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Publications

MEFGL selected publications (2001-)

2017

Llewellyn, M.S., Leadbeater, S., Garcia, C., Sylvain, F.-E., Custodio, M., Ang, K. P., Powell, F., Carvalho, G. R., Creer, S., Elliot, J. and Derome, N. 2017. Parasitism perturbs the mucosal microbiome of Atlantic Salmon. Scientific Reports 7, Article number: 43465. doi:10.1038/srep43465

de Vere, N., Jones, L.E., Gilmore, T., Moscrop, J., Lowe, A., Smith, D., Hegarty, M.J., Creer, S. and Ford, C.R. 2017. Using DNA metabarcoding to investigate honey bee foraging reveals limited flower use despite high floral availability. Scientific Reports 7, Article number: 42838. doi:10.1038/srep42838

Bista, I., Carvalho, G.R., Walsh, K., Seymour, M., Hajibabaei, M., Lallias, D., Christmas, M. and Creer, S. (2017). Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nature Communications. 8: 14087. DOI: http://dx.doi.org/10.1038/ncomms14087

Creer, S. and Seymour, M. (2017). Marine ecology: Genetics from a drop in the ocean. Nature Ecology and Evolution. 1: 037. DOI: 10.1038/s41559-016-0037

Leese, F. et al., Creer, S. et al. and Zimmermann, J. 2016. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems. Research Ideas and Outcomes 2: e11321, DOI 10.3897/rio.2.e11321

2016

Harvey, A.C., Solberg, M.F., Troianou, E., Carvalho, G.R., Taylor, M.I. Creer, S., Dyrhovden, L., Matre, I.H. and Glover, K.A. 2016. 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? BMC Evolutionary Biology. 16:264 DOI: 10.1186/s12862-016-0841-7

Harvey, A.C., Solberg, M. F., Glover, K. A., Taylor, M. I., Creer, S., and Carvalho, G.R. Plasticity in response to feed availability - does feeding regime influence the relative growth performance of domesticated, wild and hybrid Atlantic salmon Salmo salar parr? Journal of Fish biology. DOI: 10.1111/jfb.13076

Harvey, A.C., Juleff, G., Carvalho, G.R., Taylor, M.I., Solberg, M.F., Creer, S.,"Dyrhovden, L., Matre, I.-H., Glover, K.A. 2016. Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions? Royal Society Open Science. DOI: 10.1098/rsos.160152

Sinniger, F., Pawlowski, J., Harii, S., Gooday, A.J., Yamamoto, H.,Chevaldonne, P., Cedhagen, T., Carvalho, G.R., and Creer, S. 2016.Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos. Frontiers in Marine Science.
http://dx.doi.org/10.3389/fmars.2016.00092

Creer, S., Deiner, K., Frey, S., Porazinska, D., Taberlet, P., Thomas, W.K., Potter, C. and Bik, H.M. 2016. The ecologist’s field guide to sequence-based identification of biodiversity. Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12574 Methods in Ecology and Evolution Podcast available here.

Derycke, S., De Meester, N., Rigaux, A., Creer, S., Bik, H., Thomas, W.K. and Moens, T. 2016. Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability. Molecular Ecology. doi/10.1111/mec.13597/full

Harvey, A. C., Glover, K. A., Taylor, M. I., Creer, S. and Carvalho, G. R. (2016), A common garden design reveals population-specific variability in potential impacts of hybridization between populations of farmed and wild Atlantic salmon, Salmo salar L. Evolutionary Applications. doi: 10.1111/eva.12346

2015

Llewellyn, M.S., McGinnity, P., Dionne, M., Letourneau, J., Thonier, F., Carvalho, G.R., Creer, S. and Derome, N. 2015. The biogeography of the atlantic salmon (Salmo salar) gut microbiome. The ISME Journal. doi:10.1038/ismej.2015.189 http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2015189a.html

Gray. C., Bista, I., Creer, S., Demars, B.O.L., Falciani, F., Monteith, D.T., Sun, X. and Woodward, G. 2015. Freshwater Conservation and Biomonitoring of Structure and Function: Genes to Ecosystems. In: Aquatic Functional Biodiversity. An ecological and evolutionary perspective. Eds Belgrano, A, Woodward, G. and Jacob, U. Elsevier Academic Press. Pp. 241-271.

Lallias, D., Fonseca, V.G., Gaspar, J., Hiddink, J., Sung, W., Neill, S.P., Barnes, N., Ferrero, T., Hall, T., Lambshead, P.J., Packer, M., Thomas, W.K. and Creer, S. 2015. Environmental metabarcoding reveal heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems. The ISME Journal 9, 1208-1221 doi:10.1038/ismej.2014.213

2014

Bohmann K*, Evans A*, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Yu DW, de Bruyn M (2014) Environmental DNA for wildlife biology and biomonitoring. Trends in Ecology and Evolution. 29: 358-367. (* joint first authors)

http://www.sciencedirect.com/science/article/pii/S016953471400086X

Casewell, N.C., S.C. Wagstaff, W. Wüster, D.A.N. Cool, F.M.S. Bolton, S.I. King, D. Pla, L. Sanz, J.J. Calvete & R.A. Harrison (2014) Medically important differences in snake venom composition are dictated by distinct post-genomic mechanisms. PNAS http://www.pnas.org/content/early/2014/06/04/1405484111.abstract

