Estimation of divergence times for major lineages of galliform birds: Evidence from complete mitochondrial genome sequences

African Journal of Biotechnology

Volumn 9, Issue 21, 2010, Pages 3073-3078

  Kan, Xian Zhao ^a   Li, Xi Feng ^a   Lei, Zu Pei ^b   Chen, Lei ^a   Gao, Hui ^c   Yang, Zu Yu ^c   Yang, Jian Ke ^a   Guo, Zhi Chun ^a   Yu, Lei ^a   Zhang, Li Qin ^a   Qian, Chao Ju ^a  

^a ANHUI NORMAL UNIVERSITY   (China)

^b The Administration Bureau of Wuyanling National Nature Reserve   (China)

^c INSTITUTE OF BOTANY   (China)

Author keywords

Divergence time; Galliformes; Mitochondrial genome; Relaxed molecular clock

Indexed keywords

ARBOROPHILINAE; ARTICLE; BAYES THEOREM; CONTROLLED STUDY; COTURNICINAE; CRETACEOUS; EOCENE; FOSSIL; GALLIFORMES; GALLININAE; GALLINULOIDES; GALLUS BRAVARDI; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; MEGAPODIIDAE; MELEAGRIDINAE; MITOCHONDRIAL GENOME; MOLECULAR CLOCK; MONTE CARLO METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; NUMIDIDAE; OLIGOCENE; PALEOGENE; PAVONINAE; PHASIANIDAE; PHASIANINAE; PROBABILITY; SCHAUBORTYX;

AVES; GALLIFORMES; GALLINULOIDES; GALLUS; MEGAPODIIDAE; MELEAGRIDINAE; NUMIDIDAE; PHASIANIDAE; PHASIANINAE;

EID: 77958171615     PISSN: 16845315     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (40)

