Collins, Allen G.
Research Zoologist
0000-0002-3664-9691
Collins, Allen G.
Research Zoologist
My research focuses on the biodiversity and evolutionary history of cnidarians (jellyfishes, corals, etc.) and sponges. I document species ranges and use genetic and morphological data to delimit species. In addition, I generate and use evolutionary trees, known as phylogenetic hypotheses, to better understand how the amazing biodiversity of these groups -- in terms of morphology, life history, and genetics -- has come to be.
Positions
- Affiliated Scientist / Curator, National Museum of Natural History 2004 -
- Research Zoologist, National Systematics Lab of NOAA's Fisheries 2004 -
- Director, National Systematics Lab of NOAA's Fisheries 2016 -
Geographic Focus
- Global Transnational Region
Background And Education
Education And Training
- B.A., Amherst College
- Ph.D., University of California, Berkeley
Research And Grants
Co-principal Investigator On
- Assembly of Marine Biodiversity Along Geographic and Anthropogenic Stress Gradients 2013 - 2018
- Augmenting Scientific Research and Education through Biodiversity Research in Indonesia 2014 - 2015
- A Systematic Framework for Understanding Jellyfish Blooms and Invasive Species: Taxonomy of Semaeostome Scyphomedusae (Cnidaria) 2008 - 2010
Investigator On
Publications
Selected Publications
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Article
- Fonfría, Eva S., Straehler-Pohl, Ilka, Stampar, Sérgio N., Collins, Allen G., Hoverd, William Alan, and Bordehore, Cesar. 2024. "Copula lucentia sp. nov., a new box jellyfish (Cnidaria: Cubozoa: Carybdeida) from Western Mediterranean Sea." Marine Biodiversity, 54, (5). https://doi.org/10.1007/s12526-024-01460-6. 2024
- Tan, Kei Chloe, Ames, Cheryl Lewis, and Collins, Allen G. 2024. "Complete linear mitochondrial genomes for Cephea cephea and Mastigias albipunctata (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships." Mitochondrial DNA Part B: Resources, 9, (11) 1544–1548. https://doi.org/10.1080/23802359.2024.2429644. 2024
- Molinari, Clarissa G., Collins, Allen G., and Morandini, Andre C. 2023. "A morphological review of the jellyfish genus Nausithoe Kolliker,1853 (Nausithoideae, Coronatae, Scyphozoa, Cnidaria)." Zootaxa, 5336, (1) 1–32. https://doi.org/10.11646/zootaxa.5336.1.1. 2023
- Molinari, Clarissa G., Collins, Allen G., and Morandini, Andre C. 2023. "A morphological review of the jellyfish genus Nausithoe K & ouml;lliker,1853 (Nausithoideae, Coronatae, Scyphozoa, Cnidaria)." Zootaxa, 5336, (1) 1–32. https://doi.org/10.11646/zootaxa.5336.1.1. 2023
- Molinari, Clarissa G., Collins, Allen G., and Morandini, André C. 2023. "A morphological review of the jellyfish genus Nausithoe Kölliker, 1853 (Nausithoideae, Coronatae, Scyphozoa, Cnidaria)." Zootaxa, 5336, (1) 1–32. https://doi.org/10.11646/zootaxa.5336.1.1. 2023
- Goodheart, Jessica A., Collins, Allen G., Cummings, Michael P., Egger, Bernhard, and Rawlinson, Kate A. 2023. "A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution." Royal Society Open Science, 10, (3). https://doi.org/10.1098/rsos.220939. 2023
- Verhaegen, Gerlien, Sangekar, Mehul Naresh, Bentlage, Bastian, Hoving, Henk‐Jan, Collins, Allen G., and Lindsay, Dhugal. 2023. "Drivers behind the diversity and distribution of a widespread midwater narcomedusa." Limnology and Oceanography, https://doi.org/10.1002/lno.12408. 2023
- Montenegro, Javier, Collins, Allen G., Hopcroft, Russell R., Questel, Jennifer M., Thuesen, Erik V., Bachtel, Tiffany S., Bergman, Leah A., Sangekar, Mehul N., Drazen, Jeffrey C., and Lindsay, Dhugal J. 2023. "Heterogeneity in diagnostic characters across ecoregions: A case study with Botrynema (Hydrozoa: Trachylina: Halicreatidae)." Frontiers in Marine Science, 9. https://doi.org/10.3389/fmars.2022.1101699. 2023
- Peterson, Miles, I., Tan, Kei Chloe, Collins, Allen, Kitano, Satoshi, Kusuoka, Yasushi, Suzuki, Takahito G., Migita, Masao, Iesa, Iffah, Pirro, Stacy, Lindsay, Dhugal, and Ames, Cheryl Lewis. 2022. "A description of a novel swimming behavior in a dioecious population of Craspedacusta sowerbii, the rediscovery of the elusive Astrohydra japonica and the first genetic analysis of freshwater jellyfish in Japan." Plankton & Benthos Research, 17, (2) 231–248. https://doi.org/10.3800/pbr.17.231. 2022
