A time-calibrated phylogenetic approach to assessing the phylogeography, colonization history and phenotypic evolution of snakes in the Japanese Izu Islands

Journal of Biogeography

Volumn 38, Issue 2, 2011, Pages 259-271

  Kuriyama, Takeo ^a   Brandley, Matthew C ^b,e   Katayama, Akira ^c   Mori, Akira ^c   Honda, Masanao ^d   Hasegawa, Masami ^a  

^a TOHO UNIVERSITY   (Japan)

^b YALE UNIVERSITY   (United States)

^c KYOTO UNIVERSITY   (Japan)

^d UNIVERSITY OF TSUKUBA   (Japan)

^e UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Bayesian phylogeny; Colubridae; Elaphe quadrivirgata; Island biogeography; Izu Islands; lagrange; Multiple colonization; Ratsnakes; Relaxed molecular clock; Reptiles

Indexed keywords

BODY SIZE; COLONIZATION; EVOLUTIONARY BIOLOGY; ISLAND; MELANISM; MORPHOLOGY; NATURAL SELECTION; PHENOTYPE; PHYLOGENETICS; PHYLOGEOGRAPHY; SNAKE; ZOOGEOGRAPHY;

CHUBU; HONSHU; IZU ISLANDS; JAPAN; PACIFIC COAST [JAPAN]; SHIZUOKA [CHUBU];

COLUBRIDAE; ELAPHE QUADRIVIRGATA; REPTILIA; SERPENTES; VERTEBRATA;

EID: 78751475547     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2010.02403.x     Document Type: Article

References (67)

