DNA barcoding of freshwater zooplankton in Lake Kasumigaura, Japan

Baek SY, Jang KH, Choi EH, Ryu SH, Kim SK, Lee JH et al (2016) DNA barcoding of metazoan zooplankton copepods from South Korea. PLoS One 11:e0157307. doi:10.1371/journal.pone.0157307 Ban S, Makino W, SakanoH Haruna H, Ueda H (2013) Annual variation in biomass and the community structure of crustacean zooplankton over 5 years in Lake Toya, Japan. Limnology 14:59–70. doi:10.1007/s10201-012-0387-3 Bekker EI, Karabanov DP, Galimov YR, Kotov AA (2016) DNA Barcoding reveals high cryptic diversity in the North Eurasian Moina species (Crustacea: Cladocera). PLoS One 11:e0161737. doi:10.1371/journal.pone.0161737 Benzie JAH (2005) Cladocera: the genus Daphnia (including Daphniopsis). Backhuys Publishers, Leiden Briski E, Cristescu ME, Bailey SA, MacIssac HJ (2011) Use of DNA barcode to detect invertebrate invasive species from diapausing eggs. Biol Invasion 13:1325–1340. doi:10.1007/s10530-010-9892-7 Briski E, Ghabooli S, Bailey SA, MacIsaac HJ (2016) Are genetic databases sufficiently populated to detect non-indigenous species? Biol Invasions 18:1911–1922. doi:10.1007/s10530-016-1134-1 Cieplinski A, Weisse T, Obertegger U (2016) High diversity in Keratella cochlearis (Rotifera, Monogononta): morphological and genetic evidence. Hydrobiologia. doi:10.1007/s10750-016-2781-z Costa FO, deWaard FR, Boutillier F, Ratnasingham S, Dooh ST, Hajibabael M, Hebert PDN (2007) Biological identifications through DNA barcodes: the case of the Crustacea. Can J Fish Aquat Sci 64:272–295. doi:10.1139/f07-008 Costello MJ, May RM, Stork NE (2013) Can we name earth’s species before they go extinct? Science 329:413–416. doi:10.1126/science.1230318 Cristescu MEA, Hebert PDN (2002) Phylogeny and adaptive radiation in the Onychopoda (Crustacea, Cladocera): evidence from multiple gene sequences. J Evol Biol 15:838–849. doi:10.1046/j.1420-9101.2002.00466.x De Melo R, Hebert PDN (1994) A taxonomic reevaluation of North American Bosminidae. Can J Zool 72:1808–1825. doi:10.1139/z94-245 Defaye D, Kawabata K (1993) Mesocyclops dissimilis n. sp. from Lake Biwa, Japan. Hydrobiologia 257:121–126. doi:10.1007/BF00005952 Deiner K, Fronhofer EA, Mächler E, Walser J-C, Altermatt F (2015) Envornmental DNA reveals that rivers are conveyer belt of biodiversity information. Nat Commun 7:12544. doi:10.1038/ncomms12544 Dumont HJ, Negrea S (2002) Introduction to the class Branchiopoda. Backhuys Publishers, Leiden Einsle U (1996) Copepoda: Cyclopoida. SPB Academic Publishing, Amsterdam, Genera Cyclops, Megacyclops, Acanthocyclops Elías-Gutiérrez M, Jerónimo FM, Ivanova NV, Valdez-Moreno M, Hebert PDN (2008) DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries. Zootaxa 1839:1–42 Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotech 3:294–299 Frey DG (1982) Questions concerning cosmopolitanism in Cladocera. Arch Hydrobiol 93:484–502 García-Morales AE, Elías-Gutiérrez M (2013) DNA barcoding of freshwater rotifera in Mexico: evidence of cryptic speciation in common rotifers. Mol Ecol Res 13:1097–1107. doi:10.1111/1755-0998.12080 Geller J, Meyer C, Parker M, Hawk H (2013) Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Mol Ecol Resour 13:851–861. doi:10.1111/1755-0998.12138 Geng X, Zhang L, Xu M, Deng D, Zhang H (2014) PCR amplication and sequence analysis of CO I genes