Directional biases in phylogenetic structure quantification: a Mediterranean case study

Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly differ depending on phylogenetic tree shape

Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information?

Appendix 1. (extra analyses). (ZIP 4769 kb

A generalized framework to expand incomplete phylogenies using non-molecular phylogenetic information

Aim: The increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the world's biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. This prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms. Innovation: Here, we present a completely generalized and flexible framework to expand incomplete phylogenies. The framework is implemented in the R package “randtip”, a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. Although randtip can generate fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the “blind” expansion of phylogenies using “quick-and-dirty” approaches often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step tutorial that was designed to provide guidelines to non-specialist users. Main Conclusions: Phylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete phylogenies and thereby account for phylogenetic uncertainty in quantitative analysesMinistry of Science and Innovation of Spain, Grant/Award Number: CGL2017- 86926-P; Regional Government of Madrid, Spain, Grant/Award Number: CM/ JIN/2019-00

Phylogenetic patterns of extinction risk in the endemic flora of a Mediterranean hotspot as a guiding tool for preemptive conservation actions

Climate change is a major driver of biodiversity decline with pervasive effects in biodiversity hotspots, where many endemic and threatened species thrive. However, the biological drivers of extinction susceptibility remain largely elusive, which hampers the implementation of effective conservation policies. Here, we advocate for the use of phylogenies as a complementary tool to inform policy makers. If we assume that the traits that determine extinction susceptibility are somewhat evolutionarily conserved, identifying the clades that accumulate a disproportionate amount of threatened species may help to mitigate potential increases in extinction risk among currently unthreatened species in these clades, even if the underlying biological drivers are unknown. We focused on the complete endemic angiosperm flora of a Mediterranean hotpot (Iberian Peninsula) to examine phylogenetic patterns in extinction risk expressed as IUCN categories (Least Concern “LC”, Near Threatened “NT”, Vulnerable “VU”, Endangered “EN” and Critically Endangered “CR”) using alpha and beta diversity metrics, comparative methods and a “hot node” approach. Phylogenetic diversity was significantly low for EN species and marginally significant for NT and CR, while LC and VU categories showed random pattern. Phylogenetic beta diversity (PBD) between IUCN categories was intermediate (0.40 – 0.61) and predominantly due to the “true” turnover component of PBD. Phylogenetic turnover was significantly low between NT – VU and VU – EN, suggesting that closely related species tend to show different threat status. In contrast, the comparisons involving the CR category sit toward the higher tail of the distribution, indicating a somewhat higher degree of clade specificity for CR species. In line with these patterns, phylogenetic signal in extinction risk was rather low (lambda = 0.23). Several of the “hot” clades that accumulated a significantly high number of species with the same threat status were specific to certain IUCN categories, yet few of them were observed across the categories. Most notably, the Caryophyllales stood out as the main threat-accumulating lineage, particularly within the Plumbaginaceae. All in all, our results indicate that few phylogenetic clades concentrate a great fraction of the extinction-risk gradient in the endemic flora of the western Mediterranean, and monitoring programs should pay particular attention to these extinction-prone lineagesThis paper contributes to the project REMEDINAL TE (P2018/EMT-4338) from the Regional Government of the Community of Madri

Biogeographic deconstruction of phylogenetic and functional diversity provides insights into the formation of regional assemblages

Evolutionary history and environmental filtering shape the phylogenetic and functional structure of regional assemblages. However, detecting the footprint of such eco-evolutionary drivers is challenging because these may often counter each other's signature. Here, we examined whether a biogeographic deconstruction approach of phylogenetic (PD) and functional diversity (FD) patterns may help in identifying eco-evolutionary signals in extant regional assemblages. As model system, we used forest understorey angiosperms found in three regions of Italy (Alpine, Mediterranean, Continental). We quantified PD and FD of all species inhabiting the three regions (regional assemblages). Then, we computed PD and FD for the subsets of species restricted to each region (biogeographic elements), also examining diversity patterns of species found across the three regions (widespread element). We used aboveground and belowground traits capturing major plant functions to calculate FD. Additionally, we assessed FD patterns decoupled from phylogeny. We found that species restricted to climatically harsh regions (Alpine and Mediterranean elements) were phylogenetically and functionally clustered, whereas widespread species were characterised by overdispersion. Species confined to the climatically intermediate (Continental) region were randomly sorted. By including all species occurring within a region, the patterns found for the region-restricted species blurred. Phylogenetically decoupled FD patterns were qualitatively similar to non-decoupled ones with the exception of the Alpine element, where we detected a clear signature of functional differentiation between closely related species. This suggests that recent speciation events contributed to shaping the Alpine flora. Compared to the belowground compartment, aboveground traits showed a more coherent pattern with that of all-trait FD – likely because most biomass is allocated aboveground in forest understoreys. This biogeographic deconstruction study illustrates which type of eco-evolutionary insights can be gained by implementing multifaceted and integrated approaches at the macroecological scal

Biogeographic deconstruction of phylogenetic and functional diversity provides insights into the formation of regional assemblages

