Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

Molecular Ecology Resources

Volumn 16, Issue 3, 2016, Pages 742-754

  Blischak, Paul D ^a   Kubatko, Laura S ^a   Wolfe, Andrea D ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

Allelic dosage uncertainty; Genotyping by sequencing; Hierarchical Bayesian modelling; Polyploidy; Population genomics; RADseq

Indexed keywords

BIOSTATISTICS; DNA SEQUENCE; GENE FREQUENCY; GENOTYPE; HIGH THROUGHPUT SEQUENCING; POLYPLOIDY; POPULATION GENETICS; PROCEDURES;

BIOSTATISTICS; GENE FREQUENCY; GENETICS, POPULATION; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYPLOIDY; SEQUENCE ANALYSIS, DNA;

EID: 84952360815     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12493     Document Type: Article

References (73)

1. Allendorf FW, Thorgaard GH (1984) Tetraploidy and the Evolution of Salmonid Fishes. In: Evolutionary Genetics of Fishes (ed. Turner BJ), pp. 1-53. Plenum Press, New York.
2. Anithakumari A, Tang J, van Eck H et al. (2010) A pipeline for high throughput detection and mapping of SNPs from EST databases. Molecular Breeding, 26, 65-75.
3. Arnold B, Bomblies K, Wakeley J (2012) Extending coalescent theory to autotetraploids. Genetics, 192, 195-204.
4. Arnold B, Corbett-Detig RB, Hartl D, Bomblies K (2013) RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Molecular Ecology, 22, 3179-3190.
5. Baird NA, Etter PD, Atwood TS et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PloS ONE, 3, e3376.
6. Barlow N (1913) Preliminary note on heterostylism in Oxalis and Lythrum. Journal of Genetics, 3, 53-65.
7. Barlow N (1923) Inheritance of the three forms in trimorphic plants. Journal of Genetics, 13, 133-146.
8. Buerkle CA, Gompert Z (2013) Population genomics based on low coverage sequencing: how low should we go? Molecular Ecology, 22, 3028-3035.
9. Cannon SB, McKain MR, Harkess A et al. (2014) Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes. Molecular Biology and Evolution, 32, 193-210.
10. Clark LV, Jasieniuk M (2011) polysat: an R package for polyploid microsatellite analysis. Molecular Ecology Resources, 11, 562-566.
11. Clausen J, Keck DD, Hiesey WM (1940) Experimental Studies on the Nature of Species. I. Effect of Varied Environments on Western American Plants. Carnegie Institution of Washington Publication, Washington, District of Columbia.
12. Clausen J, Keck DD, Hiesey WM (1945) Experimental Studies on the Nature of Species. II. Plant Evolution through Amphiploidy and Autoploidy, with Examples from Madiinae. Carnegie Institution of Washington Publication, Washington, District of Columbia.
13. Cui L, Wall PK, Leebens-Mack JH et al. (2006) Widespread genome duplications throughout the history of flowering plants. Genome Research, 16, 738-749.
14. Dufresne F, Stift M, Vergilino R, Mable BK (2014) Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Molecular Ecology, 23, 40-69.
15. Eaton DAR, Hipp AL, González-Rodríguez A, Cavender-Bares J (2015) Historical introgression among the American live oaks and the comparative nature of tests for introgression. Evolution, 69, 2587-2601.
16. Eddelbuettel D (2013) Seamless R and C++ Integration with Rcpp. Springer, New York.
17. Eddelbuettel D, François R (2011) Rcpp: seamless R and C++ integration. Journal of Statistical Software, 40, 1-18.
18. Eddelbuettel D, Sanderson C (2014) RcppArmadillo: accelerating R with high-performance C++ linear algebra. Computational Statistics and Data Analysis, 71, 1054-1063.
19. Esselink GD, Nybom H, Vosman B (2004) Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting-peak ratios) method. Theoretical and Applied Genetics, 109, 402-408.
