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Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations

  • J. M. Prystupa (a1) (a2), R. Juras (a3), E. G. Cothran (a3), F. C. Buchanan (a1) and Y. Plante (a1) (a2)...
Abstract

As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated that 13.3% of genetic diversity was explained by breed differences, whereas 84.6% and 2.1% of diversity came from within and among individuals, respectively. The average effective number of alleles and allelic richness was the lowest in the Eriskay (2.51 and 3.98) and Lac La Croix (2.83 and 4.01) populations, whereas it was highest in the New Forest (4.31 and 6.01) and Welsh (4.33 and 5.87) breeds, followed closely by the Newfoundland-CDN (4.23 and 5.86) population. Expected heterozygosities varied from 0.61 in the Lac La Croix to 0.74 in the Welsh and in Newfoundland. Observed heterozygosities ranged from 0.57 in the Exmoor and 0.58 in the Sable Island herd to 0.77 in the Kerry Bog and 0.76 in the New Forest breeds. Structure and admixture analyses revealed that the most likely number of clusters was 21, although some substructure was also observed when K = 16, compared with the 24 predefined populations. Information gathered from this study should be combined with other available phenotypic and pedigree data to develop, or amend, a suitable conservation strategy for all populations examined.

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E-mail: jmp479@mail.usask.ca
References
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Aberle, KS, Hamann, H, Drögemüller, C, Distl, O 2004. Genetic diversity in German draught horse breeds compared with a group of primitive, riding and wild horses by means of microsatellite DNA markers. Animal Genetics 35, 270277.
Achmann, R, Curik, I, Dovc, P, Kavar, T, Bodo, I, Habe, F, Marti, E, Sölkner, J, Brem, G 2004. Microsatellite diversity, population subdivision and gene flow in the Lipizzan horse. Animal Genetics 35, 285292.
Behl, R, Behl, J, Gupta, N, Gupta, SC 2008. Evaluation of microsatellite genotyping based individual assignment in five Indian horse breeds. Indian Journal of Animal Sciences 78, 384387.
Bowcock, AM, Ruiz-Linares, A, Tomfohrde, J, Minch, E, Kidd, JR, Cavalli-Sforza, LL 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368, 455457.
Caballero, A, Toro, MA 2002. Analysis of genetic diversity for the management of conserved subdivided populations. Conservation Genetics 3, 289299.
Cañon, J, Checa, ML, Carleos, C, Vega-Pla, JL, Vallejo, M, Dunner, S 2000. The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Animal Genetics 31, 3948.
Cothran, EG 2004. Genetic analysis of the Lac La Croix pony. Retrieved February 24, 2011, from http://www.laclacroixindianpony.com/pdfs/cothranDNAreport.pdf
D'Arnoldi, CT, Foulley, JL, Ollivier, L 1998. An overview of the Weitzman approach to diversity. Un apercu sur l'approche de la diversite selon Weitzman 30, 149161.
DeAssis, JB, DeLaat, DM, Peixoto, MG, Bergmann, JA, Fonseca, CG, Carvalho, MR 2009. Genetic diversity and population structure in Brazilian Mangalarga Marchador horses. Genetics and Molecular Research 8, 15191524.
Dieringer, D, Schlötterer, C 2003. Microsatellite Analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes 3, 167169.
Earl, DA 2009. Structure Harvester. Retrieved February 24, 2011, from http://taylor0.biology.ucla.edu/struct_harvest/
Eggert, LS, Powell, DM, Ballou, JD, Malo, AF, Turner, A, Kumer, J, Zimmerman, C, Fleischer, RC, Maldonado, JE 2010. Pedigrees and the study of the wild horse population of assateague island national seashore. Journal of Wildlife Management 74, 963973.
Eriskay Pony Mother Stud Book Society 2010. Our Stallions1. Retrieved February 24, 2011, from http://www.eriskaypony.org.uk/
Equus Survival Trust 2008. Equine conservation list. Retrieved February 24, 2011, from http://www.equus-survival-trust.org/
Evanno, G, Regnaut, S, Goudet, J 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology 14, 26112620.
Excoffier, L, Lischer, HEL 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10, 564567.
Food and Agriculture Organization (FAO) 2007. The State of the World's Animal Genetic Resources for Food and Agriculture (ed. Rischkowsky B and Pilling D). FAO, Rome.
Felsenstein, J 1989–2006. ‘Phylip’(phylogeny inference package) v. 3.66. Retrieved February 24, 2011, from http://evolution.genetics.washington.edu/phylip/getme.html
Glowatzki-Mullis, ML, Muntwyler, J, Pfister, W, Marti, E, Rieder, S, Poncet, PA, Gaillard, C 2006. Genetic diversity among horse populations with a special focus on the Franches–Montagnes breed. Animal Genetics 37, 3339.
Goudet, J 2001. FSTAT: a program to estimate and test gene diversities and fixation indices, version 2.9.3. Retrieved February 24, 2011, from http://www2.unil.ch/popgen/softwares/fstat.htm
Gutiérrez, JP, Royo, LJ, Álvarez, I, Goyache, F 2005. MolKin v2.0: a computer program for genetic analysis of populations using molecular coancestry information. Journal of Heredity 96, 718721.
