Resultados totales (Incluyendo duplicados): 35611
Encontrada(s) 3562 página(s)
Encontrada(s) 3562 página(s)
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281362
Dataset. 2017
DATA FROM: THE DOMINANT DETRITUS-FEEDING INVERTEBRATE IN ARCTIC PEAT SOILS DERIVES ITS ESSENTIAL AMINO ACIDS FROM GUT SYMBIONTS
- Larsen, Thomas
- Ventura, Marc
- Maraldo, Kristine
- Triadó-Margarit, Xavier
- Casamayor, Emilio O.
- Wang, Yiming V.
- Andersen, Nils
- O'Brien, Diane M.
13C values of amino acids
Sample 13C values (‰) of amino acids. Each sample was analyzed in triplicate (mean ± SD). NA indicates missing values or replicates. The values are compiled from this study and Larsen et al. (Plos One 2013) (marked with asterisk under sample code).
Larsen_13CAA.csv, Supplementation of nutrients by symbionts enables consumers to thrive on resources that might otherwise be insufficient to meet nutritional demands. Such nutritional subsidies by intracellular symbionts has been well studied; however, supplementation of de novo synthesized nutrients to hosts by extracellular gut symbionts is poorly documented, especially for generalists with relatively undifferentiated intestinal tracts. Although gut symbionts facilitate degradation of resources that would otherwise remain inaccessible to the host, such digestive actions alone cannot make up for dietary insufficiencies of macronutrients such as essential amino acids (EAA). Documenting whether gut symbionts also function as partners for symbiotic EAA supplementation is important because the question of how some detritivores are able to subsist on nutritionally insufficient diets has remained unresolved. To answer this poorly-understood nutritional aspect of symbiont-host interactions, we studied the enchytraeid worm, a bulk soil feeder that thrives in arctic peatlands. In a combined field and laboratory study, we employed stable isotope fingerprinting of amino acids to identify the biosynthetic origins of amino acids to bacteria, fungi and plants in enchytraeids. Enchytraeids collected from arctic peatlands derived more than 80% of their EAA from bacteria. In a controlled feeding study with the enchytraeid Enchytraeus crypticus, EAA derived almost exclusively from gut bacteria when the worms fed on higher fiber diets, whereas most of the enchytraeids' EAA derived from dietary sources when fed on lower fiber diets. Our gene sequencing results of gut microbiota showed that the worms harbor several taxa in their gut lumen absent from their diets and substrates. Almost all gut taxa are candidates for EAA supplementation because almost all belong to clades capable of biosynthesizing EAA. Our study provides the first evidence of extensive symbiotic supplementation of EAA by microbial gut symbionts, and demonstrate that symbiotic bacteria in the gut lumen appear to function as partners for both symbiotic EAA supplementation as well as for digestion of insoluble plant fibers., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.6f798" target="_blank">http://hdl.handle.net/10261/281362, http://datadryad.org/stash/dataset/doi:10.5061/dryad.6f798
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281362
HANDLE: dataset/doi:10.5061/dryad.6f798" target="_blank">http://hdl.handle.net/10261/281362, http://datadryad.org/stash/dataset/doi:10.5061/dryad.6f798
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281362
PMID: dataset/doi:10.5061/dryad.6f798" target="_blank">http://hdl.handle.net/10261/281362, http://datadryad.org/stash/dataset/doi:10.5061/dryad.6f798
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281362
Ver en: dataset/doi:10.5061/dryad.6f798" target="_blank">http://hdl.handle.net/10261/281362, http://datadryad.org/stash/dataset/doi:10.5061/dryad.6f798
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281362
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281373
Dataset. 2017
DATA FROM: DEVELOPMENTAL MECHANISMS OF STRIPE PATTERNS IN RODENTS
- Mallarino, Ricardo
- Henegar, Corneliu
- Mirasierra, Mercedes
- Manceau, Marie
- Schradin, Carsten
- Vallejo, Mario
- Beronja, Slobodan
- Barsh, Gregory S.
