Resultados totales (Incluyendo duplicados): 34260
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Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281669
Dataset. 2021

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

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


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

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

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

Proyecto: //

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

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

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

Proyecto: //

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

DATA FROM: A FATHER EFFECT EXPLAINS SEX-RATIO BIAS

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

Proyecto: //

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

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

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

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281707
Dataset. 2017

DATA FROM: HOST NEST SITE CHOICE DEPENDS ON RISK OF CUCKOO PARASITISM IN MAGPIE HOSTS

  • Expósito-Granados, Mónica
  • Parejo, Deseada
  • Martínez, Juan Gabriel
  • Precioso, Marta
  • Molina-Morales, Mercedes
  • Avilés, Jesús M.
Data from "Host nest site choice depends on risk of cuckoo parasitism in magpie hosts" Data to analyze the parasitism risk proximity of induced cuckoo risk of parasitism for magpie nests during the experimental year 2013 and the individual magpie site fidelity of magpies between consecutive years 2012-2013. ExpositoGranados_et_al_2017BEHECO_data.xls, Avian brood parasites impose large fitness costs on their hosts and, thus, brood parasitism has selected for an array of host defensive mechanisms to avoid them. So far most studies have focused on antiparasite defenses operating at the egg and chick stages and neglected defenses that may work prior to parasite egg deposition. Here, we experimentally explore the possibility that hosts, as part of a front-line defense, might minimize parasitism costs through informed nest site choice based on perceived risk of cuckoo parasitism. We conducted a large-scale manipulation of visual and auditory cues potentially informing on the risk of great spotted cuckoo Clamator glandarius parasitism during the nest site choice period of the magpie Pica pica host to investigate its effect on host’s nest settlement and individual year to year site fidelity. Early breeding magpies preferentially placed their nests in safe areas (i.e., in sites of low perceived risk of parasitism), and, this effect diluted with time elapsed since risk of parasitism was manipulated. Site fidelity of individual magpies decreased with risk of cuckoo parasitism, for those that were not parasitized in the previous year. Our results constitute the first strong evidence showing that hosts can minimize the costs of cuckoo parasitism through informed nest-site choice, calling for future consideration of defenses potentially operating prior to parasite egg deposition to achieve a better understanding of cuckoo-host coevolution., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281713
Dataset. 2017

DATA FROM: THE CHICKEN OR THE EGG? ADAPTATION TO DESICCATION AND SALINITY TOLERANCE IN A LINEAGE OF WATER BEETLES

  • Pallarés, Susana
  • Arribas, Paula
  • Bilton, David T.
  • Millán, Andrés
  • Velasco, Josefa
  • Ribera, Ignacio
Alignments Alignments of the mitochondrial and nuclear genes (or gene fragments) sequenced to obtain the phylogeny of the subgenus Lumetus (genus Enochrus, family Hydrophilidae, order Coleoptera) in FASTA format alignments.rar, Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e., the ability to osmoregulate in hyperosmotic media) and habitat transitions in the water beetle genus Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced desiccation resistance evolved before increases in hyporegulation ability or vice versa, or whether the two mechanisms evolved in parallel. The most recent ancestor of Lumetus was inferred to have high desiccation resistance and moderate hyporegulation ability. There were repeated shifts between habitats with differing levels of salinity in the radiation of the group, those to the most saline habitats generally occurring more rapidly than those to less saline ones. Significant and accelerated changes in hyporegulation ability evolved in parallel with smaller and more progressive increases in desiccation resistance across the phylogeny, associated with the colonization of meso- and hypersaline waters during global aridification events. All species with high hyporegulation ability were also desiccation-resistant, but not vice versa. Overall, results are consistent with the hypothesis that desiccation resistance mechanisms evolved first and provided the physiological basis for the development of hyporegulation ability, allowing these insects to colonize and diversify across meso- and hypersaline habitats., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281745
Dataset. 2017

DATA FROM: INTRASPECIFIC GENETIC STRUCTURE, DIVERGENCE AND HIGH RATES OF CLONALITY IN AN AMPHI-ATLANTIC STARFISH

  • García-Cisneros, Álex
  • Palacín, Cruz
  • Rezende Ventura, Carlos Renato
  • Feital, Barbara
  • Paiva, Paulo Cesar
  • Pérez-Portela, R.
Genotypes and sequences of sampled individuals Microsatellite genotypes in an excel sheet and all sequences obtained in fasta format. Sequences and genotypes coscinasterias tenuispina.zip, Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species’ distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the south-western Atlantic and the other along the north-eastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations where found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intra-population genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations’ genetic divergence could be observed between some populations., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281750
Dataset. 2017

