Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Lippold, Sebastian ^a   Matzke, Nicholas J ^b   Reissmann, Monika ^c   Hofreiter, Michael ^d  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HUMBOLDT UNIVERSITY   (Germany)

^d UNIVERSITY OF YORK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARRAY; BAYESIAN ANALYSIS; DATA SET; DIVERGENCE; DOMESTIC SPECIES; DOMESTICATION; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; HORSE; MITOCHONDRIAL DNA; PARSIMONY ANALYSIS; PHYLOGENETICS; POPULATION STRUCTURE; SPECIES DIVERSITY; WILD POPULATION;

ANIMALIA; EQUIDAE; EQUUS CABALLUS; EQUUS PRZEWALSKII;

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; EVOLUTION; FEMALE; GENETICS; HORSE; MITOCHONDRIAL GENOME; MITOCHONDRION; PHYLOGENY; WILD ANIMAL;

ANIMALS; ANIMALS, WILD; BAYES THEOREM; BIOLOGICAL EVOLUTION; DNA, MITOCHONDRIAL; FEMALE; GENOME, MITOCHONDRIAL; HORSES; MITOCHONDRIA; PHYLOGENY;

EID: 81055124180     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-328     Document Type: Article

References (61)

1. Multiple maternal origins of native modern and ancient horse populations in China. Lei CZ, Su R, Bower MA, Edwards CJ, Wang XB, Weining S, Liu L, Xie WM, Li F, Liu RY, et al. Animal Genetics 2009 40 933 944 10.1111/j.1365-2052.2009. 01950.x 19744143
2. Ancient DNA provides new insights into the origin of the Chinese domestic horse. Cai DW, Tang ZW, Han L, Speller CF, Yang DYY, Ma XL, Cao JE, Zhu H, Zhou H, Journal of Archaeological Science 2009 36 835 842 10.1016/j.jas.2008.11.006
3. Mitochondrial DNA analysis of Bronze Age horses recovered from Chifeng region, Inner Mongolia, China. Cai DW, Han L, Xie CZ, Li SN, Zhou H, Zhu H, Progress in Natural Science 2007 17 544 550 10.1080/10020070708541034 (Pubitemid 46886744)
4. Evidence for biogeographic patterning of mitochondrial DNA sequences in Eastern horse populations. McGahern A, Bower MAM, Edwards CJ, Brophy PO, Sulimova G, Zakharov I, Vizuete-Forster M, Levine M, Li S, MacHugh DE, Hill EW, Animal Genetics 2006 37 494 497 10.1111/j.1365-2052.2006.01495.x 16978180 (Pubitemid 44410837)
5. The origins of Iberian horses assessed via mitochondrial DNA. Royo LJ, Alvarez I, Beja-Pereira A, Molina A, Fernandez I, Jordana J, Gomez E, Gutierrez JP, Goyache F, Journal of Heredity 2005 96 663 669 10.1093/jhered/esi116 16251517 (Pubitemid 41668786)
6. Molecular methods and equine genetic diversity. Cunningham EP, Conservation Genetics of Endangered Horse Breeds 2005 15 24
7. Domestication of the horse: results based on microsatellite and mitochondrial DNA markers. Aberle KS, Distl O, Archiv Fur Tierzucht-Archives of Animal Breeding 2004 47 517 535 (Pubitemid 39622849)
8. Mitochondrial DNA and the origins of the domestic horse. Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C, Weber J, Olek K, Proc Natl Acad Sci USA 2002 99 10905 10910 10.1073/pnas.152330099 12130666
9. Widespread Origins of Domestic Horse Lineages. Vil C, Leonard JA, Götherström A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H, Science 2001 291 474 477 10.1126/science.291.5503.474 11161199 (Pubitemid 32097069)
10. Phylogenetic relationships of Cheju horses to other horse breeds as determined by mtDNA D-loop sequence polymorphism. Kim KI, Yang YH, Lee SS, Park C, Ma R, Bouzat JL, Lewin HA, Animal Genetics 1999 30 102 108 10.1046/j.1365-2052.1999.00419.x 10376300 (Pubitemid 29275813)
11. Mitochondrial-DNA sequences of various species of the genus equus with special reference to the phylogenetic relationship between Przewalskiis wild horse and domestic horse. Ishida N, Oyunsuren T, Mashima S, Mukoyama H, Saitou N, Journal of Molecular Evolution 1995 41 180 188 7666447
12. A survey of equid mitochondrial DNA: Implications for the evolution, genetic diversity and conservation of Equus. Oakenfull EA, Lim H, Ryder O, Conservation Genetics 2000 1 341 355 10.1023/A:1011559200897
13. Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses. Lira J, Linderholm A, Olaria C, Durling MB, Gilbert MTP, Ellegren H, Willerslev E, Liden K, Arsuaga JL, Gotherstrom A, Molecular Ecology 2010 19 64 78 10.1111/j.1365-294X.2009.04430.x 19943892
14. Domestication of the horse: Genetic relationships between domestic and wild horses. Kavar T, Dovc P, Livestock Science 2008 116 1 14 10.1016/j.livsci.2008.03.002
15. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Morin PA, Archer FI, Foote AD, Vilstrup J, Allen EE, Wade P, Durban J, Parsons K, Pitman R, Li L, et al. Genome Res 2010 20 908 916 10.1101/gr.102954.109 20413674
16. Direct multiplex sequencing (DMPS)-a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M, Genome Res 2009 19 1843 1848 10.1101/gr.095760.109 19635845
17. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Gilbert MTP, Drautz DI, Lesk AM, Ho SYW, Qi J, Ratan A, Hsu CH, Sher A, Dalen L, Gotherstrom A, et al. Proceedings of the National Academy of Sciences of the United States of America 2008 105 8327 8332 10.1073/pnas.0802315105 18541911 (Pubitemid 351904755)
18. Mitochondrial genomes of extinct aurochs survive in domestic cattle. Achilli A, Olivieri A, Pellecchia M, Uboldi C, Colli L, Al-Zahery N, Accetturo M, Pala M, Kashani BH, Perego UA, et al. Current Biology 2008 18 157 R158 10.1016/j.cub.2008.01.019 18302915 (Pubitemid 351258346)
19. Proboscidean mitogenomics: Chronology and mode of elephant evolution using mastodon as outgroup. Rohland N, Malaspinas AS, Pollack JL, Slatkin M, Matheus P, Hofreiter M, Plos Biology 2007 5 1663 1671 (Pubitemid 47328271)
20. Sampling Properties of DNA Sequence Data in Phylogenetic Analysis. Cummings MP, Otto SP, Wakeley J, Molecular Biology and Evolution 1995 12 814 822 7476127
21. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Meyer M, Kircher M, Cold Spring Harb Protoc 2010 2010 pdb prot5448
22. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Hodges E, Rooks M, Xuan ZY, Bhattacharjee A, Gordon DB, Brizuela L, McCombie WR, Hannon GJ, Nature Protocols 2009 4 960 974 10.1038/nprot.2009.68 19478811
23. Clustal W and clustal X version 2.0. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Bioinformatics 2007 23 2947 2948 10.1093/bioinformatics/btm404 17846036 (Pubitemid 350162903)
24. Bayesian coalescent inference of past population dynamics from molecular sequences. Drummond AJ, Rambaut A, Shapiro B, Pybus OG, Molecular Biology and Evolution 2005 22 1185 1192 10.1093/molbev/msi103 15703244 (Pubitemid 40577756)
25. Approximate Bayesian-inference with the weighted likelihood bootstrap. Newton MA, Raftery AE, Davison AC, Bacha M, Celeux G, Carlin BP, Clifford P, Lu C, Sherman M, Tanner MA, et al. J R Stat Soc Ser B-Methodol 1994 56 3 48
26. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond AJ, Rambaut A, BMC Evolutionary Biology 2007 7 214 10.1186/1471-2148-7-214 17996036 (Pubitemid 351253125)
27. Bayes Factors. Kass RE, Raftery AE, J Am Stat Assoc 1995 90 773 795 10.2307/2291091
28. mtDNA Data Indicate a Single Origin for Dogs South of Yangtze River, Less Than 16,300 Years Ago, from Numerous Wolves. Pang J-F, Kluetsch C, Zou X-J, Zhang A-b, Luo L-Y, Angleby H, Ardalan A, Ekstrom C, Skollermo A, Lundeberg J, et al. Molecular Biology and Evolution 2009 26 2849 2864 10.1093/molbev/msp195 19723671
29. The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome. Achilli A, Bonfiglio S, Olivieri A, Malusa A, Pala M, Kashani BH, Perego UA, Ajmone-Marsan P, Liotta L, Semino O, et al. PLoS One 2009 4 7
30. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. vonHoldt BM, Pollinger JP, Lohmueller KE, Han EJ, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, et al. Nature 2010 464 898 U109 10.1038/nature08837 20237475
31. Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, et al. Science 2009 326 865 867 10.1126/science.1178158 19892987
32. Coat Color Variation at the Beginning of Horse Domestication. Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann GA, Castanos P, Cieslak M, Lippold S, Llorente L, Malaspinas AS, et al. Science 2009 324 485 485 10.1126/science.1172750 19390039
33. Holocene survival of the wild horse in Europe: a matter of open landscape? Sommer RS, Benecke N, Lugas L, Nelle O, Schmölcke U, Journal of Quaternary Science 2011
34. Bayesian inference of population expansions in domestic bovines. Finlay EK, Gaillard C, Vahidi SMF, Mirhoseini SZ, Jianlin H, Qi XB, El-Barody MAA, Baird JF, Healy BC, Bradley DG, Biology Letters 2007 3 449 452 10.1098/rsbl.2007.0146 17535790
