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:10261/281306
Dataset. 2018
DATA FROM: THE TIMING OF FRUGIVORE-MEDIATED SEED DISPERSAL EFFECTIVENESS
- González-Varo, Juan P.
- Arroyo, Juan M.
- Jordano, Pedro
seed_rain_pistacia
Data on the magnitude of seed rain in seed traps placed in different microhabitat types and in each of the study periods (early, mid and late) of the 2014–2015 fruiting season of Pistacia lentiscus (FIGURE 2a).
viability_seeds_fruits
Data on the viability test (‘flotation/sink’ method) conducted on depulped seeds from Pistacia lentiscus ripe (black) fruits (Figure S3 in Supplementary Material).
seed_predation_pistacia
Data on the seed predation experiment (FIGURE 3b). Each row corresponds to an individual Pistacia lentiscus seed within a seed depot.
sowing_experiment_pistacia
Data on the sowing experiment of Pistacia lentiscus seeds to assess seed germination (FIGURE 3c) and seedling survival (FIGURE 3d). Each row corresponds to an individual Pistacia lentiscus seed within a sowing station.
timing_sde_pistacia
Mean values of multiple demographic processes used to calculate the quantity (QT) and (QL) components of seed dispersal effectiveness (SDE) for different bird species groups contributing to seed dispersal in different periods and microhabitat types (FIGURE 4).
seeds_pistacia_barcoding_viability
Data on the Pistacia lentiscus seeds sampled for DNA barcoding analyses, which includes the bird species responsible for dispersal (FIGURE 2b) and the outcome of the viability test (FIGURE 3a)., The seed dispersal effectiveness framework allows assessing mutualistic services from frugivorous animals in terms of quantity and quality. Quantity accounts for the number of seeds dispersed and quality for the probability of recruitment of dispersed seeds. Research on this topic has largely focused on the spatial patterns of seed deposition because seed fates often vary between microhabitats due to differences in biotic and abiotic factors. However, the temporal dimension has remained completely overlooked despite these factors – and even local disperser assemblages – can change dramatically during long fruiting periods. Here, we test timing effects on seed dispersal effectiveness, using as study case a keystone shrub species dispersed by frugivorous birds and with a fruiting period of nine months. We evaluated quantity and quality in different microhabitats of a Mediterranean forest and different periods of the fruiting phenophase. We identified the bird species responsible for seed deposition through DNA barcoding and evaluated the probability of seedling recruitment through a series of field experiments on sequential demographic processes. We found that timing matters: the disperser assemblage was temporally structured, seed viability decreased markedly during the plant’s fruiting phenophase, and germination was lower for viable seeds dispersed in the fruiting peak. We show how small contributions to seed deposition by transient migratory species can result in a relevant effectiveness if they disperse seeds in a high-quality period for seedling recruitment. This study expands our understanding of seed dispersal effectiveness, highlighting the importance of timing and infrequent interactions for population and community dynamics., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.3c4n8nc" target="_blank">http://hdl.handle.net/10261/281306, http://datadryad.org/stash/dataset/doi:10.5061/dryad.3c4n8nc
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281306
HANDLE: dataset/doi:10.5061/dryad.3c4n8nc" target="_blank">http://hdl.handle.net/10261/281306, http://datadryad.org/stash/dataset/doi:10.5061/dryad.3c4n8nc
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281306
PMID: dataset/doi:10.5061/dryad.3c4n8nc" target="_blank">http://hdl.handle.net/10261/281306, http://datadryad.org/stash/dataset/doi:10.5061/dryad.3c4n8nc