Collins, C.J.; Rawlence, N.J.; Prost, S.; Anderson, C.; Knapp, M.; Scofield, R.P.; Robertson, B.C., Smith, I.; Matisoo-Smith, E.A.; Chilvers, B.L.; Waters, J.M. (2014): Extinction and recolonization of coastal megafauna following human arrival in New Zealand. Proceeedings of the Royal Society B. 281: 20140097. http://dx.doi.org/10.1098/rspb.2014.0097

de Bruyn M*, Stelbrink B*, Morley RJ, Hall R, Carvalho GR, Cannon CH, van den Bergh G, Meijaard E, Metcalfe I, Boitani L, Maiorano L, Shoup R, von Rintelen T (2014) Borneo and Indochina are major evolutionary hotspots for Southeast Asian biodiversity. Systematic Biology, 63(6), 879-901 (* joint first authors) http://sysbio.oxfordjournals.org/content/63/6/879.full

de Bruyn M, Pinsky M, Hall B, Koch P, Baroni C, Hoelzel AR (2014) Rapid increase in southern elephant seal genetic diversity after a founder event. Proceedings of the Royal Society B, 281, 20133078. http://rspb.royalsocietypublishing.org/content/281/1779/20133078.full.pdf

Fonseca, V.G., Carvalho, G.R., Nichols, B., Quince, C., Johnson, H., Neill, S., Lambshead, P.J.D., Thomas, W.K., Power, D. and Creer, S. (2014). Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Global Ecology and Biogeography. 23, 1293-1302.

Goldberg, J.; Knapp, M.;, Emberson, R.M.; Townsend, J.I.; Trewick, S.A. (2014): Species Radiation of Carabid Beetles (Broscini: Mecodema) in New Zealand. PLoS ONE 9(1): e86185. doi:10.1371/journal.pone.0086185

Helyar SJ, Lloyd HD, de Bruyn M, Leake J, Bennett N, Carvalho GR (2014) Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing. PLoS One, 9(6), e98691.

Knapp, M.; Hofreiter, M. (2014): Ancient Human DNA: Phylogenetic Applications. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0005143.pub3

Morgan, M. J., Bass, D., Bik, H., Birky, C. W., Blaxter, M., Crisp, M. D., Derycke, S., Fitch, D., Fontaneto, D., Hardy, C. M., King, A. J., Kiontke, K. C., Moens, T., Pawlowski, J. W., Porazinska, D., Tang, C. Q., Thomas, W. K., Yeates, D. K., Creer, S. (2014). A critique of Rossberg et al.: noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets. Proceedings of the Royal Society, Series B. 281: no. 1783, 20133076.

Nylinder S, Lemey P, de Bruyn M, Suchard MA, Pfeil BE, Walsh N, Anderberg AE (2014) On the biogeography of Centipeda: a species tree diffusion approach. Systematic Biology, 63(2), 178-191. http://sysbio.oxfordjournals.org/content/early/2013/12/12/sysbio.syt102.abstract

Seddon AR, et al. de Bruyn M, et al. (2014) Looking forward through the past: Identification of fifty priority research questions in palaeoecology. Journal of Ecology, 102, 156-165. http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12195/abstract

2013

Stiller, M.; Molak, M.; Prost, S.; Rabeder, G.; Baryshnikov, G.; Rosendahl, W.; Münzel, S.; Bocherens, H.; Grandal-d'Anglade, A.; Hilpert, B.; Germonpré, M.; Stasyk, O.; Pinhasi, R.; Tintori, A.; Rohland, N.; Mohandesan, E.; Ho, S.Y.W.; Hofreiter, M.; Knapp, M. (2013): Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex. Quaternary International. Early online: http://dx.doi.org/10.1016/j.quaint.2013.09.023.

Dabney, J.; Knapp, M.; Glocke, I.; Gansauge, M-T.; Weihmann, A.; Nickel, B.; Valdiosera, C.; Garcia, N.;  Pääbo, S.; Arsuaga, J-L.; Meyer, M. (2013): A complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultra-short DNA fragments. Proceedings of the National Academy of Sciences of the U.S.A.110, 15758-15763.

Collins, C.J.; Rawlence, N.J.; Worthy, T.H.; Scofield, R.P.; Tennyson, A.J.D.; Smith, I.; Knapp, M.; Waters, J.M. (2013): Pre-human New Zealand sea lion (Phocarctos hookeri) rookeries on mainland New Zealand. Journal of the Royal Society of New Zealand. Early online. http://dx.doi.org/10.1080/03036758.2013.828761.

Vonk, F.J., N.R. Casewell, C.V. Henkel, A. Heimberg, R.J.R. McCleary, H.M.E. Kerkkamp, R. Vos, E. McGlinn, I. Guerreiro, J.J. Calvete, W. Wüster, J.M. Logan, A.E. Woods, R.A. Harrison, T.A. Castoe, A.P.J. de Koning, D.D. Pollock, C. Renjifo, R.B. Currier, D. Salgado, D. Pla, L. Sanz, H.P. Spaink, H.J. Jansen, A.S. Hyder, J.M.C. Ribeiro, P.W. Arntzen, G.E.E.J. van den Thillart, M. Boetzer, W. Pirovano, R.P. Dirks, D. Duboule, R.M. Kini & M.K. Richardson (2013) King cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. PNAS 110 (51): 20651-20656. http://www.pnas.org/content/110/51/20651

Casewell, N.R., W. Wüster, F.J. Vonk, R.A. Harrison & B.G. Fry (2013) Complex cocktails: the evolutionary novelty of venoms. Trends in Ecology and Evolution. 28: 219-229. https://db.tt/T7usfmen

Barlow, A., K. Baker, C.R. Hendry, L. Peppin, T. Phelps, K.A. Tolley, C.E. Wüster & W. Wüster (2013) Phylogeography of the widespread African puff adder (Bitis arietans) reveals multiple Pleistocene refugia in southern Africa. Molecular Ecology, 22: 1134-1157. https://db.tt/h60pkdzT

Phillips, MJ, Page, TJ, de Bruyn, M, Huey, JA, Humphreys, WF, Hughes, JM, Santos, SR, Schmidt, DJ, Waters, JM (2013) The linking of plate tectonics and evolutionary divergence. Current Biology, 23(14). R305-R307.
http://www.cell.com/current-biology/fulltext/S0960-9822%2813%2900691-X

de Bruyn M, Stelbrink B, Page TJ, Phillips MJ, Lohman DJ, Albrecht C, Hall R, von Rintelen K, Ng PKL, Shih H-T, Carvalho GR, von Rintelen T (2013) Time and space in biogeography: response to Parenti & Ebach (2013). Journal of Biogeography, 40, 2204-2206.

