Phylogenetic analysis and species allocation of individual equids using microsatellite data

Journal of Animal Breeding and Genetics, Supplement

Volumn 122, Issue 1, 2005, Pages 78-86

  Kruger K ^a,b   Gaillard, C ^c   Stranzinger, G ^a,b   Rieder, S ^a,d  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c UNIVERSITY OF BERN   (Switzerland)

^d Swiss College of Agriculture   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EQUIDAE; EQUUS HEMIONUS KULAN; EQUUS HEMIONUS ONAGER; EQUUS KIANG;

EID: 16844374282     PISSN: 17424488     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1439-0388.2005.00505.x     Document Type: Article

References (51)

1. Achmann R., Huber T., Wallner B., Dove P., Müller M., Brem G. (2001) Base substitutions in the sequences flanking microsatellite markers HMS3 and ASB2 interfere with parentage testing in the Lipizzan horse. Anim. Genet., 32, 52.
2. Belkhir K., Borsa P., Chikhi L., Raufaste N., Bonhomme F. (1996-2002) GENETIX 4.03, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, F.
3. Bjørnstad G., Røed K.H. (2001) Breed demarcation and potential for breed allocation of horses assessed by microsatellite markers. Anim. Genet., 32, 59-65.
4. Bjørnstad G., Røed K.H. (2002) Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses. Anim. Genet., 33, 264-270.
5. Bjørnstad G., Nilsen N.O., Roed K.H. (2003) Genetic relationship between Mongolian and Norwegian horses. Anim. Genet., 34, 55-58.
6. Bowcock A.M., Ruiz-Linares A., Tomfohrde J., Minch E., Kidd J.R., Cavalli-Sforza L.L. (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature, 368, 455-457.
7. Breen M., Downs P., Irvin Z., Bell K. (1994) Intrageneric amplification of horse microsatellite markers with emphasis on the Przewalski's horse (E. przewalskii). Anim. Genet., 25, 401-405.
8. Cañon J., Checa M.L., Carleos C., Vega-Pla J.L., Vallejo M., Dunner S. (2000) The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Anim. Genet., 31, 39-48.
9. Cavalli-Sforza L.L. (1998) The DNA revolution in population genetics. Trends Genet., 14, 60-65.
10. Chowdhary B.P., Raudsepp T. (2000) Cytogenetics and physical gene maps. In: A.T. Bowling, A. Ruvinsky (eds), The Genetics of the Horse. CAB International, Oxen, UK, pp. 171-241.
11. Chowdhary B.P., Raudsepp T., Kata S.R., Goh G., Millon L.V., Allan V., Piumi F., Guérin G., Swinburne J., Binns M., Lear T.L., Mickelson J., Murray J., Antczak D.F., Womack J.E., Skow L.C. (2003) The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res., 13, 742-751.
12. Clutton-Brock J. (1992) Horse Power: A History of the Horse and the Donkey in Human Societies. Natural History Museum Publication, London, UK.
13. Cornuet J.M., Piry S., Luikart G., Estoup A., Solignac M. (1999) New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics, 153, 1989-2000.
14. Davies N., Villablanca F.X., Roderick G.K. (1999) Determining the source of individuals: multilocus genotyping in nonequilibrium population genetics. Trend Ecol. Evol., 14, 17-21.
15. Denzau G., Denzau H. (1999) Wildesel. Jan Thorbecke Verlag, Stuttgart, D.
16. Driscoll C.A., Menotti-Raymond M., Nelson G., Goldstein D., O'Brien S.J. (2002) Genomic microsatellites as evolutionary chronometers: a test in wild cats. Genome Res., 12, 414-423.
17. Feh C., Shah N., Rowen M., Reading R., Goyal S.P. (2002) Status and Action Plan for the Asiatic Wild Ass (Equus hemionus). In: P. Moehlman (ed.), Equids: Zebras, Asses and Horses. Status survey and Conservation Action Plan. The World Conservation Union (IUCN), Equid Specialist Group, Gland, Switzerland, pp. 61-71.
18. Felsenstein J. (1985) Confidence limits on phylogenies: an approach using bootstrap. Evolution, 339, 783-791.
19. Felsenstein J. (1995) PHYLIP (Phylogeny Inference Package; version 3, 57c). Department of Genetics, University of Washington, Seattle, WA, USA. http://evolution.genetics.washington.edu/phylip.html.
20. Forstén A. (1992) Mitochondrial-DNA time-table and the evolution of Equus: comparison of molecular and paleontological evidence. Ann. Zool. Fenn., 28, 301-309.
21. Goldstein D.B., Ruiz-Linares A., Feldmann M., Cavalli-Sforza L.L. (1995) Genetic absolute dating based on microsatellites and origin of modern humans. Proc. Natl Acad. Sci. USA, 96, 6720-6727.
22. Groves C.P. (2002) Taxonomy of living equidae. In: P. Moehlman (ed.), Equids: Zebras, Asses and Horses. Status Survey and Conservation Action Plan. The World Conservation Union (IUCN), Equid Specialist Group, Gland, Switzerland, pp. 94-107.
23. Groves C.P., Ryder O.A. (2000) Systematics and phylogeny of the horse. In: A.T. Bowling, A. Ruvinsky (eds), The Genetics of the Horse. CAB International, Oxen, UK, pp. 1-24.
24. Guérin G., Bailey E., Bernoco D., Anderson I., Antczak D.F., Bell K., Biros I., Bjørnstad G., Bowling A.T., Brandon R., Caetano A.R., Cholewinski G., Colling D., Eggleston M., Ellis N., Flynn J., Gralak B., Hasegawa T., Ketchum M., Lindgren G., Lyons L.A., Millon L.V., Mariat D., Murray J., Neau A., Roed K., Sandberg K., Skow L.C., Tammen I., Tozaki T., Dyk E.V., Weiss B., Young A., Ziegle J. (2003) The second generation of the International Equine Gene Mapping Workshop half-sibling linkage map. Anim. Genet., 34, 161-168.
