Bernie Degnan

publications


2013

Felipe Aguilera, Carmel McDougall and Bernard M Degnan. 2013. Origin, evolution and classification of type-3 copper proteins: lineage-specific gene expansions and losses across the Metazoa. BMC Evolutionary Biology 2013, 13:96 doi:10.1186/1471-2148-13-96.

McDougall Carmel, Aguilera Felipe, Degnan BM. 2013. Rapid evolution of pearl oyster shell matrix proteins with repetitive, low-complexity domains.  J Royal Society Interface 10 (82), 20130041

2012

Steinmetz PRH, Kraus JEM, Larroux C, Hammel JU, Amon-Hassenzahl A, Houliston E, Wörheide G, Nickel M, Degnan BM, Technau U. 2012. Independent evolution of striated muscles in cnidarians and bilaterians. Nature 487, 231-234

Conaco C, Bassett DS, Zhou H, Arcila ML, Degnan SM, Degnan BM, Kosik KS. 2012. Functionalization of a proto-synaptic gene expression network. Proc Natl Acad Sci USA 109, 10612-10618

Fahey B, Degnan BM. 2012. Origin and evolution of laminin gene family diversity. Mol Biol Evol 29, 1823-1836

Richards GS, Degnan BM. 2012. The expression of Delta ligands in the sponge Amphimedon queenslandica suggests an ancient role for Notch signaling in metazoan development. EvoDevo 3, e15

Rivera AS, Ozturk N, Fahey B, Plachetzki DC, Degnan BM, Sancar A, Oakley TH. 2012. Blue light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsins. J Exp Biol 215, 1278-1286

Conaco C, Neveu P, Zhou H, Bassett DS, Arcila ML, Degnan SM, Degnan BM, Kosik KS. 2012. Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions. BMC Genomics 13, e209

York PS, Cummins SF, Degnan SM, Woodcroft BJ, Degnan BM. 2012. Marked changes in neuropeptide expression accompany broadcast spawnings in the gastropod Haliotis asinina. Front Zool 9, e9

Jackson DJ, Degnan SM, Degnan BM. 2012. Variation in rates of early Haliotis asinina development generate competent larvae of different ages. Front Zool 9, e2

Wollesen T, Nishiguchi MK, Seixas P, Degnan BM, Wanninger A. 2012. The VD(1)/RPD(2) α1-neuropeptide is highly expressed in the brain of cephalopod mollusks. Cell Tissue Res 348, 439-452

Kuanpradit C, Stewart MJ, York PS, Degnan BM, Sobhon P, Hanna PJ, Chavadej J, Cummins SF. 2012. Characterization of mucus associated proteins from abalone (Haliotis): candidates for chemical signaling. FEBS J 279, 437-450

York PS, Cummins SF, Lucas T, Blomberg SP, Degnan SM, Degnan BM. 2012. Differential expression of neuropeptides correlates with growth rate in cultivated Haliotis asinina (Vetigastropoda: Mollusca). Aquaculture 334-337, 159-168

Erpenbeck D, Schmitz J, Churakov G, Huchon D, Wörheide G, Degnan BM 2012. First evidence of miniature transposable elements in Porifera. Hydrobiologia 687, 43-47

2011

Cummins SF, Boal JG, Buresch KC, Kuanpradit C, Sobhon P, Holm JB, Degnan BM, Nagle GT, Hanlon RT. 2011. Extreme aggression in male squid induced by a beta-MSP-like pheromone. Curr Biol 21, 322-327

Erpenbeck D, Voigt O, Adamski M, Woodcroft BJ, Hooper JNA, Wörheide G, Degnan BM. 2011. NUMTs in the sponge genome reveal conserved transposition mechanisms in metazoans. Mol Biol Evol 28, 1-5

Kerner P, Degnan SM, Marchand L, Degnan BM, Vervoort M. 2011. Evolution of RNA-binding proteins in animals: insights from genome-wide analysis in the sponge Amphimedon queenslandica. Mol Biol Evol 28, 2289-2303

Sebé-Pedrós A, de Mendoza A, Lang FB, Degnan BM, Ruiz-Trillo I. 2011. Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Mol Biol Evol 28, 1241-1254

McDougall C, Degnan BM. 2011. Modularity of gene regulatory networks revealed in sea star development. BMC Biol 9, 6 (commentary)

Cummins SF, Tollenaere A, Degnan BM, Croll RP. 2011. Molecular analysis of two FMRFamide-encoding transcripts expressed during the development of the tropical abalone Haliotis asinina. J Comp Neurol 519, 2043-2059

McDougall C, Green K, Jackson DJ, Degnan BM. 2011. Ultrastructure of the mantle of the gastropod Haliotis asinina and mechanisms of shell regionalization. Cells Tissues Organs 194, 103-107

Adamska A, Zwafink C, Green K, Degnan BM. 2011. What sponges can tell us about the evolution of developmental processes. Zoology 114, 1-10

