Population genomics is an increasingly popular approach to investigate the genetic basis of adaptation and speciation at the genome scale. However, it has so far largely failed to go beyond the mere ...identification of anonymous markers displaying selection signatures. Will population genomics ever be up to our expectations and able to really pinpoint genes underlying adaptation and speciation processes? In this issue of Molecular Ecology, Namroud et al. use population genomics to investigate local adaptation in natural populations of a conifer tree, the white spruce (Picea glauca). They show how population and functional genomics can finally converge with the deployment of the next generation of genome scans, which target gene‐rich regions rather than the whole genome.
Environmental DNA (eDNA) metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa such as soil organisms. Increasing sample ...sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guideline for best practices so far. Here, we assessed the impact of four methods of soil sample preservation that can be conveniently used also in metabarcoding studies targeting remote or difficult to access areas. Tested methods include: preservation at room temperature for 6 hr, preservation at 4°C for 3 days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6 hr at room temperature and preservation for 21 days. For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under ideal conditions (i.e., extraction of eDNA immediately after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in molecular operational taxonomic units (MOTU) richness of bacteria, fungi and eukaryotes across treatments, but MOTU richness was similar across preservation methods if rare taxa were not considered. All the approaches were able to identify differences in community structure among habitats, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.
There is a growing interest in identifying ecological factors that influence adaptive genetic diversity patterns in both model and nonmodel species. The emergence of large genomic and environmental ...data sets, as well as the increasing sophistication of population genetics methods, provides an opportunity to characterize these patterns in relation to the environment. Landscape genetics has emerged as a flexible analytical framework that connects patterns of adaptive genetic variation to environmental heterogeneity in a spatially explicit context. Recent growth in this field has led to the development of numerous spatial statistical methods, prompting a discussion of the current benefits and limitations of these approaches. Here we provide a review of the design of landscape genetics studies, the different statistical tools, some important case studies, and perspectives on how future advances in this field are likely to shed light on important processes in evolution and ecology.
Subterranean environments host a substantial amount of biodiversity, however assessing the distribution of species living underground is still extremely challenging. Environmental DNA (eDNA) ...metabarcoding is a powerful tool to estimate biodiversity in poorly known environments and has excellent performance for soil organisms. Here, we tested 1) whether eDNA metabarcoding from cave soils/sediments allows to successfully detect springtails (Hexapoda: Collembola) and insects (Hexapoda: Insecta); 2) whether eDNA mostly represents autochthonous (cave-dwelling) organisms or it also incorporates information from species living in surface environments; 3) whether eDNA detection probability changes across taxa with different ecology. Environmental DNA metabarcoding analyses detected a large number of Molecular Operational Taxonomic Units (MOTUs) for both insects and springtails. For springtails, detection probability was high, with a substantial proportion of hypogean species, suggesting that eDNA provides good information on the distribution of these organisms in caves. Conversely, for insects most of MOTUs represented taxa living outside caves, and the majority of them represented taxa/organisms living in freshwater environments (Ephemeroptera, Plecoptera and Trichoptera). The eDNA of freshwater insects was particularly abundant in deep sectors of caves, far from the entrance. Furthermore, average detection probability of insects was significantly lower than the one of springtails. This suggests that cave soils/sediments act as “conveyer belts of biodiversity information”, possibly because percolating water lead to the accumulation of eDNA of organisms living in nearby areas. Cave soils hold a complex mix of autochthonous and allochthonous eDNA. eDNA provided unprecedented information on the understudied subterranean cave organisms; analyses of detection probability and occupancy can help teasing apart local eDNA from the eDNA representing spatially-integrated biodiversity for whole landscape.
Display omitted
•We tested the usefulness of eDNA from cave soil to study subterranean biodiversity.•A complex pattern of allochthonous and autochthonous eDNA has been observed.•Cave soils act as conveyer belts of biodiversity information.
Although genotyping errors affect most data and can markedly influence the biological conclusions of a study, they are too often neglected. Errors have various causes, but their occurrence and effect ...can be limited by considering these causes in the production and analysis of the data. Procedures that have been developed for dealing with errors in linkage studies, forensic analyses and non-invasive genotyping should be applied more broadly to any genetic study. We propose a protocol for estimating error rates and recommend that these measures be systemically reported to attest the reliability of published genotyping studies.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping ...techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (
Coenonympha sp.
) and several populations of common beech (
Fagus sylvatica
). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.
