Correcting principal component maps for effects of spatial autocorrelation in population genetic data

Frontiers in Genetics

Volumn 3, Issue NOV, 2012, Pages

  Frichot, Eric ^a   Schoville, Sean ^a   Bouchard, Guillaume ^b   François, Olivier ^a  

^a UNIV GRENOBLE ALPES   (France)

^b XEROX RESEARCH CENTRE EUROPE   (France)

Author keywords

Isolation by distance; Principal component analysis; Spatial autocorrelation; Spatial factor analysis

Indexed keywords

EID: 84876132518     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00254     Document Type: Article

References (29)

1. Ahmed, N., Natarajan, T., and Rao, K. R. (1974). Discrete cosine transform. IEEE Trans. Comput. C-23, 90-93.
2. Borcard, D., and Legendre, P. (2002). All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecol. Modell. 153, 51-68.
3. Borcard, D., Legendre, P., Avois-Jacquet, C., and Tuomisto, H. (2004). Dissecting the spatial structure of ecological data at multiple scales. Ecology 85, 1826-1832.
4. Cressie, N. A. C. (1993). Statistics for Spatial Data, Revised Edition. New York: Wiley.
5. Diaconis, P., Goel, S., and Holmes, S. (2008). Horseshoes in multidimensional scaling and local kernel methods. Ann. Appl. Stat. 2, 777-807.
6. Dray, S., Legendre, P., and Peresneto, P. (2006). Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM).Ecol. Modell.196, 483-493.
7. Durand, E., Jay, F., Gaggiotti, O. E., and François, O. (2009). Spatial inference of admixture proportions and secondary contact zones. Mol. Biol. Evol. 26, 1963-1973.
8. Engelhardt, B. E., and Stephens, M. (2010). Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet. 6, e1001117. doi:10.1371/journal.pgen.1001117
9. François, O., Currat, M., Ray, N., Han, E., Excoffier, L., and Novem-bre, J. (2010). Principal component analysis under population genetic models of range expansion and admixture. Mol. Biol. Evol. 27, 1257-1268.
10. François, O., and Durand, E. (2010). Spatially explicit bayesian clustering models in population genetics. Mol. Ecol. Resour. 10, 773-784.
11. Hudson, R. R. (2002). Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337-338.
12. Jolliffe, I. T. (1986). Principal Component Analysis. New York: Springer Verlag.
13. Jombart, T., Devillard, S., Dufour, A.-B., and Pontier, D. (2008). Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity 101, 92-103.
14. Kimura, M., and Weiss, G. H. (1964). The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 49, 561-576.
15. Legendre, P., and Gallagher, E. (2001). Ecologically meaningful transformations for ordination of species data. Oecologia 129, 271-280.
16. Malécot, G. (1948). Les Mathématiques de l'Hérédité. Paris: Masson.
17. Mardia, K. V., Kent, J. T., and Bibby, J. M. (1979). Multivariate Analysis. London: Academic Press.
18. McVean, G. (2009). A genealogical interpretation of principal components analysis. PLoS Genet. 5, e1000686. doi:10.1371/journal. pgen.1000686
19. Meirmans, P. G. (2012). The trouble with isolation by distance. Mol. Ecol. 21, 2839-2846.
20. Novembre, J., and Stephens, M. (2008). Interpreting principal component analyses of spatial population genetic variation. Nat. Genet. 40, 646-649.
21. Patterson, N., Price, A. L., and Reich, D. (2006). Population structure and eigenanalysis. PLoS Genet. 2, e190. doi:10.1371/journal.pgen.0020190
22. Patterson, N. J., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., et al. (2012). Ancient admixture in human history. Genetics 192, 1065-1093.
23. Powell, G. T., Yang, H., Tyler-Smith, C., and Xue, Y. (2007). The population history of the Xibe in northern China: a comparison of auto-somal, mtDNA and Y-chromosomal analyses of migration and gene flow. Forensic Sci. Int. Genet. 1, 115-119.
24. Pritchard, J. K., Stephens, M., and Donnelly, P. (2000). Inference of population structure using multi-locus genotype data. Genetics 155, 945-959.
25. Rosenberg, N., Pritchard, J., Weber, J., Cann, H., Kidd, K., Zhivotovsky, L., et al. (2002). Genetic structure of human populations. Science 298, 2381-2385.
26. Rousset, F. (1997). Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145, 1219-1228.
27. Tipping, M. E., and Bishop, C. M. (1999). Probabilistic principal component analysis. J. R. Stat. Soc. 61, 611-622. doi:10.1111/1467-9868.00196
28. Wright, S. (1943). Isolation by distance. Genetics 28, 114-138.
29. Zhang, F., Su, B., Zhang, Y., and Jin, L. (2007). Genetic studies of human diversity in East Asia. Philos. Trans. R. Soc. Lond. B Biol. Sci. 362, 987-996.