Detecting inter- and intra-island genetic diversity: population structure of the endangered crocodile newt, Echinotriton andersoni, in the Ryukyus

  • Takeshi IgawaEmail author
  • Hirotaka Sugawara
  • Masanao Honda
  • Atsushi Tominaga
  • Shohei Oumi
  • Seiki Katsuren
  • Hidetoshi Ota
  • Masafumi Matsui
  • Masayuki Sumida
Research Article


The endangered crocodile newt, Echinotriton andersoni, is a relatively large species of the family Salamandridae and is distributed on six islands in the central part of the Ryukyu Archipelago, Japan. Because of an originally small distribution range and recent habitat loss, this species has been steadily declining in number. To elucidate fine-scale population structure, which is essential for effective conservation management, we analyzed genetic diversity and gene flow based on nine microsatellite loci. Our results identified three different island groups (Amamioshima, Tokunoshima, and Okinawajima) and multiple genetic assemblages within the Amami and Okinawa island groups. The gross genetic variation within each island was positively correlated with island size. Population structure followed a latitudinal cline and isolation by distance, even among geographically isolated islands. In northern Okinawajima, relatively complex genetic structure was observed. This unexpected population structure seems to reflect historical migration and distribution expansion through the formation of land bridges and shifted coastlines in the Pleistocene. We also found that small islands showed little genetic variation (Ukeshima, Sesokojima, and Tokashikijima). In particular, our findings revealed that the Tokashikijima population is at greater risk for extinction than the other populations because it has the smallest effective population size.


Island population Amphibian Microsatellite Population genetics Population structure 



We thank Noriko Iwai and Kazuki Yamamuro for their field assistance. Echinotriton andersoni was designated as a natural monument by Kagoshima and Okinawa Prefectural Governments, and its handling is thus regulated by law. Our sampling was conducted with permission from the Boards of Education of both governments. Moreover, sampling was completed prior to designation of this newt as a rare species of wild fauna and flora of Japan by the national government in 2016.


This work was supported by a Grant-in-Aid for Scientific Research (B and C) (Grant Nos. 24310173, 20510216) to M. S. and a Grant-in-Aid for Young Scientists (B) (Grant Nos. 23710282, 26830144) to T. I. from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Amphibian Research Center, Hiroshima UniversityHigashi-HiroshimaJapan
  2. 2.Graduate School of Science and EngineeringTokyo Metropolitan UniversityHachiojiJapan
  3. 3.Faculty of Life and Environmental SciencesUniversity of TsukubaTsukubaJapan
  4. 4.Faculty of EducationUniversity of the RyukyusNishiharaJapan
  5. 5.Section of Agriculture and ForestAmami City GovernmentAmamiJapan
  6. 6.Biology and Ecology GroupOkinawa Prefectural Institute of Health and EnvironmentNanjoJapan
  7. 7.Institute of Natural and Environmental Sciences, University of Hyogo, and Museum of Nature and Human ActivitiesSandaJapan
  8. 8.Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan

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