Radiation of the, Drosophila" subgenus (Drosophilidae, Diptera) in the Neotropics

Journal of Zoological Systematics and Evolutionary Research

Volumn 48, Issue 4, 2010, Pages 310-321

  Robe, Lizandra J ^a,b   Loreto, Elgion L S ^a,b   Valente, Vera L S ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b FEDERAL UNIVERSITY OF SANTA MARIA   (Brazil)

Author keywords

amd gene; ddc gene; Divergence times estimates; Drosophila" subgenus; Phylogeny

Indexed keywords

DIVERGENCE; FLY; GENE; NEOTROPIC ECOZONE; PHYLOGENETICS;

DIPTERA; DROSOPHILIDAE;

EID: 78649481322     PISSN: 09475745     EISSN: 14390469     Source Type: Journal    
DOI: 10.1111/j.1439-0469.2009.00563.x     Document Type: Article

References (75)

1. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, De Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Siden-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Woodage T, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC (2000) The genome sequence of Drosophila melanogaster. Science 287:2185-2195.
2. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Automat Contr 19:716-723.
3. Bächli G (2009) TaxoDros: The Database on Taxonomy of Drosophilidae, v.1.03, Database 2009/08. Available at (Last accessed on 19 June 2009).
4. Beverley SM, Wilson AC (1984) Molecular evolution in Drosophila and the higher Diptera II. A time scale for fly evolution. J Mol Evol 21:1-13.
5. Bremer K (1988) The limits of amino acid sequence data in angiosperm phylogenetics reconstruction. Evolution 42:795-803.
6. Bremer K (1994) Branch support and tree stability. Cladistics 10:295-304.
7. Brisson JA, Wilder J, Hollocher H (2006) Phylogenetic analysis of the cardini group of Drosophila with respect to changes in pigmentation. Evolution 60:1228-1247.
8. Brncic D, Koref-Santibañez S (1957) The mesophragmatica species group of Drosophila. Evolution 11:300-310.
9. Brncic D, Nair PS, Wheeler MR (1971) Cytotaxonomic relationships within the mesophragmatica species group of Drosophila. Univ Texas Publ 7103:1-16.
10. DaLage JL, Dergoat GJ, Maczkowiak F, Silvain JF, Cariou ML, Lachaise D (2007) A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries. J Zoolog Syst Evol Res 45:47-63.
11. DeSalle R (1992a) The phylogenetic relationships of flies in the family Drosophilidae deduced from mtDNA sequences. Mol Phylogenet Evol 1:31-40.
12. DeSalle R (1992b) The origin and possible time of divergence of the Hawaiian Drosophilidae: evidence from DNA sequences. Mol Biol Evol 9:905-916.
13. Eveleth DD, Marsh JL (1986) Evidence for evolutionary duplication of genes in the dopa decarboxylase region of Drosophila. Genetics 114:469-483.
14. Farris JS, Källersjö M, Kluge A, Bult C (1994) Testing significance of congruence. Cladistics 10:315-320.
15. Farris JS, Källersjö M, Kluge A, Bult C (1995) Constructing a significance test for incongruence. Syst Biol 44:570-572.
16. Felsenstein J (1985) Confidence limits on phylogenies: an approaching using bootstrap. Evolution 39:783-791.
17. Flores SV, Evans AL, McAllister BF (2008) Independent origns of new sex-linked chromosomes in the melanica and robusta species groups of Drosophila. BMC Evol Biol 8:33.
18. Frota-Pessoa O (1954) Revision of the tripunctata group of Drosophila with description of fifteen new species (Drosophilidae, Diptera). Arq Mus Paranaense X:253-304.
19. Galtier N, Gouy M (1995) Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci U S A 92:11317-11321.
20. Galtier N, Gouy M (1998) Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol 15:871-879.
21. Grimaldi DA (1987) Amber fossil Drosophilidae (Diptera), with particular reference to the Hispaniolan taxa. Am Mus Novit 2880:1-23.
22. Grimaldi DA (1990) A phylogenetic, revised classification of the genera in the Drosophilidae (Diptera). Bull Am Mus Nat Hist 197:1-139.
23. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704.
24. Haffer J (1997) Alternative models of vertebrate speciation in Amazonia: an overview. Biodivers Conserv 6:451-476.
25. Hatadani LM, McInerney JO, Medeiros HF, Junqueira ACM, Azeredo-Espin AM, Klaczko LB (2009) Molecular phylogeny of the Drosophila tripunctata and closely related groups (Diptera: Drosophilidae). Mol Phylogenet Evol 51:595-600.
26. Heed WB (1962) Genetic characteristics of island populations. Univ Texas Publ 6205:173-206.
27. Heed WB, Russell JS (1971) Phylogeny and population structure in island and continental species on the cardini group of Drosophila studied by inversion analysis. Univ Texas Publ 7103:91-130.
28. Hooghiemstra H, Van Der Hammen T (1998) Neogene and Quaternary development of the Neotropical rain forest: the forest refugia hypothesis, and a literature overview. Earth-Sci Rev 44:147-183.
29. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
30. Kastritsis CD (1969) The chromosomes of some species of the guarani group of Drosophila. J Hered 60:51-57.
31. Katoh T, Tamura K, Aotsuka T (2000) Phylogenetic position of the subgenus Lordiphosa of the genus Drosophila (Diptera: Drosophilidae) inferred from Alcohol Dehydrogenase (Adh) gene sequences. J Mol Evol 51:122-130.
32. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5:150-163.
33. Kwiatowski J, Ayala FJ (1999) Phylogeny of Drosophila and related genera: conflict between molecular and anatomical analyses. Mol Phylogenet Evol 13:319-328.
34. Kwiatowski J, Krawczyk M, Jaworski M, Skarecky D, Ayala FJ (1997) Erratic Evolution of Glycerol-3-Phophate Dehydrogenase in Drosophila, Chymomyza, and Ceratitis. J Mol Evol 44:9-22.
35. Van Der Linde K, Houle D (2008) A supertree analysis and literature review of the genus Drosophila and closely related genera (Diptera, Drosophilidae). Insect Syst Evol 39:241-267.
36. Lockhart PJ, Stell MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11:605-612.
37. Malogolowkin C (1953) Sobre a genitália de drosofilídeos. IV. A genitália masculina no subgênero Drosophila (Diptera, Drosophilidae). Rev Bras Biol 13:245-264.
38. Markow TA, O'Grady PM (2006) Phylogenetic relationships of Drosophilidae. In: Markow TA, O'Grady PM (eds), Drosophila: A Guide to Species Identification and Use. Academic Press, London, pp. 3-64.
39. Mota NR, Robe LJ, Valente VLS, Budnik M, Loreto ELS (2008) Phylogeny of the Drosophila mesophragmatica group (Diptera, Drosophilidae): an example of Andean evolution. Zoolog Sci 25:526-532.
40. Nair PS, Brncic D, Kojima KI (1971) II. Isozyme variations and evolutionary relationships in the mesophragmatica species group of Drosophila. Univ Texas Publ VI:17-28.
41. Napp M, Cordeiro AR (1981) Interespecific relationships in the cardini group of Drosophila studied by electrophoresis. Rev Bras Biol 4:537-547.
42. Nylander JAA (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Center, Uppsala University, Uppsala, Sweden.
43. O'Grady P, DeSalle R (2008) Out of Hawaii: the origin and biogeography of the genus Scaptomyza (Diptera: Drosophilidae). Biol Lett 4:195-199.
44. Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Mol Biol Evol 5:568-583.
45. Pélandakis M, Solignac M (1993) Molecular phylogeny of Drosophila based on ribosomal RNA sequences. J Mol Evol 37:525-543.
46. Pollard DA, Iyer VN, Moses AM, Eisen MB (2006) Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet 2:e173.
47. Posada C, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
48. Remsen J, DeSalle R (1998) Character congruence and multiple data partitions and the origin of the Hawaiian Drosophilidae. Mol Phylogenet Evol 9:225-235.
49. Remsen J, O'Grady PO (2002) Phylogeny of Drosophilinae (Diptera: Drosopilidae) with comments on combined analysis and character support. Mol Phylogenet Evol 24:249-264.