2010

Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier MEA, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki D, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson D, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, Manning G, Degnan BM, Rokhsar DS. 2010. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466, 720-726

Jackson DJ, McDougall CL, Woodcroft BJ, Moase P, Rose R, Kube M, Reinhardt R, Rokhsar DS, Montagnani C, Joubert C, Piquemal D, Degnan BM. 2010. Parallel evolution of nacre building gene sets in molluscs. Mol Biol Evol 27, 591-608

Degnan SM, Degnan BM. 2010. The initiation of metamorphosis as an ancient polyphenic trait and its role in metazoan life cycle evolution. Phil Trans R Soc B 365, 641-651

Bridgham JT, Eick GN, Larroux C, Deshpande K, Harms MJ, Gauthier MAE,  Ortlund EA, Degnan BM, Thornton JW. 2010. Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor. PLoS Biol 8, e1000497

Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, Holst J, Ritchie W, Wong JJ-L, Rasko JEJ, Rokhsar DS, Degnan BM, Mattick JS. 2010. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nature Struct Mol Biol 17, 1030-1034             

Srivastava M, Larroux C, Lu DR, Mohanty K, Chapman J, Degnan B, Rokhsar DS. 2010. Early evolution of the LIM homeobox gene family. BMC Biol 8, 4

Degnan BM. 2010. The rise of genomics sheds light on the dawn of animals. Evol Dev 12, 425-427

Adamska M, Larroux C, Adamski M, Green K, Lovas E, Koop D, Richards GS, Zwafink C, Degnan BM. 2010. Structure and expression of conserved Wnt pathway components in the demosponge Amphimedon queenslandica. Evol Dev 12, 492-518

Gauthier MEA, Du Pasquier L, Degnan BM. 2010. The genome of the sponge Amphimedon queenslandica provides new perspectives into the origin of Toll-like and Interleukin1 receptor pathways. Evol Dev 12, 519-533

Fahey B, Degnan BM. 2010. Origin of animal epithelia: insights from the sponge genome. Evol Dev 12, 601-617

Jackson DJ, Meyer NP, Seaver E, Pang K, McDougall C, Moy VN, Gordon K, Degnan BM, Martindale MQ, Burke RD, Peterson KJ. 2010. Developmental expression of COE across the Metazoa supports a conserved role in neuronal cell-type specification and mesodermal development. Dev Genes Evol 220, 221-234

Callaghan TR, Degnan BM, Sellars MJ. 2010. Expression of sex and reproduction related genes in Marsupenaeus japonicus. Mar Biotech 12, 664-677

Shimeld SM, Degnan BM, Luke GN. 2010. Evolutionary genomics of the Fox genes: Origin of gene families and the ancestry of gene clusters. Genomics 95,256-260

Kranz AM, Tollenaere A, Norris BJ, Degnan BM, Degnan SM. 2010. Identifying the germ-line in an equally cleaving mollusc: Vasa and Nanos expression during embryonic and larval development of the vetigastropod Haliotis asinina. J Exp Zool B (Mol Dev Evol) 314B, 267-279

Cummins SF, Nuurai P, Nagle GT, Degnan BM. 2010. Conservation of the egg laying hormone neuropeptide and attractin pheromone in the spotted sea hare, Aplysia dactylomela. Peptides 31, 394-401

Wollesen T, Cummins SF, Degnan BM, Wanninger A. 2010. FMRFamide gene and peptide expression during CNS development of the cephalopod mollusk, Idiosepius notoides. Evol Dev 12, 113-130

Wollesen T, Degnan BM, Wanninger A. 2010. Expression of serotonin (5-HT) during CNS development of the cephalopod mollusk, Idiosepius notoides. Cell Tissue Res 342, 161-178

Marie B, Marie A, Jackson DJ, Dubost L, Degnan BM, Milet C, Marin F. 2010. Proteomic analysis of the organic matrix of the abalone Haliotis asinina calcified shell. Proteomics 8, 54

Izumi H, Gauthier M, Degnan BM, Ng YK, Hewavitharana  AK, Shaw PN, Fuerst JA. 2010. Diversity of Mycobacterium species from marine sponges and their sensitivity to antagonism by sponge-derived rifamycin-synthesizing actinobacteria in genus Salinispora. FEMS Microbiol Lett 313, 33-40

York PS, Cummins SF, Degnan SM, Woodcroft BJ, Degnan BM. 2010. Identification of genes differentially expressed in the ganglia of growing Haliotis asinina. J Shellfish Res 29, 741-752

Maritz K, Calcino A, Fahey B, Degnan BM, Degnan SM. 2010. Remarkable consistency of larval supply in the spermcast-mating demosponge Amphimedon queenslandica (Hooper and van Soest). Open Mar Biol J 4, 57-64

