Resultados totales (Incluyendo duplicados): 33743
Encontrada(s) 3375 página(s)
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281568
Dataset. 2022

DATA_HDR_A ; DATA_HDR_B; DATA_HDR_C [DATASET] OF UNDERSTANDING LIFE AT HIGH TEMPERATURES. RELATIONSHIPS OF MOLECULAR CHANNELS IN ENZYMES OF METHANOGENIC ARCHAEA AND THEIR GROWTH TEMPERATURES

  • Ginsbach, Laura F.
  • González Grau, Juan Miguel
Los datos de estos tres excels pertenecen al trabajo Ginsbach, Laura F.; González Grau, Juan Miguel: of Understanding life at high temperatures. Relationships of molecular channels in enzymes of methanogenic Archaea and their growth temperatures, Figure 3. Molecular tunnel dimensions, length (A, D, G), surface (B, E, H) and volume (C, F, I)(in Å), predicted for the heterodisulfide reductase (Hdr) gene subunits, A (A, B, C), B (D, E, F) and C (G, H, I), from numerous methanogenic Archaea as a function of their optimum growth rates. Dark color filled symbols correspond to predicted protein structures; Light color filled symbols correspond to resolved model structures from the Protein Data Bank., This is funding from the Ministry of Science and Innovation, project EQC2019-005634-P (cofunded by FEDER) and PID2020-119373GB-I00., Peer reviewed

DOI: http://hdl.handle.net/10261/281568, https://doi.org/10.20350/digitalCSIC/14770
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281568
HANDLE: http://hdl.handle.net/10261/281568, https://doi.org/10.20350/digitalCSIC/14770
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281568
PMID: http://hdl.handle.net/10261/281568, https://doi.org/10.20350/digitalCSIC/14770
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281568
Ver en: http://hdl.handle.net/10261/281568, https://doi.org/10.20350/digitalCSIC/14770
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281568

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281573
Dataset. 2022

DATA_MCOM_RED_ALPHA; DATA_MCOM_RED_BETA; DATA_MCOM_RED_GAMMA [DATASET] OF UNDERSTANDING LIFE AT HIGH TEMPERATURES. RELATIONSHIPS OF MOLECULAR CHANNELS IN ENZYMES OF METHANOGENIC ARCHAEA AND THEIR GROWTH TEMPERATURES

  • Ginsbach, Laura F.
  • González Grau, Juan Miguel
Los datos de estos tres excels pertenecen al trabajo Ginsbach, Laura F.; González Grau, Juan Miguel: of Understanding life at high temperatures. Relationships of molecular channels in enzymes of methanogenic Archaea and their growth temperatures, Figure 2. Molecular tunnel dimensions, length (A, D, G), surface (B, E, H) and volume (C, F, I) (in Å), predicted for the methyl-CoM reductase (Mmr) gene subunits, alpha (A, B, C), beta (D, E, F) and gamma (G, H, I), from numerous methanogenic Archaea as a function of their optimum growth rates. Dark color filled symbols correspond to predicted protein structures. Light color filled symbols correspond to resolved model structures from the Protein Data Bank., This is funding from the Ministry of Science and Innovation, project EQC2019-005634-P (cofunded by FEDER) and PID2020-119373GB-I00., Peer reviewed

DOI: http://hdl.handle.net/10261/281573, https://doi.org/10.20350/digitalCSIC/14771
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281573
HANDLE: http://hdl.handle.net/10261/281573, https://doi.org/10.20350/digitalCSIC/14771
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281573
PMID: http://hdl.handle.net/10261/281573, https://doi.org/10.20350/digitalCSIC/14771
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281573
Ver en: http://hdl.handle.net/10261/281573, https://doi.org/10.20350/digitalCSIC/14771
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281573

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281576
Dataset. 2021

DATA FROM: ANNUAL AND PERENNIAL MEDICAGO SHOW SIGNATURES OF PARALLEL ADAPTATION TO CLIMATE AND SOIL IN HIGHLY CONSERVED GENES

