Assessing population genetic structure via the maximisation of genetic distance

Genetics Selection Evolution

Volumn 41, Issue 1, 2009, Pages

  Rodríguez Ramilo, Silvia T ^a,b   Toro, Miguel A ^a,c   Fernndez, Jess ^a  

^a INIA   (Spain)

^b UNIVERSITY OF VIGO   (Spain)

^c Electrotechnical Section   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN ANALYSIS; DATA SET; GENETIC MARKER; GENETIC STRUCTURE; POPULATION GENETICS; POPULATION STRUCTURE; SIMULATION;

ALGORITHM; BIOLOGICAL MODEL; COMPUTER PROGRAM; EVALUATION STUDY; GENETIC LINKAGE; GENETIC VARIABILITY; HUMAN; POPULATION GENETICS; PROCEDURES;

ALGORITHMS; GENETIC LINKAGE; GENETIC STRUCTURES; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; SOFTWARE;

EID: 77949856216     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/1297-9686-41-49     Document Type: Article

References (46)

1. Evolution in mendelian populations. S Wright, Genetics 1931 16 97 159 17246615
2. Sex-biased dispersal in a migratory bat: a characterization using sex-specific demographic parameters. E Petit F Balloux J Goudet, Evolution 2001 55 635 640 10.1554/0014-3820(2001)055[0635:SBDIAM]2.0.CO;2 11327171
3. Inference of population structure using multilocus genotype data. JK Pritchard M Stephens P Donnelly, Genetics 2000 155 945 959 10835412
4. A Bayesian approach to the identification of panmictic populations and the assignment of individuals. KJ Dawson K Belkhir, Genet Res 2001 78 59 77 10.1017/S001667230100502X 11556138
5. Bayesian analysis of genetic differentiation between populations. J Corander P Waldmann MJ Sillanpaa, Genetics 2003 163 367 374 12586722
6. Inference of population structure under a Dirichlet process model. JP Huelsenbeck P Andolfatto, Genetics 2007 175 1787 1802 17237522 10.1534/genetics.106.061317 (Pubitemid 46789963)
7. The Bayesian revolution in genetics. MA Beaumont B Rannala, Nat Rev Genet 2004 5 251 261 10.1038/nrg1318 15131649
8. A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. H Gao S Williamson CD Bustamante, Genetics 2007 176 1635 1651 17483417 10.1534/genetics.107.072371
9. Assignment methods: matching biological questions with appropriate techniques. S Manel OE Gaggiotti RS Waples, Trends Ecol Evol 2005 20 136 142 10.1016/j.tree.2004.12.004 16701357
10. Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. EK Latch G Dharmarajan JC Glaubitz OE Rhodes, Conserv Genet 2006 7 295 302 10.1007/s10592-005-9098-1 (Pubitemid 43873283)
11. Estimation of individual admixture: Analytical and study design considerations. H Tang J Peng P Wang NJ Risch, Genet Epidemiol 2005 28 289 301 10.1002/gepi.20064 15712363
12. PSMIX: an R package for population structure inference via maximum likelihood method. BL Wu NJ Liu HY Zhao, BMC Bioinformatics 2006 7 317 16792813 10.1186/1471-2105-7-317 (Pubitemid 44251341)
13. GENELAND: a computer package for landscape genetics. G Guillot F Mortier A Estoup, Mol Ecol Notes 2005 5 712 715 10.1111/j.1471-8286.2005.01031.x (Pubitemid 41716893)
14. Bayesian clustering using hidden Markov random fields in spatial population genetics. O François S Ancelet G Guillot, Genetics 2006 174 805 816 16888334 10.1534/genetics.106.059923 (Pubitemid 44656469)
15. Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. C Chen E Durand F Forbes O Francois, Mol Ecol Notes 2007 7 747 756 10.1111/j.1471-8286.2007.01769.x (Pubitemid 47329398)
16. WOMBSOFT: an R package that implements the Wombling method to identify genetic boundary. A Crida S Manel, Mol Ecol Notes 2007 7 588 591 10.1111/j.1471-8286.2007.01753.x (Pubitemid 47035521)
17. A simulated annealing approach to define the genetic structure of populations. I Dupanloup S Schneider L Excoffier, Mol Ecol 2002 11 2571 2581 10.1046/j.1365-294X.2002.01650.x 12453240
18. Geographic patterns of (genetic, morphologic, linguistic) variation: How barriers can be detected by using Monmonier's algorithm. F Manni E Guerard E Heyer, Hum Biol 2004 76 173 190 10.1353/hub.2004.0034 15359530
19. Alleles In Space (AIS): Computer software for the joint analysis of interindividual spatial and genetic information. MP Miller, J Hered 2005 96 722 724 10.1093/jhered/esi119 16251514
20. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. D Falush M Stephens JK Pritchard, Genetics 2003 164 1567 1587 12930761
21. BAPS 2: enhanced possibilities for the analysis of genetic population structure. J Corander P Waldmann P Marttinen MJ Sillanpaa, Bioinformatics 2004 20 2363 2369 10.1093/bioinformatics/bth250 15073024
