An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding

Perry, W. B., Seymour, M., Orsini, L., Jâms, I. B., Milner, N., Edwards, F., Harvey, R., de Bruyn, M., Bista, I., Walsh, K., Emmett, B., Blackman, R., Altermatt, F., Lawson Handley, L., Mächler, E., Deiner, K., Bik, H. M., Carvalho, G., Colbourne, J., Cosby, B. J., Durance, I. & Creer, S., 23 May 2024, In: Nature Communications. 15, 1, p. 4372

Research output: Contribution to journal › Article › peer-review

Comparative population genomics of manta rays has global implications for management

Humble, E., Hosegood, J., Carvalho, G., De Bruyn, M., Creer, S., Stevens, G. M. W., Armstrong, A., Bonfil, R., Deakos, M., Fernando, D., Froman, N., Peel, L. R., Pollett, S., Ponzo, A., Stewart, J. D., Wintner, S. & Ogden, R., 23 Nov 2023, (E-pub ahead of print) In: Molecular Ecology.

Research output: Contribution to journal › Article › peer-review

Environmental DNA metabarcoding for fish diversity assessment in a macrotidal estuary: A comparison with established fish survey methods

Gibson, T., Carvalho, G., Ellison, A., Gargiulo, E., Hatton-Ellis, T., Handley, L. L., Mariani, S., Collins, R. A., Sellers, G., Distaso, M., Zampieri, C. & Creer, S., 1 Nov 2023, In: Estuarine, Coastal and Shelf Science. 294, 108522.

Research output: Contribution to journal › Article › peer-review

Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

Holman, L. E., Parker-Nance, S., de Bruyn, M., Creer, S., Carvalho, G. & Rius, M., 14 Mar 2022, In: Philosophical Transactions of The Royal Society B: Biological Sciences. 377, 1846, 20210025.

Research output: Contribution to journal › Article › peer-review

Domestication-induced reduction in eye size revealed in multiple common garden experiments: The case of Atlantic salmon (Salmo salar L.)

Perry, W. B., Kaufmann, J., Solberg, M. F., Brodie, C., Medina, A. M. C., Pillay, K., Egerton, A., Harvey, A., Phillips, K. P., Coughlan, J., Egan, F., Grealis, R., Hutton, S., Leseur, F., Ryan, S., Poole, R., Rogan, G., Ryder, E., Schaal, P., Waters, C., Wynne, R., Taylor, M., Prodohl, P., Creer, S., Llewellyn, M., McGinnity, P., Carvalho, G. & Glover, K. A., 28 Sept 2021, In: Evolutionary Applications. 14, 9, p. 2319-2332 14 p.

Research output: Contribution to journal › Article › peer-review

Animals, protists and bacteria share marine biogeographic patterns

Holman, L. E., De Bruyn, M., Creer, S., Carvalho, G., Robidart, J. & Rius, M., 1 Jun 2021, In: Nature Ecology and Evolution. 5, 6, p. 738–746

Research output: Contribution to journal › Article › peer-review

Environmental DNA provides higher resolution assessment of riverine biodiversity and ecosystem function via spatio-temporal nestedness and turnover partitioning

Seymour, M., Edwards, F. K., Cosby, B. J., Bista, I., Scarlett, P. M., Brailsford, F., Glanville, H., de Bruyn, M., Carvalho, G. & Creer, S., 3 May 2021, In: Communications Biology. 4, 1, 512.

Research output: Contribution to journal › Article › peer-review

Molecular characterization of a marine turtle tumor epizootic, profiling external, internal and postsurgical regrowth tumors

Yetsko, K., Farrell, J., Blackburn, N. B., Whitmore, L., Stammnitz, M. R., Whilde, J., Eastman, C., Ramia, D. R., Thomas, R., Krstic, A., Linser, P., Creer, S., Carvalho, G., Devlin, M. A., Nahvi, N., Leandro, A. C., deMaar, T. W., Burkhalter, B., Murchison, E. P., Schnitzler, C. & Duffy, D., 1 Feb 2021, In: Communications Biology. 4, 1, 152.