DATA FROM: AGRICULTURE SHAPES THE TROPHIC NICHE OF A BAT PREYING ON MULTIPLE PEST ARTHROPODS ACROSS EUROPE: EVIDENCE FROM DNA METABARCODING

  • Aizpurua, Ostaizka
  • Budinski, Ivana
  • Georgiakakis, Panagiotis
  • Gopalakrishnan, Shyam
  • Ibáñez, Carlos
  • Mata, Vanessa
  • Rebelo, Hugo
  • Russo, Danilo
  • Szodoray-Parádi, Farkas
  • Zhelyazkova, Violeta
  • Zrncic, Vida
  • Gilbert, M. Thomas P.
  • Alberdi, Antton
Zeale sequences Sequences filtered by DAMe using 2/3 filtering strategy and a minimum copy number of 2. zeale_sequences.zip Epp sequences Sequences filtered by DAMe using 2/3 filtering strategy and a minimum copy number of 2. epp_sequences.zip, The interaction between agricultural production and wildlife can shape, and even condition, the functioning of both systems. In this study we i) explored the degree to which a widespread European bat, namely the common bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at a continental scale, and ii) tested whether its dietary niche is shaped by the extension and type of agricultural fields. We employed a dual-primer DNA metabarcoding approach to characterise arthropod 16S and COI DNA sequences within bat faecal pellets collected across 16 Southern European localities, to first characterise the bat species’ dietary niche, secondly measure the incidence of agricultural pests across their ranges, and thirdly assess whether geographical dietary variation responds to climatic, landscape diversity, agriculture type and vegetation productivity factors. We detected 12 arthropod orders, among which lepidopterans were predominant. We identified >200 species, 44 of which are known to cause agricultural damage. Pest species were detected at all but one sampling site and in 94% of the analysed samples. Furthermore, the dietary diversity of M. schreibersii exhibited a negative linear relation with the area of intensive agricultural fields, thus suggesting crops restrict the dietary niche of bats to prey taxa associated with agricultural production within their foraging range. Overall our results imply that M. schreibersii might be a valuable asset for biological pest suppression in a variety of agricultural productions, and highlight the dynamic interplay between wildlife and agricultural systems., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/281753
Dataset. 2017

DATA FROM: THE CURIOUS CASE OF BRADYPUS VARIEGATUS SLOTHS: POPULATIONS IN THREATENED HABITATS ARE BIODIVERSITY COMPONENTS NEEDING PROTECTION

  • Marques Silva, Sofia
  • Dávila, José A.
  • Voirin, Bryson
  • Lopes, Susana
  • Ferrand, Nuno
  • Moraes-Barros, Nadia
Bradypus_microsatellites Microsatellite genotypes. Missing data is coded as 0. Bradypus_dryad.xlsx, Studying Neotropical wild populations is of particular interest. While this region is facing an escalating habitat degradation, it also has remarkable biodiversity levels, whose origin we are only beginning to understand. A myriad of processes might have had idiosyncratic effects on its numerous species. Within the hottest Neotropical biodiversity hotspot, the Atlantic Forest (AF), species and genetic diversities are organized latitudinally, with decreasing diversity levels southwards. Bradypus variegatus, the brown-throated three-toed sloth, was one of the first species observed to present such pattern. Moreover, within AF, B. variegatus populations seem to be geographically isolated and genetically differentiated. Whether AF B. variegatus isolation, differentiation, and loss of genetic diversity are historical or contemporary (anthropogenic-driven), result from species-specific or general historical events, and if this is of conservation concern remains unclear. Here, we combine micro-evolutionary, multilocus, and high-throughput sequencing approaches to detail the processes responsible for the patterns of genetic diversity on B. variegatus populations in AF, and further understand AF biogeographic history. Few studies made use of similar approaches on Neotropical biodiversity. Our results agree with recent re-interpretations on the AF refugia model and support a species-specific refugium in southern AF, characterized by a metapopulation formation. Finally, we present compelling evidences of the need for conservation actions on AF B. variegatus populations, by comparing genetic diversity levels between populations of different Bradypus species. As far as we know, this is the most comprehensive assessment on Bradypus nuclear DNA diversity., Peer reviewed

Proyecto: //

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