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281306
Ver en: dataset/doi:10.5061/dryad.3c4n8nc" target="_blank">http://hdl.handle.net/10261/281306, http://datadryad.org/stash/dataset/doi:10.5061/dryad.3c4n8nc
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281306
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281311
Dataset. 2018
DATA FROM: PREDATION RISK DETERMINES PIGMENTATION PHENOTYPE IN NUTHATCHES BY MELANIN-RELATED GENE EXPRESSION EFFECTS
- Galván, Ismael
Dataset used in the study
Predation risk - Dryad.xls
Predation risk - Dryad readme.txt, Pigments determine the appearance of organisms. However, pigment production can be associated to physiological constraints as in the case of pheomelanin, the sulphurated form of melanin whose synthesis in melanocytes consumes cysteine and consequently reduces the availability of glutathione (GSH) to exert antioxidant protection. Pheomelanogenesis may thus increase the susceptibility to suffer chronic oxidative stress. I investigated the possibility that environmental lability in the expression of genes regulating pheomelanogenesis protects from oxidative stress, a situation in which GSH is most required. By broadcasting adult alarm calls, I manipulated the perception of predation risk, a natural source of oxidative stress, in free-living Eurasian nuthatch Sitta europaea nestlings developing pheomelanin-pigmented flank feathers. The manipulation affected the consumption of GSH that resulted from the expression of two genes (Slc7a11 and Slc45a2) influencing cysteine/GSH availability in cells, as these genes were downregulated in the feather melanocytes of the nestlings with lowest intracellular antioxidant capacity (i.e., lowest GSH levels). Systemic oxidative damage increased with Slc7a11 expression in feather melanocytes, suggesting that the observed downregulation was physiologically advantageous. The nestlings exposed to an increased perception of predation risk developed flank feathers of reduced color intensity. These results indicate that perceived predation risk can determine the pigmentation phenotype by (probably epigenetic) effects on gene expression that protect from physiological constraints imposed by pheomelanin production., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.6rb12hk" target="_blank">http://hdl.handle.net/10261/281311, http://datadryad.org/stash/dataset/doi:10.5061/dryad.6rb12hk
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281311
HANDLE: dataset/doi:10.5061/dryad.6rb12hk" target="_blank">http://hdl.handle.net/10261/281311, http://datadryad.org/stash/dataset/doi:10.5061/dryad.6rb12hk
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281311
PMID: dataset/doi:10.5061/dryad.6rb12hk" target="_blank">http://hdl.handle.net/10261/281311, http://datadryad.org/stash/dataset/doi:10.5061/dryad.6rb12hk
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281311
Ver en: dataset/doi:10.5061/dryad.6rb12hk" target="_blank">http://hdl.handle.net/10261/281311, http://datadryad.org/stash/dataset/doi:10.5061/dryad.6rb12hk
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281311
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281323
Dataset. 2018
DATA FROM: BAYESIAN VECTOR TRANSMISSION MODEL DETECTS CONFLICTING INTERACTIONS FROM TRANSGENIC DISEASE‐RESISTANT GRAPEVINES
- Zeilinger, Adam R.
- Turek, Daniel
- Cornara, Daniele
- Sicard, Anne
- Lindow, Steven E.
- Almeida, Rodrigo P. P.
Vector transmission from DSF grapevines data set
Data from vector transmission experiment for Xylella fastidiosa from DSF transgenic grapevines. File is an .rds file for loading directly into R. The file is a list of length 2. The first item in the list is metadata describing each variable of the data set, including total sample size. The second item is the data set itself.