Tropical forests shelter an unparalleled biological diversity. The relative influence of environmental selection (i.e., abiotic conditions, biotic interactions) and stochastic–distance‐dependent ...neutral processes (i.e., demography, dispersal) in shaping communities has been extensively studied for various organisms, but has rarely been explored across a large range of body sizes, in particular in soil environments. We built a detailed census of the whole soil biota in a 12‐ha tropical forest plot using soil DNA metabarcoding. We show that the distribution of 19 taxonomic groups (ranging from microbes to mesofauna) is primarily stochastic, suggesting that neutral processes are prominent drivers of the assembly of these communities at this scale. We also identify aluminium, topography and plant species identity as weak, yet significant drivers of soil richness and community composition of bacteria, protists and to a lesser extent fungi. Finally, we show that body size, which determines the scale at which an organism perceives its environment, predicted the community assembly across taxonomic groups, with soil mesofauna assemblages being more stochastic than microbial ones. These results suggest that the relative contribution of neutral processes and environmental selection to community assembly directly depends on body size. Body size is hence an important determinant of community assembly rules at the scale of the ecological community in tropical soils and should be accounted for in spatial models of tropical soil food webs.
see also the Perspective by Dumbrell
Soil microbial communities play a key role in plant nutrition and stress tolerance. This is particularly true in sites contaminated by trace metals, which often have low fertility and stressful ...conditions for woody plants in particular. However, we have limited knowledge of the abiotic and biotic factors affecting the richness and composition of microbial communities inhabiting the rhizosphere of plants in contaminated sites. Using high-throughput amplicon sequencing, we studied the rhizospheric bacterial and fungal community structures of 14 woody plant families planted in three contrasting sites contaminated by metals (Pb, Cd, Zn, Mn, Fe, S). The rhizospheric bacterial communities in the given sites showed no significant difference between the various woody species but did differ significantly between sites. The Proteobacteria phylum was dominant, accounting for over 25 % of the overall relative abundance, followed by Actinobacteria, Bacteroidetes and Gemmatimonadetes. Site was also the main driver of fungal community composition, yet unlike bacteria, tree species identity significantly affected fungal communities. The Betulaceae, Salicaceae and Fagaceae families had a high proportion of Basidiomycota, particularly ectomycorrhizal fungi, and the lowest diversity and richness. The other tree families and the unplanted soil harboured a greater abundance of Ascomycota and Mucoromycota. Consequently, for both bacteria and fungi, the site effect significantly impacted their community richness and composition, while the influence of plants on the richness and composition of rhizospheric microbial communities stayed consistent across sites and was dependent on the microbial kingdom. Finally, we highlighted the importance of considering this contrasting response of plant rhizospheric microbial communities in relation to their host identity, particularly to improve assisted revegetation efforts at contaminated sites.
Display omitted
•Rhizospheric fungal and bacterial communities were assessed at three different sites.•Fungal communities are mainly driven by soil parameters and tree species.•Two groups of tree species were identified as a function of their fungal communities.•Uncultured and rhizospheric soils shared the same bacterial communities.•The fungal communities differed depending on the site at which the trees were cultivated.
While many studies have analyzed the diet of marine consumers using traditional morphology-based methods, the integral diet of many species of functionally important groups such as benthic ...invertebrates remains poorly resolved. This hinders our ability to precisely establish trophic links among species, which is necessary to understand food webs and ecosystem dynamics. Here, we applied DNA metabarcoding to obtain a high resolution picture of the animal fraction of the diet of six species of crustaceans in the Bay of Biscay; the edible crab Cancer pagurus, the velvet crab Necora puber, the circular crab Atelecyclus undecimdentatus, the spider crab Maja brachydactyla, the shrimp Crangon crangon, and the hermit crab Pagurus bernhardus. We used two pairs of primers targeting the 18S rDNA (generalist) and 12S rDNA (fish-specific) regions to identify prey that makes up the animal fraction of the diet. Based on occurrence data, 54 prey taxa belonging to 5 different phylum mostly represented by teleost fishes and malacostracans were identified. Through a high-level of prey detection, results indicate a scavenging strategy across all consumers mostly based on the consumption of preys likely originating from fishing discards. This study also reveals patterns of niche overlaps among consumers differentiating C. crangon from others and suggesting high overlap in animal resource use between N. puber and M. brachydactyla as well as C. pagurus. High resolution diet description revealed the complexity of trophic interactions on a local scale.
•The dietary profiles of six crustaceans were studied.•DNA metabarcoding on gut content provides an accurate detection of prey items.•Teleost fishes and malacostracans were the main prey items across the consumers.•Necora puber trophic niche is common to Maja brachydactyla and Cancer pagurus ones.•Scavenging is a significant energetic pathway that probably structure communities.
PDF
