基于线粒体控制区探讨红腹锦鸡种群进化历史
|
摘要
红腹锦鸡(Chrysolophus pictus),又名金鸡,我国特有物种,国家二级保护动物。利用线粒体DNA分子标记研究红腹锦鸡种内及种间的群体遗传结构和系统发生关系,将对该物种的有效保护起到重要作用。本研究以线粒体DNA控制区的448bp高变区序列为分子标记,利用PCR和直接测序方法,采用序列分析技术,对红腹锦鸡的12个种群的212个个体进行了实验,探讨各群体间与个体间的遗传变异、系统发育及种群进化关系和种群历史动态,研究结果如下：
1)所分析的序列有57个变异位点(12.93%),其中单可变位点15个,简约信息位点42个,有插入和缺失现象。57个变异位点定义了38种单倍型,出现频率最高的为单倍型H2(73/212),并存在于11个种群中。单倍型多样性和核苷酸多样性水平均较高,分别为0.907和9.115%。陕西秦岭个体的单倍型多样性和核苷酸多样性水平在12个种群中是相对最高的,其单倍型种类也最丰富,由此推断,秦岭种群是较为原始的种群。
2)根据种群不同群体划分模式下的分子变异分析,结合遗传距离的远近,将本研究的12个种群分为3大群体是比较合理的,令为QL群体、中部地区群体和SC群体。
3) NETWORK图显示单倍型并没有依采样地区域形成各自的分支(clade), QL种群的单倍型遍布整个网络图。以单倍型H2作为中心向其他单倍型发散,推断H2是这些单倍型的历史基因流,视为古老单倍型。单倍型H1也形成一个小的中心,含有个体数也较多。表明H1也是古老单倍型之一。在中部地区的种群里,H1和H2单倍型保留最多,分布最广。中部地区群体的独享单倍型与QL、SC群体,QL与SC群体的单倍型之间相互连接,表明了三大群体存在连续的系统进化关系,群体内个体之间发生相互迁移和扩散。
4)AMOVA分析显示红腹锦鸡种群的分子变异主要来自于种群内变异(87.13%)。种群内分化程度要大于地理区内群体间的分化,地理区间分化指数FCT很低,表明红腹锦鸡的地理区间分化并不明显,地理区间群体间存在着较高水平的基因交流,亦暗示红腹锦鸡种群能够快速地扩张。各种群遗传多样性不存在显著的地理差异,个体呈现出混杂的分布格局。
5)红腹锦鸡所有种群的中性检验和错配分布曲线显示,种群整体处于动态平衡,趋向稳定,并未发生扩张和明显数量增长。各群体内积累了较多的基因突变,主要为中、低频率的变异,QL和JG种群在历史上曾发生过扩张历史事件,中部地区群体可能存在较多基因搭载现象或经历了自然选择。
6)综合分析12个种群的遗传多样性和系统发育,QL种群为较原始种群,单倍型H1和H2是主导单倍型,并在中部地区群体广泛分布,需施以更加合理的保护和管理措施。
Golden pheasant (Chrysolophus pictus) is also named as golden chicken. It's a kind of specific pheasants in our country. Studying the genetic structures and phylogenesis within and among populations through mtDNA molecular marker will resort to protect this species effectively. In this study,448bp hypervariable gene sequences of mitochondrial control region were applied to investigate the genetic variance, phylogenetic development, evolutionary relationships among populations and the dynamics of group history through PCR, directly sequencing and sequential analysis technology, which point at 12 populations, 212 species of golden pheasant. The main results are as follows:
1. There were 57 variable sites (12.93%) on the sequences, including 15 singleton variable sites and 42 parsimony informative sites. Some sites were alignment gaps or missing data. The chicken samples falled into 38 haplotypes. Haplotype H2 distributed most widely, and existed in 11 populations. In the whole populations, haplotype diversity was 0.907 and nucleotide diversity was 9.115%. The haplotype diversity and nucleotide diversity were the highest in QL population of Shanxi province. What' more, QL polulation carried the most haplotypes. It may inferred that QL population was the most primitive.
2. On the strength of hierarchial AMOVA analysis referring to different clustering combining with genetic distance, it indicated it was reasonable that 12 chicken populations should be falled into three groups in our study, which were named as QL, central and SC groups.
3. The NETWORK picture showed that the haplotypes didn't form clades corresponding to the geographical sites. QL population almost spreaded all over the whole network. Haplotype H2 was surrouneded by other haplotypes. This character suggested H2 was the orign of its surrouding ones, which was referred as an old haplotype.H1 also formed a small center, which indicted that it was one of the old haplotypes and was the origin to its surrounding ones. In the central group, excellent haplotypes were retained and distributed the most. The only sharing haplotypes by central group interconnected with QL and SC groups, the same as QL group and SC group, which indicted there had a successive phyletic evolutional relationships among these three groups and in the meanwhile the individuals in the three groups migrated or diffused mutually.
4. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation consisted in that among populations. Differentiation level(87.13%) among populations were greater than populations within a geographic region. Geographic region differentiation indexes FCT was very low, which indicted that differentiation was not obvious among geographic regions of 12 goldern pheasant populations and there were magor gene exchanges populations within geographic regions. Above all, these conclusions implied golden pheasant populations can expand quickly. Their genetic diversity of populations was high and had no geographical difference. Individuals of different water system distributed motleyly.
5. The neutral tests and mismatch distribution curve of all golden pheasant populations indicted that the whole was in dynamic balance and not expanding or remarkable quantity increase. Many mutations accumulated in each population, and they were almost mutations with middium or lower frequency. QL and JG may experience population expansion. The central group may carry more genetic hitchkiking experiments or experience natural selection.
