Resultados totales (Incluyendo duplicados): 33526
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Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281792
Dataset. 2016

DATA FROM: DEEP-SEA, DEEP-SEQUENCING: METABARCODING EXTRACELLULAR DNA FROM SEDIMENTS OF MARINE CANYONS

  • Guardiola, Magdalena
  • Uriz, María Jesús
  • Taberlet, Pierre
  • Coissac, Eric
  • Wangensteen, Owen S.
  • Turon, Xavier
obitools commands used in the analysis of data This file contains the obitools commands used to manipulate sequence reads, filter sequences, and assign taxonomy obitools commands.txt Database of MOTUs and sequences This database contains the number of reads of the different MOTUs in the samples studied, together with information on taxonomic assignment and the sequences themselves database corrected.txt, Marine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environmental DNA metabarcoding. We used a new primer set targeting a short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed to obtain extractions enriched in extracellular DNA from replicated sediment corers. With this strategy we captured information from DNA (local or deposited from the water column) that persists adsorbed to inorganic particles and buffered short-term spatial and temporal heterogeneity. We analysed replicated samples from 20 localities including 2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range 100–2,250 m). We identified 1,629 MOTUs, among which the dominant groups were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles, and Rhizaria. There was a marked small-scale heterogeneity as shown by differences in replicates within corers and within localities. The spatial variability between canyons was significant, as was the depth component in one of the canyons where it was tested. Likewise, the composition of the first layer (1 cm) of sediment was significantly different from deeper layers. We found that qualitative (presence-absence) and quantitative (relative number of reads) data showed consistent trends of differentiation between samples and geographic areas. The subset of exclusively benthic MOTUs showed similar patterns of β-diversity and community structure as the whole dataset. Separate analyses of the main metazoan phyla (in number of MOTUs) showed some differences in distribution attributable to different lifestyles. Our results highlight the differentiation that can be found even between geographically close assemblages, and sets the ground for future monitoring and conservation efforts on these bottoms of ecological and economic importance., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281798
Dataset. 2016

DATA FROM: MARINE BIODIVERSITY IN JUAN FERNÁNDEZ AND DESVENTURADAS ISLANDS, CHILE: GLOBAL ENDEMISM HOTSPOTS

  • Friedlander, Alan M.
  • Ballesteros, Enric
  • Caselle, Jennifer E.
  • Gaymer, Carlos F.
  • Palma, Alvaro T.
  • Petit, Ignacio
  • Varas, Eduardo
  • Muñoz Wilson, Alex
  • Sala, Enric
Desventuradas_Juan_Fernandes_Fish Underwater counts of fishes on transects Desventuradas_Juan_Fernandes_mobile_inverts Underwater counts of mobile invertebrates Desventuradas_Juan_Fernandes_Sessile_Benthos Underwater counts of sessile benthos, The Juan Fernández and Desventuradas islands are among the few oceanic islands belonging to Chile. They possess a unique mix of tropical, subtropical, and temperate marine species, and although close to continental South America, elements of the biota have greater affinities with the central and south Pacific owing to the Humboldt Current, which creates a strong biogeographic barrier between these islands and the continent. The Juan Fernández Archipelago has ~ 700 people, with the major industry being the fishery for the endemic lobster, Jasus frontalis. The Desventuradas Islands are uninhabited except for a small Chilean military garrison on San Félix Island. We compared the marine biodiversity of these islands across multiple taxonomic groups. At San Ambrosio Island (SA), in Desventuradas, the laminarian kelp (Eisenia cokeri), which is limited to Desventuradas in Chile, accounted for >50% of the benthic cover at wave exposed areas, while more sheltered sites were dominated by sea urchin barrens. The benthos at Robinson Crusoe Island (RC), in the Juan Fernández Archipelago, comprised a diverse mix of macroalgae and invertebrates, a number of which are endemic to the region. The biomass of commercially targeted fishes was > 2 times higher in remote sites around RC compared to sheltered locations closest to port, and overall biomass was 35% higher around SA compared to RC, likely reflecting fishing effects around RC. The number of endemic fish species was extremely high at both islands, with 87.5% of the species surveyed at RC and 72% at SA consisting of regional endemics. Remarkably, endemics accounted for 99% of the numerical abundance of fishes surveyed at RC and 96% at SA, which is the highest assemblage-level endemism known for any individual marine ecosystem on earth. Our results highlight the uniqueness and global significance of these biodiversity hotspots exposed to very different fishing pressures., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281800
Dataset. 2016

