were generally shorter (warmer) except for a decade with very long and severe winters around AD 1260–1270 (following the AD 1258 volcanic eruption). The 16th and 17th centuries and the beginning of the 19th century experienced very long severe winters. Comparison with other European cold-season reconstructions and atmospheric indices for this region indicates that large parts of the winter variability (reconstructed DB4 °C) is due to the interplay between the oscillations of the zonal flow controlled by the North Atlantic Oscillation (NAO) and the influence of continental anticyclonic systems (Siberian High, East Atlantic/Western Russia pattern). Differences with other European records are attributed to geographic climatological differences between Poland and Western Europe (Low Countries, Alps). Striking correspondence between the combined volcanic and solar forcing and the DB4 °C reconstruction prior to the 20th century suggests that winter climate in Poland responds mostly to natural forced variability (volcanic and solar) and the influence of unforced variability is low.

Intermediate Kinematics Produce Inferior Feeding Performance in a Classic Case of Natural Hybridization

Selection on naturally occurring hybrid individuals is a key component of speciation theory, but few studies examine the functional basis of hybrid performance. We examine the functional consequences of hybridization in nature, using the freshwater sunfishes (Centrarchidae), where natural hybrids have been studied for more than a century and a half. We examined bluegill (Lepomis macrochirus), green sunfish (Lepomis cyanellus), and their naturally occurring hybrid, using prey-capture kinematics and morphology to parameterize suction-feeding simulations on divergent parental resources. Hybrid individuals exhibited kinematics intermediate between those of the two parental species. However, performance assays indicated that hybrids display performance most similar to the worse-performing species for a given parental resource. Our results show that intermediate hybrid phenotypes can be impaired by a less-than-intermediate performance and hence suffer a larger loss in fitness than could be inferred from morphology alone.

A below-ground herbivore shapes root defensive chemistry in natural plant populations

Plants display extensive intraspecific variation in secondary metabolites. However, the selective forces shaping this diversity remain often unknown, especially below ground. Using Taraxacum officinale and its major native insect root herbivore Melolontha melolontha, we tested whether below-ground herbivores drive intraspecific variation in root secondary metabolites. We found that high M. melolontha infestation levels over recent decades are associated with high concentrations of major root latex secondary metabolites across 21 central European T. officinale field populations. By cultivating offspring of these populations, we show that both heritable variation and phenotypic plasticity contribute to the observed differences. Furthermore, we demonstrate that the production of the sesquiterpene lactone taraxinic acid β-d-glucopyranosyl ester (TA-G) is costly in the absence, but beneficial in the presence of M. melolontha, resulting in divergent selection of TA-G. Our results highlight the role of soil-dwelling insects for the evolution of plant defences in nature.