6. On the strength of comprehensive analysis of genetic diversity and phyletic development, QL population was more primitive population; H1 and H2 were the leading haplotypes and distributed generally in central group. They all needed more reasonable protection and supervision.
1)所分析的序列有57个变异位点(12.93%),其中单可变位点15个,简约信息位点42个,有插入和缺失现象。57个变异位点定义了38种单倍型,出现频率最高的为单倍型H2(73/212),并存在于11个种群中。单倍型多样性和核苷酸多样性水平均较高,分别为0.907和9.115%。陕西秦岭个体的单倍型多样性和核苷酸多样性水平在12个种群中是相对最高的,其单倍型种类也最丰富,由此推断,秦岭种群是较为原始的种群。
2)根据种群不同群体划分模式下的分子变异分析,结合遗传距离的远近,将本研究的12个种群分为3大群体是比较合理的,令为QL群体、中部地区群体和SC群体。
3) NETWORK图显示单倍型并没有依采样地区域形成各自的分支(clade), QL种群的单倍型遍布整个网络图。以单倍型H2作为中心向其他单倍型发散,推断H2是这些单倍型的历史基因流,视为古老单倍型。单倍型H1也形成一个小的中心,含有个体数也较多。表明H1也是古老单倍型之一。在中部地区的种群里,H1和H2单倍型保留最多,分布最广。中部地区群体的独享单倍型与QL、SC群体,QL与SC群体的单倍型之间相互连接,表明了三大群体存在连续的系统进化关系,群体内个体之间发生相互迁移和扩散。
4)AMOVA分析显示红腹锦鸡种群的分子变异主要来自于种群内变异(87.13%)。种群内分化程度要大于地理区内群体间的分化,地理区间分化指数FCT很低,表明红腹锦鸡的地理区间分化并不明显,地理区间群体间存在着较高水平的基因交流,亦暗示红腹锦鸡种群能够快速地扩张。各种群遗传多样性不存在显著的地理差异,个体呈现出混杂的分布格局。
5)红腹锦鸡所有种群的中性检验和错配分布曲线显示,种群整体处于动态平衡,趋向稳定,并未发生扩张和明显数量增长。各群体内积累了较多的基因突变,主要为中、低频率的变异,QL和JG种群在历史上曾发生过扩张历史事件,中部地区群体可能存在较多基因搭载现象或经历了自然选择。
6)综合分析12个种群的遗传多样性和系统发育,QL种群为较原始种群,单倍型H1和H2是主导单倍型,并在中部地区群体广泛分布,需施以更加合理的保护和管理措施。
Golden pheasant (Chrysolophus pictus) is also named as golden chicken. It's a kind of specific pheasants in our country. Studying the genetic structures and phylogenesis within and among populations through mtDNA molecular marker will resort to protect this species effectively. In this study,448bp hypervariable gene sequences of mitochondrial control region were applied to investigate the genetic variance, phylogenetic development, evolutionary relationships among populations and the dynamics of group history through PCR, directly sequencing and sequential analysis technology, which point at 12 populations, 212 species of golden pheasant. The main results are as follows:
1. There were 57 variable sites (12.93%) on the sequences, including 15 singleton variable sites and 42 parsimony informative sites. Some sites were alignment gaps or missing data. The chicken samples falled into 38 haplotypes. Haplotype H2 distributed most widely, and existed in 11 populations. In the whole populations, haplotype diversity was 0.907 and nucleotide diversity was 9.115%. The haplotype diversity and nucleotide diversity were the highest in QL population of Shanxi province. What' more, QL polulation carried the most haplotypes. It may inferred that QL population was the most primitive.
2. On the strength of hierarchial AMOVA analysis referring to different clustering combining with genetic distance, it indicated it was reasonable that 12 chicken populations should be falled into three groups in our study, which were named as QL, central and SC groups.
3. The NETWORK picture showed that the haplotypes didn't form clades corresponding to the geographical sites. QL population almost spreaded all over the whole network. Haplotype H2 was surrouneded by other haplotypes. This character suggested H2 was the orign of its surrouding ones, which was referred as an old haplotype.H1 also formed a small center, which indicted that it was one of the old haplotypes and was the origin to its surrounding ones. In the central group, excellent haplotypes were retained and distributed the most. The only sharing haplotypes by central group interconnected with QL and SC groups, the same as QL group and SC group, which indicted there had a successive phyletic evolutional relationships among these three groups and in the meanwhile the individuals in the three groups migrated or diffused mutually.
4. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation consisted in that among populations. Differentiation level(87.13%) among populations were greater than populations within a geographic region. Geographic region differentiation indexes FCT was very low, which indicted that differentiation was not obvious among geographic regions of 12 goldern pheasant populations and there were magor gene exchanges populations within geographic regions. Above all, these conclusions implied golden pheasant populations can expand quickly. Their genetic diversity of populations was high and had no geographical difference. Individuals of different water system distributed motleyly.
5. The neutral tests and mismatch distribution curve of all golden pheasant populations indicted that the whole was in dynamic balance and not expanding or remarkable quantity increase. Many mutations accumulated in each population, and they were almost mutations with middium or lower frequency. QL and JG may experience population expansion. The central group may carry more genetic hitchkiking experiments or experience natural selection.
6. On the strength of comprehensive analysis of genetic diversity and phyletic development, QL population was more primitive population; H1 and H2 were the leading haplotypes and distributed generally in central group. They all needed more reasonable protection and supervision.
引文
Avise J.C., Arnold J., Ball R.M., et al(1987). Intraspecific Phylogeography:The Mitochondrial DNA Bridge Between Population Genetics and Systematics. Annual Review of Ecology and Systematics.18:489-522.