- Lawley, Jonathan W., Gamero-Mora, Edgar, Maronna, Maximiliano M., Chiaverano, Luciano M., Stampar, Sérgio N., Hopcroft, Russell R., Collins, Allen G., and Morandini, André C. 2022. "Morphology is not always useful for diagnosis, and that's ok: Species hypotheses should not be bound to a class of data. Reply to Brown and Gibbons (S Afr J Sci. 2022;118(9/10), Art. #12590)." South African Journal of Science, 118, (9). https://doi.org/10.17159/sajs.2022/14495. 2022
- Hoban, Mykle L., Whitney, Jonathan, Collins, Allen G., Meyer, Christopher, Murphy, Katherine R., Reft, Abigail J., and Bemis, Katherine E. 2022. "Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing." PeerJ, 10. https://doi.org/10.7717/peerj.13790. 2022
- O'Brien, Kristin M., Crockett, Elizabeth L., Adams, Byron J., Amsler, Charles D., Appiah-Madson, Hannah, Collins, Allen, Desvignes, Thomas, Detrich, H. William, III, Distel, Daniel L., Eppley, Sarah M., Frable, Benjamin W., Franz, Nico M., Grim, Jeffrey M., Kocot, Kevin M., Mahon, Andrew R., Mayfield-Meyer, Teresa, Mikucki, Jill A., Moser, William E., Schmull, Michaela, Seid, Charlotte A., Smith, Craig R., Todgham, Anne E., and Watkins-Colwell, Gregory. 2022. "The time is right for an Antarctic biorepository network." Proceedings of the National Academy of Sciences of the United States of America, 119, (50). https://doi.org/10.1073/pnas.2212800119. 2022
- Miranda, Thais P., Fernandez, Marina O., Genzano, Gabriel N., Pena Cantero, Alvaro L., Collins, Allen G., and Marques, Antonio C. 2021. "Biodiversity and biogeography of hydroids across marine ecoregions and provinces of southern South America and Antarctica." Polar Biology, https://doi.org/10.1007/s00300-021-02909-1. 2021
- Casey, Jordan M., Ransome, Emma, Collins, Allen G., Mahardini, Angka, Kurniasih, Eka M., Sembiring, Andrianus, Schiettekatte, Nina M. D., Cahyani, Ni Kadek Dita, Wahyu Anggoro, Aji, Moore, Mikaela, Uehling, Abby, Belcaid, Mahdi, Barber, Paul H., Geller, Jonathan B., and Meyer, Christopher P. 2021. "DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity." Environmental DNA, 3, (6) 1229–1246. https://doi.org/10.1002/edn3.245. 2021
- Ames, Cheryl L., Ohdera, Aki H., Colston, Sophie M., Collins, Allen G., Fit, William K., Morandini, André C., Erickson, Jefferey S., and Vora, Gary J. 2021. "Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States." Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.640527. 2021
- Astarini, Ida Ayu, Ningsih, Enex Yuniarti, Simanungkalit, Devy, Ardiana, Shella Ayu, Al Malik, M. Danie, Yusmalinda, Ni Luh Astria, Sembiring, Andrianus, Pertiwi, Ni Putu Dian, Cahyani, Ni Kadek Dita, and Collins, Allen. 2021. "Genetic variation of longtail tuna Thunnus tonggol landed in four fish markets in Indonesia based on mitochondrial DNA." Biodiversitas Journal of Biological Diversity, 22, (4). https://doi.org/10.13057/biodiv/d220408. 2021
- Klompen, Anna M. L., Kayal, Ehsan, Collins, Allen G., and Cartwright, Paulyn. 2021. "Phylogenetic and Selection Analysis of an Expanded Family of Putatively Pore-Forming Jellyfish Toxins (Cnidaria: Medusozoa)." Genome Biology and Evolution, 13, (6). https://doi.org/10.1093/gbe/evab081. 2021
- Bentlage, Bastian and Collins, Allen G. 2021. "Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput." Peerj, 9. https://doi.org/10.7717/peerj.12104. 2021
- Meyer, Christopher P., Duffy, J. Emmett, Collins, Allen G., Paulay, Gustav, and Wetzer, Regina. 2021. "The U.S. Ocean Biocode." Marine Technology Society Journal, 55, (3) 140–141. https://doi.org/10.4031/MTSJ.55.3.33. 2021
- Lawley, Jonathan W., Gamero-Mora, Edgar, Maronna, Maximiliano M., Chiaverano, Luciano M., Stampar, Sergio N., Hopcroft, Russell R., Collins, Allen G., and Morandini, Andre C. 2021. "The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa)." Peerj, 9. https://doi.org/10.7717/peerj.11954. 2021
