Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

PeerJ

Volumn 2014, Issue 1, 2014, Pages 1-14

  Kamvar, Zhian N ^a   Tabima, Javier F ^a   Gr̈unwald, Niklaus J ^a,b  

^a OREGON STATE UNIVERSITY   (United States)

^b HORTICULTURAL CROPS RESEARCH LABORATORY   (United States)

Author keywords

Bootstrap; Bruvo's distance; Clonality; Clone correction; Genotypic diversity; Hierarchy; Index of association; Minimum spanning networks; Permutation; Population genetics

Indexed keywords

ALLELE; ARTICLE; BIOLOGY; BOOTSTRAPPING; CLONAL VARIATION; CODING ALGORITHM; COMPUTER PROGRAM; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC DISTANCE; GENETIC VARIABILITY; GENOTYPE; INFORMATION PROCESSING; NONHUMAN;

EID: 84895752138     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.281     Document Type: Article

References (38)

1. Agapow PM, Burt A. 2001. Indices of multilocus linkage disequilibrium. Molecular Ecology Notes 1:101-102
2. Anderson JB, Kohn LM. 1995. Clonality in soilborne, plant-pathogenic fungi. Annual Review of Phytopathology 33:369-391
3. Brown A, Feldman M, Nevo E. 1980. Multilocus structure of natural populations of Hordeum spontaneum. Genetics 96:523-536.
4. Bruvo R,Michiels NK, D'Souza TG, Schulenburg H. 2004. A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level. Molecular Ecology 13:2101-2106
5. Burt A, Carter DA, Koenig GL,White TJ, Taylor JW. 1996. Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis. Proceedings of the National Academy of Sciences 93:770-773
6. Clark L, Jasieniuk M. 2011. Polysat: an R package for polyploid microsatellite analysis. Molecular Ecology Resources 11:562-566
7. Cooke DE, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, Gr̈unwald NJ, Hein I,MacLean D,McNicol JW, Randall E, Oliva RF, Pel MA, Shaw DS, Squires JN, Taylor MC, Vleeshouwers VG, Birch PR, Lees AK, Kamoun S. 2012. Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen. PLoS Pathogens 8:e1002940
8. Csardi G, Nepusz T. 2006. The igraph software package for complex network research. Inter Journal, Complex Systems 1695:1695.
9. Goss EM, Larsen M, Chastagner GA, Givens DR, Gr̈unwald NJ. 2009. Population genetic analysis infers migration pathways of Phytophthora ramorum in US nurseries. PLoS Pathogens 5:e1000583
10. Gr̈unwald NJ, Goss EM. 2011. Evolution and population genetics of exotic and re-emerging pathogens: novel tools and approaches. Annual Review of Phytopathology 49:249-267
11. Gr̈unwald NJ, Goodwin SB,Milgroom MG, Fry WE. 2003. Analysis of genotypic diversity data for populations of microorganisms. Phytopathology 93:738-746
12. Gr̈unwald NJ, Hoheisel G. 2006. Hierarchical analysis of diversity, selfing, and genetic differentiation in populations of the oomycete Aphanomyces euteiches. Phytopathology 96:1134-1141. Available at http://dx.doi.org/10.6084/m9.figshare.877104 DOI 10.1094/PHYTO-96-1134.
13. Hartl DL, Clark AG. 1997. Principles of population genetics. Second edition. Sunderland, MA: Sinauer Associates, Inc.
14. Haubold B, Hudson RR. 2000. LIAN 3.0: detecting linkage disequilibrium in multilocus data. Bioinformatics 16:847-849
15. Heck KL, Belle GV, Simberloff D. 1975. Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56:1459-1461
16. Hurlbert SH. 1971. The nonconcept of species diversity: a critique and alternative parameters. Ecology 52:577-586
17. Jombart T. 2008. Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403-1405
18. Jombart T, Ahmed I. 2011. Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27:3070-3071
19. Ludwig J, Reynolds J. 1988. Statistical ecology. A primer on methods and computing. New York, USA: John Wiley and Sons.
20. Mascheretti S, Croucher P, Vettraino A, Prospero S, Garbelotto M. 2008. Reconstruction of the sudden oak death epidemic in California through microsatellite analysis of the pathogen Phytophthora ramorum. Molecular Ecology 17:2755-2768
21. McDonald BA. 1997. The population genetics of fungi: tools and techniques. Phytopathology 87:448-453
22. Meirmans PG, Van Tienderen PH. 2004. Genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes 4:792-794
23. Milgroom MG. 1996. Recombination and the multilocus structure of fungal populations. Annual Review of Phytopathology 34:457-477.
24. Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590.
25. Nielsen R, Slatkin M. 2013. An introduction to population genetics: theory and applications. Sunderland, MA: Sinauer Associates, Inc.
26. Oksanen J, Blanchet FG, Kindt R, Legendre P,Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH,Wagner H. 2013. vegan: Community Ecology Package. R package version 2.0-7. Available at http://CRAN.R-project.org/package=vegan.
27. Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290
28. Peakall R, Smouse PE. 2006. GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6:288-295
29. Peever TL, MilgroomMG. 1994. Genetic structure of Pyrenophora teres populations determined with random amplified polymorphic DNA markers. Canadian Journal of Botany 72:915-923
30. Peng B, Amos CI. 2008. Forward-time simulations of non-random mating populations using simupop. Bioinformatics 24:1408-1409
31. Pielou E. 1975. Ecological diversity. New York: Wiley.
32. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
33. R Core Team. 2013. R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. Available at http://www.R-project.org/ (accessed 16 May 2013).
34. Schliep K. 2011. Phangorn: phylogenetic analysis in R. Bioinformatics 27:592-593
35. Shannon CE. 1948. A mathematical theory of communication. Bell Systems Technical Journal 27:379-423
36. Smith JM, Smith NH, O'Rourke M, Spratt BG. 1993. How clonal are bacteria?. Proceedings of the National Academy of Sciences 90:4384-4388
37. Stoddart JA, Taylor JF. 1988. Genotypic diversity: estimation and prediction in samples. Genetics 118:705-711.
38. Weir BS. 1996. Genetic data analysis II. Sunderland, MA: Sinauer Associates, Inc.