Abstract
Rhodeus atremius is an endemic bitterling fish from Japan comprising two endangered subspecies, R. a. atremius and R. a. suigensis. The latter subspecies, which had dramatically declined in last decades, was reported to contain two distinct mtDNA lineages. In order to estimate the optimized units for conservation management, the genetic structure of R. atremius was inferred by analyzing mtDNA and microsatellite markers (MS). Allelic richness and heterozygosity of MS in R. a. suigensis was less than half that in R. a. atremius. In R. a. suigensis, not only within-population genetic diversity but also among-population genetic divergence was low, with the exception of population Ah1, while the diversity was high and the divergence showed isolation by distance in R. a. atremius. In mtDNA and MS, R. a. suigensis concordantly formed a single lineage, while R. a. atremius encompassed four mtDNA lineages, two of which were completely admixed into one group on the basis of MS. In population Ah1 a striking introgression between the two subspecies was suggested by a Bayesian-based assignment test, with the presence of mtDNA haplotype of R. a. atremius. Contrary to the prevailing theory, R. a. suigensis corresponds to a single conservation unit, while three units seem appropriate for R. a. atremius. In addition, low genetic diversity of R. a. suigensis might have arisen mainly as a result of recent bottlenecks before population fragmentation, followed by current anthropogenic effects. Genetic introgression in population Ah1 was probably the result of human transplantation of R. a. atremius.
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References
Akaike H (1974) A new look at the statistical model identification. IEEE Trans Auto Control 19:716–723
Allendorf FW, Luikart G (2006) Conservation and the genetics of populations. Blackwell, Malden, MA
Arai R, Akai Y (1988) Acheilognathus melanogaster, a senior synonym of A. moriokae, with a revision of the genera of the subfamily Acheilognathinae (Cypriniformes, Cyprinidae). Bull Natl Sci Mus Tokyo Ser A 14:199–213
Arai R, Fujikawa H, Nagata Y (2007) Four new subspecies of Acheilognathus bitterlings (Cyprinidae: Acheilognathinae) from Japan. Bull Nat Sci Mus Tokyo Ser A Suppl 1:1–28
Asahida T, Kobayashi T, Saitoh K, Nakayama I (1996) Tissue preservation and total DNA extraction from fish stored at ambient temperature using buffers containing high concentration of urea. Fish Sci 62:727–730
Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MA
Bânârescu P (1990) Zoogeography of fresh waters, vol 1. AULA-Verlag, Wiesbaden
Brown JH, Kodric-Brown A (1977) Turnover rates in insular biogeography: effect of immigration on extinction. Ecology 58:445–449
Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014
Dawson DA, Burland TM, Douglas A, Comber SCL, Bradshaw M (2003) Isolation of microsatellite loci in the freshwater fish, the bitterling Rhodeus sericeus (Teleostei: Cyprinidae). Mol Ecol Notes 3:199–202
Degnan SM (1993) The perils of single gene trees—mitochondrial versus single-copy nuclear DNA variation in white-eyes (Aves: Zosteropidae). Mol Ecol 2:219–225
Di Rienzo A, Peterson AC, Garza JC et al (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci USA 91:3166–3170
Earl DA, Louie KD, Bardeleben C, Swift CC, Jacobs DK (2010) Rangewide microsatellite phylogeography of the endangered tidewater goby, Eucyclogobius newberryi (Teleostei: Gobiidae), a genetically subdivided coastal fish with limited marine dispersal. Conserv Genet 11:103–114
El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree (Argania spinosa (L.) Skeels) endemic of Morocco. Theor Appl Genet 92:832–839
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620
Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491
Excoffier L, Laval G, Schneider S (2005) ARLEQUIN version 3.0: an integrated software package for population genetics data analysis. Evol Bioinform 1:47–50
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587
Felsenstein J (2005) Phylogeny inference package (PHYLIP), version 3.65. University of Washington, Seattle, WA
Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge
Froese R, Pauly D (2010) FishBase. http://www.fishbase.org/search.php. Cited 1 April 2010
Fujiwara H (1998) Search for the origin of rice cultivation. Iwanami Shoten, Tokyo, Japan
Gompert Z, Nice CC, Fordyce JA, Forister ML, Shapiro AM (2006) Identifying units for conservation using molecular systematics: the cautionary tale of the Karner blue butterfly. Mol Ecol 15:1759–1768
Goudet J (2001) FSTAT: a program to estimate and test gene diversities and fixation indices. Version 2.9.3. http://www2.unil.ch/popgen/softwares/fstat.htm