and their flanking regions of mitochondrial DNA from three Daphnia species. J Nanjing Agricultural Univ 37:44–50. doi:10.7685/j.issn.1000-2030.2014.03.006 Hanazato T, Aizaki M (1991) Changes in species composition of cladoceran community in Lake Kasumigaura during 1986–1989: occurrence of Daphnia galeata and its effect on algal biomass. Jpn J Limnol 52:45–55. doi:10.3739/rikusui.52.45 Hanazato T, Yasuno M (1985) Occurrence of Daphnia ambigua Scourfield in Lake Kasumigaura. Jpn J Limnol 46:212–214. doi:10.3739/rikusui.46.212 Hanazato T, Yasuno M (1987) Characteristics of biomass and production of cladoceran zooplankton in Lake Kasumigaura. Jpn J Limnol 48:S45–S57. doi:10.3739/rikusui.48.Special_45 Hebert PDN, Cywinska A, Ball SL, deWaaard JR (2003a) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321. doi:10.1098/rspb.2002.2218 Hebert PDN, Ratnasingham S, deWaard DR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc London B 270(Suppl 1):S96–S99. doi:10.1098/rsbl.2003.0025 Hebert PDN, Witt JDS, Adamowicz SJ (2003c) Phylogeographical patterning in Daphnia ambigua: regional divergence and intercontinental cohesion. Limnol Oceanogr 48:261–268. doi:10.4319/lo.2003.48.1.0261 Ishida T (2002) Illustrated fauna of the freshwater cyclopoid copepods in Japan. Bull Biogeogr Soc Jpn 57:37–106 (in Japanese with English abstract) Jeppesen E, Leavitt PR, De Meester L, Jensen JP (2001) Functional ecology and palaeolimnology: using cladoceran remains to reconstruct anthropogenic impact. Trends Ecol Evol 16:191–198. doi:10.1016/S0169-5347(01)02100-0 Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 Knebelsberger T, Dunz AR, Neumann D, Geiger MF (2015) Molecular diversity of Gemany’s freshwater fishes and lampreys assessed by DNA barcoding. Mol Ecol Res 15:562–572 Kotov AA, Ishida S, Taylor DJ (2009) Revision of the genus Bosmina Baird, 1845 (Cladocera: Bosminidae), based on evidence from male morphological characters and molecular phylogenies. Zool J Linnean Soc 156:1–51. doi:10.1111/j.1096-3642.2008.00475.x Kotov A, Forró L, Korovchinsky NM, Petrusek A (2013) World checklist of freshwater Cladocera species. World Wide Web electronic publication. http://fada.biodiversity.be/group/show/17. Accessed 24 Sept 2015 Lakatos C, Urabe J, Makino W (2015) Cryptic diversity of Japanese Diaphanosoma (Crustacea: Cladocera) revealed by morphological and molecular assessments. Inland Wat 5:253–262. doi:10.5268/IW-5.3.847 Lampert W, Sommer U (1997) Limnoecology. The ecology of lakes and streams. Oxford University Press, Oxford Lim NKM, Tay YC, Srivathsan A, Tan JWT, Kwik JTB, Baloğlu B, Meier R, Yeo DCJ (2016) Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities. R Soc Open Sci 3:160635. doi:10.1098/rsos.160635 Ma X, Wolinska J, Petrusek A, Gießler S, Hu W, Yin M (2016) The phenotypic plasticity in Chinese populations of Daphnia similoides sinensis: recurvate helmeted forms are associated with the presence of predators. J Plankton Res 38:855–864. doi:10.1093/plankt/fbw031 Makino W, Ban S (1998) Diel changes in vertical overlap between Cyclops strenuus (Copepoda; Cyclopoida) and its prey in oligotrophic Lake Toya, Hokkaido, Japan. J Mar Syst 15:139–148. doi:10.1016/S0924-7963(97)00073-0 Makino W, Tanabe AS (2009) Extreme population genetic differentiation and secondary contact in the freshwater copepod