Viruses transmitted by Aedes mosquitoes are an increasingly important global cause of disease. Defining common determinants of host susceptibility to this large group of het- erogenous pathogens is key for informing the rational design of panviral medicines. Infection of the vertebrate host with these viruses is enhanced by mosquito saliva, a complex mixture of salivary-gland-derived factors and microbiota. We show that the enhancement of infection by saliva was dependent on vascular function and was inde-...

Supplementary Material 1

Supplementary Material 2

Additional file 4: Supplementary Table S4. Accuracy of each pipeline in re-constructing the mock community at genus level.

Additional file 9: Supplementary Figure S5. Reproducibility of beta diversity at different read truncation lengths. Reproducibility of sequenced technical replicates by measuring the Bray-Curtis (A and C) and Jaccard distances (B and D) of the microbiome composition among technical replicate samples. Two datasets were used to represent different biomes and amplicon technologies using (A, B) human faecal samples (16S rRNA primer, N=40 replicates) and (C, D) soil samples (16S rRNA, V4-V5 region primers, N=50 replicates)....

Temperature has a profound effect on the growth and development of ectothermic animals. However, the extent to which ecologically-driven selection pressures can adjust thermal plastic responses in growth schedules is not well understood. Comparing temperature-induced plastic responses between sexes provides a promising but underexploited approach to evaluating the evolvability of thermal reaction norms: males and females share largely the same genes and immature environments but typically experience different ecological selection pressures. We proceed from the...

Additional file 1: Supplementary Table S1. Read counts and number of OTUs/ASVs in the OTU/ASV matrix of each pipeline.

The ecology and evolution of reproductive timing and synchrony has been a topic of great interest in evolutionary ecology for decades. Originally motivated by questions related to behavioural and reproductive adaptation to environmental conditions, the topic has acquired new relevance in the face of climate change. However, there has been relatively little research on reproductive phenology in mammalian carnivores. The Eurasian lynx (Lynx lynx) occurs across the Eurasian continent, covering three of the four main...

Additional file 14: Supplementary information.

Additional file 2: Supplementary Table S2. Significance of differences between each pipeline in the reproducibility of beta diversity between the technical replicates. Significance of differences in Bray-Curtis distance between the pipelines were calculated based on the Tukey’s HSD test.

Additional file 6: Supplementary Figure S2. Reproducibility and data usage efficiency respective to dereplication filtering. A, D and G) Data usage efficiency of each tested pipeline at different dereplication parameters of LotuS2 (from strictest to least strict dereplication: 20:1,12:3,6:2; 15:1,9:3,12:2; 10:1,6:3,8:2; 8:1,4:2,3:3 (default); 4:1; 2:1, and 1:1) using DADA2 or CD-HIT clustering for 16S and ITS datasets, respectively, by comparing the number of sequence clusters (OTUs/ASVs) to retrieved read counts in final output matrix.The dereplication...

Additional file 8: Supplementary Figure S4. Data usage efficiency of different amplicon sequence data analysis pipelines. Data usage efficiency on gut 16S rRNA (gut- 16S) and soil 16S rRNA (soil-16S) amplicons tested with different pipelines at different read truncation lengths (170, 200, and 230 & 170, 200, and 220 bases for the gut and soil datasets, respectively), by comparing the number of sequence clusters (ASVs /OTUs) to retrieved read counts in the final output matrix...

Drought is expected to increase in future climate scenarios. Although responses to drought of individual functional traits are relatively well-known, simultaneous changes across multiple traits in response to water scarcity remain poorly understood despite its importance to understand alternative strategies to resist drought. We grew 52 herbaceous species in monocultures under drought and control treatments and characterized the functional space using seven measured above- and belowground traits: plant height, leaf area, specific leaf area, leaf...

The degree to which variation in adult food availability affects the population dynamics of a species depends on its position on the capital-income breeding continuum. The long-lived butterflies that feed on fruits as adults constitute an example of Lepidoptera with a high degree of income breeding. For three species of fruit-feeding butterflies in Uganda, we assessed the contribution of the income to breeding in the wild, and the consequences of variation in fruit availability for...

Migration patterns in birds vary in space and time. Spatial patterns include chain, leap frog, and telescopic migration. Temporal patterns such as migration duration, number and duration of stopovers may vary according to breeding latitude, sex and season. This study aimed to verify these patterns in a long-distance migrant, the Eurasian curlew (Numenius arquata arquata), and to provide a synopsis of spatio-temporal migration patterns in this species of concern throughout the East Atlantic Flyway. We...

To analyze time trends in incidence, causes and risk factors for traumatic spinal cord injuries (TSCI) in Estonia between 1997–2007 and 2008–2018. Retrospective, population-based cohort study. Specialized trauma centres in Estonia. Medical records of patients with TSCI from 1997 to 2018. None. Demographical data, crude and age- and sex-adjusted incidence rates, causes of TSCI, level and extent of injury, associated injuries. A total of 940 new patients with TSCI were identified for the period of...

Additional file 10: Supplementary Figure S6. Reproducibility of alpha diversity between technical replicates. OTU/ASV richness was calculated for A) gut-16S, B) soil-16S, and C) soil-ITS datasets. Samples were rarefied to an equal number of reads per sample before calculating richness, and any samples whose replicate pair was removed after rarefaction (because of having lower number of reads than the rarefaction depth) were excluded from further analysis. LotuS1 results for soil-16S were removed due to too...

Additional file 11: Supplementary Figure S7. Observed composition of the mock community compared to the composition predicted by each pipeline. A) Relative abundances of the 16 orders having the highest abundance. B) Bray-Curtis distance based PCoA of the observed composition of the mock sample and composition predicted by each pipeline

Additional file 13: Supplementary Figure S9. Accuracy of each pipeline in predicting the mock community composition at species level. For benchmarking we compared the fraction of reads assigned to true taxa and both correctly and erroneously recovered taxa at the species level from the mock community.

1. Mycorrhizas are known to increase plant resistance to herbivores and climatic stress. However, it is unknown if particularly hostile environments select for increased investment of plants into mycorrhiza. 2. We studied hostile biotic environments: phylogenetically proximate neighbourhoods known to increase herbivory and pedoclimatic stress. In a common garden, we studied the resistances, tri-trophic interactions and microclimate of 28-years-old oaks (Quercus petraea), descending from provenances of contrasting phylogenetic neighbourhoods. 3. We found that oaks descending...

Supplementary Material 3

Additional file 7: Supplementary Figure S3. Reproducibility of the technical replicates respective to different LotuS2 non-default parameters. Bray-Curtis distances between technical replicates of A) gut-16S, B) soil-16S, and C) soil-ITS datasets using default and non-default parameters (LotuS2 flags: -lulu 0, -xtalk 1, -keepUnclassified 1, -ITSx 0, where 1 means the option is activated; 0 means deactivated). When activated, -lulu option uses LULU R package [24] to merge OTUs/ASVs based on their co-occurrences; -xtalk option checks...

Abstract Background Amplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (less OTU scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences. Results In LotuS2, six...