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Department of Invertebrate Zoology

Image of "stalked jellyfish"

This "stalked jellyfish" lives on marine algae off the coast of California and represents a new species of Stauromedusae, Haliclystus californiensis Kahn et al., 2010 (Holotype USNM 1106657; Paratypes USNM 1139484, 1139485, 1106654).

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Allen G. Collins Zoologist, NMFS, NOAA
National Systematics Lab


Miranda, Lucilia S., Branch, George M., Collins, Allen Gilbert, Hirano, Yayoi M., Marques, Antonio C. and Griffiths, Charles L. 2017. Stalked jellyfishes (Cnidaria: Staurozoa) of South Africa, with the description of Calvadosia lewisi sp nov.. Zootaxa, 4227(3): 369-389. doi:10.11646/zootaxa.4227.3.5

Miranda, Lucília S., Mills, Claudia E., Hirano, Yayoi M., Collins, Allen G. and Marques, Antonio C. 2017. A review of the global diversity and natural history of stalked jellyfishes (Cnidaria, Staurozoa). Marine Biodiversity, doi:10.1007/s12526-017-0721-4

Lindsay, Dhugal John, Grossmann, Mary Matilda, Bentlage, Bastian, Collins, Allen Gilbert, Minemizu, Ryo, Hopcroft, Russell Ross, Miyake, Hiroshi, Hidaka-Umetsu, Mitsuko and Nishikawa, Jun 2017. The perils of online biogeographic databases: a case study with the 'monospecific' genus Aegina (Cnidaria, Hydrozoa, Narcomedusae). Marine Biology Research, : 1-19. doi:10.1080/17451000.2016.1268261

Miranda, Lucília S., García-Rodríguez, Jimena, Collins, Allen G., Morandini, André C. and Marques, Antonio C. 2017. Evolution of the claustrum in Cnidaria: comparative anatomy reveals that it is exclusive to some species of Staurozoa and absent in Cubozoa. Organisms Diversity & Evolution, doi:10.1007/s13127-017-0342-6

Goodheart, Jessica A., Bazinet, Adam L., Valdés, Ángel, Collins, Allen G. and Cummings, Michael P. 2017. Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia). BMC Evolutionary Biology, 17(1): 221 doi:10.1186/s12862-017-1066-0

Bayha, Keith M., Collins, Allen G. and Gaffney, Patrick M. 2017. Multigene phylogeny of the scyphozoan jellyfish family Pelagiidae reveals that the common U.S. Atlantic sea nettle comprises two distinct species (Chrysaora quinquecirrha and C. chesapeakei). PeerJ, 5 doi:10.7717/peerj.3863

Ames, Cheryl L., Ryan, Joseph F., Bely, Alexandra E., Cartwright, Paulyn and Collins, Allen Gilbert. 2016. [Dataset:] Supplemental Information for A new transcriptome and transcriptome profiling of adult and larval tissue in the box jellyfish Alatina alata: an emerging model for studying venom, vision and sex.. : .

Ames, Cheryl Lewis, Ryan, Joseph F., Bely, Alexandra E., Cartwright, Paulyn and Collins, Allen Gilbert 2016. Erratum to: A new transcriptome and transcriptome profiling of adult and larval tissue in the box jellyfish Alatina alata: an emerging model for studying venom, vision and sex. BMC Genomics, 17(1): 980 doi:10.1186/s12864-016-3305-y

Lawley, Jonathan W., Ames, Cheryl Lewis, Bentlage, Bastian, Yanagihara, Angel, Goodwill, Roger, Kayal, Ehsan, Hurwitz, Kikiana and Collins, Allen Gilbert 2016. Box Jellyfish Alatina alata Has a Circumtropical Distribution. The Biological bulletin, 231(2): 152-169. doi:10.1086/690095

