Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla

Molecular Phylogenetics and Evolution

Volumn 28, Issue 2, 2003, Pages 276-284

  Nikaido, Masato ^a   Cao, Ying ^b   Harada, Masashi ^c   Okada, Norihiro ^a   Hasegawa, Masami ^b,d  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^c OSAKA CITY UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^d GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ERINACEIDAE; EUTHERIA; HEMIECHINUS AURITUS; HYLOMYINAE; MOGERA WOGURA; NEUROTRICHUS GIBBSII; SORICIDAE; UROTRICHUS TALPOIDES;

MITOCHONDRIAL DNA;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; HEDGEHOG; MOLECULAR GENETICS; PHYLOGENY; STATISTICAL MODEL;

AMINO ACID SEQUENCE; ANIMALS; DNA, MITOCHONDRIAL; HEDGEHOGS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 0141721417     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00120-9     Document Type: Conference Paper

References (38)

1. Adachi, J., Hasegawa, M., 1996. "MOLPHY: Programs for Molecular Phylogenetics, ver.2.3," Institute of Statistical Mathematics, Tokyo.
2. Blin, N., Stafford, D.W., 1976. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 3, 2303-2308.
3. Butler, P.M., 1988. Phylogeny of the insectivores. In: The Phylogeny and Classification of the Tetrapods. In: Benton, M.J. (Ed.), Mammals, vol. 2. Clarendon, Oxford, pp. 117-141.
4. Cao, Y., Fujiwara, M., Nikaido, M., Okada, N., Hasegawa, M., 2000. Interordinal relationships and time-scale of eutherian evolution as inferred from mitochondrial genome data. Gene 259, 149-158.
5. D'Erchia, A.M., Gissi, C., Pesole, G., Saccone, C., Arnason, U., 1996. The guinea-pig is not a rodent. Nature 381, 597-600.
6. de Jong, W.W., Zweers, A., Goodman, M., 1981. Relationship of aardvark to elephants, hyraxes and sea cows from α-crystallin sequences. Nature 292, 538-540.
7. Douady, C.J., Chatelier, P.I., Madsen, O., de Jong, W.W., Catzeflis, F., Springer, M.S., Stanhope, M.J., 2002. Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews. Mol. Phylogenet. Evol. 25, 200-209.
8. Gregory, W.K., 1910. The orders of mammals. Amer. Mus. Nat. Hist. Bull. 27, 1-524.
9. Kishino, H., Hasegawa, M., 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29, 170-179.
10. Krettek, A., Gullberg, A., Arnason, U., 1995. Sequence analysis of the complete mitochondrial DNA molecule of the hedgehog, Erinaceus europaeus, and the phylogenetic position of the Lipotyphla. J. Mol. Evol. 41, 952-957.
11. Lake, J.A., 1994. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc. Natl. Acad. Sci. USA 91, 1455-1459.
12. Lin, Y.H., McLenachan, P.A., Gore, A.R., Phillips, M.J., Ota, R., Hendy, M.D., Penny, D., 2002. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol. Biol. Evol. 19, 2060-2070.
13. Lockhart, P.J., Steel, M.A., Hendy, M.D., Penny, D., 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11, 605-612.
14. MacPhee, R.D.E., Novacek, M.J., 1993. Definition and relationships of Lipotyphla. In: Szalay, F.S., Novacek, M.J., McKenna, M.C. (Eds.), Mammal Phylogeny: Placentals. Springer, New York, pp. 13-31.
15. Madsen, O., Scally, M., Douady, C.J., Kao, D.J., DeBry, R.W., Adkins, R., Amrine, H.M., Stanhope, M.J., de Jong, W.W., Springer, M.S., 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409, 610-614.
16. McKenna, M.C., Bell, S.K., 1997. Classification of Mammals: Above the Species Level, Columbia University Press, New York.
17. Mouchaty, S.K., Gullberg, A., Janke, A., Arnason, U., 2000. The phylogenetic position of the Talpidae within Eutheria based on analysis of complete mitochondrial sequences. Mol. Biol. Evol. 17, 60-67,
