Publications

Found 57 results
Filters: Author is L. Chen  [Clear All Filters]
2013
H. L. Wang, Li, Z. X., Chen, L., Yang, J., Wang, L. J., He, H., Niu, F. B., Liu, Y., Guo, J. Z., and Liu, X. L., Polymorphism in PGLYRP-2 gene by PCR-RFLP and its association with somatic cell score and percentage of fat in Chinese Holstein, vol. 12, pp. 6743-6751, 2013.
L. Chen, Yang, D. Y., Liu, T. F., Nong, X., Huang, X., Xie, Y., Fu, Y., Zheng, W. P., Zhang, R. H., Wu, X. H., Gu, X. B., Wang, S. X., Peng, X. R., and Yang, G. Y., Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes, vol. 12, pp. 587-596, 2013.
Brown WM, George M Jr and Wilson AC (1979). Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. U. S. A. 76: 1967-1971. http://dx.doi.org/10.1073/pnas.76.4.1967 PMid:109836 PMCid:383514   Bulmer M (1991). The selection-mutation-drift theory of synonymous codon usage. Genetics 129: 897-907. PMid:1752426 PMCid:1204756   Chiapello H, Lisacek F, Caboche M and Henaut A (1998). Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene 209: GC1-GC38. http://dx.doi.org/10.1016/S0378-1119(97)00671-9   Duret L and Mouchiroud D (1999). Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 96: 4482-4487. http://dx.doi.org/10.1073/pnas.96.8.4482 PMid:10200288 PMCid:16358   Fadiel A, Lithwick S, Wanas MQ and Cuticchia AJ (2001). Influence of intercodon and base frequencies on codon usage in filarial parasites. Genomics 74: 197-210. http://dx.doi.org/10.1006/geno.2001.6531 PMid:11386756   Fadiel AA, Lithwick S and Gamra MM (2002). Codon usage analysis of Ascaris species influence of base and intercodon frequencies on the synonymous codon usage. J. Egypt. Soc. Parasitol. 32: 625-638. PMid:12214939   Fickett JW (1982). Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10: 5303-5318. http://dx.doi.org/10.1093/nar/10.17.5303 PMid:7145702 PMCid:320873   Grantham R, Gautier C, Gouy M, Mercier R, et al. (1980). Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8: r49-r62. http://dx.doi.org/10.1093/nar/8.1.197-c PMid:6986610 PMCid:327256   Hua J and Lee RW (2012). Factors affecting codon bias in the mitochondrial genomes of the streptophyte Mesostigma viride and the chlorophyte Chlamydomonas reinhardtii. J. Eukaryot. Microbiol. 59: 287-289. http://dx.doi.org/10.1111/j.1550-7408.2011.00613.x PMid:22340021   Ikemura T (1981). Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151: 389-409. http://dx.doi.org/10.1016/0022-2836(81)90003-6   Jia W and Higgs PG (2008). Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol. Biol. Evol. 25: 339-351. http://dx.doi.org/10.1093/molbev/msm259 PMid:18048402   Karlin S and Mrazek J (1996). What drives codon choices in human genes? J. Mol. Biol. 262: 459-472. http://dx.doi.org/10.1006/jmbi.1996.0528 PMid:8893856   Liu H, He R, Zhang H, Huang Y, et al. (2010). Analysis of synonymous codon usage in Zea mays. Mol. Biol. Rep. 37: 677-684. http://dx.doi.org/10.1007/s11033-009-9521-7 PMid:19330534   Liu Q, Feng Y and Xue Q (2004). Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa. Mitochondrion 4: 313-320. http://dx.doi.org/10.1016/j.mito.2004.06.003 PMid:16120394   Lloyd AT and Sharp PM (1992). Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae. Nucleic Acids Res. 20: 5289-5295. http://dx.doi.org/10.1093/nar/20.20.5289 PMid:1437548 PMCid:334333   Luo XL, Xu JG and Ye CY (2011). Analysis of synonymous codon usage in Shigella flexneri 2a strain 301 and other Shigella and Escherichia coli strains. Can. J. Microbiol. 57: 1016-1023. http://dx.doi.org/10.1139/w11-095 PMid:22112197   Ma J, Zhou T, Gu W, Sun X, et al. (2002). Cluster analysis of the codon use frequency of MHC genes from different species. Biosystems 65: 199-207. http://dx.doi.org/10.1016/S0303-2647(02)00016-3   Martin AP, Naylor GJ and Palumbi SR (1992). Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357: 153-155. http://dx.doi.org/10.1038/357153a0 PMid:1579163   Moriyama EN and Powell JR (1998). Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res. 26: 3188-3193. http://dx.doi.org/10.1093/nar/26.13.3188 PMid:9628917 PMCid:147681   Musto H, Cruveiller S, D'Onofrio G, Romero H, et al. (2001). Translational selection on codon usage in Xenopus laevis. Mol. Biol. Evol. 18: 1703-1707. http://dx.doi.org/10.1093/oxfordjournals.molbev.a003958 PMid:11504850   Oresic M and Shalloway D (1998). Specific correlations between relative synonymous codon usage and protein secondary structure. J. Mol. Biol. 281: 31-48. http://dx.doi.org/10.1006/jmbi.1998.1921 PMid:9680473   Osawa S, Ohama T, Yamao F, Muto A, et al. (1988). Directional mutation pressure and transfer RNA in choice of the third nucleotide of synonymous two-codon sets. Proc. Natl. Acad. Sci. U. S. A. 85: 1124-1128. http://dx.doi.org/10.1073/pnas.85.4.1124 PMid:2448791 PMCid:279718   Powell JR and Moriyama EN (1997). Evolution of codon usage bias in Drosophila. Proc. Natl. Acad. Sci. U. S. A. 94: 7784-7790. http://dx.doi.org/10.1073/pnas.94.15.7784 PMid:9223264 PMCid:33704   Ramirez V, Savoie P and Morais R (1993). Molecular characterization and evolution of a duck mitochondrial genome. J. Mol. Evol. 37: 296-310. http://dx.doi.org/10.1007/BF00175506 PMid:8230253   Romero H, Zavala A and Musto H (2000). Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res. 28: 2084-2090. http://dx.doi.org/10.1093/nar/28.10.2084 PMid:10773076 PMCid:105376   Sau K and Deb A (2009). Temperature influences synonymous codon and amino acid usage biases in the phages infecting extremely thermophilic prokaryotes. In Silico Biol. 9: 1-9. PMid:19537157   Sharp PM and Li WH (1986). Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 14: 7737-7749. http://dx.doi.org/10.1093/nar/14.19.7737 PMid:3534792 PMCid:311793   Sloan DB and Taylor DR (2010). Testing for selection on synonymous sites in plant mitochondrial DNA: the role of codon bias and RNA editing. J. Mol. Evol. 70: 479-491. http://dx.doi.org/10.1007/s00239-010-9346-y PMid:20424833   Wang B, Liu J, Jin L, Feng XY, et al. (2010). Complex mutation and weak selection together determined the codon usage bias in bryophyte mitochondrial genomes. J. Integr. Plant Biol. 52: 1100-1108. http://dx.doi.org/10.1111/j.1744-7909.2010.00998.x PMid:21106008   Wang B, Yuan J, Liu J, Jin L, et al. (2011). Codon usage bias and determining forces in green plant mitochondrial genomes. J. Integr. Plant Biol. 53: 324-334. http://dx.doi.org/10.1111/j.1744-7909.2011.01033.x PMid:21332641   Whittle CA, Sun Y and Johannesson H (2011). Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta. Genome Biol. Evol. 3: 332-343. http://dx.doi.org/10.1093/gbe/evr018 PMid:21402862 PMCid:3089379   Wright F (1990). The 'effective number of codons' used in a gene. Gene 87: 23-29. http://dx.doi.org/10.1016/0378-1119(90)90491-9   Xie T and Ding D (1998). The relationship between synonymous codon usage and protein structure. FEBS Lett. 434: 93-96. http://dx.doi.org/10.1016/S0014-5793(98)00955-7   Zhang Y, Liu Y, Liu W, Zhou J, et al. (2011). Analysis of synonymous codon usage in hepatitis A virus. Virol. J. 8: 174. http://dx.doi.org/10.1186/1743-422X-8-174 PMid:21496278 PMCid:3087699   Zhou M and Li X (2009). Analysis of synonymous codon usage patterns in different plant mitochondrial genomes. Mol. Biol. Rep. 36: 2039-2046. http://dx.doi.org/10.1007/s11033-008-9414-1 PMid:19005776
2012
X. J. Chen, Li, Z. B., Chen, L., Cao, Y. Y., and Li, Q. H., Isolation and characterization of new microsatellite markers in the pen shell Atrina pectinata (Pinnidae), vol. 11, pp. 2884-2887, 2012.