- Hoekstra, Hopi E.
De novo assembly of Rhabdomys pumilio transcriptome and detailed differential gene expression results
This dataset contains a fasta file, including the de novo assembly of Rhabdomys pumilio transcriptome (built from RNA-Seq data using the Trinity suite of de novo transcriptome assembly tools - https://github.com/trinityrnaseq/trinityrnaseq/wiki), as well as a tab separated text file indicating the gene annotations corresponding to each assembly contig, obtained by mapping the de novo assembly to the human reference transcriptome, as described in the manuscript. A third Excel file contains the detailed results of RNA-Seq differential gene expression study in skin obtained from three dorsal regions, as described in the manuscript.
Rhabdomys_pumilio.zip, Mammalian colour patterns are among the most recognizable characteristics found in nature and can have a profound impact on fitness. However, little is known about the mechanisms underlying the formation and subsequent evolution of these patterns. Here we show that, in the African striped mouse (Rhabdomys pumilio), periodic dorsal stripes result from underlying differences in melanocyte maturation, which give rise to spatial variation in hair colour. We identify the transcription factor ALX3 as a regulator of this process. In embryonic dorsal skin, patterned expression of Alx3 precedes pigment stripes and acts to directly repress Mitf, a master regulator of melanocyte differentiation, thereby giving rise to light-coloured hair. Moreover, Alx3 is upregulated in the light stripes of chipmunks, which have independently evolved a similar dorsal pattern. Our results show a previously undescribed mechanism for modulating spatial variation in hair colour and provide insights into how phenotypic novelty evolves., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.7v222" target="_blank">http://hdl.handle.net/10261/281373, http://datadryad.org/stash/dataset/doi:10.5061/dryad.7v222
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281373
HANDLE: dataset/doi:10.5061/dryad.7v222" target="_blank">http://hdl.handle.net/10261/281373, http://datadryad.org/stash/dataset/doi:10.5061/dryad.7v222
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281373
PMID: dataset/doi:10.5061/dryad.7v222" target="_blank">http://hdl.handle.net/10261/281373, http://datadryad.org/stash/dataset/doi:10.5061/dryad.7v222
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281373
Ver en: dataset/doi:10.5061/dryad.7v222" target="_blank">http://hdl.handle.net/10261/281373, http://datadryad.org/stash/dataset/doi:10.5061/dryad.7v222
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281373
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281381
Dataset. 2017
DATA FROM: SPATIO-TEMPORAL MONITORING OF DEEP-SEA COMMUNITIES USING METABARCODING OF SEDIMENT DNA AND RNA
- Guardiola, Magdalena
- Wangensteen, Owen S.
- Taberlet, Pierre
- Coissac, Eric
- Uriz, María Jesús
- Turon, Xavier
MOTUdataset
This excel file presents filtered data found in the samples with the 18S_allshorts primers. It contains the number of occurrences of each MOTU in the different samples, as well as different columns related to the taxonomic identification of the MOTUs and the representative sequences of them
assembled sequences
Fasta file containing the raw assembled sequences (singletons eliminated). For each sequence the codes of the samples where the sequence has been found are indicated, as well as the number of reads in each, the total counts of the sequence, and the sequence length
assembled seqs.fasta
code equivalences
This excel file provides the equivalences of sample codes between the file MOTUdataset.xlsx and the file assembled seqs.fasta
codes.xlsx, We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.4kn05" target="_blank">http://hdl.handle.net/10261/281381, http://datadryad.org/stash/dataset/doi:10.5061/dryad.4kn05
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281381
HANDLE: dataset/doi:10.5061/dryad.4kn05" target="_blank">http://hdl.handle.net/10261/281381, http://datadryad.org/stash/dataset/doi:10.5061/dryad.4kn05
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281381
PMID: dataset/doi:10.5061/dryad.4kn05" target="_blank">http://hdl.handle.net/10261/281381, http://datadryad.org/stash/dataset/doi:10.5061/dryad.4kn05
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281381
Ver en: dataset/doi:10.5061/dryad.4kn05" target="_blank">http://hdl.handle.net/10261/281381, http://datadryad.org/stash/dataset/doi:10.5061/dryad.4kn05
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281381
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281390
Dataset. 2017
DATA FROM: A NOVEL LOCUS ON CHROMOSOME 1 UNDERLIES THE EVOLUTION OF A MELANIC PLUMAGE POLYMORPHISM IN A WILD SONGBIRD
- Bourgeois, Yann X. C.
