Adaptive radiation of gobies in the interstitial habitats of gravel beaches accompanied by body elongation and excessive vertebral segmentation

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Yamada, Tomohiko ^a   Sugiyama, Tomoshige ^a   Tamaki, Nana ^a   Kawakita, Atsushi ^a   Kato, Makoto ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; GENOMIC DNA; MITOCHONDRIAL DNA;

ADAPTIVE RADIATION; ANIMAL TISSUE; ARTICLE; CLADISTICS; CYTOCHROME B GENE; FISH; FISH GENETICS; GENE; JAPAN; LUCIOGOBIUS ADAPEL; LUCIOGOBIUS ELONGATUS; LUCIOGOBIUS GRANDIS; LUCIOGOBIUS PARVULUS; LUCIOGOBIUS PLATYCEPHALUS; MICROHABITAT; MORPHOLOGICAL ADAPTATION; NONHUMAN; PHYLOGENY; SEASHORE; SPECIES DIFFERENTIATION; SPECIES DIVERSITY; SPECIES HABITAT; VERTEBRA; ADAPTATION; ANIMAL; DNA SEQUENCE; ECOSYSTEM; GENETICS; HISTOLOGY; MOLECULAR EVOLUTION; PERCIFORMES; SEQUENCE ALIGNMENT; SPINE;

GOBIIDAE; LUCIOGOBIUS; PISCES; VERTEBRATA;

ADAPTATION, BIOLOGICAL; ANIMALS; DNA, MITOCHONDRIAL; ECOSYSTEM; EVOLUTION, MOLECULAR; PERCIFORMES; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPINE;

EID: 67650478674     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-145     Document Type: Article

References (48)

