Morphological and molecular investigation of Gomphonema longissimum and related taxa from Malili lakes (Indonesia) with comments on diatom evolution in ancient lakes

References

• Amossé, A. (1969). Note sur des Diatomées récoltées en Indochine. Revue Algologique, Nouvelle Série, 9: 326‒344.
   Google Scholar
• Bramburger, A.J., Haffner, G.D. & Hamilton, P.B. (2004). Examining the distributional patterns of the diatom flora of the Malili Lakes, Sulawesi, Indonesia. In Proceedings of the 17th International Diatom Symposium (Poulin, M., editor), 11–25. Biopress, Bristol.
   Google Scholar
• Bramburger, A.J., Haffner, G.D., Hamilton, P.B., Hinz, F. & Hehanussa, P.E. (2006). An examination of species within the genus Surirella from the Malili Lakes, Sulawesi Island, Indonesia, with descriptions of 11 new taxa. Diatom Research, 21: 1–56.
   Web of Science ®Google Scholar
• Bramburger, A.J., Hamilton, P.B., Hehanussa, P.E. & Haffner, G.D. (2008). Processes regulating the community composition and relative abundance of taxa in the diatom communities of the Malili Lakes, Sulawesi Island, Indonesia. Hydrobiologia, 615: 215–224.
   Web of Science ®Google Scholar
• Bramburger, A.J., Hamilton, P.B. & Haffner, G.D. (2014). Effects of a simulated upwelling event on the littoral epilithic diatom community of an ancient tropical lake (Lake Matano, Sulawesi Island, Indonesia). Hydrobiologia, 739: 133–143.
   Web of Science ®Google Scholar
• Darriba, D., Taboada, G.L., Doallo, R. & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9: 772.
   PubMed Web of Science ®Google Scholar
• Eastman, J.T. & McCune, A.R. (2000). Fishes on the Antarctic continental shelf: evolution of a marine species flock? Journal of Fish Biology, 57: 84–102.
   Web of Science ®Google Scholar
• Genkal, S.I., Kulikovskiy, M.S. & Kuznetsova, I.V. (2013). New data on Centrophyceae (Bacillariophyta) of Lake Baikal, Russia. International Journal on Algae, 15: 50–64.
   Google Scholar
• Glaubrecht, M. & Rintelen, T.v. (2008). The species flocks of lacustrine gastropods: Tylomelania on Sulawesi as models in speciation and adaptive radiation. Hydrobiologia, 615: 181–199.
   Web of Science ®Google Scholar
• Glushchenko, A.M., Kulikovskiy, M.S. & Kociolek, J.P. (2017). New diatom species from Gomphonema subtile-group in Southeast Asia. Phytotaxa, 329: 223‒232.
   Web of Science ®Google Scholar
• Greenwood, P.H. (1974). The haplochromine fishes of Lake Victoria, East Africa: the biology and evolution of a species flock. Bulletin of the British Museum of Natural History Zoology, 6: 1‒134.
   Google Scholar
• Greenwood, P.H. (1984). African cichlids and evolutionary theories. In Evolution of Fish Species Flocks (Echelle, A.A. & Kornfield, I., editors), 93‒110. University of Maine, Orono.
   Google Scholar
• Guillard, R.R.L. & Lorenzen, C.J. (1972). Yellow-green algae with chlorophyllide C. Journal of Phycology, 8: 10‒14.
   Web of Science ®Google Scholar
• Haffner, G., Hehanussa, P.E. & Hartoto, D. (2001). The biology and physical processes of large lakes of Indonesia: Lakes Matano and Towuti. In The Great Lakes of the World. Food-web, Health and Integrity (Munawar, M. & Hecky, R.E., editors), 183‒192. Backhuys Publishers, Leiden.
   Google Scholar
• Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95–98.