Hashiguchi Y, Kado T, Kimura S, Tachida H (2006) Comparative phylogeography of two bitterlings, Tanakia lanceolata and T. limbata (Teleostei, Cyprinidae), in Kyushu and adjacent districts of Western Japan, based on mitochondrial DNA analysis. Zool Sci 23:309–322
Hedrick PW (2010) Genetics of populations, 4th edn. Jones & Bartlett Publishers, Sudbury, MA
Holsbeek G, Maes GE, Meester DE, Volckaert FAM (2009) Conservation of the introgressed European water frog complex using molecular tools. Mol Ecol 18:1071–1087
Hosoya K (1997) The endangered Japanese freshwater fishes. In: Nagata Y, Hosoya K (eds) Circumstances in endangered Japanese freshwater fishes and their protection. Midori Shobo, Tokyo, pp 3–21
Kalinowski S (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189
Katano O, Mori S (2005) Distribution and ecology of endangered freshwater fishes. In: Katano O, Mori S (eds) The present and future of endangered freshwater fishes—scenario of fruitful conservation. Shinzansha, Tokyo, pp 1–10
Kawamura K (2003) Rhodeus atremius suigensis. In: Ministry of the Environment (ed) Threatened wildlife of Japan. Red data book, 2nd edn, vol 4. Pisces: brackish and fresh water fishes. Japan wildlife research center, Tokyo, pp 46–47
Kawamura K (2005a) Low genetic variation and inbreeding depression in small isolated populations of the Japanese rosy bitterling, Rhodeus ocellatus kurumeus. Zool Sci 22:517–524
Kawamura K (2005b) Values of Rhodeus atremius suigensis. In: Katano O, Mori S (eds) The present and future of endangered freshwater fishes—scenario of fruitful conservation. Shinzansha, Tokyo, pp 142–143
Kawamura K, Ueda T, Arai R et al (2001) Genetic introgression by the rose bitterling, Rhodeus ocellatus ocellatus, into the Japanese rose bitterling, R. o. kurumeus (Teleostei: Cyprinidae). Zool Sci 18:1027–1039
Kawamura K, Katayama M, Miyake T et al (2009) Mechanisms of extinction of native species caused by exotic-related species. Jpn J Ecol 59:131–143
Kimura S (2003) Rhodeus atremius atremius. In: Ministry of the Environment (ed) Threatened wildlife of Japan. Red data book, 2nd edn, vol 4. Pisces: brackish and fresh water fishes. Japan wildlife research center, Tokyo, pp 152–153
Konishi M, Hosoya K, Takata K (2003) Natural hybridization between endangered and introduced species of Pseudorasbora, with their genetic relationships and characteristics inferred from allozyme analyses. J Fish Biol 63:213–231
Kubota H, Watanabe K, Suguro N et al. (2010) Genetic population structure and management units of the endangered Tokyo bitterling, tanakia tanago (cyprinidae). Conserv Genet (in press). doi:10.1007/s10592-10010-10120-x
Leary RF, Allendorf FW, Forbes SH (1993) Conservation genetics of bull trout in the Columbia and Klamath River drainages. Conserv Biol 7:856–865
Luikart G, Cornuet J-M (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv Biol 12:228–237
Luikart G, Allendorf FW, Cornuet J-M, Sherwin WB (1998a) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 89:238–247
Luikart G, Sherwin WB, Steele BM, Allendorf FW (1998b) Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Mol Ecol 7:963–974
Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220
Masembe C, Muwanika VB, Nyakaana S, Arctander P, Siegismund HR (2006) Three genetically divergent lineages of the Oryx in eastern Africa: evidence for an ancient introgressive hybridization. Conserv Genet 7:551–562
Ministry of the Environment (2006) Law for the conservation of endangered species of wild fauna and flora, National endangered species of wild fauna and flora. http://www.env.go.jp/nature/yasei/hozonho/list_domestic.pdf. Cited 1 Jan 2010
Ministry of the Environment (2007) Biodiversity Center of Japan, Japan Integrated Biodiversity Information System. http://www.env.go.jp/press/file_view.php?serial=9944& hou_id=8648. Cited 1 Jan 2010
Miyake T, Kawamura K, Hosoya K, Okazaki T, Kitagawa T (2007) Discovery of the Japanese rosy bitterling, Rhodeus ocellatus kurumeus, in Nara Prefecture. Jpn J Ichthyol 54:139–148
Miyake T, Nakajima J, Komaru A, Kawamura K (2008) Recent distribution of japanese rosy bitterling rhodeus ocellatus kurumeus in kyushu, inferred from mitochondrial DNA and morphology. Nippon Suisan Gakkaishi 74:1060–1067
Mori S, Katano O (2005) The problem and prospect of endangered freshwater fishes conservation. In: Katano O, Mori S (eds) The present and future of endangered freshwater fishes—scenario of fruitful conservation. Shinzansha, Tokyo, pp 13–31
Moritz C (1994) Defining ‘Evolutionarily Significant Units’ for conservation. Trends Ecol Evol 9:373–375
Murakami O, Washitani I (2002) Alien species and invasive alien species issues. In: The Ecological Society of Japan (ed) Handbook of alien species in Japan. Chijin-shokan, Tokyo, pp 3–4
