Bayesian molecular clock dating and the divergence times of angiosperms and primates

The explosive increase of molecular sequence data has produced unprecedented opportunities for addressing a number of evolutionary problems. Specially, the species divergence time estimation is fundamental because our understanding of history of life depends critically on knowledge of the ages of major clades. This thesis explores the use of molecular data (genome-scale datasets), combined with statistical summaries of the fossil record, to date the origin of angiosperms (flowering plants) and the divergence times of its major groups in an attempt to resolve the apparent conflict between the molecular dates and fossil evidence. Moreover, because fossil calibrations are the major source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis, several strategies for converting fossil calibrations into the prior on times are evaluated. Chapter one introduces the diversity and evolution of angiosperms, reviews the current literature that is based predominantly on systematics, phylogenetics, palaeobotany and plant molecular evolution. In introducing the early evolution of angiosperms this chapter highlights the questions associated with the origin of angiosperms and presents aims of the thesis. Chapter two focuses on molecular clock dating methods. It discusses different approaches for estimating divergence times, with emphasis on Bayesian molecular clock dating methods. Chapter three uses a powerful Bayesian method to analyze a molecular dataset of 83 genes from 644 taxa of vascular plants, combined with a suite of 52 fully-justified fossil calibrations to disentangle the pattern of angiosperm diversification. The results indicate that crown angiosperms originated during the Triassic to the Jurassic interval, long prior to the Cretaceous Terrestrial Revolution. This analysis demonstrates that even though many sources of uncertainty are explored, attempts to control for these factors still do not bring clock estimates and earliest confident fossil occurrences into agreement. A post-Jurassic origin of angiosperms was rejected, supporting the notion of a cryptic early history of angiosperms. The main factors affecting the estimates in this study are also discussed. Subsequently, in chapter four different strategies for summarizing fossil information to construct calibration priors were assessed employing an a priori procedure for deriving accurate calibration densities in Bayesian divergence dating. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. The results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis. Finally, chapter five draws together key finding from chapters three and four, and reviews how this work advances our understanding of the origin and evolution of angiosperms and on molecular clock dating using fossil calibrations. This chapter also highlights new gaps in our understanding of early evolution of angiosperms and in the implementation of fossil calibrations in Bayesian molecular clock dating, and discusses several areas for future research. Overall, this thesis highlights that more room for improvement might lie in refining our knowledge and use of fossil calibrations, the resulting improvements to molecular estimates of timescales will lead to a better understanding of angiosperm evolution. I speculate that these results will also shed light on dating discrepancies in other major clades

Molecular timetrees using relaxed clocks and uncertain phylogenies

A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to infer phylogeny and times jointly to incorporate phylogenetic errors into molecular dating. We compared the performance of these two alternatives in reconstructing evolutionary timetrees using computer-simulated and empirical datasets. We found sequential and joint analyses to produce similar divergence times and phylogenetic relationships, except for some nodes in particular cases. The joint inference performed better when the phylogeny was not well resolved, situations in which the joint inference should be preferred. However, joint inference can be infeasible for large datasets because available Bayesian methods are computationally burdensome. We present an alternative approach for joint inference that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals, incorporating phylogeny uncertainty. The new method alleviates the high computational burden imposed by Bayesian methods while achieving a similar result

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution.

Through the lens of the fossil record, angiosperm diversification precipitated a Cretaceous Terrestrial Revolution (KTR) in which pollinators, herbivores and predators underwent explosive co-diversification. Molecular dating studies imply that early angiosperm evolution is not documented in the fossil record. This mismatch remains controversial. We used a Bayesian molecular dating method to analyse a dataset of 83 genes from 644 taxa and 52 fossil calibrations to explore the effect of different interpretations of the fossil record, molecular clock models, data partitioning, among other factors, on angiosperm divergence time estimation. Controlling for different sources of uncertainty indicates that the timescale of angiosperm diversification is much less certain than previous molecular dating studies have suggested. Discord between molecular clock and purely fossil-based interpretations of angiosperm diversification may be a consequence of false precision on both sides. We reject a post-Jurassic origin of angiosperms, supporting the notion of a cryptic early history of angiosperms, but this history may be as much as 121 Myr, or as little as 23 Myr. These conclusions remain compatible with palaeobotanical evidence and a more general KTR in which major groups of angiosperms diverged later within the Cretaceous, alongside the diversification of pollinators, herbivores and their predators

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.

Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene

Stability and pKa Modulation of Aminophenoxazinones and Their Disulfide Mimics by Host-Guest Interaction with Cucurbit[7]uril. Direct Applications in Agrochemical Wheat Models