   Google Scholar
• Hamsher, S.E., Graeff, C.L., Stepanek, J.G. & Kociolek, J.P. (2014). Frustular morphology and polyphyly in freshwater Denticula (Bacillariophyceae) species, and the description of Tetralunata gen. nov. (Epithemiaceae, Rhopalodiales). Plant Ecology and Evolution, 147: 346‒365.
   Web of Science ®Google Scholar
• Herder, F., Nolte, A.W., Pfaender, J., Schwarzer, J., Hadiaty, R.K. & Schliewen, U.K. (2006). Adaptive radiation and hybridization in Wallace’s Dreamponds: evidence from sailfin silversides in the Malili Lakes of Sulawesi. Proceedings of the Royal Society B: Biological Sciences, 273: 2209‒2217.
   Google Scholar
• Herder, F., Pfaender, J. & Schliewen, U.K. (2008). Adaptive sympatric speciation of polychromatic “roundfin” sailfin silverside fish in Lake Matano (Sulawesi). Evolution, 62: 2178‒2195.
   PubMed Web of Science ®Google Scholar
• Hustedt, F. (1942). Süßwasser-Diatomeen des indomalayischen Archipels und der Hawaii-Inseln. Int. Rev. Gesamten Hydrobiol. Hydrogr., 42: 1–252.
   Google Scholar
• Kapustin, D.A. & Kulikovskiy, M.S. (2018). Transfer of Stenopterobia and Surirella taxa (Bacillariophyceae) described from the insular Southeast Asia to the genus Iconella. Nova Hedwigia, Beiheft, 147: 237–245.
   Google Scholar
• Kapustin, D.A., Kulikovskiy, M.S. & Kociolek, J.P. (2017). Celebesia gen. nov., a new cymbelloid diatom genus from the ancient Lake Matano (Sulawesi Island, Indonesia). Nova Hedwigia, Beiheft, 146: 147‒155.
   Google Scholar
• Katoh, K. & Toh, H. (2010). Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics, 26: 1899–1900.
   PubMed Web of Science ®Google Scholar
• Katsev, S., Crowe, S.A., Mucci, A., Sundby, B., Nomosatryo, S., Haffner, G.D. & Fowle, D.A. (2010). Mixing and its effects on biogeochemistry in the persistently stratified, deep, tropical Lake Matano, Indonesia. Limnology and Oceanography, 55: 763–776.
   Web of Science ®Google Scholar
• Kociolek, J.P. & Stoermer, E.F. (1993). Freshwater gomphonemoid diatom phylogeny: preliminary results. Hydrobiologia, 269/270: 31–38.
   Web of Science ®Google Scholar
• Kociolek, J.P., Balasubramanian, K., Blanco, S., Coste, M., Ector, L., Liu, Y., Kulikovskiy, M., Lundholm, N., Ludwig, T., Potapova, M., Rimet, F., Sabbe, K., Sala, S., Sar, E., Taylor, J., Van de Vijver, B., Wetzel, C.E., Williams, D.M., Witkowski, A. & Witkowski, J. (2019). DiatomBase. http://www.diatombase.org on 2019- 06-15.
   Google Scholar
• Kociolek, J.P., Kulikovskiy, M.S. & Solak, C.N. (2013). The diatom genus Gomphoneis Cleve (Bacillariophyceae) from Lake Baikal, Russia. Phytotaxa, 154: 1‒37.
   Web of Science ®Google Scholar
• Kociolek, J.P., Glushchenko, A.M. & Kulikovskiy, M.S. (2015). Typification, valve ultrastructure, and systematic position of Gomphonema gomphopleuroides Amossé ex Kociolek, Glushchenko & Kulikovskiy, an endemic diatom from Southeast Asia. Diatom Research, 30: 247‒255.
   Web of Science ®Google Scholar
• Kociolek, J.P., Kapustin, D.A. & Kulikovskiy, M.S. (2018a). A new, large species of Gomphonema Ehrenberg from ancient Lake Matano, Indonesia. Diatom Research, 33: 241–250.