Li Q (2006). Development of microsatellite DNA markers and their applications in genetic studies in marine mollusks. J. Fish. Sci. China 3: 503-509.   Liang XQ, Fang JZ and Yang HQ (1996). Aquatic Biology (Morphological Character and Classification). China Agriculture Press, Beijing.   Ren J and Guo Y (2005). Current status of study on pen shell Atrina pectinata and its prospects of application and exploitation. Mar. Fish. Res. 26: 84-87.   Rice WR (1989). Analyzing tables of statistical tests. Evol. Int. J. Org. Evol. 43: 223-225. http://dx.doi.org/10.2307/2409177   Van Oosterhaut C, Hutchinson WF and Shipley P (2004). MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4: 535-538. http://dx.doi.org/10.1111/j.1471-8286.2004.00684.x   Waples RS (1998). Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. J. Hered. 89: 438-450. http://dx.doi.org/10.1093/jhered/89.5.438   Yeh FC, Yang R, Boyle TJ, Ye Z, et al (2000). PopGene32, Microsoft Windows-Based Freeware for Population Genetic Analysis. Version 1.32, Molecular Biology and Biotechnology Centre. University of Alberta, Edmonton.   Zane L, Bargelloni L and Patarnello T (2002). Strategies for microsatellite isolation: a review. Mol. Ecol. 11: 1-16. http://dx.doi.org/10.1046/j.0962-1083.2001.01418.x PMid:11903900
Z. L. Yao, Wang, H., Chen, L., Zhou, K., Ying, C. Q., and Lai, Q. F., Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress, vol. 11, pp. 2200-2246, 2012.
Brindley DN and Pilquil C (2009). Lipid phosphate phosphatases and signaling. J. Lipid. Res. 50: S225-S230. http://dx.doi.org/10.1194/jlr.R800055-JLR200 PMid:19066402 PMCid:2674702   Claiborne JB, Edwards SL and Morrison-Shetlar AI (2002). Acid-base regulation in fishes: cellular and molecular mechanisms. J. Exp. Zool. 293: 302-319. http://dx.doi.org/10.1002/jez.10125 PMid:12115903   Dennis G Jr, Sherman BT, Hosack DA, Yang J, et al. (2003). DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4: 3. http://dx.doi.org/10.1186/gb-2003-4-5-p3   Evans TG (2010). Co-ordination of osmotic stress responses through osmosensing and signal transduction events in fishes. J. Fish Biol. 76: 1903-1925. http://dx.doi.org/10.1111/j.1095-8649.2010.02590.x PMid:20557646   Fiol DF and Kültz D (2007). Osmotic stress sensing and signaling in fishes. FEBS J. 274: 5790-5798. http://dx.doi.org/10.1111/j.1742-4658.2007.06099.x PMid:17944942   Gibson G (2008). The environmental contribution to gene expression profiles. Nat. Rev. Genet. 9: 575-581. http://dx.doi.org/10.1038/nrg2383 PMid:18574472   Gilmour KM and Perry SF (2009). Carbonic anhydrase and acid-base regulation in fish. J. Exp. Biol. 212: 1647-1661. http://dx.doi.org/10.1242/jeb.029181 PMid:19448075   Goss GG, Wood CM, Laurent P and Perry SF (1994). Morphological responses of the rainbow trout (Oncorhynchus mykiss) gill to hyperoxia, base (NaHCO3) and acid (HCl) infusions. Fish Physiol. Biochem. 12: 465-477. http://dx.doi.org/10.1007/BF00004449   Green TJ and Barnes AC (2010). Reduced salinity, but not estuarine acidification, is a cause of immune-suppression in the Sydney rock oyster Saccostrea glomerata. Mar. Ecol. Prog. Ser. 402: 161-170. http://dx.doi.org/10.3354/meps08430   Hirayama M, Nakaniwa M, Mitani H and Watabe S (2005). Gene expression profiles for medaka Olyzias latipes associated with cold and warm temperatures in cDNA microarray. Comp. Biochem. Phys. 141: S354-S355.   