http://onlinelibrary.wiley.com/doi/10.1111/jbi.12166/full

de Bruyn M, et al., Carvalho GR. (2013) Paleo-drainage basin connectivity predicts evolutionary relationships across three Southeast Asian biodiversity hotspots. Systematic Biology, 62, 398-410.

http://sysbio.oxfordjournals.org/content/early/2013/02/07/sysbio.syt007.abstract?keytype=ref&ijkey=jzqCm9cdFjVKW6Q

van Wijk, SJ, Taylor, MI, Creer, S, Dreyer, C, Rodrigues, FM, Ramnarine, IW, van Oosterhout, C and Carvalho, GR (2013) Experimental harvesting of fish populations drives genetically-based shifts in body size and maturation. Frontiers Ecol. Environ. 2013; doi:10.1890/120229; available from: http://www.esajournals.org/toc/fron/0/0

Pascoal, S, Carvalho, GR, Vasieva, O, Hughes, R, Cossins, A, Fang, Y, Ashelford, K, Olohan, L, Barroso, C, Mendo, S, Creer, S (2013) Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus. Molecular Ecology, 22, 1589-1608. (Perspective on paper : Contaminants and impoSEX: transcriptomics of contaminant-induced sex change. Molecular Ecology, 22, 1485-1487)

Briscoe, A.G., Goodacre, S., Masta, S., Taylor, M.I., Arnedo, M.A., Penney, D., Kenny, J. and Creer, S. 2013. Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae). PLoS One. http://dx.plos.org/10.1371/journal.pone.0062404

 

2012

Casewell, N.R., G.A. Huttley & W. Wüster (2012) Dynamic evolution of venom proteins in squamate reptiles. Nature Communications, 3(1066): 1-10. https://db.tt/0iD46mNu

Barlow, A., W. Grail, M. de Bruyn & W. Wüster (2012) Anonymous nuclear markers for the African adders (Serpentes: Viperidae: Bitis). Conservation Genetics Resources, 4:967-969.  PDF: https://db.tt/1wZ1aBmK

Fry, B.G.,, N.R. Casewell, W. Wüster, N. Vidal, B. Young & T.N.W. Jackson (2012) The structural and functional diversification of the Toxicofera reptile venom system. Toxicon, 60: 434-448.  PDF: https://db.tt/L4y28z3W

Richards, D.P., A. Barlow & W. Wüster. (2012) Venom lethality and diet: Differential responses of natural prey and model organisms to the venom of the saw-scaled vipers (Echis), Toxicon, 59: 110-116.  PDF: https://db.tt/HYuX7kDw

Mat Jafaar TNA, Taylor MI, Mohd Nor SA, de Bruyn M, Carvalho GR (2012) DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PLoS One, 7(11), e49623

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049623

Limborg T, Helyar SJ, de Bruyn M, Taylor MI, Nielsen EE, Ogden R, Carvalho GR, FPT Consortium, Bekkevold D (2012) Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus). Molecular Ecology, 21, 3686-3703.

http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2012.05639.x/abstract

de Bruyn M, von Rintelen K, von Rintelen T, Mather PB, Carvalho GR (2012) Molecular biogeography and phylogeography of the freshwater fauna of the Indo-Australian Archipelago. In: Biotic Evolution and Environmental Change in SouthEast Asia, Systematics Association Volume - Cambridge University Press, UK

http://www.cambridge.org/gb/knowledge/isbn/item6796393/?site_locale=en_GB

Nielsen, EE, Cariani, A, Mac Aoidh, E, Maes, GE, Milano, I, Ogden, R, Taylor, MI, Hemmer-Hansen, J, Babbucci, M, Bargelloni, L, Bekkevold, D, Diopere, E, Grenfell, L, Helyar, S, Limborg, MT, Martinsohn, JT, McEwing, R, Panitz, F, Patarnello, T, Tinti, F, Van Houdt, J, Volckaert, FAM, Waples, RS, FishPopTrace consortium & GR Carvalho (2012). Gene-associated markers provide tools for tackling illegal fishing and false eco-certification. Nature Communications 3, Article number: 851 doi:10.1038/ncomms1845

Bik, H., Porazinska, D.L., Creer, S., Caporaso, J.G., Knight, R. and Thomas, W.K. (2012). Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution. http:/dx.doi.org/10.1016/).tree.2011.11.010

Creer, S. and Sinniger, F. 2012. Cosmopolitanism of microbial eukaryotes in the global deep seas. Molecular Ecology. 21: 1033-1035.

Fonseca V.G., Nichols, B., Lallias, D., Quince, C., Carvalho G.R., Power, D.M. and Creer, S. 2012. Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Research: doi: 10.1093/nar/gks002

Pascoal, S., Carvalho, G., Creer, S., Rock, J., Kawaii, K., Mendo, S., Hughes, R. 2012. Plastic and heritable components of phenotypic variation in Nucella lapillus: an assessment using reciprocal transplant and common garden experiments. PLoS One 7(1): e30289. doi:10.1371/journal.pone.0030289

2011

Casewell, N.R., S.C. Wagstaff, R.A. Harrison, C.Renjifo & W. Wüster (2011) Domain loss facilitates accelerated evolution and neofunctionalization of duplicate snake venom metalloproteinase toxin genes. Molecular Biology and Evolution 28: 2637-2649. PDF: https://db.tt/UCKImI6U

Williams, D.J., J.-M. Gutiérrez, J.J. Calvete, W. Wüster, K. Ratanabanangkoon, O. Paiva, N.I. Brown, N.R. Casewell, R.A. Harrison, P.D. Rowley, M. O’Shea, S.D. Jensen, K.D. Winkel & D.A. Warrell (2011) Ending the drought: new strategies for improving the flow of affordable, effective antivenoms in Asia and Africa. Journal of Proteomics, 74: 1735-1767.  PDF: https://db.tt/uBm9zfge

