Afrotherian phylogeny as inferred from complete mitochondrial genomes

Molecular Phylogenetics and Evolution

Volumn 28, Issue 2, 2003, Pages 253-260

  Murata, Yumie ^a   Nikaido, Masato ^a   Sasaki, Takeshi ^a   Cao, Ying ^b   Fukumoto, Yukio ^c   Hasegawa, Masami ^b,d   Okada, Norihiro ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^c Hiroshima City Asa Zoological Park   (Japan)

^d GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHRYSOCHLORIDAE; ELEPHANT; EUTHERIA; MAMMALIA; PROCAVIIDAE;

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; MAMMAL; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; DNA, MITOCHONDRIAL; LIKELIHOOD FUNCTIONS; MAMMALS; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 0141498022     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00035-6     Document Type: Conference Paper

References (32)

1. Adachi, J., Hasegawa, M., 1996. MOLPHY: Programs for Molecular Phylogenetics, ver. 2.3. Institute of Statistical Mathematics, Tokyo.
2. Amrine, H.M., Springer, M.S., 1999. Maximum-likelihood analysis of the Tethythere hypothesis based on a multigene data set and a comparison of different models of sequence evolution. J. Mammal. Evol. 6, 161-176.
3. Arnason, U., Gullberg, A., Janke, A., 1997. Phylogenetic analyses of mitochondrial DNA suggest a sister group relationship between Xenarthra (Edentata) and Ferungulates. Mol. Biol. Evol. 14, 762-768.
4. Arnason, U., Gullberg, A., Janke, A., 1999. The mitochondrial DNA molecule of the aardvark, Orycteropus afer, and the position of the Tubulidentata in the eutherian tree. Proc. R. Soc. Lond. B 266, 339-345.
5. Arnason, U., Adegoke, J.A., Bodin, K., Born, E.W., Esa, Y.B., Gullberg, A., Nilsson, M., Short, R.V., Xu, X., Janke, A., 2002. Mammalian mitogenomic relationships and the root of the eutherian tree. Proc. Natl. Acad. Sci. USA 99, 8151-8156.
6. Blin, N., Stafford, D.W., 1976. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 3, 2303-2308.
7. 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.
8. 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.
9. Felsenstein, J., 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27, 401-410.
10. Hauf, J., Waddell, P.J., Chalwatzis, N., Joger, U., Zimmermann, F.K., 1999. The complete mitochondrial genome sequence of the African elephant (Loxodonta africana), phylogenetic relationships of Proboscidea to other mammals, and D-loop heteroplasmy. Zoology 102, 184-195.
11. 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.
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. 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.
14. Mouchaty, S.K., Gullberg, A., Janke, A., Arnason, U., 2000a. The phylogenetic position of the Talpidae within Eutheria based on analysis of complete mitochondrial sequences. Mol. Biol. Evol. 17, 60-67.
15. Mouchaty, S.K., Gullberg, A., Janke, A., Arnason, U., 2000b. Phylogenetic position of the Tenrecs (Mammalia: Tenrecidae) of Madagascar based on analysis of the complete mitochondrial genome sequence of Echinops telfairi. Zool. Scripta 29, 307-317.
16. 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.
17. 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.
18. 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.
19. 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.
20. Nikaido, M., Cao, Y., Okada, N., Hasegawa, M., 2003a. The Phylogenetic relationships of insectivores with special reference to the lesser hedgehog tenrec as inferred from the complete sequence of their mitochondria. Genes Genet. Syst. 78, 107-112.
21. Nikaido, M., Nishihara, H., Fukumoto, Y., Okada, N., 2003b. Ancient SINEs from African endemic mammals. Mol. Biol. Evol. 20, 522-527.
22. Scally, M., Madsen, O., Douady, C.J., de Jong, W.W., Stanhope, M.J., Springer, M.S., 2001. Molecular evidence for the major clades of placental mammals. J. Mammal. Evol. 8, 239-277.
23. Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
24. Shoshani, J., 1998. Understanding proboscidean evolution: a formidable task. TREE 13, 480-487.
25. 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.
26. Stanhope, M.J., Madsen, O., Waddell, V.G., Cleven, G.C., de Jong, W.W., Springer, M.S., 1998. Highly congruent molecular support for a diverse superordinal clade of endemic African mammals. Mol. Phylogenet. Evol. 9, 501-508.
27. Strimmer, K., von Haeseler, A., 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964-969.
28. 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.
29. Waddell, P.J., Okada, N., Hasegawa, M., 1999a. Towards resolving the interordinal relationships of placental mammals. Syst. Biol. 48, 1-5.
30. 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.
31. Waddell, P.J., Kishino, H., Ota, R., 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Inform. 12, 141-154.
32. Yang, Z., 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13, 555-556.