Miranda, Lucília S., Hirano, Yayoi M., Mills, Claudia E., Falconer, Audrey, Fenwick, David, Marques, Antonio C. and Collins, Allen Gilbert 2016. Systematics of stalked jellyfishes (Cnidaria: Staurozoa). PeerJ, 4 doi:10.7717/peerj.1951

Kayal, Ehsan, Bentlage, Bastian and Collins, Allen Gilbert 2016. Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa). RNA biology, 13(9): 799-809. doi:10.1080/15476286.2016.1194161

Pyataeva, Sofia V., Hopcroft, Russell R., Lindsay, Dhugal J. and Collins, Allen Gilbert 2016. DNA barcodes unite two problematic taxa: the meiobenthic Boreohydra simplex is a life-cycle stage of Plotocnide borealis (Hydrozoa: Aplanulata). Zootaxa, 4150(1): 85-92. doi:10.11646/zootaxa.4150.1.5

Lasley, Robert M., Ames, Cheryl Lewis, Erdman, Robert, Parks, Sheri and Collins, Allen Gilbert 2016. First record of the box jellyfish Tripedalia cystophora (Cnidaria: Cubozoa: Tripedaliidae) in the Gulf of Mexico. Proceedings of the Biological Society of Washington, 129(1): 164-172. doi:10.2988/0006-324X-129.Q2.164

Ames, Cheryl Lewis, Ryan, Joseph F., Bely, Alexandra E., Cartwright, Paulyn and Collins, Allen Gilbert 2016. A new transcriptome and transcriptome profiling of adult and larval tissue in the box jellyfish Alatina alata: an emerging model for studying venom, vision and sex. BMC Genomics, 17(1): 650 doi:10.1186/s12864-016-2944-3

Lindsay, Dhugal J., Grossmann, Mary M., Nishikawa, Jun, Bentlage, Bastian and Collins, Allen Gilbert 2015. DNA Barcoding of Pelagic Cnidarians: Current Status and Future Prospects. Bulletin- Plankton Society of Japan, 62(1): 39-43.

Miranda, L. S., Collins, Allen Gilbert and Marques, A. C. 2015. Is Haootia quadriformis related to extant Staurozoa (Cnidaria)? Evidence from the muscular system reconsidered. Proceedings of the Royal Society B: Biological Sciences, 282(1803) doi:10.1098/rspb.2014.2396

Goodheart, Jessica A., Bazinet, Adam L., Collins, Allen Gilbert and Cummings, Michael P. 2015. Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation. Royal Society Open Science, 2(9): 150196 doi:10.1098/rsos.150196

Zapata, Felipe, Goetz, Freya E., Smith, Stephen A., Howison, Mark, Siebert, Stefan, Church, Samuel H., Sanders, Steven M., Ames, Cheryl Lewis, McFadden, Catherine S., France, Scott C., Daly, Marymegan, Collins, Allen Gilbert, Haddock, Steven H. D., Dunn, Casey W. and Cartwright, Paulyn 2015. Phylogenomic Analyses Support Traditional Relationships within Cnidaria. PloS One, 10(10) doi:10.1371/journal.pone.0139068

Kayal, Ehsan, Bentlage, Bastian, Cartwright, Paulyn, Yanagihara, Angel A., Lindsay, Dhugal J., Hopcroft, Russell R. and Collins, Allen Gilbert 2015. Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription. PeerJ, 3 doi:10.7717/peerj.1403

Bracken-Grissom, Heather, Collins, Allen Gilbert, Collins, Timothy, Crandall, Keith, Distel, Daniel, Dunn, Casey, Giribet, Gonzalo, Haddock, Steven, Knowlton, Nancy, Martindale, Mark, Medina, Monica, Messing, Charles, O'Brien, Stephen J., Paulay, Gustav, Putnam, Nicolas, Ravasi, Timothy, Rouse, Greg W., Ryan, Joseph F., Schulze, Anja, Worheide, Gert, Adamska, Maja, Bailly, Xavier, Breinholt, Jesse, Browne, William E., Diaz, M. Christina, et al 2014. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. Journal of Heredity, 105(1): 1-18. doi:10.1093/jhered/est084