La luz natural como generadora del espacio arquitectónico de la catedral gótica

La historia de la construcción de las catedrales góticas es la historia de la búsqueda de la luz. Esta afirmación casi metafísica, recoge una realidad asumida por todos los historiadores tanto de la arquitectura antigua como del resto de las artes. La luz en el gótico ha sido descrita bajo múltiples matices como son su carácter simbólico, cromático e incluso místico, sin embargo no existe, en el estudio del conocimiento de la luz gótica, ninguna referencia a la misma como realidad física cuantificable, cualificable y por tanto, clasificable. La presente tesis doctoral aborda el concepto de la iluminación gótica desde una perspectiva nueva. Demuestra, con un método analítico inédito, que la iluminación gótica es cuantificable y cualificable. Para ello analiza en profundidad la iluminación de una selección de 6 edificios muestra, las catedrales de Gerona, Toledo, Sevilla y León, la basílica de Santa María del Mar y la capilla de la Sainte Chapelle de París, mediante una toma de datos “in situ” de iluminación y su comparación con los datos lumínicos obtenidos por un programa de soleamiento de la simulación en tres dimensiones de los distintos proyectos originales góticos. El análisis exhaustivo de las muestras y su introducción en el método analítico descrito, permite determinar, en primer lugar, unas cualidades inéditas que identifican la luz de los espacios góticos según unos parámetros nuevos como son la intensidad, expresividad, recorrido, distorsión y color. También describe cuales son los factores determinantes, de nuevo inéditos, que modulan cada una de las cualidades y en que proporción lo hacen cada uno de ellos. Una vez establecidas las cualidades y los factores que las definen, la tesis doctoral establece los rangos en los que se mueven las distintas cualidades y que conformarán la definitiva clasificación según “tipos de cualidad lumínica”. Adicionalmente, la tesis propone un procedimiento abreviado de acercamiento a la realidad de la iluminación gótica a través de unas fórmulas matemáticas que relacionan los factores geométricos detectados y descritos en la tesis con el resultado luminoso del espacio en lo que concierne a las dos cualidades más importantes de las reflejadas, la intensidad y la expresividad. Gracias a este método y su procedimiento abreviado, la clasificación se hace extensible al resto de catedrales góticas del panorama español y europeo y abre el camino a nuevas clasificaciones de edificios históricos de distintas épocas, iniciando un apasionante camino por recorrer en la recuperación de “la luz original”. Esta clasificación y sus cualidades podrán a su vez, ser utilizadas como herramientas de conocimiento de un factor determinante a la hora de describir cualquier espacio gótico y su aportación pretende ser un nuevo condicionante a tener en cuenta en el futuro, ayudando a entender y respetar, en las posibles intervenciones a realizar sobre el patrimonio arquitectónico, aquello que fue en su inicio motor principal del proyecto arquitectónico y que hoy día no se valora suficientemente tan solo por falta de conocimiento: su luz. The history of the construction of the Gothic cathedrals is the history of the search for light. This almost etaphysical statement reflects a reality accepted by all historians both of ancient architecture and other arts. Light in the Gothic period has been described under multiple approaches such as its symbolic, chromatic and even mystical character. However, in the study of the Gothic light, no references exist to it as a physical quantifiable and qualifiable reality and therefore, classifiable. This dissertation deals with the concept of Gothic light from a new perspective. With a new analytical method, it shows that Gothic lighting is quantifiable and can be classified regarding quality. To this end, a selection of 6 buildings light samples are analyzed; the cathedrals of Gerona, Toledo, Seville and León, the basilica of Santa María of the Sea and the Sainte Chapelle in Paris. "In situ" lighting data is collected and it is compared with lighting data obtained by a program of sunlight of the 3D simulation of various Gothic original projects. The comprehensive analysis of the samples and the data introduced in the analytical method described, allows determining, first, important qualities that identify the light of Gothic spaces according to new parameters such as intensity, expressiveness, trajectory, distortion and color. It also describes the determinant factors, which modulate each of the qualities and in what proportion they do it. Once the qualities and factors that define them have been established, in this doctoral dissertation the ranges regarding different qualities are set, which will make up the final classification according to "types of light quality". In addition, this work proposes an abbreviated procedure approach to the reality of the Gothic lighting through some mathematical formulae, relating the geometric factors identified and described in the study with the bright result of space regarding the two most important qualities of the light,intensity and expressiveness. Thanks to this method and to the abbreviated procedure, the classification can be applied to other Spanish and European Gothic cathedrals and opens up the way to new classifications of historic buildings from different eras, starting an exciting road ahead in the recovery of the "original light". This classification and its qualities may in turn be used as tools to know a determinant factor when describing any Gothic space. Its contribution is intended to be a new conditioning factor to keep in mind in the future, helping to understand and respect, in possible interventions on the architectural heritage, what was the main engine to start the architectural project and which today is not valued enough due to the lack knowledge: the light.

Sentence selection for improving the tuning process of a statistical machine translation system

Este artículo describe una estrategia de selección de frases para hacer el ajuste de un sistema de traducción estadístico basado en el decodificador Moses que traduce del español al inglés. En este trabajo proponemos dos posibilidades para realizar esta selección de las frases del corpus de validación que más se parecen a las frases que queremos traducir (frases de test en lengua origen). Con esta selección podemos obtener unos mejores pesos de los modelos para emplearlos después en el proceso de traducción y, por tanto, mejorar los resultados. Concretamente, con el método de selección basado en la medida de similitud propuesta en este artículo, mejoramos la medida BLEU del 27,17% con el corpus de validación completo al 27,27% seleccionando las frases para el ajuste. Estos resultados se acercan a los del experimento ORACLE: se utilizan las mismas frases de test para hacer el ajuste de los pesos. En este caso, el BLEU obtenido es de 27,51%.