  • Blanco-Pastor, J.L.
  • Liberal, Isabel.M.
  • Sakiroglu, M
  • Wei, Y
  • Brummer, E.C.
  • Andrew, R.L.
  • Pfeil, B.E.
Human induced environmental change may require rapid adaptation of plant populations and crops, but the genomic basis of environmental adaptation remain poorly understood. We analyzed polymorphic loci from the perennial crop Medicago sativa (alfalfa or lucerne) and the annual legume model species M. truncatula to search for a common set of candidate genes that might contribute to adaptation to abiotic stress in both annual and perennial Medicago species. We identified a set of candidate genes of environmental adaptation associated with environmental gradients along the distribution of the two Medicago species. Candidate genes for each species were detected in homologous genomic linkage blocks using genome-environment (GEA) and genome-phenotype association analyses. Hundreds of GEA candidate genes were species-specific, of these, 13.4% (M. sativa) and 24% (M. truncatula) were also significantly associated with phenotypic traits. A set of 168 GEA candidates were shared by both species, which was 25.4% more than expected by chance. When combined, they explained a high proportion of variance for certain phenotypic traits associated with adaptation. Genes with highly conserved functions dominated among the shared candidates and were enriched in Gene Ontology terms that have shown to play a central role in drought avoidance and tolerance mechanisms by means of cellular shape modifications and other functions associated with cell homeostasis. Our results point to the existence of a molecular basis of adaptation to abiotic stress in Medicago determined by highly conserved genes and gene functions. We discuss these results in light of the recently proposed omnigenic model of complex traits., European Commission, Award: 625308 Marie Curie Intra‐European Fellowship., Peer reviewed

Proyecto: EC/FP7/625308
DOI: http://hdl.handle.net/10261/281576
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281576
HANDLE: http://hdl.handle.net/10261/281576
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281576
PMID: http://hdl.handle.net/10261/281576
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281576
Ver en: http://hdl.handle.net/10261/281576
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281576

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281599
Dataset. 2017

DATA FROM: EVOLVABILITY MEETS BIOGEOGRAPHY: EVOLUTIONARY POTENTIAL DECREASES AT HIGH AND LOW ENVIRONMENTAL FAVOURABILITY

  • Martínez-Padilla, Jesús
  • Estrada, Alba
  • Early, Regan
  • García-González, Francisco
Data from: Evolvability meets biogeography: evolutionary potential decreases at high and low environmental favourability Fav_CVa_wildbirds.xlsx Data from: Evolvability meets biogeography: evolutionary potential decreases at high and low environmental favourability Fav_Ia_wildbirds.xlsx Species distribution and environmental variables Here we provide the environmental variables used to construct the SDM for each species. Description of the variables are given in the ESM of the paper Sps_environmental_variables.csv, Understanding and forecasting the effects of environmental change on wild populations requires knowledge on a critical question: do populations have the ability to evolve in response to that change? However, our knowledge on how evolution works in wild conditions under different environmental circumstances is extremely limited. We investigated how environmental variation influences the evolutionary potential of phenotypic traits. We used published data to collect or calculate 135 estimates of evolvability of morphological traits of European wild bird populations. We characterized the environmental favourability of each population throughout the species' breeding distribution. Our results suggest that the evolutionary potential of morphological traits decreases as environmental favourability becomes high or low. Strong environmental selection pressures and high intra-specific competition may reduce species' evolutionary potential in low- and high- favourability areas, respectively. This suggests that species may be least able to adapt to new climate conditions at their range margins and at the centre. Our results underscore the need to consider the evolutionary potential of populations when studying the drivers of species distributions, particularly when predicting the effects of environmental change. We discuss the utility of integrating evolutionary dynamics into a biogeographical perspective to understand how environmental variation shapes evolutionary patterns. This approach would also produce more reliable predictions about the effect of environmental change on population persistence and therefore on biodiversity., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281622
Dataset. 2017

DATA FROM: ABRUPT CHANGES IN THE COMPOSITION AND FUNCTION OF FUNGAL COMMUNITIES ALONG AN ENVIRONMENTAL GRADIENT IN THE HIGH ARCTIC

