BUSCADOR RECOLECTA

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

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

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

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

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

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

Simón-Porcar_etal_2015_AJB Genetic database of 31 populations of Narcissus papyraceus in the western Mediterranean, genotyped with 8 microsatellite markers. Genotyped individuals are either long-styled (L) or short-styled (S)., Premise of the study: Theoretical models state that natural selection and mating patterns account for floral morph ratio in style- polymorphic plants. However, the demographic history of populations can also influence variation in morph ratios. If so, we hypothesize an association between the morph ratios and the genetic structure across populations. Methods: We used nuclear microsatellites to assess genetic variation and structure in populations of Narcissus papyraceus, a style-dimorphic plant whose floral morph ratios (L-morph to S-morph) gradually vary throughout its distribution range in the southwestern SW Mediterranean Basin. We implemented analyses to relate the genetic features of populations with their morph ratios. Key results: We found greater frequencies of the S-morph in central populations and declining frequencies toward the periphery. This geographic pattern was not associated with the genetic structure of populations. Instead, we found two distinct genetic groups, mainly separated by the Strait of Gibraltar, with a mixture of morph ratios within each one. Overall, there was a weak genetic structure. Genetic diversity was greater in central and southern dimorphic populations than in northern L-monomorphic populations. Conclusions: Altogether, our results do not support the hypothesis that the demographic history of populations can account for the observed geographical pattern of morph ratios in N. papyraceus. We suggest that adaptive processes shown in previous studies in the species are the main determinant of the existing variation in the morph composition of populations., Peer reviewed

All Tribolium Genotypes This file includes all the genotypes scored as part of this study in GenPop format. Sample names include either Fam (indicating that they are the first offspring from each family in the inbreeding assey) or Ind (indicating that these are additional individuals from the selection lines also included in the sample name). Allgenotypes.xlsx Per locus heterozygosity The estimated heterozygosities for each locus for each population produced by GenPop. Het by locus.xlsx Tribolium linear models R script The R script used to fit linear models to the heterozygosities and plot the graph. Tribolium_linear_models_Nature.R, Reproduction through sex carries substantial costs, mainly because only half of sexual adults produce offspring. It has been theorized that these costs could be countered if sex allows sexual selection to clear the universal fitness constraint of mutation load. Under sexual selection, competition between (usually) males and mate choice by (usually) females create important intraspecific filters for reproductive success, so that only a subset of males gains paternity. If reproductive success under sexual selection is dependent on individual condition, which is contingent to mutation load, then sexually selected filtering through ‘genic capture’ could offset the costs of sex because it provides genetic benefits to populations. Here we test this theory experimentally by comparing whether populations with histories of strong versus weak sexual selection purge mutation load and resist extinction differently. After evolving replicate populations of the flour beetle Tribolium castaneum for 6 to 7 years under conditions that differed solely in the strengths of sexual selection, we revealed mutation load using inbreeding. Lineages from populations that had previously experienced strong sexual selection were resilient to extinction and maintained fitness under inbreeding, with some families continuing to survive after 20 generations of sib × sib mating. By contrast, lineages derived from populations that experienced weak or non-existent sexual selection showed rapid fitness declines under inbreeding, and all were extinct after generation 10. Multiple mutations across the genome with individually small effects can be difficult to clear, yet sum to a significant fitness load; our findings reveal that sexual selection reduces this load, improving population viability in the face of genetic stress., Peer reviewed

