To cite adegenet:

Jombart T.(2008)adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics24: 1403-1405. doi: 10.1093/bioinformatics/btn129 [linkto a free pdf]

Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. doi: 10.1093/bioinformatics/btr521 [link to the bublisher's website]

Related publications:

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

- 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]

First 200 publications citing adegenet (433 citations on google scholar as of 13-05-2014):

[1] Cohas A, Yoccoz NG, Bonenfant C, Goossens B, Genton C, Galan M, Kempenaers B, Allainé D (2007) Thegenetic similarity between pair members influences the frequency of extrapair paternity in alpine marmots. Animal Behaviour76: 87-95.

[2] Satkoski JA,  Malhi RS, Kanthaswamy S, Tito RY, Malladi VS, Smith DG (2008) Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta). BMC Genomics9: 256.

Kanthaswamy S, Satkoski J, George D, Kou A, Erickson BJ, Smith DG. (2008). Interspecies hybridization and the stratification of nuclear genetic variation of rhesus (Macaca mulatta) and long-tailed macaques (Macaca fascicularis). Int J Primatol 29: 1295-1311.

[4] Kidd, AG, Bowman J, Lesbarrères D, Schulte-Hostedde AI (2009). Hybridization between escaped domestic and wild American mink (Neovison vison). Molecular Ecology 18: 1175-1186.

[5] Cohas E, Bonenfant C, Kempaners B, Allainé D (2009). Age-specific effect of heterozygosity on survival in alpine marmots, Marmota marmota.Molecular Ecology 18: 1491-1503.

[6] O'Brien J, Devillard S, Say L, Vanthomme A, Léger F, Ruette S, Pontier D (2009). Preserving genetic integrity in a hybridising world:
are European Wildcats (Felis silvestris silvestris) in eastern France distinct from sympatric feral domestic cats? Biodivers Conserv 18: 2351-2360.

[7] Kanthaswamy S et al. (2009). Canine Population Data Generated from a Multiplex STR Kit for Use in Forensic Casework. Journal of Forensic Sciences 54: 829-840.

[8] Lankau R A, Nuzzo V, Spyreas G, Davis A S (2009). Evolutionary limits ameliorate the negative impact of an invasive plant. Proceedings of the National Academy of Sciences 106: 15362-15367.

[9] Dutech C, Fabreguettes O, Capdevielle X, Robin C (2009) Multiple introductions of divergent genetic lineages in an invasive fungal pathogen, Cryphonectria parasitica, in France. Heredity (advanced online) doi: 10.1038/hdy.2009.164.

[10] L Y Rutledge, C J Garroway, K M Loveless and B R Patterson (2010) Genetic differentiation of eastern wolves in Algonquin Park despite bridging gene flow between coyotes and grey wolves.Heredity (advanced online) doi: 10.1038/hdy.2010.6.

[11] Jennifer Paul, Nicole Vachon, Colin J. Garroway and Joanna R. Freeland (2010) Molecular data provide strong evidence of natural hybridization between native and introduced lineages of Phragmites australis in North America. Biological Invasions. doi: 10.1007/s10530-010-9699-6.

[12] C. BERTHOULY, D. DO NGOC, S. THÉVENON, D. BOUCHEL, T. NHU VAN, C. DANES, V. GROSBOIS, H. HOANG THANH, C. VU CHI, J.-C. MAILLARD (2009) How does farmer connectivity influence livestock genetic structure? A case-study in a Vietnamese goat population. Molecular Ecology 18: 3980-3991

[13] COLIN J. GARROWAY, JEFF BOWMAN, TARA J. CASCADEN, GILLIAN L. HOLLOWAY, CAROLYN G. MAHAN, JAY R. MALCOLM, MICHAEL A. STEELE, GREGORY TURNER and PAUL J. WILSON (2009) Climate change induced hybridization in flying squirrels. Global Change Biology 16: 113-121.

[14] JOSSELIN MONTARRY, DIDIER ANDRIVON, ISABELLE GLAIS, ROSELYNE CORBIERE, GLADYS MIALDEA and FRANCOIS DELMOTTE (2010) Microsatellite markers reveal two admixed genetic groups and an ongoing displacement within the French population of the invasive plant pathogen Phytophthora infestans. Molecular Ecology 19: 1965-1977

[15] Gwenaelle Comont, Marie-France Corio-Costet, Philippe Larignon and François Delmotte (2010) AFLP markers reveal two genetic groups in the French population of the grapevine fungal pathogen Phaeomoniella chlamydospora. European Journal of Plant Pathology Doi: 10.1007/s10658-010-9611-3

[16] Michelle F. DiLeo, Jeffrey R. Row and Stephen C. Lougheed (2010) Discordant patterns of population structure for two co-distributed snake species across a fragmented Ontario landscape. Diversity and Distributions. Doi: 10.1111/j.1472-4642.2010.00667.x

Francisco Balao, Luis M. Valente, Pablo Vargas , Javier Herrera and Salvador Talavera (2010) Radiative evolution of polyploid races of the Iberian carnation Dianthus broteri (Caryophyllaceae).New Phytologist. Doi:10.1111/j.1469-8137.2010.03280.x

Gadieux P, Caffier V , Devaux M , Le Cam B(2010) Host-specific differentiation among populations of Venturia inaegualis causing scab on apple, pyracantha and loquat. FUNGAL GENETICS AND BIOLOGY , 47:  511-521

