Potential gene flow in natural populations of the Drosophila ananassae species cluster inferred from a nuclear mitochondrial pseudogene

Molecular Phylogenetics and Evolution

Volumn 48, Issue 3, 2008, Pages 1087-1093

  Sawamura, Kyoichi ^a   Koganebuchi, Kae ^a   Sato, Hajime ^b   Kamiya, Koichi ^c   Matsuda, Muneo ^b   Oguma, Yuzuru ^a  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b KYORIN UNIVERSITY   (Japan)

^c NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

Drosophila ananassae; Introgression; Phylogeography; Pseudogene

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CELL NUCLEUS; CHROMOSOME; DROSOPHILA; FEMALE; GENE FLOW; GENETICS; GEOGRAPHY; MALE; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PAPUA NEW GUINEA; PHYLOGENY; PSEUDOGENE; SPECIES DIFFERENCE; ULTRASTRUCTURE;

ANIMALS; BASE SEQUENCE; CELL NUCLEUS; CHROMOSOMES; DNA, MITOCHONDRIAL; DROSOPHILA; FEMALE; GENE FLOW; GEOGRAPHY; MALE; MOLECULAR SEQUENCE DATA; PAPUA NEW GUINEA; PHYLOGENY; PSEUDOGENES; SPECIES SPECIFICITY;

DROSOPHILA ANANASSAE; DROSOPHILA PALLIDOSA;

EID: 50249101192     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.06.007     Document Type: Article

References (44)

1. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., et al. The genome sequence of Drosophila melanogaster. Science 287 (2000) 2185-2195
2. Amador A., and Juan E. Nonfixed duplication containing the Adh gene and a truncated form of the Adhr gene in the Drosophila funebris species group: different modes of evolution of Adh relative to Adhr in Drosophila. Mol. Biol. Evol. 16 (1999) 1439-1456
3. Bachtrog D., Thornton K., Clark A., and Andolfatto P. Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group. Evolution 60 (2006) 292-302
4. Baines J.F., Das A., Mousset S., and Stephan W. The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae. Genetics 168 (2004) 1987-1998
5. Begun D.J., and Aquadro C.F. Levels of naturally occurring DNA polymorphism are correlated with recombination rates in Drosophila melanogaster. Nature 356 (1992) 519-520
6. Bensasson D., Zhang D.X., Hartl D.L., and Hewitt G.M. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Genet. 16 (2001) 314-321
7. Berry A.J., Ajioka J.W., and Kreitman M. Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics 129 (1991) 1111-1117
8. Bock I.R., and Wheeler M.R. The Drosophila melanogaster species group. Univ. Tex. Publ. 7213 (1972) 1-102
9. Burge C., and Karlin S. Prediction of complete gene structure in human genomic DNA. J. Mol. Biol. 268 (1997) 78-94
10. Chen Y., Marsh B.J., and Stephan W. Joint effects of natural selection and recombination on gene flow between Drosophila ananassae populations. Genetics 155 (2000) 1185-1194
11. Da Lage J.L., Kergoat G.J., Maczkowiak F., Silvain J.F., Cariou M.L., and Lachaise D. A phylogeny of Drosophilidae using the Amyrel gene questioning the Drosophila melanogaster species group boundaries. J. Zoolog. Syst. Evol. Res. 45 (2007) 47-63
12. Das A., Mohanty S., and Stephan W. Inferring the population structure and demography of Drosophila ananassae from multilocus data. Genetics 168 (2004) 1975-1985
13. Devor E.J. Primate microRNAs miR-220 and miR-492 lie within processed pseudogenes. J. Hered. 97 (2006) 186-190
14. Doi, M., 1997. Genetic studies on reproductive isolation and speciation in the Drosophila ananassae complex. Ph.D. dissertation submitted to University of Tsukuba, Tsukuba.
15. Drosophila 12 Genomes Consortium, 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218.
16. Futch D.G. A study of speciation in South Pacific populations of Drosophila ananassae. Univ. Tex. Publ. 6615 (1966) 79-120
17. Futch D.G. On the ethological differentiation of Drosophila ananassae and Drosophila pallidosa in Samoa. Evolution 27 (1973) 456-467
18. Hey J., and Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167 (2004) 747-760
19. Hilton H., Kliman R.M., and Hey J. Using hitchhiking genes to study adaptation and divergence during speciation within the Drosophila melanogaster species complex. Evolution 48 (1994) 1900-1913
20. Hochman B. The fourth chromosome of Drosophila melanogaster. In: Ashburner M., and Novitski E. (Eds). The Genetics and Biology of Drosophila vol. 1b (1975), Academic Press, London 903-928
21. Hudson R.R., Slatkin M., and Maddison W.P. Estimation of levels of gene flow from DNA sequence data. Genetics 132 (1992) 583-589
22. Kaneshiro K., and Wheeler M.R. Preliminary report on the species of the ananassae subgroup. Drosophila Inf. Serv. 45 (1970) 143
23. Lemeunier F., David J., Tsacas L., and Ashburner M. The melanogaster species group. In: Ashburner M., Carson H., and Thompson Jr. J.N. (Eds). The Genetics and Biology of Drosophila vol. 3e (1986), Academic Press, London 147-256
24. Machado C.A., and Hey J. The causes of phylogenetic conflict in a classic Drosophila species group. Proc. R. Soc. Lond. B 270 (2003) 1193-1202
25. Mishmar D., Ruiz-Pesini E., Brandon M., and Wallace D.C. Mitochondrial DNA-like sequences in the nucleus (NUMTs): insights into our African origins and the mechanism of foreign DNA integration. Hum. Mut. 23 (2004) 125-133
26. Moriwaki D., and Tobari Y.N. Catalog of mutants. In: Tobari Y.N. (Ed). Drosophila ananassae: Genetical and Biological Aspects (1993), Japan Scientific Societies Press, Tokyo 209-259
27. Nei M. Molecular Evolutionary Genetics (1987), Columbia University Press, New York 1-512
28. Nichols R. Gene trees and species trees are not the same. Trends Ecol. Evol. 16 (2001) 358-364
29. Noor M.A.F., and Kliman R.M. Variability on the dot chromosome in the Drosophila simulans clade. Genetica 118 (2003) 51-58
30. Perna N.T., and Kocher T.D. Mitochondrial DNA: molecular fossils in the nucleus. Curr. Biol. 6 (1996) 128-129
31. Pollard D.A., Iyer V.N., Moses A.M., and Eisen M.B. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. Publ. Libr. Sci. Genet. 2 (2006) 1634-1647
32. Richly E., and Leister D. NUMTs in sequenced eukaryotic genomes. Mol. Biol. Evol. 21 (2004) 1081-1084
33. Schug M.D., Regulski E.E., Pearce A., and Smith S.G. Isolation and characterization of dinucleotide repeat microsatellites in Drosophila ananassae. Genet. Res. 83 (2004) 19-29
34. Schug M.D., Smith S.G., Tozier-Pearce A., and McEvey S.F. The genetic structure of Drosophila ananassae populations from Asia, Australia and Samoa. Genetics 175 (2007) 1429-1440
35. Schug M.D., Baines J.F., Killon-Atwood A., Mohanty S., Das A., Grath S., Smith S.G., Zargham S., McEvey S.F., and Stephan W. Evolution of mating isolation between populations of Drosophila ananassae. Mol. Ecol. 17 (2008) 2706-2721
36. Smith C.D., Edgar R.C., Yandell M.D., Smith D.R., Celniker S.E., Myers E.W., and Karpen G.H. Improved repeat identification and masking in Dipterans. Gene 389 (2007) 1-9
37. Stephan W., and Mitchell S.J. Reduced levels of DNA polymorphism and fixed between-population differences in the centromeric region of Drosophila ananassae. Genetics 132 (1992) 1039-1045
38. Stone W.S., Wheeler M.R., Wilson F.D., Gerstenberg V.L., and Yang H. Genetic studies of natural populations of Drosophila .II. Pacific island populations. Univ. Tex. Publ. 6615 (1966) 1-36
39. Tobari Y.N. Geographical distribution. In: Tobari Y.N. (Ed). Drosophila ananassae: Genetical and Biological Aspects (1993), Japan Scientific Societies Press, Tokyo 9-22
40. Tomimura Y., Matsuda M., and Tobari Y.N. Polytene chromosome variations of Drosophila ananassae and its close relatives. In: Tobari Y.N. (Ed). Drosophila ananassae: Genetical and Biological Aspects (1993), Japan Scientific Societies Press, Tokyo 39-151
41. Vogl C., Das A., Beaumont M., Mohanty S., and Stephan W. Population subdivision and molecular sequence variation: theory and analysis of Drosophila ananassae data. Genetics 165 (2003) 1385-1395
42. Wang W., Thornton K., Berry A., and Long M. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295 (2002) 134-137
43. Yamada H., Sakai T., Tomaru M., Doi M., Matsuda M., and Oguma Y. Search for species-specific mating signal in courtship songs of sympatric sibling species, Drosophila ananassae and D. pallidosa. Genes Genet. Syst. 77 (2002) 97-106
44. Zhang D.X., and Hewitt G.M. Nuclear integrations: challenges for mitochondrial DNA markers. Trends Ecol. Evol. 11 (1996) 247-251