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A Molecular Analysis of the Evolutionary History of Mushroom Corals (Scleractinia: Fungiidae) and Its Consequences for Taxonomic Classifi Cation

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A Molecular Analysis of the Evolutionary History of Mushroom Corals (Scleractinia: Fungiidae) and Its Consequences for Taxonomic Classifi Cation The evolutionary history of parasitic gastropods and their coral hosts in the Indo-Pacific Gittenberger, Adriaan Citation Gittenberger, A. (2006, November 29). The evolutionary history of parasitic gastropods and their coral hosts in the Indo-Pacific. Retrieved from https://hdl.handle.net/1887/5415 Version: Corrected Publisher’s Version Licence agreement concerning inclusion of doctoral thesis in the License: Institutional Repository of the University of Leiden Downloaded from: https://hdl.handle.net/1887/5415 Note: To cite this publication please use the final published version (if applicable). 3 A molecular analysis of the evolutionary history of mushroom corals (Scleractinia: Fungiidae) and its consequences for taxonomic classifi cation Adriaan Gittenberger, Bastian T. Reijnen and Bert W. Hoeksema A molecular analysis of the evolutionary history of mushroom corals (Scleractinia: Fungiidae) and its consequences for taxonomic classifi cation Adriaan Gittenberger, Bastian T. Reijnen and Bert W. Hoeksema National Museum of Natural History, P.O. Box 9517, NL 2300 RA Leiden. E-mail: [email protected] Key words: coral reefs; Scleractinia; Fungiidae; Fungia; taxonomy; Cytochrome Oxidase I; Internal Transcribed Spacer I & II; Indo-Pacifi c Abstract Contents DNA samples from fungiid corals were used to reconstruct the Introduction ......................................................................... 37 phylogeny of the Fungiidae (Scleractinia), based on the mark- Material and methods .......................................................... 38 ers COI and ITS I & II. In some cases coral DNA was isolated Sampling ............................................................................. 38 and sequenced from parasitic gastropods that have eaten from DNA extraction and sequencing ......................................... 38 their host corals, by using fungiid-specifi c primers. Even Sequence alignment and phylogenetic analyses ................. 39 though the present molecular phylogeny reconstructions Results ................................................................................. 42 largely refl ect the one based on morphological characters by General discussion .............................................................. 43 Hoeksema (1989), there are some distinct differences. Most One source for two sequences ......................................... 44 of these are probably linked to parallel or convergent evolution. Excluding intraspecifi c variation .................................... 44 Most fungiid coral species live fi xed to the substrate in juvenile A classifi cation of the Fungiidae ..................................... 47 stage and become detached afterwards. A loss of this ability Cantharellus Hoeksema and Best, 1984 ..................... 47 to become free-living, appears to have induced similar revers- Ctenactis Verrill, 1864 ................................................ 47 als independently in two fungiid species. These species express Fungia Lamarck, 1801 ................................................ 49 ancestral, plesiomorphic character states, known from the Cycloseris Milne Edwards and Haime, 1849 .............. 49 closest relatives of the Fungiidae, like encrusting and multi- Danafungia Wells, 1966 ............................................. 51 stomatous growth forms. Consequently, they were both placed Lobactis Verrill, 1864 .................................................. 53 in the genus Lythophyllon by Hoeksema (1989). However, the Pleuractis Verrill, 1864 ............................................... 53 present molecular analysis indicates that these species are not Verrillofungia Wells, 1966 .......................................... 54 even closely related. Another discrepancy is formed by the Halomitra Dana, 1846 ................................................ 54 separate positions of Ctenactis crassa, away from its conge- Heliofungia Wells, 1966 ............................................. 54 ners, in various cladograms that were based on either of the Herpolitha Eschcholtz, 1825 ...................................... 54 two markers. This may have been caused by one or more bot- Lithophyllon Rehberg, 1892 ........................................ 54 tleneck events in the evolutionary history of that species, which Podabacia Milne Edwards and Haime, 1849 ............. 55 resulted in a much faster average DNA mutation rate in Cten- Polyphyllia Blainville, 1830 ....................................... 55 actis crassa as compared to the other fungiid species. Further- Sandalolitha Quelch, 1884 .......................................... 