Casewell, N.R., S.C. Wagstaff, R.A. Harrison & W. Wüster (2011) Gene tree parsimony of multi-locus snake venom protein families reveals species tree conflict as a result of multiple parallel gene loss. Molecular Biology and Evolution, 28: 1157–1172.  PDF: https://db.tt/lIi1mb7c

Alexandrou, M., Oliveira, C., Maillard, M., McGill, R.A.R., Newton, J., Creer, S. and M. I. Taylor. Competition and phylogeny determine community structure in Müllerian co-mimics. Nature 469:84–88, 2011. DOI:10.1038/nature09660

de Bruyn M., Hoelzel A.R., Carvalho G.R., Hofreiter M. (2011) Faunal histories from Holocene ancient DNA. Trends in Ecology and Evolution, 26, 405-413 . http://www.sciencedirect.com/science/article/pii/S0169534711000917

de Bruyn M, Parenti L.R. & Carvalho G.R. (2011) Successful extraction of DNA from archived ‘white-eye’ alcohol-fixed fish specimens using an ancient DNA protocol. Journal of Fish Biology, 78, 2074-2079. PDF

Lohman D.*, de Bruyn M.*, et al. Carvalho G.R., et al.(2011) Biogeography of the Indo-Australian Archipelago. Annual Review of Ecology, Evolution and Systematics, 42, 205-226. (* joint first authors)

http://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-102710-145001

Matzen, J., Creer, S., dos Santos, A., Costa, A.C., Cunha M.R., Costa, F.O. and Carvalho, G.R. (2011). Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS One. 6: e19449

Matzen, J., dos Santos, A., Cunha M.R., Costa, F.O., Creer, S. and Carvalho, G.R. (2011). Multigene molecular systematics confirm species status of morphologically convergent Pagurus hermit crabs. PLoS One. http://dx.plos.org/10.1371/journal.pone.0028233

B.K. Mable, M.A. Alexandrou and M.I. Taylor. (2011). Genome duplication in amphibians and fish: an extended synthesis. Journal of Zoology, 284: 151-182.

2010

Casewell, N.R., D.A.N. Cook, S.C. Wagstaff, A. Nasidi, N. Durfa, W. Wüster & R.A. Harrison (2010) Pre-clinical assays predict pan-African Echis viper efficacy for a species-specific antivenom. PLoS Neglected Tropical Diseases, 4: e851. DOI: 10.1371/journal.pntd.0000851

Antonelli, A., A. Quijada-Mascareñas, A.J. Crawford, J.M. Bates, P.M. Velazco & W. Wüster (2010) Molecular studies and phylogeography of Amazonian tetrapods and their relation to geological and climatic models. In Amazonia: Landscape and Species Evolution (C. Hoorn, F. Wesselingh & H. Vonhoff, eds.), p. 386-404. Blackwell Publishing, Oxford.  PDF: https://db.tt/znZzRJdJ

Andre, C, Larsson, LC, Laikre, L, Bekkevold, D, Brigham, J, Carvalho, GR, Dahlgren, TG, Hutchinson, W, Mariana, S, Mudde, K, Ruzzante, D, Ryman, N (2010) Detecting population structure in a high gene flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral versus putatively selected loci. Heredity, In Press

Carvalho, G.R., Creer, S., Allen M., Costa F.O., Tsigenopoulos C.S., Le Goff-Vitry M., Magoulas A.M., Medlin L. & Metfies K. (In Press) Genomics in the discovery and monitoring of marine biodiversity. In: An Introduction to Marine Genomics, (eds.) Boyen C and Cock, M. Springer-Verlag, pp.1-32.

Costa, FO & Carvalho, GR (2010) New insights into molecular evolution: prospects from the Barcode of Life Initiative (BOLI). Theory in Biosciences, DOI 10.1007/s12064-010-0091-y

Creer, S. 2010. Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists. Molecular Ecology. 19:2829-2831

Creer, S., Fonseca, V.G., Porazinska D.L., Giblin-Davies, R.M., Sung, W., Power, D.M., Packer, M., Carvalho, G.R., Blaxter, M.L., Lambshead, P.J.D. and Thomas, W.K. 2010. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises . Molecular Ecology 19.4-20.

de Bruyn M, Grail W, Barlow A, Carvalho GR (2010) Anonymous nuclear markers for SE Asian halfbeaks (genus Dermogenys). Conservation Genetics Resources DOI: 10.1007/s12686-010-9228-z

Domingues C.P., Creer S., Taylor MI., Queiroga H., Carvalho GR. Genetic structure of Carcinus maenas withinits native range: larval dispersal and oceanographic variability. Marine Ecology Progress Series 410: 111–123, 2010 DOI: 10.3354/meps08610 PDF

Domingues CP., Creer S., Taylor MI., Queiroga H.,Carvalho GR. Temporal genetic homogeneity among shore crab(Carcinus maenas) larval events supplied to an estuarine system on the Portuguese northwest coast. Heredity (2010), 1–9 PDF

Fonseca, V.G., Carvalho, GR, Sung, W, Johnson, HF, Power, DM, Neill, SP, Packer, M, Blaxter, ML, Lambshead, PJD, Thomas, WK, & Creer, S (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity.

Nature Communications DOI:http://dx.doi.org/10.038/ncomms1095

Genner MJ, Knight ME, Haesler MP, Turner GF (2010) Establishment and expansion of Lake Malawi rock fish populations after a dramatic Late Pleistocene lake level rise. Molecular Ecology, 19, 170-182

Genner, M.J., Nichols, P., Shaw, P.W., Carvalho, G.R., Robinson, R.L.& Turner, G.F. (2010) Population structure on breeding grounds of Lake Malawi’s ‘twilight zone’ cichlid fishes. J. Biogeog 37, 258-269


Young, E, Meredith, M, Murphy, EJ & Carvalho, GR (2010) High-resolution modelling of the shelf and open ocean adjacent to South Georgia, Southern Ocean. Deep Sea Research II. In Press.

