An empirical assessment of individual-based population genetic statistical techniques: Application to British pig breeds

Heredity

Volumn 106, Issue 2, 2011, Pages 261-269

  Wilkinson, S ^a   Haley, C ^a,b   Alderson, L ^c   Wiener, P ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b WESTERN GENERAL HOSPITAL   (United Kingdom)

^c Countrywide Livestock Ltd ^*  (United Kingdom)

Author keywords

Bayesian; domestic pig; genetic structure; livestock breeds; microsatellites

Indexed keywords

ASSESSMENT METHOD; BAYESIAN ANALYSIS; CLUSTER ANALYSIS; DATA SET; EMPIRICAL ANALYSIS; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GENETIC MARKER; GENETIC STRUCTURE; GENOTYPE; LIVESTOCK; PHYLOGENETICS; PIG; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS; REPRODUCTIVE BEHAVIOR; STATISTICAL ANALYSIS;

ANIMAL; ARTICLE; BAYES THEOREM; COMPARATIVE STUDY; GENE FREQUENCY; GENETIC VARIABILITY; GENETICS; GENOTYPE; PHYLOGENY; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS; STATISTICAL MODEL; SWINE; UNITED KINGDOM;

ANIMALS; BAYES THEOREM; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; GREAT BRITAIN; MODELS, STATISTICAL; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; SWINE;

ANIMALIA; SUIDAE; SUS SCROFA DOMESTICA;

EID: 78751641617     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2010.80     Document Type: Article

References (43)

1. Beaumont MA, Rannala B (2004). The Bayesian revolution in genetics. Nat Rev Genet 5: 251-261.
2. 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: 455-457.
3. BPA, (2002). British Pig Breeds. British Pig Association, Cambridge.
4. Bruford MW, Bradley DG, Luikart G (2003). DNA markers reveal the complexity of livestock domestication. Nat Rev Genet 4: 900-910.
5. Corander J, Marttinen P (2006). Bayesian identification of admixture events using multi-locus molecular markers. Mol Ecol 15: 2833-2843.
6. Corander J, Marttinen P, Mantuniemi S (2006). A Bayesian method for identificaiton of stock mixtures from molecular marker data. Fish Bull 104: 9.
7. Corander J, Marttinen P, Sirén J, Tang J (2008). Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9: 539-552.
8. DEFRA (2006). UK National Action Plan on Farm Animal Genetic Resources. DEFRA.
9. Dinno A (2009). pp paran-Horn's Parallel Analysis of Components/Factors. http://cran.r-project.org/web/ packages/paran/index. html.
10. Eding H, Bennewitz J (2007). Measuring genetic diversity in farm animals. In: Oldenbroek K (ed). Utilisation and Conservation of Farm Animal Genetic Resources. Wageningen Academic Publishers.
11. Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
12. Excoffier L, Smouse PE, Quattro JM (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
13. Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M et al. (2003). Traces of human migrations in helicobacter pylori populations. Science 299: 1582-1585.
14. Felsenstein J (1989). PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
15. Frantz A, Pourtois JT, Heuertz M, Flamand M, Krier A, Bertouille S et al. (2006). Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population. Mol Ecol 15: 3191-3203.
16. Guillot G, Estoup A, Mortier F, Cosson JF (2005). A spatial statistical model for landscape genetics. Genetics 170: 1261-1280.
17. Guillot G, Leblois R, Coulon A, Frantz AC (2009). Statistical methods in spatial genetics. Mol Ecol 18: 4734-4756.
18. Hall SJG, Clutton-Brock J (1988). Two Hundred Years of British Farm Livestock. British Museum (Natural History): London.
19. Hartl D, Clark A (1989). Principles of Population Genetics. Sinauer Associates.
20. Huelsenbeck JP, Andolfatto P (2007). Inference of population structure under a Dirichlet process prior. Genetics 175: 1787-1802.
21. Koskinen MT (2003). Individual assignment using microsatellite DNA reveals unambiguous breed identification in the domestic dog. Animal Genet 4: 297-301.
22. Latch E, Dharmarajan G, Glaubitz J, Rhodes O (2006). Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conserv Genet 7: 295-302.
23. Li M, Tapio I, Vilkki J, Ivanova Z, Kiselyova T, Marzanov N et al. (2007). The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservation. Mol Ecol 16: 3839-3853.
24. MacHugh D, Loftus R, Cunningham P, Bradley D (1998). Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers. Animal Genet 29: 333-340.
25. MacHugh DE, Bradley DG (2001). Livestock genetic origins: goats buck the trend. Proc Natl Acad Sci USA 98: 5382-5384.
26. Megens H-J, Crooijmans RPMA, Cristobal MS, Hui X, Li N, Groenen MAM (2008). Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication. Genet Sel Evol 40: 103-128.
27. Menotti-Raymond M, David VA, Pflueger SM, Lindblad-Toh K, Wade CM, O'Brien SJ et al. (2008). Patterns of molecular genetic variation among cat breeds. Genomics 91: 1-11.
28. Menozzi P, Piazza A, Cavalli-Sforza L (1978). Synthetic maps of human gene frequencies in Europeans. Science 201: 786-792.
29. Minch E, Ruiz-Linares A, Goldstein D, Feldman M, Cavalli-Sforza L (1997). pp Microsat v.1.5d : a computer program for calculating various statistics on microsatellite allele data (http://hpgl.stanford.edu/projects/microsat).
30. O'Connor B (2000). SPSS and SAS programs for determining the number of components using parallel analysis and velicer's MAP test. Behav Res Meth Instr Comput 32: 396-402.
31. Paradis E, Claude J, Strimmer K (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.
32. Patterson N, Price AL, Reich D (2006). Population structure and eigenanalysis. PLoS Genet 2: e190.
33. Pearse DE, Crandall KA (2004). Beyond FST: analysis of population genetic data for conservation. Conserv Genet 5: 585-602.
34. Porter V (1993). Pigs. A handbook to the Breeds of the World. Helm Information, Ltd.
35. Pritchard J, Wen W (2004). Department of Human Genetics, Univerity of Chicago, 920 E 58th st, CLCS 507, Chicago IL 60637, USA.
36. Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
37. R Development Core Team (2009). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http:// www.R-project.org.
38. Rosenberg NA, Burke T, Elo K, Feldman MW, Freidlin PJ, Groenen MAM et al. (2001). Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159: 699-713.
39. Rousset F (2008). Genepop 0007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resources 8: 103-106.
40. Rowe G, Beebee JC (2007). Defining population boundaries: use of three Bayesian approaches with microsatellite data from British natterjack toads (Bufo calamita). Mol Ecol 16: 785-796.
41. SanCristobal M, Chevalet C, Haley CS, Joosten R, Rattink AP, Harlizius B et al. (2006). Genetic diversity within and between European pig breeds using microsatellite markers. Animal Genet 37: 189-198.
42. Toro MA, Caballero A (2005). Characterization and conservation of genetic diversity in subdivided populations. Phil Trans Roy Soc Lond, B 360: 1367-1378.
43. Waples R, Gaggiotti O (2006). What is a population? an empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol 15: 1419-1439.