[adegenet-commits] r1051 - www

Tue Nov 13 11:43:46 CET 2012

Author: jombart
Date: 2012-11-13 11:43:45 +0100 (Tue, 13 Nov 2012)
New Revision: 1051

Modified:
   www/literature.html
Log:
+2 ref

Modified: www/literature.html
===================================================================

--- www/literature.html	2012-11-13 10:18:01 UTC (rev 1050)
+++ www/literature.html	2012-11-13 10:43:45 UTC (rev 1051)
@@ -1,10 +1,10 @@
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <html>
-<head>
-  <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
-  <title>documentation</title>
-  <script type="text/javascript">
+  <head>
+    <meta content="text/html; charset=ISO-8859-1"
+      http-equiv="content-type">
+    <title>documentation</title>
+    <script type="text/javascript">
 
   var _gaq = _gaq || [];
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@@ -17,968 +17,1337 @@
   })();
 
   </script>
-  <meta http-equiv="content-type"
- content="text/html; charset=ISO-8859-1">
-</head>
-<body>
-<br>
-<br>
-<br>
-<div style="margin-left: 40px;"><span
- style="text-decoration: underline;">To cite adegenet:</span><br>
-<br>
-<span style="color: rgb(0, 153, 0);">Jombart T</span><span
- style="color: rgb(0, 153, 0);">.</span><span
- style="color: rgb(0, 153, 0);"> (</span><span
- style="font-style: italic; color: rgb(0, 153, 0);"></span><span
- style="color: rgb(0, 153, 0);">2008)</span><span
- style="font-weight: bold; color: rgb(0, 153, 0);"> </span><span
- style="color: rgb(0, 153, 0);">adegenet: a R package for the
-multivariate analysis of genetic markers. </span><span
- style="font-style: italic; color: rgb(0, 153, 0);">Bioinformatics</span><span
- style="color: rgb(0, 153, 0);"> </span><span
- style="font-weight: bold; color: rgb(0, 153, 0);">24</span><span
- style="color: rgb(0, 153, 0);">: 1403-1405. doi:
-10.1093/bioinformatics/btn129 [</span><a style="color: rgb(0, 153, 0);"
- href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129?ijkey=6sqx5BTXCdYtBZz&keytype=ref">link</a><span
- style="color: rgb(0, 153, 0);"> to a free pdf]</span><br>
-<br>
-<span style="color: rgb(0, 153, 0);">Jombart T. and Ahmed I. (2011) </span><span
- style="font-style: italic; color: rgb(0, 153, 0);">adegenet 1.3-1</span><span
- style="color: rgb(0, 153, 0);">: new tools for the analysis of
-genome-wide SNP data. </span><span
- style="font-style: italic; color: rgb(0, 153, 0);">Bioinformatics</span><span
- style="color: rgb(0, 153, 0);">. doi: 10.1093/bioinformatics/btr521 [</span><a
- style="color: rgb(0, 153, 0);"
- href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
-to
-the
-bublisher's
-website</a><span style="color: rgb(0, 153, 0);">]</span> <br
- style="color: rgb(0, 153, 0);">
-<br>
-<br style="color: rgb(0, 153, 0);">
-<br>
-<span style="text-decoration: underline;">Related publications:<br>
-<br style="text-decoration: underline;">
-</span>- a review of applications of multivariate analyses to genetic
-markers data:<br>
-<b>Jombart T</b>, Pontier D, Dufour AB. (2009) <span
- style="font-style: italic;"></span> Genetic markers in the playground
-of multivariate analysis. <span style="font-style: italic;">Heredity </span><span
- style="font-weight: bold;">102</span>: 330-341.