Nagata Y (2002) Rhodeus atremius. In: Kawanabe H, Mizuno N, Hosoya K (eds) Freshwater fishes of Japan. Yamakei Press, Tokyo, pp 331, 360–366
Nagata Y, Fukuhara S (1998) Rhodeus atremius atremius. In: Fisheries Agency in Japan (ed) Basic data of rare wild aquatic organisms in Japan (V). Japan Fisheries Resource Conservation Association, Tokyo, pp 41–45, 50
Nakamura M (1969) Cyprinid fishes of Japan. Research Institute for Natural Resources, Tokyo
Nei M (1972) Genetic distance between populations. Am Nat 106:283–292
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590
Neki A, Neki O (1997) Small ecology system of fishes in the area of water: way for irrigation, and the pernicious influence to this system by the improvement and its restoration: as a case study of the Okayama plains. Bull Nagaoka Univ Technol 19:141–150
Okazaki M, Naruse K, Shima A, Arai R (2001) Phylogenetic relationships of bitterlings based on mitochondrial 12S ribosomal DNA sequences. J Fish Biol 58:89–106
Onikura N, Nakajima J, Eguchi K et al (2006) Change in distribution of bitterlings, and effects of urbanization on populations of bitterlings and unionid mussels in Tatara River system, Kyushu, Japan. J Jpn Soc Water Environ 29:837–842
Onikura N, Nakajima J, Eguchi K et al (2007) Relationships between the appearances and populations of freshwater fish species and the revetment conditions in the creeks around sea of Ariake, northwestern Kyushu island, Japan. J Jpn Soc Water Environ 30:277–282
Piry S, Luikart G, Cornuet J-M (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90:502–503
Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Raymond M, Rousset F (1995) GENEPOP version 1.2: population genetics software for exact tests and ecumenicism. J Hered 86:248–249
Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225
Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228
Ryder OA (1986) Species conservation and systematics: the dilemma of subspecies. Trends Ecol Evol 1:9–10
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Slatkin M (1985) Rare alleles as indicators of gene flow. Evolution 39:53–65
Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462
Smith C, Reichard M, Jurajda P, Przybylski M (2004) The reproductive ecology of the European bitterling (Rhodeus sericeus). J Zool 262:107–124
Suzuki N (1995) Rhodeus atremius suigensis. In: Fisheries Agency in Japan (ed) Basic data of rare wild aquatic organisms in Japan (II). Japan Fisheries Resource Conservation Association, Tokyo, pp 308–313, 386
Suzuki N, Hibiya T (1984) Development of eggs and larvae of two bitterlings, Rhodeus atremius and R. suigensis (Cyprinidae). Jpn J Ichthyol 31:287–296
Swofford AR (1999) PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods), version 4.0. Sinauer, Sunderland
Tabe M (1993) Genetic research of Rhodeus atremius suigensis in Ashida river. A School Board of Fukuyama, Hiroshima
Taki Y (1993) History of earth told by fish. Gihodo Shuppan, Tokyo
van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538
Vrijenhoek RC (1998) Conservation genetics of freshwater fish. J Fish Biol 53(Supplement A):394–412
Waples RS (2002) Definition and estimation of effective population size in the conservation of endangered species. In: Beissinger SR, McCullough DR (eds) Population viability analysis. The University of Chicago Press, Chicago, pp 147–168
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370
Wiepkema PR (1961) An ethological analysis of the reproductive behavior of the bitterling (Rhodeus amarus Bloch). Arch Neerl Zool 14:103–199
Acknowledgments
We thank the staff of the Ministry of the Environment of Japan and Okayama Prefecture Environmental Conservation Agency for supplying samples of R. a. suigensis. We also thank Carl Smith (University of St. Andrews, UK) for comments and English revision. We express sincere thanks to two anonymous reviewers for the critical comments and useful suggestions that have helped us to improve our paper considerably. This study was carried out as a part of a conservation project for R. a. suigensis organized by the Ministry of Environment of Japan, the Fisheries Agency in Japan and Okayama Prefectural Office. This study was partly supported by Interdisciplinary Research Institute of Environmental Sciences.
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Miyake, T., Nakajima, J., Onikura, N. et al. The genetic status of two subspecies of Rhodeus atremius, an endangered bitterling in Japan. Conserv Genet 12, 383–400 (2011). https://doi.org/10.1007/s10592-010-0146-0
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DOI: https://doi.org/10.1007/s10592-010-0146-0