Research output: Contribution to journal › Article › peer-review

Ecological community dynamics: 20 years of moth sampling reveals the importance of generalists for community stability

Carvalho, G., Seymour, M., Brown, N., Wood, C., Goertz, S. & de Bruyn, M., 1 Dec 2020, In: Basic and Applied Ecology. 49, p. 34-44 10 p.

Research output: Contribution to journal › Article › peer-review

Phylogenomics and species delimitation for effective conservation of manta and devil rays

Hosegood, J., Humble, E., Ogden, R., De Bruyn, M., Creer, S., Stevens, G. M. W., Abudaya, M., Bassos-Hull, K., Bonfil, R., Fernando, D., Foote, A., Hipperson, H., Jabado, R. W., Kaden, J., Moazzam, M., Peel, L. R., Pollett, S., Ponzo, A., Poortvliet, M., Salah, J., Senn, H., Stewart, J. D., Wintner, S. & Carvalho, G., Dec 2020, In: Molecular Ecology. 29, 24, p. 4783-4796

Research output: Contribution to journal › Article › peer-review

Disentangling the effects of sex, life history and genetic background in Atlantic salmon: growth, heart and liver under common garden conditions

Perry, W. B., Solberg, M. F., Brodie, C., Medina, A. C., Pillay, K. G., Egerton, A., Harvey, A., Creer, S., Llewellyn, M., Taylor, M., Carvalho, G. & Glover, K. A., 7 Oct 2020, In: Royal Society Open Science. 7, 10, 200811.

Research output: Contribution to journal › Article › peer-review

Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks

Seymour, M., Edwards, F., Cosby, B., Kelly, M., de Bruyn, M., Carvalho, G. & Creer, S., 10 Aug 2020, In: Science of the Total Environment. 729, 138801.

Research output: Contribution to journal › Article › peer-review

Comparative genetic stock structure in three species of commercially exploited Indo-Malay Carangidae (Teleosteii, Perciformes)

Jaafar, T. N. A. M., Taylor, M. I., Nor, S. A. M., de Bruyn, M. & Carvalho, G. R., 20 Feb 2020, In: Journal of Fish Biology. 96, 2, p. 337-349

Research output: Contribution to journal › Article › peer-review

Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface

Besnier, F., Solberg, M. F., Harvey, A., Carvalho, G., Bekkevold, D., Taylor, M. I., Creer, S., Nielsen, E. E., Skaala, O., Ayllon, F., Dahle, G. & Glover, K. A., 7 Feb 2020, In: BMC Genetics. 21, 1, 13.

Research output: Contribution to journal › Article › peer-review

Demographic reconstruction from ancient DNA supports rapid extinction of the great auk

Thomas, J., Carvalho, G., Haile, J., Rawlence, N. J., Martin, M. D., Ho, S. Y., Sigfússon, A. Þ., Jósefsson, V. A., Frederiksen, M., Linnebjerg, J. F., Samaniego Castruita, J. A., Niemann, J., Sinding, M.-H. S., Sandoval-Velasco, M., Soares, A. E., Lacy, R., Barilaro, C., Best, J., Brandis, D., Cavallo, C., Elorza, M., Garrett, K. L., Groot, M., Johansson, F., Lifjeld, J. T., Nilson, G., Serjeanston, D., Sweet, P., Fuller, E., Hufthammer, A. K., Meldgaard, M., Fjeldsa, J., Shapiro, B., Hofreiter, M., Stewart, J. R., Gilbert, M. T. P. & Knapp, M., 26 Nov 2019, In: Elife. 8, e47509.

Research output: Contribution to journal › Article › peer-review

Environmental DNA size sorting and degradation experiment indicates the state of Daphnia magna mitochondrial and nuclear eDNA is subcellular

Moushomi, R., Wilgar, G., Carvalho, G., Creer, S. & Seymour, M., 29 Aug 2019, In: Scientific Reports. 9, 12500 (2019.

Research output: Contribution to journal › Article › peer-review

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

Holman, L. E., de Bruyn, M., Creer, S., Carvalho, G., Robidart, J. & Rius, M., 9 Aug 2019, In: Scientific Reports. 9, 11559.

