Isochore evolution in mammals: A human-like ancestral structure

Genetics

Volumn 150, Issue 4, 1998, Pages 1577-1584

  Galtier, Nicolas ^a,b   Mouchiroud, Dominique ^a,c  

^a LABORATOIRE DE BIOMÉTRIE ET BIOLOGIE EVOLUTIVE   (France)

^b CNRS   (France)

^c UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA; GUANINE; NUCLEAR PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CODON USAGE; DNA SEQUENCE; EVOLUTION; GENE MUTATION; HUMAN; ISOCHORE; MAMMAL; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL;

ANIMALS; CYTOSINE; EVOLUTION, MOLECULAR; GUANINE; HUMANS; MAMMALS; MICE; MODELS, GENETIC; PHYLOGENY;

EUTHERIA; MAMMALIA; MURIDAE;

EID: 0031762570     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (45)

1. ALVAREZ-VALIN, F., K. JABBARI and G. BERNARDI, 1998 Synonymous and nonsynonymous substitutions in mammalian genes: intragenic correlations. J. Mol. Evol. 46: 37-53.
2. BERNARDI, G., 1993 The vertebrate genome: isochores and evolution. Mol. Biol. Evol. 10: 186-204.
3. BERNARDI, G., and G. BERNARDI, 1990 Compositional patterns in the nuclear genome of cold-blooded vertebrates. J. Mol. Evol. 31: 265-281.
4. BERNARDI, G., B. OLOFSSON, J. FILIPSKI, M. ZERIAL, J. SALINAS et al., 1985 The mosaic genome of warm-blooded vertebrates. Science 228: 953-958.
5. BERNARDI, G., S. HUGHES and D. MOUCHIROUD, 1997 The major compositional transition in the vertebrate genome. J. Mol. Evol. 44: 44-51.
6. CAO, Y., N. OKADA and M. HASEGAWA, 1997 Phylogenetic position of Guinea pigs revisited. Mol. Biol. Evol. 14: 461-464.
7. CLAY, O., S. CACCIO, S. ZOUBAK, D. MOUCHIROUD and G. BERNARDI, 1996 Human coding and non-coding DNA: compositional correlations. Mol. Phylogenet. Evol. 5: 2-12.
8. CROSS, S. H., M. LEE, V. H. CLARK, J. M. CRAIG, A. P. BIRD et al., 1997 The chromosomal distribution of CpG islands in the mouse: evidence for genome scrambling in the rodent lineage. Genomics 40: 454-461.
9. D'ERCHIA, A. M., C. GISSI, G. PESOLE, C. SACCONE and U. ARNASON, 1996 The guinea-pig is not a rodent. Nature 381: 597-600.
10. DURET, L., D. MOUCHIROUD and M. GOUY, 1994 HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res. 22: 2360-2365.
11. DURET, L., D. MOUCHIROUD and C. GAUTIER, 1995 Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40: 308-317.
12. EYRE-WALKER, A., 1992 Evidence that both G + C rich and G + C poor isochores are replicated early and late in the cell cycle. Nucleic Acids Res. 20: 1497-1501.
13. FELSENSTEIN, J., 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376.
14. GALTIER, N., and M. GOUY, 1998 Inferring pattern and process: maximum-likelihood implementation of a new, non-homogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15: 871-879.
15. GALTIER, N., M. GOUY and C. GAUTIER, 1996 SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comp. Appl. Biosci. 12: 543-548.
16. GRAUR, D., W. A. HIDE and W.-H. LI, 1991 Is the guinea-pig a rodent? Nature 351: 649-651.
17. GRAUR, D., L. DURET and M. GOUY, 1996 Phylogenetic position of the order Lagomorpha (rabbits, hares and allies). Nature 379: 333-335.
18. HART, R. W., and R. B. SETLOW, 1974 Correlation between deoxyribonucleic acid excision-repair and life-span in a number of mammalian species. Science 71: 2169-2173.
19. HASEGAWA, M., H. KISHINO and T. YANO, 1985 Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
20. HOLMQUIST, G. P., and J. FILIPSKI, 1994 Organization of mutations along the genome: a prime determinant of genome evolution. TREE 9: 65-68.
21. HUGUENEY, M., and P. MEIN, 1993 A comment on the earliest Spalacinae (Rodentia, Muroidea). J. Mammal. Evol. 1: 215-223.
22. JACOBS, L. L., and W. R. DOWNS, 1994 The evolution of murine rodents in Asia, pp. 149-156 in Rodent and Lagomorph Families of Asian Origin and Diversification, edited by Y. TOMIDA, C. LI and T. SETOGUCHI. National Science Museum, Tokyo.