-doi:10.1038/hdy.2008.130<span style="font-style: italic;">. </span>[<a
- href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy2008130a.pdf">link</a>
-to the journal's pdf - <a target="_new"
- href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy2008130a.html">free
-abstract</a>]<br>
-<br>
-- the paper presenting the <span style="font-style: italic;">spatial
-principal component analysis</span> (<span style="font-style: italic;">sPCA</span>,
-function
-<span style="font-family: monospace; color: rgb(255, 0, 0);">spca</span>),
-
-global
-and
-local
-tests
-(<span style="font-family: monospace; color: rgb(255, 0, 0);">global.rtest</span>
-and <span style="font-family: monospace; color: rgb(255, 0, 0);">local.rtest</span>):<br>
-<b>Jombart T, </b>Devillard S, Dufour AB, Pontier D<b> </b>(2008)<b> </b>Revealing
-
-cryptic
-spatial
-patterns
-in
-genetic variability by a new multivariate
-method.  <span style="font-style: italic;">Heredity</span> <span
- style="font-weight: bold;">101</span>: 92-103. doi:
-10.1038/hdy.2008.34 [<a
- href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy200834a.pdf">link</a>
-on the journal's website - <a target="_new"
- href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy200834a.html">free
-abstract</a>]<br>
-</div>
-<br>
-<div style="margin-left: 40px;"><span
- style="font-family: monospace; font-weight: bold;"></span><span
- style="font-family: monospace; font-weight: bold;"></span>- the paper
-presenting the <span style="font-style: italic;">SeqTrack </span>algorithm
-(<span style="font-family: monospace; color: rgb(255, 0, 0);">seqTrack</span>),
-and
-simulations
-of
-genealoies
-of
-haplotypes
-(<span style="font-family: monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
-<b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010) Reconstructing
-disease outbreaks from genetic data: a graph approach. <span
- style="font-style: italic;">Heredity</span>. Doi: 10.1038/hdy.2010.78<br>
-<br>
-- the paper introducing the <span style="font-style: italic;">Discriminant
-Analysis
-of
-Principal
-Components</span> (<span style="font-style: italic;">DAPC</span>,
-functions <span style="font-family: monospace;"><span
- style="color: rgb(255, 0, 0);">find.clusters</span> </span>and <span
- style="font-family: monospace; color: rgb(255, 0, 0);">dapc</span>):<br>
-<b>Jombart T</b>, Devillard S and Balloux F <b> </b>(2010)
-Discriminant analysis of principal components: a new method for the
-analysis of genetically structured populations. <i>BMC Genetics</i> <strong>11</strong><strong>:</strong>94.
-<span>doi:10.1186/1471-2156-11-94</span> [<a href="files/DAPCpaper.pdf">free
-pdf</a>] [<a href="http://www.biomedcentral.com/1471-2156/11/94">free
-html version</a>] [<a href="reviewDAPC.html">evaluation by Laurent
-Excoffier on F1000</a>] <br>
-<br>
-<br>
-<br>
-<span style="text-decoration: underline;">Publications citing adegenet:</span><br
- style="text-decoration: underline;">
-<br>
-[1] Cohas A, Yoccoz NG, Bonenfant C, Goossens B, Genton C, Galan M,
-Kempenaers B, Allainé D (2007) The<span
- style="color: rgb(0, 0, 0);"> genetic similarity between pair members
-influences the frequency of extrapair paternity in alpine marmots</span>.
-<i>Animal Behaviour</i><i> </i><span style="font-weight: bold;">76</span>:
-87-95.<br>
-<br>
-[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 (<em>Macaca mulatta</em>). <span
- class="citation-abbreviation"><span style="font-style: italic;">BMC
-Genomics</span></span><span class="citation-publication-date"> </span><span
- style="font-weight: bold;" class="citation-volume">9</span><span
- class="citation-issue"></span>: 256.<br>
-<div><span class="citation-flpages"><br>
-[3] </span>Kanthaswamy S, Satkoski J, George D, Kou A, Erickson BJ,
-Smith DG. (2008). Interspecies hybridization and the stratification of
-nuclear genetic variation of rhesus (<span style="font-style: italic;">Macaca
-mulatta</span>) and long-tailed macaques (<span
- style="font-style: italic;">Macaca </span><span
- style="font-style: italic;">fascicularis</span>). <span
- style="font-style: italic;">Int J Primatol</span> <span
- style="font-weight: bold;">29</span>: 1295-1311.<br>
-<br>
-[4] Kidd, AG, Bowman J, Lesbarrères D, Schulte-Hostedde AI
-(2009). Hybridization between escaped domestic and wild American mink (<span
- style="font-style: italic;">Neovison vison</span>). <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 1175-1186.<br>
-<br>
-[5] Cohas E, Bonenfant C, Kempaners B, Allainé D (2009).
