期刊论文详细信息
BMC Genetics
Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens
Jaime Gongora2  Simon YW Ho3  Bruce Baskerville1  Spiridoula Kraitsek2  Shannan M Langford S2 
[1] Kingston & Arthur’s Vale Historic Area, Norfolk Island Government, Kingston, NI 2899, Australia;Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia;School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
关键词: Ferals;    Chickens;    Network analysis;    Mitochondrial DNA;    Norfolk Island;   
Others  :  1086619
DOI  :  10.1186/1471-2156-14-91
 received in 2012-12-20, accepted in 2013-09-12,  发布年份 2013
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【 摘 要 】

Background

Norfolk Island has a population of feral chickens which could be the result of domestic stock introduced onto the island by British settlers in 1788. However, there is ongoing debate about their origins because multiple human arrivals to the island may have brought chickens with them. Here we investigate the genetic origins of these feral chickens by sequencing their mitochondrial control region. We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world.

Results

Eleven control region haplotypes were found among the Norfolk Island feral and Australian mainland domestic chickens. Six of the Norfolk Island haplotypes fall within haplogroup E, but given the worldwide distribution of this haplogroup, the putative European origin of these chickens requires further investigation. One haplotype common among Norfolk Island and Australian samples belonged to a subgroup of haplogroup D, which appears to be restricted to chickens from Indonesia, Vanuatu and Guam.

Conclusions

Our data show that at least two mitochondrial DNA haplogroups (D and E) have contributed to the genetic make-up of Norfolk Island feral chickens. In addition, we have provided insights into the discrete geographical distribution and diversity of the chicken haplogroup D. In view of the worldwide interest in the characterisation of poultry resources, further assessment of chicken populations of Island Southeast Asia and the Pacific region is warranted.