  • Grau, Oriol
  • Geml, József
  • Pérez-Haase, A.
  • Ninot, Josep M.
  • Semenova-Nelsen, Tatiana A.
  • Peñuelas, Josep
Z1 (Fell field-Bare ground-Plot 1) Z1.fastq Z2 (Fell field-Salix-Plot 1) Z2.fastq Z3 (Fell field-Dryas-Plot 1) Z3.fastq Z4 (Fell field-Bare ground-Plot 2) Z4.fastq Z5 (Fell field-Salix-Plot 2) Z5.fastq Z6 (Fell field-Dryas-Plot 2) Z6.fastq Z7 (Fell-field-Bare ground-Plot 3) Z7.fastq Z8 (Fell field-Dryas-Plot 3) Z8.fastq Z9 (Fell field-Salix-Plot 3) Z9.fastq Z10 (Heath-Bare ground-Plot 2) Z10.fastq Z11 (Snowbed-Bare ground-Plot 1) Z11.fastq Z12 (Snowbed-Salix-Plot 1) Z12.fastq Z13 (Snowbed-Bare ground-Plot 3) Z13.fastq Z14 (Snowbed-Salix-Plot 3) Z14.fastq Z15 (Snowbed-Dryas-Plot 3) Z15.fastq Z16 (Snowbed-Bare ground-Plot 2) Z16.fastq Z17 (Snowbed-Salix-Plot 2) Z17.fastq Z18 (Snowbed-Dryas-Plot 2) Z18.fastq Z19 (Snowbed-Dryas-Plot 1) Z19.fastq Z20 (Heath-Dryas-Plot 2) Z20.fastq Z21 (Heath-Salix-Plot 2) Z21.fastq Z22 (Heath-Bare ground-Plot 1) Z22.fastq Z23 (Heath-Dryas-Plot 1) Z23.fastq Z24 (Heath-Salix-Plot 1) Z24.fastq Z25 (Heath-Bare ground-Plot 3) Z25.fastq Z26 (Heath-Salix-Plot 3) Z26.fastq Z27 (Heath-Dryas-Plot 3) Z27.fastq, Fungi play a key role in soil-plant interactions, nutrient cycling, and carbon flow and are essential for the functioning of arctic terrestrial ecosystems. Some studies have shown that the composition of fungal communities is highly sensitive to variations in environmental conditions, but little is known about how the conditions control the role of fungal communities (i.e. their ecosystem function). We used DNA metabarcoding to compare taxonomic and functional composition of fungal communities along a gradient of environmental severity in Northeast Greenland. We analysed soil samples from fell fields, heaths, and snowbeds, three habitats with very contrasting abiotic conditions. We also assessed within-habitat differences by comparing three widespread microhabitats (patches with high cover of Dryas, Salix, or bare soil). The data suggest that, along the sampled mesotopographic gradient, the greatest differences in both fungal richness and community composition are observed among habitats, while the effect of microhabitat is weaker, although still significant. Furthermore, we found that richness and community composition of fungi are shaped primarily by abiotic factors and to a lesser, though still significant extent, by floristic composition. Along this mesotopographic gradient, environmental severity is strongly correlated with richness in all fungal functional groups: positively in saprotrophic, pathogenic, and lichenised fungi, and negatively in ectomycorrhizal and root-endophytic fungi. Our results suggest complex interactions amongst functional groups, possibly due to nutrient limitation or competitive exclusion, with potential implications on soil carbon stocks. These findings are important in light of the environmental changes predicted for the Arctic., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281669
Dataset. 2021

BAYESIAN MORPHOLOGICAL CLOCK VERSUS PARSIMONY: AN INSIGHT INTO THE RELATIONSHIPS AND DISPERSAL EVENTS OF POSTVACUUM CRICETIDAE (RODENTIA, MAMMALIA)

  • López-Antoñanzas, Raquel
  • Peláez-Campomanes, Pablo
[Methods] The material and methods section of the article contains all details concerning the methods used in this study. [Usage Notes] The readme file contains an explanation of each file uploaded in supplementary files., Establishing an evolutionary timescale is fundamental for tackling a great variety of topics in evolutionary biology, including the reconstruction of patterns of historical biogeography, coevolution and diversification. However, the tree of life is pruned by extinction and very generally molecular data cannot be gathered for extinct lineages. Methodological challenges have prevented until recently the application of tip-dating Bayesian approaches in morphology-based fossil-only datasets. Herein we present a morphological dataset for a group of cricetid rodents to which we apply a battery of methods fairly new in palaeontology that can be used by palaeontologists for the analysis of entirely extinct clades. We compare the tree topologies obtained by traditional parsimony, Bayesian dated and undated phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods seem to outperform parsimony in the case of our dataset, which includes highly homoplastic morphological characters. Regardless, all three topologies support the monophyly of Megacricetodontinae, Democricetodontinae and Cricetodontinae. Dispersal and speciation events inferred through Bayesian Binary Markov chain Monte Carlo and biodiversity analyses provide evidence for a correlation between biogeographic events, climatic changes and diversification in cricetids., Consejo Superior de Investigaciones Científicas, Award: PGC2018-094122-B-100 (MICU/AEI/FEDER,EU). European Commission, Award: ES-TAF-2579., Peer reviewed


Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281687
Dataset. 2017

DATA FROM: RESOLVING RECENT PLANT RADIATIONS: POWER AND ROBUSTNESS OF GENOTYPING-BY-SEQUENCING

  • Fernández-Mazuecos, Mario
  • Mellers, Greg
  • Vigalondo, Beatriz
  • Sáez, Llorenç
  • Vargas, Pablo
  • Glover, Beverley J.
Online Appendices Online Appendices 1 and 2 Supplementary Figures Supplementary Figures S1-S9 Supplementary Tables Supplementary Tables S1-S6 SNP matrices Unlinked SNP matrices used in genetic structure analyses. See text for dataset nomenclature SNPs.zip Allele files Sequence datasets used in phylogenetic analyses. Allele files produced by pyRAD are provided. See text for dataset nomenclature alleles.zip, Disentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, inter-specific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genus Linaria that radiated in the Quaternary. After confirming the morphological and genetic distinctness of eight species, we evaluated the relative performances of concatenation and coalescent methods to resolve phylogenetic relationships. Specifically, we focused on assessing the robustness of both approaches to variations in the parameter used to estimate sequence orthology (clustering threshold). Concatenation analyses suffered from strong systematic bias, as revealed by the high statistical support for multiple alternative topologies depending on clustering threshold values. By contrast, topologies produced by two coalescent-based methods (NJst, SVDquartets) were robust to variations in the clustering threshold. Reticulate evolution may partly explain incongruences between NJst, SVDquartets and concatenated trees. Integration of morphometric and coalescent-based phylogenetic results revealed (1) extensive morphological divergence associated with recent splits between geographically close or sympatric sister species, and (2) morphological convergence in geographically disjunct species. These patterns are particularly true for floral traits related to pollinator specialisation, including nectar spur length, tube width and corolla colour, suggesting pollinator-driven diversification. Given its relatively simple and inexpensive implementation, GBS is a promising technique for the phylogenetic and systematic study of recent radiations, but care must be taken to evaluate the robustness of results to variation of data assembly parameters., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281688
Dataset. 2021

DATA FROM: FACILITATION ENHANCES ECOSYSTEM FUNCTION WITH NON-RANDOM SPECIES GAINS

  • Verdú, Miguel
  • Goberna, M.
  • Navarro-Cano, J. A.
[Methods] We selected 25 plots under the nurse plant (Ononis tridentata) canopy and 25 adjacent gaps of the same size to estimate the cover of each plant. The size of the plots varied with the size of the nurse plant, ranging from 11435 to 21980 cm2. The cover of facilitated plants was estimated by adding the number of cm that each plant species occupied along a variable number of parallel linear transects established under the canopy of the nurse plant. To estimate the contribution of different processes to the BEF relationship, we followed the CAFE approach described in Bannar-Martin et al (2017; Ecol. Lett. 21, 167-180)., Facilitation, an ecological interaction assembling plant communities worldwide, has been shown to modulate both species richness and ecosystem functions. Such a Biodiversity-Ecosystem Functioning (BEF) relationship can be decomposed into different components not only related to species losses and gains but also to the identity of the species and the context in which they live. Using an extension of the classical BEF approach named CAFE (Community Assembly and the Functioning of Ecosystems), we quantified the contribution of these components to the BEF relationship in a Spanish semiarid plant community shaped by facilitation. We used species richness as a measure for biodiversity and plant cover as a proxy of multiple ecosystem functions including plant productivity, soil protection, soil fertility and microbial productivity. Nurse plants doubled the number of species that live beneath them relative to open ground, but caused a five-fold increase in plant cover. The disproportionate increase of plant cover was a consequence of the identity of the species enhanced by nurse plants, which were more productive than the average. We discuss these results in terms of sampling effects (i.e., the higher probability of richer communities to harbour hyperproductive species) and complementary effects (i.e., richer communities enhancing productivity through resource partitioning, abiotic facilitation, or biotic feedbacks). The enhancement of ecosystem functions that plant facilitation produces by incorporating species with high functional values to the community may reverberate among other trophic levels and propagate beyond the local scale where the ecological interaction is produced., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281698
Dataset. 2017

