References
- Allen GR. 1972. Anemonefishes: their classification and biology. Neptune (NJ): T.F.H Publications. p. 1–272.
- Allen GR. 1975. The anemonefishes: their classification and biology. Neptune (NJ): T.F.H Publications. p. 1–352.
- Allen GR, Drew J, Fenner D. 2010. Amphiprion pacificus, a new species of anemonefish (Pomacentridae) from Fiji, Tonga, Samoa, and Wallis Island. Aqua, International Journal of Ichthyology. 16(3):129–139.
- Allen GR, Steene R, Humann P, Deloach N. 2005. Reef fish identification: tropical pacific. 2nd ed. Jacksonville, FL: New World Publications. p. 64–67.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology. 215:403–410. DOI:10.1016/S0022-2836(05)80360-2.
- Astakhov DA. 2002. Species composition of anemonefishes (Perciformes, Pomacentridae) and their symbiotic sea anemones (Cnidaria, Actiniaria) in the Khanhhoa province (South Vietnam). Journal of Ichthyology. 42(1):37–50.
- Astakhov DA, Savinkin OV, Ponomarev SA. 2016. Fauna of anemonefishes (Pomacentridae, Amphiprioninae) and their host sea anemones (Cnidaria, Actiniaria) on reefs of Phu Quy, Con Son, and An Thoi islands (South China Sea, South Vietnam, and Gulf of Thailand) and a review of these groups from the coasta. Journal of Ichthyology. 56:832–847. DOI:10.1134/S0032945216060011.
- Balbuena JA, Míguez-Lozano R, Blasco-Costa I. 2013. PACo: a novel procrustes application to cophylogenetic analysis. PLoS One. 8:e61048. DOI:10.1371/journal.pone.0061048.
- Baudet C, Donati B, Sinaimeri B, Crescenzi P, Gautier C, Matias C, Sagot M-F. 2015. Cophylogeny reconstruction via an approximate Bayesian computation. Systematic Biology. 416–431. DOI:10.1093/sysbio/syu129.
- Burke KS, Nedosyko A. 2016. Sea anemones and anemonefish: a match made in heaven. In: Goffredo S, Dubinsky Z, editors. The Cnidaria, past, present and future. 1st ed. Cham, Switzerland: Springer International Publishing; p. 425–438.
- Charleston MA, Perkins SL. 2006. Traversing the tangle: algorithms and applications for cophylogenetic studies. Journal of Biomedical Informatics. 39:62–77. DOI:10.1016/j.jbi.2005.08.006.
- Charleston MA, Robertson DL. 2002. Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Systematic Biology. 51:528–535. DOI:10.1080/10635150290069940.
- Chen CA, Yu JK. 2000. Universal primers for amplification of mitochondrial small subunit ribosomal RNA-encoding gene in Scleractinian corals. Marine Biotechnology. 2:146–153. DOI:10.1007/s101269900018.
- Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R. 2010. Jane: a new tool for the cophylogeny reconstruction problem. Algorithms for Molecular Biology. 5:16. DOI:10.1186/1748-7188-5-16.
- Cruaud A, Rønsted N, Chantarasuwan B, Chou LS, Clement WL, Couloux A, Cousins B, Genson G, Harrison RD, Hanson PE, Hossaert-McKey M, et al. 2012. An extreme case of plant-insect codiversification: figs and fig-pollinating wasps. Systematic Biology. 61:1029–1047. DOI:10.1093/sysbio/sys068.
- Daly M, Chaudhuri A, Gusmão L, Rodríguez E. 2008. Phylogenetic relationships among sea anemones (Cnidaria: Anthozoa: Actiniaria). Molecular Phylogenetics and Evolution. 48:292–301. DOI:10.1016/j.ympev.2008.02.022.
- Daly M, Gusmão LC, Reft AJ, Rodríguez E. 2010. Phylogenetic signal in mitochondrial and nuclear markers in sea anemones (Cnidaria, Actiniaria). Integrative and Comparative Biology. 50:371–388. DOI:10.1093/icb/icq081.