23. JANKE, A., X. XU and U. ARNASON, 1997 The complete mitochondrial genome of Wallaroo (Macropus robustus) and the phylogenetic relationship among Monotrema, Marsupialia and Eutheria. Proc. Natl. Acad. Sci. USA 94: 1276-1281.
24. LI, W.-H., D. L. ELLSWORTH, J. KRUSHKAL, B. J. H. CHANG and D. HEWETT-EMETT, 1996 Rates of nucleotide substitution in primates and rodents and the generation time hypothesis. Mol. Phylogenet. Evol. 5: 182-187.
25. MATSUO, K., O. CLAY, T. TAKAHASHI, J. SILKE and W. SCHAFFNER, 1993 Evidence for erosion of mouse CpG island during mammalian evolution. Somatic Cell. Mol. Genet. 19: 543-555.
26. MOUCHIROUD, D., and G. BERNARDI, 1993 Compositional properties of coding sequences and Mammalian phylogeny. J. Mol. Evol. 37: 109-116.
27. MOUCHIROUD, D., and C. GAUTIER, 1990 Codon usage changes and sequence dissimilarity between human and rat. J. Mol. Evol. 31: 81-91.
28. MOUCHIROUD, D., C. GAUTIER and G. BERNARDI, 1988 The compositional distribution of coding sequences and DNA molecules in humans and murids. J. Mol. Evol. 27: 311-320.
29. NEDBAL, M. A., R. L. HONEYCUTT and D. A. SCHLITTER, 1996 Higher-level systematics of rodents (Mammalia:Rodentia): evidence from the mitochondrial 12S rRNA gene. J. Mammal. Evol. 3: 201-237.
30. ROBINSON, M., C. GAUTIER and D. MOUCHIROUD, 1997a Evolution of isochores in rodents. Mol. Biol. Evol. 14: 823-828.
31. ROBINSON, M., F. CATZEFLIS, J. BRIOLAY and D. MOUCHIROUD, 1997b Molecular phylogeny of rodents, with special emphasis on murids: evidence from nuclear gene LCAT. Mol. Phylogenet. Evol. 8: 423-434.
32. SABEUR, G., G. MACAYA, F. KADI and G. BERNARDI, 1993 The isochore pattern of mammalian genomes and their phylogenetic implications. J. Mol. Evol. 37: 93-108.
33. SACCONE, C., S. CACCIO, P. PERANI, L. ANDREOZZI, A. RAPISARDA et al., 1997 Compositional mapping of mouse chromosomes and the identification of the gene-rich regions. Chromosome Res. 5: 293-300.
34. SAITOU, N., and M. NEI, 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
35. SALINAS, J., M. ZERIAL, J. FILIPSKI and G. BERNARDI, 1986 Gene distribution and nucleotide sequence organization in the mouse genome. Eur. J. Biochem. 160: 469-478.
36. SHARP, P. M., M. AVEROF, A. T. LLOYD, G. MATASSI and J. F. PEDEN, 1995 DNA sequence evolution: the sounds of silence. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 349: 241-247.
37. STEEL, M. A., 1993 Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett. 7: 19-23.
38. TAMURA, K., 1992 Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol. Biol. Evol. 9: 678-687.
39. THOMPSON, J. D., D. G. HIGGINS and T. J. GIBSON, 1994 CLUSTAL W: improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
40. VIEGAS-PEQUINOT, E., D. PETIT , T. BENAZZOU, M. PROD'HOMME, M. LOMBARD et al., 1986 Phylogénie chromosomique chez les Sciuridés, Gerbillidae et Muridae, et étude d'espèces appartenant à d'autres familles de Rongeurs. Mammalia 50: 164-202.
41. WILSON, D. E., and D. M. REEDER, 1993 Mammal Species of the World. A Taxonomic and Geographic Reference. Smithsonian Institution Press, Washington, DC and London.
42. WOLFE, K. W., P. M. SHARP and W.-H. LI, 1989 Mutation rates differ among regions of the mammalian genome. Nature 337: 283-285.
43. YANG, Z., 1994 Maximum-likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39: 105-111.
44. YANG, Z., N. GOLDMAN and A. FRIDAY, 1994 Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 12: 451-458.
45. ZOUBAK, S., G. D'ONOFRIO, S. CACCIO, G. BERNARDI and G. BERNARDI, 1995 Specific compositional pattern of synonymous positions in homologous mammalian genes. J. Mol. Evol. 40: 293-307.