Cummins SF, Degnan BM. 2010. Sensory sea slugs: Towards decoding the molecular toolkit required for a mollusc to smell. Comm Int Biol 3, 423-426

Kuanpradit C, Cummins SF, Degnan BM, Sretarugsa P, Hanna PJ, Sobhon P, Chavadej J. 2010 Identification of an attractin-like pheromone in the mucus-secreting hypobranchial gland of the abalone Haliotis asinina Linnaeus. J Shellfish Res 29, 699-704

Koene JM, Sloo W, Montagne-Wajer K, Cummins SF, Degnan BM, Smith JS, Nagle GT, ter Maat A. 2010. Male accessory gland peptide reduces egg laying in simultaneous hermaphrodite. PLoS ONE 5, e10117

2009

Wade NW, Tollenaere A, Hall MR, Degnan BM. 2009. Evolution of a novel carotenoid binding protein responsible for crustacean shell color. Mol Biol Evol 26, 1851–1864

Richards GS, Degnan BM. 2009. The dawn of developmental signaling in the Metazoa. Cold Spring Harb Symp Quant Biol 74, 81-90

Degnan BM, Vervoort M, Larroux C, Richards GS. 2009. Early evolution of metazoan transcription factors. Curr Op Genet Dev Biol 19, 591-599

Cummins SF, Erpenbeck D, Zou Z, Claudianos C, Moroz LL, Nagle GT, Degnan BM. 2009. Candidate chemoreceptor subfamilies differentially expressed in the chemosensory organs of the mollusc. Aplysia. BMC Biol 7, 28

Degnan BM, Adamska M, Craigie A, Degnan SM, Fahey B, Gauthier M, Hooper JNA, Larroux C, Leys SP, Lovas E, Richards GS. 2009. The demosponge Amphimedon queenslandica: reconstructing the ancestral metazoan genome and deciphering the origin of animal multicellularity. In Emerging Model Organisms: A Laboratory Manual, Volume 1. Cold Spring Harbor Laboratory Press, New York, pp 139-166

Williams EA, Degnan BM, Gunter H, Jackson DJ, Woodcroft BJ, Degnan SM. 2009. Widespread transcriptional changes pre-empt the critical pelagic-benthic transition in the vetigastropod Haliotis asinina. Mol Ecol 18, 1006-1025

Tompkins-MacDonald GJ, Gallin WJ, Sakarya O, Degnan B, Leys SP, Boland LM. 2009. Expression of a poriferan potassium channel: insights into the evolution of ion channels in metazoans. J Exp Biol 212, 761-767

Gazave E, Lapébie P, Richards GS, Brunet F, Ereskovsky AV, Degnan BM, Borchiellini C, Vervoort M, Renard E. 2009. Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes. BMC Evol Biol 9, 249

Tiozzo S, Murray M, Degnan BM, De Tomaso AW, Croll RP. 2009. Development of the neuromuscular system during asexual regeneration in a primitive chordate. Dev Dyn 238, 2081-2094

Cummins SF, Leblanc L, Degnan BM, Nagle GT. 2009. Molecular identification of candidate chemoreceptor genes and signal transduction components in the sensory epithelium of Aplysia. J Exp Biol 212, 2037-2044

Robertson AJ, Larroux C, Degnan BM,, Coffman JA. 2009. The evolution of Runx genes II The C-terminal Groucho recruitment motif is present in both eumetazoans and homoscleromorphs but absent in a haplosclerid demosponge. BMC Res Rep 2, 59

Panasophonkul S, Apisawetakan S, Cummins,SF, York PS, Degnan BM, Hanna PJ, Saitongdee P, Sobhon P, Sretarugsa P. 2009. Molecular characterization and analysis of a truncated serotonin receptor gene expressed in neural and reproductive tissues of abalone. Histochem Cell Biol 131, 629-642

Roper KE, Beamish H, Garson MJ, Skilleter GA, Degnan BM. 2009. Convergent antifouling activities from structurally distinct bioactive compounds synthesized within two sympatric Haliclona demosponges. Mar Biotech 11, 188-198

Cummins SF, York PS, Hanna PH, Degnan BM, Croll RP. 2009. Expression of prohormone convertase 2 and the generation of neuropeptides in the developing nervous system of the gastropod Haliotis. Intl J Dev Biol 53, 1081-1088

Marie B, Le Roy N, Marie A, Dubost L, Milet C, Bedouet L, Becchi M, Zanella-Cleon I, Jackson D, Degnan B, Luquet G, Marin F. 2009. Nacre evolution: A proteomic approach. Mat Res Soc Symp Proc 1187, 3-8

2008

Richards GS, Simionato E, Perrron M, Adamska M, Vervoort M, Degnan BM. 2008. Sponge genes provide new insight into the evolutionary origin of the neurogenic circuit. Curr Biol 18, 1156-1161         

Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP. 2008. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455, 1193-1197   