Modelo basado en técnicas de procesamiento de lenguaje natural para extraer y anotar información de publicaciones científicas

La rápida evolución experimentada en los últimos años por las tecnologías de Internet ha estimulado la proliferación de recursos software en varias disciplinas científicas, especialmente en bioinformática. En la mayoría de los casos, la tendencia actual es publicar dichos recursos como servicios accesibles libremente a través de Internet, utilizando tecnologías y patrones de diseño definidos para la implementación de Arquitecturas Orientadas a Servicios (SOA). La combinación simultánea de múltiples servicios dentro de un mismo flujo de trabajo abre la posibilidad de crear aplicaciones potencialmente más útiles y complejas. La integración de dichos servicios plantea grandes desafíos, tanto desde un punto de vista teórico como práctico, como por ejemplo, la localización y acceso a los recursos disponibles o la coordinación entre ellos. En esta tesis doctoral se aborda el problema de la identificación, localización, clasificación y acceso a los recursos informáticos disponibles en Internet. Con este fin, se ha definido un modelo genérico para la construcción de índices de recursos software con información extraída automáticamente de artículos de la literatura científica especializada en un área. Este modelo consta de seis fases que abarcan desde la selección de las fuentes de datos hasta el acceso a los índices creados, pasando por la identificación, extracción, clasificación y “curación” de la información relativa a los recursos. Para verificar la viabilidad, idoneidad y eficiencia del modelo propuesto, éste ha sido evaluado en dos dominios científicos diferentes—la BioInformática y la Informática Médica—dando lugar a dos índices de recursos denominados BioInformatics Resource Inventory (BIRI) y electronic-Medical Informatics Repository of Resources(e-MIR2) respectivamente. Los resultados obtenidos de estas aplicaciones son presentados a lo largo de la presente tesis doctoral y han dado lugar a varias publicaciones científicas en diferentes revistas JCR y congresos internacionales. El impacto potencial y la utilidad de esta tesis doctoral podrían resultar muy importantes teniendo en cuenta que, gracias a la generalidad del modelo propuesto, éste podría ser aplicado en cualquier disciplina científica. Algunas de las líneas de investigación futuras más relevantes derivadas de este trabajo son esbozadas al final en el último capítulo de este libro. ABSTRACT The rapid evolution experimented in the last years by the Internet technologies has stimulated the proliferation of heterogeneous software resources in most scientific disciplines, especially in the bioinformatics area. In most cases, current trends aim to publish those resources as services freely available over the Internet, using technologies and design patterns defined for the implementation of Service-Oriented Architectures (SOA). Simultaneous combination of various services into the same workflow opens the opportunity of creating more complex and useful applications. Integration of services raises great challenges, both from a theoretical to a practical point of view such as, for instance, the location and access to the available resources or the orchestration among them. This PhD thesis deals with the problem of identification, location, classification and access to informatics resources available over the Internet. On this regard, a general model has been defined for building indexes of software resources, with information extracted automatically from scientific articles from the literature specialized in the area. Such model consists of six phases ranging from the selection of data sources to the access to the indexes created, covering the identification, extraction, classification and curation of the information related to the software resources. To verify the viability, feasibility and efficiency of the proposed model, it has been evaluated in two different scientific domains—Bioinformatics and Medical Informatics—producing two resources indexes named BioInformatics Resources Inventory (BIRI) and electronic-Medical Informatics Repository of Resources (e-MIR2) respectively. The results and evaluation of those systems are presented along this PhD thesis, and they have produced different scientific publications in several JCR journals and international conferences. The potential impact and utility of this PhD thesis could be of great relevance considering that, thanks to the generality of the proposed model, it could be successfully extended to any scientific discipline. Some of the most relevant future research lines derived from this work are outlined at the end of this book.