Hwang PP and Lee TH (2007). New insights into fish ion regulation and mitochondrion-rich cells. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 148: 479-497. http://dx.doi.org/10.1016/j.cbpa.2007.06.416 PMid:17689996   Inoue K and Takei Y (2002). Diverse adaptability in oryzias species to high environmental salinity. Zoolog. Sci. 19: 727- 734. http://dx.doi.org/10.2108/zsj.19.727 PMid:12149572   Kanehisa M and Goto S (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28: 27-30. http://dx.doi.org/10.1093/nar/28.1.27 PMid:10592173 PMCid:102409   Kang CK, Tsai SC, Lee TH and Hwang PP (2008). Differential expression of branchial Na+/K+-ATPase of two medaka species, Oryzias latipes and Oryzias dancena, with different salinity tolerances acclimated to fresh water, brackish water and seawater. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 151: 566-575. http://dx.doi.org/10.1016/j.cbpa.2008.07.020 PMid:18692588   Kasahara M, Naruse K, Sasaki S, Nakatani Y, et al. (2007). The medaka draft genome and insights into vertebrate genome evolution. Nature 447: 714-719. http://dx.doi.org/10.1038/nature05846 PMid:17554307   Kültz D (2001). Evolution of osmosensory MAP kinase signaling pathways. Am. Zool. 41: 743-757. http://dx.doi.org/10.1668/0003-1569(2001)041[0743:EOOMKS]2.0.CO;2   Kültz D (2005). Molecular and evolutionary basis of the cellular stress response. Annu. Rev. Physiol. 67: 225-257. http://dx.doi.org/10.1146/annurev.physiol.67.040403.103635 PMid:15709958   Kurosawa Y and Hashimoto K (1997). How did the primordial T cell receptor and MHC molecules function initially? Immunol. Cell Biol. 75: 193-196. http://dx.doi.org/10.1038/icb.1997.28 PMid:9107575   Lang F, Bohmer C, Palmada M, Seebohm G, et al. (2006). (Patho)physiological significance of the serum- and glucocorticoid-inducible kinase isoforms. Physiol. Rev. 86: 1151-1178. http://dx.doi.org/10.1152/physrev.00050.2005 PMid:17015487   Lockwood BL, Sanders JG and Somero GN (2010). Transcriptomic responses to heat stress in invasive and native blue mussels (genus Mytilus): molecular correlates of invasive success. J. Exp. Biol. 213: 3548-3558. http://dx.doi.org/10.1242/jeb.046094 PMid:20889835   Loffing J, Flores SY and Staub O (2006). Sgk kinases and their role in epithelial transport. Annu. Rev. Physiol. 68: 461- 490. http://dx.doi.org/10.1146/annurev.physiol.68.040104.131654 PMid:16460280   Parra JEG and Baldisserotto B (2007). Effect of Water pH and Hardness on Survival and Growth of Freshwater Teleosts. In: Fish Osmoregulation (Baldisserotto B, Mancera JM and Kapoor BG, eds.). Science Publishers, Enfield, 139.   Perry SF and Gilmour KM (2006). Acid-base balance and CO2 excretion in fish: unanswered questions and emerging models. Respir. Physiol. Neurobiol. 154: 199-215. http://dx.doi.org/10.1016/j.resp.2006.04.010 PMid:16777496   Podrabsky JE and Somero GN (2004). Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J. Exp. Biol. 207: 2237-2254. http://dx.doi.org/10.1242/jeb.01016 PMid:15159429   Prophete C, Carlson EA, Li Y, Duffy J, et al. (2006). Effects of elevated temperature and nickel pollution on the immune status of Japanese medaka. Fish Shellfish Immunol. 21: 325-334. http://dx.doi.org/10.1016/j.fsi.2005.12.009 PMid:16529948   Randall DJ and Tsui TK (2006). Tribute to R. G. Boutilier: acid-base transfer across fish gills. J. Exp. Biol. 209: 1179- 1184. http://dx.doi.org/10.1242/jeb.02100 PMid:16547290   Rodrigues PN, Hermsen TT, van Maanen A, Taverne-Thiele AJ, et al. (1998). Expression of MhcCyca class I and class II molecules in the early life history of the common carp (Cyprinus carpio L.). Dev. Comp. Immunol. 