50. Robe LJ, Cordeiro J, Loreto ELS, Valente VLS (2010) Taxonomic boundaries, phylogenetic relationships and biogeography of the Drosophila willistoni subgroup (Diptera: Drosophilidae). Genetica. doi.
51. Robe LJ, Valente VLS, Budnik M, Loreto ELS (2005) Molecular phylogeny of the subgenus Drosophila (Diptera, Drosophilidae) with an emphasis on Neotropical species and groups: a nuclear versus mitochondrial gene approach. Mol Phylogenet Evol 36:623-640.
52. Rodríguez-Trelles F, Tarrío R, Ayala FJ (2000) Fluctuating mutation bias and the evolution of base composition in Drosophila. J Mol Evol 50:1-10.
53. Rull V (2008) Speciation timing and neotropical biodiversity: the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence. Mol Ecol 17:2722-2729.
54. Russo CAM, Takezaki N, Nei M (1995) Molecular phylogeny and divergence times of Drosophilid species. Mol Biol Evol 12:391-404.
55. Sassi AK, Heredia F, Loreto ELS, Valente VLS, Rohde C (2005) Transposable elements P and gypsy in natural populations of Drosophila willistoni. Genet Mol Biol 28:734-739.
56. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114-1116.
57. Sorenson MD, Franzosa EA (2007) TreeRot Version 3. Boston University, Boston.
58. Staden R (1996) The Staden sequence analysis package. Mol Biotechnol 5:233-241.
59. Swofford DL (2003) PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. Sinauer Associates, Massachusetts.
60. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK (eds), Molecular Systematics. Sinauer, Sunderland, pp. 407-514.
61. Tamura K, Subramanian S, Kumar S (2004) Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21:36-44.
62. Tatarenkov A, Ayala FJ (2001) Phylogenetic relationships among species groups of the virilis-repleta radiation of Drosophila. Mol Phylogenet Evol 21:327-331.
63. Tatarenkov A, Kwiatowski J, Sharecky D, Barrío E, Ayala FJ (1999) On the evolution of Dopa decarboxylase (Ddc) and Drosophila systematics. J Mol Evol 48:445-462.
64. Tatarenkov A, Zurovcová M, Ayala FJ (2001) Ddc and Amd sequences resolve phylogenetic relationships of Drosophila. Mol Phylogenet Evol 20:321-325.
65. Templeton AR (1983) Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data. In: Weir B (ed.), Statistical Analysis of DNA Sequence Data. Marcel Dekker, New York, pp. 151-179.
66. Thorne JL, Kishino H (2002) Divergence time and evolutionary rate estimation with multilocus data. Syst Biol 51:689-702.
67. Thorne JL, Kishino H, Painter IS (1998) Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 15:1647-1657.
68. Throckmorton LH (1962) The problem of phylogeny in the genus Drosophila. Univ Texas Publ 6205:207-343.
69. Throckmorton LH (1975) The phylogeny, ecology and geography of Drosophila. In: King RC (ed.), Handbook of Genetics. Plenun, New York, pp. 421-469.
70. Vidal NM, Ludwig A, Loreto ELS (2009) Evolution of Tom, 297, 17.6 and rover retrotransposons in Drosophilidae species. Mol Genet Genomics 282:351-362.
71. Wang B, Park J, Watabe H, Gao J, Xiangyu J, Aotsuka T, Chen H, Zhang Y (2006) Molecular phylogeny of the Drosophila virilis section (Diptera: Drosophilidae) based on mitochondrial and nuclear sequences. Mol Phylogenet Evol 40:484-500.
72. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. BACIOS 13:555-556.
73. Yotoko KSC, Medeiros HF, Solferini VN, Klaczko LB (2003) A molecular study of the systematics of the Drosophila tripunctata group and the tripunctata radiation. Mol Phylogenet Evol 28:614-619.
74. Zachos FE (2009) Gene trees and species trees - mutual influences and interdependences of population genetics and systematics. J Zoolog Syst Evol Res 47:209-218.
75. Zachos J, Pagani H, Sloan L, Thomas E, Billups K (2001) Trends, rhythms, and aberrations in global climate 65 ma to present. Science 292:686-693.