- Deng J, Yu F, Bin LH, Gebiola M, Desdevises Y, Wu SA, Zhang YZ. 2013. Cophylogenetic relationships between Anicetus parasitoids (Hymenoptera: Encyrtidae) and their scale insect hosts (Hemiptera: Coccidae). BMC Evolutionary Biology. 13:275. DOI:10.1186/1471-2148-13-275.
- Doña J, Sweet AD, Johnson KP, Serrano D, Mironov S, Jovani R. 2017. Cophylogenetic analyses reveal extensive host-shift speciation in a highly specialized and host-specific symbiont system. Molecular Phylogenetics and Evolution. 115:190–196. DOI:10.1016/j.ympev.2017.08.005.
- Dunn DF. 1981. The clownfish sea anemones: Stichodactylidae (Coelenterata: Actiniaria) and other sea anemones symbiotic with pomacentrid fishes. Transactions of the American Philosophical Society. 71:3–115. DOI:10.2307/1006382.
- Elliott JK, Lougheed SC, Bateman B, McPhee LK, Boag PT. 1999. Molecular phylogenetic evidence for the evolution of specialization in anemonefishes. Proceedings of the Royal Society B: Biological Sciences. 266:677–685. DOI:10.1098/rspb.1999.0689.
- Emblem Å, Okkenhaug S, Weiss ES, Denver DR, Karlsen BO, Moum T, Johansen SD. 2014. Sea anemones possess dynamic mitogenome structures. Molecular Phylogenetics and Evolution. 75:184–193. DOI:10.1016/j.ympev.2014.02.016.
- Fautin DG. 1991. The anemonefish symbiosis: what is known and what is not. Symbiosis. 10:23–46.
- Fautin DG. 2008. Sea anemones (Cnidaria: Anthozoa: Actiniaria) of Moreton Bay. Memoirs of the Queensland Museum. Nature 54(1):35–64.
- Fautin DG. 2016. Catalog to families, genera, and species of orders Actiniria and Corallimorpharia (Cnidaria: Anthozoa). Zootaxa. 4145(1):1–449. DOI:10.11646/zootaxa.4145.1.1.
- Fautin DG, Allen GR. 1997. Anemonefishes and their host anemones: a guide for aquarists and divers. Perth: Western Australian Museum. p. 1–160.
- Filipiak A, Zając K, Kübler D, Kramarz P. 2016. Coevolution of host-parasite associations and methods for studying their cophylogeny. Invertebrate Survival Journal. 13:56–65.
- Fountain ED, Pauli JN, Mendoza JE, Carlson J, Peery MZ. 2017. Cophylogenetics and biogeography reveal a coevolved relationship between sloths and their symbiont algae. Molecular Phylogenetics and Evolution. 110:73–80. DOI:10.1016/j.ympev.2017.03.003.
- Godinot C, Chadwick NE. 2009. Phosphate excretion by anemonefish and uptake by giant sea anemones: demand outstrips supply. Bulletin of Marine Science. 85:1–9.
- Godwin J, Fautin DG. 1992. Defense of host Actinians by anemonefishes. Copeia. 1992:902. DOI:10.2307/1446171.
- Hall TA. 1999. Bioedit: a user-frendly biolobical senquence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 41:95–98.
- Holbrook SJ, Schmitt RJ. 2004. Population dynamics of a damselfish: effects of a competitor that also is an indirect mutualist. Ecology. 85:979–985. www.jstor.org/stable/3450313 doi: 10.1890/03-0406
- Holbrook SJ, Schmitt RJ. 2005. Growth, reproduction and survival of a tropical sea anemone (Actiniaria): benefits of hosting anemonefish. Coral Reefs. 24:67–73. DOI:10.1007/s00338-004-0432-8.
