A biogeographic view of Apodemus in Asia and Europe inferred from nuclear and mitochondrial gene sequences

Biochemical Genetics

Volumn 46, Issue 5-6, 2008, Pages 329-346

  Suzuki, Hitoshi ^a   Filippucci, Maria Grazia ^b   Chelomina, Galina N ^c   Sato, Jun J ^d   Serizawa, Keiko ^a   Nevo, Eviatar ^e  

^a HOKKAIDO UNIVERSITY   (Japan)

^b UNIVERSITY OF ROME TOR VERGATA   (Italy)

^c INSTITUTE OF BIOLOGY AND SOIL SCIENCE   (Russian Federation)

^d FUKUYAMA UNIVERSITY   (Japan)

^e UNIVERSITY OF HAIFA   (Israel)

Author keywords

Apodemus; Biogeography; Late Tertiary; Molecular phylogeny; Wood mice

Indexed keywords

ADAPTIVE RADIATION; APODEMUS AGRARIUS; APODEMUS ARGENTEUS; APODEMUS GURKHA; APODEMUS MYSTACINUS; APODEMUS PENINSULAE; APODEMUS SEMOTUS; APODEMUS SPECIOSUS; APODEMUS SYLVATICUS; ARTICLE; BIOGEOGRAPHY; BOOTSTRAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC LINKAGE; LATE QUATERNARY; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; RODENT; SPECIES DISTRIBUTION; TERTIARY (PERIOD); UNINDEXED SEQUENCE;

ANIMALS; ASIA; CELL NUCLEUS; CYTOCHROMES B; EUROPE; EYE PROTEINS; HOMEODOMAIN PROTEINS; MITOCHONDRIA; MURINAE; PHYLOGENY; RECEPTORS, ODORANT; RETINOL-BINDING PROTEINS; VON WILLEBRAND FACTOR;

APODEMUS; APODEMUS AGRARIUS; APODEMUS ARGENTEUS; APODEMUS GURKHA; APODEMUS MYSTACINUS; APODEMUS PENINSULAE; APODEMUS SEMOTUS; APODEMUS SPECIOSUS; APODEMUS SYLVATICUS; MUS;

EID: 43049148304     PISSN: 00062928     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10528-008-9149-7     Document Type: Article

References (69)

