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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

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

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

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

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

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

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

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

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