1. JS Nelson, Fishes of the World New York: John Wiley & Sons, Inc. 4 2006
2. Particle size and shape in pebble-beach sedimentation. AT Williams NE Caldwell, Mar Geol 1988 82 199 215 10.1016/0025-3227(88)90141-7 (Pubitemid 18662488)
3. Rocky shore-gravelly beach transition, and storm/post-storm changes of a Holocene gravelly beach (Kos Island, Aegean Sea): stratigraphic significance. DI Sanders, Facies 2000 42 227 244 10.1007/BF02562574
4. Concepts in gravel beach dynamics. D Buscombe G Masselink, Earth-Science Reviews 2006 79 33 52 10.1016/j.earscirev.2006.06.003
5. O Giere, Meiobenthology: The Microscopic Fauna in Aquatic Sediments Berlin: Springer-Verlag 1993
6. A review of the gobioid fishes of Japan with descriptions of twenty-one new species. DS Jordan JO Snyder, Proceedings of the United States National Museum 1901 24 33 132
7. The fishes of the gobiid genus Luiciogobius Gill. CT Regan, Annals and Magazine of Natural History 1949 5 462 465
8. A new species of a goby with a synopsis of the species of the genus Luciogobius and its two allied genera. Y Dotu, Journal of the Faculty of Agriculture, Kyushu University 1957 11 69 76
9. Luciogobius grandis, a new goby from Japan and Korea. R Arai, Bulletin of the National Science Museum, Tokyo 1970 13 199 206
10. Two new species of the genus Luciogobius (family Gobiidae) from Japan. M Shiogaki Y Dotsu, Japanese Journal of Ichthyology 1976 23 125 129
11. Luciogobius adapel, a new species of gobiid fish from Japan. M Okiyama, Bulletin of the National Science Museum, Tokyo, Series A 2001 27 141 149
12. Gobioidei. Akihito M Hayashi T Yoshino K Shimada H Seno T Yamamoto, The fishes of the Japanese archipelago Tokyo: Tokai University Press, Masuda H, Amaoka K, Araga C, Uyeno T, Yoshino T, 1984 228 276
13. Gobioidei. Akihito K Sakamoto Y Ikeda A Iwata, Fishes of Japan with Pictoral Key to the Species Tokyo: Tokai University Press, Nakabo T, 2 2000 1139 1310
14. Fishes of Luciogobius and Inu (Gobiidae) from the Izu Peninsula, Central Japan. R Arai, Memoirs of the National Science Museum 1981 14 151 166
15. Genus Luciogobius. T Suzuki K Shibukawa, A photographic guide to the gobioid fishes of Japan Tokyo: Heibonsha Press, Seno H, 2004 59 60
16. The Life History of the Gobiid Fish, Expedio parvulus. M Shiogaki Y Dotsu, Bulletin of the Faculty of Fisheries, Nagasaki University 1971 32 17 25
17. The Life History of the Gobiid Fish, Luciogobius elongatus. M Shiogaki Y Dotsu, Bulletin of the Faculty of Fisheries, Nagasaki University 1972 34 9 18
18. The Life History of the Gobiid Fish, Luciogobius platycephalus. M Shiogaki Y Dotsu, Japanese Journal of Ichthyology 1977 24 43 48
19. The Life History of the Gobiid Fish, Luciogobius grandis. M Shiogaki N Miura Y Dotsu, Bulletin of the Faculty of Fisheries, Nagasaki University 1974 38 57 64
20. Late Cenozoic palaeogeography of Japan. S Kaizuka, GeoJournal 1980 4 101 109 10.1007/BF00705517
21. Paleogeographic maps of the Japanese Islands: Plate tectonic synthesis from 750 Ma to the present. S Maruyama Y Isozaki G Kimura M Terabayashi, The Island Arc 1997 6 121 142 10.1111/j.1440-1738.1997.tb00043.x
22. Tectonic Evolution of the Japanese Island Arc System. A Taira, Annu Rev Earth Planet Sci 2001 29 109 134 10.1146/annurev.earth.29.1.109
23. Phylogenies and the comparative method. J Felsenstein, Am Nat 1985 125 1 15 10.1086/284325
24. Genetic differentiation of the gobies Gymnogobius castaneus and G. taranetzi in the region surrounding the Sea of Japan as inferred from a mitochondrial gene genealogy. T Sota T Mukai T Shinozaki H Sato K Yodoe, Zoolog Sci 2005 22 87 93 10.2108/zsj.22.87 15684588
25. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. MJ Sanderson, Mol Biol Evol 2002 14 1218 1231
26. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. SYW Ho MJ Phillips A Cooper AJ Drummond, Mol Biol Evol 2005 22 1561 1568 10.1093/molbev/msi145 15814826
27. Comparative historical biogeography of Plateumaris leaf beetles (Coleoptera: Chrysomelidae) in Japan: interplay between fossil and molecular data. T Sota M Hayashi, J Biogeogr 2007 34 977 993 10.1111/j.1365-2699.2006. 01672.x
28. Evolution of subterranean diving beetles (Coleoptera: Dytiscidae: Hydroporini, Bidessini) in the arid zone of Australia. R Leys CHS Watts SJB Copper WF Humphreys, Evolution 2003 57 2819 2834 14761060 (Pubitemid 38078362)
29. Brazos River Bar: A study in the significance of grain size parameters. RL Folk WC Ward, J Sediment Petrol 1957 27 3 26
30. Intraspecific mitochondrial DNA phylogeny of a Japanese brackish water goby, Luciogobius guttatus. T Mukai M Nishida, Japanese Journal of Ichthyology 2004 51 157 161 (Pubitemid 44465156)
31. D Schluter, The Ecology of Adaptive Radiation Oxford: Oxford University Press 2000
32. The life history of the goby, Luciogobius guttatus Gill. Y Dotu, Science bulletin of the Faculty of Agriculture, Kyushu University 1957 16 93 100
33. On the Blind Gobioid Fish, Luciogobius albus REGAN. Y Dotu, Doubutsugaku zasshi 1963 72 1 5
34. Luciogobius pallidus REGAN. T Yoshida Y Dotsu, Freshwater Fishes of Japan Tokyo: Yama to Keikoku Sha, Kawanabe H, Mizuno N, Hosoya K, 3 2001 628 629
35. A blind goby, Luciogobius pallidus REGAN, collected from a burrow of a mud shrimp, Upogebia yokoyai MAKAROV. G Itani N Aizawa H Tanase, Nanki Seibutu 1996 38 53 54
36. Note sur un nouveau poisson chinos appartenant au genre Luciogobius. JTF Chen, Bulletin du Musee d'Histoire Naturelle de Paris, (Série 2) 1932 4 648 650 fig. 1, 2.
37. Miscellanea Ichthyologica. V. Un nuovo Gobiide della Cina meridionale. L Di Caporiacco, Bollettino di pesca, piscialtura e idrobiologia 1947 2 193 205
38. MM Miyamoto J Cracraft, Phylogenetic analysis of DNA sequences Oxford: Oxford University Press 1991
39. DL Swofford, PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods). Version 4.0b10 Sunderland, Massachusetts: Sinauer Associates 2002
40. Modeltest: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 817 818 10.1093/bioinformatics/14.9.817 9918953 (Pubitemid 28552116)
41. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 696 704 10.1080/10635150390235520 14530136
42. MrModeltest 2.2. JAA Nylander, Program distributed by the author Uppsala, Sweden: Evolutionary Biology Centre, Uppsala University 2004
43. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/btg180 12912839
44. WP Maddison DR Maddison, Mesquite: a modular system for evolutionary analysis, Version 2.6 2009 http://mesquiteproject.org
45. PE Midford TJ Garland WP Maddison, PDAP Package of Mesquite. Version 1.07 2005 http://mesquiteproject.org/pdap-mesquite/
46. Procedures for the analysis of comparative data using phylogenetically independent contrasts. T Garland JPH Harvey AR Ives, Syst Biol 1992 41 18 32
47. Phylogenetic relationships of four specie of floating gobies (Gymnogobius) as inferred from partial mitochondrial cytochrome b gene sequences. S Harada SR Jeon I Kinoshita M Tanaka M Nishida, Ichthyological Research 2002 49 324 332 10.1007/s102280200048 (Pubitemid 36064677)
48. J Felsenstein, PHYLIP (phylogeny inference package), v. 3.6 Seattle, Washington: Department of Genetics, University of Washington 2005