Rocha, L. A., Aleixo, A., Allen, G., Almeda, F., Baldwin, Carole C., Barclay, M. V. L., Bates, J. M., Bauer, A. M., Benzoni, F., Berns, C. M., Berumen, M. L., Blackburn, D. C., Blum, S., Bolanos, F., Bowie, R. C. K., Britz, R., Brown, R. M., Cadena, C. D., Carpenter, K., Ceriaco, L. M., Chakrabarty, P., Chaves, G., Choat, J. H., Clements, K. D., Collette, Bruce B., et al 2014. Specimen collection: An essential tool. Science, 344(6186): 814-815. doi:10.1126/science.344.6186.814

Grossmann, Mary M., Collins, Allen Gilbert and Lindsay, Dhugal J. 2014. Description of the eudoxid stages of Lensia havock and Lensia leloupi (Cnidaria: Siphonophora: Calycophorae), with a review of all known Lensia eudoxid bracts. Systematics and Biodiversity, 12(2): 163-180. doi:10.1080/14772000.2014.902867

Kayal, Ehsan, Roure, Béatrice, Philippe, Hervé, Collins, Allen Gilbert and Lavrov, Dennis V. 2013. Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evolutionary Biology, 13: 5 doi:10.1186/1471-2148-13-5

Marques, Antonio C., Maronna, Maximiliano M. and Collins, Allen Gilbert 2013. Putting GenBank Data on the Map. Science, 341(6152): 1341 doi:10.1126/science.341.6152.1341-a

Lewis, Cheryl, Bentlage, Bastian, Yanagihara, Angel, Gillan, William, Blerk, Johan Van, Keil, Daniel P., Bely, Alexandra E. and Collins, Allen Gilbert 2013. Redescription of Alatina alata (Reynaud, 1830) (Cnidaria: Cubozoa) from Bonaire, Dutch Caribbean. Zootaxa, 3737(4): 473-487. doi:10.11646/zootaxa.3737.4.8

Nawrocki, Annalise M., Collins, Allen Gilbert, Hirano, Yayoi M., Schuchert, Peter and Cartwright, Paulyn 2013. Phylogenetic placement of Hydra and relationships within Aplanulata (Cnidaria: Hydrozoa). Molecular phylogenetics and evolution, 67(1): 60-71. doi:10.1016/j.ympev.2012.12.016

Hill, Malcolm S., Hill, April L., Lopez, Jose, Peterson, Kevin J., Pomponi, Shirley, Diaz, Maria C., Thacker, Robert W., Adamska, Maja, Boury-Esnault, Nicole, Cárdenas, Paco, Chaves-Fonnegra, Andia, Danka, Elizabeth, De Laine, Bre-Onna, Formica, Dawn, Hajdu, Eduardo, Lobo-Hajdu, Gisele, Klontz, Sarah, Morrow, Christine C., Patel, Jignasa, Picton, Bernard, Pisani, Davide, Pohlmann, Deborah, Redmond, Niamh E., Reed, John, Richey, Stacy, et al 2013. Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes. PLoS ONE, 8(1): e50437 doi:10.1371/journal.pone.0050437

Diaz, Maria C., Thacker, Robert W., Redmond, Niamh E., Matterson, Kenan O. and Collins, Allen Gilbert 2013. Phylogenetic Novelties and Geographic Anomalies among Tropical Verongida. Integrative & Comparative Biology, 53(3): 482-494. doi:10.1093/icb/ict033

Klautau, Michelle, Azevedo, Fernanda, Cóndor-Luján, Báslavi, Rapp, Hans Tore, Collins, Allen Gilbert and Russo, Claudia A. 2013. A molecular phylogeny for the order Clathrinida rekindles and refines Haeckel's taxonomic proposal for calcareous sponges. Integrative & Comparative Biology, 53(3): 447-461. doi:10.1093/icb/ict039