Balakrishnan, C.N., Monfort, S.L., Gaur, A., Singh, L. and Sorenson, M.D. (2003). Phylogeography and conservation genetics of Eld's deer (Cervus eldi). Molecular Ecology.12:1-10.
Baker, A.J. and Marshall, H. D.(1997). Mitochondrial control region sequences as tools for understanding evolution. In:Mindell, D.P. (Ed), Avian Molecular Evolution and Systematics. Academic Press, San Diego,11:51-82
Barrowclough, G.F., Groth, J.G., Mertz, L,A,, and Gutierrez, R.J. (2005). Genetic structure, introgression, and a narrow hybrid zone between northern and California spotted owls (Strix occidentalis). Molecular Ecology.14:1109-1120.
Bermingham E, Martin A P.(1998) Comparative mtDNA phylogeography of neotropical freshwater fishes:testing shared history to infer the evolutionary landscape of lower Central America. [J]. Mol Ecol.,7(4):499-517.
Brown, G.G., Gadaleta, G., Pepe, G., Saccone, C. and Sbisa(1986) Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. Journal of Molecular Biology.192:503-511.
Cann, R. L., Brown, W. M., and Wilson, A. C. (1984). Polymorphic sites and the mechanism of evolution in human mitochondrial DNA. Genetics 106:479-499.
Carlos T. Moraes, Sarika Srivastava, Ilias Kirkinezos, Jose Oca-Cossio, Corina vanWaveren, Markus Woischnick, Francisco Diaz(2000). Mitochondrial DNA structure and function,International Review of Neurobiology. Volume 53:3-23
Case, M.A., Mlodozeniec, H.T., Wallace, L.E., Weldy, T.W. (1998). Conservation genetics and taxonomic status of the rare Kentucky Lady's slipper:Cypripedium kentuckiense (Orchidaceae). American Journal of Botany.85:1779-1786.
Chang, D.and Clayton, D., (1986). Identification of primary transcription start sites of mouse mitochondrial DNA:Accurate in vitro initiation of both heavy and light-strand transcriptions. Molecular Cell Biology.6:1446-1453.
Clayton, D. A. (1992). Transcription and replication of animal mitochondrial DNAs. International Review Of Cytology-A Survey Of Cell Biology.141:217-232.
Clayton, D. A. (1991). Replication and transcription of vertebrate mitochondrial DNA. Annual Review of Cell Biology.7:453-478.
Desjardins, P., and Morais, R. (1990). Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. Journal of Molecular Biology.212:599-634
Desjardins,P.and R.Morais(1999). Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome. Journal of Molecular Evolution.32:153-161.
DeYoung, R.W., Demarais, S., Honeycutt, R.L. (2003). Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi. Molecular Ecology.12:3237-3252.
Dupanloup,Schneider and Excoffier(2002). A simulated annealing approach to define the genetic structure of populations.IN. Molecular Ecology Issue. 12:2571-2581.
Edwards,S.V.(1993). Long-distance gene flow in a cooperative breeder detected in genealogies of mitochondrial DNA sequence.Proceedings of the Royal Society of London Series B.252:177-185.
Excoffier L, Laval G, Schneider S. Arlequin (version 3.0)(2005). An integrated software package for population genetics data analysis.[J]. Evol Bioinform Online.1:47-50.
Excoffier L, Smouse P E. (1994).Using allele frequencies and geographic subdivision to reconstruct gene trees within a species:molecular variance parsimony.[J]. Genetics.136(1):343-359.
Fu Y X, Li W H (1993). Statistical tests of neutrality of mutations. Genetics.133(3): 693-709.
Frankham R, Ballou J D, Briscoe D A et al. (2002). Introduction to conservation genetics. New York:Cambridge University Press.
Glenn, T.C., Stephan, W. and Braun, M.J. (1999). Effects of a population bottleneck on Whooping Crane mitochondiral DNA variation. Conservation Biology.13: 1097-1107.
Godoy, J.A., Negro, J.J., Hiraldo, F., and Donazar, J.A. (2004). Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L) as revealed by mitochondrial DNA. Molecular Ecology. 13:371-390.
Goldstein, P.Z., DeSalle, R., Amato, G., Vogler, A.P.(2000). Conservation genetics at the species boundary. Conservation Biology.11:120-131.
Grani V. (1999). The Evolution Proeess:A Critieal study of Evolutionary Theory (2nd ed.). New York:Columbia University Press.
Grant W A S, Bowen B W. (1998). Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation[J]. The Journal of Heredity.89:415-426.
Grunwald, C, Stabile, J., Waldman, R., Gross, R. and Wirgin, I. (2002). Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequences. Molecular Ecology.11:1885-1898.
Guindon, S.& Gascuel, O. (2003). A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology.52:696-704.
Hoelzel AR, Green A (1998). PCR protocols and population analysis by direct DNA sequencing and PCR-based DNA fingerpriting. In:Molecular Genetic Analysis of Populations (ed.Hoelzer AR). Oxford University Press, Oxford, UK.4: 201-235.
Holsinger, K.E. (1996). The scope and the limits of conservation genetics. Evolution. 50:2558-2561.
Hwang U W, (1999). Isoenzyme patterns and phylogenetic relationships in Acanthamoeba spp. Isolated from contact lens containers in Korea. Korean Journal of Parasitology.37:215-228.
Idaghdour, Y., D. Broderick, et al. (2004). Mitochondrial control region diversity of the houbara bustard Chlamydotis undulata complex and genetic structure along the Atlantic seaboard of North Africa. Molecular Ecology.13(1):43-54.
J. C. Fay, C. I. Wu(2000). Hitchhiking under positive Darwinian selection. Genetics. 155:1405-1413.
Kretzmann, M.B., Gilmartin, W.G., Meyer, A., Zegers, G.P., Fain, S.R., Taylor, B.F. and Costa, D.P. (1997). Low Genetic Variability in the Hawaiian Monk Seal. Conservation Biology.11:482-490.