Acanthodiaptomus pacificus in the Japanese Archipelago. Mol Ecol 18:3699–3713. doi:10.1111/j.1365-294X.2009.04307.x Makino W, Haruna H, Ban S (1996) Diel vertical migration and feeding rhythm of Daphnia longispina and Bosmina coregoni in Lake Toya, Hokkaido, Japan. Hydrobiologia 337:133–143. doi:10.1007/BF00028514 Makino W, Ohtsuki H, Urabe J (2013) Finding copepod footprints: a protocol for molecular identification of diapausing eggs in lake sediments. Limnology 14:269–282. doi:10.1007/s10201-013-0404-1 Marrone F, Lo Brutto S, Hundsdoerfer AK, Arculeo M (2013) Overlooked cryptic endemism in copepods: systematics and natural history of the calanoid subgenus Occidodiaptomus Borutzky 1991 (Copepoda, Calanoda, Diaptomidae). Mol Phylogenet Evol 66:190–202. doi:10.1016/j.ympev.2012.09.016 Mills S, Alcántara-Rodríguez JA, Ciros-Pérez J, Gómez A, Hagiwara A, Galindo KH, Jersabek CD, Malekzadeh-Viayeh R, Leasi F, Lee J-S, Welch DBM, Papakostas S, Riss S, Segres H, Serra M, Shiel R, Smolak R, Snell TW, Stelzer C-P, Tang CQ, Wallace RL, Fontaneto D, Walsh EJ (2016) Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) trough DNA taxonomy. Hydrobiologia. doi:10.1007/s10750-016-2725-7 Mizuno T, Takahashi E (eds) (2000) An illustrated guide to freshwater zooplankton in Japan (in Japanese). Tokai University Press, Tokyo Obertegger U, Fontaneto D, Flaim G (2012) Using DNA taxonomy to investigate the ecological determinants of plankton diversity: explaining the occurrence of Synchaeta spp. (Rotifera, Monogononta) in mountain lakes. Freshwat Biol 57:1545–1553. doi:10.1111/j.1365-2427.2012.02815.x Obertegger U, Flaim G, Fontaneto D (2014) Cryptic diversity within the rotifer Polyarthra dolichoptera along an altitudinal gradient. Freshwat Biol 59:2413–2427. doi:10.1111/fwb.12447 Pace ML (1986) An empirical analysis of zooplankton community size structure across lake trophic gradients. Limnol Oceanogr 31:45–55. doi:10.4319/lo.1986.31.1.0045 Popova EV, Petrusek A, Kořínek V, Mergeay J, Bekker EI, Karabanov DP, Galimov YR, Neretina TV, Taylor DJ, Kotov AA (2016) Revision of the Old World Daphnia (Ctenodaphnia) similis group (Cladocera, Daphniidae). Zootaxa 4161:1–40. doi:10.11646/zootaxa.4161.1.1 Prosser S, Martínez-Arce A, Elías-Gutiérrez M (2013) A new set of primers for COI amplification from freshwater microcrustaceans. Mol Ecol Res 13:1151–1155. doi:10.1111/1755-0998.12132 Puillandre N, Lambert A, Brouillet S, Achaz G (2012) ABGD, Automated Barcode Gap Discovery for primary species delimitation. Mol Ecol 21:1864–1877. doi:10.1111/j.1365-294X.2011.05239.x Sarri C, Stamatis C, Sarafidou T, Galara I, Godosopoulos V, Kolovos M, Liakou C, Tastsoglou S, Mamuris Z (2014) A new set of 16S rRNA universal primers for identification of animal species. Food Control 43:35–41. doi:10.1016/j.foodcont.2014.02.036 Segers H (2007) Annotated checklist of the rotifers (Phylum Rotifera), with notes on nomenclature, taxonomy and distribution. Zootaxa 1564:1–104 Sørensen MV, Giribet G (2006) A modern approach to rotiferan phylogeny: combining morphological and molecular data. Mol Phylogenet Evol 40:585–608. doi:10.1016/j.ympev.2006.04.001 Takamura N, Nakagawa M, Hanazato T (2017) Zooplankton abundance in the pelagic region of Lake Kasumigaura (Japan): monthly data since 1980. Ecol Res 32:1–1. doi:10.1007/s11284-016-1406-3 