Thacker, Robert W., Hill, April L., Hill, Malcom S., Redmond, Niamh E., Collins, Allen Gilbert, Morrow, Christine C., Spicer, Lori, Carmack, Cheryl A., Zappe, Megan E., Pohlmann, Deborah, Hall, Chelsea, Diaz, Maria C. and Bangalore, PurushothamV 2013. Nearly Complete 28S rRNA Gene Sequences Confirm New Hypotheses of Sponge Evolution. Integrative & Comparative Biology, 53(3): 373-387. doi:10.1093/icb/ict071

Morrow, Christine C., Redmond, Niamh E., Picton, Bernard E., Thacker, Robert W., Collins, Allen Gilbert, Maggs, Christine A., Sigwart, Julia D. and Allcock, A. Louise 2013. Molecular Phylogenies Support Homoplasy of Multiple Morphological Characters Used in the Taxonomy of Heteroscleromorpha (Porifera: Demospongiae). Integrative & Comparative Biology, 53(3): 428-446. doi:10.1093/icb/ict065

Redmond, Niamh E., Morrow, Christine C., Thacker, Robert W., Diaz, Maria C., Boury-Esnault, N., Cárdenas, P., Hajdu, E., Lôbo-Hajdu, G., Picton, B. E., Pomponi, S. A., Kayal, E. and Collins, Allen Gilbert 2013. Phylogeny and Systematics of Demospongiae in Light of New Small-Subunit Ribosomal DNA (18S) Sequences. Integrative & Comparative Biology, 53(3): 388-415. doi:10.1093/icb/ict078

Hajdu, Eduardo, de Paula, Thiago S., Redmond, Niamh E., Cosme, Bruno, Collins, Allen Gilbert and Lôbo-Hajdu, Gisele 2013. Mycalina: Another Crack in the Poecilosclerida Framework. Integrative and Comparative Biology, 53(3): 462-472. doi:10.1093/icb/ict074

Harrison, Genelle F., Kim, Kiho and Collins, Allen Gilbert 2013. Low genetic diversity of the putatively introduced, brackish water hydrozoan, Blackfordia virginica (Leptothecata: Blackfordiidae), throughout the United States, with a new record for Lake Pontchartrain, Louisiana. Proceedings of the Biological Society of Washington, 126(2): 91-102. doi:10.2988/0006-324X-126.2.91

Grossmann, Mary M., Lindsay, Dhugal J. and Collins, Allen G. 2013. The end of an enigmatic taxon: Eudoxia macra is the eudoxid stage of Lensia cossack (Siphonophora, Cnidaria). Systematics and Biodiversity, 11(3): 381-387. doi:10.1080/14772000.2013.825658

Dohrmann, Martin, Vargas, Sergio, Janussen, Dorte, Collins, Allen Gilbert and Wörheide, Gert 2012. Molecular paleobiology of early-branching animals: integrating DNA and fossils elucidates the evolutionary history of hexactinellid sponges. Paleobiology, 39(1): 95-108. doi:10.1666/0094-8373-39.1.95

Kayal, Ehsan, Bentlage, Bastian, Collins, Allen Gilbert, Kayal, Mohsen, Pirro, Stacy and Lavrov, Dennis V. 2012. Evolution of Linear Mitochondrial Genomes in Medusozoan Cnidarians. Genome Biology and Evolution, 4(1): 1-12. doi:10.1093/gbe/evr123

Smith, David Roy, Kayal, Ehsan, Yanagihara, Angel A., Collins, Allen Gilbert, Pirro, Stacy and Keeling, Patrick J. 2012. First Complete Mitochondrial Genome Sequence from a Box Jellyfish Reveals a Highly Fragmented Linear Architecture and Insights into Telomere Evolution. Genome Biology and Evolution, 4(1): 52-58. doi:10.1093/gbe/evr127

Weigt, Lee A., Driskell, Amy C., Ormos, Andrea, Meyer, Christopher P. and Collins, Allen Gilbert 2012. Introduction to animal DNA barcoding protocols. In: DNA Barcodes: Methods and Protocols. : ,(Methods in molecular biology) pp.11-16.