Evolutionary history and environmental filtering shape the phylogenetic and functional structure of regional assemblages. However, detecting the footprint of such eco-evolutionary drivers is challenging because these may often counter each other's signature. Here, we examined whether a biogeographic deconstruction approach of phylogenetic (PD) and functional diversity (FD) patterns may help in identifying eco-evolutionary signals in extant regional assemblages. As model system, we used forest understorey angiosperms found in three regions of Italy (Alpine, Mediterranean, Continental). We quantified PD and FD of all species inhabiting the three regions (regional assemblages). Then, we computed PD and FD for the subsets of species restricted to each region (biogeographic elements), also examining diversity patterns of species found across the three regions (widespread element). We used aboveground and belowground traits capturing major plant functions to calculate FD. Additionally, we assessed FD patterns decoupled from phylogeny. We found that species restricted to climatically harsh regions (Alpine and Mediterranean elements) were phylogenetically and functionally clustered, whereas widespread species were characterised by overdispersion. Species confined to the climatically intermediate (Continental) region were randomly sorted. By including all species occurring within a region, the patterns found for the region-restricted species blurred. Phylogenetically decoupled FD patterns were qualitatively similar to non-decoupled ones with the exception of the Alpine element, where we detected a clear signature of functional differentiation between closely related species. This suggests that recent speciation events contributed to shaping the Alpine flora. Compared to the belowground compartment, aboveground traits showed a more coherent pattern with that of all-trait FD – likely because most biomass is allocated aboveground in forest understoreys. This biogeographic deconstruction study illustrates which type of eco-evolutionary insights can be gained by implementing multifaceted and integrated approaches at the macroecological scal

Comparing and Tuning Machine Learning Algorithms to Predict Type 2 Diabetes Mellitus

The main goals of this work is to study and compare machine learning algorithms to predict the development of type 2 diabetes mellitus. Four classifi cation algorithms have been considered, studying and comparing the accuracy of each one to predict the incidence of type 2 diabetes mellitus seven years in advance. Specifically, the techniques studied are: Decision Tree, Random Forest, kNN (k-Nearest Neighbors) and Neural Networks. The study not only involves the comparison among these techniques, but also, the tuning of the meta-parameters in each algorithm. The algorithms have been implemented using the language R. The data base used is obtained from the nation-wide cohort [email protected] study. The conclusions will include the accuracy of each algorithm and therefore the best technique for this problem. The best meta-parameters for each algorithm will be also provided.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Mirador mas parador en los Chacayes.

37 p.El Mirador mas Parador en los Chacayes es el resultado de Ia búsqueda de materialización de una idea, a su vez la idea obedece a Ia investigación particular realizada durante el proceso de titilación año 2006 y consiste en hacer aparecer un lugar, construir un artefacto que sumado a la tierra y al paisaje existente subraye un acontecimiento. En este lugar me siento, descanso hago una pausa en el camino observo, juego o salto busco mi sitio. La Forma es aquella que sin ser un adorno connota y distingue los sitios escogidos en un paisaje seco y homogéneo. La Materia es Ia propia tierra, las piedras, madera y hormigón que al ser intervenidas se transforman abandonan su estado inerte para ser Ia generatriz de La propuesta, ellas condicionan y cualifican la construcción

Conglomerado De Relevancias En El Discurso De Un Niño Llanero Sobre La Naturaleza.

La presente comunicación atiende al discurso sobre la naturaleza de Alfredo por medio de los Conglomerados de Relevancias (Molina 2000, 2012; Venegas 2012a,2012b) donde se exponen los diferentes criterios de valor (Naturalista, utilidad,Espacial, Ético–Estético-Emocional) de sus ideas sobre la naturaleza y lajerarquización a los mismos; se muestra la importancia de los criterios naturalista yde utilidad. La comunicación se configura desde la tesis doctoral “DiversidadCultural, Enseñanza de las Ciencias e Ideas de Naturaleza de Niños y Niñas”.Cabe resaltar que su discurso hace referencia a una construcción histórica de lospueblos de la Orinoquia colombiana, donde se reconoce la emergencia de lainclusión de estos saberes en la clase de ciencias y el papel de los mismos en laescuela para una enseñanza no colonialista. Palabras Clave Conglomerados de Relevancias, Ethos llanero, Ideas de Naturaleza

Alumbrado controlado por dimmer y temporizado

Unidad número 49 perteneciente al Módulo 2 del bloque 2 del curso de instalaciones eléctricas. En este capítulo se enseñará a efectuar instalaciones de alumbrado controladas por Dimmers y a hacer instalaciones de alumbrado contraladas por temporizadores e interruptores pulsadoresUnit number 49 belonging to Module 2 of block 2 of the course of electrical installations. This chapter will teach you how to carry out lighting installations controlled by Dimmers and to make lighting installations controlled by timers and pushbutton switchesEquipos, herramientas y materiales – Controles – Temporizados o minuteros – Protecciones – Esquema de circuitos especiales de alumbrado eléctrico, alimentados con corriente alterna monofásica – Proceso de ejecución de las instalacione