Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds

References

• Bandelt, H. J., P. Forster, and A. Röhl. 1999. “Median-Joining Networks for Inferring Intraspecific Phylogenies.” Molecular Biology and Evolution 16 (1): 37–48. doi:10.1093/oxfordjournals.molbev.a026036.
   PubMed Web of Science ®Google Scholar
• Bao, W. B., J. T. Shu, and C. B. Wang. 2008. “Analysis of Genetic Diversity and Phylogenetic Relationship among Chinese Domestic Fowls and Red Jungle Fowls.” Chinese Journal of Animal and Veterinary Science 39 (11): 1449–1459. In Chinese.
   Google Scholar
• Chen, G. H., K. H. Wang, J. Y. Wang, C. Ding, and N. Yang. 2004. Poultry Genetic Resources in China. Shanghai: Shanghai Scientific and Technological Press. In Chinese.
   Google Scholar
• Cuc, N. T. K., H. Simianer, L. F. Groeneveld, and S. Weigend. 2011. “Multiple Maternal Lineages of Vietnamese Local Chickens Inferred by Mitochondrial D-Loop Sequences.” Asian Australasian Journal of Animal Sciences 24: 155–161. doi:10.5713/ajas.2011.10155.
   Web of Science ®Google Scholar
• Felsenstein, J. 1985. “Confidence Limits on Phylogenies: An Approach Using the Bootstrap.” Evolution 39: 783–791. doi:10.2307/2408678.
   PubMed Web of Science ®Google Scholar
• Gong-Pian, P. T., L. X. Liu, and D. L. Li. 2011. “The Investigation of Genetic Diversity of Piao Chicken Based on Mitochondrial DNA D-Loop Region Sequence.” Journal of Yunnan Agricultural University (Nutural Sciences) 2: 211–214. In Chinese.
   Google Scholar
• Han, D. F., S. H. Wang, Y. X. Hu, Y. Y. Zhang, X. G. Dong, Z. Yang, J. K. Wang, J. Y. Li, and X. M. Deng. 2015. “Hyperpigmentation Results in Aberrant Immune Development in Silky Fowl (Gallus Gallus Domesticus Brisson).” PLoS One 10 (6): e0125686. doi:10.1371/journal.pone.0125686.
   PubMed Web of Science ®Google Scholar
• Harumi, T., A. Sano, T. Minematsu, and M. Naito. 2011. “Allele-Specific PCR Typing and Sequencing of the Mitochondrial D-Loop Region in Four Layer Breeds.” Animal Science Journal 82: 223–226. doi:10.1111/asj.2011.82.issue-2.
   PubMed Web of Science ®Google Scholar
• Hoque, M. R., N. R. Choi, and H. Sultana. 2013. “Phylogenetic Analysis of a Privately-Owned Korean Native Chicken Population Using Mtdna D-Loop Variations.” Asian Australasian Journal of Animal Sciences 26 (2): 157–162. doi:10.5713/ajas.2012.12459.
   PubMed Web of Science ®Google Scholar
• Hoque, M. R., S. H. Lee, K. C. Jung, B. S. Kang, M. N. Park, H. K. Lim, K. D. Choi, and J. H. Lee. 2011. “Discrimination of Korean Native Chicken Populations Using SNPs from mtDNA and MHC Polymorphisms.” Asian Australasian Journal of Animal Sciences 24: 1637–1643. doi:10.5713/ajas.2011.11144.
   Web of Science ®Google Scholar
• Kawabe, K., R. Worawut, S. Taura, T. Shimogiri, T. Nishida, and S. Okamoto. 2014. “Genetic Diversity of mtDNA D-Loop Polymorphisms in Laotian Native Fowl Populations.” Asian Australasian Journal of Animal Sciences 27: 19–23. doi:10.5713/ajas.2013.13443.
   PubMed Web of Science ®Google Scholar
• Kimura, M. 1980. “A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide Sequences.” Journal of Molecular Evolution 16: 111–120. doi:10.1007/BF01731581.
   PubMed Web of Science ®Google Scholar
• Kumar, S., S. Edu, and K. Tamura. 2007. “MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0.” Molecular Biology and Evolution 24 (8): 1596–1599. doi:10.1093/molbev/msm092.