[19] Joost S, Colli L, Baret PV, et al. (2010) Integrating geo-referenced multiscale and multidisciplinary data for the management of biodiversity in livestock genetic resources. Animal Genetics 41: 47-63.
[20] Denis Laloë, Katayoun Moazami-Goudarzi, Johannes A. Lenstra, Paolo Ajmone Marsan, Pedro Azor, Roswitha Baumung, Daniel G. Bradley, Michael W. Bruford, Javier Cañón, Gaudenz Dolf, Susana Dunner, Georg Erhardt, Godfrey Hewitt, Juha Kantanen, Gabriela Obexer-Ruff, Ingrid Olsaker, Clemen Rodellar, Alessio Valentini, Pamela Wiener and European Cattle Genetic Diversity Consortium and Econogene Consortium (2010) Spatial Trends of Genetic Variation of Domestic Ruminants in Europe. Diversity 2010, 2(6), 932-945; doi:10.3390/d2060932

[21] Gautier M, Laloë D, Moazami-Goudarzi K, 2010 Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds. PLoS ONE5(9): e13038. doi:10.1371/journal.pone.0013038a

[22] Morris, C. E., D. C. Sands, J. L. Vanneste, J. Montarry, B. Oakley, et al. 2010. Inferring the evolutionary history of the plant pathogen Pseudomonas syringae from its biogeography in headwaters of rivers in North America, Europe, and New Zealand. mBio 1(3):e00107-10. doi:10.1128/mBio.00107-10.

[23] Bower MA, Campana MG, Whitten M, Edwards CJ, Jones H, Barrett E, Cassidy R, Nisbet RE, Hill EW, Howe CJ, Binns M (2010) The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares. Biol Lett.2010 Oct 6. [Epub ahead of print]

[24] SANTOS, H., BURBAN, C., ROUSSELET, J., ROSSI, J.-P., BRANCO, M. and KERDELHUÉ, C. , Incipient allochronic speciation in the pine processionary moth (Thaumetopoea pityocampa, Lepidoptera, Notodontidae). Journal of Evolutionary Biology, no. doi: 10.1111/j.1420-9101.2010.02147.x

[25] Giorgia Ferrara, Rita Cannas, Marco Stagioni, Giulia Riccioni, Piero Addis, Angelo Cau, Corrado Piccinetti, FaustoTinti (2010) Fishery genetics of mediterranean bluefin tuna: review of existing data, on-going studies and perspectives. Collect. Vol. Sci. Pap. ICCAT, 65(3): 988-995

[26] Vandewoestijne S, Van Dyck H, 2010 Population Genetic Differences along a Latitudinal Cline between Original and Recently Colonized Habitat in a Butterfly. PLoS ONE5(11): e13810. doi:10.1371/journal.pone.0013810

[27] Lagisz, M., Port, G. and Wolff, K. (2011) Living in a jar: genetic variation and differentiation among laboratory strains of the red flour beetle. Journal of Applied Entomology, no. doi: 10.1111/j.1439-0418.2010.01593.x

[28] Jessica A. Satkoski Trask, Ripan S. Malhi, Sree Kanthaswamy, Jesse Johnson, Wendy T. Garnica, Venkat S. Malladi and David Glenn Smith.(2011) The effect of SNP discovery method and sample size on estimation of population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta). Primates:  DOI: 10.1007/s10329-010-0232-4

[29] HELYAR, S. J., HEMMER-HANSEN, J., BEKKEVOLD, D., TAYLOR, M. I., OGDEN, R., LIMBORG, M. T., CARIANI, A., MAES, G. E., DIOPERE, E., CARVALHO, G. R. and NIELSEN, E. E. , Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources, no. doi: 10.1111/j.1755-0998.2010.02943.x

BARDIN, JACQUI A. SHYKOFF and TATIANA GIRAUD (in press) Temporal isolation explains host-related genetic differentiation in a group of widespread mycoparasitic fungi. Molecular Ecology.

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[35] HORNE, J. B., MOMIGLIANO, P., WELCH, D. J., NEWMAN, S. J. and Van HERWERDEN, L. (2011), Limited ecological population connectivity suggests low demands on self-recruitment in a tropical inshore marine fish (Eleutheronema tetradactylum: Polynemidae). Molecular Ecology, 20: no. doi: 10.1111/j.1365-294X.2011.05097.x

[36] Simwami SP, Khayhan K, Henk DA, Aanensen DM, Boekhout T, et al. 2011 Low Diversity Cryptococcus neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin. PLoS Pathog7(4): e1001343. doi:10.1371/journal.ppat.1001343

[37] CRISCIONE, C. D., VILAS, R., PANIAGUA, E. and BLOUIN, M. S. (2011), More than meets the eye: detecting cryptic microgeographic population structure in a parasite with a complex life cycle. Molecular Ecology, 20: no. doi: 10.1111/j.1365-294X.2011.05113.x

[38] A. Mercier, D. Ajzenberg, S.Devillard, M.P. Demar, B. de Thoisy, H. Bonnabau, F. Collinet, R. Boukhari, D. Blanchet, S. Simon, B. Carme, M.-L. Dardé (in press) Human impact on genetic diversity of Toxoplasma gondii: Example of the anthropized environment from French Guiana.
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