22: 493-506. http://dx.doi.org/10.1016/S0145-305X(97)00059-1   Rozen S and Skaletsky HJ (2000). Primer 3 on the WWW for General Users and for Biologist Programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (Krawetz S and Misener S, eds.). Humana Press, Totowa, 365-386. PMid:10547847   Schmittgen TD and Livak KJ (2008). Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 3: 1101- 1108. http://dx.doi.org/10.1038/nprot.2008.73 PMid:18546601   Scott GR, Richards JG, Forbush B, Isenring P, et al. (2004). Changes in gene expression in gills of the euryhaline killifish Fundulus heteroclitus after abrupt salinity transfer. Am. J. Physiol. Cell Physiol. 287: C300-C309. http://dx.doi.org/10.1152/ajpcell.00054.2004 PMid:15044150   Takeda H and Shimada A (2010). The art of medaka genetics and genomics: what makes them so unique? Annu. Rev. Genet. 44: 217-241. http://dx.doi.org/10.1146/annurev-genet-051710-151001 PMid:20731603   Todgham AE and Hofmann GE (2009). Transcriptomic response of sea urchin larvae Strongylocentrotus purpuratus to CO2-driven seawater acidification. J. Exp. Biol. 212: 2579-2594. http://dx.doi.org/10.1242/jeb.032540 PMid:19648403   Tseng YC and Hwang PP (2008). Some insights into energy metabolism for osmoregulation in fish. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 148: 419-429.   Tufts BL, Esbaugh A and Lund SG (2003). Comparative physiology and molecular evolution of carbonic anhydrase in the erythrocytes of early vertebrates. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 136: 259-269. http://dx.doi.org/10.1016/S1095-6433(03)00159-4   Vijayan M, Morgan J, Sakamoto T, Grau E, et al. (1996). Food-deprivation affects seawater acclimation in tilapia: hormonal and metabolic changes. J. Exp. Biol. 199: 2467-2475. PMid:9320394   Wang YS, Gonzalez RJ, Patrick ML, Grosell M, et al. (2003). Unusual physiology of scale-less carp, Gymnocypris przewalskii, in Lake Qinghai: a high altitude alkaline saline lake. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 134: 409-421. http://dx.doi.org/10.1016/S1095-6433(02)00317-3   Wilkie MP and Wood CM (1996). The adaptations of fish to extremely alkaline environments. Comp. Biochem. Phys. B 113: 665-673. http://dx.doi.org/10.1016/0305-0491(95)02092-6   Yao ZL, Lai QF, Zhou K, Rizalita RE, et al. (2010). Developmental biology of medaka fish (Oryzias latipes) exposed to alkalinity stress. J. Appl. Ichthyol. 26: 397-402. http://dx.doi.org/10.1111/j.1439-0426.2009.01360.x   Yum S, Woo S, Kagami Y, Park HS, et al. (2010). Changes in gene expression profile of medaka with acute toxicity of Arochlor 1260, a polychlorinated biphenyl mixture. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 151: 51-56.   Zhang Z, Ju Z, Wells MC and Walter RB (2009). Genomic approaches in the identification of hypoxia biomarkers in model fish species. J. Exp. Mar. Biol. Ecol. 381: S180-S187. http://dx.doi.org/10.1016/j.jembe.2009.07.021 PMid:20161383 PMCid:2782826
2010
X. Z. Kan, Li, X. F., Zhang, L. Q., Chen, L., Qian, C. J., Zhang, X. W., and Wang, L., Characterization of the complete mitochondrial genome of the Rock pigeon, Columba livia (Columbiformes: Columbidae), vol. 9, pp. 1234-1249, 2010.
