Littlefair, J. E. | Search bioRxiv

bioRxiv2020

Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes

The effective use of metabarcoding in biodiversity science has brought important analytical challenges due to the need to generate accurate taxonomic assignments. The assignment of sequences to a generic or species level is critical for biodiversity surveys and biomonitoring, but it is particularly challenging. Researchers must select the approach that best recovers information on species composition. This study evaluates the performance and accuracy of seven methods in recovering the species composition of mock communities which vary in species number and specimen abundance, while holding upstream molecular and bioinformatic variables constant. It also evaluates the impact of parameter optimization on the quality of the predictions. Despite the general belief that BLAST top hit underperforms newer methods, our results indicate that it competes well with more complex approaches if optimized for the mock community under study. For example, the two machine learning methods that were benchmarked proved more sensitive to the reference database heterogeneity and completeness than methods based on sequence similarity. The accuracy of assignments was impacted by both species and specimen counts which will influence the selection of appropriate software. We urge the usage of realistic mock communities to allow optimization of parameters, regardless of the taxonomic assignment method used.

bioinformatics↗

bioRxiv2020

Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes

Significant advances have been made towards surveying animal and plant communities using DNA isolated from environmental samples. Despite rapid progress, we lack a comprehensive understanding of the "ecology" of environmental DNA (eDNA), particularly its temporal and spatial distribution and how this is shaped by abiotic and biotic processes. Here, we tested how seasonal variation in thermal stratification and animal habitat preferences influence the distribution of eDNA in lakes. We sampled eDNA depth profiles of five dimictic lakes during both summer stratification and autumn turnover, each containing warm- and cool-water fishes as well as the cold-water stenotherm, lake trout (Salvelinus namaycush). Habitat use by lake trout was validated by acoustic telemetry and was significantly related to eDNA distribution during stratification. Fish eDNA became "stratified" into layers during summer months, reflecting lake stratification and the thermal niches of the species. During summer months, lake trout, which rarely ventured into shallow waters, could only be detected at the deepest layers of the lakes, whereas the eDNA of warm-water fishes was much more abundant above the thermocline. By contrast, during autumn lake turnover, the fish species assemblage as detected by eDNA was homogenous throughout the water column. These findings contribute to our overall understanding of the "ecology" of eDNA within lake ecosystems, illustrating how the strong interaction between seasonal thermal structure in lakes and thermal niches of species on very localised spatial scales influences our ability to detect species.

ecology↗