Biology subjects

Harper, L. R.

Publications and source records attributed to Harper, L. R..

3 recordsLinked to original sources

bioRxiv2018

Development of environmental DNA surveillance for the threatened crucian carp (Carassius carassius)

O_LIThe crucian carp (Carassius carassius) is one of few fish species associated with small ponds in the UK. These populations contain genetic diversity not found in Europe and are important to conservation efforts for the species, which has declined across its range. Detection and monitoring of extant crucian carp populations are crucial for conservation success. Environmental DNA (eDNA) analysis could be very useful in this respect as a rapid, cost-efficient monitoring tool.\nC_LIO_LIWe developed a species-specific quantitative PCR (qPCR) assay for eDNA surveillance of crucian carp to enable non-invasive, large-scale distribution monitoring. We compared fyke netting and eDNA at ponds with (N = 10) and without (N = 10) crucian carp for presence-absence detection and relative abundance estimation, specifically whether DNA copy number reflected catch-per-unit-effort (CPUE) estimate. We examined biotic and abiotic influences on eDNA detection and quantification, and compared qPCR to standard PCR. Notably, eDNA occurrence and detection probabilities in relation to biotic and abiotic factors were estimated using a hierarchical occupancy model.\nC_LIO_LIeDNA analysis achieved 90% detection for crucian carp (N = 10), failing in only one pond where presence was known. We observed an overall positive trend between DNA copy number and CPUE estimate, but this was not significant. Macrophyte cover decreased the probability of eDNA occurrence at ponds, whereas CPUE and conductivity had positive and negative influences on eDNA detection probability in qPCR replicates respectively. Conductivity also had a negative effect on DNA copy number, but copy number increased with temperature and percentage of macrophyte cover. PCR was comparable to qPCR for species detection and may provide semi-quantitative information.\nC_LIO_LIOur results demonstrate that eDNA could enable detection of crucian carp populations in ponds and benefit ongoing conservation efforts, but imperfect species detection in relation to biotic and abiotic factors and eDNA workflow requires further investigation. Nonetheless, we have established an eDNA framework for crucian carp and sources of imperfect detection which future investigations can build upon.\nC_LI

molecular biology↗

bioRxiv2018

Understanding biodiversity at the pondscape using environmental DNA: a focus on great crested newts

Environmental DNA (eDNA) metabarcoding is revolutionising biodiversity monitoring, but has unrealised potential for ecological hypothesis generation and testing. Here, we validate this potential in a large-scale analysis of vertebrate community data generated by eDNA metabarcoding of 532 UK ponds. We test biotic associations between the threatened great crested newt (Triturus cristatus) and other vertebrates as well as abiotic factors influencing T. cristatus detection at the pondscape. Furthermore, we test the status of T. cristatus as an umbrella species for pond conservation by assessing whether vertebrate species richness is greater in ponds with T. cristatus and higher T. cristatus Habitat Suitability Index (HSI) scores. T. cristatus detection was positively correlated with amphibian and waterfowl species richness. Specifically, T. cristatus was positively associated with smooth newt (Lissotriton vulgaris), common coot (Fulica atra), and common moorhen (Gallinula chloropus), but negatively associated with common toad (Bufo bufo). T. cristatus detection did not significantly decrease as fish species richness increased, but negative associations with common carp (Cyprinus carpio), three-spined stickleback (Gasterosteus aculeatus) and ninespine stickleback (Pungitius pungitius) were identified. T. cristatus detection was negatively correlated with mammal species richness, and T. cristatus was negatively associated with grey squirrel (Sciurus carolinensis). T. cristatus detection was negatively correlated with larger pond area, presence of inflow, and higher percentage of shading, but positively correlated with HSI score, supporting its application to T. cristatus survey. Vertebrate species richness was significantly higher in T. cristatus ponds and broadly increased as T. cristatus HSI scores increased. We reaffirm reported associations (e.g. T. cristatus preference for smaller ponds) but also provide novel insights, including a negative effect of pond inflow on T. cristatus. Our findings demonstrate the prospects of eDNA metabarcoding for ecological hypothesis generation and testing at landscape scale, and dramatic enhancement of freshwater conservation, management, monitoring and research.

ecology↗

bioRxiv2017

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of great crested newt (Triturus cristatus)

Environmental DNA (eDNA) analysis is a rapid, cost-effective, non-invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and metabarcoding have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA. We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real-time quantitative PCR (qPCR) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using High-Throughput Sequencing technology. With qPCR and a detection threshold of 1/12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4/12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species-specific surveys.

molecular biology↗