zeilinger_dsf_transmission_dataset.rds, Effective management of vector-borne plant pathogens often relies on disease-resistant cultivars. While heterogeneity in host resistance and in pathogen population density at the host population level play important and well-recognized roles in epidemiology, the effects of resistance traits on pathogen distribution at the individual host level, and the epidemiological consequences in turn, are poorly understood. Transgenic disease-resistant plants that produce bacterial Diffusible Signaling Factor (DSF) could provide resistance to the vector-borne bacterium Xylella fastidiosa by impeding plant colonization and reducing virulence. However, the effects of constitutive in planta production of DSF on insect vector transmission has remained unresolved. We investigated the transmission biology of X. fastidiosa in DSF and wild-type (WT) grapevines with the efficient vector Graphocephala atropunctata. We also developed a novel Bayesian hierarchical model to improve statistical inference on the multiple components of the vector transmission process. We found that insect vectors had a greater colonization efficiency on DSF plants—meaning they acquired a greater population size of X. fastidiosa—than on WT plants. However, DSF plants also maintained much lower X. fastidiosa populations. These apparently conflicting processes resulted in a lower but highly variable probability of transmission from DSF plants compared to WT plants. Our Bayesian model improved statistical inference compared to widely used frequentist statistics in part by estimating and correcting for imperfect detection of X. fastidiosa in plant and insect tissues. Overall, our results support current models on the roles that DSF plays in vector transmission of X. fastidiosa. In line with our hypothesis, DSF production reduced mean X. fastidiosa population density but increased heterogeneity within host plants. While DSF-producing plants could potentially improve disease management, our results suggest that they could, under some conditions, facilitate X. fastidiosa spread., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.16dp926" target="_blank">http://hdl.handle.net/10261/281323, http://datadryad.org/stash/dataset/doi:10.5061/dryad.16dp926
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281323
HANDLE: dataset/doi:10.5061/dryad.16dp926" target="_blank">http://hdl.handle.net/10261/281323, http://datadryad.org/stash/dataset/doi:10.5061/dryad.16dp926
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281323
PMID: dataset/doi:10.5061/dryad.16dp926" target="_blank">http://hdl.handle.net/10261/281323, http://datadryad.org/stash/dataset/doi:10.5061/dryad.16dp926
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281323
Ver en: dataset/doi:10.5061/dryad.16dp926" target="_blank">http://hdl.handle.net/10261/281323, http://datadryad.org/stash/dataset/doi:10.5061/dryad.16dp926
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281323
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281339
Dataset. 2018
DATA FROM: THE EVOLUTION OF IRIS COLOUR IN RELATION TO NOCTURNALITY IN OWLS
- Passarotto, Arianna
- Parejo, Deseada
- Cruz-Miralles, Ángel
- Avilés, Jesús M.
data for dryads
Raw data used for comparative analyses on eye colour in owls, Birds, due to their multiple colourful displays, constitute a classic paradigm for the study of colour evolution. Although avian eyes are remarkably coloured, the functional basis behind inter‐specific variability in iris colouration remains poorly understood. Owls are an ideal system to shed light on the role of ecology in promoting iris colour evolution as they show inter‐specific variation in iris colour and in niche specialization with some species being strictly nocturnal and others active during the day. Owls perching for hunting at night might be unnoticed by both predators and their prey if they had dark irises, which would predict that dark irises were more likely to evolve in strictly nocturnal species than in diurnal ones. Using phylogenetic comparative models, we tested the camouflage hypothesis for eye colour. Ancestral state reconstruction revealed that the owl ancestor of the family Strigidae was more likely bright‐irided whereas the ancestor of the family Tytonidae was more likely dark‐irided. We found that iris colour and activity rhythm have more likely evolved in concert than independently, and a non‐significant trend of dark eyes to evolve more easily in owl species presenting strictly nocturnal habits than in diurnal species. The transition from diurnality to nocturnality was a previous requisite for the evolution of dark irises in owls. Taken together our results are only partly consistent with the camouflage hypothesis suggesting that dark irises in owls have primarily evolved to enhance concealment in nocturnal conditions., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.32j0040" target="_blank">http://hdl.handle.net/10261/281339, http://datadryad.org/stash/dataset/doi:10.5061/dryad.32j0040
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281339
HANDLE: dataset/doi:10.5061/dryad.32j0040" target="_blank">http://hdl.handle.net/10261/281339, http://datadryad.org/stash/dataset/doi:10.5061/dryad.32j0040
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281339
PMID: dataset/doi:10.5061/dryad.32j0040" target="_blank">http://hdl.handle.net/10261/281339, http://datadryad.org/stash/dataset/doi:10.5061/dryad.32j0040
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281339
Ver en: dataset/doi:10.5061/dryad.32j0040" target="_blank">http://hdl.handle.net/10261/281339, http://datadryad.org/stash/dataset/doi:10.5061/dryad.32j0040
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281339
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344
Dataset. 2018
DATA FROM: GENOME-WIDE SIGNALS OF DRIFT AND LOCAL ADAPTATION DURING RAPID LINEAGE DIVERGENCE IN A SONGBIRD
- Friis, Guillermo
- Fandos, Guillermo
- Zellmer, Amanda J.