Lewis, Cheryl, Migita, Masao, Hashimoto, Hiroshi and Collins, Allen Gilbert 2012. On the occurrence of freshwater jellyfish in Japan 1928-2011: eighty-three years of records of mamizu kurage (Limnomedusae, Olindiidae). Proceedings of the Biological Society of Washington, 125(2): 165-179. doi:10.2988/11-31.1

Appeltans, Ward, Ahyong, Shane T, Anderson, Gary, Angel, Martin V, Artois, Tom, Bailly, Nicolas, Bamber, Roger, Barber, Anthony, Bartsch, Ilse, Berta, Annalisa, Blazewicz-Paszkowycz, Magdalena, Bock, Phil, Boxshall, Geoff, Boyko, Christopher B, Brandão, Simone Nunes, Bray, Rod A, Bruce, Niel L, Cairns, Stephen D., Chan, Tin-Yam, Cheng, Lanna, Collins, Allen Gilbert, Cribb, Thomas, Curini-Galletti, Marco, Dahdouh-Guebas, Farid, Davie, Peter J F., et al 2012. The Magnitude of Global Marine Species Diversity. Current Biology, 22(23): 2189-2202. doi:10.1016/j.cub.2012.09.036

Orellana, Evan R. and Collins, Allen Gilbert 2011. First report of the box jellyfish Tripedalia cystophora (Cubozoa: Tripedaliidae) in the continental USA, from Lake Wyman, Boca Raton, Florida. Marine Biodiversity Records, 4: e54 doi:10.1017/S1755267211000133

Collins, Allen Gilbert, Bentlage, Bastian, Gillan, William (Bud), Lynn, Tara H., Morandini, Andre C. and Marques, Antonio C. 2011. Naming the Bonaire banded box jelly, Tamoya ohboya, n. sp. (Cnidaria: Cubozoa: Carybdeida: Tamoyidae). Zootaxa, 2753: 53-68.

Bentlage, Bastian, Cartwright, Paulyn, Yanagihara, Angel A., Lewis, Cheryl, Richards, Gemma S. and Collins, Allen Gilbert 2010. Evolution of box jellyfish (Cnidaria: Cubozoa), a group of highly toxic invertebrates. Proceedings of the Royal Society B: Biological Sciences, 277(1680): 493-501. doi:10.1098/rspb.2009.1707

Miranda, Lucilia S., Collins, Allen Gilbert and Marques, Antonio C. 2010. Molecules Clarify a Cnidarian Life Cycle - The "Hydrozoan'' Microhydrula limopsicola Is an Early Life Stage of the Staurozoan Haliclystus antarcticus. Plos One, 5(4): e10182 doi:10.1371/journal.pone.0010182

Kahn, Amanda S., Matsumoto, George I., Hirano, Yayoi M. and Collins, Allen Gilbert 2010. Haliclystus californiensis, a "new" species of stauromedusa (Cnidaria: Staurozoa) from the northeast Pacific, with a key to the species of Haliclystus. Zootaxa, 2518: 49-59.

Bayha, Keith M., Dawson, Michael N., Collins, Allen Gilbert, Barbeitos, Marcos S. and Haddock, Steven H. D. 2010. Evolutionary Relationships Among Scyphozoan Jellyfish Families Based on Complete Taxon Sampling and Phylogenetic Analyses of 18S and 28S Ribosomal DNA. Integrative and Comparative Biology, 50(3): 436-455. doi:10.1093/icb/icq074

Dohrmann, M., Collins, Allen Gilbert and Woerheide, G. 2009. New insights into the phylogeny of glass sponges (Porifera, Hexactinellida): Monophyly of Lyssacinosida and Euplectellinae, and the phylogenetic position of Euretidae. Molecular phylogenetics and evolution, 52: 257-262.

