- To cite adegenet:
+

To cite adegenet:

Jombart T.2008)adegenet: a R package for the - multivariate - analysis of genetic markers. BioinformaticsBioinformatics24: 1403-1405. doi: 10.1093/bioinformatics/btn129 @@ -41,17 +40,16 @@ style="color: rgb(0, 153, 0);">to a free pdf]

Jombart T. and Ahmed I. - (2011) - adegenet - 1.3-1: new tools for - the - analysis of genome-wide SNP data. 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]

@@ -60,74 +58,69 @@ Related publications:

- a review of applications of multivariate analyses to - genetic markers - data:
+ 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. [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 + + 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 [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), +

- 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: + 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 + 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]
+ Excoffier on F1000]

@@ -135,111 +128,90 @@ adegenet:

[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.
+ 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 GenomicsMacaca mulatta). BMC + Genomics9: 256.
-

-
+

[3] 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 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 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.
+ 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:
+ 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.
+ 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.
+ (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.
+ 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.
+ 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.
+ 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: + 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
+ 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, @@ -255,52 +227,45 @@ GREGORY TURNER and PAUL J. WILSON - (2009) - Climate change induced hybridization in flying squirrels. - Global Change Biology 16: 113-121.
+ (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: 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: + 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
+ 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

[17] Francisco Balao, @@ -312,28 +277,23 @@ class="surname">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
+ evolution of polyploid races of the Iberian carnation Dianthus broteri (Caryophyllaceae).New Phytologist. + Doi:10.1111/j.1469-8137.2010.03280.x

[18] 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
+ 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.
+ 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, @@ -355,21 +315,17 @@ style="white-space: nowrap;">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
+ 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 + class="citation_article_title">Insights into the Genetic + History of French Cattle from Dense SNP Data on 47 Worldwide Breeds. PLoS ONE5(9): @@ -378,1046 +334,793 @@ class="citation_author">a

[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 + 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]
+ 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
+ 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. + 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 Van Dyck H, + 2010 Population Genetic - Differences along a - Latitudinal Cline between Original and Recently Colonized - Habitat in a - Butterfly. PLoS ONE5(11): 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
+ 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: + 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. [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/adegenet -r 1070 From noreply at r-forge.r-project.org Fri Feb 8 19:05:08 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 8 Feb 2013 19:05:08 +0100 (CET) Subject: [adegenet-commits] r1071 - pkg/R Message-ID: <20130208180508.DFEA91847C9@r-forge.r-project.org> Author: jombart Date: 2013-02-08 19:05:08 +0100 (Fri, 08 Feb 2013) New Revision: 1071 Modified: pkg/R/import.R Log: fixed an issue in fasta2genlight when there was no SNPs Modified: pkg/R/import.R =================================================================== --- pkg/R/import.R 2013-02-06 10:51:39 UTC (rev 1070) +++ pkg/R/import.R 2013-02-08 18:05:08 UTC (rev 1071) @@ -1111,6 +1111,10 @@ ## POOL <- lapply(POOL, setdiff, "-") nb.alleles <- sapply(POOL, length) snp.posi <- nb.alleles==2 + if(all(!snp.posi)){ + warning("No polymorphism in the alignment - returning empty object") + return(new("genlight")) + } sec.all <- unlist(lapply(POOL[snp.posi], function(e) e[2])) From noreply at r-forge.r-project.org Thu Feb 14 15:32:59 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 14 Feb 2013 15:32:59 +0100 (CET) Subject: [adegenet-commits] r1072 - www Message-ID: <20130214143259.5B6D6183912@r-forge.r-project.org> Author: jombart Date: 2013-02-14 15:32:58 +0100 (Thu, 14 Feb 2013) New Revision: 1072 Modified: www/literature.html Log: +1ref Modified: www/literature.html =================================================================== --- www/literature.html 2013-02-08 18:05:08 UTC (rev 1071) +++ www/literature.html 2013-02-14 14:32:58 UTC (rev 1072) @@ -50,6 +50,7 @@ href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link to + the bublisher's website]

@@ -69,10 +70,12 @@ to the journal's pdf - free + abstract]

- the paper presenting the spatial + principal component analysis (sPCA, function spca), global and @@ -80,6 +83,7 @@ 0, 0);">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: @@ -88,6 +92,7 @@ on the journal's website - free + abstract]

@@ -98,6 +103,7 @@ style="font-family: monospace; color: rgb(255, 0, 0);">seqTrack), and + simulations of genealoies of haplotypes (haploGen):
Jombart T, Eggo RM, Dodd PJ, Balloux F (2010) @@ -108,6 +114,7 @@ - the paper introducing the Discriminant Analysis + of Principal Components (DAPC, functions find.clusters @@ -129,16 +136,16 @@
[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.
+ rgb(0, 0, 0);">genetic 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.
@@ -155,13 +162,16 @@ [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.