Kurland, C.G. (1992). Evolution of mitochondrial genomes and the genetic code. BioEssays.14:709-714
Li M., Ding, C.Q., Wei, F.W., and Tamate, B.H. (2003). Molecular phylogeny of Crested Ibis, Nipponia Nippon, inferred from mitochondrial cytochrome-B gene sequence. Acta Zootaxonomica Sinica 28:1-4.
Marshall,H.D.and A.J.Baker(1997). Structural conservation and variation in the mitochondrial control region of fringilline finches(Fringilla spp.)and the greenfinch(Carduelis chloris). Molecular Biology and Evolution,14:173-184.
Martinez-Cruz. B., Godoy, J.A., and Negro, J.J. (2004). Population genetics after fragmentation:the case of the endangered Spanish imperial eagle (Aquila adalberti). Molecular Ecology.13:2243-2255.
Matthee, C.A. and Robinson, T.J. (1999). Mitochondrial DNA population structure of roan and sable antelope:implications for the translocation and conservation of the species. Molecular Ecology.8:227-238.
Mindell, D. P., Sorenson, M. D., and Dimcheff, D. E. (1998). Multiple independent origins of mitochondrial gene order in birds. Proceeding s of the National Academy of Sciences of the USA.95:10693-10697.
Milligan B, Lynch M, (1994). Analysis of population genetic structure with RAPD markers. Molecular Ecology.3:91-99.
Milligan, B.G., Leebens-Mack, J. Strand, A.E. (1994). The maintenance. Molecular Ecology.3:423-435.
Monique Barat, Catherine Dufresne, Hubert Pinon, Monique Tourte, Jean-Claude Mounolo(1977). Mitochondrial DNA synthesis in large and mature oocytes of Xenopus laevis Developmental Biology.1:59-68.
Mundy, N.I., Winchell, C.S., and Woodruff D.S. (1996). Tandem Repeats and Heteroplasmy in the Mitochondrial DNA control region of the Loggerhead Shrike (Lanius ludovicianus). Journal of Heredity.87:21-26.
Nadiya M. Druzhyna, Glenn L. Wilson, Susan P. LeDoux(2008). Mitochondrial DNA repair in aging and disease. Mechanisms of Ageing and Development,7(8): 383-390.
Pestano, J., Brown, R.P., Rodriguez, F. and Moreno, A. (2000). Mitochondrial DNA control region diversity in the endangered blue chaffinch, Fringilla teydea. Molecular Ecology.9:1421-1425.
Quinn, T. W., (1992). The genetic legacy of mother goose-Phylogeographic patterns of lessor snow goose Chen caerulescens caerulescens maternal lineages. Molecular Ecology.1:105-117.
Quinn, T. W., (1997). Molecular Evolution of Mitochondrial Genome. In:Mindell, D.P. (Ed), Avian Molecular Evolution and Systematics. Academic Press. Pp:3-27.
Quinn,T.W. et al.(1993). Wilson.Sequence evolution in and around the mitochondrial control region in birds. Journal of Molecular Evolution.39:417-425.
Ramirez,V.,P.Savoies and R.Morais(1993). Molecular characterization and evolution of a duck mitochondrial genome. Journal of Molecular Evolution.37:296-310.
Ritchie, P.A., and Lambert, D.M. (2000). A repeat complex in the mitochondrial control region of Adelie penguins from Antarctica.Genome.43:613-618.
Robin, E. D., and Wong, R. (1988). Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. Journal of Cell Physiology.136:507-513
Ruokonen, M. and Kvist, L. (2002). Structure and evolution of the avian mitochondrial control region. Molecular Phylogenetics and Evolution.34:111-130.
Saccone, C., Gissi, C., Lanave, C., Larizza, A., Pesole, G., Reyes, A. (2000). Evolution of the mitochondrial genetic system:an overview. Gene.261:153-159.
Schmitz, A., Brandley, M.C., Mausfeld, P., Vences, M., Glaw, F., Nussbaum, R.A., Reeder, T.W. (2005). Opening the black box:phylogenetics and morphological evolution of the Malagasy fossorial lizards of the subfamily "Scincinae". Molecular Phylogenetics and Evolution.34:118-133.
Soule, M. E. Hillis, L. S. (1998). No need to isolated genetics. Science. 282:1658-1659.
TajimaF. (1989). Statistieal method for testing the neutral mutation hypothesis byDNA polymorphism. Genetics.123(3):585-595.
Tamura K, Dudley J, Nei M, et al. MEGA4(2007). Molecular Evolutionary Genetics Analysis software version 4.0.[J]. Mol Biol Evol..24(8):1596-1599.24.
Teske, P.R., Cherry, M.I., and Matthee, C.A. (2003) Population genetics of the endangered Knysna seahorse, Hippocampus capensis. Molecular Ecology. 12:1703-1715.
Thompson W.W. Hauswirth, P.J. Laipis, M.E. Gilman, T.W. O'Brien, G.S. Michaels, M.A. Rayfield(1980). Genetic mapping of bovine mitochondrial DNA from a single animal,Gene.2:193-209.
Thompson J D, Gibson T J, Plewniak, et al(1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools [J]. Nucleic Acids Research.25(24):4876-4882.
Wan, Q.H., Wu, H., Fujihara, T., Fang, S.G. (2004). Which genetic marker for which conservation genetics issue. Electrophoresis.25:2165-2176.
Wenink,P.W., A.J.Baker and M.G.J. Tilanus(1994). Mitochondrial control region sequences in two shorebird species,the Turnstone and Dunlin,and their utility in population genetic studies.Molecular Biology and Evolution.11:22-31.