20. Fisher RA (1943) Allowance for double reduction in the calculation of genotype frequencies with polysomic inheritance. Annals of Eugenics, 12, 169-171.
21. Furlong RF, Holland PWH (2001) Were vertebrates octoploid? Philosophical Transactions of the Royal Society B: Biological Sciences, 357, 531-544.
22. Gelman A, Carlin JB, Stern HS, Dunson DB, Vehtari A, Rubin DB (2014) Bayesian Data Analysis, 3rd edn. Chapman & Hall/CRC Press, Boca Raton, Florida.
23. Gompert Z, Buerkle CA (2011) A hierarchical Bayesian model for next-generation population genomics. Genetics, 187, 903-917.
24. Gompert Z, Buerkle CA (2012) bgc: software for Bayesian estimation of genomic clines. Molecular Ecology Resources, 12, 1168-1176.
25. Grant V (1971) Plant Speciation. Columbia University Press, New York.
26. Gregory TR, Mable BK (2005) Polyploidy in animals. In: The Evolution of the Genome (eds Gregory TR), pp. 427-517. Elsevier, San Diego, California.
27. Haldane JBS (1930) Theoretical genetics of autopolyploids. Journal of Genetics, 22, 359-372.
28. Hardy OJ (2015) Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate. Molecular Ecology Resources, doi: 10.1111/1755-0998.12431 [Epub ahead of print].
29. Hernández JL, Weir BS (1989) A disequilibrium coefficient approach to Hardy-Weinberg testing. Biometrics, 45, 53-70.
30. Jiao Y, Wickett NJ, Ayyampalayam S et al. (2011) Ancestral polyploidy in seed plants and angiosperms. Nature, 473, 97-100.
31. Jones G, Sagitov S, Oxelman B (2013) Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Systematic Biology, 62, 467-478.
32. Lawrence WJC (1929) The genetics and cytology of Dahlia species. Journal of Genetics, 21, 125-158.
33. Logan-Young CJ, Yu JZ, Verma SK, Percy RG, Pepper AE (2015) SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing. Applications in Plant Sciences, 3, 1400077.
34. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research, 17, 240-248.
35. Moody ML, Mueller LD, Soltis DE (1993) Genetic variation and random drift in autotetraploid populations. Genetics, 134, 649-657.
36. Muller HJ (1914) A new mode of segregation in gregory's tetraploid primulas. American Naturalist, 48, 508-512.
37. Ogden R, Gharbi K, Mugue N et al. (2013) Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing. Molecular Ecology, 22, 3112-3123.
38. Ohno S (1970) Evolution by Gene Duplication. Springer, New York.
39. Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annual Review of Genetics, 34, 401-437.
40. Parisod C, Holderegger R, Brochmann C (2010) Evolutionary consequences of autopolyploidy. New Phytologist, 186, 5-17.
41. Pennell MW, FitzJohn RG, Cornwell WK, Harmon LJ (2015) Model adequacy and the macroevolution of angiosperm functional traits. American Naturalist, 186, E100.
42. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS ONE, 7, e37135.
43. Plummer M, Best N, Cowles K, Vines K (2006) CODA: Convergence Diagnostics and Output Analysis for MCMC. R News, 6, 7-11.
44. Puritz JB, Matz MV, Toonen RJ, Weber JN, Bolnick DI, Bird CE (2014) Demystifying the RAD fad. Molecular Ecology, 23, 5937-5942.
45. R Core Team (2014) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
46. Ramsey J (2011) Polyploidy and ecological adaptation in wild yarrow. Proceedings of the National Academy of Sciences, 108, 7096-7101.
47. Ramsey J, Ramsey TS (2014) Ecological studies of polyploidy in the 100 years following its discovery. Philosophical Transactions of the Royal Society B: Biological Sciences, 369, 20130352.
