Biology subjects

Harper, K. J.

Publications and source records attributed to Harper, K. J..

2 recordsLinked to original sources

bioRxiv2024

Extending sampling approaches for great crested newt (Triturus cristatus) eDNA monitoring

O_LIEnvironmental DNA (eDNA) monitoring has been used for great crested newt (Triturus cristatus) survey in the UK since the publication of a Defra-funded trial in 2014. If eDNA results are to be used in support of a great crested newt licence, surveys must be performed during a 76-day survey window (15 April - 30 June) to coincide with peak great crested newt activity, and must follow the approved ethanol precipitation protocol. However, eDNA detection is possible in other months and filtration may be a more effective method of eDNA capture. C_LIO_LIWe investigated whether the great crested newt eDNA survey season could be extended and filtration could be used for great crested newt eDNA capture by reviewing the available evidence and conducting a field study from April to October 2022. Paired water samples for ethanol precipitation and filtration were collected from 25 ponds once a month, resulting in 124 samples of each type. All samples (N = 248) were analysed with the approved great crested newt quantitative PCR assay. C_LIO_LIOur results indicate that great crested newts can be reliably detected using both eDNA capture methods from April to August, with detection rates decreasing in September and October. Great crested newt eDNA detection was comparable or higher with filtration than ethanol precipitation. C_LIO_LIPractical implication. Acceptance of filtration for great crested newt eDNA surveys could allow more water to be processed for robust and reliable estimates of great crested newt presence. Extending the great crested newt eDNA survey season to August could allow more waterbodies to be surveyed for great crested newt presence (but not absence), and identification of sites that provide important habitat for great crested newts outside of the breeding season. This would also remove logistical challenges and costs associated with completing sampling within 11 weeks and laboratory analysis within 10 working days from sample receipt. Furthermore, great crested newt eDNA surveys could be more frequently carried out alongside monitoring for other species, which are typically surveyed from April to September/October or year-round with conventional methods or eDNA surveys using filtration. This could enable infrastructure projects to develop more effective mitigation measures as well as reduce time required from surveyors and survey costs. C_LI

ecology↗

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↗