@@ -202,6 +212,7 @@ 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.
@@ -346,11 +357,13 @@ 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
@@ -361,15 +374,18 @@ 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
@@ -387,6 +403,7 @@ population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta). Primates: + DOI: 10.1007/s10329-010-0232-4

@@ -441,6 +458,7 @@ 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

@@ -453,6 +471,7 @@ class="citation_date">2011 Low Diversity Cryptococcus + neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin. PLoS @@ -471,6 +490,7 @@ class="hit">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.
@@ -492,6 +512,7 @@ Jindřich ; Plačková, Ivana ;Mráz, Patrik (2001) Allozyme Variation in Diploid, Polyploid and Mixed-Ploidy Populations of the Pilosella + alpicola Group (Asteraceae): Relation to Morphology, Origin of Polyploids and Breeding System . Folia Geobotanica: 1-24. Doi: 10.1007/s12224-011-9102-0
@@ -652,9 +673,8 @@ [67] R.M. Fewster, S.D. Miller, and J. Ritchie (2011) DNA profiling – a management tool for rat eradication. Pages 426-431 In: Veitch, C. R.; Clout, M. N. and Towns, D. R. (eds.). Island - invasives: eradication and management. 426 Gland, - Switzerland.
+ style="font-style: italic;">Island invasives: eradication and + management. 426 Gland, Switzerland.

[68] Monteil, C. L., Guilbaud, C., Glaux, C., Lafolie, F., Soubeyrand, S. and Morris, C. E. (2011), Emigration of the plant @@ -702,6 +722,7 @@ genetic signal of current connectivity among populations. GENETICA - Online first. DOI: + 10.1007/s10709-012-9640-2

[76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright, @@ -1150,7 +1171,13 @@ Kolfschoten, Michael Hofreiter and Klaas Vrieling (2013) Losing Ground: Past history and future fate of Arctic small mammals in a changing climate. Global Change Biology. doi: - 10.1111/gcb.12157

+ 10.1111/gcb.12157
+

[152] Koen EL, Bowman J, Garroway CJ, Wilson PJ (2013) The + Sensitivity of Genetic Connectivity Measures to Unsampled and + Under-Sampled Sites. PLoS ONE 8(2): e56204. + doi:10.1371/journal.pone.0056204
+

From noreply at r-forge.r-project.org Mon Feb 18 16:56:00 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 18 Feb 2013 16:56:00 +0100 (CET) Subject: [adegenet-commits] r1073 - www Message-ID: <20130218155600.C1A8A183F3C@r-forge.r-project.org> Author: jombart Date: 2013-02-18 16:56:00 +0100 (Mon, 18 Feb 2013) New Revision: 1073 Modified: www/literature.html Log: +1 ref Modified: www/literature.html =================================================================== --- www/literature.html 2013-02-14 14:32:58 UTC (rev 1072) +++ www/literature.html 2013-02-18 15:56:00 UTC (rev 1073) @@ -51,6 +51,7 @@ to + the bublisher's website]

@@ -71,11 +72,13 @@ href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy2008130a.html">free + abstract]

- the paper presenting the spatial + principal component analysis (sPCA, function spca), global and @@ -84,6 +87,7 @@ monospace; color: rgb(255, 0, 0);">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: @@ -93,6 +97,7 @@ href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy200834a.html">free + abstract]

@@ -104,6 +109,7 @@ and + simulations of genealoies of haplotypes (haploGen):
Jombart T, Eggo RM, Dodd PJ, Balloux F (2010) @@ -115,6 +121,7 @@ Analysis + of Principal Components (DAPC, functions find.clusters @@ -146,6 +153,7 @@ identification in the rhesus macaque (Macaca mulatta). BMC + Genomics9: 256.
@@ -163,6 +171,7 @@ AI (2009). Hybridization between escaped domestic and wild American mink (Neovison vison). + Molecular Ecology 18: 1175-1186.

@@ -170,8 +179,10 @@ Age-specific effect of heterozygosity on survival in alpine marmots, Marmota + marmota.Molecular + Ecology 18: 1491-1503.