35. The Earliest Horse Harnessing and Milking. Outram AK, Stear NA, Bendrey R, Olsen S, Kasparov A, Zaibert V, Thorpe N, Evershed RP, Science 2009 323 1332 1335 10.1126/science.1168594 19265018
36. Molecular clocks: when timesare a-changin'. Ho SYW, Larson G, Trends in Genetics 2006 22 79 83 10.1016/j.tig.2005.11.006 16356585 (Pubitemid 43152025)
37. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Kircher M, Stenzel U, Kelso J, Genome Biol 2009 10 83 10.1186/gb-2009-10-8-r83 19682367
38. The Complete Mitochondrial-DNA Sequence of the Horse, Equus-Caballus-Extensive Heteroplasmy of the Control Region. Xu XF, Arnason U, Gene 1994 148 357 362 10.1016/0378-1119(94)90713-7 7958969 (Pubitemid 24333700)
39. Fast and accurate short read alignment with Burrows-Wheeler transform. Li H, Durbin R, Bioinformatics 2009 25 1754 1760 10.1093/bioinformatics/btp324 19451168
40. Genome Project Data P: The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Bioinformatics 2009 25 2078 2079 10.1093/bioinformatics/btp352 19505943
41. High altitude adaptation and phylogenetic analysis of Tibetan horse based on the mitochondrial genome. Xu S, Luosang J, Hua S, He J, Ciren A, Wang W, Tong X, Journal of Genetics and Genomics 2007 34 720 729 10.1016/S1673-8527(07) 60081-2 17707216 (Pubitemid 47247621)
42. PAUP*: phylogenetic analysis using parsimony (* and other methods), version 4.0 b10. Swofford DL, Sunderland, MA: Sinauer Associates 2002
43. TNT, a free program for phylogenetic analysis. Goloboff PA, Farris JS, Nixon KC, Cladistics 2008 24 774 786 10.1111/j.1096-0031.2008.00217.x
44. Quantitative phyletics and the evolution of anurans. Kluge AG, Farris JS, Systematic Zoology 1969 18 1 32 10.2307/2412407
45. The retention index and homoplasy excess. Farris JS, Systematic Biology 1989 38 406
46. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Bremer K, Evolution 1988 42 795 803 10.2307/2408870
47. Branch support and tree stability. Bremer K, Cladistics 1994 10 295 304 10.1111/j.1096-0031.1994.tb00179.x
48. PRAP - computation of Bremer support for large data sets. Müller K, Molecular Phylogenetics and Evolution 2004 31 780 782 10.1016/j.ympev.2003.12. 006 15062810 (Pubitemid 38504464)
49. Inferring phylogenies. Felsenstein J, Sinauer Associates Sunderland, MA 2004
50. A rapid bootstrap algorithm for the RAxML Web servers. Stamatakis A, Hoover P, Rougemont J, Systematic Biology 2008 57 758 771 10.1080/ 10635150802429642 18853362
51. Modeltest: testing the model of DNA substitution. Posada D, Crandall KA, Bioinformatics 1998 14 817 10.1093/bioinformatics/14.9.817 9918953
52. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Posada D, Buckley TR, Systematic Biology 2004 53 793 808 10.1080/10635150490522304 15545256 (Pubitemid 39568279)
53. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Guindon S, Gascuel O, Systematic Biology 2003 52 696 704 10.1080/10635150390235520 14530136 (Pubitemid 37365050)
54. MrModeltest v2. 2. Nylander JAA, Program distributed by the author Evolutionary Biology Centre, Uppsala University 2004
55. Bayesian analysis of molecular evolution using MrBayes. Huelsenbeck J, Ronquist F, Statistical methods in molecular evolution 2005 183 226
56. MrBayes 3: Bayesian phylogenetic inference under mixed models. Ronquist F, Huelsenbeck JP, Bioinformatics 2003 19 1572 10.1093/bioinformatics/btg180 12912839 (Pubitemid 37038874)
57. PAML 4: phylogenetic analysis by maximum likelihood. Yang Z, Molecular Biology and Evolution 2007 24 1586 10.1093/molbev/msm088 17483113 (Pubitemid 47236688)
58. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Sanderson MJ, Bioinformatics 2003 19 301 302 10.1093/bioinformatics/19.2.301 12538260 (Pubitemid 36181923)
59. r8s version 1.71. Sanderson MJ, Software and documentation 2006 http://loco.biosci.arizona.edu/r8s/
60. Revising the recent evolutionary history of equids using ancient DNA. Orlando L, Metcalf JL, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M, Martin F, Eisenmann V, Mashkour M, Morello F, et al. Proceedings of the National Academy of Sciences 2009 106 21754 21759 10.1073/pnas.0903672106
61. Pedigree analysis in the Andalusian horse: population structure, genetic variability and influence of the Carthusian strain. Valera M, Molina A, Gutiérrez JP, Gámez J, Goyache F, 2005 95 57 66