Wenink,P.W., A.J.Baker and M.G.J.Tilanus(1993). Hypervariable-controlregion sequences reveal global population structuring in a long-distance migrant shorebird,the Dunlin(Calidris alpina). Proceedings of the National Academy of Sciences of the USA.90:94-98.
Williams, C.L., Serfass, T.L., Cogan, R., Rhodes JR., O.E.(2002). Microsatellite variation in the reintroduced Pennsylvania elk herd. Molecular Ecology. 11:1299-1310.
Wyner, Y.M., Amato, G., and Desalle, R. (1999). Captive breeding, reintroduction, and the conservation genetics of black and white ruffed lemurs, Varecia variegate variegate. Molecular Ecology.8:107-118.
http://amuseum.cdstm.cn/AMuseum/dongwu/page/animal_detail_4733.html
Dobzhansky T.遗传学与物种起源[M].谈家祯等,译。北京：科学出版社,1993.
方盛国,万秋红等,大熊猫保护遗传学,2008.
吴华,梅花鹿的保护遗传学研究,2005.
张蓓,朱鹮线粒体DNA及MHCⅡ类B基因的多态性研究,浙江大学,2005.
张姣,刘迺发.基于线粒体控制区分析雉鸡甘肃亚种的种群遗传结构与保护遗传研究[D].兰州大学,2005.
余志刚,蒋鸿,梁伟,红腹锦鸡繁殖生态研究[J].动物学杂志,1997,32(1)：41-42.
黄族豪,龙进等,从线粒体DNA控制区探讨红腹锦鸡和白腹锦鸡的分类关系,2006.
尚玥,雉科四种鸟类线粒体DNAR的分子进化,2003.
黄族豪,刘迺发等,从线粒体DNA控制区基因比较石鸡和大石鸡的遗传变异,2006.
黄族豪,刘迺发等,大石鸡兰州亚种的mtDNA种群遗传结构、单倍型分析和遗传多样性,2006.
邵晨,红腹锦鸡的冬季栖息地[J],动物学杂志,1998,33(2)：38.
包文斌,舒婧婷等,中国家鸡和红色原鸡mtDNA控制区遗传多态性及系统进化分析,2008.
刘铸,杨春文等,鸟类线粒体DNA结构特点及在鸟类研究中的作用,2009.
梁伟,郑光美,张正旺等,利用无线电遥测位点分析红腹锦鸡的生境利用[J].动物学报,2003,49(2)：178-183.
徐宏发,王静波,分子系统学研究进展[J].2001.
丘城锋,林岳光,庆宁,华南西部及海南岛美丽小条鳅种群遗传变异与亲缘地理[J],动物学报,2008,54(5)：805-813.
闫华超,高超,线粒体DNA遗传特性的研究进展,生物技术,第13卷第六期： 63—66,2003.
林弘都,台湾与中国大陆地区鲤科鱼类之亲缘地理研究[D],台南国立成功大学(台湾),2008.
刘忠权,中国泽蛙线粒体基因组结构及种群系统地理学研究[D],南京师范大学,2003.
赵生国,中国地方鸡种线粒体DNA遗传多样性研究[D],甘肃农业大学,2006.
武玉珍,濒危鸟类褐马鸡遗传多样性及保护研究[D],黄土高原研究所,2005.
王继文,主要主要家鹅品种分子系统进化研究[D],四川农业大学,2003.
张红霞,鹤性别鉴定及线粒体遗传多样性与鹤系统发育研究[D],扬州大学,2008.
杨志松,我国石鸡属鸟类系统地理结构及其种间杂交的研究[D],兰州大学,2005.
向余劲功,杨岚,张亚平,白腹锦鸡和红腹锦鸡的遗传分化[J].遗传,2000.
王培欣,斗鱼属鱼类分子系统发育与叉尾斗鱼亲缘地理研究[D],上海海洋大学,2009.
张德禄,俞诗源,张育康.,3只红腹锦鸡小肠的显微结构观察[J],西北师范大学学报(自然科学版),2000,36(3)：63.
张德禄,俞诗源.,3只红腹锦鸡食管和大肠的显微结构观察[J],西北师范大学学报(自然科学版),2000,36(4)：69-72.
张德禄,俞诗源,红腹锦鸡胃的血供[J],西北师范大学学报,2000,36(2)：58-61.
张德禄,俞诗源,刘世倩等,红腹锦鸡肝脏的显微结构观察[J],西北师范大学学报(自然科学版),2002,38(2)：61-63.
俞诗源,红腹锦鸡肺毛细血管铸型的扫描电镜观察[J],兰州大学学报(自然科学版),1995,31：4-5.
俞诗源,司克媛,王子仁等,红腹锦鸡和小白鼠肾小球微血管铸型的扫描电镜观察[J],动物学杂志,2002,37(6)：17.
张录强,杨振才,孙儒泳,人工饲养红腹锦鸡卵、肌肉营养组成及氨基酸构成模式研究[J],北京师范大学学报(自然科学版),2004,(4)：670-675.
孙淑霞,薛会明,赵立香,红腹锦鸡的生物学特性及饲养技术[J],动物科学与动物医学,2001,18(4)：65-66.
刘佩红,沈莉萍,沈素芳,红腹锦鸡大肠杆菌与鸡异刺线虫混合感染的诊治[J], 中国家禽,2001,23(14)：10-12.
谢恩义,红腹锦鸡的胚胎发育及饲养管理与疾病防治[J],怀化学院学报,2002,21(2)：62-64.
李丽霞,张宏杰等,红腹锦鸡研究现状,2006.黄族豪,廖信军,红腹锦鸡线粒体DNA控制区结构和遗传变异研究,2011.