DATA FROM: DETECTION OF TEPHRA LAYERS IN ANTARCTIC SEDIMENT CORES WITH HYPERSPECTRAL IMAGING

  • Aymerich, Ismael F.
  • Oliva, Marc
  • Giralt, Santiago
  • Martín-Herrero, Julio
Data_IsmaelAymerich_PLOSONE_2015 Excel file containing hyperspectral signatures of tephra and No-tephra samples extracted from an Antarctic sediment core. Tephra signatures are labelled 1, while No-tephra spectra are labelled 0., Tephrochronology uses recognizable volcanic ash layers (from airborne pyroclastic deposits, or tephras) in geological strata to set unique time references for paleoenvironmental events across wide geographic areas. This involves the detection of tephra layers which sometimes are not evident to the naked eye, including the so-called cryptotephras. Tests that are expensive, time-consuming, and/or destructive are often required. Destructive testing for tephra layers of cores from difficult regions, such as Antarctica, which are useful sources of other kinds of information beyond tephras, is always undesirable. Here we propose hyperspectral imaging of cores, Self-Organizing Map (SOM) clustering of the preprocessed spectral signatures, and spatial analysis of the classified images as a convenient, fast, non-destructive method for tephra detection. We test the method in five sediment cores from three Antarctic lakes, and show its potential for detection of tephras and cryptotephras., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281805
Dataset. 2016

DATA FROM: BET-HEDGING AS A MECHANISM FOR THE EVOLUTION OF POLYANDRY, REVISITED

  • Yasui, Yukio
  • García-González, Francisco
Yasui and Garcia-Gonzalez polyandry bet-hedging raw data All simulation results described in the paper intrinsic male quality scenario (binomial quality distribution) Fujitsu F-BASIC for Windows V6.0 program source code for the intrinsic male quality scenario (binomial quality distribution) intrinsic male quality scenario (continuous quality distribution with SD0.167) Fujitsu F-BASIC for Windows V6.0 program source code for the intrinsic male quality scenario (continuous quality distribution) gametophytic genetic compatibility scenario Fujitsu F-BASIC for Windows V6.0 program source code for the genetic incompatibility scenario (gametophytic incompatibility) Instruction manual for simulation programs Instruction manual for 3 program files Instruction_manual_for_simulation_programs.txt, Females that mate with multiple males (polyandry) may reduce the risk that their eggs are fertilized by a single unsuitable male. About 25 years ago it was hypothesized that bet-hedging could function as a mechanism favoring the evolution of polyandry, but this idea is controversial because theory indicates that bet-hedging via polyandry can compensate the costs of mating only in small populations. Nevertheless, populations are often spatially structured, and even in the absence of spatial structure, mate choice opportunity can be limited to a few potential partners. We examined the effectiveness of bet-hedging in such situations with simulations carried out under two scenarios; (1) intrinsic male quality, with offspring survival determined by male phenotype (male's ability to generate viable offspring), and (2) genetic incompatibility (offspring fitness determined non-additively by parental genotypes). We find higher fixation probabilities for a polyandrous strategy compared to a monandrous strategy if complete reproductive failure due to male effects or parental incompatibility is pervasive in the population. Our results also indicate that bet-hedging polyandry can delay the extinction of small demes. Our results underscore the potential for bet-hedging to provide benefits to polyandrous females and have valuable implications for conservation biology., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281810
Dataset. 2016

DATA FROM: THE ROLE OF SELECTION AND HISTORICAL FACTORS IN DRIVING POPULATION DIFFERENTIATION ALONG AN ELEVATIONAL GRADIENT IN AN ISLAND BIRD