- Jang-Liaw N-H, Tang KL, Hui C, Shao K. 2002. Molecular phylogeny of 48 species of damselfishes (Perciformes: Pomacentridae) using 12S mtDNA sequences. Molecular Phylogenetics and Evolution. 25:445–454. doi: 10.1016/S1055-7903(02)00278-6
- Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 33:1870–1874. DOI:10.1093/molbev/msw054.
- Larson PG, Daly M. 2016. Phylogenetic analysis reveals an evolutionary transition from internal to external brooding in Epiactis Verrill (Cnidaria: Anthozoa: Actiniaria) and rejects the validity of the genus Cnidopus Carlgren. Molecular Phylogenetics and Evolution. 94:548–558. DOI:10.1016/j.ympev.2015.10.008.
- Lauron EJ, Loiseau C, Bowie RCK, Spicer GS, Smith TB, Melo M, Sehgal RNM. 2015. Coevolutionary patterns and diversification of avian malaria parasites in African sunbirds (family Nectariniidae). Parasitology. 142:635–647. DOI:10.1017/S0031182014001681.
- Lefoulon E, Bain O, Makepeace BL, d’Haese C, Uni S, Martin C, Gavotte L. 2016. Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts. PeerJ. 4:e1840. DOI:10.7717/peerj.1840.
- Legendre P, Desdevises Y, Bazin E. 2002. A statistical test for host – parasite coevolution. Systematic Biology. 51:217–234. DOI:10.1080/10635150252899734.
- Li J, Chen X, Kang B, Liu M. 2015. Mitochondrial DNA genomes organization and phylogenetic relationships analysis of eight anemonefishes (Pomacentridae: Amphiprioninae). PLoS One. 10(4). DOI:10.1371/journal.pone.0123894.
- Litsios G, Pearman PB, Lanterbecq D, Tolou N, Salamin N. 2014. The radiation of the clownfishes has two geographical replicates. Journal of Biogeography. 41:2140–2149. DOI:10.1111/jbi.12370.
- Litsios G, Sims CA, Wüest RO, Pearman PB, Zimmermann NE, Salamin N. 2012. Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evolutionary Biology. 12(212). DOI:10.1186/1471-2148-12-212.
- Mariscal RN. 1970. The nature of the symbiosis between Indo-Pacific anemone fishes and sea anemones. Marine Biology. 6:58–65. DOI:10.1007/BF00352608.
- Martínez-Aquino A. 2016. Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees. Current Zoology. 62:393–403. DOI:10.1093/cz/zow018.
- Mebs D. 2009. Chemical biology of the mutualistic relationships of sea anemones with fish and crustaceans. Toxicon. 54:1071–1074. doi: 10.1016/j.toxicon.2009.02.027
- Merkle D, Middendorf M, Wieseke N. 2010. A parameter-adaptive dynamic programming approach for inferring cophylogenies. BMC Bioinformatics. 11:1–10. DOI:10.1186/1471-2105-11-S1-S60.
- Nelson LA, Davies KA, Scheffer SJ, Taylor GS, Purcell MF, Giblin-Davis RM, Thornhill AH, Yeates DK. 2014. An emerging example of tritrophic coevolution between flies (Diptera: Fergusoninidae) and nematodes (Nematoda: Neotylenchidae) on myrtaceae host plants. Biological Journal of the Linnean Society. 111:699–718. DOI:10.1111/bij.12237.
- Nguyen H-TT, Tran A-NT, Dang BT, Ha LTL, Ngo DN, Geffen AJ. 2019. Host choice and fitness of anemonefish Amphiprion ocellaris (Perciformes: Pomacentridae) living with host anemones (Anthozoa: Actiniaria) in captive conditions. Journal of Fish Biology. 94:937–947. DOI:10.1111/jfb.13910.
- Ollerton J, Mccollin D, Fautin DG, Allen GR. 2007. Finding NEMO : nestedness engendered by mutualistic organization in anemonefish and their hosts. Proceedings of the Royal Society B: Biological Sciences. 274:591–598. DOI:10.1098/rspb.2006.3758.
