16S-raw-.001-abundance.representative.sequences

This fasta file includes 16S sequence data from different environmental samples. Within QIIME2, DADA2 was used to remove primer sequences from the reads, perform error correction, identify sequence variants, and remove chimeric sequences. Sequence variants were then classified by a naive Bayes classifier within QIIME2 using release of 128 of the Silva SSU database. An abundance filter was applied, and sequence variants that did not compose at least 0.1% of at least one library were removed from all libraries. The fasta file includes all variants that passed the abundance filter

ITS-dna-sequences

Following ITS sequencing, reads were demultiplexed using the 2017.10 release of QIIME2 requiring a barcode match. Because the forward and reverse reads do not overlap for this amplicon, DADA2 was used to trim forward and reverse reads to 200 and 100bp respectively. Cutadapt was used to trim primer sequences from the sequence variants identified by DADA2. Sequences that did not contain these primer sequences were discarded. VSEARCH was used to perform de novo chimera detection and removal. The remaining ITS sequence variants were clustered into operational taxonomic units (OTUs) at 97% similarity using Abundant OTU+. The software package ITSx was then used to filter non-ITS and non-fungal OTUs from our data set

Data from: Diplogastrellus nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host

A recent accumulation of studies has demonstrated that nongenetic, maternally transmitted factors are often critical to the health and development of offspring and can therefore play a role in ecological and evolutionary processes. In particular, microorganisms such as bacteria have been championed as heritable, symbiotic partners capable of conferring fitness benefits to their hosts. At the same time, parents may also pass various nonmicrobial organisms to their offspring, yet the roles of such organisms in shaping the developmental environment of their hosts remain largely unexplored. Here, we show that the nematode Diplogastrellus monhysteroides is transgenerationally inherited and sexually transmitted by the dung beetle Onthophagus taurus. By manipulating artificial chambers in which beetle offspring develop, we demonstrate that the presence of D. monhysteroides nematodes enhances the growth of beetle offspring, empirically challenging the paradigm that nematodes are merely commensal or even detrimental to their insect hosts. Finally, our research presents a compelling mechanism whereby the nematodes influence the health of beetle larvae: D. monhysteroides nematodes engineer the bacterial and fungal communities that also inhabit the beetle developmental chambers, including specific taxa known to be involved in biomass degradation, possibly allowing larval beetles better access to their otherwise recalcitrant, plant-based diet. Thus, our findings illustrate that nongenetic inheritance can include intermediately sized organisms that live and proliferate in close association with, and in certain cases enhance, the development of their hosts’ offspring

Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents

Evolutionary biology today tries to explain a natural world that appears remarkably different from the nature of the past century. It is a dynamic world, where symbiosis and phenotypic plasticity are the rules, not the exceptions. High-throughput sequencing has uncovered a world of complex interactions between developing organisms and the biotic and abiotic components of their environments. This newfound awareness of the dependency of phenotypes on other species and environmental conditions presents additional layers of complexity for evolutionary theory and raises many questions that are being addressed by new research programmes. The field of ecological evolutionary developmental biology (EcoEvo-Devo) attempts to study and model this new view of nature by organizing concepts such as developmental symbiosis and developmental plasticity into evolutionary theory 11 , different bacterial symbionts can generate reproductive isolation. Developmental plasticity -the ability of larval or embryonic organisms to react to environmental input with a change in form, physiology or behaviour 12 -is also ubiquitous. A single genome can generate different phenotypes depending on environmental cues. This means that the environment is not merely a selective agent; it also shapes the production of phenotypes. Such developmental plasticity can be critical in evolution. First, such plasticity can provide the phenotypic ranges within which animals can accommodate to environmental challenges such as climate changes 13,14 As such, it is crucial in ecosystem modelling. Second, developmental plasticity can facilitate niche construction, the process whereby an organism actively alters its environment 15 . Abstract | The integration of research from developmental biology and ecology into evolutionary theory has given rise to a relatively new field, ecological evolutionary developmental biology (Eco-Evo-Devo). This field integrates and organizes concepts such as developmental symbiosis, developmental plasticity, genetic accommodation, extragenic inheritance and niche construction. This Review highlights the roles that developmental symbiosis and developmental plasticity have in evolution. Developmental symbiosis can generate particular organs, can produce selectable genetic variation for the entire animal, can provide mechanisms for reproductive isolation, and may have facilitated evolutionary transitions. Developmental plasticity is crucial for generating novel phenotypes, facilitating evolutionary transitions and altered ecosystem dynamics, and promoting adaptive variation through genetic accommodation and niche construction. In emphasizing such non-genomic mechanisms of selectable and heritable variation, Eco-Evo-Devo presents a new layer of evolutionary synthesis

Diapause in a tropical oil-collecting bee: molecular basis unveiled by RNA-Seq

Abstract Background Diapause is a natural phenomenon characterized by an arrest in development that ensures the survival of organisms under extreme environmental conditions. The process has been well documented in arthropods. However, its molecular basis has been mainly studied in species from temperate zones, leaving a knowledge gap of this phenomenon in tropical species. In the present study, the Neotropical and solitary bee Tetrapedia diversipes was employed as a model for investigating diapause in species from tropical zones. Being a bivoltine insect, Tetrapedia diversipes produce two generations of offspring per year. The first generation, normally born during the wet season, develops faster than individuals from the second generation, born after the dry season. Furthermore, it has been shown that the development of the progeny, of the second generation, is halted at the 5th larval instar, and remains in larval diapause during the dry season. Towards the goal of gaining a better understanding of the diapause phenomenon we compared the global gene expression pattern, in larvae, from both reproductive generations and during diapause. The results demonstrate that there are similarities in the observed gene expression patterns to those already described for temperate climate models, and also identify diapause-related genes that have not been previously reported in the literature. Results The RNA-Seq analysis identified 2275 differentially expressed transcripts, of which 1167 were annotated. Of these genes, during diapause, 352 were upregulated and 815 were downregulated. According to their biological functions, these genes were categorized into the following groups: cellular detoxification, cytoskeleton, cuticle, sterol and lipid metabolism, cell cycle, heat shock proteins, immune response, circadian clock, and epigenetic control. Conclusion Many of the identified genes have already been described as being related to diapause; however, new genes were discovered, for the first time, in this study. Among those, we highlight: Niemann-Pick type C1, NPC2 and Acyl-CoA binding protein homolog (all involved in ecdysteroid synthesis); RhoBTB2 and SASH1 (associated with cell cycle regulation) and Histone acetyltransferase KAT7 (related to epigenetic transcriptional regulation). The results presented here add important findings to the understanding of diapause in tropical species, thus increasing the comprehension of diapause-related molecular mechanisms