- Pappalardo, Paula, Collins, Allen G., Pagenkopp Lohan, Katrina M., Hanson, Kate M., Truskey, Sarit B., Jaeckle, William, Ames, Cheryl Lewis, Goodheart, Jessica A., Bush, Stephanie L., Biancani, Leann M., Strong, Ellen E., Vecchione, Michael, Harasewych, M. G., Reed, Karen, Lin, Chan, Hartil, Elise C., Whelpley, Jessica, Blumberg, Jamie, Matterson, Kenan, Redmond, Niamh E., Becker, Allison, Boyle, Michael J., and Osborn, Karen J. 2021. "The role of taxonomic expertise in interpretation of metabarcoding studies." ICES Journal of Marine Science, 78, (9) 3397–3410. https://doi.org/10.1093/icesjms/fsab082. 2021
- Ford, Michael, Bezio, Nicholas, and Collins, Allen. 2020. "Duobrachium sparksae (incertae sedis Ctenophora Tentaculata Cydippida): A new genus and species of benthopelagic ctenophore seen at 3,910 m depth off the coast of Puerto Rico." Plankton and Benthos Research, 15, (4) 296–305. https://doi.org/10.3800/pbr.15.296. 2020
- Castello-Branco, Cristiana, Collins, Allen G., and Hajdu, Eduardo. 2020. "A collection of hexactinellids (Porifera) from the deep South Atlantic and North Pacific: new genus, new species and new records." PeerJ, 8. https://doi.org/10.7717/peerj.9431. 2020
- Ames, Cheryl L., Klompen, Anna M. L., Badhiwala, Krishna, Muffett, Kade, Reft, Abigail J., Kumar, Mehr, Janssen, Jennie D., Schultzhaus, Janna N., Field, Lauren D., Muroski, Megan E., Bezio, Nick, Robinson, Jacob T., Leary, Dagmar H., Cartwright, Paulyn, Collins, Allen G., and Vora, Gary J. 2020. "Cassiosomes are stinging-cell structures in the mucus of the upside-down jellyfish Cassiopea xamachana." Communications Biology, 3, (1) Article 67. https://doi.org/10.1038/s42003-020-0777-8. 2020
- Fernandez, Marina O., Collins, Allen G., and Marques, Antonio C. 2020. "Gradual and rapid shifts in the composition of assemblages of hydroids (Cnidaria) along depth and latitude in the deep Atlantic Ocean." Journal of Biogeography, 47, (7) 1541–1551. https://doi.org/10.1111/jbi.13853. 2020
- Fernandez, Marina Oliveira, Collins, Allen G., Gittenberger, Arjan, Roy, Kaustuv, and Marques, Antonio Carlos. 2020. "Traits and depth: What do hydroids tell us about morphology and life‐history strategies in the deep sea?" Global Ecology and Biogeography, 29, (5) 908–924. https://doi.org/10.1111/geb.13074. 2020
- Cunha, Amanda F., Collins, Allen G., and Marques, Antonio C. 2020. "When morphometry meets taxonomy: morphological variation and species boundaries in Proboscoida (Cnidaria: Hydrozoa)." Zoological Journal of the Linnean Society, 190, (2) 417–447. https://doi.org/10.1093/zoolinnean/zlz166. 2020
- Ohdera, Aki, Ames, Cheryl L., Dikow, Rebecca B., Kayal, Ehsan, Chiodin, Marta, Busby, Ben, La, Sean, Pirro, Stacy, Collins, Allen G., Medina, Mónica, and Ryan, Joseph F. 2019. "Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa)." GigaScience, 8, (7). https://doi.org/10.1093/gigascience/giz069. 2019
- Miranda, Lucilia Souza and Collins, Allen Gilbert. 2019. "Eyes in Staurozoa (Cnidaria): a review." Peerj, 7, (e6693). https://doi.org/10.7717/peerj.6693. 2019
- Morrow, Christine, Cardenas, Paco, Boury-Esnault, Nicole, Picton, Bernard, Mccormack, Grace, Van Soest, Rob, Collins, Allen, Redmond, Niamh, Maggs, Christine, Sigwart, Julia, and Allcock, Louise A. 2019. "Integrating morphological and molecular taxonomy with the revised concept of Stelligeridae (Porifera: Demospongiae)." Zoological Journal of the Linnean Society, 187, (1) 31–81. https://doi.org/10.1093/zoolinnean/zlz017. 2019
- Moura, Carlos J., Collins, Allen G., Santos, Ricardo S., and Lessios, Harilaos. 2019. "Predominant east to west colonizations across major oceanic barriers: Insights into the phylogeographic history of the hydroid superfamily Plumularioidea, suggested by a mitochondrial DNA barcoding marker." Ecology and Evolution, 1–16. https://doi.org/10.1002/ece3.5608. 2019
- Miranda, Lucília S., Mills, Claudia E., Hirano, Yayoi M., Collins, Allen G., and Marques, Antonio C. 2018. "A review of the global diversity and natural history of stalked jellyfishes (Cnidaria, Staurozoa)." Marine Biodiversity, 48, (4) 1695–1714. https://doi.org/10.1007/s12526-017-0721-4. 2018
