The speciation history of the Drosophila nasuta complex

Genetical Research

Volumn 88, Issue 1, 2006, Pages 13-26

  Bachtrog, Doris ^a  

^a University of California at San Diego   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA; NUCLEOTIDE;

ARTICLE; CONTROLLED STUDY; DROSOPHILA; DROSOPHILA ALBOMICANS; DROSOPHILA MELANOGASTER; DROSOPHILA NASUTA; EVOLUTION; FEMALE; GENE FLOW; GENE LOCUS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME; INSECT GENETICS; NONHUMAN; PHYLOGENY; REPRODUCTION; SEX CHROMOSOME; SOUTHEAST ASIA; SPECIES DIFFERENTIATION; TAXONOMY; Y CHROMOSOME;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; DROSOPHILA; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENETIC VARIATION; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEX CHROMOSOMES; VARIATION (GENETICS);

DROSOPHILA NASUTA; MELANOGASTER; NASUTA SUBGROUP;

EID: 33749428115     PISSN: 00166723     EISSN: 14695073     Source Type: Journal    
DOI: 10.1017/S0016672306008330     Document Type: Article

References (50)

1. Abraham, I. & Lucchesi, J. (1974). Dosage compensation of genes on left and right arms of X-chromosome of Drosophila pseudoobscura and Drosophila willistoni. Genetics 78, 1119-11226.
2. Andolfatto, P. (2005). Adaptive evolution of non-coding DNA in Drosophila. Nature 437, 1149-1152.
3. Andolfatto, P. & Przeworski, M. (2000). A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156, 257-268.
4. Andolfatto, P. & Wall, J. (2003). Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster. Genetics 165, 1289-1305.
5. Bachtrog, D. (2005). Sex chromosome evolution: Molecular aspects of Y chromosome degeneration in Drosophila. Genome Research 15, 1393-1401.
6. Bachtrog, D. & Charlesworth, B. (2002). Reduced adaptation of a non-recombining neo-Y chromosome. Nature 416, 323-326.
7. Bachtrog, D., Thornton, K., Clark, A. & Andolfatto, P. (2006). Extensive introgression of mitochondrial DNA relative to nuclear gene flow in the Drosophila yakuba species group. Evolution 60, 292-302.
8. Ballard, J. (2000). When one is not enough: Introgression of mitochondrial DNA in Drosophila. Molecular Biology and Evolution 17, 1126-1130.
9. Ballard, J., Chernoff, B. & James, A. (2002). Divergence of mitochondrial DNA is not corroborated by nuclear DNA, morphology, or behavior in Drosophila simulans. Evolution 56, 527-545.
10. Bone, J. R. & Kuroda, M. I. (1996). Dosage compensation regulatory proteins and the evolution of sex chromosomes in Drosophila. Genetics 144, 705-713.
11. Carvalho, A. & Clark, A. (2005). Y chromosome of D. pseudoobscura is not homologous to the ancestral Drosophila Y. Science 307, 108-110.
12. Chang, H. Y., Wang, D. G. & Ayala, F. J. (1989). Mitochondrial DNA evolution in the Drosophila nasuta subgroup of species. Journal of Molecular Evolution 28, 337-348.
13. Charlesworth, B. & Charlesworth, D. (2000). The degeneration of Y chromosomes. Philosophical Transactions of the Royal Society of London B: Biological Sciences 355, 1563-1572.
14. Fay, J. C. & Wu, C. I. (2000). Hitchhiking under positive Darwinian selection. Genetics 155, 1405-1413.
15. Felsenstein, J. (1988). Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetics 22, 521-565.
16. Haddrill, P., Thornton, K., Charlesworth, B. & Andolfatto, P. (2005). Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Research 15, 790-799.
17. Hatsumi, M., Morishige, Y. & Wakahama, K. (1988). Metaphase chromosomes of four species of the Drosophila nasuta subgroup. Japanese Journal of Genetics 63, 435-444.
18. Hudson, R. R. (1990). Gene genealogies and the coalescent process. In Oxford Surveys in Evolutionary Biology (ed. J. Antonovics & D. Futuyma), pp. 1-44. Oxford: Oxford University Press.
19. Hudson, R. (2002). Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337-338.
20. Hudson, R. R., Kreitman, M. & Aguade, M. (1987). A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153-159.
21. Kitagawa, O. (1991). Evolutions of Populations. Tokyo: Tokyo University Press.
22. Kitagawa, O., Wakahama, K. I., Fuyama, Y., Shimada, Y., Takanashi, E., et al. (1982). Genetic study of Drosophila nasuta subgroup, with notes on distribution and morphology. Japanese Journal of Genetics 57, 113-141.
