Systematic revision of the Japanese freshwater snail

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19, 1655–1664. doi:10.1101/gr.094052.109

Andy L, Matthew W (2002) Classification and regression by randomForest. R News 2, 18–22.

Annandale N (1916) Zoological results of a tour in the Far East. The Mollusca of Lake Biwa, Japan. Records of the Indian Museum 6, 41–74. doi:10.5962/bhl.title.46524

Boettger O (1886) Zur Kenntniss der Melanien Chinas und Japans. Jahrbücher der Deutschen Malakozoologischen Gesellschaft 13, 1–16.

Breiman L (2001) Random Forests. Machine Learning 45, 5–32. doi:10.1023/A:1010933404324

Brot A (1877) Die Melaniaceen (Melanidae) in Abbildungen nach der Natur mit Beschreibunge. In ‘Systematisches Conchylien-Cabinet von Martini und Chemnitz, Ersten Bandes, Vierundzwanzigste Abtheilung (1) 24 (259)’. (Eds HC. Küster, W Kobelt.) pp. 193–352. (Bauer & Raspe: Nürnberg, Germany)

Burch JB (1968) Cytotaxonomy of some Japanese Semisulcospira (Streptoneura: Pleuroceridae). Journal de Conchyliologie 107, 3–51.

Burch JB, Davis GM (1967) A taxonomic study of some species of the freshwater snail genus Semisulcospira in Japan. Annual Reports for 1967, 36–38.

Callomon P (2017) Research on the collections of the Museum 1. Hirase Malacological collection. The Kyoto University Museum Newsletter 41, 8–9.

Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890. doi:10.1093/bioinformatics/bty560

Covich AP (2010) Winning the biodiversity arms race among freshwater gastropods: competition and coexistence through shell variability and predator avoidance. Hydrobiologia 653, 191–215. doi:10.1007/s10750-010-0354-0

Davis GM (1969) A taxonomic study of some species of Semisulcospira in Japan (Mesogastropoda: Pleuroceridae). Malacologia 7, 211–294.

Du L-N, Guo-Hua Y, Jun-xing Y (2019) Systematic relationships of Chinese freshwater semisulcospirids (Gastropoda, Cerithioidea) revealed by mitochondrial sequences. Zoological Research 40, 1–11. doi:10.24272/j.issn.2095-8137.2019.033

Fukuoka G (1933) Ecological distribution of the freshwater snail Semisulcospira in the environs of Kyôto. Venus 4, 114–118. doi:10.18941/venusomsj.4.2_114

Goto Y, Poppe G (1996) ‘A listing of living mollusca. Part II. Volume I’. (L'Informatore Piceno: Ancona, Italy)

Gould AA (1859) Descriptions of shells collected in the North Pacific Exploring Expedition under Captain Ringgold and Rodgers. Proceedings of the Boston Society of Natural History 7, 40–48. doi:10.1017/CBO9781107415324.004

Habe T (1968) ‘Color Books 157) Japanese shellfish’. (Hoikusha Publishing Co. , Ltd.: Osaka, Japan)

Habe T (1970) Papers on the taxonomy of the Japanese Semisulcospira. Venus 28, 191–192. doi:10.18941/venusjjm.28.4_191

Habe T (1978) Fresh water molluscs in Korea and Japan as the intermediate hosts of trematodes. Yonsei Reports on Tropical Medicine 9, 91–96.

Habe T (1984) Type specimens of the Japanese land and freshwater molluscs collected during the Vega Expedition and housed in the Swedish Natural History Museum in Stockholm. Venus 43, 305–313. doi:10.18941/venusjjm.43.4_305

Habe T, Kosuge S (1967) ‘Common Shells of Japan in Color. 21th Edition’. (Hoikusha Publishing Co., Ltd.: Osaka, Japan)

Higo S, Goto Y (1993) ‘A Systematic List of Molluscan Shells from the Japanese Is. and the Adjacent Area’. (Elle Scientific Publications, Yao, Japan)

Hirase S, Taki I (1951) ‘An Illustrated Handbook of Shells in Natural Colors from the Japanese Islands and Adjacent Territory’. (Bunkyokaku: Tokyo, Japan)

Holomuzki JR, Biggs BJF (2006) Habitat-specific variation and performance trade-offs in shell armature of New Zealand mudsnails. Ecology 87, 1038–1047. doi:10.1890/0012-9658(2006)87[1038:HVAPTI]2.0.CO;2

International Commisson on Zoological Nomenclature (1999) ‘International Code of Zoological Nomenclature’. (International Trust for Zoological Nomenclature: London, UK)

Iwakawa T (1919) ‘Catalogue of Japanese Mollusca in the Natural History Department, Tokyo Imperial Museum’. (Tokyo Imperial Museum: Tokyo, Japan)

Kajiyama H, Habe T (1961) Two new forms of the Japanese melanians, Semisulcospira. Venus 21, 167–176.