Jankowski, T., Collins, Allen Gilbert and Campbell, R. 2008. Global diversity of inland water cnidarians. Hydrobiologia, 595: 35-40.

Tabachnick, K. R. and Collins, Allen Gilbert 2008. Glass sponges (Porifera, Hexactinellida) of the northern Mid-Atlantic Ridge. Marine Biology Research, 4: 25-47.

Evans, Nathaniel M., Lindner, A., Raikova, E. V., Collins, Allen Gilbert and Cartwright, Paulyn 2008. Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria. BMC Evolutionary Biology, 8: 139

Dohrmann, Martin, Janussen, Dorte, Reitner, Joachim, Collins, Allen Gilbert and Wörheide, Gert 2008. Phylogeny and Evolution of Glass Sponges (Porifera, Hexactinellida). Systematic Biology, 57(3): 388-405. doi:10.1080/10635150802161088

Lewis, Cheryl, Kubota, Shin, Migotto, Alvaro E. and Collins, Allen Gilbert 2008. Sexually Dimorphic Cubomedusa Carybdea sivickisi (Cnidaria: Cubozoa) in Seto, Wakayama, Japan. Publications of the Seto Marine Biological Laboratory, 40(5/6): 1-8.

Kilvington, C. C., Collins, Allen Gilbert, Kosevich, I. A., Pyataeva, S. V. and Robson, E. A. 2008. Protohydra leuckarti near Plymouth. Journal of the Marine Biological Association of the United Kingdom, 88: 1555-1557.

Cartwright, Paulyn, Evans, Nathaniel M., Dunn, Casey W., Marques, Antonio C., Miglietta, Maria Pia, Schuchert, Peter and Collins, Allen Gilbert 2008. Phylogenetics of Hydroidolina (Hydrozoa: Cnidaria). Journal of the Marine Biological Association of the United Kingdom, 88: 1663-1672.

Collins, Allen Gilbert, Bentlage, Bastian, Lindner, Alberto, Lindsay, Dhugal, Haddock, Steven H. D., Jarms, Gerhard, Norenburg, Jon L., Jankowski, Thomas and Cartwright, Paulyn 2008. Phylogenetics of Trachylina (Cnidaria: Hydrozoa) with new insights on the evolution of some problematical taxa. Journal of the Marine Biological Association of the United Kingdom, 88: 1673-1685.

Fukami, Hironobu, Chen, Chaolun Allen, Budd, Ann F., Collins, Allen Gilbert, Wallace, Carden, Chuang, Yao-Yang, Chen, Chienhsun, Dai, Chang-Feng, Iwao, Kenji, Sheppard, Charles and Knowlton, Nancy 2008. Mitochondrial and Nuclear Genes Suggest that Stony Corals Are Monophyletic but Most Families of Stony Corals Are Not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria). PLoS ONE, 3(9): e3222 doi:10.1371/journal.pone.0003222

Daly, M., Brugler, M. R., Cartwright, Paulyn, Collins, Allen Gilbert, Dawson, M. N., Fautin, D. G., France, S. C., McFadden, C. S., Opresko, Dennis M., Rodriguez, E., Roman, S. L. and Stake, J. L. 2007. The phylum Cnidaria: A review of phylogenetic patterns and diversity 300 years after Linnaeus. Zootaxa, 1668: 127-182.