Exposito J-Y, Larroux C, Cluzel C, Valcourt U, Lethias C, Degnan BM. 2008. Demosponge and sea anemone fibrillar collagen diversity reveals the early emergence of A/C clades and the maintenance of the modular structure of type V/XI collagens from sponge to human. J Biol Chem 283, 28226-28235   

Gauthier M, Degnan BM. 2008. Partitioning of genetically distinct cell populations in chimeric juveniles of the sponge Amphimedon queenslandica. Dev Comp Immun 32, 1270-1280

Larroux C, Luke GN, Koopman P, Rokhsar DS, Shimeld SM , Degnan BM. 2008. Genesis and expansion of metazoan transcription factor gene classes. Mol Biol Evol 25, 980-996       

Fahey B, Larroux C, Woodcroft BJ, Degnan BM. 2008. Does the high gene density in the sponge NK homeobox gene cluster reflect limited regulatory capacity? Biol Bull 214, 205-217

Gauthier M, Degnan BM. 2008. The transcription factor NF-κB in the sponge Amphimedon queenslandica: insights into the evolutionary origin of the Rel homology domain. Dev Genes Evol 218, 23-32

Gostling NJ, Thomas C, Greenwood JM, Dong X, Bengtson S, Raff EC, Raff RA, Degnan BM, Stampanoni M, Donoghue PCJ. 2008. Deciphering the fossil record of early bilaterian embryonic development in light of experimental taphonomy. Evol Dev 10, 339-349

Kvennefors ECE, Leggat W, Hoegh-Guldberg O, Degnan BM, Barnes AC. 2008. An ancient and variable mannose binding lectin from the coral Acropora millepora binds both pathogens and symbionts. Dev Comp Immun 32, 1582-1592

Gunter HM, Degnan BM. 2008. The impact of ecologically relevant heat shocks on Hsp developmental function in the vetigastropod Haliotis asinina. J Exp Zool B (Mol Dev Evol) 310, 450–464

Jacobs MW, Degnan BM, Bishop JDD, Strathmann RR. 2008. Early activation of adult organ differentiation during delay of metamorphosis in solitary ascidians, and consequences for juvenile growth. Invert Biol 127, 217-236

Wade N, Melville-Smith R, Degnan BM, Hall MR. 2008. Control of shell colour changes in the lobster, Panulirus cygnus. J Exp Biol 211, 1512-1519

Cummins SF, Degnan BM, Nagle GT. 2008. Characterization of Aplysia Alb-1, a candidate water-borne protein pheromone released during egg laying. Peptides 29, 152-161

Walker SJ, Degnan BM, Hooper JNA, Skilleter GA. 2008. Will increased storm disturbance affect the biodiversity of intertidal, non-scleractinian sessile fauna on coral reefs? Global Change Biol 14, 2755–2770

Leys SP, Larroux C, Gauthier M, Adamska, M, Fahey B, Richards GS, Degnan SM, Degnan BM. 2008. Isolation of Amphimedon developmental material. Cold Spring Harb Protoc doi: 101101/pdbprot5095

Larroux C, Fahey B, Adamska M, Richards GS, Gauthier M, Green K, Lovas E, Degnan BM. 2008. Whole-mount in situ hybridization in Amphimedon. Cold Spring Harb Protoc doi: 101101/pdbprot5096

Adamska M, Degnan BM. 2008. Analysis of cell movement in Amphimedon embryos by injection of fluorescent tracers. Cold Spring Harb Protoc doi: 101101/pdbprot5097

Degnan SM, Craigie A, Degnan, BM. 2008. Genotyping individual Amphimedon embryos, larvae, and adults. Cold Spring Harb Protoc doi: 101101/pdbprot5098

Wanninger A, Koop D, Moshel-Lynch S, Degnan BM. 2008. Molluscan evolutionary development. In The Evolution and Phylogeny of the Mollusca (eds D Lindberg and W Ponder) University of California Press, pp 427-445

2007

Larroux C, Fahey B, Degnan SM, Adamski M, Rokhsar DS, Degnan BM. 2007. The NK homeobox gene cluster predates the origin of Hox genes. Curr Biol 17, 706-710

Adamska M, Degnan SM, Green KM, Adamski M, Craigie A, Larroux C, Degnan BM. 2007. Wnt and TGF-β expression in the sponge Amphimedon queenslandica and the origin of metazoan embryonic patterning. PLoS ONE 2, e1031

Jackson DJ, Macis L, Reitner J, Degnan BM, Wörheide G. 2007. Sponge paleogenomics reveals an ancient role for carbonic anhydrase in skeletogenesis. Science 316, 1893-1895

Adamska M, Matus DQ, Adamski M, Green KM, Rokhsar DS, Martindale MQ, Degnan BM. 2007. The evolutionary origin of hedgehog proteins.  Curr Biol 17, R836-837

