Assessing distribution of Didemnum vexillum in Scotland using environmental DNA

References

Abbott, C., Coulson, M., Gagné, N., Lacoursière‐Roussel, A., Parent, G.J., Bajno, R., Dietrich, C. and May-McNally, S. 2021. Guidance on the Use of Targeted Environmental DNA (eDNA) Analysis for the Management of Aquatic Invasive Species and Species at Risk. DFO Canadian Science Advisory Secretariat, Research Document, 2021/019. iv + 42 p.

Agersnap, S., Larsen, W.B., Knudsen, S.W., Strand, D., Thomsen, P.F., Hesselsøe, M., Mortensen, P.B., Vrålstad, T. and Møller, P.R. 2017. Monitoring of noble, signal and narrow-clawed crayfish using environmental DNA from freshwater samples. PLUS One, 12(6), e0179261.

Allan, E.A., Zhang, W.G., Lavery, A.C. and Govindarajan, A.F. Environmental DNA shedding and decay rates from diverse animal forms and thermal regimes. 2021. Environmental DNA, 3, 492–514.

von Ammon, U., Wood, S.A., Laroche, O., Zaiko, A., Tait, L., Lavery, S., Inglis, G.J., and Pochon, X. 2018. Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities. Scientific Reports, 8, 16290.

Andersen, J.H., Pedersen, S.A., Thaulow, J., Stuer-Lauridsen, F., Kristensen, D. and Cochrane S. 2014. Monitoring of non-indigenous species in Danish marine waters: Background and proposals for a monitoring strategy and a monitoring network. NIVA Denmark, Danish Nature Agency, pp 1-54.

Arenas, F., Bishop, J.D.D., Carlton, J.T., Dyrynda, P.J., Farnham, W.F., Gonzalez, D.J., Jacobs, M.W., Lambert, C., Lambert, G., Nielsen, S.E., Pederson, J.A., Porter, J.S., Ward, S. and Wood, C.A. 2006. Alien species and other notable records from a rapid assessment survey of marinas on the south coast of England. Journal of Marine Biological Association UK, 89, 1329–1337.

Begg, T., Graham, J. and Matejusova, I. 2019. The Marine Invasive Non-Native Species Didemnum vexillum: Loch Creran Survey – September 2019. Scottish Marine and Freshwater Science, 11, pp.17.

Beveridge, C., Cook, E.J., Brunner, L., MacLeod, A., Black, K., Brown, C. and Manson F.J. 2011. Initial response to the invasive carpet sea squirt, Didemnum vexillum, in Scotland. Scottish Natural Heritage Commissioned Report No. 413.

Bishop, J.D.D., Wood, C.A., Lévêque, L., Yunnie, A.L.E., and Viard, F. 2015. Repeated rapid assessment surveys reveal contrasting trends in occupancy of marinas by non-indigenous species on opposite sides of the western English Channel. Marine Pollution Bulletin, 95, 699–706.

Blackman, R.C.,Ho, H-C., Walser, J-C., and Altermatt, F. (2022). Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics uncovered across a river catchment using environmental DNA. Communications Biology, 5, 259.

Brown, L., Turrell, W.R., Graham, J., Gubbins, M., Hermann, G., Lacaze, J-P. and I Matejusova 2018a. The Marine Invasive Non-Native Species Didemnum vexillum: Loch Creran Surveys - October 2016. Scottish Marine and Freshwater Science, 9(10), pp. 40pp.

Brown, L., Gubbins, M., Donnan, D. and Dodd, J. 2018b. The Marine Invasive Non-Native Species Didemnum vexillum: Survey of intertidal and shallow sub-tidal artificial infrastructure in Loch Creran. Scottish Marine and Freshwater Science, 9(11), pp. 20. .