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. doi:10.1093/molbev/mst197 Tanaka S (2000) A taxonomic revision of Japanese Bosminidae (Crustacea, Cladocera). Bull Toyama Sci Museum 23:109–125 Tang CQ, Obertegger U, Fontaneto D, Barraclough TG (2014) Sexual species are separated by larger genetic gaps than asexual species in rotifers. Evolution 68:2901–2916. doi:10.1111/evo.12483 Taylor DJ, Ishikane CR, Haney RA (2002) The systematics of Holarctic bosminids and a revision that reconciles molecular and morphological evolution. Limnol Oceanogr 47:1486–1495. doi:10.4319/lo.2002.47.5.1486 Telfer A, Young M, Quinn J, Perez K, Sobel C, Sones J, Levesque-Beaudin V, Derbyshire R, Fernandez-Triana J, Rougerie R, Thevanayagam A, Boskovic A, Borisenko A, Cadel A, Brown A, Pages A, Castillo A, Nicolai A, Glenn Mockford B, Bukowski B, Wilson B, Trojahn B, Lacroix C, Brimblecombe C, Hay C, Ho C, Steinke C, Warne C, Garrido Cortes C, Engelking D, Wright D, Lijtmaer D, Gascoigne D, Hernandez Martich D, Morningstar D, Neumann D, Steinke D, Marco DeBruin D, Dobias D, Sears E, Richard E, Damstra E, Zakharov E, Laberge F, Collins G, Blagoev G, Grainge G, Ansell G, Meredith G, Hogg I, McKeown J, Topan J, Bracey J, Guenther J, Sills-Gilligan J, Addesi J, Persi J, Layton K, D’Souza K, Dorji K, Grundy K, Nghidinwa K, Ronnenberg K, Lee K, Xie L, Lu L, Penev L, Gonzalez M, Rosati M, Kekkonen M, Kuzmina M, Iskandar M, Mutanen M, Fatahi M, Pentinsaari M, Bauman M, Nikolova N, Ivanova N, Jones N, Weerasuriya N, Monkhouse N, Lavinia P, Jannetta P, Hanisch P, McMullin R, Ojeda Flores R, Mouttet R, Vender R, Labbee R, Forsyth R, Lauder R, Dickson R, Kroft R, Miller S, MacDonald S, Panthi S, Pedersen S, Sobek-Swant S, Naik S, Lipinskaya T, Eagalle T, Decaëns T, Kosuth T, Braukmann T, Woodcock T, Roslin T, Zammit T, Campbell V, Dinca V, Peneva V, Hebert P, deWaard J (2015) Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve. Biodivers Data J 3:e6313. doi:10.3897/BDJ.3.e6313 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 Trebitz AS, Hoffman JC, Grant GW, Billehus TM, Pilgrim EM (2015) Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries. Sci Rep 5:12162. doi:10.1038/srep12162 Ueda H, Reed JW (eds) (2003) Copepoda: Cyclopoida. Genera mesocyclops and thermocyclops. Backhuys Publishers, Leiden Xiang X-L, Xi Y-L, Wen X-L, Zhang J-Y, Ma Q (2010) Spatial patterns of genetic differentiation in Brachionus calyciflorus species complex collected from East China in summer. Hydrobiologia 638:67–83. doi:10.1007/s10750-009-0010-8 Xu L, Han B-P, Van Damme K, Vierstraete A, Vanfleteren JR, Dumont HJ (2011) Biogeography and evolution of the Holartic zooplankton genus Leptodora (Crustacea: Branchiopoda: Haplopoda). J Biogeogr 38:359–370. doi:10.1111/j.1365-2699.2010.02409.x Yoshida T, Kagami M, Gurung TB, Urabe J (2001) Seasonal succession of zooplankton in the north basin of Lake Biwa. Aquat Ecol 35:19–29. doi:10.1023/A:1011498202050 Young S-S, Ni M–H, Liu M–Y (2012) Systematic study of the Simocephalus sensu stricto species group (Cladocera: Daphniidae) from Taiwan by morphometric and molecular analyses. Zool Stud 51:222–231 Zhang G, Xi Y-L, Xue Y-H, Xiang X-L, Wen X-L (2015) Coal fly ash effluent affects the distribution of Brachionus calyciflorus sibling species. Ecotoxicol Environ Saf 112:60–67. doi:10.1016/j.ecoenv.2014.09.036