Sakarya O, Armstrong KA, Adamska M, Adamski M, Wang I-F, Sachdu D, Tidor B, Degnan BM, Oakley T, Kosik KS. 2007. A post-synaptic scaffold at the origin of the animal kingdom. PLoS ONE 2, e506          

Simionato E, Ledent V, Richards G, Thomas-Chollier M, Kerner P, Coornaert D, Degnan BM, Vervoort M. 2007. Origin and diversification of the basic helix-Loop-helix gene family in metazoans: insights from comparative genomics. BMC Evol Biol 7, 33

Imron, Jefferey B, Hale P, Degnan BM, Degnan SM. 2007. Pleistocene isolation and recent gene flow in Haliotis asinina, an Indo-Pacific vetigastropod with limited dispersal capacity and specific settlement requirements. Mol Ecol 16, 289-304

Erpenbeck D, Voigt O, Adamski M, Adamska M, Hooper JNA, Wörheide G,, Degnan BM. 2007. Mitochondrial diversity of early branching Metazoa is revealed by the complete mt genome of a haplosclerid demosponge. Mol Biol Evol 24, 19-22

Koop D, Richards G, Wanninger A, Gunter H, Degnan BM. 2007. The role of MAPK signalling in patterning and establishing axial symmetry in the gastropod Haliotis asinina. Dev Biol 311, 200-212

Plachetzki DC, Degnan BM, Oakley TH. 2007. The origins of novel protein interactions during animal opsin evolution. PLoS ONE 2, e1054

Jackson DJ, Wörheide G, Degnan BM. 2007. Dynamic expression of ancient and novel molluscan shell genes during ecological transitions. BMC Evol Biol 7, 160

Gunter HM, Degnan BM. 2007. Developmental expression of Hsp90, Hsp70 and HSF during morphogenesis in the vetigastropod Haliotis asininaDev Genes Evol 217, 603-612

Erpenbeck D, Nichols SA, Voigt O, Dohrmann M, Degnan BM, Hooper JNA, Wörheide G. 2007. Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches - case studies with diploblast LSU. J Mol Evol 64, 543-557

Cummins SF, Xie F, de Vries MR, Annangudi SP, Misra M, Degnan BM, Sweedler JV, Nagle GT, Schein CH. 2007. Aplysia temptin: the “glue” in the water-borne attractin pheromone complex. FEBS J 274, 5425-5437

Sellars MJ, Lyons RE, Grewe PM, Vuocolo T, Leeton L, Coman GJ, Degnan BM, Preston NP. 2007. A PL10 vasa-like gene in the Kuruma shrimp Marsupenaeus japonicus (Bate) is expressed during development in the adult gonad. Mar Biotech 9, 377-387

de la Vega E, Hall MR, Wilson KJ, Reverter A, Woods RG, Degnan BM. 2007. Stress-induced gene expression profiling in the black tiger shrimp Penaeus monodon. Physiol Genomics 19, 126-138

Sellars, MJ, Vuocolo, T, Leeton, L, Coman, GJ, Degnan, BM, Preston, NP. 2007. Real time RT‑PCR quantification of Kuruma shrimp transcripts: A comparison of relative and absolute quantification procedure. J Biotechnol 129, 391-399

de la Vega, E, Degnan, BM, Hall, MR, Wilson, KJ. 2007. Differential expression of immune-related genes and transposable elements in black tiger shrimp (Penaeus monodon) exposed to a range of environmental stressors. Fish Shellfish Immun 23, 1072-1088

Erpenbeck D, Hooper JNA, List-Armitage SE, Degnan, BM, Wörheide G, van Soest RWM. 2007. Affinities of the family Sollasellidae (Porifera, Demospongiae) II Molecular evidence. Contrib Zool 76, 95-102

Sellars MJ, Coman GJ, Callaghan, TR, Arnold SJ, Wakeling J, Degnan BM, Preston NP. 2007. The effect of ionizing irradiation of post-larvae on subsequent survival and reproductive performance in the Kuruma shrimp, Marsupenaeus japonicus (Bate). Aquaculture 264, 309–322

Erpenbeck, D, List-Armitage S, de Glasby BA, Degnan BM, Wörheide G, Hooper NA. 2007. The systematics of Raspailiidae (Demospongiae, Poecilosclerida, Microcionina) reanalysed with a ribosomal marker. J Mar Biol Assoc UK 87, 1571-1576

Erpenbeck D, Cleary DFR, Voigt O, Nichols SA, Degnan BM Hooper JNA, Wörheide G. 2007. Analysis of evolutionary, biogeographical and taxonomic patterns of nucleotide composition in demosponge rRNA. J Mar Biol Assoc UK 87, 1607-1614

2006

Larroux C, Fahey B, Liubicich D, Hinman VF, Gongora M, Green KM, Wörheide G, Leys SP, Degnan BM. 2006. Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity. Evol Dev 8, 150-173

Jackson DJ, McDougall C, Green KM, Simpson F, Wörheide G, Degnan BM. 2006. Ancient and novel secretome builds and patterns a sea shell. BMC Biol 4, e40