Kamiya S, Shimamoto M, Hashimoto T (2011) Allozyme analysis of Japanese Semisulcospira species (Gastropoda: Pleuroceridae) reveals that Lake Biwa endemic species are not monophyletic. American Malacological Bulletin 29, 23–36. doi:10.4003/006.029.0213

Kihira H, Matsuda M, Uchiyama R (2009) ‘Guide of Japanese Freshwater Shellfishes (1). Freshwater Shellfishes in Lake Biwa and Yodo River, Revised Edition’. (Pieces Publishers: Yokohama, Japan)

Kikuchi N, Ohara K, Otani Y, Katori H (1996) ‘Catalogue of the shellfish type specimens described by the late Dr. Tokubei Kuroda in the possession of Nishinomiya City’. (Nishinomiya City: Nishinomiya, Japan)

Kikuchi N, Ohara K, Otani Y, Katori H (1997) ‘Catalogue of the shellfish type specimens described by the late Dr. Tokubei Kuroda except the possession of Nishinomiya City’. (Nishinomiya City: Nishinomiya, Japan)

Kobayashi T (1986) Karyotypes of four species of the genus Semisulcospira in Japan. Venus 45, 127–137. doi:10.18941/venusjjm.45.2_127

Kobelt W (1876) Conchologische Miscellen. Jahrbücher der Deutschen Malakozoologischen Gesellschaft 3, 275–278.

Kobelt W (1879) ‘Fauna molluscorum extramarinorum Japoniae. Nach den von Professor Rein Gemachten Sammlungen’. (Christian Winter: Frankfurt, Germany) doi:10.5962/bhl.title.12881

Köhler F (2016) Rampant taxonomic incongruence in a mitochondrial phylogeny of Semisulcospira freshwater snails from Japan (Cerithioidea: Semisulcospiridae). Journal of Molluscan Studies 82, 268–281. doi:10.1093/mollus/eyv057

Köhler F (2017) Against the odds of unusual mtDNA inheritance, introgressive hybridisation and phenotypic plasticity: systematic revision of Korean freshwater gastropods (Semisulcospiridae, Cerithioidea). Invertebrate Systematics 31, 249–268. doi:10.1071/IS16077

Kubo H (1985) A sinistral specimen of Biwakomelania decipiens from Lake Biwa. Chiribotan 16, 48.

Kuroda T (1929) On Japanese Melanians. Venus 1, 179–193. doi:10.18941/venusomsj.1.5_179

Kuroda T (1941). A catalogue of molluscan shells from Taiwan (Formosa), with description of new species. Memoirs of the Faculty of Science and Agriculture, Taihoku Imperial University 22, 65–216.

Kuroda T (1962) Mollusca in Lake Biwa. Venus 22, 86–91.

Kuroda T, Habe T (1965) Semisulcospira decipiens. In ‘New Illuscrated Encyclopedia of the Fauna of Japan’. (Ed. K, Okada) p. 57. (Hukuryu-kan Publishing Co. Ltd.: Tokyo, Japan)

Kurozumi T (2007) Shellfish. In ‘Survey Report on Ecological Diversity of Fuji Five Lakes in the Northern Area of Mt. Fuji, Central Japan’. (Ed Fuji-hokuroku Ecological Study Group) pp. 61–71. (Fuji-hokuroku Ecological Study Group, Fujiyosida, Japan)

Lamarck JBPA (1799) Prodrome d’une nouvelle classification des coquilles, comprenant une rédaction appropriée des caractères génériques, et l’établissement d’un grand nombre de genres nouveaux. Mémoires de la Société d'Histoire Naturelle de Paris 1, 63–91.