  • Bertrand, Joris A. M.
  • Delahaie, Boris
  • Bourgeois, Yann X. C.
  • Duval, Thomas
  • García-Jiménez, Ricardo
  • Cornuault, Josselin
  • Pujol, Benoit
  • Thébaud, Christophe
  • Milá, Borja
ZoboGrad-GENEPOP Individual genotypes of the 401 individuals at 12 microsatellite loci. This file is provided in the universal GENEPOP format. The first section corresponds to a list of the name of the loci. Then, each row represent a single individual: first column is the individual identifier and the following columns correspond to the length (concatenation of 2 x 3 digits) of the different alleles at the 12 loci (one column each). Sampling localities are separated by a empty lines. ZoboGrad-Morpho File summarizing the morphological data for each individual. Each line corresponds to a single individual with informations about sampling localities, ringer and all the morphological variables measured: weight (g), wing length (mm), tail length (mm), tarsus length (mm), bill length (mm), bill depth (mm) and bill width (mm)., Adaptation to local environmental conditions and the range dynamics of populations can influence evolutionary divergence along environmental gradients. Thus, it is important to investigate patterns of both phenotypic and genetic variation among populations to reveal the respective roles of these two types of factors in driving population differentiation. Here, we test for evidence of phenotypic and genetic structure across populations of a passerine bird (Zosterops borbonicus) distributed along a steep elevational gradient on the island of Réunion. Using eleven microsatellite loci screened in 401 individuals from 18 localities distributed along the gradient, we found that genetic differentiation occurred at two spatial levels: (i) between two main population groups corresponding to highland and lowland areas, respectively, and (ii) within each of these two groups. In contrast, several morphological traits varied gradually along the gradient. Comparison of neutral genetic differentiation (FST) and phenotypic differentiation (PST) showed that PST largely exceeds FST at several morphological traits, which is consistent with a role for local adaptation in driving morphological divergence along the gradient. Overall, our results revealed an area of secondary contact mid-way up the gradient between two major, cryptic, population groups likely diverged in allopatry. Remarkably, local adaptation has shaped phenotypic differentiation irrespective of population history, resulting in different patterns of variation along the elevational gradient. Our findings underscore the importance of understanding both historical and selective factors when trying to explain variation along environmental gradients., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281813
Dataset. 2016

DATA FROM: COMPARATIVE SPATIAL GENETICS AND EPIGENETICS OF PLANT POPULATIONS: HEURISTIC VALUE AND A PROOF OF CONCEPT

  • Herrera, Carlos M.
  • Medrano, Mónica
  • Bazaga, Pilar
Microsatellite genotypes Genotype information from 11 microsatellite loci (Hefo1, Hefo4, Hefo10, Hefo2, Hefo11, Hefo13, Hefo9, Hefo8, Hefo7, Hefo3, Hefo5) for individual Helleborus foetidus plants sampled Microsatellite.genotypes.txt Geographical coordinates of individual Helleborus foetidus plants sampled Geographical.coordinates.xls, Despite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation-by-distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity-distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200 mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP markers. Expectations from individual-level IBD patterns were tested by means of kinship-distance regressions. Both genetic and epigenetic similarity between H. foetidus individuals conformed to theoretical expectations under individual-level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic ‘kinship excess’ tending to decrease as plant separation increased. Results suggest that moderate-to-high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H. foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating and testing hypotheses on forces shaping epigenetic diversity in wild plant populations., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281820
Dataset. 2016

DATA FROM: A COST FOR HIGH LEVELS OF SPERM COMPETITION IN RODENTS: INCREASED SPERM DNA FRAGMENTATION

  • Delbarco-Trillo, Javier
  • García-Álvarez, Olga
  • Soler, Ana J.
  • Tourmente, Maximiliano
  • Garde, José Julián
  • Roldán, Eduardo R. S.
Sperm DNA fragmentation data Total DNA fragmentation index (tDFI) and high DNA stainability (HDS) results obtained by Sperm Chromatin Structure Assay (SCSA). ALL DATA.xlsx, Sperm competition, a prevalent evolutionary process in which the spermatozoa of two or more males compete for the fertilization of the same ovum, leads to morphological and physiological adaptations, including increases in energetic metabolism that may serve to propel sperm faster but that may have negative effects on DNA integrity. Sperm DNA damage is associated with reduced rates of fertilization, embryo and foetal loss, offspring mortality, and mutations leading to genetic disease. We tested whether high levels of sperm competition affect sperm DNA integrity. We evaluated sperm DNA integrity in 18 species of rodents that differ in their levels of sperm competition using the sperm chromatin structure assay (SCSA). DNA integrity was assessed upon sperm collection, in response to incubation under capacitating or non-capacitating conditions, and after exposure to physical and chemical stressors. Sperm DNA was very resistant to physical and chemical stressors, whereas incubation in non-capacitating and capacitating conditions resulted in only a small increase in sperm DNA damage. Importantly, levels of sperm competition were positively associated with sperm DNA fragmentation across rodent species. This is the first evidence showing that high levels of sperm competition lead to an important cost in the form of increased sperm DNA damage., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281824
Dataset. 2016

DATA FROM: SELECTIVE LOGGING IN TROPICAL FORESTS DECREASES THE ROBUSTNESS OF LIANA-TREE INTERACTION NETWORKS TO THE LOSS OF HOST TREE SPECIES