   PubMed Web of Science ®Google Scholar
• Lan, D., Y. D. Hu, Q. Zhu, and Y. P. Liu. 2015. “Mitochondrial DNA Study in Domestic Chicken.” Mitochondrial DNA 2015: 1–5. doi:10.3109/19401736.2014.1003847.
   Web of Science ®Google Scholar
• Liu, Y.-P., G.-S. Wu, Y.-G. Yao, Y.-W. Miao, G. Luikart, M. Baig, A. Beja-Pereira, Z.-L. Ding, M. G. Palanichamy, and Y.-P. Zhang. 2006. “Multiple Maternal Origins of Chickens: Out of the Asian Jungles.” Molecular Phylogenetics & Evolution 38: 12–19. doi:10.1016/j.ympev.2005.09.014.
   PubMed Web of Science ®Google Scholar
• Lyu, Y. Z., J. X. Liu, and G. W. Lu. 2014. “Xichuan Black-Bone Chicken Genetic Resources Is Introduced.” Chinese Journal of Animal Husbandry 13: 65–66. In Chinese.
   Google Scholar
• Miao, Y. W., M. S. Peng, and G. S. Wu. 2013. “Chicken Domestication: An Updated Perspective Based on Mitochondrial Genomes.” Heredity 110: 277–282. doi:10.1038/hdy.2012.83.
   PubMed Web of Science ®Google Scholar
• Muchadeyi, F. C., H. Eding, and H. Simianer. 2008. “Mitochondrial DNA D-Loop Sequences Suggest a Southeast Asian and Indian Origin of Zimbabwean Village Chickens.” Animal Genetics 39: 615–622. doi:10.1111/j.1365-2052.2008.01785.x.
   PubMed Web of Science ®Google Scholar
• Niu, D., Y. Fu, and J. Luo. 2002. “The Origin and Genetic Diversity of Chinese Native Chicken Breeds.” Biochemical Genetics 40: 163–174. doi:10.1023/A:1015832108669.
   PubMed Web of Science ®Google Scholar
• Ohno, S. 1997. “The One Ancestor per Generation Rule and Three Other Rules of Mitochondrial Inheritance.” Proceedings of the National Academy of Sciences 94 (15): 8033–8035. doi:10.1073/pnas.94.15.8033.
   PubMed Web of Science ®Google Scholar
• Oka, T., Y. Ino, K. Nomura, S. Kawashima, T. Kuwayama, and H. Hanada. 2007. “Analysis of mtDNA Sequences Shows Japanese Native Chickens Have Multiple Origins.” Animal Genetics 38 (3): 287–293. doi:10.1111/j.1365-2052.2007.01604.x.
   PubMed Web of Science ®Google Scholar
• Rozas, J., J. C. Sánchez-Delbarrio, and X. Messeguer. 2003. “DnaSP DNA Polymorphism Analyses by the Coalescent and Other Methods.” Bioinformatics 19 (18): 2496–2497. doi:10.1093/bioinformatics/btg359.
   PubMed Web of Science ®Google Scholar
• Saitou, N., and M. Nei. 1987. “The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees.” Molecular Biology & Evolution 4 (4): 406–425.
   PubMed Web of Science ®Google Scholar
• Tamura, K., D. Peterson, and N. Peterson. 2011. “MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.” Molecular Biology & Evolution 28 (10): 2731–2739. doi:10.1093/molbev/msr121.
   PubMed Web of Science ®Google Scholar
• Torroni, A., T. G. Schurr, M. F. Cabell, M. D. Brown, J. V. Neel, and M. Larson. 1993. “Asian Affinities and Continental Radiation of the Four Founding Native American mtDNAs.” American Journal of Human Genetics 53 (3): 563–590.
   PubMed Web of Science ®Google Scholar
• Ward, R. H., A. Redd, D. Valencia, B. Frazier, and S. Paabo. 1993. “Genetic and Linguistic Differentiation in the Americas.” Proceedings of the National Academy of Sciences of the United States of America 90 (22): 10663–10667. doi:10.1073/pnas.90.22.10663.
   PubMed Web of Science ®Google Scholar
• Zouros, E., A. O. Ball, C. Saavedra, C. and K. R., Freeman. 1994. “Mitochondrial Dna Inheritance.” Nature 368: (6474): 818. doi: 10.1038/368818a0.
   PubMed Web of Science ®Google Scholar