-Age-specific effect of heterozygosity on survival in alpine marmots, <span
- class="i"><span style="font-style: italic;">Marmota marmota</span>.</span><span
- style="font-style: italic;"> Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 1491-1503.<br>
-<br>
-[6] O'Brien J, Devillard S, Say L, Vanthomme A, Léger F, Ruette
-S, Pontier D (2009). Preserving genetic integrity in a hybridising
-world:<br>
-are European Wildcats (<span style="font-style: italic;">Felis
-silvestris silvestris</span>) in eastern France distinct from sympatric
-feral domestic cats? <span style="font-style: italic;">Biodivers
-Conserv</span> <span style="font-weight: bold;">18</span>: 2351-2360.<br>
-<br>
-[7] Kanthaswamy S <span style="font-style: italic;">et al.</span>
-(2009). Canine Population Data Generated from a Multiplex STR Kit for
-Use in Forensic Casework. <span style="font-style: italic;">Journal of
-Forensic Sciences</span> <span style="font-weight: bold;">54</span>:
-829-840.<br>
-<br>
-[8] Lankau R A, Nuzzo V, Spyreas G, Davis A S (2009). Evolutionary
-limits ameliorate the negative impact of an invasive plant. <span
- style="font-style: italic;">Proceedings of the National Academy of
-Sciences</span> <span style="font-weight: bold;">106</span>:
-15362-15367.<br>
-<br>
-[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. <span
- style="font-style: italic;">Heredity</span> (advanced online) doi:
-10.1038/hdy.2009.164.<br>
-<br>
-[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.<span style="font-style: italic;"> Heredity</span> (advanced
-online) doi: 10.1038/hdy.2010.6.<br>
-<br>
-[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 <i>Phragmites australis</i> in North
-America. <span style="font-style: italic;">Biological Invasions</span>.
-doi:
-10.1007/s10530-010-9699-6.<br>
-<br>
-[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. <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 3980-3991<br>
-<br>
-[13] <span class="name"><span class="forenames">COLIN J.</span> <span
- class="surname">GARROWAY</span><sup><nobr></nobr></sup></span>, <span
- class="name"><span class="forenames">JEFF</span> <span class="surname">BOWMAN</span></span>,
-<span class="name"><span class="forenames">TARA J.</span> <span
- class="surname">CASCADEN</span></span>, <span class="name"><span
- class="forenames">GILLIAN L.</span> <span class="surname">HOLLOWAY</span></span>,
-<span class="name"><span class="forenames">CAROLYN G.</span> <span
- class="surname">MAHAN</span></span>, <span class="name"><span
- class="forenames">JAY R.</span> <span class="surname">MALCOLM</span></span>,
-<span class="name"><span class="forenames">MICHAEL A.</span> <span
- class="surname">STEELE</span><sup><nobr></nobr></sup></span>, <span
- class="name"><span class="forenames">GREGORY</span> <span
- class="surname">TURNER</span></span> and <span class="name"><span
- class="forenames">PAUL J.</span> <span class="surname">WILSON</span>
-(2009) </span>Climate change induced hybridization in flying
-squirrels. <span style="font-style: italic;">Global Change Biology</span>
-<span style="font-weight: bold;">16</span>: 113-121.<br>
-<br>
-[14] <span class="name"><span class="forenames">JOSSELIN</span> <span
- class="surname">MONTARRY</span></span>, <span class="name"><span
- class="forenames">DIDIER</span> <span class="surname">ANDRIVON</span>,</span>
-<span class="name"><span class="forenames">ISABELLE</span> <span
- class="surname">GLAIS</span></span>, <span class="name"><span
- class="forenames">ROSELYNE</span> <span class="surname">CORBIERE</span></span>,
-<span class="name"><span class="forenames">GLADYS</span> <span
- class="surname">MIALDEA</span></span> and <span class="name"><span
- class="forenames">FRANCOIS</span> <span class="surname">DELMOTTE
-(2010)</span></span> Microsatellite markers reveal two admixed genetic