Balakrishnan, C.N., Monfort, S.L., Gaur, A., Singh, L. and Sorenson, M.D. (2003). Phylogeography and conservation genetics of Eld's deer (Cervus eldi). Molecular Ecology.12:1-10.
Baker, A.J. and Marshall, H. D.(1997). Mitochondrial control region sequences as tools for understanding evolution. In:Mindell, D.P. (Ed), Avian Molecular Evolution and Systematics. Academic Press, San Diego,11:51-82
Barrowclough, G.F., Groth, J.G., Mertz, L,A,, and Gutierrez, R.J. (2005). Genetic structure, introgression, and a narrow hybrid zone between northern and California spotted owls (Strix occidentalis). Molecular Ecology.14:1109-1120.
Bermingham E, Martin A P.(1998) Comparative mtDNA phylogeography of neotropical freshwater fishes:testing shared history to infer the evolutionary landscape of lower Central America. [J]. Mol Ecol.,7(4):499-517.
Brown, G.G., Gadaleta, G., Pepe, G., Saccone, C. and Sbisa(1986) Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. Journal of Molecular Biology.192:503-511.
Cann, R. L., Brown, W. M., and Wilson, A. C. (1984). Polymorphic sites and the mechanism of evolution in human mitochondrial DNA. Genetics 106:479-499.
Carlos T. Moraes, Sarika Srivastava, Ilias Kirkinezos, Jose Oca-Cossio, Corina vanWaveren, Markus Woischnick, Francisco Diaz(2000). Mitochondrial DNA structure and function,International Review of Neurobiology. Volume 53:3-23
Case, M.A., Mlodozeniec, H.T., Wallace, L.E., Weldy, T.W. (1998). Conservation genetics and taxonomic status of the rare Kentucky Lady's slipper:Cypripedium kentuckiense (Orchidaceae). American Journal of Botany.85:1779-1786.
Chang, D.and Clayton, D., (1986). Identification of primary transcription start sites of mouse mitochondrial DNA:Accurate in vitro initiation of both heavy and light-strand transcriptions. Molecular Cell Biology.6:1446-1453.
Clayton, D. A. (1992). Transcription and replication of animal mitochondrial DNAs. International Review Of Cytology-A Survey Of Cell Biology.141:217-232.
Clayton, D. A. (1991). Replication and transcription of vertebrate mitochondrial DNA. Annual Review of Cell Biology.7:453-478.
Desjardins, P., and Morais, R. (1990). Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. Journal of Molecular Biology.212:599-634
Desjardins,P.and R.Morais(1999). Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome. Journal of Molecular Evolution.32:153-161.
DeYoung, R.W., Demarais, S., Honeycutt, R.L. (2003). Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi. Molecular Ecology.12:3237-3252.
Dupanloup,Schneider and Excoffier(2002). A simulated annealing approach to define the genetic structure of populations.IN. Molecular Ecology Issue. 12:2571-2581.
Edwards,S.V.(1993). Long-distance gene flow in a cooperative breeder detected in genealogies of mitochondrial DNA sequence.Proceedings of the Royal Society of London Series B.252:177-185.
Excoffier L, Laval G, Schneider S. Arlequin (version 3.0)(2005). An integrated software package for population genetics data analysis.[J]. Evol Bioinform Online.1:47-50.
Excoffier L, Smouse P E. (1994).Using allele frequencies and geographic subdivision to reconstruct gene trees within a species:molecular variance parsimony.[J]. Genetics.136(1):343-359.
Fu Y X, Li W H (1993). Statistical tests of neutrality of mutations. Genetics.133(3): 693-709.
Frankham R, Ballou J D, Briscoe D A et al. (2002). Introduction to conservation genetics. New York:Cambridge University Press.
Glenn, T.C., Stephan, W. and Braun, M.J. (1999). Effects of a population bottleneck on Whooping Crane mitochondiral DNA variation. Conservation Biology.13: 1097-1107.
Godoy, J.A., Negro, J.J., Hiraldo, F., and Donazar, J.A. (2004). Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L) as revealed by mitochondrial DNA. Molecular Ecology. 13:371-390.
Goldstein, P.Z., DeSalle, R., Amato, G., Vogler, A.P.(2000). Conservation genetics at the species boundary. Conservation Biology.11:120-131.
Grani V. (1999). The Evolution Proeess:A Critieal study of Evolutionary Theory (2nd ed.). New York:Columbia University Press.
Grant W A S, Bowen B W. (1998). Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation[J]. The Journal of Heredity.89:415-426.
Grunwald, C, Stabile, J., Waldman, R., Gross, R. and Wirgin, I. (2002). Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequences. Molecular Ecology.11:1885-1898.
Guindon, S.& Gascuel, O. (2003). A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology.52:696-704.
Hoelzel AR, Green A (1998). PCR protocols and population analysis by direct DNA sequencing and PCR-based DNA fingerpriting. In:Molecular Genetic Analysis of Populations (ed.Hoelzer AR). Oxford University Press, Oxford, UK.4: 201-235.
Holsinger, K.E. (1996). The scope and the limits of conservation genetics. Evolution. 50:2558-2561.
Hwang U W, (1999). Isoenzyme patterns and phylogenetic relationships in Acanthamoeba spp. Isolated from contact lens containers in Korea. Korean Journal of Parasitology.37:215-228.
Idaghdour, Y., D. Broderick, et al. (2004). Mitochondrial control region diversity of the houbara bustard Chlamydotis undulata complex and genetic structure along the Atlantic seaboard of North Africa. Molecular Ecology.13(1):43-54.
J. C. Fay, C. I. Wu(2000). Hitchhiking under positive Darwinian selection. Genetics. 155:1405-1413.
Kretzmann, M.B., Gilmartin, W.G., Meyer, A., Zegers, G.P., Fain, S.R., Taylor, B.F. and Costa, D.P. (1997). Low Genetic Variability in the Hawaiian Monk Seal. Conservation Biology.11:482-490.
