Environmental and spatial characterisation of an unknown fauna using DNA sequencing – an example with Himalayan Hydropsychidae (Insecta: Trichoptera)

Abstract

Summary Ecological studies of freshwater biota in understudied regions are often obstructed by poor taxonomic knowledge. We posit that molecular tools can help alleviate this issue and present an example where we combined molecular tools, environmental data and ecological statistics to investigate the distribution and community ecology of an unknown fauna of hydropsychid caddisflies along altitudinal gradients in four Himalayan river systems of Central and Eastern Nepal. A total of 484 larval specimens from 34 tributaries were examined. Phylogenetic analysis of the mitochondrial cytochrome c oxidase I (COI) and the nuclear ribosomal RNA 28S were used to delineate molecular operational taxonomic units (MOTUs) applying three analytical methods: general mixed Yule‐coalescent (GMYC) model, Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics and Phylogeography (BPP). Spatial distributional patterns and potential differences in ecological niches among MOTUs were statistically tested using regression and correlation approaches. Further, we examined the data for signs of non‐random structure in MOTU communities. MOTU diversity within the family of Hydropsychidae was generally high but varied across evaluated gene fragments and slightly among delineation methods. Yet, the subsequent evaluation of environmental and spatial drivers and resulting distributional patterns were highly consistent among the different MOTU estimates. Within each river system, we found community composition varied greatly along the altitudinal gradients, with many MOTUs associated with specific altitudinal ranges. Prevalent MOTU turnover at the river system scale indicated high β‐diversity in the hydropsychid community leading to high degrees of regional endemism. In the Langtang river system, we found fewer MOTU co‐occurrences than expected by chance. These results highlight the utility of DNA‐based approaches using variable genetic markers (mitochondrial or ribosomal nuclear) for primary biodiversity assessment of poorly studied groups or regions. Our study further shows that DNA‐based biodiversity measures are suitable for downstream applications, such as exploring fundamental questions in stream ecology.

Metacommunity structuring in Himalayan streams over large elevational gradients: the role of dispersal routes and niche characteristics

“…Our findings, along with those of Hoppeler et al . () support the assertion that highland headwaters can support considerable beta diversity (Finn et al ., ).…”

“…Hoppeler et al . () found extremely high turnover and narrow elevational ranges in genetically identified operational taxonomic units of hydropsychid caddisflies in these streams. Our findings, along with those of Hoppeler et al .…”

“…() found invertebrates, diatoms and bacteria were structured through a combination of environmental and spatial (including elevation and geographical distance) factors along a large elevational stream gradient. The clear importance of elevation in streams of this region has recently been supported at both population genetic (Hoppeler et al ., ) and community (Shah et al ., ) levels. It is important to recognize that elevation may not be the driver per se but the various chemical, physical and biotic parameters that change with elevation, including dissolved oxygen and temperature (e.g.…”

Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics

“…Using these tools is particularly beneficial for studying evolutionary or ecological patterns in taxonomically understudied areas [128, 134]. When integrated into larger databases these data on evolutionary lineages and species can be further used for large-scale evolutionary or phylogenetic studies [66].…”

Ancient landscapes of the Namib Desert harbor high levels of genetic variability and deeply divergent lineages for Collembola

“…Sequencing of the COI locus has been demonstrated to be an effective method for resolving population-level and specieslevel differences for Collembola, as well as identifying cryptic species (e.g., Hogg & Hebert, 2004;Porco, Bedos, & Deharveng, 2010;Raschmanová et al, 2016). Previous studies using multiple markers, including COI, have shown that COI is likely to be representative of overall genomic differences and is an appropriate measure of genetic differentiation between populations (e.g., Hoppeler et al, 2016;Stevens & Hogg, 2003;Saltzwedel, Scheu, & Schaefer, 2016). Here, we determine genetic variability, using COI, for Collembola across large-scale Namib Desert soil transects, and assess the spatial distribution of COI haplotypes and putative species-level groupings as an indication of population connectivity and dispersal.…”