-groups and an ongoing displacement within the French population of the
-invasive plant pathogen <span class="i"><span
- style="font-style: italic;">Phytophthora infestans</span>. <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">19</span>: <span
- style="text-decoration: underline;"></span></span>1965-1977<br>
-<br>
-[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 <i>Phaeomoniella chlamydospora. European
-Journal of Plant Pathology</i> Doi: 10.1007/s10658-010-9611-3<br>
-<br>
-[16] <span class="name"><span class="forenames">Michelle F.</span> <span
- class="surname">DiLeo</span></span>, <span class="name"><span
- class="forenames">Jeffrey R.</span> <span class="surname">Row</span></span>
-and <span class="name"><span class="forenames">Stephen C.</span> <span
- class="surname">Lougheed (2010)</span></span> Discordant patterns of
-population structure for two co-distributed snake species across a
-fragmented Ontario landscape. <span style="font-style: italic;">Diversity
-and
-Distributions.</span> Doi: <span class="doi">10.1111/j.1472-4642.2010.00667.x<br>
-<br>
-[17] </span><span class="name"><span class="forenames">Francisco</span>
-<span class="surname">Balao</span><sup><nobr></nobr></sup></span>, <span
- class="name"><span class="forenames">Luis M.</span> <span
- class="surname">Valente</span><sup><nobr></nobr></sup></span>, <span
- class="name"><span class="forenames">Pablo</span> <span
- class="surname">Vargas</span><sup><nobr></nobr></sup> </span>, <span
- class="name"><span class="forenames">Javier</span> <span
- class="surname">Herrera</span><sup><nobr></nobr></sup> </span> and <span
- class="name"><span class="forenames">Salvador</span> <span
- class="surname">Talavera</span> (2010)</span> Radiative evolution of
-polyploid races of the Iberian carnation <span class="i">Dianthus
-broteri</span> (Caryophyllaceae).<span class="name"> <sup
- style="font-style: italic;"><nobr></nobr></sup></span><span class="doi"><span
- style="font-style: italic;">New Phytologist. </span>Doi:</span><span
- class="doi"> 10.1111/j.1469-8137.2010.03280.x<br>
-<br>
-[18] </span>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. <span
- style="font-style: italic;">FUNGAL GENETICS AND BIOLOGY</span> ,
-47:  511-521<br>
-<span style="display: block;" id="records_chunks"><br>
-[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. <span
- style="font-style: italic;">Animal Genetics </span><span
- style="font-weight: bold;">41</span>: 47-63.<br>
- </span><span class="authors"><span style="white-space: nowrap;">[20]
-Denis
-Laloë</span>, <span style="white-space: nowrap;">Katayoun
-Moazami-Goudarzi</span>, <span style="white-space: nowrap;">Johannes
-A. Lenstra</span>, <span style="white-space: nowrap;">Paolo Ajmone
-Marsan</span>, <span style="white-space: nowrap;">Pedro Azor</span>, <span
- style="white-space: nowrap;">Roswitha Baumung</span>, <span
- style="white-space: nowrap;">Daniel G. Bradley</span>, <span
- style="white-space: nowrap;">Michael W. Bruford</span>, <span
- style="white-space: nowrap;">Javier Cañón</span>, <span
- style="white-space: nowrap;">Gaudenz Dolf</span>, <span
- style="white-space: nowrap;">Susana Dunner</span>, <span
- style="white-space: nowrap;">Georg Erhardt</span>, <span
- style="white-space: nowrap;">Godfrey Hewitt</span>, <span
- style="white-space: nowrap;">Juha Kantanen</span>, <span
- style="white-space: nowrap;">Gabriela Obexer-Ruff</span>, <span
- style="white-space: nowrap;">Ingrid Olsaker</span>, <span
- style="white-space: nowrap;">Clemen Rodellar</span>, <span
- style="white-space: nowrap;">Alessio Valentini</span>, <span
- style="white-space: nowrap;">Pamela Wiener</span> and <span
- style="white-space: nowrap;"> European Cattle Genetic Diversity
-Consortium and Econogene Consortium</span></span> (2010) <span