Lopes-Lima M, Hattori A, Kondo T, Hee Lee J, Ki Kim S, Shirai A, Hayashi H, Usui T, Sakuma K, Toriya T, Sunamura Y, Ishikawa H, Hoshino N, Kusano Y, Kumaki H, Utsugi Y, Yabe S, Yoshinari Y, Hiruma H, Tanaka A, Sao K, Ueda T, Sano I, Miyazaki J-I, Gonçalves D V, Klishko OK, Konopleva ES, Vikhrev I V, Kondakov A V, Yu. Gofarov M, Bolotov IN, Sayenko EM, Soroka M, Zieritz A, Bogan AE, Froufe E (2020) Freshwater mussels (Bivalvia: Unionidae) from the rising sun (Far East Asia): phylogeny, systematics, and distribution. Molecular Phylogenetics and Evolution 146, 106755. doi:10.1016/j.ympev.2020.106755

Matsuoka K (1981) Research history of Semisulcospira decipiens and its relatives in Lake Biwa. Kakitsubata 7, 3–6.

Matsuoka K (1985) Pliocene freshwater gastropods from the Iga formation of the Kobiwako group, Mie Prefecture, central Japan. Transactions and proceedings of the Paleontological Society of Japan 139, 180–195.

Matsuoka K, Nakamura T (1981) Preliminary report of the freshwater molluscs from the Pleistocene Katata Formation of the Kobiwako Group in Shiga Prefecture, Japan. Bulletin of the Mizunami Fossil Museum 8, 105–126.

Miura O, Urabe M, Mori H, Chiba S (2020) Ancient drainage networks mediated a large-scale genetic introgression in the East Asian freshwater snails. Ecology and Evolution 10, 8186–8196. doi:10.1002/ece3.6523

Miura O, Urabe M, Nishimura T, Nakai K, Chiba S (2019) Recent lake expansion triggered the adaptive radiation of freshwater snails in the ancient Lake Biwa. Evolution Letters 3, 43–54. doi:10.1002/evl3.92

MolluscaBase (2022) Semisulcospira. Available at https://www.molluscabase.org/aphia.php?p=taxdetails&id=741120

Morrison JPE (1952) World relations of the melanians. American Malacological Union. News Bulletin and Annual Report 1951, 6–9.

Nakajima J (2012) Taxonomic study of the Cobitis striata complex (Cypriniformes, Cobitidae) in Japan. Zootaxa 3586, 103–130. doi:10.11646/zootaxa.3586.1.11

Nakamura M, Wada K, Taki K, Hirayama N (2020) Evolving issues toward improvement of the Lake Biwa–Yodo River Basin governance In ‘Lake Biwa: Interactions between Nature and People. Second Edition. (Eds H Kawanabe, M Nishino, M Maehata.) pp. 485–528. (Springer International Publishing: Cham, Switzerland) doi:10.1007/978-3-030-16969-5_6

Negoro K. (1957) The water quality of Lake Biwa-ko. Japanese journal of limnology 19, 1–22. doi: 10.3739/rikusui.19.1

Nishino M (1991) ‘Benthos in Lake Biwa. Life in watersides’. (Lake Biwa Research Institute, Otsu, Japan)

Nishino M (2021) Semisulcospira (Biwamelania) ourensis, Semisulcospira (Biwamelania) rugosa, Semisulcospira (Biwamelania) dilatata, Semisulcospira (Biwamelania) nakasekoae, Semisulcospira (Biwamelania) fluvialis, Semisulcospira (Biwamelania) arenicola, Semisulcospira (Biwamelania) decipiens, Semisulcospira (Biwamelania) habei. In ‘Red data book of Shiga Prefecture 2020’. (Ed Scientific Committee for Research into the Wildlife in Shiga Prefecture) pp. 605, 607, 609, 610, 612, 620. (Sunrise Publishing Co., Ltd., Otsu, Japan)

Nishino M, Tanida K (2018) ‘Illustration of Lake Biwa benthic fauna. Second Edition’. (Incorporated Administrative Agency Japan Water Agency Lake Biwa Development Integrated Operation & Maintenance Office: Otsu, Japan)

Nishino M, Watanabe NC (2000) Evolution and endmism in Lake Biwa, with special reference to its gastropod mollusc fauna. Advances in Ecological Research 31, 151–180. doi:10.1016/s0065-2504(00)31011-x

Nomoto Y (2001) Studies on the explosive radiation in freshwater snails of the genus Biwamelania. PhD thesis. The University of Tokyo, Japan.