  • Magrach, Ainhoa
  • Senior, Rebeca A.
  • Rogers, Andrew
  • Nurdin, Deddy
  • Benedick, Suzan
  • Laurance, William F.
  • Santamaría, Luis
  • Edwards, David P.
borneo dataset Includes liana and tree species, DBH and host used by lianas across 120 sample plots in primary and logged forest, Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in species composition. Whether such changes modify interactions between species and the networks in which they are embedded remain fundamental questions to assess the ‘health’ and ecosystem functionality of logged forests. We focus on interactions between lianas and their tree hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more abundant, had higher species richness and different species compositions in logged than in primary forests. Logged forests showed heavier liana loads disparately affecting slow-growth tree species, which could exacerbate the loss of timber value and carbon storage already associated to logging. Moreover, simulation scenarios of host tree local species loss indicated that logging might decrease the robustness of liana-tree interaction networks if heavily infested trees (i.e. the most connected ones) are more likely to disappear. This effect is partially mitigated in the short term by the colonization of host trees by a greater diversity of liana species within logged forests, yet this might not compensate for the loss of preferred tree hosts in the long term. As a consequence, species interaction networks may show a lagged response to disturbance, which may trigger sudden collapses in species richness and ecosystem function in response to additional disturbances, representing a new type of “extinction debt”., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281829
Dataset. 2016

DATA FROM: CANDIDATE GENE ANALYSIS SUGGESTS UNTAPPED GENETIC COMPLEXITY IN MELANIN-BASED PIGMENTATION IN BIRDS

  • Bourgeois, Yann X. C.
  • Bertrand, Joris A. M.
  • Delahaie, Boris
  • Cornuault, Josselin
  • Duval, Thomas
  • Milá, Borja
  • Thébaud, Christophe
Phased DNA sequences and aminoacids This file contains all the phased sequences used in the study, with heterozygous gaps resolved. Fasta containing aminoacids translations are also provided for markers used in MK tests. Phased_DNA_sequences_and_amino_acids.zip Informations about individuals This file contains for each individual included in the study its identifier, its color form/morph, the locality where it was sampled and its sex. Individual_information.xlsx, Studies on melanin-based color variation in a context of natural selection have provided a wealth of information on the link between phenotypic and genetic variation. Here, we evaluated associations between melanic plumage patterns and genetic polymorphism in the Réunion grey white-eye (Zosterops borbonicus), a species in which mutations on MC1R do not seem to play any role in explaining melanic variation. This species exhibits five plumage color variants that can be grouped into three color forms which occupy discrete geographic regions in the lowlands of Réunion and a fourth form which comprises two color morphs (grey and brown), occurs at high elevation, and represents a true color polymorphism. We conducted a comprehensive survey of sequence variation in 96 individuals at a series of seven candidate genes other than MC1R that have been previously shown to influence melanin-based color patterns in vertebrates, including genes that have rarely been studied in a wild bird species before: POMC, Agouti, TYR, TYRP1, DCT, Corin and SLC24A5. Of these seven genes, two (Corin and TYRP1) displayed an interesting shift in allele frequencies between lowland and highland forms and a departure from mutation-drift equilibrium consistent with balancing selection in the polymorphic highland form only. Sequence variation at Agouti, a gene frequently involved in melanin-based pigmentation patterning, was not associated with color forms or morphs. Thus, we suggest that functionally important changes in loci other than those classically studied may beare involved in the color polymorphism exhibited by the Réunion grey white-eye and possibly many other non-model species., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281835
Dataset. 2016

DATA FROM: EVOLUTIONARY HISTORY OF ENDEMIC SULAWESI SQUIRRELS CONSTRUCTED FROM UCES AND MITOGENOMES SEQUENCED FROM MUSEUM SPECIMENS

  • Hawkins, Melissa T. R.
  • Leonard, Jennifer A.
  • Helgen, Kristofer M.
  • McDonough, Molly M.
  • Rockwood, Larry L.
  • Maldonado, Jesús E.
157k_362Loci_align_9plus Nexus file of 362 UCE loci from a minimum of nine individuals, with at least three informative sites. The total alignment is over 157,000 bp. ML tree of Mitogenomes plus UCE outgroups Mitochondrial tree, generated through Maximum Likelihood. Mitogene_Tree_DCSPrior Mitogenome BEAST xml file from this publication. FcC_info FasConCat data partitioning text file. FcC_supermatrix FasConCat supermatrix fasta file. 28ConpleteGeneTrees Subset of 28 UCE loci from complete data matrix. NJst_362LociSpTree Species tree from NJst. 157kUCEs BEAST xml file for 362 UCE loci dataset. 157k_38subsets Zipped folder containing each of the 38 data partitions selected from the k-means algorithm., Background: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi’s three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. Results: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace’s line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. Conclusions: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species., Peer reviewed

Proyecto: //

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