   Web of Science ®Google Scholar
• Kociolek, J.P., Kulikovskiy M.S., Kuznetsova, I.V., Glushchenko, A.M. & Solak, C.N. (2018b). A putative species flock in the diatom genus Gomphonema Ehrenberg (Bacillariophyta: Gomphonemataceae) from Lake Baikal, Russia: description of six new species similar to G. ventricosum W. Gregory. Cryptogamie, Algologie, 39: 365–388.
   Web of Science ®Google Scholar
• Kociolek, J.P., Woodward, J. & Graeff, C. (2016). New and endemic Gomphonema C.G. Ehrenberg (Bacillariophyceae) species from Hawaii. Nova Hedwigia, 102: 141‒171.
   Web of Science ®Google Scholar
• Kottelat, M. (1991). Sailfin silversides (Pisces: Telmatherinidae) of Lake Matano, Sulawesi, Indonesia, with descriptions of six new species. Ichthyological Exploration of Freshwaters, 1: 321‒344.
   Google Scholar
• Krammer, K. (2002). Cymbella. Diatoms of Europe, 3: 1‒584.
   Google Scholar
• Kulikovskiy, M.S. & Kociolek, J.P. (2014). The diatom genus Gomphonema Ehrenberg in Lake Baikal. I. Morphology and taxonomic history of two endemic species. Nova Hedwigia, Beiheft, 143: 507‒518.
   Google Scholar
• Kulikovskiy, M.S. & Kuznetsova, I.V. (2016). Morphology, taxonomical position, and distribution of the genera of diatoms Ochigma and Khursevichia from Lake Baikal. Inland Water Biology, 9: 226–233.
   Web of Science ®Google Scholar
• Kulikovskiy, M.S., Lange-Bertalot, H., Witkowski, A. & Khursevich, G.K. (2011). Achnanthidium sibiricum (Bacillariophyta), a new species from bottom sediments in Lake Baikal. Algological Studies, 136/137: 77‒87.
   Google Scholar
• Kulikovskiy, M.S., Lange-Bertalot, H., Metzeltin, D. & Witkowski, A. (2012a). Lake Baikal: hotspot of endemic diatoms I. Iconographia Diatomologica, 23: 7‒608.
   Google Scholar
• Kulikovskiy, M.S., Witkowski, A. & Khursevich, G.K. (2012b). Encyonema horstii sp. nov., a species of unusual valve outline from Pleistocene deposits of Lake Baikal. Nova Hedwigia, Beiheft, 141: 365–374.
   Google Scholar
• Kulikovskiy, M.S., Lange-Bertalot, H. & Witkowski, A. (2013). Gliwiczia gen. nov. a new monoraphid diatom genus from Lake Baikal with a description of four species new for science. Phytotaxa, 109: 1‒16.
   Web of Science ®Google Scholar
• Kulikovskiy, M.S., Lange-Bertalot, H., Witkowski, A. & Kuznetsova, I.V. (2014). Description of four species belonging in Cavinula D.G. Mann & Stickle from Lake Baikal with notes on family Cavinulaceae D.G. Mann in Round et al. 1990. Nova Hedwigia, 99: 487–499.
   Web of Science ®Google Scholar
• Kulikovskiy, M.S., Kociolek, J.P., Solak, C.N. & Kuznetsova, I.V. (2015a). The diatom genus Gomphonema Ehrenberg in Lake Baikal. II. Revision of taxa from Gomphonema acuminatum and Gomphonema truncatum-capitatum complexes. Phytotaxa, 233: 251‒272.
   Web of Science ®Google Scholar
• Kulikovskiy, M.S., Lange-Bertalot, H. & Kuznetsova, I.V. (2015b). Lake Baikal: hotspot of endemic diatoms II. Iconographia Diatomologica, 26: 1‒657.
   Google Scholar
• Kulikovskiy, M.S., Lange-Bertalot, H., Kuznetsova, I.V. & Khursevich, G.K. (2015c). Three new species of Eolimna Lange-Bertalot & Schiller (Bacillariophyta) from Lake Baikal. Nova Hedwigia, Beiheft, 144: 199‒209.