- Goodheart, Jessica A., Bleidißel, Sabrina, Schillo, Dorothee, Strong, Ellen E., Ayres, Daniel L., Preisfeld, Angelika, Collins, Allen G., Cummings, Michael P., and Wägele, Heike. 2018. "Comparative morphology and evolution of the cnidosac in Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)." Frontiers in Zoology, 15, (1) 43. https://doi.org/10.1186/s12983-018-0289-2. 2018
- Bentlage, Bastian, Osborn, Karen J., Lindsay, Dhugal J., Hopcroft, Russell R., Raskoff, Kevin A., and Collins, Allen G. 2018. "Corrigendum to Loss of metagenesis and evolution of a parasitic life style in a group of open-ocean jellyfish Molecular Phylogenetics and Evolution 124 (2018) 50-59." Molecular phylogenetics and evolution, 126 390–391. https://doi.org/10.1016/j.ympev.2018.06.017. 2018
- Moura, Carlos J., Lessios, Harilaos, Cortes, Jorge, Nizinski, Martha S., Reed, John, Santos, Ricardo S., and Collins, Allen G. 2018. "Hundreds of genetic barcodes of the species-rich hydroid superfamily Plumularioidea (Cnidaria, Medusozoa) provide a guide toward more reliable taxonomy." Scientific Reports, 8 17986. https://doi.org/10.1038/s41598-018-35528-8. 2018
- Bentlage, Bastian, Osborn, Karen J., Lindsay, Dhugal J., Hopcroft, Russell R., Raskoff, Kevin A., and Collins, Allen G. 2018. "Loss of metagenesis and evolution of a parasitic life style in a group of open ocean jellyfish." Molecular phylogenetics and evolution, 124 50–59. https://doi.org/10.1016/j.ympev.2018.02.030. 2018
- Kayal, Ehsan, Bentlage, Bastian, Pankey, M. Sabrina, Ohdera, Aki H., Medina, Monica, Plachetzki, David C., Collins, Allen G., and Ryan, Joseph F. 2018. "Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits." Bmc Evolutionary Biology, 18 68–68. https://doi.org/10.1186/s12862-018-1142-0. 2018
- Mendoza-Becerril, Maria A., Jaimes-Becerra, Adrian Jose, Collins, Allen G., and Marques, Antonio C. 2018. "Phylogeny and morphological evolution of the so-called bougainvilliids (Hydrozoa, Hydroidolina)." Zoologica Scripta, 47, (5) 608–622. https://doi.org/10.1111/zsc.12291. 2018
- Ohdera, Aki H., Abrams, Michael J., Ames, Cheryl L., Baker, David M., Suescún-Bolívar, Luis P., Collins, Allen G., Freeman, Christopher J., Gamero-Mora, Edgar, Goulet, Tamar L., Hofmann, Dietrich K., Jaimes-Becerra, Adrian, Long, Paul F., Marques, Antonio C., Miller, Laura A., Mydlarz, Laura D., Morandini, Andre C., Newkirk, Casandra R., Putri, Sastia P., Samson, Julia E., Stampar, Sérgio, Steinworth, Bailey, Templeman, Michelle, Thomé, Patricia E., Vlok, Marli, Woodley, Cheryl M. et al. 2018. "Upside-Down but Headed in the Right Direction: Review of the Highly Versatile Cassiopea xamachana System." Frontiers in Ecology and Evolution, 6 35. https://doi.org/10.3389/fevo.2018.00035. 2018
- Kubota, Shin and Collins, Allen G. 2017. "A single origin of bivalve-inhabiting hydrozoans (Cnidaria, Hydrozoa, Leptomedusae) in the family Eirenidae based on an analysis of 16S rRNA gene." Biogeography, 19 75–79. 2017
- 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, 17, (4) 753–766. https://doi.org/10.1007/s13127-017-0342-6. 2017
- 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 1–43. https://doi.org/10.7717/peerj.3863. 2017
- Cunha, Amanda F., Collins, Allen Gilbert, and Marques, Antonio C. 2017. "Phylogenetic relationships of Proboscoida Broch, 1910 (Cnidaria, Hydrozoa): Are traditional morphological diagnostic characters relevant for the delimitation of lineages at the species, genus, and family levels?" Molecular phylogenetics and evolution, 106 118–135. https://doi.org/10.1016/j.ympev.2016.09.012. 2017
- 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. https://doi.org/10.1186/s12862-017-1066-0. 2017
- 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. https://doi.org/10.11646/zootaxa.4227.3.5. 2017
- Ransome, Emma, Geller, Jonathan B., Timmers, Molly, Leray, Matthieu, Mahardini, Angka, Sembiring, Andrianus, Collins, Allen Gilbert, and Meyer, Christopher P. 2017. "The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo'orea coral reefs, French Polynesia." PLOS ONE, 12, (4). https://doi.org/10.1371/journal.pone.0175066. 2017