Research output: Contribution to journal › Article › peer-review

Evolutionary drivers of kype size in Atlantic salmon (Salmo salar): domestication, age and genetics

Perry, W. B., Solberg, M. F., Besnier, F., Dyrhovden, L., Matre, I. H., Fjelldal, P. G., Ayllon, F., Creer, S., Llewelyn, M., Taylor, M. I., Carvalho, G. & Glover, K. A., 17 Apr 2019, In: Royal Society Open Science. 6, 4, 190021.

Research output: Contribution to journal › Article › peer-review

Deep segregation in the open ocean: Macaronesia as an evolutionary hotspot for low dispersal marine invertebrates

Vieira, P. E., Desiderato, A., Holdich, D. M., Soares, P., Creer, S., Carvalho, G., Costa, F. O. & Queiroga, H., 1 Apr 2019, In: Molecular Ecology. 28, 7, p. 1784-1800

Research output: Contribution to journal › Article › peer-review

Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

Bista, I., Carvalho, G., Tang, M., Walsh, K., Zhou, X., Hajibabaei, M., Shokralla, S., Seymour, M., Bradley, D., Liu, S., Christmas, M. & Creer, S., Sept 2018, In: Molecular Ecology Resources. 18, 5, p. 1020-1034

Research output: Contribution to journal › Article › peer-review

Stepping stones to isolation: Impacts of a changing climate on the connectivity of fragmented fish populations

Young, E. F., Tysklind, N., Meredith, M. P., de Bruyn, M., Belchier, M., Murphy, E. J. & Carvalho, G. R., Jul 2018, In: Evolutionary Applications. 11, 6, p. 978-994

Research output: Contribution to journal › Article › peer-review

Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

Marburger, S., Alexandrou, M., Taggart, J. B., Creer, S., Carvalho, G., Oliveira, C. & Taylor, M. I., 14 Feb 2018, In: Proceedings of the Royal Society B: Biological Sciences. 285, 1872, 20172732.

Research output: Contribution to journal › Article › peer-review

Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms

Seymour, M., Durance, I., Cosby, B. J., Ransom-Jones, E., Deiner, K., Ormerod, S. J., Colbourne, J. K., Wilgar, G., Carvalho, G., De Bruyn, M., Edwards, F., Emmett, B. A., Bik, H. M. & Creer, S., 22 Jan 2018, In: Communications Biology. 1, 4.

Research output: Contribution to journal › Article › peer-review

Plio-Pleistocene phylogeography of the Southeast Asian blue panchax killifish, Aplocheilus panchax.

Beck, S., Carvalho, G., Barlow, A., Ruber, L., Tan, H. H., Nugroho, E., Wowor, D., Nor, S. A. M., Herder, F., Muchlisin, Z. A. & De Bruyn, M., 25 Jul 2017, In: PLoS ONE.

Research output: Contribution to journal › Article › peer-review

Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity

Bista, I., Carvalho, G., Walsh, K., Seymour, M., Hajibabaei, M., Lallias, D., Christmas, M. & Creer, S., Jan 2017, In: Nature Communications. 8, 14087.

Research output: Contribution to journal › Article › peer-review

Parasitism perturbs the mucosal microbiome of Atlantic Salmon

Llewellyn, M. S., Leadbeater, S., Garcia, C., Sylvain, F.-E., Custodio, M., Ang, K. P., Powell, F., Carvalho, G., Creer, S., Elliot, J. & Derome, N., 2017, In: Scientific Reports. 7, 43465.

Research output: Contribution to journal › Article › peer-review

Fish, genes and genomes: contributions to ecology, evolution and management

Carvalho, G., Hauser, L., Martinsohn, J. & Naish, K., 5 Dec 2016, In: Journal of Fish Biology. 89, 6, p. 2471-2478

Research output: Contribution to journal › Special issue › peer-review

Plasticity in growth of farmed and wild Atlantic salmon: is the increased growth rate of farmed salmon caused by evolutionary adaptations to the commercial diet?

Harvey, A., Solberg, M. F., Troianou, E., Carvalho, G., Taylor, M. I., Creer, S., Dyrhovden, L., Matre, I. H. & Glover, K. A., 1 Dec 2016, In: BMC Evolutionary Biology. 2016, 16, 264.

Research output: Contribution to journal › Article › peer-review

Plasticity in response to feed availability: Does feeding regime influence the relative growth performance of domesticated, wild and hybrid Atlantic salmon Salmo salar parr?