2009

Casewell, N.R., R.A. Harrison, W. Wüster & S.C. Wagstaff (2009) Comparative venom gland transcriptome surveys of the saw-scaled vipers (Viperidae: Echis) reveal substantial intra-family gene diversity and novel venom proteins. BMC Genomics 10: 564.  PDF: http://www.biomedcentral.com/1471-2164/10/564

Pook, C.E., U. Joger, N. Stümpel & W. Wüster (2009) When continents collide: phylogeny, historical biogeography and systematics of the medically important viper genus Echis (Squamata: Serpentes: Viperidae). Molecular Phylogenetics and Evolution 53: 792-807.  PDF: https://db.tt/aSpzbElu

Barlow, A., C.E. Pook., R.A. Harrison & W. Wüster (2009) Co-evolution of diet and prey-specific venom activity supports the role of selection in snake venom evolution. Proceedings of the Royal Society B, 276: 2443-2449.  PDF: https://db.tt/QVevGUry

Lallias D., Gomez-Raya L., Haley C.S., Arzul I., Heurtebise S., Beaumont A.R., Boudry P. and Lapègue S. (2009) Combining two-stage testing and interval mapping strategies to detect QTL for resistance to bonamiosis in the European flat oyster Ostrea edulis. Marine Biotechnology 11: 570-584.

Lallias D., Stockdale R., Boudry P., Lapègue S. and Beaumont A.R. (2009) Characterization of ten microsatellite loci in the blue mussel Mytilus edulis. Journal of Shellfish Research 28 (3): 547-551.

                          

Lallias D., Stockdale R., Boudry P., Beaumont A.R. and Lapègue S. (2009) Characterization of 27 microsatellite loci in the European flat oyster Ostrea edulis. Molecular Ecology Resources 9: 960-963.  

Chopelet. J., Helyar, S., Mann, B. and Mariani. S. (2009) Novel polymorphic microsatellite loci for the protogynous hermaphrodite slinger sea bream (Chrysoblephus puniceus, Sparidae) Molecular Ecology Resources 9 (4):1223 – 1226

de Bruyn M, Hall BL, Chauke LF, Baroni C, Koch PL & Hoelzel AR. (2009) Rapid response of a marine mammal species to Holocene climate and habitat change. PLoS Genetics, 5, e1000554

Helyar, S., Sacchi, C., Coughlan, J., and Mariani. S. (2009) Novel microsatellite loci for a deep sea fish (Macrourus berglax) and their amplification in other grenadiers (Gadiformes: Macrouridae) Conservation Genetics Resources (Online First).

Pascoal S, Creer S, Taylor M.I, Queiroga H, Carvalho G, et al. (2009) Development and Application of Microsatellites in Carcinus maenas: Genetic Differentiation between Northern and Central Portuguese Populations. PLoS ONE 4(9): e7268. doi:10.1371/journal.pone.0007268

Blais, J., Plenderleith M., Rico, C. Taylor, M. I. Seehausen, O,  Ooseterhout C. and Turner, G.F. (2009) Assortative mating among Lake Malawi cichlid fish populations is not simply predictable from male nuptial colour.  BMC Evolutionary Biology 9:53.

Tysklind, N, Neupath, T, Ashcroft, G, Taylor, M. I. Lyons, B. McCarthy, I, Carvalho, C. (2009) Isolation and characterization of 28 new microsatellite markers for European flounder (Platichthys flesus L.). Molecular Ecology Resources. In Press.

Tysklind, N, Taylor, M. I. LyB. McCarthy, I, Carvalho, C. (2009) Development of 30 microsatellite markers for dab (Limanda limanda L.): a key UK marine biomonitoring species Molecular Ecology Resources Online Early: DOI: 10.1111/j.1755-0998.2008.02513.x

Galarza JA,  Carreras-Carbonell, J, Macpherson E, Pascual M, Roques S, Turner GF & Rico C (2009) The influence of oceanographic fronts and early-life-history traits on connectivity among littoral fish species. PNAS 106, 1473-1478.

Blais J, Plenderleith M, Rico C, Taylor M I, Seehausen O, van Oosterhout C,& Turner GF (2009). Assortative mating among Lake Malawi cichlid fish populations is not simply predictable from male nuptial colour. BMC Evolutionary Biology 2009, 9: 53.

Young KA, Whitman JM & Turner GF (2009). Secondary contact during adaptive radiation: a community matrix for Lake Malawi cichlids. J. Evol. Biol. 22, 882 - 889.

Galarza JA, Turner GF, Macpherson E, & Rico C (2009) Patterns of genetic differentiation between two co-occurring demersal species: the red mullet (Mullus barbatus) and the striped red mullet (Mullus surmuletus). Can. J. Fish Aq. Sci. 66, 1478-1490.

Zidana H, Turner GF, Van Oosterhout C, Hanfling B (2009) Elevated mtDNA diversity in introduced populations of Cynotilapia afra (Gunther 1894) in Lake Malawi National Park is evidence for multiple source populations and hybridization. Molecular Ecology, 18, 4380-4389

Guerra-Varela J., Colson I., Backeljau T., Breugelmans K., Hughes R.N., Rola´n- Alvarez R. 2009. The evolutionary mechanism maintaining shell shape and molecular differentiation between two ecotypes of the dogwhelk Nucella lapillus. Evol. Ecol. 23:261–280. doi: 10.1007/s10682-007-9221-5

Hughes, R.N., Wright, P.J., Carvalho, G.R. & Hutchinson, W.F. 2009. Patterns of self compatibility, inbreeding depression, outcrossing, and sex allocation in a marine bryozoan suggest the predominating influence of sperm competition. Biological Journal of the Linnean Society, 98, 519-531.   DOI: 10.1111/j.1095-8312.2009.01312.x

Malhotra, A., Creer, S., Pook, C.E. and Thorpe R.S. 2009. Inclusion of nuclear intron sequence data helps to identify the Asian sister group of New World pitvipers. Molecular Phylogenetics and Evolution, 54: 172-178.