1. Bloomer P, Crowe TM (1998). Francolin phylogenetics: molecular, morphobehavioral, and combined evidence. Mol. Phylogenet. Evol. 9(2): 236-254.
2. Brodkorb P (1964). Catalogue of fossil birds. part 2 (Anseriformes through Galliformes). Bull. Florida State Mus. Biol. Sci. 8: 195-335.
3. Bromham L, Penny D (2003). The modern molecular clock. Nat. Rev. Genet. 4(3): 216-224.
4. Brown JW, Rest JS, Garcia-Moreno J, Sorenson MD, Mindell DP (2008). Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biol. 6: p. 6.
5. Crowe TM, Bowie RCK, Bloomer P, Mandiwana TG, Hedderson TAJ, Randi E, Pereira SL, Wakeling J (2006). Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data. Cladistics, 22(6): 495-532.
6. Drove ski SV (2003). Plio-Pleistocene climatic oscilations, Holarctic biogeography and speciation in an avian subfamily. J. Biogeogr. 30:1173-1181.
7. Drummond AJ, Rambaut A (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: p. 214.
8. Dyke GJ, Gulas BE, Crowe TM (2003). Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters. Zool. J. Linn. Soc. 137(2): 227-244.
9. Grau ET, Pereira SL, Silveira LF, Hofling E, Wajntal A (2005). Molecular phylogenetics and biogeography of Neotropical piping guans (Aves: Galliformes): Pipile Bonaparte, 1856 is synonym of Aburria Reichenbach, 1853. Mol. Phylogenet. Evol. 35(3): 637-645.
10. Guan X, Silva P, Gyenai KB, Xu J, Geng T, Tu Z, Samuels DC, Smith EJ (2009). The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo. Anim. Genet. 40(2): 134-141.
11. Guindon S, Gascuel O (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52(5): 696-704.
12. Haddrath O, Baker AJ (2001). Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc. Biol. Sci. 268(1470): 939-945.
13. He L, Dai B, Zeng B, Zhang X, Chen B, Yue B, Li J (2009). The complete mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) and a phylogenetic analysis with related species. Gene. 435(1-2): 23-28.
14. Hipsley CA, Himmelmann L, Metzler D, Muller J (2009). Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards. BMC Evol. Biol. 9: p. 151.
15. Huang Z, Liu N, Luo S, Long J (2007). Phylogeography of rusty-necklaced partridge (Alectoris magna) in northwestern China. Mol. Phylogenet. Evol. 43(2): 379-385.
16. Huang Z, Liu N, Xiao Y, Cheng Y, Mei W, Wen L, Zhang L, Yu X (2009). Phylogenetic relationships of four endemic genera of the Phasianidae in China based on mitochondrial DNA control-region genes. Mol. Phylogenet. Evol. 53(2): 378-283.
17. Kimball RT, Braun EL, Ligon JD (1997). Resolution of the phylogenetic position of the Congo peafowl, Afropavo congensis: a biogeographic and evolutionary enigma. Proc. R. Soc. B. Biol. Sci. 264: 1517-1523.
18. Lambrecht K (1933). Handbuch der Paleoornithologie. Berlin.
19. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007). Clustal W and Clustal X version 2.0. Bioinform. 23(21): 2947-2948.
20. Lucchini V, Hoglund J, Klaus S, Swenson J, Randi E (2001). Historical biogeography and a mitochondrial DNA phylogeny of grouse and ptarmigan. Mol. Phylogenet. Evol. 20(1): 149-162.
21. Nishibori M, Hayashi T, Tsudzuki M, Yamamoto Y, Yasue H (2001). Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species. Anim. Genet. 32(6): 380-385.
22. Nishibori M, Hayashi T, Yasue H (2004). Complete nucleotide sequence of Numida meleagris (Helmeted guineafowl) mitochondrial genome. J. Poult. Sci. 41: 259-268.
23. Nishibori M, Shimogiri T, Hayashi T, Yasue H (2005). Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Anim. Genet. 36(5): 367-375.
24. Nishibori M, Tsudzuki M, Hayashi T, Yamamoto Y, Yasue H (2002). Complete nucleotide sequence of the Coturnix chinensis (blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species. J. Hered. 93(6): 439-444.
25. Pereira SL, Baker AJ (2004). Vicariant speciation of curassows (Aves, Cracidae):a hypothesis based on mitochondrial DNA phylogeny. The Auk. 121(3): 682-694.
26. Pereira SL, Baker AJ (2006a). A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol. Biol. Evol. 23(9): 1731-1740.
27. Pereira SL, Baker AJ (2006b). A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites. Mol. Phylogenet. Evol. 38(2): 499-509.
28. Pereira SL, Baker AJ, Wajntal A (2002). Combined nuclear and mitochondrial DNA sequences resolve generic relationships within the Cracidae (Galliformes, Aves). Syst. Biol. 51(6): 946-958.
29. Pereira SL, Wajntal A (2008). The historical biogeography of Pteroglossus aracaris (Aves, Piciformes, Ramphastidae) based on Bayesian analysis of mitochondrial DNA sequences. Genet. Mol. Biol. 31(4): 964-973.
30. Pereira SL, Johnson KP, Clayton DH, Baker AJ (2007). Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleocene. Syst. Biol. 56(4): 656-672.
31. Randi E, Lucchini V, Armijo-Prewitt T, Kimball RT, Braun EL, Ligon JD (2000). Mitochondrial DNA phylogeny and speciation in the Tragopans. The Auk. 117(4): 1003-1015.
32. Rodriguez-Trelles F, Tarrio R, Ayala FJ (2002). A methodological bias toward overestimation of molecular evolutionary time scales. Proc. Natl. Acad. Sci. USA, 99(12): 8112-8115.
33. Sanderson MJ (1997). A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14(12): 1218-1231.
34. Shen YY, Shi P, Sun YB, Zhang YP (2009). Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. Genome Res. 19(10): 1760-1765.
35. Slack KE, Delsuc F, McLenachan PA, Arnason U, Penny D (2007). Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol. Phylogenet. Evol. 42(1):1-13.
36. Thorne JL, Kishino H (2002). Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51(5): 689-702.
37. Van Tuinen M, Dyke GJ (2004). Calibration of galliform molecular clocks using multiple fossils and genetic partitions. Mol. Phylogenet. Evol. 30(1): 74-86.
38. Xia X, Xie Z (2001). DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92(4): 371-373.
39. Xia X, Xie Z, Salemi M, Chen L, Wang Y (2003). An index of substitution saturation and its application. Mol. Phylogenet. Evol. 26(1): 1-7.
40. Zhang Y, Zhang Z-W, Zhang N. (2003). Calibration of basal Phasianidae molecular clock. J. Beijing Norm. Univ. Nat. Sci. 39(4): 525-530.