Kurland, C.G. (1992). Evolution of mitochondrial genomes and the genetic code. BioEssays.14:709-714
Li M., Ding, C.Q., Wei, F.W., and Tamate, B.H. (2003). Molecular phylogeny of Crested Ibis, Nipponia Nippon, inferred from mitochondrial cytochrome-B gene sequence. Acta Zootaxonomica Sinica 28:1-4.
Marshall,H.D.and A.J.Baker(1997). Structural conservation and variation in the mitochondrial control region of fringilline finches(Fringilla spp.)and the greenfinch(Carduelis chloris). Molecular Biology and Evolution,14:173-184.
Martinez-Cruz. B., Godoy, J.A., and Negro, J.J. (2004). Population genetics after fragmentation:the case of the endangered Spanish imperial eagle (Aquila adalberti). Molecular Ecology.13:2243-2255.
Matthee, C.A. and Robinson, T.J. (1999). Mitochondrial DNA population structure of roan and sable antelope:implications for the translocation and conservation of the species. Molecular Ecology.8:227-238.
Mindell, D. P., Sorenson, M. D., and Dimcheff, D. E. (1998). Multiple independent origins of mitochondrial gene order in birds. Proceeding s of the National Academy of Sciences of the USA.95:10693-10697.
Milligan B, Lynch M, (1994). Analysis of population genetic structure with RAPD markers. Molecular Ecology.3:91-99.
Milligan, B.G., Leebens-Mack, J. Strand, A.E. (1994). The maintenance. Molecular Ecology.3:423-435.
Monique Barat, Catherine Dufresne, Hubert Pinon, Monique Tourte, Jean-Claude Mounolo(1977). Mitochondrial DNA synthesis in large and mature oocytes of Xenopus laevis Developmental Biology.1:59-68.
Mundy, N.I., Winchell, C.S., and Woodruff D.S. (1996). Tandem Repeats and Heteroplasmy in the Mitochondrial DNA control region of the Loggerhead Shrike (Lanius ludovicianus). Journal of Heredity.87:21-26.
Nadiya M. Druzhyna, Glenn L. Wilson, Susan P. LeDoux(2008). Mitochondrial DNA repair in aging and disease. Mechanisms of Ageing and Development,7(8): 383-390.
Pestano, J., Brown, R.P., Rodriguez, F. and Moreno, A. (2000). Mitochondrial DNA control region diversity in the endangered blue chaffinch, Fringilla teydea. Molecular Ecology.9:1421-1425.
Quinn, T. W., (1992). The genetic legacy of mother goose-Phylogeographic patterns of lessor snow goose Chen caerulescens caerulescens maternal lineages. Molecular Ecology.1:105-117.
Quinn, T. W., (1997). Molecular Evolution of Mitochondrial Genome. In:Mindell, D.P. (Ed), Avian Molecular Evolution and Systematics. Academic Press. Pp:3-27.
Quinn,T.W. et al.(1993). Wilson.Sequence evolution in and around the mitochondrial control region in birds. Journal of Molecular Evolution.39:417-425.
Ramirez,V.,P.Savoies and R.Morais(1993). Molecular characterization and evolution of a duck mitochondrial genome. Journal of Molecular Evolution.37:296-310.
Ritchie, P.A., and Lambert, D.M. (2000). A repeat complex in the mitochondrial control region of Adelie penguins from Antarctica.Genome.43:613-618.
Robin, E. D., and Wong, R. (1988). Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. Journal of Cell Physiology.136:507-513
Ruokonen, M. and Kvist, L. (2002). Structure and evolution of the avian mitochondrial control region. Molecular Phylogenetics and Evolution.34:111-130.
Saccone, C., Gissi, C., Lanave, C., Larizza, A., Pesole, G., Reyes, A. (2000). Evolution of the mitochondrial genetic system:an overview. Gene.261:153-159.
Schmitz, A., Brandley, M.C., Mausfeld, P., Vences, M., Glaw, F., Nussbaum, R.A., Reeder, T.W. (2005). Opening the black box:phylogenetics and morphological evolution of the Malagasy fossorial lizards of the subfamily "Scincinae". Molecular Phylogenetics and Evolution.34:118-133.
Soule, M. E. Hillis, L. S. (1998). No need to isolated genetics. Science. 282:1658-1659.
TajimaF. (1989). Statistieal method for testing the neutral mutation hypothesis byDNA polymorphism. Genetics.123(3):585-595.
Tamura K, Dudley J, Nei M, et al. MEGA4(2007). Molecular Evolutionary Genetics Analysis software version 4.0.[J]. Mol Biol Evol..24(8):1596-1599.24.
Teske, P.R., Cherry, M.I., and Matthee, C.A. (2003) Population genetics of the endangered Knysna seahorse, Hippocampus capensis. Molecular Ecology. 12:1703-1715.
Thompson W.W. Hauswirth, P.J. Laipis, M.E. Gilman, T.W. O'Brien, G.S. Michaels, M.A. Rayfield(1980). Genetic mapping of bovine mitochondrial DNA from a single animal,Gene.2:193-209.
Thompson J D, Gibson T J, Plewniak, et al(1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools [J]. Nucleic Acids Research.25(24):4876-4882.
Wan, Q.H., Wu, H., Fujihara, T., Fang, S.G. (2004). Which genetic marker for which conservation genetics issue. Electrophoresis.25:2165-2176.
Wenink,P.W., A.J.Baker and M.G.J. Tilanus(1994). Mitochondrial control region sequences in two shorebird species,the Turnstone and Dunlin,and their utility in population genetic studies.Molecular Biology and Evolution.11:22-31.