- McCormack, John E.
- Faircloth, Brant C.
- Milá, Borja
genolike_map20_q20_snp16_maf002_ind32_430K.beagle
Input file of genotype likelihoods in Beagle format (.beagle.gz) for PCANGSD analysis.
ORJUSTRUx8_biall_dp450_q40_perpopmiss075_hwe00001_maf002_LD02_neutral01
Dataset of 16,858 independent neutral SNPs from 64 samples in vcf format for STRUCTURE analysis.
ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZ_neutral01
Dataset of 15,209 neutral SNPs used in the PCA intended for population structure correction in the redundancy analysis (RDA).
ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZ
Dataset of 15,252 SNPs used in the redundancy analysis.
ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_sel01_BAYESCENV
Subset of 49 SNP outliers identified with BayScEnv for the second redundancy analysis in the manuscript.
ORJUGEO_coords_ALLSAMPLES
Table of sample location and geographic coordinates for all sequenced samples of the study.
ORJUGEO_coords_ClimVariables
Sample data and WorldClim environmental data (Fick, S.E. and R.J. Hijmans, 2017. Worldclim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology.) for each one of the samples included in the genotype-environment association analyses., The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (i) drift in geographic isolation, (ii) differentiation along continuous selective gradients, and (iii) isolation by adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.0nb2307" target="_blank">http://hdl.handle.net/10261/281344, http://datadryad.org/stash/dataset/doi:10.5061/dryad.0nb2307
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344
HANDLE: dataset/doi:10.5061/dryad.0nb2307" target="_blank">http://hdl.handle.net/10261/281344, http://datadryad.org/stash/dataset/doi:10.5061/dryad.0nb2307
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344
PMID: dataset/doi:10.5061/dryad.0nb2307" target="_blank">http://hdl.handle.net/10261/281344, http://datadryad.org/stash/dataset/doi:10.5061/dryad.0nb2307
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344
Ver en: dataset/doi:10.5061/dryad.0nb2307" target="_blank">http://hdl.handle.net/10261/281344, http://datadryad.org/stash/dataset/doi:10.5061/dryad.0nb2307
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281344
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281351
Dataset. 2018
DATA FROM: SHOREBIRDS AS IMPORTANT VECTORS FOR PLANT DISPERSAL IN EUROPE
- Lovas-Kiss, Ádám
- Sánchez, Marta I.
- Wilkinson, David M.
- Coughlan, Neil E.
- Alves, José A.
- Green, Andy J.