Guo, P.,Malhotra, A., Creer, S., and Pook, C.E. 2009.An evaluation of the systematic value of skull morphology in the Trimeresurus radiation (Serpentes: Viperidae: Crotalinae) of Asian pitvipers. Journal of Zoological Systematics and Evolutionary Research. 47: 378-384.

Guo, P., Malhotra, A., Li, C., Creer, S., Pook, C.E. and Wen, T. 2009.Systematics of the Protobothrops jerdonii complex (Serpentes, Viperidae, Crotalinae) inferred from morphometric data and molecular phylogeny. Herpetological Journal 19: 85-96.

2008

Wüster, W., L. Peppin, C.E. Pook & D.E. Walker (2008) A nesting of vipers: phylogeny, historical biogeography and patterns of diversification of the Viperidae (Squamata: Serpentes). Molecular Phylogenetics and Evolution 49: 445-459.  PDF: https://db.tt/AD4L2y6z

Croft DP, James R, and Krause J 2008. Exploring Animal Social Networks. Princeton, NJ, Princeton University Press. 186p - predicted release date Easter 2008

Hughes RN, Gomez A, Wright PJ, Moyano HI, Cancino JM, Carvalho GR and Lunt DH 2008. Molecular phylogeny supports division of the 'cosmopolitan' taxon Celleporella (Bryozoa; Cheilostomata) into four major clades. Molecular Phylogenetics and Evolution. 46: 369-374. PDF

Lallias D, Stockdale R, Boudry P, Beaumont AR and Lapègue S. Characterization of 27 microsatellite loci in the European flat oyster Ostrea edulis. Accepted: Molecular Ecology Resources.

Thomas POR, Croft DP, Morrell LJ, Davis A, Faria JJ, Dyer JRG, Piyapong C, Ramnarine I, Ruxton GD and Krause J. Does defection during predator inspection affect social structure in wild shoals of guppies? Animal Behaviour (in press).

2007

Wüster, W., S. Crookes, I. Ineich, Y. Mane, C.E. Pook, J.-F. Trape & D.G.Broadley (2007) The phylogeny of cobras inferred from mitochondrial DNA sequences: evolution of venom spitting and the phylogeography of the African spitting cobras (Serpentes: Elapidae: Naja nigricollis complex). Molecular Phylogenetics and Evolution 45: 437-453.  PDF: https://db.tt/gBsQOIfC

Quijada-Mascareñas, J.A., J.E. Ferguson, C.E. Pook, M.G. Salomão, R.S. Thorpe & W. Wüster (2007) Phylogeographic patterns of trans-Amazonian vicariants and Amazonian biogeography: the Neotropical rattlesnake (Crotalus durissus complex) as an example. Journal of Biogeography 34: 1296–1312.   PDF: https://db.tt/JXAdYFmi

Creer S 2007. Choosing and using introns in molecular phylogenetics. Evolutionary Bioinformatics. 3: 99-108. PDF

de Bruyn M and Mather PB 2007. Molecular signatures of Pleistocene sea-level changes that affected connectivity among freshwater shrimp in Indo-Australian waters. Molecular Ecology. 16: 4295-4307. PDF

Dyer JRG, Ioannou CC, Morrell LJ, Croft DP, Couzin ID, Waters DA, Wong Y, and Krause J 2007. Collective decision making in human crowds. Animal Behaviour (in press)

Genner MJ, Seehausen O, Lunt DH, Joyce DA, Shaw, PW, Carvalho GR and Turner GF 2007. Age of cichlids: New dates for ancient lake fish radiations. Molecular Biology and Evolution. 24: 1269-1282. PDF

Genner MJ, Nichols P, Carvalho GR, Robinson RL, Shaw, PW and Turner GF 2007. Reproductive isolation among deep-water cichlid fishes of Lake Malawi differing in monochromatic male breeding dress. Molecular Ecology. 16: 651-662. PDF

Gomez A, Hughes RN, Wright PJ, Carvalho GR and Lunt DH 2007. Mitochondrial DNA phylogeography and mating compatability reveal marked genetic structuring and speciation in the NE Atlantic bryozoan Celleporella hyalina. Molecular Ecology, 16, 2173-2188. PDF

Gomez A, Wright PJ, Lunt DH, Cancino JM, Carvalho GR and Hughes RN 2007. Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proceedings of the Royal Society of London, B. 24: 199-207. PDF

Lallias D, Lapègue S, Hecquet C, Boudry P and Beaumont AR 2007. AFLP-based genetic linkage maps of the blue mussel Mytilus edulis. Animal Genetics 38: 340-349. PDF

Lallias D, Beaumont AR, Haley CS, Boudry P, Heurtebise S and Lapègue S 2007. A first genetic linkage map of the European flat oyster Ostrea edulis (L.) based on AFLP and microsatellite markers. Animal Genetics 38: 560-568. PDF

Rock J, Ironside J, Potter T, Whitely N and Lunt DE 2007. Phylogeography and environmental diversification of a highly adapted marine amphipod, Gammarus duebeni. Heredity. 99: 102-111.

