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Multi-species occupancy modeling reveals methodological and environmental effects on eDNA detection of amphibians in temporary ponds

2023-07Journal article Open access
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dc.contributor.authorPeixoto, Sara
dc.contributor.authorMota-Ferreira, Mário
dc.contributor.authorChaves, Cátia
dc.contributor.authorVelo-Antón, Guillermo
dc.contributor.authorBeja, Pedro
dc.contributor.authorEgeter, Bastian
dc.date.accessioned2024-04-02T15:24:36Z
dc.date.available2024-04-02T15:24:36Z
dc.date.issued2023-07
dc.description.abstractAquatic environmental DNA is increasingly used for biodiversity monitoring, such as surveying threatened and invasive species. Mainstreaming these methods in practi- cal applications, however, still requires significant standardization and optimisation, namely regarding DNA capture methods. Here we evaluated how filter type (standard disc filters vs high-capacity capsules), number of sampling sites, volume of water fil- tered and environmental factors affected amphibian detection in Mediterranean tem - porary ponds. The study involved water filtering until clogging at one (capsules) and five (discs) sites from 16 small and shallow ponds, where three urodele and seven anu- ran species were recorded through sweep- netting and adult observations. Detection probabilities were estimated from site occupancy models based on replicate sampling and from an adaptation of time-to-detection models relating detection probability to volume of water filtered. Discs filtered relatively small volumes (15–1250 mL), with detection probabilities of the two abundant species (Pelobates cultripes, Hyla meridi- onalis) increasing rapidly with sample size and water volume, reaching almost per- fect detection (0.95) at four and seven discs, and 420 mL and 1860 mL, respectively. However, reaching high detection probabilities for rare species (Pelodytes atlanticus, Pleurodeles waltl, Triturus pygmaeus) would require larger sampling effort than that used in our study. Despite filtering much larger volumes (600–5300 mL), filtering with capsules at a single site per pond provided lower detection probabilities for abun- dant species than filtering with discs at five sites. Rarer species showed no difference between methods, which may be due to small sample sizes and reduced statistical power for species with few detections. The effect of conductivity on species detect- ability was largely negative, while the influence of water clarity varied across species, and pH had no effects. Overall, our results suggest that eDNA amphibian surveys in Mediterranean temporary ponds need to consider filter clogging, heterogeneous DNA distribution, and highly conductive waterspt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationPeixoto, Sara, et al. “Multi‐species Occupancy Modeling Reveals Methodological and Environmental Effects on eDNA Detection of Amphibians in Temporary Ponds.” Environmental DNA, vol. 5, no. 4, July 2023, pp. 796–811.pt_PT
dc.identifier.doi10.1002/edn3.443pt_PT
dc.identifier.urihttp://hdl.handle.net/10400.5/30515
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherWileypt_PT
dc.relationNORTE-01-0246-FEDER-000063pt_PT
dc.relationTeaming to Upgrade to Excellence in Environmental Biology, Ecosystem Research and AgroBiodiversity
dc.relationIntegrative analytical framework for the study of evolutionary mechanistic forces: assessing the factors leading to the transition to viviparity in Salamandra
dc.relationNot Available
dc.relationCapacity Building at InBIO for Research and Innovation Using Environmental Metagenomics
dc.relation.publisherversionwileyonlinelibrary.com/journal/edn3pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectdisc filterspt_PT
dc.subjectDNA capture methodspt_PT
dc.subjecthigh-capacity capsulespt_PT
dc.subjectmulti-species occupancy modelspt_PT
dc.subjectspecies detection probabilitypt_PT
dc.subjecttime-to-detection modelspt_PT
dc.titleMulti-species occupancy modeling reveals methodological and environmental effects on eDNA detection of amphibians in temporary pondspt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleTeaming to Upgrade to Excellence in Environmental Biology, Ecosystem Research and AgroBiodiversity
oaire.awardTitleIntegrative analytical framework for the study of evolutionary mechanistic forces: assessing the factors leading to the transition to viviparity in Salamandra
oaire.awardTitleNot Available
oaire.awardTitleCapacity Building at InBIO for Research and Innovation Using Environmental Metagenomics
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/857251/EU
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/Investigador FCT/IF%2F01425%2F2014%2FCP1256%2FCT0013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/CEEC IND 2018/CEECIND%2F00937%2F2018%2FCP1546%2FCT0005/PT
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/668981/EU
oaire.citation.endPage811pt_PT
oaire.citation.issue4pt_PT
oaire.citation.startPage796pt_PT
oaire.citation.titleEnvironmental DNApt_PT
oaire.citation.volume5pt_PT
oaire.fundingStreamH2020
oaire.fundingStreamInvestigador FCT
oaire.fundingStreamCEEC IND 2018
oaire.fundingStreamH2020
person.familyNameCorreia de Oliveira Beja
person.givenNamePedro Rui
person.identifierA-7851-2008
person.identifier.ciencia-idC116-3331-F9E6
person.identifier.orcid0000-0001-8164-0760
person.identifier.scopus-author-id6602807125
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.nameEuropean Commission
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameEuropean Commission
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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relation.isAuthorOfPublication.latestForDiscovery834414ef-1b0f-42f8-bc30-ab39d60c36b1
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