25. Henner J., Poncet P.A., Guérin G., Hagger C., Stranzinger G., Rieder S. (2002) Genetic mapping of the (G)-locus responsible for the coat color phenotype 'progressive greying with age' in horses (Equus caballus). Mamm. Genome, 13, 535-537.
26. Ivankovic A., Kavar T., Caput P., Mioc B., Pavic V., Dove P. (2002) Genetic diversity of three donkey populations in the Creation coastal region. Anim. Genet., 33, 169-177.
27. Jansen T., Forster P., Levine M.A., Oelke H., Hurles M., Renfrew C., Weber J., Olek K. (2002) Mitochondrial DNA and the origins of the domestic horse. Proc. Natl Acad. Sci. USA, 99, 10905-10910.
28. 2: all loci are equal, but some are more equal than others. Genetics, 161, 1339-1347.
29. Laval G., SanCristobal M., Chevalet C. (2002) Measuring genetic distances between breeds: use of some distances in various short term evolution models. Genet. Sel. Evol., 34, 481-507.
30. Lebart L., Morineau A., Warwick K.M.; 1984) Multivariate Descriptive Statistical Analysis: Correspondence Analysis and Related Techniques for Large Matrices. John Wiley and Sons, New York.
31. MacHugh D.E., Shriver M.D., Loftus R.T., Cunningham P., Bradley D.G. (1997) Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics, 146, 1071-1086.
32. Manel S., Berthier P., Luikart G. (2002) Detecting wildlife poaching: identifying the origin of individuals with Bayesian assignment tests and multilocus genotypes. Conserv. Biol., 16, 650-659.
33. Marklund S., Ellegren H., Eriksson S., Sandberg K., Andersson L. (1994) Parentage testing and linkage analysis in the horse using a set of highly polymorphic microsatellites. Anim. Genet., 25, 19-23.
34. Minch E., Ruiz-Linares A., Goldstein D., Feldman M., Cavalli-Sforza L.L. (1996) Microsat (version 1.5): a computer program for calculating various statistics on microsatellite allele data, http://lotka.stanford.edu/ micorsat/microsat.html.
35. Neff B.D., Gross M.R. (2001) Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution, 55, 1717-1733.
36. Oakenfull E.A., Ryder O.A. (2002) Genetics of equid species and subspecies. In: P. Moehlman (ed.), Equids: Zebras, Asses and Horses. Status Survey and Conservation Action Plan. The World Conservation Union (IUCN), Equid Specialist Group, Gland, Switzerland, pp. 108-112.
37. Oakenfull E.A., Lim H.N., Ryder O.A. (2000) A survey of equid mitochondrial DNA: implications for the evolution, genetic diversity and conservation of equids. Conserv. Genet., 1, 341-355.
38. Ohta T., Kimura M. (1973) The model of mutation appropriate to estimate the number of the electrophoretically detectable alleles in a genetic population. Genet. Res., 22, 201-204.
39. Parker H.G., Kim L.V., Sutter N.B., Carlson S., Lorentzen T.D., Malek T.B., Johnson G.S., DeFrance H.B., Ostrander E.A., Kruglyak L. (2004) Genetic structure of the purebred domestic dog. Science, 304, 1160-1164.
40. Pritchard J.K., Stephens M., Donnelly P.J. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
41. Raymond M., Rousset F. (1995) GENEPOP, 1.2, population genetics software for exact tests and ecumenicism. J. Hered., 86, 248-249.
42. Reist-Marti S.B. (2004) Analysis of methods for efficient biodiversity conservation with focus on African cattle breeds. Thesis, ETH, Zurich, no. 15494.
43. Rieder S., Taourit S., Mariat D., Langlois B., Guérin G. (2001) Mutations in the agouti (ASIP), the extension (MC1R) and the brown (TYRP1) loci and their association to coat color phenotypes in horses. Mamm. Genome, 12, 450-455.
44. Ritz L.R., Glowatzki-Mullis M.L., MacHugh D.E., Gaillard C. (2000) Phylogenetic analysis of the tribe bovini using microsatellites. Anim. Genet., 31, 178-185.
45. Saitou N., Nei M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
46. Schaller G.B. (1998) Wildlife of the Tibetan Steppe. The University of Chicago Press, Chicago, IL, USA.
47. Schreiber A., Eisenmann V., Zimmermann W. (2000) Hemiones: pluridisciplinary quest of their identities and relationships. In: W. Zimmermann (ed.), EEP Asiatic Equid Husbandry Guidelines, Vol. 2. Münster Schilling, Verlag, D, pp. 2-39.
48. Simianer H. (2002) A bootstrap approach to reduce the bias of genetic distances estimated from population samples of different size. Poster Presentation F014, ISAG Conference, Göttingen D.
49. Swinburne J., Gerstenberg C., Breen M., Aldridge V., Lockhart L., Marti E., Antczak D., Eggleston-Stott M., Bailey E., Mickelson J., Roed K., Lindgren G., van Haeringen W., Guérin G., Bjarnason J., Allen T., Binns M. (2000) First comprehensive low-density horse linkage map based on two 3-generation, full-sibling, cross-bred horse reference families. Genomics, 66, 123-134.
50. Vilà C., Leonard J.A., Götherström A., Marklund S., Sandberg K., Lidén K., Wayne R.W., Ellegren H. (2001) Widespread origins of domestic horse lineages. Science, 291, 474-477.
51. Wallner B., Brem G., Müller M., Achmann R. (2003) Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus. Anim. Genet., 34, 453-456.