Gene and species trees reveal mitochondrial and nuclear discordance in the Drosophila cardini group (Diptera: Drosophilidae)

Invertebrate Biology

Volumn 129, Issue 4, 2010, Pages 353-367

  Cenzi De Ré, Francine ^a   Loreto, Elgion L S ^a   Robe, Lizandra J ^a  

^a FEDERAL UNIVERSITY OF SANTA MARIA   (Brazil)

Author keywords

Complete lineage sorting; Congruence; Trogression

Indexed keywords

CARDINI GROUP; CARDINI SUBGROUP; DIPTERA; DROSOPHILA CARDINI; DROSOPHILA DUNNI; DROSOPHILA NEOCARDINI; DROSOPHILIDAE; DUNNI SUBGROUP;

EID: 78649470158     PISSN: 10778306     EISSN: 17447410     Source Type: Journal    
DOI: 10.1111/j.1744-7410.2010.00207.x     Document Type: Article

References (60)

1. Akaike H 1974. A new look at the statistical model identification. IEEE Trans. Autom. Control. 19: 716-723.
2. Ané C, Larget B, Baum DA, Smith SD, & Rokas A 2007. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 24: 412-426.
3. Bächli G 2010. TaxoDros: the database on taxonomy of Drosophilidae, v.1.03. Available at (accessed January 4, 2010).
4. Ballard JWO 2000. When one is not enough: introgression of mitochondrial DNA in Drosophila. Mol. Biol. Evol. 17: 1126-1130.
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: 1228-1241.
8. 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. Zool. Syst. Evol. Res. 45: 47-63.
9. Degnan JH & Rosenberg NA 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2: 762-768.
10. Edwards SV, Liu L, & Pearl DK 2007. High-resolution species trees without concatenation. Proc Natl. Acad. Sci. USA 104: 5936-5941.
11. Farris JS, Källersjö M, Kluge A, & Bult C 1994. Testing significance of congruence. Cladistics 10: 315-320.
12. Farris JS, Källersjö M, Kluge A, & Bult C 1995. Constructing a significance test for incongruence. Syst. Biol. 44: 570-572.
13. Frota-Pessoa O 1954. Revision of the tripunctata group of Drosophila with description of fifteen new species (Drosophilidae, Diptera). Arq. Mus. Paran. X: 253-304.
14. Futch DG 1962. Hybridization studies within the cardini species group of the genus Drosophila. Univ. Texas Publ. 6205: 539-554.
15. Hatadani LM, Mc erney 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.
16. Heed WB 1962. Genetic characteristics of island populations. Univ. Texas Publ. 6205: 173-206.
17. Heed WB & Krishnamurthy NB 1959. Genetic studies on the cardini group of Drosophila in the West dies. Univ. Texas Publ. 5914: 155-179.
18. Heed WB & Russell JS 1971. Phylogeny and population structure in island and continental species of the cardini group of Drosophila studied by inversion analysis. Univ. Texas Publ. 7103: 91-130.
19. Huelsenbeck JP & Ronquist F 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
20. Jukes TH & Cantor CR 1969. Evolution of protein molecules. : Mammalian Protein Metabolism. Munro HN, ed., pp. 21-132. Academic Press, New York, NY, USA.
21. Kimura M 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
22. Kubatko LS & Degnan JH 2007. consistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56: 17-24.
23. Kumar S & Gadagkar SR 2001. Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 158: 1321-1327.
24. Larget B 2008. BUCKy-Bayesian untangling of concordance knots. Available at (accessed December 10, 2009).
25. Lee MSY & Hugall AF 2003. Partitioned likelihood support and the evaluation of data set conflict. Syst. Biol. 52: 15-22.
26. Liu L 2008. Best: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24: 2542-2543.
27. Liu L & Pearl DK 2007. Species trees from gene trees: reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56: 504-514.
28. Liu L, Pearl DK, Brumfield RT, & Edwards SV 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62: 2080-2091.
29. Maddison WP 1997. Gene trees in species trees. Syst. Biol. 46: 523-536.
30. Moriyama E & Powell J 1997. Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J. Mol. Evol. 45: 378-391.