Telfer S, Clough HE, Birtles RJ, Bennett M, Carslake D, Helyar S & Begon M 2007. Ecological differences and coexistence in a guild of microparasites: Bartonella in wild rodents. Ecology. 88: 1841–1849. PDF

2006

Creer S, Malhotra A, Thorpe RS, and Pook CE 2006. Optimal intron analyses in the Trimeresurus radiation of Asian pitvipers. Systematic Biology 55: 57-72. PDF

Culling MA, Janko K, Boroñ A, Vasil'Ev VP, Côte IM and Hewitt GM 2006. European colonization by the spined loach (Cobitis taenia) from Ponto-Caspian refugia based on mitochondrial DNA variation. Molecular Ecology 15: 173-190. PDF

Neuparth T, Bickham JW, Theodorakis CW, Costa FO and Costa MH 2006. Bulletin of Environmental Contamination and Toxicology 76: 242-248. PDF

Rock J 2006. Delayed parturition: constraint or coping mechanism in a viviparous gekkonid? Journal of Zoology 268:355-360

Rock J, Pastene L, Kaufman G, Forestell P, Matsuoka K, and Allen J 2006. East Australia Group V Stock humpback whale movement between feeding and breeding areas based on photo-identification. Journal of Cetacean Research and Management. In press.

Ruzzante, D, Mariani, S, Bekkevold, D, Andre, C, Mosegaard, H, Clausen, L, Dahlgren, T, Hutchinson, WF, Hatfield, E, Torstensen, E, Brigham, J, Simmonds, J, Laikre, L, Larsson, L, Stet, R, Ryman, N and Carvalho, GR 2006. Biocomplexity in a highly migratory pelagic marine fish, Atlantic herring. Proceedings of the Royal Society of London, B. 273: 1459-1464. PDF

2005

Wüster, W., J.E. Ferguson, J.A. Quijada-Mascareñas, C.E. Pook, M.G. Salomão & R.S. Thorpe (2005) Tracing an invasion: landbridges, refugia and the phylogeography of the Neotropical rattlesnake (Serpentes: Viperidae: Crotalus durissus). Molecular Ecology 14: 1095-1108. PDF: https://db.tt/NLCPyxWC

Wüster, W., A.J. Dumbrell, C. Hay, C.E. Pook, D.J. Williams & B.G. Fry (2005) Snakes across the Strait: Trans-Torresian phylogeographic relationships in three genera of Australasian snakes (Serpentes: Elapidae: Acanthophis, Oxyuranus and Pseudechis). Molecular Phylogenetics and Evolution 34: 1-14. PDF: https://db.tt/Py7VYH3s

Bekkevold D, Andre C, Dahlgreen TG, Clausen LAW, Torstensen E, Mosegaard H., Carvalho GR, Christensen TB and Ruzzante DE 2005. Environmental correlates of population differentiation in Atlantic herring. Evolution, 59: 2656-2668. PDF

Costa FO, Neuparth T, Correia, AD and Costa MH 2005. Multi-level assessment of chronic toxicity of estuarine sediments with the amphipod Gammarus locusta: II. Organism and population-level endpoints. Marine Environmental Research. 60: 93-110. PDF

Creer S, Malhotra A, Thorpe RS and Pook CE 2005. Targetting optimal introns for phylogenetic analyses in non-model taxa: experimental results in Asian pitvipers. Cladistics 21: 390-395. PDF

de Bruyn M, Nugroho E, Hossain MD, Wilson JC and Mather PB 2005. Phylogeographic evidence for the existence of an ancient biogeographic barrier: the Isthmus of Kra Seaway. Heredity 94: 370-378. PDF

Fox, C*, Taylor, MI*, Pereyra, Villasana RMI and Rico C 2005. Taqman DNA technology confirms likely overestimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg-based methods. Molecular Ecology 14, 879-884. * Joint first authors. PDF

Janko K, Culling MA, Ráb and Kotlík P 2005. Ice age cloning - comparison of the Quaternary evolutionary histories of sexual and clonal forms of spiny loaches (Cobitis; Teleostei) using the analysis of mitochondrial DNA variation. Molecular Ecology 14: 2991-3004. PDF

Neuparth T, Correia AD, Costa FO, Lima G and Costa MH 2005. Multi-level assessment of chronic toxicity of estuarine sediments with the amphipod Gammarus locusta: I. Biochemical endpoints. Marine Environmental Research 60: 69-91. PDF

Saccheri IJ, Lloyd HD, Helyar SJ, Brakefield PM 2005. Inbreeding uncovers fundamental differences in the genetic load affecting male and female fertility in a butterfly. Proceedings of the Royal Society of London Series B-Biological Sciences 272: 39-46. PDF
This paper was selected for Research Highlights. Nature 432: 688.PDF

Siriovski N, Woolnough C, Rock J, Joss JMP 2005. NfCR1, the first non-LTR retrotransposon characterised in the Australian lungfish genome, Neoceratodus forsteri, shows similarities to CR1-like elements. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 304B:40-49.

2004

Wüster, W. C.S.E. Allum, I.B. Bjargardóttir, K.L. Bailey, K.J. Dawson, J. Guenioui, J. Lewis, J. Mcgurk, A.G. Moore, M. Niskanen & C.P. Pollard (2004) Do aposematism and Batesian mimicry require bright colours? A test, using European viper markings. Proceedings of the Royal Society of London, Biological Sciences 271: 2495 - 2499. PDF: https://db.tt/xwsruQpV

Fry, B.G. & W. Wüster (2004) Assembling an arsenal: origin and evolution of the snake venom proteome inferred from phylogenetic analysis of toxin sequences. Molecular Biology and Evolution 21: 870–883.  PDF: https://db.tt/UppuG3F4

Albaina A and Irigoien X 2004.Relationships between frontal structures and zooplankton communities along a cross-shelf transect in the Bay of Biscay (1995 to 2003). Marine Ecology Progress Series 284: 65-75. PDF

Costa, FO, Cunha, MR, Neuparth, T, Theodorakis, CW, Costa, MH and Shugart, LR 2004. Application of RAPD DNA fingerprinting in taxonomic identification of amphipods: a case-study with Gammarus species (Crustacea: Amphipoda). Journal of the Marine Biological Association of the United Kingdom. 84, 171-178. PDF