DATA FROM: A FATHER EFFECT EXPLAINS SEX-RATIO BIAS

  • Malo, Aurelio F.
  • Martínez-Pastor, Felipe
  • García-González, Francisco
  • Garde, José Julián
  • Ballou, Jonathan D.
  • Lacy, Robert C.
Data-Malo et al 2017 Data for the main analysis of the paper entitled "A father effect explains sex-ratio bias", relating the effects of sperm nucleus area and sperm nucleus length on offspring sex ratio (figure 1), the effects of the coefficient of inbreeding on offspring sex ratio weighing each data point for the total number of offspring (figure 2), and the effects of the coefficient of inbreeding on sperm nucleus area and sperm nucleus length (figure 3)., Sex ratio allocation has important fitness consequences, and theory predicts that parents should adjust offspring sex ratio in cases where the fitness returns of producing male and female offspring vary. The ability of fathers to bias offspring sex ratios has traditionally been dismissed given the expectation of an equal proportion of X- and Y-chromosome-bearing sperm (CBS) in ejaculates due to segregation of sex chromosomes at meiosis. This expectation has been recently refuted. Here we used Peromyscus leucopus to demonstrate that sex ratio is explained by an exclusive effect of the father, and suggest a likely mechanism by which male-driven sex-ratio bias is attained. We identified a male sperm morphological marker that is associated with the mechanism leading to sex ratio bias; differences among males in the sperm nucleus area (a proxy for the sex chromosome that the sperm contains) explain 22% variation in litter sex ratio. We further show the role played by the sperm nucleus area as a mediator in the relationship between individual genetic variation and sex-ratio bias. Fathers with high levels of genetic variation had ejaculates with a higher proportion of sperm with small nuclei area. This, in turn, led to siring a higher proportion of sons (25% increase in sons per 0.1 decrease in the inbreeding coefficient). Our results reveal a plausible mechanism underlying unexplored male-driven sex-ratio biases. We also discuss why this pattern of paternal bias can be adaptive. This research puts to rest the idea that father contribution to sex ratio variation should be disregarded in vertebrates, and will stimulate research on evolutionary constraints to sex ratios—for example, whether fathers and mothers have divergent, coinciding, or neutral sex allocation interests. Finally, these results offer a potential explanation for those intriguing cases in which there are sex ratio biases, such as in humans., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281701
Dataset. 2017

DATA FROM: MULTIPLE INTERACTION NETWORKS: TOWARDS MORE REALISTIC DESCRIPTIONS OF THE WEB OF LIFE

  • García-Callejas, David
  • Molowny-Horas, Roberto
  • Araújo, Miguel B.
R script for generating results The file included is a self-contained R script that was used to produce the results and images of the manuscript. Figures obtained with this script will not exactly match the ones of the paper due to the type of analyses performed, based on random parameterizations (within given parameter intervals) of dynamic models. 0IK-04428.R, Ecological communities are defined by species interacting dynamically in a given location at a given time, and can be conveniently represented as networks of interactions. Pairwise interactions can be ascribed to one of five main types, depending on their outcome for the species involved: amensalism, antagonism (including predation, parasitism and disease), commensalism, competition or mutualism. While most studies have dealt so far with networks involving one single type of interaction at a time, often focusing on a specific clade and/or guild, recent studies are being developed that consider networks with more than one interaction type and across several levels of biological organisation. We review these developments and suggest that three main frameworks are in use to investigate the properties of multiple interactions networks: 'expanded food-webs', 'multilayer networks' and 'equal footing networks'. They differ on how interactions are classified and implemented in mathematical models, and on whether the effect of different interaction types is expressed in the same units. We analyse the mathematical and ecological assumptions of these three approaches, and identify some of the questions that can be addressed with each one of them. Since the overwhelming majority of multiple interaction studies are theoretical and use artificially generated data, we also provide recommendations for the incorporation of field data in such studies., Peer reviewed

Proyecto: //

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