Cartwright, Paulyn and Collins, Allen Gilbert 2007. Fossils and phylogenies: integrating multiple lines of evidence to investigate the origin of early major metazoan lineages. Integrative and Comparative Biology, 47(5): 744-751. doi:10.1093/icb/icm071

Cartwright, Paulyn, Halgedahl, Susan L., Hendricks, Jonathan R., Jarrard, Richard D., Marques, Antonio C., Collins, Allen Gilbert and Lieberman, Bruce S. 2007. Exceptionally Preserved Jellyfishes from the Middle Cambrian. PLoS ONE, 2(10): e1121

Collins, Allen Gilbert, Bentlage, Bastian, Matsumoto, G. I., Haddock, H. D., Osborn, Karen J. and Schierwater, B. 2006. Solution to the phylogenetic enigma of Tetraplatia, a worm-shaped cnidarian. Biology Letters, 2: 120-124.

Lutz, Richard A., Collins, Allen Gilbert, Annis, Eric R., Reed, Andrew J., Bennett, Kyle F., Halanych, Kenneth M. and Vrijenhoek, Robert C. 2006. Stauromedusan populations inhabiting deep-sea hydrothermal vents along the southern East Pacific Rise. Cahiers de Biologie Marine, 47: 409-414.

van Iten, H., Moraes Leme, J. De, Simoes, M. G., Marques, A. C. and Collins, Allen Gilbert 2006. Reassessment of the phylogenetic position of conulariids (?Ediacaran-Triassic) within the subphylum Medusozoa (phylum Cnidaria). Journal of Systematic Palaeontology, 4(2): 109-118. doi:10.1017/S1477201905001793

Medina, M., Collins, Allen Gilbert, Takaoka, T. L., Kuehl, J. V. and Boore, J. L. 2006. Naked Corals: Skeleton Loss in Scleractinia. Proceedings of the National Academy of Sciences of the United States of America, 103: 9096-9100.

Collins, Allen Gilbert, Schuchert, P., Marques, A. C., Jankowski, T., Medina, M. and Schierwater, B. 2006. Medusozoan Phylogeny and Character Evolution Clarified by New Large and Small Subunit rDNA Data and an Assessment of the Utility of Phylogenetic Mixture Models. Systematic Biology, 55(1): 97-115. doi:10.1080/10635150500433615

Collins, J. A. and Collins, Allen Gilbert 2005. Systematics as a Hypothesis-Based Science and its Fundamental Role in Understanding Oceans. In: OCEANS, 2005. Proceedings of MTS/IEEE. : ,() pp.1395-1402.

Collins, Allen Gilbert and Daly, M. 2005. A new deepwater species of Stauromedusae, Lucernaria janetae (Cnidaria, Staurozoa, Lucernariidae), and a preliminary investigation of stauromedusan phylogeny based on nuclear and mitochondrial rDNA data. Biological Bulletin, 208: 221-230.

Collins, Allen Gilbert, Cartwright, Paulyn, McFadden, C. S. and Schierwater, B. 2005. Phylogenetic context and basal metazoan model systems. Integrative and Comparative Biology, 45: 585-594.

Tomassetti, P., Voigt, O., Collins, Allen Gilbert, Porrello, S., Pearse, V. B. and Schierwater, B. 2005. Placozoans (Trichoplax adhaerens Schulze, 1883) in the Mediterranean Sea. Meiofauna Marina, 14: 5-7.

Collins, Allen Gilbert, Winkelmann, S., Hadrys, H. and Schierwater, B. 2005. Phylogeny of Capitata (Cnidaria, Hydrozoa) and Corynidae in light of mitochondrial 16S rDNA data. Zoologica Scripta, 34: 91-99.

Voigt, O., Collins, Allen Gilbert, Pearse, V. B., Pearse, J. S., Hadrys, H. and Schierwater, B. 2004. Placozoa no longer a phylum of one. Current Biology, 14: R944-R945.

Waggoner, Ben and Collins, Allen Gilbert 2004. Reductio ad absurdum: Testing the evolutionary relationships of Ediacaran and Paleozoic problematic fossils using molecular divergence dates. Journal of Paleontology, 78(1): 51-61.