23. Kliman, R., Andolfatto, P., Coyne, J., Depaulis, F., Kreitman, M., et al. (2000). The population genetics of the origin and divergence of the Drosophila simulans species complex. Genetics 156, 1913-1931.
24. Kopp, A. & Barmina, O. (2005). Evolutionary history of the Drosophila bipectinata species complex. Genetical Research 85, 23-46.
25. Kumar, S. Tamura, K. & Nei, M. (2004). MEGA3: Integrated software for molecular evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics 5, 150-163.
26. Li, W. (1997). Molecular Evolution. Sunderland, MA: Sinauer Associates.
27. Llopart, A., Lachaise, D. & Coyne, J. (2005). Multilocus analysis of introgression between two sympatric sister species of Drosophila: Drosophila yakuba and D. santomea. Genetics 171, 197-210.
28. Lucchesi, J. C. (1978). Gene dosage compensation and the evolution of sex chromosomes. Science 202, 711-716.
29. Machado, C., Kliman, R., Markert, J., & Hey, J. (2002). Inferring the history of speciation from multilocus DNA sequence data: The case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution 19, 472-488.
30. Marìn, I., Franke, A., Bashaw, G. & Baker, B. (1996). The dosage compensation system of Drosophila is coopted by newly evolved X chromosomes. Nature 383, 160-163.
31. Moriyama, E. N. & Powell, J. R. (1996). Intraspecific nuclear DNA variation in Drosophila. Molecular Biology and Evolution 13, 261-277.
32. Moriyama, E. N. & Powell, J. R. (1997). Synonymous substitution rates in Drosophila: Mitochondrial versus nuclear genes. Journal of Molecular Evolution 45, 378-391.
33. Nagaraja, J. & Ranganath, H (2004). Molecular phylogeny of the nasuta subgroup of Drosophila based on 12S rRNA, 16S rRNA and CoI mitochondrial genes, RAPD and ISSR polymorphisms. Genes and Genetic Systems 79, 293-299.
34. Osada, N. & Wu, C. (2005). Inferring the mode of speciation from genomic data: A study of the great apes. Genetics 169, 259-264.
35. Patterson, J. T. & Stone, W. S. (1952). Evolution in the Genus Drosophila. New York: Macmillan,
36. Powell, J. (1983). Interspecific cytoplasmic gene flow in the absence of nuclear gene flow: Evidence from Drosophila. Proceedings of the National Academy of Sciences of the USA 80,492-495.
37. Przeworski, M., Wall, J. D. & Andolfatto, P. (2001). Recombination and the frequency spectrum in Drosophila melanogaster and Drosophila simulans. Molecular Biology and Evolution 18, 291-298.
38. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning. A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
39. Schierup, M. & Hein, J. (2000). Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879-891.
40. Shao, H.-G., Li, D., Zhang, X-N., Yu, H.-J., Li, X., et al. (1997). Study on the recognition and evolutionary genetics of the courship song of species in Drosophila nasuta species group. Chinese Journal of Genetics 24, 311-321.
41. Steinemann, M. & Steinemann, S. (1998). Enigma of Y chromosome degeneration: Neo-Y and neo-X chromosomes of Drosophila miranda - a model for sex chromosome evolution. Genetica 102-103, 409-420.
42. Sullivan, W., Ashburner M. & Hawley, R. (2000). Drosophila Protocols. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
43. Suzuki, Y., Kitagawa, O. & Wakahama, K. (1990). Chromosomal analysis and phylogenetic relationships in the Drosophila nasuta subgroup. I. Phylogenetic relationships within the Drosophila sulfurigaster species complex. Genetica 80, 53-66.
44. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
45. Tamura, K. & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10, 512-526.
46. Thornton, K. & Andolfatto, P. (2006). Approximate bayesian inference reveals evidence for a recent, severe, bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172, 1607-1619.
47. Wakeley, J. & Hey, J. (1997). Estimating ancestral population parameters. Genetics 145, 847-855.
48. Wilson, F. D., Wheeler, M. R., Harger, M. & Kambysellis, M. (1969). Cytogenetic relations in the Drosophila nasuta subgroup of the immigrans group of species. University of Texas Publications 6918, 207-254.
49. Yi, S., Bachtrog, D. & Charlesworth, B. (2003) A survey of chromosomal and nucleotide sequence variation in Drosophila miranda. Genetics 164, 1369-1381.
50. Yu, H., Wang, W., Fang, S., Zhang, Y. P., Lin, F. J., et al. (1999). Phylogeny and evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences. Molecular Phylogenetics and Evolution 13, 556-565.