Bruce K., Blackman, R.C., Bourlat, S.J., Hellström, M., Bakker, J., Bista, I., Bohmann, K., Bouchez, A., Brys, R., Clark, K., Elbrecht, V., Fazi, S., Fonseca, V.G., Hänfling, b., Leese, F., Mächler, E., Mahon, A.R., Meissner, K., Panksep, K., Pawlowski, J., Schmidt Yáñez, P., Seymour, M., Thalinger, B., Valentini, A., Woodcock, P., Traugott, M., Vasselon, V. and Deiner, K. 2021. A practical guide to DNA-based methods for biodiversity assessment. Advanced Books, https://doi.org/10.3897/ab.e6834

Burian, A., Mauvisseau, Q., Bulling, M., Domisch. S,, Qian, S. and Sweet, M. 2021. Improving the reliability of eDNA data interpretation. Molecular Ecology Resources, 1;1–12.

Buxton, A., Matechou, E., Griffin, J., Diana, A., Griffiths, R.A. 2021. Optimising sampling and analysis protocols in environmental DNA studies. Scientific Reports, 11, 11637.

Buxton, A., Diana, A., Matechou, E., Grifin, J. and Grifths, R.A. 2022. Reliability of environmental DNA surveys to detect pond occupancy by newts at a national scale. Scientific Reports, 12, 1295.

Cottier-Cook, E.J., Minchin, D., Gielser, R., Graham, J., Mogg, A.O.M., Sayer, M.D.J. and Matejusova, I. 2019. Biosecurity implications of the highly invasive carpet sea-squirt Didemnum vexillum Kott, 2002 for a protected area of global significance. Management of Biological Invasions, 10, 311–323.

D’Alessandro, S. and Mariani, S. (2021). Sifting environmental DNA metabarcoding data sets for rapid reconstruction of marine food webs. Fish and Fisheries, 22, 822– 833.

Da Silva Neto, J.G., Sutton, W.B., Spear, S.F., Freake, M.J., Kéry, M.K. and Schmidt, B.R. 2020. Integrating species distribution and occupancy modelling to study hellbender (Cryptobranchus alleganiensis) occurrence based on eDNA surveys. Biological Conservation, 251: 08787

Diana, A., Matechou, E., Griffin, J.E., Buxton, A.S. and Griffiths, R.A. 2021. An RShiny app for modelling environmental DNA data: accounting for false positive and false negative observation error. Ecography, 44, 1838–1844.

Ficetola, G.F., Taberlet, P. and Coissac, E. 2016.: How to limit false positives in environmental DNA and metabarcoding? Molecular Ecology Resources, 16, 604–607.

Gargan, L.M., Brooks, P.R., Vye, S.R., Ironside, J.E., Jenkins, S.R., Crowe, T.P. and Carlson, J. 2021. The use of environmental DNA metabarcoding and quantitative PCR for molecular detection of marine invasive non-native species associated with artificial structures. Biological Invasions, 24, 63648.

GBNNSS. 2011. Didemnum vexillum: GB Non-native species organism risk assessment. GB Non-native species organism risk assessment scheme. https://secure.fera.defra.gov.uk/nonnativespecies/index.cfm?sectionid=51 (accessed 22 March 2011).

Goldberg, C.S., Turner, C.R., Deiner, K., Klymus, K.E., Thomsen, P.F., Murphy, M.A., Spear, S.F., McKee, A., Oyler-McCance, S.J., Cornman, R.S., Laramie, M.B., Mahon, A.R., Lance, R.F., Pilliod, D.S., Strickler, K.M., Waits, L.P., Fremier, A.K., Takahara, T., Herder, J.E. and Taberlet, P. 2016. Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods in Ecology and Evolution, 7, 1299-1307.

Griffin, J. Matechou, E., Buxton, A., Bormpoudakis, D. and Griffiths, R. 2019. Modelling environmental DNA data; Bayesian variable selection accounting for false positive and false negative errors. Journal of the Royal Statistical Society: Series C (Applied Statistics), 69, 10.1111/rssc.12390.

