Optimising high-throughput sequencing data analysis, from gene database selection to the analysis of compositional data: a case study on tropical soil nematodes

IntroductionHigh-throughput sequencing (HTS) provides an efficient and cost-effective way to generate large amounts of sequence data, providing a very powerful tool to analyze biodiversity of soil organisms. However, marker-based methods and the resulting datasets come with a range of challenges and disputes, including incomplete reference databases, controversial sequence similarity thresholds for delimitating taxa, and downstream compositional data analysis. MethodsHere, we use HTS data from a soil nematode biodiversity experiment to explore standardized HTS data processing procedures. We compared the taxonomic assignment performance of two main rDNA reference databases (SILVA and PR2). We tested whether the same ecological patterns are detected with Amplicon Sequence Variants (ASV; 100% similarity) versus classical Operational Taxonomic Units (OTU; 97% similarity). Further, we tested how different HTS data normalization methods affect the recovery of beta diversity patterns and the identification of differentially abundant taxa.ResultsAt this time, the SILVA 138 eukaryotic database performed better than the PR2 4.12 database, assigning more reads to family level and providing higher phylogenetic resolution. ASV- and OTU-based alpha and beta diversity of nematodes correlated closely, indicating that OTU-based studies represent useful reference points. For downstream data analyses, our results indicate that loss of data during subsampling under rarefaction-based methods might reduce the sensitivity of the method, e.g. underestimate the differences between nematode communities under different treatments, while the clr-transformation-based methods may overestimate effects. The Analysis of Compositions of Microbiome with Bias Correction approach (ANCOM-BC) retains all data and accounts for uneven sampling fractions for each sample, suggesting that this is currently the optimal method to analyze compositional data.DiscussionOverall, our study highlights the importance of comparing and selecting taxonomic reference databases before data analyses, and provides solid evidence for the similarity and comparability between OTU- and ASV-based nematode studies. Further, the results highlight the potential weakness of rarefaction-based and clr-transformation-based methods. We recommend future studies use ASV and that both the taxonomic reference databases and normalization strategies are carefully tested and selected before analyzing the data

Global Biodiversity and Phylogenetic Evaluation of Remipedia (Crustacea)

Remipedia is one of the most recently discovered classes of crustaceans, first described in 1981 from anchialine caves in the Bahamas Archipelago. The class is divided into the order Enantiopoda, represented by two fossil species, and Nectiopoda, which contains all known extant remipedes. Since their discovery, the number of nectiopodan species has increased to 24, half of which were described during the last decade. Nectiopoda exhibit a disjunct global distribution pattern, with the highest abundance and diversity in the Caribbean region, and isolated species in the Canary Islands and in Western Australia. Our review of Remipedia provides an overview of their ecological characteristics, including a detailed list of all anchialine marine caves, from which species have been recorded. We discuss alternative hypotheses of the phylogenetic position of Remipedia within Arthropoda, and present first results of an ongoing molecular-phylogenetic analysis that do not support the monophyly of several nectiopodan taxa. We believe that a taxonomic revision of Remipedia is absolutely essential, and that a comprehensive revision should include a reappraisal of the fossil record

Changes in diversity and community assembly of jumping spiders (Araneae: Salticidae) after rainforest conversion to rubber and oil palm plantations

Rainforest conversion into monoculture plantations results in species loss and community shifts across animal taxa. The effect of such conversion on the role of ecophysiological properties influencing communities, and conversion effects on phylogenetic diversity and community assembly mechanisms, however, are rarely studied in the same context. Here, we compare salticid spider (Araneae: Salticidae) communities between canopies of lowland rainforest, rubber agroforest (“jungle rubber”) and monoculture plantations of rubber or oil palm, sampled in a replicated plot design in Jambi Province, Sumatra, Indonesia. Overall, we collected 912 salticid spider individuals and sorted them to 70 morphospecies from 21 genera. Salticid richness was highest in jungle rubber, followed by rainforest, oil palm and rubber, but abundance of salticids did not differ between land-use systems. Community composition was similar in jungle rubber and rainforest but different from oil palm and rubber, which in turn were different from each other. The four investigated land-use systems differed in aboveground plant biomass, canopy openness and land use intensity, which explained 12% of the observed variation in canopy salticid communities. Phylogenetic diversity based on ~850 bp 28S rDNA fragments showed similar patterns as richness, that is, highest in jungle rubber, intermediate in rainforest, and lowest in the two monoculture plantations. Additionally, we found evidence for phylogenetic clustering of salticids in oil palm, suggesting that habitat filtering is an important factor shaping salticid spider communities in monoculture plantations. Overall, our study offers a comprehensive insight into the mechanisms shaping communities of arthropod top predators in canopies of tropical forest ecosystems and plantations, combining community ecology, environmental variables and phylogenetics across a land-use gradient in tropical Asia