File nymphs_replica 1.raw.zip This file contains the mass spectrometry data of iTRAQ labeled nymph sample (A. phagocytophilum-infected and uninfected control) replicate 1 (RAW.ZIP). Files may be viewed with Thermo Scientific Qual Browser. nymphs_replica 1.raw.zip File nymphs_replica 2.raw.zip This file contains the mass spectrometry data of iTRAQ labeled nymph sample (A. phagocytophilum-infected and uninfected control) replicate 2 (RAW.ZIP). Files may be viewed with Thermo Scientific Qual Browser. nymphs_replica 2.raw.zip File tissues_ replica 1.raw.zip This file contains the mass spectrometry data of iTRAQ labeled adult female gut and salivary gland sample (A. phagocytophilum-infected and uninfected control) replicate 1 (RAW.ZIP). Files may be viewed with Thermo Scientific Qual Browser. tissues_ replica 1.raw.zip File tissues_ replica 2.raw.zip This file contains the mass spectrometry data of iTRAQ labeled adult female gut and salivary gland sample (A. phagocytophilum-infected and uninfected control) replicate 2 (RAW.ZIP). Files may be viewed with Thermo Scientific Qual Browser. tissues_ replica 2.raw.zip Folder RNAseq analysis This folder contains RNAseq data analysis for A. phagocytophilum-infected and uninfected nymphs, guts and salivary glands samples replicates 1 and 2. RNAseq analysis.zip File Sample_Tissues_Ixo_all_samples.fastq.zip This file contains the reads from I. scapularis adult female tissue samples replicates 1 and 2 (FASTQ.ZIP). Sample_Tissues_Ixo_all_samples.fastq.zip File Sample_Nymphs_Ixo_all_samples.fastq.zip This file contains the reads from I. scapularis nymph samples replicates 1 and 2 (FASTQ.ZIP). Sample_Nymphs_Ixo_all_samples.fastq.zip, Anaplasma phagocytophilum is an emerging pathogen that causes human granulocytic anaplasmosis. Infection with this zoonotic pathogen affects cell function in both vertebrate host and the tick vector, Ixodes scapularis. Global tissue-specific response and apoptosis signaling pathways were characterized in I. scapularis nymphs and adult female midguts and salivary glands infected with A. phagocytophilum using a systems biology approach combining transcriptomics and proteomics. Apoptosis was selected for pathway-focused analysis due to its role in bacterial infection of tick cells. The results showed tissue-specific differences in tick response to infection and revealed differentiated regulation of apoptosis pathways. The impact of bacterial infection was more pronounced in tick nymphs and midguts than in salivary glands, probably reflecting bacterial developmental cycle. All apoptosis pathways described in other organisms were identified in I. scapularis, except for the absence of the Perforin ortholog. Functional characterization using RNA interference showed that Porin knockdown significantly increases tick colonization by A. phagocytophilum. Infection with A. phagocytophilum produced complex tissue-specific alterations in transcript and protein levels. In tick nymphs, the results suggested a possible effect of bacterial infection on the inhibition of tick immune response. In tick midguts, the results suggested that A. phagocytophilum infection inhibited cell apoptosis to facilitate and establish infection through up-regulation of the JAK/STAT pathway. Bacterial infection inhibited the intrinsic apoptosis pathway in tick salivary glands by down-regulating Porin expression that resulted in the inhibition of Cytochrome c release as the anti-apoptotic mechanism to facilitate bacterial infection. However, tick salivary glands may promote apoptosis to limit bacterial infection through induction of the extrinsic apoptosis pathway. These dynamic changes in response to A. phagocytophilum in I. scapularis tissue-specific transcriptome and proteome demonstrated the complexity of the tick response to infection and will contribute to characterize gene regulation in ticks., Peer reviewed

Vegetation surveys and mean community traits DeFrenne et al_data.xlsx, Competition for light has profound effects on plant performance in virtually all terrestrial ecosystems. Nowhere is this more evident than in forests, where trees create environmental heterogeneity that shapes the dynamics of forest-floor communities1,​2,​3. Observational evidence suggests that biotic responses to both anthropogenic global warming and nitrogen pollution may be attenuated by the shading effects of trees and shrubs4,​5,​6,​7,​8,​9. Here we show experimentally that tree shade is slowing down changes in below-canopy communities due to warming. We manipulated levels of photosynthetically active radiation, temperature and nitrogen, alone and in combination, in a temperate forest understorey over a 3-year period, and monitored the composition of the understorey community. Light addition, but not nitrogen enrichment, accelerated directional plant community responses to warming, increasing the dominance of warmth-preferring taxa over cold-tolerant plants (a process described as thermophilization6,10,​11,​12). Tall, competitive plants took greatest advantage of the combination of elevated temperature and light. Warming of the forest floor did not result in strong community thermophilization unless light was also increased. Our findings suggest that the maintenance of locally closed canopy conditions could reduce, at least temporarily, warming-induced changes in forest floor plant communities., Peer reviewed