Advertisement

Genetic Structure of Japanese Populations of Tachypleus tridentatus by mtDNA AT-Rich Region Sequence Analysis

  • Shin Nishida
  • Hiroko Koike
Chapter

Abstract

Tachypleus tridentatus is distributed from coastal Southeast Asia to western Japan. The northernmost population of this species, the Japanese population, is rapidly decreasing due to loss of tidal flats and spawning beaches, and the deterioration of coastal waters. To examine the genetic structure and the genetic diversity of the Japanese population, over 290 samples from nine localities were analyzed using hemolymph, egg, and muscle. The AT-rich region (control region, 369 base pairs) of mitochondrial DNA (mtDNA) was analyzed. Sequences of nuclear integrations of mtDNA (numt) were found in this species, with high sequence similarity to mtDNA. Therefore, to identify “true” mtDNA sequences, long PCR was conducted to amplify the majority of the circular mtDNA molecule. Specific primers were then designed for amplification of the mtDNA AT-rich region. Seven haplotypes were identified based on the sequence of the AT-rich regions from the Japanese populations. All haplotypes were related and closely connected by a single substitution. Haplotype AT1 was dominant and was observed in all regions examined. Two genetic groups were detected based on distribution of haplotypes and significant F ST or Φ ST. Sampling localities in the eastern group were almost monomorphic for AT1, with a few rare haplotypes, resulting in a low haplotype diversity, while the western group was comprised of haplotypes AT1, AT2, and AT3, and consequently higher haplotype diversity than in the eastern groups. These results suggested that the northernmost population of this species might have been formed recently and that the dispersal rate has been relatively low, leading to the formation of genetically distinct populations.

Keywords

Japanese Population Tidal Flat Sandy Beach Horseshoe Crab Western Group 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We thank the following institutions and individuals for their supports and collection of samples: Fukuoka branch of the Japan Kabutogani wo Mamoru Kai (Society of conservation for horseshoe crab, Japan), the Saikai Pearl-Sea Center, the Marine World Umino-Nakamichi, Kyushu Environmental Evaluation Association, Environmental Bureau of Fukuoka City, Federation of Fisheries Cooperative Association of Kafuri, Imari High School, Kawakami, Y., Iwaoka, C., Hayashi, O., Takahashi, S., Hayakawa, O., Sakemi, R., Sugimoto, S., Nishihara, S., Shiokawa, N., Harada, N., Ono, G., Teshima, T., Maeda, K., Wada, T., Okamura, T., Kotoh, S., Ohira, Y., Michiyama, A., Kido, Y., Shibata, K., Mansyo, M., and Hamada, M.

References

  1. Allendorf AW, Luikart G (2007) Conservation and the Genetics of Populations. Blackwell Publishing, OxfordGoogle Scholar
  2. Avise JC, Nelson WS, Sugita H (1994) A speciational history of ‘living fossils’: Molecular evolutionary patterns in horseshoe crabs. Evolution 48:1986–2001CrossRefGoogle Scholar
  3. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48PubMedCrossRefGoogle Scholar
  4. 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 131:479–491PubMedGoogle Scholar
  5. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50Google Scholar
  6. Frankham R, Ballou JD, Briscoe, DA. (2002) Introduction to Conservation Genetics. Cambridge University Press, OxfordCrossRefGoogle Scholar
  7. Harada N (2003) Long-term breeding of the Tachypleus tridentatus, egg to adult. Kabutogani 23:16–17 (In Japanese)Google Scholar
  8. Itow T (1993) Crisis in the Seto Inland Sea: the decimation of the horseshoe crab. EMECS Newslett 3:10–11Google Scholar
  9. Kawahara D (1982) Investigations on ecology of horseshoe crab larvae. Aquabiology (Kaiyou to Seibutsu) 4:380–382 (In Japanese)Google Scholar
  10. King TM, Eackles MS (2004) Microsatellite DNA markers for the study of horseshoe crab (Limulus polyphemus) population structure. Mol Ecol Note 4:394–396CrossRefGoogle Scholar
  11. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163PubMedCrossRefGoogle Scholar
  12. Lavrov DV, Boore JL, Brown WM (2000) The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus. Mol Biol Evol 17:813–824PubMedCrossRefGoogle Scholar
  13. Ministry of the Environment (2000) Red list of Threatened Wildlife of Japan: Arthropods. URL: http://www.biodic.go.jp/J-IBIS.html (In Japanese)
  14. Ministry of the Environment (2006) Threatened Wildlife of Japan -Red Data Book 2nd ed.- Volume 7, Arthropods, Japan Wildlife Research Center, TokyoGoogle Scholar
  15. Nishii H (Ed.) (1975) Kabutogani-Jiten (Encyclopedia of the Horseshoe Crabs), Add. Rev. Ed. Private Publ., Kasaoka (In Japanese)Google Scholar
  16. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New YorkGoogle Scholar
  17. Ohshima K (1990) The history of straits around the Japanese islands in the Late-Quaternary. Quatern Res 29:193–208 (In Japanese with English abstract)Google Scholar
  18. Pierce J, Tan G, Gaffney PM (2000) Delaware Bay and Chesapeake Bay population of horseshoe crab Limulus polyphemus are genetically distinct. Estuaries 23:690–698CrossRefGoogle Scholar
  19. Sakemi R (1997) Observations of larvae behavior in horseshoe crab at the Imari Bay. Kabutogani 17:30–31 (In Japanese)Google Scholar
  20. Saunders NC, Kessler LG, Avise JC (1986) Genetic variation and geographic differentiation in mitochondrial DNA of the horseshoe crab, Limulus polyphemus. Genetics 112:613–627PubMedGoogle Scholar
  21. Sekiguchi K (1988) Biology of Horseshoe Crabs. Science House, TokyoGoogle Scholar
  22. Selander RK, Yang SY, Lewontin RC, Johnson WE (1970) Genetic variation in the horseshoe crab (Limulus polyphemus), a phylogenetic ‘relic’. Evolution 24:402–414CrossRefGoogle Scholar
  23. Shuster CN Jr (1982) A pictorial review of the natural history and ecology of the horseshoe crab, Limulus polyphemus, with reference to other Limulidae. In: Bonaventura J, Bonaventura C, Tesh S (eds) Physiology and Biology of Horseshoe Crabs. Alan R. Liss, New York, pp 1–52Google Scholar
  24. Sugawara K, Yonekawa H, Tagashima Y, Sekiguchi K (1988) Mitochondrial DNA polymorphisms. In Sekiguchi K (ed) Biology of Horseshoe Crabs. Science House, Tokyo, pp 375–382Google Scholar
  25. Vila M, Björklund M (2004) The utility of the neglected mitochondrial control region for evolutionary studies in lepidoptera (insecta). J Mol Evol 58:280–290PubMedCrossRefGoogle Scholar
  26. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  27. Wright S (1951) The genetical structure of populations. Ann Eugen 15:323–354Google Scholar
  28. Yang M-C, Chen CA, Hsieh H-L, Chen C-P (2007) Population subdivision of the tri-spine horseshoe crab, Tachypleus tridentatus, in Taiwan Strait. Zool Sci 24:219–224PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Department of BiodiversityGraduate School of Social and Cultural Studies, Kyushu UniversityNishi-ku, FukuokaJapan
  2. 2.Laboratory of BiodiversityGraduate School of Social and Cultural Studies, Kyushu UniversityFukuokaJapan

Personalised recommendations