- Delahaie, Boris
- Gautier, Mathieu
- Lhuillier, Emeline
- Malé, Pierre-Jean G.
- Bertrand, Joris A. M.
- Cornuault, Josselin
- Wakamatsu, Kazumasa
- Bouchez, Olivier
- Mould, Claire
- Bruxaux, Jade
- Holota, Hélène
- Milá, Borja
- Thébaud, Christophe
Data for microsatellites, spectrophotometry and melanins dosage
This file contains 1) microsatellites data in GENPOP format, 2) morphometric data for birds included in the pedigree analysis, 3) Spectrophotometry measurements and 4) Results from the dosage of melanins for 12 individuals. Localities coordinates are also provided.
All_data_microsats_spectro_melanindosage.xlsx
Unfiltered VCF file for 42 individuals
SNPs calls for individual GBS data from the same three localities as in Pooled RAD-seq. Colors and localities for each individuals are provided in a separate excel file.
Highlands_dataset.recode.vcf
Information about individuals included in the GBS VCF file
Morph and localities for each individual included in the GBS study.
Localities_Morphs_individuals_VCF.xlsx, Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.1q9g7" target="_blank">http://hdl.handle.net/10261/281390, http://datadryad.org/stash/dataset/doi:10.5061/dryad.1q9g7
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281390
HANDLE: dataset/doi:10.5061/dryad.1q9g7" target="_blank">http://hdl.handle.net/10261/281390, http://datadryad.org/stash/dataset/doi:10.5061/dryad.1q9g7
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281390
PMID: dataset/doi:10.5061/dryad.1q9g7" target="_blank">http://hdl.handle.net/10261/281390, http://datadryad.org/stash/dataset/doi:10.5061/dryad.1q9g7
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281390
Ver en: dataset/doi:10.5061/dryad.1q9g7" target="_blank">http://hdl.handle.net/10261/281390, http://datadryad.org/stash/dataset/doi:10.5061/dryad.1q9g7
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281390
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281400
Dataset. 2017
DATA FROM: VERY HIGH MHC CLASS IIB DIVERSITY WITHOUT SPATIAL DIFFERENTIATION IN THE MEDITERRANEAN POPULATION OF GREATER FLAMINGOS
- Gillingham, Mark A. F.
- Béchet, Arnaud
- Courtiol, Alexandre
- Rendón-Martos, Manuel
- Amat, Juan A.