1. Abe, H., Matsuki, R., Ueno, S., Nashimoto, M. & Hasegawa, M. (2006) Dispersal of Camellia japonica seeds by Apodemus speciosus speciosus revealed by maternity analyses of plants and behavioral observations of animal vectors. Ecological Research, 21, 732-740.
2. Brandley, M.C., Schmitz, A. & Reeder, T.W. (2005) Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Systematic Biology, 54, 373-390.
3. Brandley, M.C., Wang, Y., Guo, X., Nieto Montes de Oca, A., Fería Ortíz, M., Hikida, T. & Ota, H. (in press) Accommodating locus-specific heterogeneity in molecular dating methods: an example using inter-continental dispersal of Plestiodon (Eumeces) lizards. Systematic Biology.
4. Burbrink, F.T. & Lawson, R. (2007) How and when did Old World ratsnakes disperse into the New World? Molecular Phylogenetics and Evolution, 43, 173-189.
5. Burbrink, F.T., Lawson, R. & Slowinksi, J.B. (2000) Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept. Evolution, 54, 2107-2118.
6. Camin, J.H. & Ehrlich, P.R. (1958) Natural selection in water snakes (Natrix sipedon L.) on islands in Lake Erie. Evolution, 12, 504-511.
7. Carstens, B.C. & Knowles, L.L. (2007) Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Systematic Biology, 56, 400-411.
8. Castoe, T.A., Doan, T.M. & Parkinson, C.L. (2004) Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophthalmid lizards. Systematic Biology, 53, 448-469.
9. Chase, J.M. (2003) Community assembly: when should history matter? Oecologia, 136, 489-498.
10. Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
11. Drummond, A.J., Ho, S.Y.W., Phillips, M.J. & Rambaut, A. (2006) Relaxed phylogenetics and dating with confidence. PLOS Biology, 4, e88.
12. Emerson, B.C. (2002) Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and process. Molecular Ecology, 11, 951-966.
13. Emerson, B.C., Oromí, P. & Hewitt, G.M. (2000) Tracking colonization and diversification of insect lineages on islands: mitochondrial DNA phylogeography of Tarphius canariensis (Coleoptera: Colydiidae) on the Canary Islands. Proceedings of the Royal Society B: Biological Sciences, 267, 2199-2205.
14. Fukami, T., Beaumont, H.J.E., Zhang, X.X. & Rainey, P.B. (2007) Immigration history controls diversification in experimental adaptive radiation. Nature, 446, 436-439.
15. Gillespie, R.G. (2004) Community assembly through adaptive radiation in Hawaiian spiders. Science, 303, 356-359.
16. Gillespie, R.G. & Roderick, G.K. (2002) Arthropods on islands: colonization, speciation, and conservation. Annual Review of Entomology, 47, 595-632.
17. Grant, P.R. & Grant, B.R. (2008) How and why species multiply: the radiation of Darwin's finches. Princeton University Press, Princeton, NJ.
18. Graur, D. & Martin, W. (2004) Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends in Genetics, 20, 80-86.
19. Hasegawa, M. (1990) Demography of an island population of the lizard, Eumeces okadae, on Miyake, Izu Islands. Researches on Population Ecology, 32, 119-133.
20. Hasegawa, M. (1994) Insular radiation in life history of the lizard Eumeces okadae in the Izu Islands, Japan. Copeia, 1994, 732-747.
21. Hasegawa, M. (1999) Impacts of introduced weasel on the insular food web. Diversity of reptiles, amphibians and other terrestrial animals on tropical islands: origin, current status and conservation (ed. by H. Ota), pp. 129-154. Elsevier Science, New York.
22. Hasegawa, M. (2003) Ecological diversification of insular terrestrial reptiles: a review of the studies on the lizard and snakes of the Izu Islands. Global Environmental Research, 7, 59-67.
23. Hasegawa, M. & Mori, A. (2008) Does a gigantic insular snake grow faster or live longer to be gigantic? Evidence from a long-term field study. South American Journal of Herpetology, 3, 145-154.
24. Hasegawa, M. & Moriguchi, H. (1989) Geographic variation in food habits, body size, and life-history traits of the snakes on the Izu Islands. Current herpetology in East Asia (ed. by M. Matsui, T. Hikida and R.C. Goris), pp. 414-432. Herpetological Society of Japan, Kyoto.
25. Hayashi, M. & Chiba, S. (2004) Enhanced colour polymorphisms in island populations of the land snail Euhadra peliomphala. Biological Journal of the Linnean Society, 81, 417-425.
26. Higuchi, H. (1976) Comparative study on the breeding of mainland and island subspecies of the varied tit, Parus varius. Tori, 25, 11-20.
27. Ho, S.Y.W., Phillips, M.J., Cooper, A. & Drummond, A.J. (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution, 22, 1561-1568.
28. Ho, S.Y.W., Shapiro, B., Phillips, M.J., Cooper, A. & Drummond, A.J. (2007) Evidence for time dependency of molecular rate estimates. Systematic Biology, 56, 515-522.
29. Huelsenbeck, J.P. & Rannala, B. (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology, 53, 904-913.
30. Inoue, K. & Amano, M. (1986) Evolution of Campanula punctata Lam. in the Izu Islands: change of pollinators and evolution of breeding systems. Plant Species Biology, 1, 89-97.
31. Inoue, K. & Kawahara, T. (1990) Allozyme differentiation and genetic structure in island and mainland Japanese populations of Campanula punctata (Campanulaceae). American Journal of Botany, 77, 1140-1448.
32. Isobe, I. & Yasuda, A. (1995) Large coastal cliff recession at the southeastern part of Niijima Island, central Japan: measurement of erosional volume of a pyroclastic cone using aerial photography. Bulletin of the Geological Survey of Japan, 46, 457-475 (in Japanese).
33. Isshiki, M. (1987) Geology of the Niijima District, Quadrangle Series. Geological Survey of Japan, Tsukuba.