- Palumbi SR, Martin A, Romano S, McMillan WO, Stice L, Grabowski G. 2002. The simple fool’s guide to PCR version 2. Honolulu, HI: University of Hawaii. p. 1–45. http://palumbi.stanford.edu/SimpleFoolsMaster.pdf .
- Paradis E, Schliep K. 2019. Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 35:526–528. DOI:10.1093/bioinformatics/bty633.
- Porat D, Chadwick-Furman NE. 2004. Effects of anemonefish on giant sea anemones: expansion behavior, growth, and survival. Hydrobiologia. 530:513–520. DOI:10.1007/s10750-004-2688-y.
- Porat D, Chadwick-Furman NE. 2005. Effects of anemonefish on giant sea anemones: ammonium uptake, zooxanthella content and tissue regeneration. Marine and Freshwater Behaviour and Physiology. 38:43–51. DOI:10.1080/10236240500057929.
- Rodríguez E, Barbeitos MS, Brugler MR, Crowley LM, Grajales A, Gusmão L, Häussermann V, Reft A, Daly M. 2014. Hidden among sea anemones: the first comprehensive phylogenetic reconstruction of the order Actiniaria (Cnidaria, Anthozoa, Hexacorallia) reveals a novel group of hexacorals. PLoS One. 9:e96998. DOI:10.1371/journal.pone.0096998.
- Rolland J, Silvestro D, Litsios G, Faye L, Salamin N. 2018. Clownfishes evolution below and above the species level. Proceedings of the Royal Society B: Biological Sciences. 285:20171796. DOI:10.1098/rspb.2017.1796.
- Roopin M, Henry RP, Chadwick NE. 2008. Nutrient transfer in a marine mutualism: patterns of ammonia excretion by anemonefish and uptake by giant sea anemones. Marine Biology. 154:547–556. DOI:10.1007/s00227-008-0948-5.
- Saenz-Agudelo P, Jones G, Thorrold S, Planes S. 2011. Detrimental effects of host anemone bleaching on anemonefish populations. Coral Reefs. 30:497–506. DOI:10.1007/s00338-010-0716-0.
- Santini S, Polacco G. 2006. Finding Nemo: molecular phylogeny and evolution of the unusual life style of anemonefish. Gene. 385:19–27. DOI:10.1016/j.gene.2006.03.028.
- Schliep KP. 2011. Phangorn: phylogenetic analysis in R. Bioinformatics. 27:592–593. DOI:10.1093/bioinformatics/btq706.
- Schmiege PFP, D’Aloia CC, Buston PM. 2017. Anemonefish personalities influence the strength of mutualistic interactions with host sea anemones. Marine Biology. 164:24. DOI:10.1007/s00227-016-3053-1.
- Scott A, Francisco B. 2006. Observations on the feeding behaviour of resident anemonefish during host sea anemone spawning. Coral Reefs. 25:451. DOI:10.1007/s00338-006-0126-5.
- Shearer TL, Gutiérrez-Rodríguez C, Coffroth MA. 2005. Generating molecular markers from zooxanthellate cnidarians. Coral Reefs. 24:57–66. DOI:10.1007/s00338-004-0442-6.
- Szczebak JT, Henry RP, Al-Horani FA, Chadwick NE. 2013. Anemonefish oxygenate their anemone hosts at night. Journal of Experimental Biology. 216:970–976. DOI:10.1242/jeb.075648.
- Tehrani JJ, Collard M, Shennan SJ. 2010. The cophylogeny of populations and cultures: reconstructing the evolution of Iranian tribal craft traditions using trees and jungles. Philosophical Transactions of the Royal Society of London B Biological Sciences. 365:3865–3874. DOI:10.1098/rstb.2010.0020.
- Titus BM, Benedict C, Laroche R, Gusmão LC, Van Deusen V, Chiodo T, Meyer CP, Berumen ML, Bartholomew A, Yanagi K, et al. 2019. Phylogenetic relationships among the clownfish-hosting sea anemones. Molecular Phylogenetics and Evolution. 139:106526. DOI:10.1016/j.ympev.2019.106526.