Estrategias, sistemas y tecnologías para el uso de luz natural y su aplicación en la rehabilitación de edificios históricos

La presente tesis investiga sobre la manera en que la arquitectura se ha construido para utilizar la luz natural, con el fin de aplicar estos conocimientos a la rehabilitación de edificios históricos. Para ello es necesario conocer aspectos técnicos en el uso de la luz, partiendo por comprender cuáles son los fenómenos físicos que debiéramos conocer los arquitectos para poder utilizarla adecuadamente. Es necesario también saber cómo es el comportamiento de los materiales frente a la luz y cómo utilizar¬los en el contexto rehabilitación. Dentro de los aspectos técnicos, se establece cuáles son las estrate¬gias, los sistemas y las tecnologías necesarias para la utilización de la luz en arquitectura, y se organiza esta información con el fin de hacerla clara, accesible y útil. Sin embargo, la luz no puede ser empleada en forma adecuada si no se conocen los requerimientos y las necesidades que el ser humano tiene respecto de ella, para habitar en forma confortable y salu¬dable. Es por eso que se establecen a su vez los requerimientos humanos respecto de la luz desde el punto de vista de sus características biológicas, su percepción y sus necesidades ergonómicas. Como la tesis se enmarca dentro de la problemática de la rehabilitación de edificios históricos, es necesario conocer cuál es la relación entre los procesos histórico-culturales y la técnica para utilizar la luz en la historia de la arquitectura. Se busca establecer la correlación entre historia y técnica, con el fin de responder en forma adecuada a los valores patrimoniales de un edificio histórico al alterar un aspecto tan importante como su iluminación natural. Con este conjunto de conocimientos técnicos, humanos e históricos establecidos en la primera parte de la tesis, se propone un protocolo de diseño para un proyecto de rehabilitación en cinco casos de estudio. Esta herramienta analiza el comportamiento actual de la luz para una determinada función, detecta los problemas lumínicos, establece criterios para la elección de soluciones y analiza el compor¬tamiento de estas soluciones. Finalmente compara los resultados lumínicos de las condiciones actua¬les y la solución propuesta. Por último, la investigación genera criterios que pueden ser aplicables a la normativa chilena de plani¬ficación territorial respecto del uso de la luz en contextos urbanos patrimoniales. ABSTRACT This thesis addresses how the architecture has been built to use natural light, in order to apply this knowledge to the historic buildings rehabilitation. This requires knowing technical aspects in the use of light, starting to understand what physical phenomena we, the architects, should know to use it properly. It is also necessary to know how materials behave in regards to light and how to use it in the rehabilitation context. Among the technical aspects, we should define strategies, systems and techno¬logies necessary for the use of light in architecture, and organize this information in order to make it clear, available and useful. However, light cannot be used properly if are not known requirements and needs that human beings have towards it, to live in comfortable and healthy way. That is why light human requirements are determined to know how light influences their cycles, perception and comfort. As the thesis is in frame of rehabilitation of historic building problem, it is necessary to know how is the relationship between historic-cultural processes and technology of light use, in the architecture history. It seeks to establish the correlation between History and technology, in order to give an ade¬quately answer to the heritage values of a historic building by altering an important aspect like its natural lighting. With this set of technical, human and historical knowledge, established in the first part of the thesis, a protocol is proposed for a rehabilitation project design in five study cases. This tool analyzes current behavior of light for a specifically function, detects lighting problems, establishes criteria for the selec¬tion of solutions and analyzes solution behaviors. Additionally, it compares results of current lighting conditions and the proposed solution. Finally this research generates criteria that may be applicable to Chilean territorial planning legislation, regarding use of light in patrimonial urban contexts.