Nomoto Y, Hirai M, Ueshima R (2001) Cloning of molluscan telomere DNA with (TTAGGG) n repeat and its chromosomal location in the freshwater snail Biwamelania habei. Zoological Science 18, 417–422. doi:10.2108/zsj.18.417

Oniwa K, Kimura M (1986) Genetic variability and relationships in six snail species of the genus Semisulcospira. The Japanese journal of genetics 61, 503–514. doi:10.1266/jjg.61.503

Pilsbry HA (1902) Revision of Japanese Viviparidæ, with notes on Melania and Bithynia. Proceedings of the Academy of Natural Sciences of Philadelphia 54, 115–121.

Prozorova LA, Rasshepkina AV (2006) On the radula and pallial gonoduct morphology of the gastropod Biwamelania decipiens and B. multigranosa (Cerithioidea: Pleuroceridae: Semisulcospirinae). Bulletin of the Russian Far East Malacological Society 10, 130–132.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC (2007) PLINK: A Tool Set for Whole- Genome Association and Population-Based Linkage Analyses. The American Journal of Human Genetics 81, 559–575. doi:10.1086/519795

R Development Core Team (2019) R for Windows, Version 3.6.1. R Foundation for Statistical Computing. Available at https://www.R-project.org/

Rintelen T von, Wilson AB, Meyer A, Glaubrecht M (2004) Escalation and trophic specialization drive adaptive radiation of freshwater gastropods in ancient lakes on Sulawesi, Indonesia. Proceedings of the Royal Society of London. Series B: Biological Sciences 271, 2541–2549. doi:10.1098/rspb.2004.2842

Rochette NC, Rivera-Colón AG, Catchen JM (2019) Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Molecular Ecology 28, 4737–4754. doi:10.1111/mec.15253

Sarasin P, Sarasin F (1897) Über die Molluskenfauna der großen Süßwasser-Seen von Central-Celebes. Zoologischer Anzeiger 539, 308–320.

Sawada N, Nakano T (2021) Revisiting a 135-year-old taxonomic account of the freshwater snail Semisulcospira multigranosa: designating its lectotype and describing a new species of the genus (Mollusca: Gastropoda: Semisulcospiridae). Zoological Studies 60, 7. doi:10.6620/ZS.2021.60-07

Sawada N, Fuke Y (2022) Diversification in ancient Lake Biwa: integrative taxonomy reveals overlooked species diversity of the Japanese freshwater snail genus Semisulcospira (Mollusca: Semisulcospiridae). Contributions to Zoology. doi: 10.1163/18759866-bja10035

Sawada N, Nakano T (2022) Insights into sex-related size and shape dimorphism in Semisulcospira niponica (Caenogastropoda: Cerithioidea: Semisulcospiridae). Journal of Molluscan Studies 88, eyac013. doi: 10.1093/mollus/eyac013

Sawada N, Toyohara H, Miyai T, Nakano T (2020) Further records of introduced Semisulcospira snails in Japan (Mollusca, Gastropoda): implications for these snails’ correct morphological identification. BioInvasions Records 9, 310–319. doi:10.3391/bir.2020.9.2.16

Sawada N, Toyohara H, Nakano T (2021) A New cleaning method for accurate examination of freshwater gastropod shell specimens covered with iron-rich deposits. Species Diversity 26, 217–224. doi:10.12782/specdiv.26.217

Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9, 671–675. doi:10.1038/nmeth.2089

Scientific Committee for Research into the Wildlife in Shiga Prefecture (2021) ‘Red data book of Shiga Prefecture 2020’. (Sunrise Publishing Co., Ltd: Hikone, Japan)

Setoguchi Y (2020) Geological History of paleo- and present Lake Biwa. In ‘Lake Biwa: Interactions between Nature and People. Second Edition’. (Eds H Kawanabe, M Nishino, M Maehata.) pp. 17–24. (Springer International Publishing: Cham, Switzerland) doi:10.1007/978-3-030-16969-5_1

Smith EA (1876) Descriptions of some new species of land and freshwater shells, and remarks on other species found in Japan. Quarterly Journal of Conchology 1, 118–127.