Degnan SM, Degnan BM. 2006. The origin of the pelagobenthic metazoan life cycle: what’s sex got to do with it? Integr Comp Biol 46, 683-690

Degnan SM, Imron, Geiger DL, Degnan BM. 2006. Evolution in temperate and tropical seas: disparate patterns in southern hemisphere abalone (Mollusca: Vetigastropoda: Haliotidae). Mol Phylogen Evol 41, 249-256

Jacobs MW, Degnan SM, Woods R, Williams E, Roper K, Green K, Degnan BM. 2006. The effect of larval age on morphology and gene expression during ascidian metamorphosis.  Integr Comp Biol 46, 760-776

Lucas T, Macbeth M, Degnan SM, Knibb W, Degnan BM. 2006. Heritability estimates for growth in the tropical abalone Haliotis asinina using microsatellites to assign parentage. Aquaculture 259, 146-152

Rice T, McGraw E, O’Brien EK, Reverter A, Jackson, DJ, Degnan BM.  2006. Parasitic castration by the digenian trematode Allopodocotyle sp alters gene expression in the brain of the host mollusc Haliotis asinina. FEBS Lett 580, 3769-3774

Sellars MJ, Degnan BM, Preston NP. 2006. Production of triploid Kuruma shrimp, Marsupenaeus (Penaeus) japonicus (Bate) nauplii through inhibition of polar body I or polar body I and II extrusion using 6-Dimethylaminopurine. Aquaculture 256, 337-345

de la Vega E, Degnan BM, Hall MR, Cowley JA, Wilson KJ. 2006. Short-term hyperthermic treatment of Penaeus monodon increases expression of heat shock protein 70 (HSP70) and reduces replication of gill associated virus (GAV). Aquaculture 253, 82-90

Jackson DJ, Degnan BM. 2006. Expressed sequence tag analysis of genes expressed during development of the tropical abalone Haliotis asinina. J Shellfish Res 25, 225-232

Sellars, MJ, Coman FE, Degnan BM, Preston NP. 2006. The effectiveness of 6‑dimethylaminopurine, heat and cold shocks for inducing tetraploidy in the Kuruma Shrimp, Penaeus (Marsupenaeus) japonicus (Bate). J Shellfish Res 25, 631-638

2005

Degnan BM, Leys SP, Larroux C. 2005. Sponge development and antiquity of animal pattern formation. Integr Comp Biol 45, 335-341

Leys SP, Rokhsar DS, Degnan BM. 2005. Sponges. Curr Biol 15, R114-R115

Wanninger A, Koop D, Degnan BM. 2005. Immunocytochemistry and metamorphic fate of the larval nervous system of Triphyllozoon mucronatum (Ectoprocta: Gymnolaemata: Cheilostomata). Zoomorph 124, 161-170

Wanninger A, Koop D, Bromham L, Noonan E, Degnan BM.  2005. Nervous and muscle system development in Phascolion strombus (Sipuncula). Dev Genes Evol 215, 509-518

Jackson DJ, Ellemor N, Degnan BM. 2005. Correlating gene expression with larval competence and the effect of larval age and parentage on rates of metamorphosis in the tropical abalone Haliotis asinina. Mar Biol 147, 681-697

Lucas T, O'Brien EK, Cribb, T, Degnan BM. 2005. Digenean trematodes infecting the tropical abalone Haliotis asinina have species-specific cercarial emergence patterns that follow daily or semilunar spawning cycles. Mar Biol 148, 285-292

Streit K, Jackson D, Degnan BM, Lieb B. 2005. Developmental expression pattern of the two Haliotis asinina hemocyanin isoforms HasH1 and HasH2. Differentiation 73, 341-349

Sellars, MJ, Degnan BM, Carrington LE, Preston NP. 2005. The effects of ionizing irradiation on the reproductive capacity of adult Penaeus (Maruspenaeus) japonicus (Bate). Aquaculture 250, 194-200

Wade N, Goulter KC, Wilson KJ, Hall MR, Degnan BM. 2005. Esterified astaxanthin levels in lobster epithelia correlate with shell colour intensity: potential role in crustacean shell colour formation. Comp Biochem Phys B 141, 307-313

Skilleter GA, Russell, BD, Degnan BM, Garson MJ. 2005. Living in a toxic environment:  comparisons of endofauna in two congeneric sponges. Mar Ecol Prog Ser 304, 67-75

2004

Campbell RK, Satoh N, Degnan BM.  2004. Piecing together evolution of the vertebrate endocrine system. Trends Genet 20, 359-366