Boore JL (1999). Animal mitochondrial genomes. Nucleic Acids Res. 27: 1767-1780. http://dx.doi.org/10.1093/nar/27.8.1767 PMid:10101183 PMCid:148383   Brown GG, Gadaleta G, Pepe G, Saccone C, et al. (1986). Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192: 503-511. http://dx.doi.org/10.1016/0022-2836(86)90272-X   Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, et al. (2001). Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409: 704-707. http://dx.doi.org/10.1038/35055536 PMid:11217857   Gibb GC, Kardailsky O, Kimball RT, Braun EL, et al. (2007). Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Mol. Biol. Evol. 24: 269-280. http://dx.doi.org/10.1093/molbev/msl158 PMid:17062634   Haddrath O and Baker AJ (2001). Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc. Biol. Sci. 268: 939-945. http://dx.doi.org/10.1098/rspb.2001.1587 PMid:11370967 PMCid:1088691   Hall AT (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symp. Ser. 41: 95-98.   Harlid A, Janke A and Arnason U (1998). The complete mitochondrial genome of Rhea americana and early avian divergences. J. Mol. Evol. 46: 669-679. http://dx.doi.org/10.1007/PL00006347 PMid:9608049   Harrison GL, McLenachan PA, Phillips MJ, Slack KE, et al. (2004). Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous. Mol. Biol. Evol. 21: 974-983. http://dx.doi.org/10.1093/molbev/msh065 PMid:14739240   Hazkani-Covo E, Zeller RM and Martin W (2010). Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet. 6: e1000834. http://dx.doi.org/10.1371/journal.pgen.1000834 PMid:20168995 PMCid:2820518   Howard R and Moore A (2003). The Howard and Moore Complete Checklist of the Birds of the World. 3rd edn. Christopher Helm, London.   L'Abbé D, Duhaime JF, Lang BF and Morais R (1991). The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. J. Biol. Chem. 266: 10844-10850. PMid:1710214   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   Lohse M, Drechsel O and Bock R (2007). OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52: 267-274. http://dx.doi.org/10.1007/s00294-007-0161-y PMid:17957369   Lowe TM and Eddy SR (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964. PMid:9023104 PMCid:146525   Mindell DP, Sorenson MD and Dimcheff DE (1998). Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. U. S. A. 95: 10693-10697. http://dx.doi.org/10.1073/pnas.95.18.10693 PMid:9724766 PMCid:27957   Moore WS (1995). Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49: 718-726. http://dx.doi.org/10.2307/2410325   Morgan-Richards M, Trewick SA, Bartosch-Harlid A, Kardailsky O, et al. (2008). Bird evolution: testing the Metaves clade with six new mitochondrial genomes. BMC Evol. Biol. 8: 20. http://dx.doi.org/10.1186/1471-2148-8-20 PMid:18215323 PMCid:2259304   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, 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   Paton T, Haddrath O and Baker AJ (2002). Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc. Biol. Sci. 269: 839-846. http://dx.doi.org/10.1098/rspb.2002.1961 PMid:11958716 PMCid:1690957   Pereira SL, Johnson KP, Clayton DH and 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: 656-672. http://dx.doi.org/10.1080/10635150701549672 PMid:17661233   Perna NT and Kocher TD (1995). Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41: 353-358. http://dx.doi.org/10.1007/BF01215182 PMid:7563121   Pratt RC, Gibb GC, Morgan-Richards M, Phillips MJ, et al. (2009). Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors. Mol. Biol. Evol. 26: 313-326. http://dx.doi.org/10.1093/molbev/msn248 PMid:18981298   Randi E and Lucchini V (1998). Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J. Mol. Evol. 47: 449-462. http://dx.doi.org/10.1007/PL00006402 PMid:9767690   Rokas A, Williams BL, King N and Carroll SB (2003). Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804. http://dx.doi.org/10.1038/nature02053 PMid:14574403   Saccone C, Pesole G and Sbisa E (1991). The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J. Mol. Evol. 33: 83-91. http://dx.doi.org/10.1007/BF02100199 PMid:1909377   Sambrook J and Russell DW (2001). Molecular Cloning: A Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, New York.   