34. Kageyama, M., Motokawa, M. & Hikida, T. (2009) Geographic variation in morphological traits of the large Japanese field mouse, Apodemus speciosus (Rodentia, Muridae) from the Izu Island group, Japan. Zoological Science, 26, 266-276.
35. Kaneoka, I., Isshiki, N. & Zashu, S. (1970) K-Ar ages of the Izu-Bonin Islands. Geochemical Journal, 4, 53-60.
36. King, R.B. & Lawson, R. (1995) Color-pattern variation in Lake Erie water snakes: the role of gene flow. Evolution, 49, 885-896.
37. Kitazato, H. (1997) Paleogeographic changes in central Honshu, Japan, during the late Cenozoic in relation to the collision of the Izu-Ogasawara Arc with the Honshu Arc. Island Arc, 6, 144-157.
38. Kocher, T.D. (2004) Adaptive evolution and explosive speciation: the cichlid fish model. Nature Review Genetics, 5, 288-298.
39. Leaché, A.D. (2009) Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus). Systematic Biology, 58, 547-559.
40. Lomolino, M.V. (1990) The target area hypothesis: the influence of island area on immigration rates of non-volant mammals. Oikos, 57, 297-300.
41. Losos, J.B. & Ricklefs, R.E. (2009) Adaptation and diversification on islands. Nature, 457, 830-835.
42. MacArthur, R. & Wilson, E.O. (1967) The theory of island biogeography. Princeton University Press, Princeton, NJ.
43. Maddison, D. & Maddison, W. (2008) MacClade version 4.08. Sinauer Associates, Inc., Sunderland, MA.
44. Maddison, W.P. (1997) Gene trees in species trees. Systematic Biology, 46, 523-536.
45. McGuire, J.A., Linkem, C.W., Koo, M., Hutchison, D.W., Lappin, A.K., Orange, D.O., Lemos-Espinal, J., Riddle, B.R. & Jaeger, J. (2007) Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards. Evolution, 61, 2879-2897.
46. Mori, A. & Hasegawa, M. (1999) Geographic differences in behavioral responses of hatchling lizards (Eumeces okadae) to snake-predator chemicals. Japanese Journal of Herpetology, 18, 45-56.
47. Mori, A. & Hasegawa, M. (2002) Early growth of Elaphe quadrivirgata from an insular gigantic population. Current Herpetology, 21, 43-50.
48. Niitsuma, N. (1991) Collision tectonics in the South Fossa Magna; central Japan (II). Modern Geology, 15, 314-411.
49. Nylander, J.A.A., Ronquist, F., Huelsenbeck, J.P. & Nieves-Aldrey, J.L. (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology, 53, 47-67.
50. Nylander, J.A.A., Wilgenbusch, J.C., Warren, D.L. & Swofford, D.L. (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics, 24, 581-583.
51. Oiki, S., Kawahara, T., Inoue, K., Ohara, M. & Maki, M. (2001) Random amplified polymorphic DNA (RAPD) variation among populations of the insular endemic plant Campanula microdonta (Campanulaceae). Annals of Botany, 87, 661-667.
52. Okamoto, T., Motokawa, J., Toda, M. & Hikida, T. (2006) Parapatric distribution of the lizards Plestiodon (formerly Eumeces) latiscutatus and P. japonicus (Reptilia: Scincidae) around the Izu Peninsula, central Japan, and its biogeographic implications. Zoological Science, 23, 419-425.
53. Parent, C.E., Caccone, A. & Petren, K. (2008) Colonization and diversification of Galápagos terrestrial fauna: a phylogenetic and biogeographical synthesis. Philosophical Transactions of the Royal Society B: Biological Sciences, 363, 3347-3361.
54. Ree, R.H. & Smith, S.A. (2008) Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology, 57, 4-14.
55. Ree, R.H., Moore, B.R., Webb, C.O. & Donoghue, M.J. (2005) A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution, 59, 2299-2311.
56. Schwarz, G. (1978) Estimating the dimension of a model. Annals of Statistics, 6, 461-464.
57. Shaw, K.L. (1995) Biogeographic patterns of two independent Hawaii cricket radiations (Laupala and Prognathogryllus). Hawaiian biogeography: evolution on a hot spot archipelago (ed. by W.L. Wagner and V.A. Funk), pp. 39-56. Smithsonian Institution Press, Washington, DC.
58. Sugihara, S., Fukuoka, T. & Ookawara, R. (2001) Volcanic eruption of Tenjosan Volcano at Kozushima and Mukaiyama volcano at Niijima, Izu Islands. Journal of Geography, 110, 94-105 (in Japanese).
59. Suzuki, H., Yasuda, S.P., Sakaizumi, M., Wakana, S., Motokawa, M. & Tsuchiya, K. (2004) Differential geographic patterns of mitochondrial DNA variation in two sympatric species of Japanese wood mice, Apodemus speciosus and A. argenteus. Genes and Genetic Systems, 79, 165-176.
60. Swofford, D.L. (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Sunderland, MA.
61. Takada, Y., Sakai, E., Uematsu, Y. & Tateishi, T. (2006) Morphological variation of large Japanese field mice, Apodemus speciosus on the Izu and Oki Islands. Mammal Study, 31, 29-40.
62. Tanaka, K., Mori, A. & Hasegawa, M. (2001) Apparent decoupling of prey recognition ability with prey availability in an insular snake population. Journal of Ethology, 19, 27-32.
63. Tomozawa, M. & Suzuki, H. (2008) A trend of central versus peripheral structuring in mitochondrial and nuclear gene sequences of the Japanese wood mouse, Apodemus speciosus. Zoological Science, 25, 273-285.
64. Tsukui, M., Saito, K. & Hayashi, K. (2006) Frequent and intensive eruptions in the 9th century, Izu Islands, Japan: revision of volcano-stratigraphy based tephras and historical document. Bulletin of Volcanological Society of Japan, 1, 327-338 (in Japanese with English abstract).
65. Whittaker, R.J. & Fernández-Palacios, J.M. (2007) Island biogeography, ecology, evolution, and conservation, 2nd edn. Oxford University Press, Oxford.
66. Whittaker, R.J., Triantis, K.A. & Ladle, R.J. (2008) A general dynamic theory of oceanic island biogeography. Journal of Biogeography, 35, 977-994.
67. Yoshida, H. (1992) Eruptive history of Nii-jima volcano. Program and abstracts of the annual meeting of the Volcanological Society of Japan in autumn of 1992, 2, 63 (in Japanese).