- Samraoui, Boudjéma
- Onmuş, Ortaç
- Sommer, Simone
- Cézilly, Frank
MHC Class II Genotype data Greater Flamingo
MHC Class IIB genoptype data of four Mediterranean breeding colonies: France, Spain, Algeria and Turkey
MHCClassIIGenotypeGreaterFlamingo.xlsx, Background: Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To date, however, evidence that adaptation to locally prevalent pathogens maintains MHC variation is limited to species with limited dispersal and, hence, reduced gene flow. On the one hand high gene flow can disrupt local adaptation in species with high dispersal rates, on the other hand such species are much more likely to experience spatial variation in pathogen pressure, suggesting that there may be intense pathogen mediated selection pressure operating across breeding sites in panmictic species. Such pathogen mediated selection pressure operating across breeding sites should therefore be sufficient to maintain high MHC diversity in high dispersing species in the absence of local adaptation mechanisms. We used the Greater Flamingo, Phoenicopterus roseus, a long-lived colonial bird showing a homogeneous genetic structure of neutral markers at the scale of the Mediterranean region, to test the prediction that higher MHC allelic diversity with no population structure should occur in large panmictic populations of long-distance dispersing birds than in other resident species. Results: We assessed the level of allelic diversity at the MHC Class IIB exon 2 from 116 individuals born in four different breeding colonies of Greater Flamingo in the Mediterranean region. We found one of the highest allelic diversity (109 alleles, 2 loci) of any non-passerine avian species investigated so far relative to the number of individuals and loci genotyped. There was no evidence of population structure between the four major Mediterranean breeding colonies. Conclusion: Our results suggest that local adaptation at MHC Class IIB in Greater Flamingos is constrained by high gene flow and high MHC diversity appears to be maintained by population wide pathogen-mediated selection rather than local pathogen-mediated selection. Further understanding of how pathogens vary across space and time will be crucial to further elucidate the mechanisms maintaining MHC diversity in species with large panmictic populations and high dispersal rates., National Science Foundation, Award: DFG Gi 1065/2-1, Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.p65s2" target="_blank">http://hdl.handle.net/10261/281400, http://datadryad.org/stash/dataset/doi:10.5061/dryad.p65s2
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281400
HANDLE: dataset/doi:10.5061/dryad.p65s2" target="_blank">http://hdl.handle.net/10261/281400, http://datadryad.org/stash/dataset/doi:10.5061/dryad.p65s2
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281400
PMID: dataset/doi:10.5061/dryad.p65s2" target="_blank">http://hdl.handle.net/10261/281400, http://datadryad.org/stash/dataset/doi:10.5061/dryad.p65s2
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281400
Ver en: dataset/doi:10.5061/dryad.p65s2" target="_blank">http://hdl.handle.net/10261/281400, http://datadryad.org/stash/dataset/doi:10.5061/dryad.p65s2
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281400
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281403
Dataset. 2017
DATA FROM: EXTREME GENETIC STRUCTURE IN A SOCIAL BIRD SPECIES DESPITE HIGH DISPERSAL CAPACITY
- Morinha, Francisco
- Dávila, José A.
- Bastos, Estela
- Cabral, João A.
- Frías, Óscar
- González, José L.
- Travassos, Paulo
- Carvalho, Diogo
- Milá, Borja
- Blanco, Guillermo
Microsatellite allele dataset
Microsatellite genotypes of all individuals (n=590) separeted by locality (n=25). Genepop format was selected to create the dataset.
chough_microsatellite_genotypes-GENEPOP.txt
Field monitoring data
The dataset includes the population of ringing, province of recapture/resighting and individual identity of the records for which the distance of movements was calculated (n = 9862).
Field_monitoring_data.xls, Social barriers have been shown to reduce gene flow and contribute to genetic structure among populations in species with high cognitive capacity and complex societies, such as cetaceans, apes and humans. In birds, high dispersal capacity is thought to prevent population divergence unless major geographic or habitat barriers induce isolation patterns by dispersal, colonization or adaptation limitation. We report that Iberian populations of the red-billed chough, a social, gregarious corvid with high dispersal capacity, show a striking degree of genetic structure composed of at least 15 distinct genetic units. Monitoring of marked individuals over 30 years revealed that long-distance movements over hundreds of kilometres are common, yet recruitment into breeding populations is infrequent and highly philopatric. Genetic differentiation is weakly related to geographic distance and habitat types used are overall qualitatively similar among regions and regularly shared by individuals of different populations, so that genetic structure is unlikely to be due solely to isolation by distance or isolation by adaptation. Moreover, most population nuclei showed relatively high levels of genetic diversity, suggesting a limited role for genetic drift in significantly differentiating populations. We propose that social mechanisms may underlie this unprecedented level of genetic structure in birds through a pattern of isolation by social barriers not yet described, which may have driven this remarkable population divergence in the absence of geographic and environmental barriers., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.684v0" target="_blank">http://hdl.handle.net/10261/281403, http://datadryad.org/stash/dataset/doi:10.5061/dryad.684v0
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281403
HANDLE: dataset/doi:10.5061/dryad.684v0" target="_blank">http://hdl.handle.net/10261/281403, http://datadryad.org/stash/dataset/doi:10.5061/dryad.684v0
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281403
PMID: dataset/doi:10.5061/dryad.684v0" target="_blank">http://hdl.handle.net/10261/281403, http://datadryad.org/stash/dataset/doi:10.5061/dryad.684v0
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281403
Ver en: dataset/doi:10.5061/dryad.684v0" target="_blank">http://hdl.handle.net/10261/281403, http://datadryad.org/stash/dataset/doi:10.5061/dryad.684v0
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281403
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281410
Dataset. 2017
DATA FROM: IMMANENT CONDITIONS DETERMINE IMMINENT COLLAPSES: NUTRIENT REGIMES DEFINE THE RESILIENCE OF MACROALGAL COMMUNITIES
- Boada, Jordi
- Arthur, Rohan
- Alonso, David
- Pagès, Jordi F.