San Mauro D, Garcia-Paris M and Zardoya R (2004). Phylogenetic relationships of discoglossid frogs (Amphibia: Anura: Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene 343: 357-366. http://dx.doi.org/10.1016/j.gene.2004.10.001 PMid:15588590   Sbisa E, Tanzariello F, Reyes A, Pesole G, et al. (1997). Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205: 125-140. http://dx.doi.org/10.1016/S0378-1119(97)00404-6   Shadel GS and Clayton DA (1997). Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66: 409-435. http://dx.doi.org/10.1146/annurev.biochem.66.1.409 PMid:9242913   Shen X, Tian M, Liu Z, Cheng H, et al. (2009). Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): the first representative from the subclass Aspidochirotacea with the echinoderm ground pattern. Gene 439: 79-86. http://dx.doi.org/10.1016/j.gene.2009.03.008 PMid:19306915   Slack KE, Janke A, Penny D and Arnason U (2003). Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302: 43-52. http://dx.doi.org/10.1016/S0378111902010533 PMid:12527195   Slack KE, Jones CM, Ando T, Harrison GL, et al. (2006). Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol. Biol. Evol. 23: 1144-1155. http://dx.doi.org/10.1093/molbev/msj124 PMid:16533822   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   Walberg MW and Clayton DA (1981). Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9: 5411-5421. http://dx.doi.org/10.1093/nar/9.20.5411 PMid:7301592 PMCid:327529   Wang C, Chen Q, Lu G, Xu J, et al. (2008). Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae. Gene 424: 96-101. http://dx.doi.org/10.1016/j.gene.2008.07.011 PMid:18706492   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   Wyman SK, Jansen RK and Boore JL (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. http://dx.doi.org/10.1093/bioinformatics/bth352 PMid:15180927   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
X. Z. Kan, Li, X. F., Lei, Z. P., Wang, M., Chen, L., Gao, H., and Yang, Z. Y., Complete mitochondrial genome of Cabot’s tragopan, Tragopan caboti (Galliformes: Phasianidae), vol. 9, pp. 1204-1216, 2010.
Boore JL (1999). Animal mitochondrial genomes. Nucleic Acids Res. 27: 1767-1780. http://dx.doi.org/10.1093/nar/27.8.1767 PMid:10101183 PMCid:148383   Brown GG, Gadaleta G, Pepe G, Saccone C, et al. (1986). Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192: 503-511. http://dx.doi.org/10.1016/0022-2836(86)90272-X   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   del Hoyo J, Elliot A and Sargatal J (1994). Handbook of the Birds of the World. Vol. 2. Lynx Editions, Barcelona, 434-557.   Deng WH and Zheng GM (2004). Landscape and habitat factors affecting Cabot's tragopan Tragopan caboti occurrence in habitat fragments. Biol. Conserv. 117: 25-32. http://dx.doi.org/10.1016/S0006-3207(03)00259-3   Dyke GJ, Gulas BE and Crowe TM (2003). Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters. Zoolog. J. Linnean Soc. 137: 227-244. http://dx.doi.org/10.1046/j.1096-3642.2003.00048.x   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   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   IUCN (2009). IUCN Red List of Threatened Species. Gland, Switzerland. Available at [http://www.iucnredlist.org]. Accessed November 9, 2009.   Kumazawa Y and Nishida M (1993). Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37: 380-398. http://dx.doi.org/10.1007/BF00178868 PMid:7508516   L'Abbe D, Duhaime JF, Lang BF and Morais R (1991). The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. J. Biol. Chem. 266: 10844-10850. PMid:1710214   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   Lohse M, Drechsel O and Bock R (2007). Organellar Genome DRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52: 267-274. http://dx.doi.org/10.1007/s00294-007-0161-y PMid:17957369   Lowe TM and Eddy SR (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964. PMid:9023104 PMCid:146525   Mindell DP, Sorenson MD and Dimcheff DE (1998). An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles. Mol. Biol. Evol. 15: 1568-1571. http://dx.doi.org/10.1093/oxfordjournals.molbev.a025884 PMid:12572620   Monroe BL and Sibley CG (1990). A World Checklist of Birds. Yale University Press, New Haven.   