Harrison, J.B., Sunday, J.M. and Rogers, S.M. 2019. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proceedings from the Royal Society Series B, 286, 1409.e

Holman, L.E., de Bruyn, M., Creer, S., Carvalho, G., Robidart, J. and Rius, M. 2019. Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water. Scientific Reports, 9, 11559.

Hurst, H. (2016). Monitoring invasive non-native species in marinas of North West England. Natural England Report, 36 pp. NW INNS report HH 2016 FINAL.pdf (livingseasnw.org.uk)

Inkscape Project, 2020. Inkscape. Version 0.92. Available from https://inkscape.org.

Kakkonen, J. E., Worsfold, T. M., Ashelby, C. W., Taylor, A., and Beaton, K. 2019. The value of regular monitoring and diverse sampling techniques to assess aquatic non-native species: a case study from Orkney. Management of Biological Invasions, 10, 46.

Klymus, K.E., Merkes, C.M., Allison, M.J., Goldberg, C.S., Helbing, C.C., Hunter, M.E., Jackson, C.A., Lance, R.F., Mangan, A.M., Monroe, E.M., Piaggio, A.J., Stokdyk, J.P., Wilson, C.S. and Richter C.A. 2020 Reporting the limits of detection and quantification for environmental DNA assays. Environmental DNA, 2, 271–282.

LeBlanc, F., Belliveau, V., Watson, E., Coomber, C., Simard, N., DiBacco, C., Bernier, R. and Gagné, N. 2020. Environmental DNA (eDNA) detection of marine aquatic invasive species (AIS) in Eastern Canada using a targeted species-specific qPCR approach. Management of Biological Invasions, 11, 201–217.

Matejusova, I., Graham, J., Bland, F., Lacaze, J-P., Herman, G., Brown, L., Dalgarno, E., Bishop, J.D., Kakkonen, J.E., Smith, K.F. and Douglas, A. 2021. Environmental DNA based surveillance for the highly invasive carpet sea squirt Didemnum vexillum: A targeted single-species approach. Frontier in Marine Sciences, 8, 728456.

Mauvisseau, Q., Burian, A., Gibson, C., Brys, R., Ramsay, A. and Sweet, M. 2019. Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches. Scientific Reports, 9, 580.

Moffat, C., Baxter, J., Berx, B., Bosley, K., Boulcott, P., Cox, M., Cruickshank, L., Gillham, K., Haynes, V., Roberts, A., Vaughan, D., and Webster, L. 2020. Scotland's Marine Assessment 2020. Scotland's Marine Assessment 2020 | Scotland's Marine Assessment 2020. Published by Scottish Government.

Nall, C., Guerin, A. and Cook, E. (2015). Rapid assessment of marine non-native species in northern Scotland and a synthesis of existing Scottish records. Aquatic Invasions, 10, 107–121.

Puntila, R., Heyer, K., Stelzer, K. and Faber, E. 2013. HELCOM 2013. HELCOM ALIENS 2- Non-native species port survey protocols, target species selection and risk assessment tools for the Baltic Sea. 34 pp.

QGIS.org, 2021. QGIS Geographic Information System. Version 3.20.2. QGIS Association. Available from http://www.qgis.org.

Rey, A., Basurko, O.C. and Rodriguez-Ezpeleta, N. 2019. Considerations for metabarcoding-based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments. Ecology and Evolution, 1 0, 2452–2465.

Roux, M.L D., Giblot-Ducray, D., Bott, N.J., Wiltshire, K.H., Deveney, M.R., Westfall, K.M., and Abbott, C.L. 2020. Analytical validation and field testing of a specific qPCR assay for environmental DNA detection of invasive European green crab (Carcinus maenas). Environmental DNA, 2, 309–320.

Seymour, M., Durance, I., Cosby, B.J., Ransom-Jones, E., Deiner, K., Ormerod, S.J., Colbourne, J.K., Wilgar, G., Carvalho, G.R., de Bruyn, M., Edwards, F., Emmett, B.A., Bik, H.M. and Creer, S. 2018. Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms. Communications Biology, 1, 4.