Aqueous solubility and stability often limit the application of aminophenoxazinones and their sulfur mimics as promising agrochemicals in a sustainable agriculture inspired by allelopathy. This paper presents a solution to the problem using host-guest complexation with cucurbiturils (CBn). Computational studies show that CB7 is the most suitably sized homologue due to its strong affinity for guest molecules and its high water solubility. Complex formation has been studied by direct titrations monitored using UV-vis spectroscopy, finding a preferential interaction with protonated aminophenoxazinone species with high binding affinities (CB7 center dot APOH+ , Ka = (1.85 +/- 0.37) x 106 M-1; CB7 center dot DiS-NH3+ , Ka = (3.91 +/- 0.53) x 104 M-1; and DiS-(NH3+)2 , Ka= (1.27 +/- 0.42) x 105M-1). NMR characterization and stability analysis were also performed and revealed an interesting pKa modulation and stabilization by cucurbiturils (2-amino-3H-phenoxazin-3-one (APO), pKa = 2.94 +/- 0.30, and CB7 center dot APO, pKa = 4.12 +/- 0.15; 2,2 '-disulfanediyldianiline (DiS-NH2), pKa = 2.14 +/- 0.09, and CB7 center dot DiS-NH2 , pKa = 3.26 +/- 0.09), thus favoring applications in different kinds of crop soils. Kinetic studies have demonstrated the stability of the CB7 center dot APO complex at different pH media for more than 90 min. An in vitro bioassay with etiolated wheat coleoptiles showed that the bioactivity of APO and DiS-NH2 is enhanced upon complexation

Aplicación de estrategias de gamificación en la enseñanza de sistemas constructivos

La coyuntura económica que atraviesa el sector construcción afecta a los estudiantes del Grado en Arquitectura Técnica de forma indirecta en cuanto a falta de motivación debido a la incertidumbre y desmotivación presente en el sector. Todo ello magnifica aún más un problema latente entre nuestro alumnado que es la inseguridad ante carreras técnicas tan amplias y complejas y nos lleva a replantearnos si el modelo tradicional de docencia universitaria es el adecuado ante estas situaciones. En la presente red se propone trasladar -de forma concreta en el grupo en inglés de la asignatura Foundamentals of Construction- la metodología docente actual de la asignatura basada en un modelo tradicional con clases magistrales, hacia una nueva metodología docente basada en estrategias dinámicas. A través de éstas se busca motivar al alumnado, fomentando el auto-aprendizaje para desarrollar competencias resolutivas y mejorar la cooperación y el trabajo colaborativo y multidisciplinar. En el presente curso se han desarrollado actividades dinámicas a modo de workshop con una visita teaching staff, pero a pesar de las mejoras detectadas todavía existen carencias. Por ello, para el próximo curso se pretende incluir nuevas estrategias de gamificacion basadas en TIC´s y su ampliación a otras asignaturas

Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.

Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of calibrations is thus expected to have a major impact on divergence time estimates even if a huge amount of molecular data is available. In Bayesian molecular clock dating, fossil calibration information is incorporated in the analysis through the prior on divergence times (the time prior). Here, we evaluate three strategies for converting fossil calibrations (in the form of minimum- and maximum-age bounds) into the prior on times, which differ according to whether they borrow information from the maximum age of ancestral nodes and minimum age of descendent nodes to form constraints for any given node on the phylogeny. We study a simple example that is analytically tractable, and analyze two real datasets (one of 10 primate species and another of 48 seed plant species) using three Bayesian dating programs: MCMCTree, MrBayes and BEAST2. We examine how different calibration strategies, the birth-death process, and automatic truncation (to enforce the constraint that ancestral nodes are older than descendent nodes) interact to determine the time prior. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. Our results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis.This research was funded by Biotechnology and Biosciences Research Council (UK) grant (BB/N000609/1) and Natural Environment Research Council (UK) grant (NE/N002067/1). J.B.-M. was supported by a CONACyT-Mexico and UCL scholarship

Aplicación de estrategias dinámicas en la enseñanza de Equipos de obra y maquinaria

La red docente en la que se ha trabajado expone una nueva metodología de trabajo para la asignatura Equipos de obra, instalaciones y medios auxiliares impartida en tercer curso del Grado en Arquitectura Técnica de la Universidad de Alicante. Con ella se quiere lograr una mayor colaboración del estudiante mediante la aplicación de estrategias dinámicas que favorezcan el trabajo colaborativo. De esta manera, se propone una estructura de trabajo donde exista el flujo de conocimiento entre los propios alumnos y entre éstos y el docente con una retroalimentación entre todos, así como, una actitud positiva para tomar decisiones y realizar exposiciones críticas, marcando el camino hacia un aprendizaje más autónomo. Con la implementación de estas estrategias, para el próximo curso 2016-2017, en el ámbito del aprendizaje de los equipos de obra que forman parte de los procesos constructivos llevados a cabo para la ejecución de una edificación, se simularán escenarios cotidianos relacionados con el área de estudio, permitiendo a los alumnos enfrentarse a problemas cotidianos durante la ejecución de la obra, con ello, tanto las sesiones teóricas como las prácticas tendrán un mayor dinamismo que permitirá al alumno interactuar con la asignatura, con los docentes y con sus propios compañeros

Unsupervised learning of satellite images enhances discovery of late Miocene fossil sites in the Urema Rift, Gorongosa, Mozambique

Paleoanthropological research focus still devotes most resources to areas generally known to be fossil rich instead of a strategy that first maps and identifies possible fossil sites in a given region. This leads to the paradoxical task of planning paleontological campaigns without knowing the true extent and likely potential of each fossil site and, hence, how to optimize the investment of time and resources. Yet to answer key questions in hominin evolution, paleoanthropologists must engage in fieldwork that targets substantial temporal and geographical gaps in the fossil record. How can the risk of potentially unsuccessful surveys be minimized, while maximizing the potential for successful surveys?SFRH/BD/122306/2016info:eu-repo/semantics/publishedVersio