Moore WS (1995). Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49: 718-726. http://dx.doi.org/10.2307/2410325   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   Perna NT and Kocher TD (1995). Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41: 353-358. http://dx.doi.org/10.1007/BF01215182 PMid:7563121   Quinn TW (1992). The genetic legacy of Mother Goose - phylogeographic patterns of lesser snow goose Chen caerulescens caerulescens maternal lineages. Mol. Ecol. 1: 105-117. http://dx.doi.org/10.1111/j.1365-294X.1992.tb00162.x PMid:1344986   Randi E and Lucchini V (1998). Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J. Mol. Evol. 47: 449-462. http://dx.doi.org/10.1007/PL00006402 PMid:9767690   Ruokonen M and Kvist L (2002). Structure and evolution of the avian mitochondrial control region. Mol. Phylogenet. Evol. 23: 422-432. http://dx.doi.org/10.1016/S1055-7903(02)00021-0   Russell RD and Beckenbach AT (2008). Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code. J. Mol. Evol. 67: 682-695. http://dx.doi.org/10.1007/s00239-008-9179-0 PMid:19030769 PMCid:2706983   Saccone C, Pesole G and Sbisa E (1991). The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J. Mol. Evol. 33: 83-91. http://dx.doi.org/10.1007/BF02100199 PMid:1909377   Sambrook J and Russell DW (2001). Molecular Cloning: A Laboratory Manual. 3rd edn. Cold Spring Harbor Laboratory Press, New York.   San Mauro D, Garcia-Paris M and Zardoya R (2004). Phylogenetic relationships of discoglossid frogs (Amphibia:Anura:Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene 343: 357- 366. http://dx.doi.org/10.1016/j.gene.2004.10.001 PMid:15588590   Sbisa E, Tanzariello F, Reyes A, Pesole G, et al. (1997). Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205: 125-140. http://dx.doi.org/10.1016/S0378-1119(97)00404-6   Shadel GS and Clayton DA (1997). Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66: 409-435. http://dx.doi.org/10.1146/annurev.biochem.66.1.409 PMid:9242913   Shen X, Tian M, Liu Z, Cheng H, et al. (2009a). Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): the first representative from the subclass Aspidochirotacea with the echinoderm ground pattern. Gene 439: 79-86. http://dx.doi.org/10.1016/j.gene.2009.03.008 PMid:19306915   Shen YY, Shi P, Sun YB and Zhang YP (2009b). 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   Slack KE, Janke A, Penny D and Arnason U (2003). Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302: 43-52. http://dx.doi.org/10.1016/S0378111902010533 PMid:12527195   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   Walberg MW and Clayton DA (1981). Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9: 5411-5421. http://dx.doi.org/10.1093/nar/9.20.5411 PMid:7301592 PMCid:327529   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   Wyman SK, Jansen RK and Boore JL (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. http://dx.doi.org/10.1093/bioinformatics/bth352 PMid:15180927   Zhang JF, Nie LW, Wang Y and Hu LL (2009). The complete mitochondrial genome of the large-headed frog, Limnonectes bannaensis (Amphibia: Anura), and a novel gene organization in the vertebrate mtDNA. Gene 442: 119-127. http://dx.doi.org/10.1016/j.gene.2009.04.018 PMid:19397958   Zhang Y and Zheng G (2007). A population viability analysis (PVA) for Cabot's tragopan (Tragopan caboti) in Wuyanling, south-east China. Bird Conserv. Int. 17: 151-161. http://dx.doi.org/10.1017/S0959270907000652
X. - Z. Kan, Yang, J. - K., Li, X. - F., Chen, L., Lei, Z. - P., Wang, M., Qian, C. - J., Gao, H., and Yang, Z. - Y., Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes, vol. 9, pp. 1625-1633, 2010.
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

Pages