Costa FO, Neuparth T, Theodorakis CW, Costa MH and Shugart LR 2004. RAPD analysis of southern populations of Gammarus locusta: comparison with allozyme data and ecological inferences. Marine Ecology Progress Series, 277: 197-207. PDF

de Bruyn M, Wilson JC and Mather PB 2004. Reconciling geography and genealogy: phylogeography of giant freshwater prawns from the Lake Carpentaria region. Molecular Ecology 13: 3515-3526. PDF

de Bruyn M, Wilson JC and Mather PB 2004. Huxley’s Line demarcates extensive genetic divergence between eastern and western forms of the giant freshwater prawn, Macrobrachium rosenbergii. Molecular Phylogenetics and Evolution 30: 251-257. PDF

Pereyra, R, Taylor, MI, Turner, GF and Rico, C 2004. Variation in habitat preference and population structure among three species of the Lake Malawi cichlid fish genus Protomelas. Molecular Ecology 13, 2691-2697. PDF

2003

Fry, B.G., N.G. Lumsden, W. Wüster, J.C. Wickramaratna, W.C. Hodgson & R.M. Kini (2003)  Isolation of a neurotoxin (alpha-colubritoxin) from a ‘non-venomous’ colubrid: evidence for early origin of venom in snakes. Journal of Molecular Evolution, 57: 446-452.   PDF: https://db.tt/omQwVfQd

Fry, B.G., W. Wüster, S.F.R. Ramjan, T. Jackson, P.  Martelli & R.M. Kini (2003) Analysis of Colubroidea snake venoms by liquid chromatography with mass spectrometry: evolutionary and toxinological implications. Rapid Communications in Mass Spectrometry 17: 2047-2062.  PDF: https://db.tt/PQ7EFnOC

Fry, B.G., W. Wüster, R.M. Kini, V. Brusic, A. Khan, D. Venkataraman & A.P. Rooney (2003). Molecular evolution and phylogeny of snake venom three finger toxins. Journal of Molecular Evolution 57: 110-129.   PDF: https://db.tt/HTjI7EqC

Wüster, W. & D.G. Broadley (2003) A new species of spitting cobra from northeastern Africa (Serpentes: Elapidae: Naja). Journal of Zoology, London 259: 345-359.   PDF: https://db.tt/1AJGadc1

Harrison, R.A., W. Wüster & R.D.G. Theakston (2003) The conserved structure of snake venom toxins confers extensive immunological cross-reactivity to toxin-specific antibody.Toxicon 41: 441-449.  https://db.tt/zWTEFPHX

Creer S, Malhotra A and Thorpe RS 2003. Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the Asian pitviper genus Trimeresurus : separate, simultaneous, and conditional data combination analyses. Molecular Biology and Evolution 20: 1240-1251. PDF

Hutchinson, WF, van Oosterhout, C, Rogers SI and Carvalho, GR 2003. Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod. Proceedings of the Royal Society, Lond., B, 270: 2125-2132. PDF

Taylor MI, Morley J, Rico C and Balshine S 2003. Evidence for genetic monogamy and female-biased dispersal in the biparental mouthbrooding cichlid Eretmodus cyanostictus from Lake Tanganyika. Molecular Ecology 12, 3173-3177. PDF

2002

Fry, B.G., J. Wickramaratna, W. Hodgson, P. Alewood, R.M. Kini, H. Ho & W. Wüster (2002) Electrospray liquid chromatography/mass spectrometry fingerprinting of Acanthophis (death adder) venoms: taxonomic and toxinological implications. Rapid Communications in Mass Spectrometry, 16: 600-608.   PDF: https://db.tt/rq3JMI69

Neuparth T, Costa, FO and Costa MH 2002. Effects of temperature and salinity on life history of the marine amphipod Gammarus locusta. Implications for ecotoxicological testing. Ecotoxicology 11: 61-73. PDF

Rock J and Cree A 2002. The effect of reproductive condition on thermoregulation in a viviparous gecko from a cool climate. Journal of Thermal Biology 27:17-27.

Rock J, Cook S, Thomas J, Murray T and Jamieson I 2002. Selected temperatures of an alpine weta Hemideina maori from Southern New Zealand. New Zealand Journal of Zoology 29:73-78.

Hauser L, Adcock GJ, Smith PJ, Bernal Ramirez, J and Carvalho, GR 2002. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper. Proceedings of the National Academy of Sciences, USA, 99: 11742-11747. PDF

Wright PJ and Hughes RN 2002. A comparison of the early astogeny and life history of Celleporella carolinensis and Celleporella hyalina. In: Wyse Jackson, P.N., Buttler, C.J. and Spencer Jones, M.E. (eds.) Bryozoan Studies 2001. Swets & Zeitlinger, Lisse.

Hughes RN, Wright P, Manríquez PH and Bishop JDD 2002. Predominance of obligate outbreeding in the simultaneous hermaphrodite Celleporella hyalina sensu lato. In: Wyse Jackson, P.N., Buttler, C.J. and Spencer Jones, M.E. (eds.) Bryozoan Studies 2001. Swets & Zeitlinger, Lisse.

2001

Puorto, G., M.G. Salomão, R.D.G. Theakston, R.S. Thorpe, D.A. Warrell & W. Wüster (2001) Combining mitochondrial DNA sequences and morphological data to infer species boundaries: phylogeography of lanceheaded pitvipers in the Brazilian Atlantic forest, and the status of Bothrops pradoi (Squamata: Serpentes: Viperidae). Journal of Evolutionary Biology, 14: 527-538.   PDF: https://db.tt/dAkpQlx3

Creer S, Malhotra A, Thorpe RS and Chou W-H 2001. Multiple causation of phylogeographical pattern as revealed by nested clade analysis of the bamboo viper (Trimeresurus stejnegeri) within Taiwan. Molecular Ecology 10: 1967-1981. PDF

Taylor MI, Rüber L and Verheyen E 2001. Microsatellites reveal high levels of population substructuring in the species-poor, Eretmodine cichlid lineage from Lake Tanganyika. Proceedings of the Royal Society of London B 268, 803-808. PDF

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