- 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. https://doi.org/10.1080/17451000.2016.1268261. 2017
- 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. https://doi.org/10.1186/s12864-016-2944-3. 2016
- 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." Biological Bulletin, 231, (2) 152–169. https://doi.org/10.1086/690095. 2016
- Miranda, Lucília S., Collins, Allen Gilbert, Hirano, Yayoi M., Mills, Claudia E., and Marques, Antonio C. 2016. "Comparative internal anatomy of Staurozoa (Cnidaria), with functional and evolutionary inferences." PeerJ, 4 e2594. https://doi.org/10.7717/peerj.2594. 2016
- 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. https://doi.org/10.11646/zootaxa.4150.1.5. 2016
- 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. https://doi.org/10.1186/s12864-016-3305-y. 2016
- 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. https://doi.org/10.2988/0006-324X-129.Q2.164. 2016
- 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. https://doi.org/10.1080/15476286.2016.1194161. 2016
- 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 e1951. https://doi.org/10.7717/peerj.1951. 2016
- 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. 2015
- Miranda, L. S., Collins, Allen Gilbert, and Marques, Antonio 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). https://doi.org/10.1098/rspb.2014.2396. 2015
- 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 e1403. https://doi.org/10.7717/peerj.1403. 2015
- 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). https://doi.org/10.1371/journal.pone.0139068. 2015
- 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. https://doi.org/10.1098/rsos.150196. 2015
- 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. https://doi.org/10.1080/14772000.2014.902867. 2014
- 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." The Journal of Heredity, 105, (1) 1–18. https://doi.org/10.1093/jhered/est084. 2014
- 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. https://doi.org/10.1093/icb/ict039. 2013
- 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. https://doi.org/10.1186/1471-2148-13-5. 2013
- Miranda, Lucília S., Collins, Allen Gilbert, and Marques, Antonio C. 2013. "Internal anatomy of Haliclystus antarcticus (Cnidaria, Staurozoa) with a discussion on histological features used in staurozoan taxonomy." Journal of Morphology, 247, (12) 1365–1383. https://doi.org/10.1002/jmor.20185. 2013
- 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. https://doi.org/10.2988/0006-324X-126.2.91. 2013
- 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. https://doi.org/10.1093/icb/ict065. 2013
- 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. https://doi.org/10.1093/icb/ict074. 2013
- 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. https://doi.org/10.1093/icb/ict071. 2013
- 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. https://doi.org/10.1093/icb/ict033. 2013
- 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. https://doi.org/10.1016/j.ympev.2012.12.016. 2013
- 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. https://doi.org/10.1093/icb/ict078. 2013
- Marques, Antonio C., Maronna, Maximiliano M., and Collins, Allen Gilbert. 2013. "Putting GenBank Data on the Map." Science, 341, (6152) 1341–1341. https://doi.org/10.1126/science.341.6152.1341-a. 2013
- 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. https://doi.org/10.1371/journal.pone.0050437. 2013
- 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. https://doi.org/10.11646/zootaxa.3737.4.8. 2013
- 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. https://doi.org/10.1080/14772000.2013.825658. 2013
- 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. https://doi.org/10.1093/gbe/evr123. 2012
- 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. https://doi.org/10.1093/gbe/evr127. 2012
- 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. https://doi.org/10.1666/0094-8373-39.1.95. 2012
- 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. https://doi.org/10.2988/11-31.1. 2012