Hoffmann, I, Ajmone Marsan, P, Barker, SF, Cothran, EG, Hanotte, O, Lenstra, JA, Milan, D, Weigend, S, Simianer, H 2004. New MoDaD marker sets to be used in diversity studies for the major farm animal species: recommendations of a joint ISAG/FAO working group. Proceedings of 29th International Conference on Animal Genetics, Tokyo, Japan, 107pp.
Huson, DH 1998. SplitsTree: Analyzing and visualizing evolutionary data. Bioinformatics 14, 6873.
Huson, DH, Bryant, D 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23, 254267.
Jakobsson, M, Rosenberg, NA 2007. CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 18011806.
Leroy, G, Callède, L, Verrier, E, Mériaux, JC, Ricard, A, Danchin-Burge, C, Rognon, X 2009. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism. Genetics Selection Evolution 41, 5.
Lucas, ZL, McLoughlin, PD, Coltman, DW, Barber, C 2009. Multiscale analysis reveals restricted gene flow and a linear gradient in heterozygosity for an island population of feral horses. Canadian Journal of Zoology 87, 310316.
Luís, C, Juras, R, Oom, MM, Cothran, EG 2007. Genetic diversity and relationships of Portuguese and other horse breeds based on protein and microsatellite loci variation. Animal Genetics 38, 2027.
Lynghaug, F 2009. The official horse breeds standards guide: the complete guide to the standards of all North American equine breed associations. Voyageur Press, Minneapolis, MN, USA.
McGahern, AM, Edwards, CJ, Bower, MA, Heffernan, A, Park, SDE, Brophy, PO, Bradley, DG, MacHugh, DE, Hill, EW 2006. Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses. Animal Genetics 37, 498502.
Nei, M 1972. Genetic distance between populations. American Naturalist 106, 283292.
Nei, M, Tajima, F, Tateno, Y 1983. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. Journal of Molecular Evolution 19, 153170.
Nova Scotia Museum of Natural History 2001. Sable Island. Retrieved February 24, 2011, from http://museum.gov.ns.ca/mnh/nature/sableisland/english_en/nature_na/horses_ho/index_ho.htm
Paetkau, D, Calvert, W, Stirling, I, Strobeck, C 1995. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 4, 347354.
Paetkau, D, Slade, R, Burden, M, Estoup, A 2004. Genetic assignment methods for the direct, real-time estimation of migration rate: A simulation-based exploration of accuracy and power. Molecular Ecology 13, 5565.
Peakall, R, Smouse, PE 2006. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288295.
Petit, RJ, Mousadik, AEL, Pons, O 1998. Identifying populations for conservation on the basis of genetic markers. Conservation Biology 12, 844855.
Plante, Y, Vega-Pla, JL, Lucas, Z, Colling, D, De March, B, Buchanan, F 2007. Genetic diversity in a feral horse population from Sable Island, Canada. Journal of Heredity 98, 594602.
Pritchard, JK, Stephens, M, Donnelly, P 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945959.
Rare Breeds Canada 2009. Horse breeds. Retrieved February 24, 2011 from http://www.rarebreedscanada.ca/horsebreeds.htm
Raymond, M, Rousset, F 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86, 248249.
Reynolds, J, Weir, BS, Cockerham, CC 1983. Estimation of the coancestry coefficient: Basis for a short-term genetic distance. Genetics 105, 767779.
Rosenberg, NA 2004. DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes 4, 137138.
Rousset, F 2008. Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Molecular Ecology Resources 8, 103106.
Saitou, N, Nei, M 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution 4, 406425.
Solis, A, Jugo, BM, Mériaux, JC, Iriondo, M, Mazón, LI, Aguirre, AI, Vicario, A, Estomba, A 2005. Genetic diversity within and among four south European native horse breeds based on microsatellite DNA analysis: implications for conservation. Journal of Heredity 96, 670678.
Tamura, K, Dudley, J, Nei, M, Kumar, S 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24, 15961599.
Troy, CS, MacHugh, DE, Bailey, JF, Magee, DA, Loftus, RT, Cunningham, P, Chamberlain, AT, Sykes, BC, Bradley, DG 2001. Genetic evidence for near-eastern origins of European cattle. Nature 410, 10881091.
Van Oosterhout, C, Hutchinson, WF, Wills, DPM, Shipley, P 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4, 535538.
Weitzman, ML 1992. On Diversity. The Quarterly Journal of Economics 107, 363405.
Weitzman, ML 1993. What to preserve? An application of diversity theory to crane conservation. The Quarterly Journal of Economics 108, 157183.
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Supplementary materials

Prystupa Supplementary Table 1
Supplementary Table 1 A detail summary including the multiplex, location, primer sequence, allele size (ISAG markers have been standardized), dye, volume and reference of each microsatellite locus utilized this study (taken and modified from Glowatzki-Mullis et al. (2006).

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Supplementary materials

Prystupa Supplementary Table 2
Supplementary Table 2 A overall summary of the statistics parameters estimated including: average number of alleles (Na), effective number of alleles (Ne), observed heterzygosity (Ho), expected heterzygosity (He), and F indices (FIS, FST, FIT) for each individual locus tested where P=0.05

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