- Pessarrodona, Albert
- Oliva, Silvia
- Ceccherelli, Giulia
- Piazzi, Luigi
- Romero, Javier
- Alcoverro, Teresa
Urchin and Algal cover survey
This file contains information on macroalgal cover to urchin biomasses from field surveys in two regions in the Mediterranean. Region 1 (high nutrient regions) and region 2 (low nutrient region). This data was obtained from 50x50cm quadrats in several locations in each region.
Algae_Urchin_2013 (TRBase).txt
Code R
This file contains the R code used to determine thresholds, Predicting where state-changing thresholds lie can be inherently complex in ecosystems characterized by nonlinear dynamics. Unpacking the mechanisms underlying these transitions can help considerably reduce this unpredictability. We used empirical observations, field and laboratory experiments, and mathematical models to examine how differences in nutrient regimes mediate the capacity of macrophyte communities to sustain sea urchin grazing. In relatively nutrient-rich conditions, macrophyte systems were more resilient to grazing, shifting to barrens beyond 1 800 g m−2 (urchin biomass), more than twice the threshold of nutrient-poor conditions. The mechanisms driving these differences are linked to how nutrients mediate urchin foraging and algal growth: controlled experiments showed that low-nutrient regimes trigger compensatory feeding and reduce plant growth, mechanisms supported by our consumer–resource model. These mechanisms act together to halve macrophyte community resilience. Our study demonstrates that by mediating the underlying drivers, inherent conditions can strongly influence the buffer capacity of nonlinear systems., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.7k300" target="_blank">http://hdl.handle.net/10261/281410, http://datadryad.org/stash/dataset/doi:10.5061/dryad.7k300
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281410
HANDLE: dataset/doi:10.5061/dryad.7k300" target="_blank">http://hdl.handle.net/10261/281410, http://datadryad.org/stash/dataset/doi:10.5061/dryad.7k300
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281410
PMID: dataset/doi:10.5061/dryad.7k300" target="_blank">http://hdl.handle.net/10261/281410, http://datadryad.org/stash/dataset/doi:10.5061/dryad.7k300
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281410
Ver en: dataset/doi:10.5061/dryad.7k300" target="_blank">http://hdl.handle.net/10261/281410, http://datadryad.org/stash/dataset/doi:10.5061/dryad.7k300
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281410
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281419
Dataset. 2017
DATA FROM: A NEW PROMISING PHYLOGENETIC MARKER TO STUDY THE DIVERSITY OF FUNGAL COMMUNITIES: THE GLYCOSIDE HYDROLASE 63 GENE
- Pérez-Izquierdo, Leticia
- Morin, Emmanuelle
- Maurice, Jean Paul
- Martin, Francis
- Rincón, Ana
- Buée, Marc
Glycoside Hydrolase Family 63 nucleotide sequences
Fasta file with nucleotide sequences of Glycoside Hydrolase Family 63 protein from different fungal strains. In the file the following information of each sequence can be found: -organism -mol_type= type of molecule -tissue_type=origin of the fungal material -country=country:location -clone=name of the strain in the fungal collection The consensus assembling of forward and reverse sequences was made using SeqMan 7v7.0.0
GH63_sequences.docx, In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.2p57p" target="_blank">http://hdl.handle.net/10261/281419, http://datadryad.org/stash/dataset/doi:10.5061/dryad.2p57p