55 more, it was investigated whether the exclusion of intraspe- Zoopilus Dana, 1846 ................................................... 55 cifi cally variable base positions from molecular data sets might Acknowledgements ............................................................. 55 improve the phylogeny reconstruction. For COI and ITS I&II References ........................................................................... 55 in fungiid corals this has three positive effects: (1) it raised the support values of most branches in the MrBayes, Parsimony and Neighbor Joining consensus trees, (2) it lowered the Introduction number of most parsimonious trees, and (3) it resulted in phylogeny reconstructions that more closely resemble the Most coral species (Scleractinia) show much morphology-based cladograms. Apparently, the exclusion of ecophenotypical variation. Because of this and the intraspecifi c variation may give a more reliable result. There- fore, the present hypotheses about the evolutionary history of low number of plesiomorph characters states, phy- the fungiid corals are based on analyses of both the data sets logeny reconstructions based on morphology are with and without intraspecifi c variation. troublesome. Molecular analyses have helped to 38 A. Gittenberger, B.T. Reijnen, B.W. Hoeksema. – The evolutionary history of mushroom corals Fig. 1. The Indo-Pacifi c region, from the Red Sea to the Hawaiian Archipelago, illustrating the localities of the material used in this study (table 1). Abbreviations: ba, Bali, Indonesia [3]; ha, Oahu, Hawaii [5]; eg, Egypt (Red Sea) [1]; su, Sulawesi, Indonesia [4]; th, Phiphi Islands, Thailand [2]. shed more light upon their evolutionary history. Material and methods Discrepancies between coral phylogeny reconstruc- tions based on either morphological or molecular data are frequently found (Fukami et al., 2004). Sampling Even though such incompatible results have been found in various animal taxa, so-called reticulate The fungiid corals of which a DNA-sample was evolution has been used most predominantly as the analysed, were collected during various expeditions most likely explanation in corals (Diekmann et al., in the Indo-Pacifi c conducted over the last thirty years 2001). Other evolutionary history scenarios, like by either the National Museum of Natural History homeostasis, parallel or convergent evolution, and Naturalis or by affi liated institutes. To get a good bottleneck events are considered less frequently. representation of intraspecifi c molecular variation, Such scenarios may at least partly be the cause of the specimens that were included for each species different mutation speeds in sister taxa or data were preferably taken from populations far apart (fi g. saturation in general. The possibility of misidenti- 1), i.e. Egypt (Red Sea), Thailand (Indian Ocean), fi cations because of e.g. the presence of cryptic Indonesia (Sulawesi and Bali: border of Indian and species is usually also neglected. Pacifi c Oceans) and Hawaii (Pacifi c Ocean). The Characters that are variable within species and coral samples were preserved on ethanol 70% or 96%. within populations are commonly used in molecular All corals were identifi ed twice, after photographs phylogeny reconstructions. Even characters varying and/or specimens, independently by B.W. Hoeksema within individuals are usually included, like the base and A. Gittenberger. positions varying between the copies of ITS se- quenced from one specimen. Such characters are often excluded in morphology-based phylogeny DNA extraction and sequencing reconstructions. Therefore we have analysed the data sets both with and without intraspecifi cally Small pieces of coral tissue and skeleton were scraped variable base positions. off each specimen with a sterile scalpel to fi ll about Parasitic gastropods and their coral hosts – Chapter 3 39 half a 1.5 ml tube. A mixture of 0.003 ml proteinase sisted of 0.0025 ml PCR buffer (10x), 0.0005 ml K (20 mg/ml) and 0.5 ml CTAB buffer, i.e. 2% CTAB, MgCl2 (50 mM), 0.0010 ml forward primer (10 pM), 1.4 M NaCl, 0.2% mercapto-ethanol, 20 mM EDTA 0.0010 ml reverse primer (10 pM), 0.0005 ml dNTP’s and 100 mM TRIS-HCl pH8, was added to the tube (10 mM), 0.0003 ml Taq polymerase (5 units / 0.001 for incubation at 60° C, for c. 15 hours. After incubation ml), 0.0132 ml MilliQ and 0.0010 ml 1:10 DNA the solution was mixed with 0.5 ml Chloroform/ stock-solution (= c. 100 ng DNA). For amplifying Isoamyl alcohol, and centrifuged for 10’at 8000 rpm. the ITS region, 0.0020 ml Qsolution (QIAGEN) was The supernatant was extracted, mixed with 0.35 ml used instead of the 0.0020 ml MilliQ. After the PCR, isopropanol, put aside for c. 15 hours at 4° C and the samples were kept on 4° C until purifi cation by fi nally centrifuged for 10’ at 8000 rpm to precipitate gel extraction using the QIAquick Gel Extraction Kit the DNA. The supernatant
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