Dataset Information

Traditional trapping methods outperform eDNA sampling for introduced semi-aquatic snakes.

ABSTRACT: Given limited resources for managing invasive species, traditional survey methods may not be feasible to implement at a regional scale. Environmental DNA (eDNA) sampling has proven to be an effective method for detecting some invasive species, but comparisons between the detection probability of eDNA and traditional survey methods using modern occupancy modeling methods are rare. We developed a qPCR assay to detect two species of watersnake (Nerodia fasciata and Nerodia sipedon) introduced to California, USA, and we compared the efficacy of eDNA and aquatic trapping. We tested 3-9 water samples each from 30 sites near the known range of N. fasciata, and 61 sites near the known range of N. sipedon. We also deployed aquatic funnel traps at a subset of sites for each species. We detected N. fasciata eDNA in three of nine water samples from just one site, but captured N. fasciata in traps at three of ten sites. We detected N. sipedon eDNA in five of six water samples from one site, which was also the only site of nine at which this species was captured in traps. Traditional trapping surveys had a higher probability of detecting watersnakes than eDNA surveys, and both survey methods had higher detection probability for N. sipedon than N. fasciata. Occupancy models that integrated both trapping and eDNA surveys estimated that 5 sites (95% Credible Interval: 4-10) of 91 were occupied by watersnakes (both species combined), although snakes were only detected at four sites (three for N. fasciata, one for N. sipedon). Our study shows that despite the many successes of eDNA surveys, traditional sampling methods can have higher detection probability for some species. We recommend those tasked with managing species invasions explicitly compare eDNA and traditional survey methods in an occupancy framework to inform their choice of the best method for detecting nascent populations.

SUBMITTER: Rose JP

PROVIDER: S-EPMC6605664 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Traditional trapping methods outperform eDNA sampling for introduced semi-aquatic snakes.

Rose Jonathan P JP Wademan Cara C Weir Suzanne S Wood John S JS Todd Brian D BD

PloS one 20190702 7

Given limited resources for managing invasive species, traditional survey methods may not be feasible to implement at a regional scale. Environmental DNA (eDNA) sampling has proven to be an effective method for detecting some invasive species, but comparisons between the detection probability of eDNA and traditional survey methods using modern occupancy modeling methods are rare. We developed a qPCR assay to detect two species of watersnake (Nerodia fasciata and Nerodia sipedon) introduced to Ca ...[more]

PMID: 31265475

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Project description:BackgroundUltraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has yet to be extensively compared with that of traditional Sanger sequencing data sets. Moreover, UCE data on invertebrates, including insects, are sparse. We compared the phylogenetic informativeness of 959 UCE loci with a multi-locus data set of ten nuclear markers obtained via Sanger sequencing, testing the ability of these two types of data to resolve and date the evolutionary history of the second most species-rich subfamily of ants in the world, the Formicinae.ResultsPhylogenetic analyses show that UCEs are superior in resolving ancient and shallow relationships in formicine ants, demonstrated by increased node support and a more resolved phylogeny. Phylogenetic informativeness metrics indicate a twofold improvement relative to the 10-gene data matrix generated from the identical set of taxa. We were able to significantly improve formicine classification based on our comprehensive UCE phylogeny. Our divergence age estimations, using both UCE and Sanger data, indicate that crown-group Formicinae are older (104-117 Ma) than previously suggested. Biogeographic analyses infer that the diversification of the subfamily has occurred on all continents with no particular hub of cladogenesis.ConclusionsWe found UCEs to be far superior to the multi-locus data set in estimating formicine relationships. The early history of the clade remains uncertain due to ancient rapid divergence events that are unresolvable even with our genomic-scale data, although this might be largely an effect of several problematic taxa subtended by long branches. Our comparison of divergence ages from both Sanger and UCE data demonstrates the effectiveness of UCEs for dating analyses. This comparative study highlights both the promise and limitations of UCEs for insect phylogenomics, and will prove useful to the growing number of evolutionary biologists considering the transition from Sanger to next-generation sequencing approaches.

Dataset Information

Traditional trapping methods outperform eDNA sampling for introduced semi-aquatic snakes.

Publications

Traditional trapping methods outperform eDNA sampling for introduced semi-aquatic snakes.

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