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281419
HANDLE: dataset/doi:10.5061/dryad.2p57p" target="_blank">http://hdl.handle.net/10261/281419, http://datadryad.org/stash/dataset/doi:10.5061/dryad.2p57p
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281419
PMID: dataset/doi:10.5061/dryad.2p57p" target="_blank">http://hdl.handle.net/10261/281419, http://datadryad.org/stash/dataset/doi:10.5061/dryad.2p57p
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281419
Ver en: dataset/doi:10.5061/dryad.2p57p" target="_blank">http://hdl.handle.net/10261/281419, http://datadryad.org/stash/dataset/doi:10.5061/dryad.2p57p
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281419
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281429
Dataset. 2017
DATA FROM: CORRELATED EVOLUTION BETWEEN COLOURATION AND AMBUSH SITE IN PREDATORS WITH VISUAL PREY LURES
- Malheiros Gawryszewski, Felipe
- Calero-Torralbo, Miguel Ángel
- Gillespie, Rosemary G.
- Rodríguez-Gironés, Miguel Ángel
- Herberstein, Marie E.
Sampled trees from the Bayesian analysis
Randomly sampled phylogenetic trees from the posterior distribution returned from the Bayesian phylogenetic inference ran in MrBayes 3.2.2. Sampled 100 trees from each one of four independent searches in MrBayes, in a total of 400 trees. Trees have been ultrametricised and pruned.
bayes.trees.pruned.nex
Bayesian phylogenetic analysis
Results from the Bayesian phylogenetic analysis ran in MrBayes 3.2.2. Four independent searches with three heated chains and one cold chain each. Default MrBayes’ priors. Searches initiated with random trees. Markov chain Monte Carlo simulations (MCMC) were run for 10 million iterations and trees sampled every 10,000 iterations.
Bayes.zip
Reflectance data
Specimen reflectance data. The first column shows wavelength (nm) values. Each one of the following columns represents the average reflectance value (%) of five measurements of one specimen. Reflectance values have been smoothed (R function 'smooth.spline' with argument 'spar'=0.7), and negative values converted to zero. Column names indicate taxon names. More detail can be found in 'specimen data.csv' file.
spec.files.csv
Specimen data
Specimen data. Columns: (1) SEQ = sequential row numbers; (2) ID = researcher’s specimen identification number; (3) Clade = taxon name; (4) family = spider taxonomic family; (5) country = country of specimen collection; (6) spectrum_file_name = reflectance data file name, same as in 'spec.files.csv' file.
specimen data.csv
Consensus tree from the Bayesian analysis
Majority rule consensus tree returned from the Bayesian analysis ran in MrBayes 3.2.2.
Tree FULL.nex
Phylogenetic tree data
Phylogenetic tree data. Columns: (1) taxon = phylogenetic tree tip labels; (2) flw.categ = flower dwelling habit, either a flower-dweller (FLW) or a non-flower dweller (NOFLW); (3) biog_reg = region of collection, either collected in Australia or in Europe plus Malaysia; (4) sample.size = reflectance data sample sizes.
tree.data.csv
Phylogenetic tree
Phylogenetic tree. Majority rule consensus tree from the Bayesian analysis ultrametricised and pruned. See file 'tree FULL.nex' for the original tree.
tree.pruned.nex
Flower-dwelling habit of Thomisidae
Number and percentage of individuals per taxon collected directly on flowers (flower) and number individuals collected on other substratum or using a sweepnet (non-flower).