@@ -213,6 +224,7 @@ (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.
@@ -358,12 +370,14 @@ 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
@@ -375,10 +389,12 @@ studies and perspectives. Collect. + Vol. Sci. Pap. ICCAT, 65(3): 988-995

[26] Vandewoestijne + S, Van Dyck H, 2010 Population Genetic @@ -386,6 +402,7 @@ Recently Colonized Habitat in a Butterfly. PLoS + ONE5(11): e13810. doi:10.1371/journal.pone.0013810
@@ -404,6 +421,7 @@ (Macaca mulatta). Primates: + DOI: 10.1007/s10329-010-0232-4

@@ -459,6 +477,7 @@ 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

@@ -472,6 +491,7 @@ class="citation_article_title">Low Diversity Cryptococcus + neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin. PLoS @@ -491,6 +511,7 @@ 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.
@@ -513,6 +534,7 @@ Allozyme Variation in Diploid, Polyploid and Mixed-Ploidy Populations of the Pilosella + alpicola Group (Asteraceae): Relation to Morphology, Origin of Polyploids and Breeding System . Folia Geobotanica: 1-24. Doi: 10.1007/s12224-011-9102-0
@@ -723,6 +745,7 @@ GENETICA - Online first. DOI: + 10.1007/s10709-012-9640-2

[76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright, @@ -1178,8 +1201,13 @@ Under-Sampled Sites. PLoS ONE 8(2): e56204. doi:10.1371/journal.pone.0056204

+ [153]* Valerie De Waele, Frederik Van den Broeck, Tine Huyse, + Guy McGrath, Isabella Higgins, Niko Speybroeck, Marco Berzano, + Pat Raleigh, Grace M. Mulcahy and Thomas M. Murphy (2013) + Panmictic structure of the Cryptosporidium parvum population in + Irish calves: Influence of prevalence and host movement. AEM. + doi: 10.1128/AEM.03613-12

-

* adegenet not or wrongly cited, but actually used in the paper.
From noreply at r-forge.r-project.org Tue Feb 19 12:49:32 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 19 Feb 2013 12:49:32 +0100 (CET) Subject: [adegenet-commits] r1074 - www Message-ID: <20130219114933.15E54184C6A@r-forge.r-project.org> Author: jombart Date: 2013-02-19 12:49:32 +0100 (Tue, 19 Feb 2013) New Revision: 1074 Modified: www/literature.html Log: +1ref Modified: www/literature.html =================================================================== --- www/literature.html 2013-02-18 15:56:00 UTC (rev 1073) +++ www/literature.html 2013-02-19 11:49:32 UTC (rev 1074) @@ -52,6 +52,7 @@ + the bublisher's website]

@@ -73,12 +74,14 @@ + abstract]

- the paper presenting the spatial + principal component analysis (sPCA, function spca), global and @@ -88,6 +91,7 @@ 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: @@ -98,6 +102,7 @@ + abstract]

@@ -110,6 +115,7 @@ + simulations of genealoies of haplotypes (haploGen):
Jombart T, Eggo RM, Dodd PJ, Balloux F (2010) @@ -122,6 +128,7 @@ + of Principal Components (DAPC, functions find.clusters @@ -154,6 +161,7 @@ class="citation-abbreviation">BMC + Genomics9: 256.
@@ -172,6 +180,7 @@ American mink (Neovison vison). + Molecular Ecology 18: 1175-1186.

@@ -180,9 +189,11 @@ marmots, Marmota + marmota.Molecular + Ecology 18: 1491-1503.

@@ -225,6 +236,7 @@ hybridization between native and introduced lineages of Phragmites + australis in North America. Biological Invasions. doi: 10.1007/s10530-010-9699-6.
@@ -371,6 +383,7 @@ letters.">Biol Lett.2010 + Oct 6. [Epub ahead of print]

[24] SANTOS, H., BURBAN, C., ROUSSELET, J., @@ -378,6 +391,7 @@ 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
@@ -390,11 +404,13 @@ + Vol. Sci. Pap. ICCAT, 65(3): 988-995

[26] Vandewoestijne + S, Van Dyck H, 2010 Population Genetic @@ -403,6 +419,7 @@ style="font-style: italic;" class="citation_journal_title">PLoS + ONE5(11): e13810. doi:10.1371/journal.pone.0013810
@@ -422,6 +439,7 @@ + DOI: 10.1007/s10329-010-0232-4

@@ -478,6 +496,7 @@ self-recruitment in a tropical inshore marine fish (Eleutheronema + tetradactylum: Polynemidae). Molecular Ecology, 20: no. doi: 10.1111/j.1365-294X.2011.05097.x