31. Mota NR, Robe LJ, Valente VL, Budnik M, & Loreto EL 2008. Phylogeny of the Drosophila mesophragmatica group (Diptera, Drosophilidae): an example of Andean evolution. Zool. Sci. 25: 526-532.
32. Napp M & Cordeiro AR 1981. terspecific relationships in the cardini group of Drosophila studied by electrophoresis. Rev. Bras. Biol. 4: 537-547.
33. Nei M & Gojobori T 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
34. Nylander JAA 2004. MrModeltest v2. Program. Distributed by the author. Evolutionary Biology Center, Uppsala University, Uppsala, Sweden.
35. Valter De Oliveira,L.F.,Da Luz Wallau,G. and Silva Loreto,E.L.2009. Isolation of high quality DNA: A protocol combining "rennet" and glass milk. Electronic Journal of Biotechnology,2009,12(2), DOI: 10.2225/vol12-issue2-fulltext-4.
36. Pamilo P & Nei M 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5: 568-583.
37. Posada C & Crandall KA 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
38. Remsen J & DeSalle R 1998. Character congruence and multiple data partitions and the origin of the Hawaiian Drosophilidae. Mol. Phylogenet. Evol. 9: 225-235.
39. 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.
40. Robe LJ, Loreto ELS, & Valente VLS 2010a. Radiation of the Drosophila subgenus (Drosophilidae, Diptera) in the Neotropics. J. Zool. Syst. Evol. Res., doi: DOI: 10.1007/s10709-009-9432-5.
41. Robe LJ, Valente VLS, & Loreto ELS 2010b. Phylogenetic relationships and macro-evolutionary patterns within the Drosophila tripunctata"radiation" (Diptera: Drosophilidae). Genetica 138: 725-735.
42. Robe LJ, Cordeiro J, Loreto ELS, & Valente VLS 2010c. Taxonomic boundaries, phylogenetic relationships and biogeography of the Drosophila willistoni subgroup (Diptera: Drosophilidae). Genetica 138: 601-617.
43. Rodriguez F, Oliver JL, Marin A, & Medina JR 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142: 485-501.
44. Ronquist F & Huelsenbeck JP 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
45. Simon C, Frati F, Beckenbach A, Crespi B, Liu H, & Flook P 1994. Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87: 651-701.
46. Sorenson MD & Franzosa EA 2007. TreeRot Version 3. Boston University, Boston, MA, USA.
47. Staden R 1996. The Staden sequence analysis package. Mol. Biotechnol. 5: 233-241.
48. Sturtevant AH 1942. The classification of the genus Drosophila, with description of five new species. Univ. Texas Publ. 4213: 5-51.
49. Swofford DL 2003. PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. Sinauer Associates, Sunderland, MA, USA.
50. Tamura K & Nei M 1993. Estimation of the number of base nucleotide substitution in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
51. Tamura K, Dudley J, Nei M, & Kumar S 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599.
52. Tatarenkov A, Kwiatowski J, Skarecky D, Barrio E, & Ayala FJ 1999. On the evolution of Dopa decarboxylase (Ddc) and Drosophilas systematics. J. Mol. Evol. 48: 445-462.
53. Templeton AR 2006. Population Genetics and Microevolutionary Theory. John Wiley & Sons, Hoboken, NJ, USA.
54. Throckmorton LH 1975. The phylogeny, ecology and geography of Drosophila. : Handbook of Genetics. King RC, ed, pp 421-469. Plenum, New York, NY, USA.
55. Vilela CR, Silva AFG, & Sene FM 2002. Preliminary data on geographical distribution of Drosophila species within morpho-climatic domains of Brazil III: the cardini group. Rev. Bras. Entomol. 46: 139-148.
56. Whitworth TL, Dawson RD, Magalon H, & Baudry E 2007. DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae). Proc. R. Soc. Lond. B: Biol. Sci. 274: 1731-1739.
57. Xia X & Xie Z 2001. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92: 371-373.
58. 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.
59. Zachos FE 2009. Gene trees and species trees-mutual influences and interdependences of population genetics and systematics. J. Zool. Syst. Evol. Res. 47: 209-218.
60. Zwickl DJ 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD Dissertation, University of Texas, Austin, TX, USA.