1. Adler GH (1995) Habitat relations within lowland grassland rodent communities in Taiwan. J Zool 237:563-576
2. Adler GH (1996) Habitat relations of two endemic species of highland forest rodents in Taiwan. Zool Stud 35:105-110
3. Bellinvia E (2004) A phylogenetic study of the genus Apodemus by sequencing the mitochondrial DNA control region. J Zool Syst Evol Res 42:289-297
4. Bryja J, Rehák Z (1998) Community of small terrestrial mammals (Insectivora, Rodentia) in dominant habitats of the Protected Landscape Area of Poodøí (Czech Republic). Folia Zool 47:249-260
5. Buck L, Axel R (1991) A novel multigene family may encode odorant receptors: A molecular basis for odor recognition. Cell 65:175-187
6. Cerling TE, Harris JM, MacFadden BJ, Leakey MG, Quade J, Eisenmann V, Ehleringer JR (1997) Global vegetation change through the Miocene/Pliocene boundary. Nature 389:153-158
7. Chelomina GN, Suzuki H (2006) Molecular evolution and phylogeography of west-Palaearctic wood mice of the genus Sylvaemus based on the data on variation of nuclear (IRBP) and mitochondrial (cyt b) DNA genes. Zool Zhurnal 85:219-234
8. Chelomina GN, Suzuki H, Tsuchiya K, Moriwaki K, Lyapunova EA, Vorontsov NN (1998) Sequencing of the mtDNA cytochrome b gene and reconstruction of the maternal relationships of wood and field mice of the genus Apodemus (Muridae, Rodentia). Russian J Genet 34:529-539
9. Chinen AA, Suzuki H, Aplin KP, Tsuchiya K, Suzuki S (2005) Preliminary genetic characterization of two lineages of black rats (Rattus rattus sensu lato) in Japan, with evidence for introgression at several localities. Genes Genet Syst 80:367-375
10. Conroy CJ, Cook JA (1999) MtDNA evidence for repeated pulses of speciation within arvicoline and murid rodents. J Mamm Evol 6:221-245
11. Corbet GB (1978) The mammals of the Palaearctic Region: a taxonomic review. British Museum (Natural History) and Cornell University Press, London and Ithaca
12. Corbet GB, Hill JE (1992) The mammals of the Indomalayan Region: a systematic review. Oxford University Press, London, 488 pp
13. Felsenstein J (1993) Phylip (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle
14. Filippucci MG (1992) Allozyme variation and divergence among European, Middle Eastern, and North African species of the genus Apodemus (Rodentia, Muridae). Isr J Zool 38:193-218
15. Filippucci MG, Simson S, Nevo E (1989) Evolutionary biology of the genus Apodemus Kaup, 1829 in Israel: allozymic and biometric analyses with description of a new species: Apodemus hermonensis (Rodentia, Muridae). Boll Zool 56:361-376
16. Filippucci MG, Storch G, Macholán M (1996) Taxonomy of the genus Sylvaemus in western Anatolia: morphological and electrophoretic evidence (Mammalia: Rodentia: Muridae). Senckenb Biol 75:1-14
17. Filippucci MG, Macholán M, Michaux JR (2002) Genetic variation and evolution in the genus Apodemus (Muridae: Rodentia). Biol J Linn Soc 75:395-419
18. Han S-H, Wakana S, Suzuki H, Hirai Y, Tsuchiya K (1996) Variation of the mitochondrial DNA and the nuclear ribosomal DNA in the striped field mouse Apodemus agrarius on the mainland and offshore islands of South Korea. Mammal Study 21:125-136
19. Hille A, Tarkhnishvili D, Meinig H, Hutterer R (2002) Morphometric, biochemical and molecular traits in Caucasian wood mice (Apodemus/Sylvaemus), with remarks on species divergence. Acta Theriol 47:389-416
20. Huchon D, Catzeflis FM, Douzery EJP (1999) Molecular evolution of the nuclear von Willebrand Factor gene in mammals and the phylogeny of rodents. Mol Biol Evol 16:577-589
21. Huchon D, Madsen O, Sibbald MJJB, Ament K, Stanhope MJ, Catzeflis F, de Jong WW, Douzery EJP (2002) Rodent phylogeny and a timescale for the evolution of glires: evidence from an extensive taxon sampling using three nuclear genes. Mol Biol Evol 19:1053-1065
22. Jansa SA, Voss RS (2000) Phylogenetic studies on didelphid marsupials I. Introduction and preliminary results from nuclear IRBP gene sequences. J Mammal Evol 7:43-77