Simpson, T.S., Dias, P.J., Snow, M., Muñoz, J. and Berry, T. 2017. Real-time PCR detection of Didemnum perlucidum (Monniot, 1983) and Didemnum vexillum (Kott, 2002) in an applied routine marine biosecurity context. Molecular Biology Resources, 17, 443–453.

Schmidt, B.R., Kéry, M., Ursenbacher, S., Hyman, O.J. and Collins, J.P. 2013. Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen. Methods in Ecology and Evolution, 4, 646–653

Spens, J., Evans, A.R., Halfmaerten, D., Knudsen, S.W., Sengupta, M.E., Mak, S.S.T., Sigsgaard, E.E. and Hellströom, M. 2017. Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter. Methods in Ecology and Evolution, 8, 635-645.

Stebbing, P., Murray, J., Whomersley, P. and Tidbury, H. 2014. Monitoring and surveillance for non-indigenous species in UK marine waters. CEFAS report ME13892, pp 1-46.

Stebbing, P., Tidbury, H., Murray, J. and Cook, A. 2016. Development and implementation of a monitoring programme for marine non-native species. CEFAS report SLA29A, pp 1-100.

Stoeckle, B.C., Beggel, S., Cerwenka, A.F., Motivans, E., Kuehn, R. and Geist, J. 2017. A: systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems. PLUS One , 12, e0189119.

Thalinger, B., Deiner, K., Harper, L.R., Rees, H.C., Blackmann, R.C., Sint, D., Traugott, M., Bruce, K. (2021). A validation scale to determine the readiness of environmental DNA assays for routine species monitoring. Environmental DNA, 3, 82836.

Tillin, H.M., Kessel, C., Sewell, J., Wood, C.A., Bishop, J.D.D. 2020. Assessing the impact of key Marine Invasive Non-Native Species on Welsh MPA habitat features, fisheries and aquaculture. NRW Evidence Report. Report No: 454, 260pp, Natural Resources Wales, Bangor.

Tingley, R., Coleman, R., Gecse, N., van Rooyen, A. and Weeks, A. 2021. Accounting for false positive detections in occupancy studies based on environmental DNA: A case study of a threatened freshwater fish (Galaxiella pusilla). Environmental DNA, 3 388–397.

von Ammon, U., Wood, S.A., Laroche, O., Zaiko, A., Tait, L., Lavery, S., Inglis, G.J. and Pochon, X. 2018. Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities. Scientific Reports, 8:16290.

Wilcox, T.M., McKelvey, K.S., Young, M.K., Jane, S.F., Lowe, W.H., Whiteley, R.J. and Schwarz, M.K. 2013. Robust detection of rare species using environmental DNA: The Importance of primer specificity. PLUS One, 8, e59520.

Williams, F., Eschen, R., Harris, A., Djeddour, D., Pratt, C., Shaw, R.S., Varia, S., Lamontagne-Godwin, J., Thomas, S.E., Murphy, S.T. 2010) The economic cost of invasive non-native species on Great Britain. CABI Europe-UK, Project No. VM10066, 199 pp.

Wood, S. A., Pochon, X., Ming, W., von Ammon, U., Woods, C., Carter, M., Smith, M., Inglis, G. and Zaiko, A. 2019. Considerations for incorporating real-time PCR assays into routine marine biosecurity surveillance programmes: a case study targeting the Mediterranean fanworm (Sabella spallanzanii) and club tunicate (Styela clava). Genome, 62, 137–146.

Wood, L., Davison, P., Matejusova, I., Marsh, M., Clark, K., Bishop, J., Wood, C., Rius, M., Briscoe, A., Ainsley, T., Cooper, A., Bass, D., Tidbury, H., Stone, D., Waine, A. and Edwards, M. 2020. Defra Centre of Excellence for DNA Methods ‘Marine Non-Indigenous Species Monitoring Workshop’ Report. Cefas Report C8021, pp 1-40.