@@ -492,6 +511,7 @@ + neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin. PLoS @@ -512,6 +532,7 @@ Carme, M.-L. Dardé (in + press) Human impact on genetic diversity of Toxoplasma gondii: Example of the anthropized environment from French Guiana.
@@ -535,6 +556,7 @@ Populations of the Pilosella + alpicola Group (Asteraceae): Relation to Morphology, Origin of Polyploids and Breeding System . Folia Geobotanica: 1-24. Doi: 10.1007/s12224-011-9102-0
@@ -746,6 +768,7 @@ + 10.1007/s10709-012-9640-2

[76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright, @@ -1208,6 +1231,12 @@ Irish calves: Influence of prevalence and host movement. AEM. doi: 10.1128/AEM.03613-12

+ [154] LUMLEY, L. M. and CUSSON, M. (2013), Linking adaptation, + delimitation of evolutionarily significant units (ESUs), and + gene function: a case study using hemlock looper ecotypes. + Systematic Entomology. doi: 10.1111/syen.12005
+
+

* adegenet not or wrongly cited, but actually used in the paper.
From noreply at r-forge.r-project.org Thu Feb 21 19:28:37 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 21 Feb 2013 19:28:37 +0100 (CET) Subject: [adegenet-commits] r1075 - www Message-ID: <20130221182837.E844318094B@r-forge.r-project.org> Author: jombart Date: 2013-02-21 19:28:37 +0100 (Thu, 21 Feb 2013) New Revision: 1075 Modified: www/literature.html Log: +1ref Modified: www/literature.html =================================================================== --- www/literature.html 2013-02-19 11:49:32 UTC (rev 1074) +++ www/literature.html 2013-02-21 18:28:37 UTC (rev 1075) @@ -53,6 +53,7 @@ + the bublisher's website]

@@ -75,6 +76,7 @@ + abstract]

- the paper presenting the spatial @@ -82,6 +84,7 @@ + principal component analysis (sPCA, function spca), global and @@ -92,6 +95,7 @@ + cryptic spatial patterns in genetic variability by a new multivariate method. Heredity 101: 92-103. doi: @@ -103,6 +107,7 @@ + abstract]

@@ -116,6 +121,7 @@ + simulations of genealoies of haplotypes (haploGen):
Jombart T, Eggo RM, Dodd PJ, Balloux F (2010) @@ -129,6 +135,7 @@ + of Principal Components (DAPC, functions find.clusters @@ -162,6 +169,7 @@ + Genomics9: 256.
@@ -181,6 +189,7 @@ + Molecular Ecology 18: 1175-1186.

@@ -190,10 +199,12 @@ + marmota.Molecular + Ecology 18: 1491-1503.

@@ -237,6 +248,7 @@ + australis in North America. Biological Invasions. doi: 10.1007/s10530-010-9699-6.
@@ -384,6 +396,7 @@ + Oct 6. [Epub ahead of print]

[24] SANTOS, H., BURBAN, C., ROUSSELET, J., @@ -392,6 +405,7 @@ + pityocampa, Lepidoptera, Notodontidae). Journal of Evolutionary Biology, no. doi: 10.1111/j.1420-9101.2010.02147.x
@@ -405,12 +419,14 @@ + Vol. Sci. Pap. ICCAT, 65(3): 988-995

[26] Vandewoestijne + S, Van Dyck H, 2010 Population Genetic @@ -420,6 +436,7 @@ + ONE5(11): e13810. doi:10.1371/journal.pone.0013810
@@ -440,6 +457,7 @@ + DOI: 10.1007/s10329-010-0232-4

@@ -497,6 +515,7 @@ + tetradactylum: Polynemidae). Molecular Ecology, 20: no. doi: 10.1111/j.1365-294X.2011.05097.x

@@ -512,6 +531,7 @@ + neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin. PLoS @@ -533,6 +553,7 @@ + press) Human impact on genetic diversity of Toxoplasma gondii: Example of the anthropized environment from French Guiana.
@@ -557,6 +578,7 @@ + alpicola Group (Asteraceae): Relation to Morphology, Origin of Polyploids and Breeding System . Folia Geobotanica: 1-24. Doi: 10.1007/s12224-011-9102-0
@@ -769,6 +791,7 @@ + 10.1007/s10709-012-9640-2

[76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright, @@ -1236,7 +1259,12 @@ gene function: a case study using hemlock looper ecotypes. Systematic Entomology. doi: 10.1111/syen.12005

+ [155] Pierpaolo Maisano Delser, Silvia Fuselli (2013) Human loci + involved in drug biotransformation: worldwide genetic variation, + population structure, and pharmacogenetic implications. Human + Genetics. doi:10.1007/s00439-013-1268-5

+

* adegenet not or wrongly cited, but actually used in the paper.