Woods RG, Roper K, Gauthier M, Bebell L, Sung, K, Lavin MF, Degnan BM.  2004. Gene expression during early ascidian metamorphosis requires signaling by Hemps, an EGF-like protein. Development 131, 2921-2933

de la Vega E, Degnan BM, Hall MR, Cowley JA, Wilson KJ. 2004. Quantitative real-time RT-PCR Assay for GAV demonstrates that handling stress leads to rapid increases in viral titre in Penaeus monodon. Dis Aqua Org 59, 195-203

2003

Hinman VF, O'Brien EK, Richards GS, Degnan BM. 2003. Expression of anterior Hox genes in larvae of the gastropod Haliotis asinina. Evol Dev 5, 508-521

Yagi K, Satou Y, Mazet F, Shimeld SM, Degnan B, Rokhsar D, Levine M, Kohara Y, Satoh N. 2003. A genomewide survey of developmental genes in Ciona intestinalis: III Genes for Fox, ETS, nuclear receptors and NF- kB. Dev Genes Evol 213, 235-244

Yamada L, Kobayashi K, Degnan B, Satoh N, Satou Y. 2003. A genomewide survey of developmental genes in Ciona intestinalis: IV Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail. Dev Genes Evol 213, 245-253

Satou Y Sasakura Y, Yamada L, Imai KS Satoh N, Degnan B. 2003. A genomewide survey of developmentally relevant genes in Ciona intestinalis: V Genes for receptor tyrosine kinase pathway and Notch signaling pathway. Dev Genes Evol 213, 254-263

O’Brien EK, Degnan BM. 2003. Expression of Pax258 in the gastropod statocyst: insights into the antiquity of metazoan geosensory organs.  Evol Dev 5, 572-578

Wörheide G, Degnan BM, Hooper JNA, Reitner J. 2003. Phylogeography and taxonomy of the Indo-Pacific reef cave dwelling coralline demosponge Astrosclera 'willeyana' - new data from nuclear internal transcribed spacer sequences. Proc 9th Int Coral Reef Sym 1, 339-346

Russell BD, Degnan BM, Garson MJ, Skilleter GA. 2003. Distribution of a nematocyst-bearing sponge in relation to potential coral donors. Coral Reefs 22, 11-16

2002

Dehal P, Satou Y, Campbell, RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein D, Harafuji N, Hastings K, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang H, Awazu S, Azumi K, Boore J, Branno M, Chin-bow S, DeSantis R, Doyle S, Francino P, Keys D, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee B, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita, T, Miura S, Nakayama,A, Nishizaka S, Nomoto,H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Sin-I T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar D. 2002. The draft genome sequence of the ascidian Ciona intestinalis: insights into the evolutionary origins of chordates and vertebrates. Science 298, 2157-2167

O’Brien EK, Degnan BM. 2002. Pleiotropic developmental expression of HasPOUIII, a class III POU gene, in the gastropod Haliotis asinina. Mech Dev 114, 129-132

Wörheide G, Hooper JNA, Degnan BM. 2002. Phylogeography of western Pacific Leucetta ‘chagosensis’ (Porifera: Calcarea) from ribosomal DNA sequences: implications for population history and conservation of the Great Barrier Reef World Heritage Area (Australia). Mol Ecol 11, 1753-1768

O’Brien E, Degnan BM. 2002. Developmental expression of a class IV POU gene in the gastropod Haliotis asinina supports a conserved role in sensory cell development in bilaterians. Dev Genes Evol 212, 394-398

Leys SP, Degnan BM. 2002. Embryogenesis and metamorphosis in a haplosclerid demosponge: gastrulation and transdifferentiation of larval ciliated cells to choanocytes. Invert Biol 121, 171-189

Hinman VF, Degnan BM. 2002. Mox homeobox expression in muscle lineage of the gastropod Haliotis asinina: evidence for a conserved role in bilaterian myogenesis. Dev Genes Evol 212, 141-144

Jackson D, Leys SP, Hinman VF, Woods R, Lavin MF, Degnan BM. 2002. Ecological regulation of development: induction of marine invertebrate metamorphosis. Int J Dev Biol 46, 679-686

Devine C Hinman VF, Degnan BM. 2002. Evolution and developmental expression of nuclear receptor genes in the ascidian Herdmania. Intl J Dev Biol 46, 687-692

Leys SP, Cronin TW, Degnan BM, Marshall JN. 2002. Spectral sensitivity in a sponge larva. J Comp Physiol A 188, 199-202

Green KM, Russell BD, Clark RJ, Jones MK, Garson MJ, Skilleter, GA, Degnan BM. 2002. Sponge allelochemical induces ascidian settlement but inhibits metamorphosis.  Mar Biol 140, 355-363

Wang S, Duncan PF, Knibb W, Degnan BM. 2002. Byssal attachment and movement of Amusium balloti (Bivalvia: Pectinidae) spat. J Shellfish Res 21, 563-569

2001

Leys SP, Degnan BM. 2001. The cytological basis of photoresponsive behavior in a sponge larva.  Biol Bull 201, 323-338