Harvey, A., Solberg, M. F., Glover, K. A., Taylor, M. I., Creer, S. & Carvalho, G., 1 Sept 2016, In: Journal of Fish Biology. 89, 3, p. 1754-1768

Research output: Contribution to journal › Article › peer-review

Does density influence relative growth performance of farmed, wild, and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions?

Harvey, A., Carvalho, G., Taylor, M., Solberg, M. F., Creer, S., Dyrhovden, L., Matre, I. H. & Glover, K. A., 6 Jul 2016, In: Royal Society Open Science. 3, 7, 160152.

Research output: Contribution to journal › Article › peer-review

Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos

Sinniger, F., Pawlowski, J., Harii, S., Gooday, A. J., Yamamoto, H., Chevaldonne, P., Cedhagen, T., Carvalho, G. & Creer, S., 14 Jun 2016, In: Frontiers in Marine Science. 3, 92

Research output: Contribution to journal › Article › peer-review

No loss of genetic diversity in the exploited and recently collapsed population of Bay of Biscay anchovy (Engraulis encrasicolus, L.)

Montes, I., Irondo, M., Manzano, C., Santos, M., Conklin, D., Carvalho, G., Irigoien, X. & Estonba, A., May 2016, In: Marine Biology. 163, 98.

Research output: Contribution to journal › Article › peer-review

The biogeography of the atlantic salmon (Salmo salar) gut microbiome

Llewellyn, M. S., McGinnity, P., Dionne, M., Letourneau, J., Thonier, F., Carvalho, G., Creer, S. & Derome, N., May 2016, In: ISME Journal. 10, p. 1280-1284

Research output: Contribution to journal › Article › peer-review

A common garden design reveals population-specific variability in potential impacts of hybridization between populations of farmed and wild Atlantic salmon, Salmo salar L.

Harvey, A., Glover, K. A., Taylor, M., Creer, S. & Carvalho, G., 1 Mar 2016, In: Evolutionary Applications. 9, 3, p. 435-449

Research output: Contribution to journal › Article › peer-review

Evaluating genetic traceability methods for captive-bred marine fish and their applications in fisheries management and wildlife forensics

Bylemans, J., Maes, G. E., Diopere, E., Cariani, A., Senn, H., Taylor, M. I., Helyar, S., Bargelloni, L., Bonaldo, A., Carvalho, G., Guarniero, I., Komen, H., Martinsohn, J. T., Nielsen, E. E., Tinti, F., Volckaert, F. A. M. & Ogden, R., 25 Feb 2016, In: Aquaculture Environment Interactions. 8, p. 131-145

Research output: Contribution to journal › Article › peer-review

Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species

Young, E. F., Belchier, M., Hauser, L., Horsburgh, G. J., Meredith, M. P., Murphy, E. J., Pascoal, S., Rock, J., Tysklind, N. & Carvalho, G. R., 16 Apr 2015, In: Evolutionary Applications. 8, 5, p. 486-509

Research output: Contribution to journal › Article › peer-review

Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring

Bekkevold, D., Helyar, S. J., Limborg, M. T., Nielsen, E. E., Hemmer-Hansen, J., Clausen, L. A. & Carvalho, G. R., 23 Feb 2015, In: ICES Journal of Marine Science. 72, 6, p. 1790-1810

Research output: Contribution to journal › Article › peer-review

Borneo and Indochina are Major Evolutionary Hotspots for Southeast Asian Biodiversity

De Bruyn, M., de Bruyn, M., Stelbrink, B., Morley, R. J., Hall, R., Carvalho, G. R., Cannon, C. H., van den Bergh, G., Meijaard, E., Metcalfe, I., Boitani, L., Maiorano, L. & Shoup, R. V., 30 Nov 2014, In: Systematic Biology. 63, 6, p. 879-901

Research output: Contribution to journal › Article › peer-review

DNA barcoding for species assignment: the case of Mediterranean marine fishes

Carvalho, G. R., Landi, M. D., Arculeo, M., Biondo, G., Martins, R. & Carneiro, M., 15 Sept 2014, In: PLoS ONE. 9, 9