- class="title">Spatial Trends of Genetic Variation of Domestic
-Ruminants in Europe</span>. <span class="idnt"><em>Diversity</em> <b>2010</b>,
-<em>2</em>(6), 932-945; doi:10.3390/d2060932</span><br>
-<span style="display: block;" id="records_chunks"><br>
-</span><span class="citation_author">[21] Gautier M, </span> <span
- class="citation_author">Laloë D, </span> <span
- class="citation_author">Moazami-Goudarzi K, </span> <span
- class="citation_date">2010</span> <span class="citation_article_title">Insights
-
-into
-the
-Genetic
-History
-of French Cattle from Dense SNP Data on 47
-Worldwide Breeds. </span> <span style="font-style: italic;"
- class="citation_journal_title">PLoS ONE</span><span
- class="citation_issue"> <span style="font-weight: bold;">5(9)</span>:</span>
-<span class="citation_start_page">e13038.</span> <span
- class="citation_doi">doi:10.1371/journal.pone.0013038</span><span
- class="citation_author">a<br>
-<br>
-</span>[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 <em>Pseudomonas syringae</em> from its biogeography in
-headwaters of rivers in North America, Europe, and New Zealand. <span
- style="font-style: italic;">mBio </span>1(3):e00107-10.
-doi:10.1128/mBio.00107-10. <br>
-<p class="auth_list"><a title="Biology letters.">[23] </a>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. <a
- style="font-style: italic;" title="Biology letters.">Biol Lett.</a><span
- style="font-style: italic;"> </span>2010 Oct 6. [Epub ahead of print]<br>
-</p>
-<p class="auth_list">[24] SANTOS, H., BURBAN, C., ROUSSELET, J., ROSSI,
-J.-P., BRANCO, M. and KERDELHUÉ, C. , Incipient allochronic
-speciation in the pine processionary moth (<em>Thaumetopoea pityocampa</em>,
-Lepidoptera,
-Notodontidae).
-<span style="font-style: italic;">Journal
-of Evolutionary Biology</span>, no.
-doi: 10.1111/j.1420-9101.2010.02147.x<br>
-</p>
-<p class="auth_list">[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. <span
- style="font-style: italic;">Collect. Vol. Sci. Pap. ICCAT</span>,
-65(3): 988-995</p>
-<p class="intro">[26] <span class="citation_author">Vandewoestijne S, </span>
-<span class="citation_author">Van Dyck H, </span> <span
- class="citation_date">2010</span> <span class="citation_article_title">Population
-
-Genetic
-Differences
-along
-a
-Latitudinal Cline between Original and
-Recently Colonized Habitat in a Butterfly. </span> <span
- style="font-style: italic;" class="citation_journal_title">PLoS ONE</span><span
- class="citation_issue"> 5(11):</span> <span
- class="citation_start_page">e13810.</span> <span class="citation_doi">doi:10.1371/journal.pone.0013810<br>
-</span></p>
-<p class="intro">[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. <span style="font-style: italic;">Journal
-of
-Applied
-Entomology</span>, no.
-doi: 10.1111/j.1439-0418.2010.01593.x<br>
-</p>
-<p class="authors">[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 (<i>Macaca mulatta</i>). <span
- style="font-style: italic;">Primates:  </span><span class="doi"><span
- class="label">DOI:</span> <span class="value">10.1007/s10329-010-0232-4<br>
-</span></span></p>
-<p class="auth_list">[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. <span style="font-style: italic;">Molecular Ecology
-Resources</span>, no. doi: 10.1111/j.1755-0998.2010.02943.x<br>
-</p>
-<p class="auth_list">[30] LEVENTE KISS,ALEXANDRA PINTYE,GABOR M.
-KOVACS, TUNDE JANKOVICS, MICHAEL C. FONTAINE, NICK HARVEY, XIANGMING
-XU, PHILIPPE C. NICOT, MARC<br>
-BARDIN, JACQUI A. SHYKOFF and TATIANA GIRAUD (<span
- style="font-style: italic;">in press</span>) Temporal isolation
-explains host-related genetic differentiation in a group of widespread
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To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1051
