detecting population structure by PCA

(1) several papers:

A genealogical interpretation of principal components analysis 

http://www.ncbi.nlm.nih.gov/sites/entrez/19834557?dopt=Abstract&holding=f1000,f1000m,isrctn

Genome-wide patterns of population structure and admixture in West Africans and African Americans

http://www.ncbi.nlm.nih.gov/sites/entrez/20080753?dopt=Abstract&holding=f1000,f1000m,isrctn

Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis

http://www.ncbi.nlm.nih.gov/sites/entrez/20862358?dopt=Abstract&holding=f1000,f1000m,isrctn

(2) adegent

- a review of applications of multivariate analyses to genetic markers data:

Jombart T, Pontier D, Dufour AB. (2009) Heredity 102: 330-341. doi:10.1038/hdy.2008.130. [link to the journal's pdf - free abstract] Genetic markers in the playground of multivariate analysis.

- the paper presenting the spatial principal component analysis (sPCA, function spca), global and local tests (global.rtest and local.rtest):
Jombart T, Devillard S, Dufour AB, Pontier D (2008) Revealing cryptic spatial patterns in genetic variability by a new multivariate method.  Heredity 101: 92-103. doi: 10.1038/hdy.2008.34 [link on the journal's website - free abstract]

- the paper presenting the SeqTrack algorithm (seqTrack), and simulations of genealoies of haplotypes (haploGen): 

Jombart T, Eggo RM, Dodd PJ, Balloux F (2010) Reconstructing disease outbreaks from genetic data: a graph approach. Heredity. Doi: 10.1038/hdy.2010.78 

- the paper introducing the Discriminant Analysis of Principal Components (DAPC, functions find.clusters and dapc): 

Jombart T , Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11:94. doi:10.1186/1471-2156-11-94 [free pdf] [free html version] [evaluation by Laurent Excoffier on F1000]