Human impact and species richness of terrestrial vertebrate: a review at different macroecological scales

El impacto humano es una variable fundamental en biogeografía de la conservación. Para explorar su efecto sobre la riqueza de especies revisamos la literatura científica para vertebrados terrestres (anfibios, reptiles, mamíferos y aves) sobre este tema. Se realizó una búsqueda de bibliografía en inglés para el período 2000-2013 en la base de datos “ISI Web of Knowledge” filtrando por palabras claves. Analizamos la distribución de publicaciones por área biogeográfica, la influencia del tamaño de grano, extensión geográfica, grupo taxonómico y del signo de los coeficientes de correlación impacto humano-riqueza de especies. Encontramos 30 publicaciones que cumplían nuestros criterios de búsqueda. Estas se concentran mayoritariamente en el Paleártico. Aves y mamíferos son los grupos con mayor disponibilidad de publicaciones. Los estudios más frecuentes se ubican a una extensión regional y continental. Por último, la distribución de frecuencias de las correlaciones entre impacto humano y riqueza de especies muestra que dominan las correlaciones positivas, sobre todo a extensiones amplias. A tamaño de grano <1000 km2, encontramos una correlación negativa dominante, que podría estar mediada por procesos de pérdida y fragmentación de hábitat o cambios del uso del suelo. Estos resultados sirven para orientar aquellas regiones biogeográficas, grupos taxonómicos y escalas que precisan de mayor atención a la hora de planificar estudios futuros, que serán de vital interés para comprender las respuestas de la biodiversidad ante escenarios de cambio global.Human impact is a fundamental variable in conservation biogeography. To explore its effect on species richness, we reviewed the scientific literature for terrestrial vertebrates (amphibians, reptiles, mammals and birds) on this topic. The search was conducted using literature in English for the period 2000-2013 in the "ISI Web of Knowledge" database and filtering keywords. We analyze the distribution of publications by biogeographical area, the role of grain size, geographical extent, taxonomic group and the sign of the correlation coefficients in the relationships between humans-species richness. We found 30 publications that met our criteria. These are mainly concentrated in the Palearctic. Birds and mammals are the groups with higher availability of publications. Most studies are found at regional and continental level. Finally, the frequency distribution of correlations between human impact and species richness shows that positive correlations dominate at large scales. At a grain size <1000 km2, we find a dominantly negative correlation, which could be mediated by processes of habitat loss and fragmentation and/or land use changes. These results will serve to orient future studies to be focused on those biogeographic regions, taxonomic groups and scales that remain underrepresented and of vital interest to understand the responses of biodiversity to global change scenarios

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics

Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. It has been developed as a web server that integrates a suite of different tools selected among the most popular stand-alone programs in phylogenetic and evolutionary analysis. It has been conceived as a natural response to the increasing demand of data analysis of many experimental scientists wishing to add a molecular evolution and phylogenetics insight into their research. Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. Phylemon has several features that differentiates it from other resources: (i) It offers an integrated environment that enables the direct concatenation of evolutionary analyses, the storage of results and handles required data format conversions, (ii) Once an outfile is produced, Phylemon suggests the next possible analyses, thus guiding the user and facilitating the integration of multi-step analyses, and (iii) users can define and save complete pipelines for specific phylogenetic analysis to be automatically used on many genes in subsequent sessions or multiple genes in a single session (phylogenomics). The Phylemon web server is available at http://phylemon.bioinfo.cipf.es

A framework for genomic sequencing on clusters of multicore and manycore processors

[EN] The advances in genomic sequencing during the past few years have motivated the development of fast and reliable software for DNA/RNA sequencing on current high performance architectures. Most of these efforts target multicore processors, only a few can also exploit graphics processing units, and a much smaller set will run in clusters equipped with any of these multi-threaded architecture technologies. Furthermore, the examples that can be used on clusters today are all strongly coupled with a particular aligner. In this paper we introduce an alignment framework that can be leveraged to coordinately run any single-node aligner, taking advantage of the resources of a cluster without having to modify any portion of the original software. The key to our transparent migration lies in hiding the complexity associated with the multi-node execution (such as coordinating the processes running in the cluster nodes) inside the generic-aligner framework. Moreover, following the design and operation in our Message Passing Interface (MPI) version of HPG Aligner RNA BWT, we organize the framework into two stages in order to be able to execute different aligners in each one of them. With this configuration, for example, the first stage can ideally apply a fast aligner to accelerate the process, while the second one can be tuned to act as a refinement stage that further improves the global alignment process with little cost.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: The researchers from the University Jaume I were supported by the MINECO/CICYT (grant numbers TIN2011-23283 and TIN2014-53495-R) and FEDER.Martínez, H.; Barrachina, S.; Castillo, M.; Tárraga, J.; Medina, I.; Dopazo, J.; Quintana Ortí, ES. (2018). A framework for genomic sequencing on clusters of multicore and manycore processors. 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Concurrent and Accurate RNA Sequencing on Multicore Platforms

In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, named HPG-Aligner, leverages the speed of the Burrows-Wheeler Transform to map a large number of RNA fragments (reads) rapidly, as well as the accuracy of the Smith-Waterman algorithm, that is employed to deal with conflictive reads. The aligner is complemented with a careful strategy to detect splice junctions based on the division of RNA reads into short segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing useful information for the successful alignment of the complete reads. Experimental results on platforms with AMD and Intel multicore processors report the remarkable parallel performance of HPG-Aligner, on short and long RNA reads, which excels in both execution time and sensitivity to an state-of-the-art aligner such as TopHat 2 built on top of Bowtie and Bowtie 2

Concurrent and Accurate Short Read Mapping on Multicore Processors

We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA1, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100–400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.This work has been supported by the Bull-CIPF Chair for Computational Genomics. The researchers from the Jaume I University were supported by project TIN2011-23283 and FEDER

A new parallel pipeline for DNA methylation analysis of long reads datasets.

BACKGROUND: DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete. RESULTS: In this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while yielding a better level of sensitivity, particularly for datasets composed of long reads. This strategy can be exported to other methylation, DNA and RNA analysis tools. CONCLUSIONS: The developed software tool achieves execution times one order of magnitude shorter than the existing tools, while yielding equal sensitivity for short reads and even better sensitivity for long reads

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments

We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at