23. Jansa SA, Goodman SM, Tucker PK (1999) Molecular phylogeny and biogeography of Madagascar's native rodents (Muridae: Nesomyinae): a test of the single origin hypothesis. Cladistics 15:253-270
24. Kimura M (1980) A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
25. Kostenko VA (2000) Rodents (Rodentia) of the Russian Far East. Institute of Biology and Soil Sciences, Russian Academy of Sciences, Far East Branch, Dalnauka, Vladivostok, 210 pp (in Russia)
26. Krautwurst D, Yau KW, Reed RR (1998) Identification of ligands for olfactory receptors by functional expression of a receptor library. Cell 95:917-926
27. Krystufek B (1985) Variability of Apodemus agrarius (Pallas, 1771) (Rodentia, Mammalia) in Yugoslavia and some data on its distribution in the northwestern part of the country. Bioloski Vestnik 33:27-40
28. Liu W, Wei F, Li M, Jiang X, Feng Z, Hu J (2004) Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species. Mol Phylogenet Evol 33:1-15
29. Macholán M, Filippucci MG, Benda P, Frynta D, Sadlova J (2001) Allozyme variation and systematics of the genus Apodemus (Muridae: Rodentia) in Asia Minor and Iran. J Mammal 82:799-813
30. Mancuso DJ, Tuley EA, Westfield LA, Worrall NK, Shelton-Inloes BB, Sorace JM, Alevy YG, Sadler JE (1989) Structure of the gene for human von Willebrand factor. J Biol Chem 264:19514-19527
31. Martin Y, Gerlach G, Schloetterer C, Meyer A (2000) Molecular phylogeny of European muroid rodents based on complete cytochrome b sequences. Mol Phylogenet Evol 16:37-47
32. May-Collado LJ, Agnarsson I (2006) Cytochrome b and Bayesian inference of whale phylogeny. Mol Phylogenet Evol 38:344-354
33. McShea WJ, Pagels J, Orrock J, Harper E, Koy K (2003) Mesic deciduous forest as patches of small-mammal richness within an Appalachian Mountain Forest. J Mammal 84:627-643
34. Mezhzherin SV, Mikhailenko AG (1991) On the species identity of Apodemus sylvaticus tscherga (Rodentia, Muridae) of the Altai Mts. Vestnik Zoologii 1991:35-44 (in Russian with English summary)
35. Michaux JR, Chevret P, Filippucci MG, Macholán M (2002) Phylogeny of the genus Apodemus with a special emphasis to the subgenus Sylvaemus using the nuclear IRBP gene and two mitochondrial markers: cytochrome b and 12S rRNA. Mol Phylogenet Evol 23:123-136
36. Michaux JR, Magnanou E, Paradis E, Nieberding C, Libois R (2003) Mitochondrial phylogeography of the woodmouse (Apodemus sylvaticus) in the Western Palearctic region. Mol Ecol 12:685-697
37. Michaux JR, Libois R, Paradis E, Filippucci MG (2004) Phylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East. Mol Phylogenet Evol 32:788-798
38. Michaux JR, Bellinvia E, Lymberakis P (2005) Taxonomy, evolutionary history and biogeography of the broad-toothed field mouse (Apodemus mystacinus) in the eastern Mediterranean area based on mitochondrial and nuclear genes. Biol J Linn Soc 85:53-63
39. Millien V (2004) Relative effects of climate change, isolation and competition on body-size evolution in the Japanese field mouse, Apodemus argenteus. J Biogeogr 31:1267-1276
40. Musser GG, Carleton MD (1993) Family muridae. In: Wilson DE, Reeder DM (eds) Mammal species of the world, 2nd edn. Smithsonian Institution Press, Washington and London, pp 501-755
41. Musser GG, Carleton MD (2005) Family muridae. In: Wilson DE, Reeder DM (eds) Mammal species of the world, 3rd edn. Johns Hopkins University Press, Baltimore, pp 894-1531
42. Musser GG, Brothers EM, Carleton MD, Hutterer R (1996) Taxonomy and distributional records of Oriental and European Apodemus, with a review of the Apodemus-Sylvaemus problem. Bonner Zool Beitr 46:143-190
43. Orlov VN, Bulatova NS, Nadjafova RS, Kozlovsky AI (1996) Evolutionary classification of European wood mice of the subgenus Sylvaemus based on allozyme and chromosome data. Bonner Zool Beitr 46:191-202
44. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793-808
45. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818
46. Reutter BA, Petit E, Bruenner H, Vogel P (2003) Cytochrome b haplotype divergences in West European Apodemus. Mammal Biol 68:153-164
47. Rietschel S, Storch G (1974) Außgewöhlich erhaltene Waldmäuse (Apodemus atavus Heller, 1936) aus dem ober-Pliozän von Willerhausen am Harz. Senkenberg Lethaea 54:491-519
48. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574
49. Rutschmann F (2005) Bayesian molecular dating using PAML/multidivtime: a step-by-step manual. University of Zurich, Switzerland. http://www.plant.ch
50. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
51. Sato JJ, Suzuki H (2004) Phylogenetic relationships and divergence times of the genus Tokudaia within Murinae (Muridae; Rodentia) inferred from the nucleotide sequences encoding the mitochondrial cytochrome b gene and nuclear recombination-activating gene 1 and interphotoreceptor retinoid-binding protein. Can J Zool 82:1343-1351
52. Sato JJ, Hosoda T, Wolsan M, Suzuki H (2004) Molecular phylogeny of arctoids (Mammalia: Carnivora) with emphasis on phylogenetic and taxonomic positions of the ferret-badgers and skunks. Zool Sci 21:111-118
53. Sekijima T, Sone K (1994) Role of interspecific competition in the coexistence of Apodemus argenteus and A. speciosus (Rodentia, Muridae). Ecol Res 9:237-244
54. Serizawa K, Suzuki H, Tsuchiya K (2000) A phylogenetic view on species radiation in Apodemus inferred from variation of nuclear and mitochondrial genes. Biochem Genet 38:27-40
55. Shimada T (2001) Hoarding behaviors of two wood mouse species: different preference for acorns of two Fagaceae species. Ecol Res 16:127-133
56. Springer MS, Burk A, Kavanagh JR, Waddell VG, Stanhope MJ (1997) The interphotoreceptor retinoid binding protein gene in therian mammals: implications for higher level relationships and evidence for loss of function in the marsupial mole. Proc Natl Acad Sci USA 94:13754-13759
57. Stanhope MJ, Czelusniak J, Si J-S, Nickerson J, Goodman M (1992) A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly. Mol Phylogenet Evol 1:148-160
58. Stanhope MJ, Smith MR, Waddell VG, Porter CA, Shivji MS, Goodman M (1996) Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades. J Mol Evol 43:83-92
59. Storch G (1975) Eine Mittelpleistozäne Nager-Fauna von der Insel Chios, Ägäis (Mammalia, Rodentia). Senckenb Biol 56:165-189
60. Storch G (1977) Die Ausbreitung der Felsenmaus (Apodemus mystacinus): zur Problematik der Inselbesiedlung und tiergeographie der Ägäis. Natur Mus 107:174-182
61. Suzuki H, Tsuchiya K, Sakaizumi M, Wakana S, Sakurai S (1994) Evolution of restriction sites of ribosomal DNA in natural populations of the field mouse, Apodemus speciosus. J Mol Evol 38:107-112
62. Suzuki H, Tsuchiya K, Takezaki N (2000) A molecular phylogenetic framework for the Ryukyu endemic rodents Tokudaia osimensis and Diplothrix legata (Rodentia, Mammalia). Mol Phylogenet Evol 15:15-24
63. Suzuki H, Sato JJ, Tsuchiya K, Luo J, Zhang Y-P, Wang Y-X, Jiang X-L (2003) Molecular phylogeny of wood mice (Apodemus, Muridae) in East Asia. Biol J Linn Soc 80:469-481
64. Suzuki H, Shimada T, Terashima M, Tsuchiya K, Aplin K (2004) Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences. Mol Phylogenet Evol 33:626-646
65. Swofford DL (2003) PAUP: phylogenetic analysis using parsimony (and other methods). Version 4. Sinauer Associates, Sunderland, MA
66. Thorne JL, Kishino H, Painter IS (1998) Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 15:1647-1657
67. Vorontsov NN, Boyeskorov GG, Mezhzherin SV, Lyapunova EA, Kandaurov AS (1992) Systematics of the Caucasian wood mice of the subgenus Sylvaemus (Mammalia, Rodentia, Apodemus). Zool Zh 71:119-131 (in Russian with English summary)
68. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
69. Yang Z, Yoder AD (2003) Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst Biol 52:705-716