Raw data on intact seeds in shorebirds
This file contains data of the faecal samples collected from the field in different locations with date, faeces sample mass, plant species name, and the number of seeds per taxon. This file was made with Microsoft Excel 2016
shorebird.xlsx, Shorebirds (Charadriiformes) undergo rapid migrations with potential for long-distance dispersal (LDD) of plants. We studied the frequency of endozoochory by shorebirds in different parts of Europe covering a broad latitudinal range and different seasons. We assessed whether plants dispersed conformed to morphological dispersal syndromes. A total of 409 excreta samples (271 faeces and 138 pellets) were collected from redshank (Tringa totanus), black-winged stilt (Himantopus himantopus), pied avocet (Recurvirostra avosetta), northern lapwing (Vanellus vanellus), Eurasian curlew (Numenius arquata) and black-tailed godwit (Limosa limosa) in south-west Spain, north-west England, southern Ireland and Iceland in 2005 and 2016, and intact seeds were extracted and identified. Godwits were sampled just before or after migratory movements between England and Iceland. The germinability of seeds was tested. Intact diaspores were recovered from all bird species and study areas, and were present in 13% of samples overall. Thirteen plant families were represented, including Charophyceae and 26 angiosperm taxa. Only four species had an "endozoochory syndrome". Four alien species were recorded. Ellenberg values classified three species as aquatic and 20 as terrestrial. Overall, 89% of seeds were from terrestrial plants, and 11% from aquatic plants. Average seed length was higher in redshank pellets than in their faeces. Six species were germinated, none of which had an endozoochory syndrome. Seeds were recorded during spring and autumn migration. Plant species recorded have broad latitudinal ranges consistent with LDD via shorebirds. Crucially, morphological syndromes do not adequately predict LDD potential, and more empirical work is required to identify which plants are dispersed by shorebirds. Incorporating endozoochory by shorebirds and other migratory waterbirds into plant distribution models would allow us to better understand the natural processes that facilitated colonization of oceanic islands, or to improve predictions of how plants will respond to climate change, or how alien species spread., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.3b333s8" target="_blank">http://hdl.handle.net/10261/281351, http://datadryad.org/stash/dataset/doi:10.5061/dryad.3b333s8
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281351
HANDLE: dataset/doi:10.5061/dryad.3b333s8" target="_blank">http://hdl.handle.net/10261/281351, http://datadryad.org/stash/dataset/doi:10.5061/dryad.3b333s8
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281351
PMID: dataset/doi:10.5061/dryad.3b333s8" target="_blank">http://hdl.handle.net/10261/281351, http://datadryad.org/stash/dataset/doi:10.5061/dryad.3b333s8
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281351
Ver en: dataset/doi:10.5061/dryad.3b333s8" target="_blank">http://hdl.handle.net/10261/281351, http://datadryad.org/stash/dataset/doi:10.5061/dryad.3b333s8
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281351
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281352
Dataset. 2018
DATA FROM: FITTER FROGS FROM POLLUTED PONDS: THE COMPLEX IMPACTS OF HUMAN-ALTERED ENVIRONMENTS
- Brady, Steven P.
- Zamora-Camacho, Francisco J.
- Eriksson, Fredrik A. A.
- Goedert, Debora
- Comas, Mar
- Calsbeek, Ryan
Adult wood frog traits
Jumping performance, adult size, and other morphometrics
AdultWoodFrogTraits2014.xls, Human-modified habitats rarely yield outcomes that are aligned with conservation ideals. Landscapes that are subdivided by roads are no exception, precipitating negative impacts on populations due to fragmentation, pollution, and road kill. Although many populations in human modified habitats show evidence for local adaptation, rarely does environmental change yield outright benefits for populations of conservation interest. Contrary to expectations, we report surprising benefits experienced by amphibian populations breeding and dwelling in proximity to roads. We show that roadside populations of the wood frog, Rana sylvatica, exhibit better locomotor performance and higher measures of traits related to fitness compared with frogs from less disturbed environments located further away from roads. These results contrast previous evidence for maladaptation in roadside populations of wood frogs studied elsewhere. Our results indicate that altered habitats might not be unequivocally detrimental, and at times might contribute to metapopulation success. While the frequency of such beneficial outcomes remains unknown, their occurrence underscores the complexity of inferring consequences of environmental change., National Science Foundation, Award: DEB-1655092, Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.2v41qr7" target="_blank">http://hdl.handle.net/10261/281352, http://datadryad.org/stash/dataset/doi:10.5061/dryad.2v41qr7
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281352
HANDLE: dataset/doi:10.5061/dryad.2v41qr7" target="_blank">http://hdl.handle.net/10261/281352, http://datadryad.org/stash/dataset/doi:10.5061/dryad.2v41qr7
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281352
PMID: dataset/doi:10.5061/dryad.2v41qr7" target="_blank">http://hdl.handle.net/10261/281352, http://datadryad.org/stash/dataset/doi:10.5061/dryad.2v41qr7
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281352
Ver en: dataset/doi:10.5061/dryad.2v41qr7" target="_blank">http://hdl.handle.net/10261/281352, http://datadryad.org/stash/dataset/doi:10.5061/dryad.2v41qr7
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281352
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281353
Dataset. 2018
DATA FROM: QUANTITATIVE ANALYSIS OF CONNECTIVITY IN POPULATIONS OF A SEMI-AQUATIC MAMMAL USING KINSHIP CATEGORIES AND NETWORK ASSORTATIVITY
- Escoda, Lídia
- Fernández-González, Ángel
- Castresana, José
ddRAD reads
Quality-filtered reads for each sample in FASTA format.