Silberman, Jeffrey D., Collins, Allen Gilbert, Gershwin, Lisa-ann, Johnson, Patricia J. and Roger, Andrew J. 2004. Ellobiopsids of the Genus Thalassomyces are Alveolates. Journal of eukaryotic microbiology, 51(2): 246-252.

Marques, Antonio C. and Collins, Allen Gilbert 2004. Cladistic analysis of Medusozoa and cnidarian evolution. Invertebrate Biology, 123(1): 23-42.

Medina, Monica, Collins, Allen Gilbert, Taylor, John W., Valentine, James W., Lipps, Jere H., Amaral-Zettler, Linda and Sogin, Mitchell L. 2003. Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa. Intenrational journal of astrobiology, 2(3): 203-211.

Roy, Kaustuv, Collins, Allen Gilbert, Becker, Bonnie J., Begovic, Emina and Engle, John M. 2003. Anthropogenic impacts and historical decline in body size of rocky intertidal gastropods in southern California. Ecology Letters, 6: 205-211.

Winkel, Kenneth D., Hawdon, Gabrielle M., Fenner, Peter J., Gershwin, Lisa-Ann, Collins, Allen Gilbert and Tibballs, James 2003. Jellyfish antivenom: Past, Present and Future. Toxin Reviews, 22(1): 115-127.

Gershwin, Lisa-Ann and Collins, Allen Gilbert 2002. A preliminary phylogeny of Pelagiidae (Cnidaria, Scyphozoa) , with new observations of Chrysaora colorata comb. nov.. Journal of Natural History, 36(2): 127-148. doi:10.1080/00222930010003819

Castilla, J. C., Collins, Allen Gilbert, Meyer, Christopher P., Guinez, R. and Lindberg, D. R. 2002. Recent introduction of the dominant tunicate, Pyura praeputialis (Urochordata, Pyuridae) to Antofagasta, Chile. Molecular ecology, 11: 1579-1584.

Medina, Monica, Collins, Allen Gilbert, Silberman, Jeffrey D. and Sogin, Mitchell L. 2001. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proceedings of the National Academy of Sciences of the United States of America, 98(17): 9707-9712.

Collins, Allen Gilbert and Valentine, J. W. 2001. Defining phyla: evolutionary pathways to metazoan body plans. Evolution & Development, 3(6): 432-442.

Hamilton, H., Caballero, S., Collins, Allen Gilbert and Brownell, Robert L., Jr. 2001. Evolution of river dolphins. Proceedings of the Royal Society B: Biological Sciences, 268(1466): 549-556.

Collins, Allen Gilbert 2000. Towards understanding the phylogenetic history of Hydrozoa: hypothesis testing with 18S gene sequence data. Scientia Marina, 64(1): 5-22.

Collins, Allen Gilbert, Lipps, J. H. and Valentine, J. W. 2000. Modern mucociliary creeping trails and the bodyplans of Neoproterozoic trace-makers. Paleobiology, 26(1): 47-55.

Valentine, James W. and Collins, Allen Gilbert 2000. The significance of moulting in Ecdysozoan evolution. Evolution & development, 2(3): 152-156.

Collins, Allen Gilbert 1999. Molecules and evolutionary history. In: Springer, Dale A. and Scotchmoor, Judith G. (eds.), Evolution : investigating the evidence. [Pittsburgh, PA]: Paleontological Society,(Paleontological Society Papers) pp.

Collins, Allen Gilbert 1998. Evaluating multiple alternative hypotheses for the origin of Bilateria: an analysis of 18S rRNA molecular evidence. Proceedings of the National Academy of Sciences of the United States of America, 95(26): 15458-15463.

Valentine, James W., Collins, Allen Gilbert and Meyer, Christopher P. 1994. Morphological complexity increase in metazoans. Paleobiology, 20(2): 131-142.

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