ESM Table 2.xlsx, The evolution of a visual signal will be affected by signaller and receiver behaviour, and by the physical properties of the environment where the signal is displayed. Crab spiders are typical sit-and-wait predators found in diverse ambush sites, such as tree bark, foliage and flowers. Some of the flower-dweller species present a UV+-white visual lure that makes them conspicuous and attractive to their prey. We hypothesised that UV+-white colouration was associated with the evolution of a flower-dwelling habit. In addition, following up on results from a previous study we tested whether the UV+-white colouration evolved predominantly in flower-dwelling species occurring in Australia. We measured the reflectance of 1149 specimens from 66 species collected in Australia and Europe, reconstructed a crab spider phylogeny, and applied phylogenetic comparative methods to test our hypotheses. We found that the flower-dwelling habit evolved independently multiple times, and that this trait was correlated with the evolution of the UV+-white colouration. However, outside Australia non-flower-dwelling crab spiders also express a UV+-white colouration. Therefore, UV+-white reflectance is probably a recurring adaptation of some flower-dwellers for attracting pollinators, although it may have other functions in non-flower-dwellers, such as camouflage., National Science Foundation, Award, Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.8567b" target="_blank">http://hdl.handle.net/10261/281429, http://datadryad.org/stash/dataset/doi:10.5061/dryad.8567b
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281429
HANDLE: dataset/doi:10.5061/dryad.8567b" target="_blank">http://hdl.handle.net/10261/281429, http://datadryad.org/stash/dataset/doi:10.5061/dryad.8567b
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281429
PMID: dataset/doi:10.5061/dryad.8567b" target="_blank">http://hdl.handle.net/10261/281429, http://datadryad.org/stash/dataset/doi:10.5061/dryad.8567b
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281429
Ver en: dataset/doi:10.5061/dryad.8567b" target="_blank">http://hdl.handle.net/10261/281429, http://datadryad.org/stash/dataset/doi:10.5061/dryad.8567b
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281429
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281440
Dataset. 2021
METAPOPULATION STRUCTURE MODULATES SEXUAL ANTAGONISM
- Rodríguez-Expósito, Eduardo
- García-González, Francisco
Explanations are given in the files and further information is provided in the Appendix of the study (available online together with the article), and in the article., Despite the far-reaching evolutionary implications of sexual conflict, the effects of metapopulation structure, when populations are subdivided into several demes connected to some degree by migration, on sexual conflict dynamics are unknown. Here, we used experimental evolution in an insect model system, the seed beetle Callosobruchus maculatus, to assess the independent and interacting effects of selection histories associated with mating system (monogamy vs. polygamy) and population subdivision on sexual conflict evolution. We confirm traditional predictions from sexual conflict theory by revealing increased resistance to male harm in females from populations with a history of intense sexual selection (polygamous populations) compared to females from populations with a history of relaxed sexual selection (monogamous populations). However, selection arising from metapopulation structure reversed the classic pattern of sexually antagonistic coevolution and led to reduced resistance in females from polygamous populations. These results underscore that population spatial structure moderates sexual selection and sexual conflict, and more broadly, that the evolution of sexual conflict is contingent on ecological context. The findings also have implications for population dynamics, conservation biology and biological control., Spanish Ministry of Economy, Award: CGL2012-34685.
Spanish Ministry of Science, Innovation and Universities, Award: CGL2016-76173-P.
Spanish Ministry of Science, Innovation and Universities, Award: PID2019-105547GB-I00.
Spanish Research Council, Award: 201730I034.
Spanish Ministry of Economy, Award: BES‐2013‐065192.
Spanish Ministry of Economy, Award: CGL2012-34685.
Spanish Research Council, Award: 201730I034., Peer reviewed
DOI: http://hdl.handle.net/10261/281440
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281440
HANDLE: http://hdl.handle.net/10261/281440
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281440
PMID: http://hdl.handle.net/10261/281440
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281440
Ver en: http://hdl.handle.net/10261/281440
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281440
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