ddRAD_reads.zip
Genotype_counts.pl
Perl script for calculating genotype counts from a PED file to be used in the VCF2LR program.
Genotype_counts.zip
Assortativity.pl
Perl script for calculating the assortativity coefficient between two groups or sectors and example file.
Assortativity.zip
SNP dataset
SNP dataset in PED and VCF formats.
SNP_dataset.zip, Analyzing the impact of anthropogenic and natural river barriers on the dispersal of aquatic and semi-aquatic species may be critical for their conservation, but no adequate genetic methods have been developed for quantifying the effect of specific barriers on current connectivity. Knowledge of kinship relationships between individuals and reconstructions of pedigrees obtained using genomic data can be extremely useful, not only for studying the social organization of animals, but also inferring how the last few generations of offspring have dispersed. In this study, we used kinship data to analyze connectivity patterns in a small semi-aquatic mammal, the Pyrenean desman, in an area comprising two river systems with close headwaters and dams of various sizes. Using a large SNP dataset from 70 specimens, we obtained kinship categories and reconstructed pedigrees. To quantify the barrier effect of specific obstacles, we constructed kinship networks and devised a method based on the assortativity coefficient, which measures the proportion between observed and expected kinship relationships across a barrier. The estimation of this parameter enabled us to infer that the most important barrier in the area was the watershed divide between the rivers, followed by a dam on one of the rivers. Other barriers did not significantly reduce the expected number of kinship relationships across them. This strategy and the information obtained with it may be crucial in determining the most important connectivity problems in an area and help develop conservation plans aimed at improving genetic exchange between populations of threatened species., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.rq583" target="_blank">http://hdl.handle.net/10261/281353, http://datadryad.org/stash/dataset/doi:10.5061/dryad.rq583
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281353
HANDLE: dataset/doi:10.5061/dryad.rq583" target="_blank">http://hdl.handle.net/10261/281353, http://datadryad.org/stash/dataset/doi:10.5061/dryad.rq583
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281353
PMID: dataset/doi:10.5061/dryad.rq583" target="_blank">http://hdl.handle.net/10261/281353, http://datadryad.org/stash/dataset/doi:10.5061/dryad.rq583
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281353
Ver en: dataset/doi:10.5061/dryad.rq583" target="_blank">http://hdl.handle.net/10261/281353, http://datadryad.org/stash/dataset/doi:10.5061/dryad.rq583
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281353
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281357
Dataset. 2017
DATA FROM: TACKLING INTRASPECIFIC GENETIC STRUCTURE IN DISTRIBUTION MODELS BETTER REFLECTS SPECIES GEOGRAPHICAL RANGE
- Marcer, Arnald
- Méndez-Vigo, Belén
- Alonso-Blanco, Carlos
- Picó, F. Xavier
Arabidopsis_data_279accessions_20jan16, Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms’ distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole-species and genetic-unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.vv804" target="_blank">http://hdl.handle.net/10261/281357, http://datadryad.org/stash/dataset/doi:10.5061/dryad.vv804
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281357
HANDLE: dataset/doi:10.5061/dryad.vv804" target="_blank">http://hdl.handle.net/10261/281357, http://datadryad.org/stash/dataset/doi:10.5061/dryad.vv804
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281357
PMID: dataset/doi:10.5061/dryad.vv804" target="_blank">http://hdl.handle.net/10261/281357, http://datadryad.org/stash/dataset/doi:10.5061/dryad.vv804
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281357
Ver en: dataset/doi:10.5061/dryad.vv804" target="_blank">http://hdl.handle.net/10261/281357, http://datadryad.org/stash/dataset/doi:10.5061/dryad.vv804
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281357
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281358
Dataset. 2017
DATA FROM: GENETIC AND EPIGENETIC DIVERGENCE BETWEEN DISTURBED AND UNDISTURBED SUBPOPULATIONS OF A MEDITERRANEAN SHRUB: A 20-YEAR FIELD EXPERIMENT
- Herrera, Carlos M.