【 授权许可】

   
2013 Langford S et al.; licensee BioMed Central Ltd.

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【 参考文献 】
  • [1]Kirch PV: Polynesia’s mystery islands Archaeology. 1988, 41:26-31.
  • [2]Anderson A, Higham T, Wallace R: The radiocarbon chronology of the Norfolk Island archaeological sites. In The Prehistoric Archaeology of Norfolk Island, Southwest Pacific. Edited by White AAP. Sydney, Australia: Ausrtalian Museum; 2001:33-42.
  • [3]Anderson A, White P: The Prehistoric Archaeology of Norfolk Island, Southwest Pacific. Edited by. Australian Museum: White AAP; 2001.
  • [4]Wright R: Land Usage. In Norfolk Islad and its first settlement 1788–1814. Edited by Nobbs R. North Ryde, North Sydney: Library of Australian History; 1988.
  • [5]Kanginakudru S, Metta M, Jakati RD, Nagaraju J: Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC evolutionary biology 2008, 8:174. BioMed Central Full Text
  • [6]Liu YP, Wu GS, Yao YG, Miao YW, Luikart G, Baig M, Beja-Pereira A, Ding ZL, Palanichamy MG, Zhang YP: Multiple maternal origins of chickens: out of the Asian jungles. Molecular phylogenetics and evolution 2006, 38:12-19.
  • [7]Berthouly-Salazar C, Rognon X, Nhu Van T, Gély M, Vu Chi C, Tixier-Boichard M, Bed’Hom B, Bruneau N, Verrier E, Maillard JC, Michaux JP: Vietnamese chickens: a gate towards Asian genetic diversity. BMC Genet 2010, 11:53.
  • [8]Dancause KN, Vilar MG, Steffy R, Lum JK: Characterizing Genetic Diversity of Contemporary Pacific Chickens Using Mitochondrial DNA Analyses. PloS one 2011, 6(2):e16843. doi:10.1371/journal.pone.0016843
  • [9]Gongora J, Rawlence NJ, Mobegi VA, Jianlin H, Alcalde JA, Matus JT, Hanotte O, Moran C, Austin JJ, Ulm S, Anderson AJ, Larson G, Cooper A: Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proc Natl Acad Sci U S A 2008, 105:10308-10313.
  • [10]Oka T, Ino Y, Nomura K, Kawashima S, Kuwayama T, Hanada H, Amano T, Takada M, Takahata N, Hayashi Y, Akishinonomiya F: Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Animal genetics 2007, 38:287-293.
  • [11]Storey AA, Ramirez JM, Quiroz D, Burley DV, Addison DJ, Walter R, Anderson AJ, Hunt TL, Athens JS, Huynen L, Matisoo-Smith EA: Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile. Proc Natl Acad Sci U S A 2007, 104:10335-10339.
  • [12]Christian M: Norfolk Island…the birds. Norfolk Island: Green Eyes Publications; 2005.
  • [13]Ponder WF: Conservation status, threats and habitat requirements of Australian terrestrial and freshwater mollusca. Memoirs of the Museumof Victoria 1997, 56:421-430.
  • [14]Lee YJ, Bhuiyan MSA, Chung HJ, Jung WY, Choi KD, Jang BG, Paek WK, Jeon JT, Park CS, Lee JH: Mitochondrial DNA Diversity of Korean Ogol Chicken. Asian-Aust J Anim Sci 2007, 20:477-481.
  • [15]Mwacharo JM, Bjornstad G, Mobegi V, Nomura K, Hanada H, Amano T, Jianlin H, Hanotte O: Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. Molecular phylogenetics and evolution 2011, 58:374-382.
  • [16]Razafindraibe H, Mobegi VA, Ommeh SC, Rakotondravao ML, Bjornstad G, Hanotte O, Jianlin H: Mitochondrial DNA origin of indigenous malagasy chicken. Ann N Y Acad Sci 2008, 1149:77-79.
  • [17]Miao Y-W, Peng M-S, Wu G-S, Ouyang Y-N, Yang Z-Y, Yu N, Liang J-P, Pianchou G, Beja-Pereira A, Mitra B, Palanichamy MG, Baig M, Chaudhuri TK, Shen Y-Y, Kong Q-P, Murphy RW, Yao Y-G, Zhang Y-P: Chicken domesitcation: an updated perspective based on mitochondrial genomes. Heredity 2013, 110:277-282.
  • [18]Sulandari S, Arifin Zein MS, Sartika T: Molecular Charactertzation of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequence. HAYATI Joumal of Bioscience 2008, 15:145-154.
  • [19]Storey AA, Athens JS, Bryant D, Carson M, Emery K, Higham C, Huynen L, Intoh M, Jones S, Kirch PV, Ladefoged T, McCoy P, Morales- Muñiz A, Quiroz D, Reitz E, Robins J, Walter R, Matisoo-Smith E, deFrance S: Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures. PloS one 2012, 7:e39171.
  • [20]Storey AA, Spriggs M, Bedford S, Hawkins SC, Robins JH, Huynen L, Matisoo-Smith E: Mitochondrial DNA from 3000-year old chickens at the Teouma site, Vanuatu. J Archaeol Sci 2010, 37:2459-2468.
  • [21]Katoh K, Toh H: Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008, 9:286-298.
  • [22]Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999, 41:95-98.
  • [23]Villesen P: FaBox: an online toolbox for fasta sequences. Mol Ecol Notes 2007, 7:965-968.
  • [24]Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011, 28:2731-2739.
  • [25]Bandelt H-J, Forster P, Röhl A: Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999, 16:37-48.
  • [26]Ronquist F, Huelsenbeck JP: MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
  • [27]Darriba D, Taboada GL, Doallo R, Posada D: jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 2012, 9:772.
  • [28]Guindon S, Gascuel O: A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood”. Syst Biology 2003, 52:696-704.
  • [29]Akaike H: A new look at the statistical model indentification. IEEE Trans Autom Control 1974, 19:716-722.
  • [30]Lima-Rosa CAV, Dalla C, Possamai MHP, Herkenho ME, Pértille F, Paludo E, Costa FJ, Battilana J: Genetic diversity of the control region (D-loop) in mitochondrial DNA in caipira’s chickens lineages. Águas de Lindóia, Brasil: 57° Congresso Brasileiro de Genética: 2011; 2011:147.
  • [31]Mtileni BJ, Muchadeyi FC, Maiwashe A, Chimonyo M, Groeneveld E, Weigend S, Dzama K: Diversity and origin of South African chickens. Poultry science 2011, 90:2189-2194.
  • [32]Cobley J: Sydney Cove 1788: in the words of Australia’s first settlers : the true story of a nation’s birth. North Ryde, N.S.W.: Angus & Robertson; 1987.
  • [33]King J: The First Fleet: The Convict Voyage That Founded Australia 1787–88. 1st edition. South Melbourne: The Macmillan Company of Australia Pty Ltd; 1982.
  • [34]Cobley J: Sydney Cove, 1788. London: London Hodder and Stoughton; 1962.
  • [35]Edgecombe J: Norfolk Island - South Pacific : island of history and many delights. 2nd edition. Thornleigh NSW Australia: Jean Edgecombe; 1999.
  • [36]Holdaway RN, Anderson A: Avifauna from the Emily Bay settlement site, Norfolk Island: a preliminary account. In The Prehistoric Archaeology of Norfolk Island, Southwest Pacific. 27th edition. Edited by White AAaP. Sydney: Australian Museum; 2001:85-100.
  • [37]Hoare M: Norfolk Island: A history through illustration 1774–1974 Canberra. Australia: Australian Government Publishing Service; 1979.
  • [38]Hoare M: Norfolk Island: An outline of its history 1774–1977. In. Brisbane, Australia: University of Queensland Press; 1972.
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