22. Bayesian analysis of population structure based on linked molecular information. J Corander J Tang, Math Biosci 2007 205 19 31 10.1016/j.mbs.2006. 09.015 17087977
23. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. G Evanno S Regnaut J Goudet, Mol Ecol 2005 14 2611 2620 10.1111/j.1365-294X.2005.02553.x 15969739
24. Measuring genetic distances between breeds: use of some distances in various short term evolution models. G Laval M Sancristobal C Chevalet, Genet Sel Evol 2002 34 481 507 12270106 10.1186/1297-9686-34-4-481
25. M Nei, Molecular evolutionary genetics New York: Columbia University Press 1987
26. Analysis of genetic diversity for the management of conserved subdivided populations. A Caballero MA Toro, Conserv Genet 2002 3 289 299 10.1023/A:1019956205473
27. G Malécot, Les mathématiques de l'héré dité Paris: Masson 1948
28. Equation of state calculations by fast computing machines. N Metropolis AW Rosenbluth MN Rosenbluth AH Teller E Teller, J Chem Phys 1953 21 1087 1092 10.1063/1.1699114
29. Optimization by simulated annealing. S Kirpatrick CD Gelatt MP Vecchi, Science 1983 220 671 680 10.1126/science.220.4598.671 17813860
30. The use of mathematical programming to control inbreeding in selection schemes. J Fernndez MA Toro, J Anim Breed Genet 1999 116 447 466 10.1046/j.1439-0388.1999.00196.x
31. EASYPOP (Version 1.7): A computer program for population genetics simulations. F Balloux, J Hered 2001 92 301 302 10.1093/jhered/92.3.301 11447253
32. The combination of linkage values, and the calculation of distance between the loci of linked factors. JBS Haldane, J Genet 1919 8 299 309 10.1007/BF02983270
33. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. M Raymond F Rousset, J Hered 1995 86 248 249
34. Genetic structure of human populations. NA Rosenberg JK Pritchard JL Weber HM Cann KK Kidd LA Zhivotovsky MW Feldman, Science 2002 298 2381 2385 10.1126/science.1078311 12493913
35. Detecting population structure using STRUCTURE software: effect of background linkage disequilibrium. R Kaeuffer D Réale DW Coltman D Pontier, Heredity 2007 99 374 380 10.1038/sj.hdy.6801010 17622269
36. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. RS Waples O Gaggiotti, Mol Ecol 2006 15 1419 1439 10.1111/j.1365-294X.2006.02890.x 16629801
37. Genotype, haplotype and copy-number variation in worldwide human populations. M Jakobsson SW Scholz P Scheet JR Gibbs JM VanLiere HC Fung ZA Szpiech JH Degnan K Wang R Guerreiro JM Bras JC Schymick DG Hernandez BJ Traynor J Simon-Sanchez M Matarin A Britton J van de Leemput I Rafferty M Bucan HM Cann JA Hardy NA Rosenberg AB Singleton, Nature 2008 451 998 1003 10.1038/nature06742 18288195
38. Worldwide human relationships inferred from genome-wide patterns of variation. JZ Li DM Absher H Tang AM Southwick AM Casto S Ramachandran HM Cann GS Barsh M Feldman LL Cavalli-Sforza M Myers R, Science 2008 319 1100 1104 10.1126/science.1153717 18292342
39. Geography is a better determinant of human genetic differentiation than ethnicity. A Manica F Prugnolle F Balloux, Hum Genet 2005 118 366 371 16189711 10.1007/s00439-005-0039-3 (Pubitemid 43091208)
40. Going the distance: human population genetics in a clinal world. LJ Handley A Manica J Goudet F Balloux, Trends Genet 2007 23 432 439 10.1016/j.tig.2007.07.002 17655965
41. An African origin for the intimate association between humans and Helicobacter pylori. B Linz F Balloux Y Moodley A Manica H Liu P Roumagnac D Falush C Stamer F Prugnolle SW van der Merwe Y Yamaoka DY Graham E Perez-Trallero T Wadstrom S Suerbaum M Achtman, Nature 2007 445 915 918 17287725 10.1038/nature05562 (Pubitemid 46309836)
42. Evidence for gradients of human genetic diversity within and among continents. D Serre SP Pääbo, Genome Res 2004 14 1679 1685 15342553 10.1101/gr.2529604 (Pubitemid 39276424)
43. Estimating F-statistics for the analysis of population structure. BS Weir CC Cokerham, Evolution 1984 38 1358 1370 10.2307/2408641
44. Estimating relatedness using genetic markers. DC Queller KF Goodnight, Evolution 1989 43 258 275 10.2307/2409206
45. Estimation of coancestry in Iberian pigs using molecular markers. MA Toro C Barragn C vilo J Rodrig̃ez C Rodríguez L Siliá Conserv Genet 2002 3 309 320 10.1023/A:1019921131171
46. Moment estimation of population diversity and genetic distance from data on recessive markers. WG Hill BS Weir, Mol Ecol 2004 13 895 908 10.1046/j.1365-294X.2004.02103.x 15012764