Society for the Study of Aquatic Life (1989) ‘Report on research commissioned by the Lake Biwa Research Institute. Studies on the taxonomic reconsideration of the major benthic fauna’. (Lake Biwa Research Institute, Otsu, Japan)

Strong EE, Köhler F (2009) Morphological and molecular analysis of ‘Melania’ jacqueti Dautzenberg and Fischer, 1906: From anonymous orphan to critical basal offshoot of the Semisulcospiridae (Gastropoda: Cerithioidea). Zoologica Scripta 38, 483–502. doi:10.1111/j.1463-6409.2008.00385.x

Suyama Y, Matsuki Y (2015) MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. Scientific Reports 5, 16963. doi:10.1038/srep16963

Tabata R, Kakioka R, Tominaga K, Komiya T, Watanabe K (2016) Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan. Ecology and Evolution 6, 2601–2623. doi:10.1002/ece3.2070

Takami A (1994) The number and size of newborns in Semisulcospira nakasekoae and S. habei (Prosobranchia: Pleuroceridae). Venus 53, 201–209. doi: 10.18941/venusjjm.53.3_201

Takami A (2013) Karyotypes of three lotic species of the genus Semisulcospira (Neotaenioglossa: Pleuroceridae) in Japan. Venus 71, 97–103. doi:10.18941/venus.71.1-2_97

Takami A (2019) Reexamination of the karyotypes of three species of the genus Semisulcospira (Neotaenioglossa: Pleuroceridae). Venus 77, 37–43. doi:10.18941/venus.77.1-4_37

Takigawa Y, Kato S, Nakano T, Nakai K, Tomikawa K, Ishiwata S, Fujita T, Hosoya K, Kawase S, Senou H, Yoshino T, Nishino M (2020) The Vega collection at the end of the nineteenth-century survey of Lake Biwa. In ‘Lake Biwa: Interactions between Nature and People. Second Edition’. (Eds H Kawanabe, M Nishino, M Maehata.) pp. 248–257. (Springer International Publishing: Cham, Switzerland) doi:10.1007/978-3-030-16969-5_2

The Lake Biwa Canal Promotion Council (2022) The Lake Biwa Canal. Available at: https://biwakososui.city.kyoto.lg.jp/en/story/

Troschel FH (1856–1863) ‘Das Gebiss der Schnecken zur Begründung einer natürlichen Classification. Vol. 1.’ (Nicolaische Verlagsbuchhandlung: Berlin, Germany)

Urabe M (1998) Contribution of genetic and environmental factors to shell shape variation in the lotic snail Semisulcospira reiniana (Prosobranchia: Pleuroceridae). Journal of Molluscan Studies 64, 329–343. doi:10.1093/mollus/64.3.329

Urabe M (2000) Phenotypic modulation by the substratum of shell sculpture in Semisulcospira reiniana (Prosobranchia: Pleuroceridae). Journal of Molluscan Studies 66, 53–60. doi:10.1093/mollus/66.1.53

Urabe M (2007) Note on Melania niponica var. minor (Gastropoda: Pleuroceridae). Chiribotan 38, 80–87.

Verhaegen G, Herzog H, Korsch K, Kerth G, Brede M, Haase M (2019) Testing the adaptive value of gastropod shell morphology to flow: a multidisciplinary approach based on morphometrics, computational fluid dynamics and a flow tank experiment. Zoological Letters 5, 5. doi:10.1186/s40851-018-0119-6

Watanabe NC (1970) Studies on three species of Semisulcospira in Lake Biwa : i) Comparative studies of shell form and habitat. Venus 29, 13–30. doi:10.18941/venusjjm.29.1_13

Watanabe NC (1984) Studies on taxonomy and distribution of the freshwater snails, genus Semisulcospira in the three islands inside Lake Biwa. Venus 45, 194–203. doi:10.3739/rikusui.45.194

Watanabe NC, Nishino M (1995) A study on taxonomy and distribution of the freshwater snail, genus Semisulcospira in Lake Biwa, with descriptions of eight new species. Lake Biwa Study Monographs 6, 1–36.

Wenz W (1939) Gastropoda. Teil 3: Prosobranchia. In ‘Handbuch der Paläozoologie Band 6 Lieferung 4’. (Ed. OH, Schindewolf.) pp. 481–720. (Bornträger: Berlin, Germany)

Westerlund A (1883) Von der Vega-expedition in Asien gesammelte Binnen mollusken. Nachrichtsblatt der Deutschen Malakozoologischen Gesellschaft. 15, 48–59.

Yusa Y, Sugiura N, Wada T (2006) Predatory potential of freshwater animals on an invasive agricultural pest, the apple snail Pomacea canaliculata (Gastropoda: Ampullariidae), in southern Japan. Biological Invasions 8, 137–147. doi:10.1007/s10530-004-1790-4