48. Reid NM, Hird SM, Brown JM et al. (2014) Poor fit to the multispecies coalescent is widely detectable in empirical data. Systematic Biology, 63, 322-333.
49. Rheindt FE, Fujita MK, Wilton PR, Edwards SV (2014) Introgression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): population genetic and phylogenetic inferences from genome-wide SNPs. Systematic Biology, 63, 134-152.
50. Ripplinger J, Sullivan J (2010) Assessment of substitution model adequacy using frequentist and Bayesian methods. Molecular Biology and Evolution, 27, 2790-2803.
51. Scarpino SV, Levin DA, Meyers LA (2014) Polyploid formation shapes flowering plant diversity. American Naturalist, 184, 456-465.
52. Selmecki AM, Maruvka YE, Richmond PA et al. (2015) Polyploidy can drive rapid adaptation in yeast. Nature, 519, 349-352.
53. Serang O, Mollinari M, Garcia AAF (2012) Efficient exact maximum a posteriori computation for Bayesian SNP genotyping in polyploids. PloS ONE, 7, e30906.
54. Soltis PS, Soltis DE (2009) The role of hybridization in plant speciation. Annual Review of Plant Biology, 60, 561-588.
55. Soltis DE, Soltis PS, Tate JA (2003) Advances in the study of polyploidy since plant speciation. New Phytologist, 161, 173-191.
56. Soltis DE, Soltis PS, Schemske DW et al. (2007) Autopolyploidy in angiosperms: have we grossly underestimated the number of species? Taxon, 56, 13-30.
57. Soltis DE, Albert VA, Leebens-Mack J et al. (2009) Polyploidy and angiosperm diversification. American Journal of Botany, 96, 336-348.
58. Soltis DE, Buggs RJA, Doyle JJ, Soltis PS (2010) What we still don't know about polyploidy. Taxon, 59, 1387-1403.
59. Soltis DE, Visger CJ, Soltis PS (2014) The polyploidy revolution then...and now: Stebbins revisited. American Journal of Botany, 101, 1057-1078.
60. Stebbins GL (1950) Variation and Evolution in Plants. Columbia University Press, New York.
61. Stift M, Berenos C, Kuperus P, van Tienderen PH (2008) Segregation models for disomic, tetrasomic and intermediate inheritance in tetraploids: a general procedure applied to Rorippa (yellow cress) microsatellite data. Genetics, 179, 2113-2123.
62. Voorrips R, Gort G, Vosman B (2011) Genotype calling in tetraploid species from bi-allelic marker data using mixture models. BMC Bioinformatics, 12, 172.
63. Wagner WH (1970) Biosystematics and evolutionary noise. Taxon, 19, 146-151.
64. Wang N, Thomson M, Bodles WJA et al. (2013) Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Molecular Ecology, 22, 3098-3111.
65. Weir BS (1996) Genetic Data Analysis II. Sinauer Associates, Sunderland, MA.
66. Wickham H (2007) Reshaping data with the reshape package. Journal of Statistical Software, 21, 1-20.
67. Wickham H (2009) ggplot2: Elegant Graphics for Data Analysis. Springer, New York.
68. Winge Ö (1917) The chromosomes: their number and general importance. Comptes rendus des travaux du Laboratoire Carlsberg, 13, 131-275.
69. Winkler H (1916) Über die experimentelle Erzeugung von Pflanzen mit abweichenden Chromosomenzahlen. Zeitschrift für induktive Abstammungs- und Vererbungslehre, 8, 417-531.
70. Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH (2009) The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences, 106, 13875-13879.
71. Wright S (1938) The distribution of gene frequencies in populations of polyploids. Proceedings of the National Academy of Sciences, 24, 372-377.
72. Wright S (1951) The genetical structure of populations. Annals of Eugenics, 15, 323-354.
73. de Silva H, Hall A, Rikkerink E, McNeilage M, Fraser L (2005) Estimation of allele frequencies in polyploids under certain patterns of inheritance. Heredity, 95, 327-334.