Publications

Abascal F, Zardoya R and Posada D (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105. http://dx.doi.org/10.1093/bioinformatics/bti263 PMid:15647292   Birks SM and Edwards SV (2002). A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences. Mol. Phylogenet. Evol. 23: 408-421. http://dx.doi.org/10.1016/S1055-7903(02)00002-7   Brom TG and Dekker RWRJ (1992). Current studies on megapode phylogeny. Zool. Verhandelingen 278: 7-17.   Cracraft J (1981). Toward a phylogenetic classification of the recent birds of the world (class Aves). Auk 98: 681-714.   Crowe TM (1988). Molecules vs. morphology in systematics: a non-controversy. Trans. R. Soc. S. Afr. 46: 317-334. http://dx.doi.org/10.1080/00359198809520135   Crowe TM, Bowie RCK, Bloomer P, Mandiwana TG, et al. (2006). Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data. Cladistics 22: 495-532. http://dx.doi.org/10.1111/j.1096-0031.2006.00120.x   Cummings MP, Otto SP and Wakeley J (1995). Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12: 814-822. PMid:7476127   del Hoyo J, Elliot A and Sargatal J (1994). Handbook of the Birds of the World. Vol. 2. Lynx Editions, Barcelona, 434-557.   Dimcheff DE, Drovetski SV and Mindell DP (2002). Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes. Mol. Phylogenet. Evol. 24: 203-215. http://dx.doi.org/10.1016/S1055-7903(02)00230-0   Dyke GJ, Gulas BE and Crowe TM (2003). Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters. Zool. J. Linn. Soc. 137: 227-244. http://dx.doi.org/10.1046/j.1096-3642.2003.00048.x   Felsenstein J (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791. http://dx.doi.org/10.2307/2408678   Guan X, Silva P, Gyenai KB, Xu J, et al. (2009). The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo. Anim. Genet. 40: 134-141. http://dx.doi.org/10.1111/j.1365-2052.2008.01810.x PMid:19067672 PMCid:2664387   Guindon S and Gascuel O (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52: 696-704. http://dx.doi.org/10.1080/10635150390235520 PMid:14530136   He L, Dai B, Zeng B, Zhang X, et al. (2009). The complete mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) and a phylogenetic analysis with related species. Gene 435: 23-28. http://dx.doi.org/10.1016/j.gene.2009.01.001 PMid:19393190   Hockey PAR, Dean WRJ and Ryan PG (2005). Roberts-Birds of Southern Africa. 5th edn. The Trustees of the John Voclcker Bird Book Fund, Cape Town.   Huelsenbeck JP and Ronquist F (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755. http://dx.doi.org/10.1093/bioinformatics/17.8.754 PMid:11524383   Kan XZ, Li XF, Lei ZP, Wang M, et al. (2010). Complete mitochondrial genome of Cabot's tragopan, Tragopan caboti (Galliformes: Phasianidae). Genet. Mol. Res. 9: 1204-1216. http://dx.doi.org/10.4238/vol9-2gmr820 PMid:20589618   Kimball RT, Braun EL, Zwartjes PW, Crowe TM, et al. (1999). A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic. Mol. Phylogenet. Evol. 11: 38-54. http://dx.doi.org/10.1006/mpev.1998.0562 PMid:10082609   Larkin MA, Blackshields G, Brown NP, Chenna R, et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. http://dx.doi.org/10.1093/bioinformatics/btm404 PMid:17846036   Livezey BC and Zusi RL (2007). Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zool. J. Linn. Soc. 149: 1-95. http://dx.doi.org/10.1111/j.1096-3642.2006.00293.x PMid:18784798 PMCid:2517308   Nishibori M, Hayashi T, Tsudzuki M, Yamamoto Y, et al. (2001). Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species. Anim. Genet. 32: 380-385. http://dx.doi.org/10.1046/j.1365-2052.2001.00795.x PMid:11736810   Nishibori M, Tsudzuki M, Hayashi T, Yamamoto Y, et al. (2002). Complete nucleotide sequence of the Coturnix chinensis (blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species. J. Hered. 93: 439-444. http://dx.doi.org/10.1093/jhered/93.6.439 PMid:12642645   Nishibori M, Hayashi T and Yasue H (2004). Complete nucleotide sequence of Numida meleagris (Helmeted guineafowl) mitochondrial genome. J. Poult. Sci. 41: 259-268. http://dx.doi.org/10.2141/jpsa.41.259   Nishibori M, Shimogiri T, Hayashi T and Yasue H (2005). Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Anim. Genet. 36: 367-375. http://dx.doi.org/10.1111/j.1365-2052.2005.01318.x PMid:16167978   Pereira SL and Baker AJ (2009). Waterfowl and Gamefowl (Galloanserae). In: The Timetree of Life (Hedges SB and Kumar S, eds.). Oxford University Press, New York, 415-418. PMCid:2719981   Peters JL (1934). Checklist of the Birds of the World. Vol. 2. Harvard University Press, Cambridge.   Posada D (2008). jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25: 1253-1256. http://dx.doi.org/10.1093/molbev/msn083 PMid:18397919   Rich PV and van Tets GF (1985). Kadimakara: Extinct Vertebrates of Australia. Pioneer Design Studio, Lilydale.   Shen YY, Shi P, Sun YB and Zhang YP (2009). Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. Genome Res. 19: 1760-1765. http://dx.doi.org/10.1101/gr.093138.109 PMid:19617397 PMCid:2765268   Sibley CG and Ahlquist J (1990). Phylogeny and Classification of the Birds. Yale University Press, New Haven.   Sibley CG and Monroe BL (1990). The Distribution and Taxonomy of the Birds of the Word. Yale University Press, New Haven.   Sibley C, Ahlquist JE and Monroe BL (1988). A classification of the living birds of the world based on DNA-DNA hybridization studies. Auk 105: 409-423.   Slack KE, Delsuc F, McLenachan PA, Arnason U, et al. (2007). Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol. Phylogenet. Evol. 42: 1-13. http://dx.doi.org/10.1016/j.ympev.2006.06.002 PMid:16854605   Swofford D (2002). PAUP*. Phylogenetic analysis using parsimony (and other methods). Version 4. Sinauer Associates, Inc., Sunderland. PMid:12504223   Talavera G and Castresana J (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56: 564-577. http://dx.doi.org/10.1080/10635150701472164 PMid:17654362   Van Tuinen M and Dyke GJ (2004). Calibration of galliform molecular clocks using multiple fossils and genetic partitions. Mol. Phylogenet. Evol. 30: 74-86. http://dx.doi.org/10.1016/S1055-7903(03)00164-7   Wetmore A (1960). A classification for the birds of the world. Smithson. Misc. Collect. 139: 1-37.   Wolstenholme DR (1992). Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141: 173-216. http://dx.doi.org/10.1016/S0074-7696(08)62066-5   Xia X and Xie Z (2001). DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92: 371-373. http://dx.doi.org/10.1093/jhered/92.4.371 PMid:11535656   Xia X, Xie Z, Salemi M, Chen L, et al. (2003). An index of substitution saturation and its application. Mol. Phylogenet. Evol. 26: 1-7. http://dx.doi.org/10.1016/S1055-7903(02)00326-3