Counihan RT, McNamara DC, Souter DC, Jebreen EJ, Preston NP, Johnson CR, Degnan BM. 2001. Pattern, synchrony and predictability of spawning of the tropical abalone Haliotis asinina from Heron Reef, Australia. Mar Ecol Prog Ser 213, 193-202

Hinman VF, Degnan BM. 2001. Homeobox genes, retinoic acid and the development and evolution of dual body plans in the ascidian Herdmania curvataAmer Zool 41, 664-675

Selvamani MJP, Degnan SM, Degnan BM. 2001. Microsatellite genotyping of individual abalone larvae: parentage assignment in aquaculture. Marine Biotech 3, 478-485

Degnan BM. 2001. Settlement and metamorphosis of the ascidian Herdmania curvata. In Biology of Ascidians (eds CC Lambert, H Yokosawa and H Sawada) Springer-Verlag, Tokyo, pp 258-263

Jackson D, Williams K, Degnan BM. 2001.  Suitability of Australian formulated diets for the aquaculture of the tropical abalone Haliotis asinina Linneus.  J Shellfish Res 20, 627-636

2000

Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G. 2000. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408, 86-89.

Hinman VF, Degnan BM. 2000. Retinoic acid perturbs Otx gene expression in the ascidian pharynx. Dev Genes Evol 210, 129-139

Giusti AF, Hinman, VF, Degnan SM, Degnan BM, Morse DE. 2000. Expression of a Hox5 gene in the larval central nervous system of the gastropod Haliotis, a non-segmented spiralian lophotrochozoan. Evol Dev 2, 294-302

Hinman VF, Becker E, Degnan BM. 2000. Neuroectodermal and endodermal expression of the ascidian Cdx gene is separated by metamorphosis. Dev Genes Evol 210, 212-216

O’Brien EK, Degnan BM. 2000. Pax, POU and Sox genes are expressed in the ganglia of the tropical abalone Haliotis asininaMarine Biotech 2, 545-557

Selvamani MJP, Degnan SM, Paetkau D, Degnan BM. 2000. High polymorphisms in microsatellite loci in the Heron Reef population of the tropical abalone Haliotis asinina. Mol Ecol 9, 1184-1185

Tan SW, Degnan BM, Lehnert S. 2000. The Penaeus monodon Chitinase 1 gene is differentially expressed in the hepatopancreas during the molt cycle. Marine Biotech 2, 126-135

Jebreen EJ, Counihan RT, Fielder DT, Degnan BM. 2000. Synchronous oogenesis during the semilunar spawning cycle of the tropical abalone Haliotis asinina. J Shellfish Res 19, 845-852

pre2000 – select representative papers

Bromham LD, Degnan BM. 1999. Hemichordates and deuterostome evolution: robust molecular phylogenetic support for a hemichordate+echinoderm clade. Evol Dev 1, 166-171

Eri R, Arnold JM, Hinman VF, Green KM, Jones,MK, Degnan BM, Lavin MF. 1999.  Hemps, a novel EGF-like protein, plays a central role in ascidian metamorphosis. Development 126, 5809-5818

Degnan BM, Johnson CR. 1999. Inhibition of settlement and metamorphosis of the ascidian Herdmania curvata by non-geniculate coralline algae. Biol Bull 197, 332-340

Hinman VF, Degnan BM. 1998. Retinoic acid disrupts ectodermal and endodermal development in ascidian larvae and postlarvae. Dev Genes Evol 208, 336-345

Degnan BM, Souter D, Degnan SM, Long SC. 1997. Induction of metamorphosis in larvae of the ascidian Herdmania momus with potassium ions requires attainment of competence and an anterior signalling center. Dev Genes Evol 206, 370-376

Degnan BM, Degnan SM, Giusti A, Morse DE. 1995. A Hox/HOM homeobox gene in sponges. Gene 156, 175-178

Degnan BM, Morse DE. 1995. Developmental and morphogenetic gene regulation in Haliotis rufescens larvae at metamorphosis Amer Zool 35, 391-398

Degnan BM, Groppe JC, Morse DE. 1995. Chymotrypsin mRNA expression in digestive gland amoebocytes: cell specification occurs prior to metamorphosis and gut morphogenesis in the gastropod Haliotis rufescens. Roux's Arch Dev Biol 205, 97-101

Degnan BM, Degnan SM, Naganuma T, Morse DE. 1993. The ets multigene family is conserved throughout the Metazoa. Nucleic Acids Res 21, 3479-3484

Degnan BM, Morse, DE. 1993. Identification of eight homeobox-containing transcripts expressed during larval development and at metamorphosis in the gastropod mollusc Haliotis rufescens. Mol Mar Biol Biotech 2, 1-9

Degnan BM, Yan J, Hawkins CJ, Lavin MF. 1990. rRNA genes from the lower chordate Herdmania momus; structural similarity with higher eukaryotes. Nucleic Acids Res 18, 7063-7070