   Google Scholar
• Kulikovskiy, M.S., Lange-Bertalot, H., Witkowski, A., Khursevich, G.K. & Kociolek, J.P. (2015d). New species of Eunotia (Bacillariophyta) from Lake Baikal with comments on morphology and biogeography of the genus. Phycologia, 54: 248‒260.
   Web of Science ®Google Scholar
• Kulikovskiy, M.S., Lange-Bertalot, H., Witkowski, A., Khursevich, G.K. & Kuznetsova, I.V. (2015e). Lectotypification of diatoms from Lake Baikal. I. Some species described by A.P. Skabitschewsky. Nova Hedwigia, 100: 215–223.
   Web of Science ®Google Scholar
• Kulikovskiy, M.S., Glushchenko, A.M., Genkal, S.I. & Kuznetsova, I.V. (2016a). Identification Book of Diatoms from Russia. Yaroslavl, Filigran, 1‒804.
   Google Scholar
• Kulikovskiy, M.S, Lange-Bertalot, H., Annenkova, N.V., Gusev, E.S. & Kociolek, J.P. (2016b). Morphological and molecular evidence support description of two new diatom species from the genus Ulnaria in Lake Baikal. Fottea, 16: 34‒42.
   Web of Science ®Google Scholar
• Kulikovskiy, M.S., Lange-Bertalot, H. & Kuznetsova, I.V. (2016c). Cocconeis nanoburyatica sp. nov. – a new monoraphid diatom species from Lake Baikal. Inland Water Biology, 9: 112‒115.
   Web of Science ®Google Scholar
• Kulikovskiy, M.S., Maltsev, Y., Andreeva, S.A., Glushchenko, A.M., Gusev, E.S., Podunay, Y., Ludwig, T.V., Tusset, E. & Kociolek, J.P. (2019). Description of a new diatom genus Dorofeyukea gen. nov. with remarks on phylogeny of the family Stauroneidaceae. Journal of Phycology, 55: 173–185.
   PubMed Web of Science ®Google Scholar
• Levkov, Z., Krstic, S., Metzeltin, D. & Nakov, T. (2007). Diatoms from Lakes Prespa and Ohrid. Iconographia Diatomologica, 16: 1–603.
   Google Scholar
• Levkov, Z., Mitic-Kopanja, D. & Reichardt, E. (2016). The diatom genus Gomphonema from the Republic of Macedonia. Diatoms of Europe, 8: 1‒552.
   Google Scholar
• Maltsev, Y.I., Andreeva, S.A., Kulikovskiy, M.S. & Kociolek, J.P. (2017). Molecular phylogeny of the diatom genus Envekadea (Bacillariophyceae, Naviculales). Nova Hedwigia, Beiheft, 146: 241–252.
   Google Scholar
• Metzeltin, D. & Lange-Bertalot, H. (2007). Tropical diatoms of South America II. Iconographia Diatomologica, 18: 1‒876.
   Google Scholar
• Poettinger, T. & Schubart, C.D. (2014). Molecular diversity of freshwater crabs from Sulawesi and the sequential colonization of ancient lakes. Hydrobiologia, 739: 73–84.
   Web of Science ®Google Scholar
• Pfaender, J., Schliewen, U.K. & Herder, F. (2010). Phenotypic traits meet patterns of resource use in the radiation of “sharpfin” sailfin silverside fish in Lake Matano. Evolutionary Ecology, 24: 957–974.
   Web of Science ®Google Scholar
• Reichardt, E. (2005). Die Identität von Gomphonema entolejum Østrup (Bacillariophyceae) sowie. Revision ähnlicher Arten mit weiter Axialarea. Nova Hedwigia, 81: 115‒144.
   Google Scholar
• Reichardt, E. (2015). Taxonomy and distribution of Gomphonema subtile Ehrenberg (Bacillariophyceae) and six related taxa. Fottea, 15: 27‒38.
