Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders

Abstract

Species Distribution Models (SDMs) have been reported as a useful tool for the risk assessment and modeling of the pathways of dispersal of freshwater invasive alien species (IAS). Environmental DNA (eDNA) is a novel tool that can help detect IAS at their early stage of introduction and additionally improve the data available for a more efficient management. SDMs rely on presence and absence of the species in the study area to infer the predictors affecting species distributions. Presence is verified once a species is detected, but confirmation of absence can be problematic because this depends both on the detectability of the species and the sampling strategy. eDNA is a technique that presents higher detectability and accuracy in comparison to conventional sampling techniques, and can effectively differentiate between presence or absence of specific species or entire communities by using a barcoding or metabarcoding approach. However, a number of potential bias can be introduced during (i) sampling, (ii) amplification, (iii) sequencing, or (iv) through the usage of bioinformatics pipelines. Therefore, it is important to report and conduct the field and laboratory procedures in a consistent way, by (i) introducing eDNA independent observations, (ii) amplifying and sequencing control samples, (iii) achieving quality sequence reads by appropriate clean-up steps, (iv) controlling primer amplification preferences, (v) introducing PCR-free sequence capturing, (vi) estimating primer detection capabilities through controlled experiments and/or (vii) post-hoc introduction of "site occupancy-detection models." With eDNA methodology becoming increasingly routine, its use is strongly recommended to retrieve species distributional data for SDMs.

Contrasting seasonal and spatial distribution of native and invasive Codium seaweed revealed by targeting species‐specific eDNA

“…Early detection of seaweed species in the aquatic environment can significantly improve AIS management and potential eradication (Jerde et al, 2013), with more efficient monitoring and containment of its spread (Tréguier et al, 2014), predicting its dispersal through spatial distribution models (Muha, Rodríguez-Rey, Rolla, & Tricarico, 2017), or influencing management and policy decisions (Kelly et al, 2014). As we have demonstrated here, eDNA can be used to assess the spatial and seasonal distribution patterns of invasive and native green seaweed algae.…”

Assessing the effect of landscape features on pond colonisation by an elusive amphibian invader using environmental DNA

“…Environmental DNA surveys have been used to estimate population density and biomass (Buxton, Groombridge, Zakaria, & Griffiths, 2017;Goldberg et al, 2016;Smart, Tingley, Weeks, Van Rooyen, & Mccarthy, 2015;Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012), monitor temporal and spatial changes in species distribution and biodiversity (Bista et al, 2017;Deiner, Fronhofer, Mächler, Walser, & Altermatt, 2016;Pansu et al, 2015;Thomsen & Willerslev, 2015;Yoccoz, 2012), or validate species distribution models (Muha, Rodríguez-Rey, Rolla, & Tricarico, 2017;Neto, 2018). Environmental DNA surveys have been used to estimate population density and biomass (Buxton, Groombridge, Zakaria, & Griffiths, 2017;Goldberg et al, 2016;Smart, Tingley, Weeks, Van Rooyen, & Mccarthy, 2015;Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012), monitor temporal and spatial changes in species distribution and biodiversity (Bista et al, 2017;Deiner, Fronhofer, Mächler, Walser, & Altermatt, 2016;Pansu et al, 2015;Thomsen & Willerslev, 2015;Yoccoz, 2012), or validate species distribution models (Muha, Rodríguez-Rey, Rolla, & Tricarico, 2017;Neto, 2018).…”

“…The benefits of using eDNA go beyond merely detecting target species. Environmental DNA surveys have been used to estimate population density and biomass (Buxton, Groombridge, Zakaria, & Griffiths, 2017;Goldberg et al, 2016;Smart, Tingley, Weeks, Van Rooyen, & Mccarthy, 2015;Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012), monitor temporal and spatial changes in species distribution and biodiversity (Bista et al, 2017;Deiner, Fronhofer, Mächler, Walser, & Altermatt, 2016;Pansu et al, 2015;Thomsen & Willerslev, 2015;Yoccoz, 2012), or validate species distribution models (Muha, Rodríguez-Rey, Rolla, & Tricarico, 2017;Neto, 2018). More recently, this technique has been used to identify environmental and habitat predictors of species occurrence at different spatial scales (Collins, 2017;Pitt et al, 2017), and investigate the loss of habitat connectivity for fishes in dammed rivers (Yamanaka & Minamoto, 2016).…”

Impacts of climate change on the global potential distribution of two notorious invasive crayfishes

“…Our results have important implications for the management of both invasive species. Early detection of alien crayfish species may be performed using environmental DNA (eDNA) techniques(Muha, Rodríguez-Rey, Rolla, & Tricarico, 2017). Early monitoring programmes and preventative measures should be considered to control spread of the two invasive species in Europe.…”