- Appeltans, Ward, Ahyong, Shane T, Anderson, Gary, Angel, Martin V, Artois, Tom, Bailly, Nicolas, Bamber, Roger, Barber, Anthony, Bartsch, Ilse, Berta, Annalisa, Błażewicz-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. https://doi.org/10.1016/j.cub.2012.09.036. 2012
- 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. https://doi.org/10.1017/S1755267211000133. 2011
- 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. 2011
- 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. https://doi.org/10.1098/rspb.2009.1707. 2010
- 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. https://doi.org/10.1093/icb/icq074. 2010
- 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. 2010
- 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. https://doi.org/10.1371/journal.pone.0010182. 2010
- 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. 2009
- 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. 2008
- Tabachnick, K. R. and Collins, Allen Gilbert. 2008. "Glass sponges (Porifera, Hexactinellida) of the northern Mid-Atlantic Ridge." Marine Biology Research, 4 25–47. 2008
- Jankowski, T., Collins, Allen Gilbert, and Campbell, R. 2008. "Global diversity of inland water cnidarians." Hydrobiologia, 595 35–40. 2008
- 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. https://doi.org/10.1371/journal.pone.0003222. 2008
- 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. 2008
- 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. 2008
- 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. 2008
- 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. https://doi.org/10.1080/10635150802161088. 2008
- 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. 2008
- 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. 2007
- 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. https://doi.org/10.1093/icb/icm071. 2007
- Daly, M., Brugler, Mercer 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. 2007
- A preliminary phylogeny of Pelagiidae (Cnidaria, Scyphozoa) , with new observations of Chrysaora colorata comb. nov.. Journal of Natural History. 36:127-148. 2002
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Chapter
- 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. 11–16. In Methods in molecular biology, 858. https://doi.org/10.1007/978-1-61779-591-6_2. 2012
- Collins, Allen G. 2009. "Recent Insights into Cnidarian Phylogeny." In Proceedings of the Smithsonian Marine Science Symposium. 139–149. Washington, D.C.: Smithsonian Institution Scholarly Press. In Smithsonian Contributions to the Marine Sciences, 38. https://doi.org/10.5479/si.01960768.38.139. 2009
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Conference Paper
- Girasek, Quinn, Copeland, Adrienne, Egan, Katharine, and Collins, Allen G. 2021. "Investigating Mesopelagic Organism Occurrence Along the Southeastern United States." from American Geophysical Union Fall Meeting. https://doi.org/10.1002/essoar.10509752.1. 2021
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Dataset
- Goodheart, Jessica, Collins, Allen, Cummings, Michael P., Egger, Bernhard, and Rawlinson, Kate. 2022. [Dataset] Phylogenomics suggests that larvae are ancestral in polyclads, but not homologous to the trochophore. Distributed by Dryad. https://doi.org/10.6076/D1JG60. 2022
- Pappalardo, Paula, Collins, Allen G., Pagenkopp Lohan, Katrina M., Hanson, Kate M., Truskey, Sarit B., Jaeckle, William, Lewis Ames, Cheryl, Goodheart, Jessica A., Bush, Stephanie L., Biancani, Leann M., Strong, Ellen E., Vecchione, Michael, Harasewych, M. G., Reed, Karen, Lin, Chan, Hartil, Elise, Whelpley, Jessica, Blumberg, Jamie, Matterson, Kenan, Redmond, Niamh E., Becker, Allison, Boyle, Michael J., and Osborn, Karen J. 2021. [Dataset] Data from: The role of taxonomic expertise in interpretation of metabarcoding studies. Distributed by Dryad. https://doi.org/10.5061/DRYAD.TDZ08KPZX. 2021
- 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. https://doi.org/10.6084/m9.figshare.3471425.v6. 2016
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- National Museum of Natural History Academic Department