   Web of Science ®Google Scholar
• Ribbink, A.J. (1984). Is the species flock concept tenable? In Evolution of Fish Species Flocks (Echelle, A.A. & Kornfield, I., editors), 21‒25. University of Maine, Orono.
   Google Scholar
• Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012). MRBAYES 3.2: Efficient Bayesian phylogenetic inference and model selection across a large model space. Systematic Biology, 61: 539–542.
   PubMed Web of Science ®Google Scholar
• Round, F.E., Crawford, R.M. & Mann, D.G. (1990). The Diatoms. Biology and Morphology of the Genera. Cambridge: Cambridge University Press, 1–747.
   Google Scholar
• Roy, D., Docker, M.F., Haffner, G.D. & Heath, D.D., 2007. Body shape vs. colour associated initial divergence in the Telmatherina radiation in Lake Matano, Sulawesi, Indonesia. Journal of Evolutionary Biology, 20: 1126‒1137.
   PubMed Web of Science ®Google Scholar
• Ruck, E.C. & Theriot, E.C. (2011). Origin and evolution of the canal raphe system in diatoms. Protist, 162: 723–737.
   PubMed Web of Science ®Google Scholar
• Schluter, D. (1996). Adaptive radiation along genetic lines of least resistance. Evolution, 50: 1766‒1774.
   Web of Science ®Google Scholar
• Schmidt, A. et al. (1874–1959). Atlas der Diatomaceenkunde. Aschersleben, Leipzig, Heft 1–120, Tafeln 1–460.
   Google Scholar
• Schubart, C.D., Santl, T. & Koller, P. (2008). Mitochondrial patterns of intra- and interspecific differentiation among endemic freshwater crabs of ancient lakes in Sulawesi. Contributions to Zoology, 77: 83‒90.
   Web of Science ®Google Scholar
• Simonsen, R. (1987). Atlas and Catalogue of the Diatom Types of Friedrich Hustedt. Volume 3. J. Cramer, Berlin-Stuttgart, pp. 1‒620.
   Google Scholar
• Stamatakis, A., Hoover, P. & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web-servers. Systems Biology, 75: 758–771.
   Google Scholar
• Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution, 30: 2725–2729.
   PubMed Web of Science ®Google Scholar
• Vaillant, J., Haffner, G.D. & Cristescu, M.E. (2011). The ancient lakes of Indonesia: towards integrated research on speciation. Integrative and Comparative Biology, 51: 634–643.
   PubMed Web of Science ®Google Scholar
• van Bemmelen, R.W. (1970). The Geology of Indonesia. 2nd Edition. Martinus Nijhoff, The Hague.
   Google Scholar
• Vishnyakov, V.S., Kulikovskiy, M.S., Genkal, S.I. & Kuznetsova, I.V. (2015). Comparative morphological characteristic of diatoms of genus Hannaea Patrick of the two largest lakes of the Baikal rift zone with a description of the new species. Inland Water Biology, 8: 222–231.
   Web of Science ®Google Scholar
• von Rintelen, T., Marwoto, R.M., Haffner, G.D. & Herder, F. (2014). Preface: species research in ancient lakes – classic concepts and new approaches. Hydrobiologia, 739: 1–6.
   Web of Science ®Google Scholar
• Wallace, A.R. (1860). On the zoological geography of the Malay Archipelago. Zoological Journal of the Linnean Society, 4: 172–184.
   Google Scholar
• Walter, R.P., Haffner, G.D. & Heath, D.D. (2009). Dispersal and population genetic structure of Telmatherina antoniae, an endemic freshwater Sailfin silverside from Sulawesi, Indonesia. Journal of Evolutionary Biology, 22: 314–323.
   PubMed Web of Science ®Google Scholar
• Zimmermann, J., Jahn, R. & Gemeinholzer, B. (2011). Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Organisms Diversity & Evolution, 11: 173–192.
   Web of Science ®Google Scholar