- Bazaga, Pilar
AFLP profiles for the plants of Lavandula latifolia sampled for the study
Markers are identified by primer combination and size (base pairs)
AFLP.scores.xlsx
MSAP profiles for the plants of Lavandula latifolia sampled for the study
Markers are identified by primer combination and size (base pairs).
MSAP.scores.xlsx
Spatial coordinates of Lavandula latifolia plants sampled for the study
Coordinates are expressed in meters and the origin (0,0) is the lower left corner of the plot as depicted in the figures.
Plant.coordinates.xlsx, Little is known on the potential of ecological disturbance to cause genetic and epigenetic changes in plant populations. We take advantage of a long-term field experiment initiated in 1986 to study the demography of the shrub Lavandula latifolia, and compare genetic and epigenetic characteristics of plants in two adjacent subplots, one experimentally disturbed and one left undisturbed, 20 years after disturbance. Experimental setup was comparable to an unreplicated ‘Before-After-Control-Impact’ (BACI) design where a single pair of perturbed and control areas were compared. When sampled in 2005, plants in the two subplots had roughly similar ages, but they had established in contrasting environments: dense conspecific population (‘Undisturbed’ subpopulation) versus open area with all conspecifics removed (‘Disturbed’ subpopulation). Plants were characterized genetically and epigenetically using amplified fragment length polymorphism (AFLP) and two classes of methylation-sensitive AFLP (MSAP) markers. Subpopulations were similar in genetic diversity but differed in epigenetic diversity and multilocus genetic and epigenetic characteristics. Epigenetic divergence between subpopulations was statistically unrelated to genetic divergence. Bayesian clustering revealed an abrupt linear boundary between subpopulations closely coincident with the arbitrary demarcation line between subplots drawn 20 years back, which supports that genetic and epigenetic divergence between subpopulations was caused by artificial disturbance. There was significant fine-scale spatial structuring of MSAP markers in both subpopulations, which in the Undisturbed one was indistinguishable from that of AFLP markers. Genetic differences between subpopulations could be explained by divergent selection alone, while the concerted action of divergent selection and disturbance-driven appearance of new methylation variants in the Disturbed subpopulation is proposed to explain epigenetic differences. This study provides the first empirical evidence to date suggesting that relatively mild disturbances could leave genetic and epigenetic signatures on the next adult generation of long-lived plants., Peer reviewed
Proyecto: //
DOI: dataset/doi:10.5061/dryad.v4192" target="_blank">http://hdl.handle.net/10261/281358, http://datadryad.org/stash/dataset/doi:10.5061/dryad.v4192
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281358
HANDLE: dataset/doi:10.5061/dryad.v4192" target="_blank">http://hdl.handle.net/10261/281358, http://datadryad.org/stash/dataset/doi:10.5061/dryad.v4192
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281358
PMID: dataset/doi:10.5061/dryad.v4192" target="_blank">http://hdl.handle.net/10261/281358, http://datadryad.org/stash/dataset/doi:10.5061/dryad.v4192
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281358
Ver en: dataset/doi:10.5061/dryad.v4192" target="_blank">http://hdl.handle.net/10261/281358, http://datadryad.org/stash/dataset/doi:10.5061/dryad.v4192
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281358
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