Rainforest conversion to monocultures favors generalist ants with large colonies

Abstract The conversion of natural ecosystems to agricultural land is one of the most important drivers of biodiversity decline worldwide, particularly in the tropics. Species loss is typically trait‐associated, leading to filtering of disturbance‐resistant species during community assembly, which affects ecosystem functioning and evolutionary potential of communities. To understand the ecological and phylogenetic impact of rainforest conversion to agricultural systems, we combine analysis of nesting habit, feeding habit, colony size, and body size of canopy ants (Formicidae) with a phylogenetic analysis of species collected in four land‐use systems in Sumatra, Indonesia: (1) lowland tropical rainforest, (2) jungle rubber (extensive rubber agroforest), and smallholder plantations of (3) rubber and (4) oil palm. Canopy ant communities in these land‐use systems differed in trait composition, with a larger proportion of generalist nesting and generalist‐omnivore feeding species in oil palm compared to rainforest and a larger proportion of generalist nesters and species with large colonies (>1000 individuals) in rubber than in rainforest. Traits of canopy ant communities in jungle rubber were more similar to those in rainforest than to those in rubber and oil palm plantations. In rainforest, mean pairwise phylogenetic distance was lower than expected for random community assembly, but did not differ from random in the other land‐use systems. Of the traits nesting habit, feeding habit, and colony size, only feeding habit exhibited phylogenetic signal. Our results show that rainforest conversion to agricultural systems is accompanied by shifts in trait composition of canopy ant communities. Further, our results argue against environmental filtering of closely related canopy ant species as the major community assembly mechanism in plantation systems, but suggest that the Sumatran lowland rainforests harbor recently diverged endemic ant species that are particularly vulnerable to rainforest conversion to agricultural systems. Given the importance of ants for tropical ecosystems, the ecological differences among ant communities along the land‐use gradient might have important consequences for ecosystem functioning and services in plantation systems

50% majority-rule consensus tree of Remipedia and outgroup taxa based on a Bayesian analysis of CO1 sequence data.

<p>Bayesian posterior probability values of clades are noted at the nodes of the tree. Remipede lineages currently assigned to the family Speleonectidae and Godzilliidae are indicated in blue and red, respectively. Outgroup lineages are indicated in black.</p

Map of the larger Caribbean region.

<p>Names of islands and regions, where Remipedia occur are indicated. For detailed information on the distribution of Remipedia see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019627#pone-0019627-g004" target="_blank">Figure 4</a>. Map (modified) with kind permission of Demis (<a href="http://www.demis.nl" target="_blank">www.demis.nl</a>).</p

Global distribution of anchialine caves.

<p>Epicontinental anchialine cave systems are indicated by dots and anchialine waters on isolated seamount islands by triangles. Remipedia show a disjunct global distribution pattern, with all known species restricted to epicontinental anchialine caves. The majority of remipede species inhabit the larger Caribbean region (A), including the Yucatán Peninsula, Cuba, the Dominican Republic, the Turks and Caicos Islands and the Bahamas. Isolated species occur in caves on the Canarian Island of Lanzarote (B) and in Western Australia (C). Map (modified) with kind permission of Demis (<a href="http://www.demis.nl" target="_blank">www.demis.nl</a>).</p

Holotype of <i>Tesnusocaris goldichi</i> (Remipedia, Enantiopoda).

<p>The holotype (catalogue number USNM 124173a) has a length of approximately 77 cm; it was collected by S. S. Goldich (1939) in the Tesnus Formation (Pennsylvanian), West of Rough Creek, Dove Mountain Quadrangle, Brewster County, Texas.</p