18. Murata, Y., Nikaido, M., Sasaki, T., Fukumoto, Y., Hasegawa, M., Okada, N., 2003. Afrotherian phylogeny as inferred from complete mitochondrial genomes. Mol. Phylogenet. Evol. (in press).
19. Murphy, W.J., Eizirik, E., Johnson, W.E., Zhang, Y.P., Ryder, O.A., O'Brien, S.J., 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409, 614-618.
20. Murphy, W.J., Eizirik, E., O'Brien, S.J., Madsen, O., Scally, M., Douady, C.J., Teeling, E., Ryder, O.A., Stanhope, M.J., de Jong, W.W., Springer, M.S., 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294, 2348-2351.
21. Nikaido, M., Cao, Y., Okada, N., Hasegawa, M., 2003. The phylogenetic relationships of insectivores with special reference to the lesser hedgehog tenrecs as inferred from the complete sequence of their mitochondrial genome. Genes Genet. Syst. 78, 107-111.
22. Nikaido, M., Harada, M., Cao, Y., Hasegawa, M., Okada, N., 2000. Monophyletic origin of the order Chiroptera and its phylogenetic position among Mammalia inferred from the complete mitochondrial DNA sequence of a Japanese megabat, Ryukyu flying fox (Pteropus dasymallus). J. Mol. Evol. 51, 318-328.
23. Nikaido, M., Kawai, K., Cao, Y., Harada, M., Tomita, S., Okada, N., Hasegawa, M., 2001. Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevaluation of the phylogeny of bats and insectivores. J. Mol. Evol. 53, 508-516.
24. Novacek, M.J., 1992. Mammalian phylogeny: shaking the tree. Nature 356, 121-125.
25. Penny, D., Hasegawa, M., Waddell, P.J., Hendy, M.D., 1999. Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition. Syst. Biol. 48, 76-93.
26. Reyes, A., Gissi, C., Pesole, G., Catzeflis, F.M., Saccone, C., 2000. Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris. Mol. Biol. Evol. 17, 979-983.
27. Shimodaira, H., 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51, 492-508.
28. Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
29. Shimodaira, H., Hasegawa, M., 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247.
30. Springer, M.S., Cleven, G.C., Madsen, O., de Jong, W.W., Waddell, V.G., Amrine, H.M., Stanhope, M.J., 1997. Endemic African mammals shake the phylogenetic tree. Nature 388, 61-64.
31. Stanhope, M.J., Madsen, O., Waddell, V.G., Cleven, G.C., de Jong, W.W., Springer, M.S., 1998a. Highly congruent molecular support for a diverse superordinal clade of endemic African mammals. Mol. Phylogenet. Evol. 9, 501-508.
32. Stanhope, M.J., Waddell, V.G., Madsen, O., de Jong, W.W., Hedges, S.B., Cleven, G.C., Kao, D., Springer, M.S., 1998b. Molecular evidence for multiple origins of insectivora and for a new order of endemic African insectivore mammals. Proc. Natl. Acad. Sci. USA 95, 9967-9972.
33. Strimmer, K., von Haeseler, A., 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964-969.
34. Sullivan, J., Swofford, D.L., 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mammal. Evol. 4, 77-86.
35. van Dijk, M.A.M., Madsen, O., Catzeflis, F., Stanhope, M.J., de Jong, W.W., Pagel, M., 2001. Protein sequence signatures support the African clade of mammals. Proc. Natl. Acad. Sci. USA 98, 188-193.
36. Waddell, P.J., Okada, N., Hasegawa, M., 1999a. Towards resolving the interordinal relationships of placental mammals. Syst. Biol. 48, 1-5.
37. Waddell, P.J., Cao, Y., Hauf, J., Hasegawa, M., 1999b. Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant. Syst. Biol. 48, 31-53.
38. Yang, Z., 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13, 555-556.