Research output: Contribution to journal › Article › peer-review

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes

Fonseca, V. G., Carvalho, G. R., Nichols, B., Quince, C., Johnson, H. F., Neill, S. P., Lambshead, J. D., Thomas, W. K., Power, D. M. & Creer, S., 25 Aug 2014, In: Global Ecology and Biogeography. 23, 11, p. 1293–1302

Research output: Contribution to journal › Article › peer-review

Fish Product Mislabelling: Failings of Traceability in the Production Chain and Implications for Illegal, Unreported and Unregulated (IUU) Fishing

De Bruyn, M., Helyar, S. J., Lloyd, H., de Bruyn, M., Leake, J., Bennett, N. & Carvalho, G. R., 12 Jun 2014, In: PLoS ONE. 9, 6, p. e98691

Research output: Contribution to journal › Article › peer-review

Environmental DNA for Wildlife Biology and Biodiversity Monitoring

Evans, A. R., Bohmann, K., Evans, A., Gilbert, M. T., Carvalho, G. R., Creer, S., Knapp, M., Yu, D. W. & De Bruyn, M., 10 May 2014, In: Trends in Ecology and Evolution. 29, 6, p. 358-367

Research output: Contribution to journal › Article › peer-review

A reliable DNA barcode reference library for the identification of the North European shelf fish fauna

Knebelsberger, T., Landi, M., Neumann, H., Sell, A. F., Campbell, P. D., Laakmann, S., Raupach, M. J., Carvalho, G. R. & Costa, F. O., 12 Mar 2014, In: Molecular Ecology Resources. 14, 5, p. 1060-1071

Research output: Contribution to journal › Article › peer-review

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Milano, I., Babbucci, M., Cariani, A., Atanassova, M., Bekkevold, D., Carvalho, G., Espineira, M., Fiorentino, F., Garofalo, G., Geffen, A., Hansen, J. H., Helyar, S. J., Nielsen, E. E., Ogden, R., Patarnello, T., Stagioni, M., Tinti, F. & Bargelloni, L., 18 Nov 2013, In: Molecular Ecology. 23, 1, p. 118-135

Research output: Contribution to journal › Article › peer-review

Combination of genetics and spatial modelling highlights the sensitivity of cod (Gadus morhua) population diversity in the North Sea to distributions of fishing

Carvalho, G. R., Heath, M. R., Culling, M. A., Crozier, W. W., Fox, C. J., Gurney, W. S., Hutchinson, W. F., Nielsen, E. E., O'Sullivan, M., Preedy, K. F., Righton, D. A., Speirs, D. C., Taylor, M. I. & Wright, P. J., 17 Nov 2013, In: ICES Journal of Marine Science. 71, 4, p. 794-807

Research output: Contribution to journal › Article › peer-review

Time and space in biogeography: response to Parenti & Ebach

De Bruyn, M., de Bruyn, M., Stelbrink, B., Page, T. J., Phillips, M. J., Lohman, D. J., Albrecht, C., Hall, R., von Rintelen, K., Ng, P. K., Shih, H. T., Carvalho, G. R. & von Rintelen, T., 1 Nov 2013, In: Journal of Biogeography. 40, 11, p. 2204-2206

Research output: Contribution to journal › Article › peer-review

Population genetics provides new insights into biomarker prevalence in dab (Limanda limanda L.): a key marine biomonitoring species

Tysklind, N., Taylor, M. I., Lyons, B. P., Goodsir, F., McCarthy, I. D. & Carvalho, G. R., 1 Sept 2013, In: Evolutionary Applications. 6, 6, p. 891-909

Research output: Contribution to journal › Article › peer-review

SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing

Montes, I., Conklin, D., Albania, A., Creer, S., Carvalho, G. R., Santos, M. & Estonba, A., 1 Aug 2013, In: PLoS ONE. 8, 8, p. e70051

Research output: Contribution to journal › Article › peer-review

Investigating the molecular systematic relationships amongst selected Plesionika (Decapoda: Pandalidae) from the Northeast Atlantic and Mediterranean Sea

da Silva, J. M., dos Santos, A., Cunha, M. R., Costa, F. O., Creer, S. & Carvalho, G. R., 1 Jun 2013, In: Marine Ecology. 34, 2, p. 157-170

Research output: Contribution to journal › Article › peer-review