Wenink,P.W., A.J.Baker and M.G.J.Tilanus(1993). Hypervariable-controlregion sequences reveal global population structuring in a long-distance migrant shorebird,the Dunlin(Calidris alpina). Proceedings of the National Academy of Sciences of the USA.90:94-98.
Williams, C.L., Serfass, T.L., Cogan, R., Rhodes JR., O.E.(2002). Microsatellite variation in the reintroduced Pennsylvania elk herd. Molecular Ecology. 11:1299-1310.
Wyner, Y.M., Amato, G., and Desalle, R. (1999). Captive breeding, reintroduction, and the conservation genetics of black and white ruffed lemurs, Varecia variegate variegate. Molecular Ecology.8:107-118.
http://amuseum.cdstm.cn/AMuseum/dongwu/page/animal_detail_4733.html
Dobzhansky T.遗传学与物种起源[M].谈家祯等,译。北京：科学出版社,1993.
方盛国,万秋红等,大熊猫保护遗传学,2008.
吴华,梅花鹿的保护遗传学研究,2005.
张蓓,朱鹮线粒体DNA及MHCⅡ类B基因的多态性研究,浙江大学,2005.
张姣,刘迺发.基于线粒体控制区分析雉鸡甘肃亚种的种群遗传结构与保护遗传研究[D].兰州大学,2005.
余志刚,蒋鸿,梁伟,红腹锦鸡繁殖生态研究[J].动物学杂志,1997,32(1)：41-42.
黄族豪,龙进等,从线粒体DNA控制区探讨红腹锦鸡和白腹锦鸡的分类关系,2006.
尚玥,雉科四种鸟类线粒体DNAR的分子进化,2003.
黄族豪,刘迺发等,从线粒体DNA控制区基因比较石鸡和大石鸡的遗传变异,2006.
黄族豪,刘迺发等,大石鸡兰州亚种的mtDNA种群遗传结构、单倍型分析和遗传多样性,2006.
邵晨,红腹锦鸡的冬季栖息地[J],动物学杂志,1998,33(2)：38.
包文斌,舒婧婷等,中国家鸡和红色原鸡mtDNA控制区遗传多态性及系统进化分析,2008.
刘铸,杨春文等,鸟类线粒体DNA结构特点及在鸟类研究中的作用,2009.
梁伟,郑光美,张正旺等,利用无线电遥测位点分析红腹锦鸡的生境利用[J].动物学报,2003,49(2)：178-183.
徐宏发,王静波,分子系统学研究进展[J].2001.
丘城锋,林岳光,庆宁,华南西部及海南岛美丽小条鳅种群遗传变异与亲缘地理[J],动物学报,2008,54(5)：805-813.
闫华超,高超,线粒体DNA遗传特性的研究进展,生物技术,第13卷第六期： 63—66,2003.
林弘都,台湾与中国大陆地区鲤科鱼类之亲缘地理研究[D],台南国立成功大学(台湾),2008.
刘忠权,中国泽蛙线粒体基因组结构及种群系统地理学研究[D],南京师范大学,2003.
赵生国,中国地方鸡种线粒体DNA遗传多样性研究[D],甘肃农业大学,2006.
武玉珍,濒危鸟类褐马鸡遗传多样性及保护研究[D],黄土高原研究所,2005.
王继文,主要主要家鹅品种分子系统进化研究[D],四川农业大学,2003.
张红霞,鹤性别鉴定及线粒体遗传多样性与鹤系统发育研究[D],扬州大学,2008.
杨志松,我国石鸡属鸟类系统地理结构及其种间杂交的研究[D],兰州大学,2005.
向余劲功,杨岚,张亚平,白腹锦鸡和红腹锦鸡的遗传分化[J].遗传,2000.
王培欣,斗鱼属鱼类分子系统发育与叉尾斗鱼亲缘地理研究[D],上海海洋大学,2009.
张德禄,俞诗源,张育康.,3只红腹锦鸡小肠的显微结构观察[J],西北师范大学学报(自然科学版),2000,36(3)：63.
张德禄,俞诗源.,3只红腹锦鸡食管和大肠的显微结构观察[J],西北师范大学学报(自然科学版),2000,36(4)：69-72.
张德禄,俞诗源,红腹锦鸡胃的血供[J],西北师范大学学报,2000,36(2)：58-61.
张德禄,俞诗源,刘世倩等,红腹锦鸡肝脏的显微结构观察[J],西北师范大学学报(自然科学版),2002,38(2)：61-63.
俞诗源,红腹锦鸡肺毛细血管铸型的扫描电镜观察[J],兰州大学学报(自然科学版),1995,31：4-5.
俞诗源,司克媛,王子仁等,红腹锦鸡和小白鼠肾小球微血管铸型的扫描电镜观察[J],动物学杂志,2002,37(6)：17.
张录强,杨振才,孙儒泳,人工饲养红腹锦鸡卵、肌肉营养组成及氨基酸构成模式研究[J],北京师范大学学报(自然科学版),2004,(4)：670-675.
孙淑霞,薛会明,赵立香,红腹锦鸡的生物学特性及饲养技术[J],动物科学与动物医学,2001,18(4)：65-66.
刘佩红,沈莉萍,沈素芳,红腹锦鸡大肠杆菌与鸡异刺线虫混合感染的诊治[J], 中国家禽,2001,23(14)：10-12.
谢恩义,红腹锦鸡的胚胎发育及饲养管理与疾病防治[J],怀化学院学报,2002,21(2)：62-64.
李丽霞,张宏杰等,红腹锦鸡研究现状,2006.黄族豪,廖信军,红腹锦鸡线粒体DNA控制区结构和遗传变异研究,2011.