Planning and Management of Mobility in Natural Protected Areas

The paper describes some relevant results of an on-going research aiming to elaborate a methodology to help the mobility management in natural parks, compatible with their protection missions: it has been developed a procedure to reproduce the mobility-environment relationships in various operational conditions. The final purpose is the identification of: a) the effects of various choices in transport planning, both at long term and strategic level; b) the most effective policies of mobility management. The work is articulated in the following steps: 1) definition of protected area on the basis of ecological and socio-economic criteria and legislative constraints; 2) analysis of mobility needs in the protected areas; 3) reconstruction of the state of the art of mobility management in natural parks at European level; 4) analysis of used traffic flows measurement methods; 5) analysis of environmental impacts due to transport systems modelling (air pollution and noise only); 6) identification of mitigation measures to be potentially applied. The whole methodology has been tested and validated on Italian case studies: i) the concerned area has been zoned according to the land-use peculiarities; ii) the local situations of transport infrastructure (roads and parking), services (public transport systems) and rules (traffic regulations) have been mapped with references to physical and functional attributes; iii) the mobility, both systematic and touristic, has been represented in an origin-destination matrix. By means of an assignment model the flows have been distributed and the corresponding average speeds to quantify gaseous and noise emissions was calculated, the criticalities in the reference scenario have been highlighted, as well as some alternative scenarios, including both operational and infrastructural measures have been identified. The comparison between projects and reference scenario allowed the quantification of effects (variation of emissions) for each scenario and a selection of the most effective management actions to be taken.

Planning and management of mobility in natural protected areas

The final purpose is the identification of: a) the effects of various choices in transport planning, both at long term and strategic level; b) the most effective policies of mobility management. The preliminary work was articulated in the following steps: 1) definition of protected area on the basis of ecological and socio-economic criteria and legislative constraints; 2) analysis of mobility needs in the protected areas; 3) reconstruction of the state of the art of mobility management in natural parks at European level; 4) analysis of used traffic flows measurement methods; 5) analysis of environmental impacts due to transport systems modelling (limited to air pollution and noise); 6) identification of mitigation measures to the potentially applied. The whole methodology has been firstly tested on the case study of the National Park of ?Gran Sasso and Monti della Laga? and further validated on the National Park of ?Gargano?, both located Italy: i) the concerned area has been zoned according to the land-use peculiarities; ii) the local situations of transport infrastructure (roads and parking), services (public transport systems) and rules (traffic regulations) have been mapped with references to physical and functional attributes; iii) the mobility, both systematic and touristic, has been synthetically represented in an origin-destination matrix. By means of an assignment model it has been determined the distribution of flows and the corresponding average speeds to quantify gaseous and noise emissions. On this basis the environmental criticalities in the reference scenario have been highlighted, as well as some alternative scenarios including both operational and infrastructural measures have been identified. The comparison between the projects and the reference scenario allowed the quantification of the effects (variation of emissions) for each scenario and a selection of the most effective management actions to be taken.

Major histocompatibility complex (MHC) class I KbDb −/− deficient mice possess functional CD8+ T cells and natural killer cells

We obtained mice deficient for major histocompatibility complex (MHC) molecules encoded by the H-2K and H-2D genes. H-2 KbDb −/− mice express no detectable classical MHC class I-region associated (Ia) heavy chains, although β2-microglobulin and the nonclassical class Ib proteins examined are expressed normally. KbDb −/− mice have greatly reduced numbers of mature CD8+ T cells, indicating that selection of the vast majority (>90%) of CD8+ T cells cannot be compensated for by β2-microglobulin-associated molecules other than classical H-2K and D locus products. In accord with the greatly reduced number of CD8+ T cells, spleen cells from KbDb −/− mice do not generate cytotoxic responses in primary mixed-lymphocyte cultures against MHC-disparate (allogeneic) cells. However, in vivo priming of KbDb −/− mice with allogeneic cells resulted in strong CD8+ MHC class Ia-specific allogeneic responses. Thus, a minor population of functionally competent peripheral CD8+ T cells capable of strong cytotoxic activity arises in the complete absence of classical MHC class Ia molecules. KbDb −/− animals also have natural killer cells that retain their cytotoxic potential.

Possible ecological risks of transgenic organism release when transgenes affect mating success: Sexual selection and the Trojan gene hypothesis

Widespread interest in producing transgenic organisms is balanced by concern over ecological hazards, such as species extinction if such organisms were to be released into nature. An ecological risk associated with the introduction of a transgenic organism is that the transgene, though rare, can spread in a natural population. An increase in transgene frequency is often assumed to be unlikely because transgenic organisms typically have some viability disadvantage. Reduced viability is assumed to be common because transgenic individuals are best viewed as macromutants that lack any history of selection that could reduce negative fitness effects. However, these arguments ignore the potential advantageous effects of transgenes on some aspect of fitness such as mating success. Here, we examine the risk to a natural population after release of a few transgenic individuals when the transgene trait simultaneously increases transgenic male mating success and lowers the viability of transgenic offspring. We obtained relevant life history data by using the small cyprinodont fish, Japanese medaka (Oryzias latipes) as a model. Our deterministic equations predict that a transgene introduced into a natural population by a small number of transgenic fish will spread as a result of enhanced mating advantage, but the reduced viability of offspring will cause eventual local extinction of both populations. Such risks should be evaluated with each new transgenic animal before release.

Negative frequency-dependent selection maintains a dramatic flower color polymorphism in the rewardless orchid Dactylorhiza sambucina (L.) Soò

The orchid Dactylorhiza sambucina shows a stable and dramatic flower-color polymorphism, with both yellow- and purple-flowered individuals present in natural populations throughout the range of the species in Europe. The evolutionary significance of flower-color polymorphisms found in many rewardless orchid species has been discussed at length, but the mechanisms responsible for their maintenance remain unclear. Laboratory experiments have suggested that behavioral responses by pollinators to lack of reward availability might result in a reproductive advantage for rare-color morphs. Consequently, we performed an experiment varying the relative frequency of the two color morphs of D. sambucina to test whether rare morph advantage acted in the natural habitat of the species. We show here clear evidence from this manipulative experiment that rare-color morphs have reproductive advantage through male and female components. This is the first demonstration, to our knowledge, that negative frequency-dependent selection through pollinator preference for rare morphs can cause the maintenance of a flower-color polymorphism.

Exploring the active site of chorismate mutase by combinatorial mutagenesis and selection: the importance of electrostatic catalysis.

Chorismate mutase (EC 5.4.99.5) catalyzes the intramolecular rearrangement of chorismate to prephenate. Arg-90 in the active site of the enzyme from Bacillus subtilis is in close proximity to the substrate's ether oxygen and may contribute to efficient catalysis by stabilizing the presumed dipolar transition state that would result upon scission of the C--O bond. To test this idea, we have developed a novel complementation system for chorismate mutase activity in Escherichia coli by reengineering parts of the aromatic amino acid biosynthetic pathway. The codon for Arg-90 was randomized, alone and in combination with that for Cys-88, and active clones were selected. The results show that a positively charged residue either at position 88 (Lys) or 90 (Arg or Lys) is essential. Our data provide strong support for the hypothesis that the positive charge is required for stabilization of the transition state of the enzymatic chorismate rearrangement. The new selection system, in conjunction with combinatorial mutagenesis, renders the mechanism of the natural enzyme(s) accessible to further exploration and opens avenues for the improvement of first generation catalytic antibodies with chorismate mutase activity.

Maintenance of pre-mRNA secondary structure by epistatic selection.

Linkage disequilibrium between polymorphisms in a natural population may result from various evolutionary forces, including random genetic drift due to sampling of gametes during reproduction, restricted migration between subpopulations in a subdivided population, or epistatic selection. In this report, we present evidence that the majority of significant linkage disequilibria observed in introns of the alcohol dehydrogenase locus (Adh) of Drosophila pseudoobscura are due to epistatic selection maintaining secondary structure of precursor mRNA (pre-mRNA). Based on phylogenetic-comparative analysis and a likelihood approach, we propose secondary structure models of Adh pre-mRNA for the regions of the adult intron and intron 2 where clustering of linkage disequilibria has been observed. Furthermore, we applied the likelihood ratio test to the phylogenetically predicted secondary structure in intron 1. In contrast to the other two structures, polymorphisms associated with the more conserved stem-loop structure of intron 1 are in low frequency, and linkage disequilibria have not been observed. These findings are qualitatively consistent with a model of compensatory fitness interactions. This model assumes that mutations disrupting pairing in a secondary structural element are individually deleterious if they destabilize a functionally important structure; a second "compensatory" mutation, however, may restabilize the structure and restore fitness.