[adegenet-commits] r980 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 19 14:35:33 CET 2011
Author: jombart
Date: 2011-12-19 14:35:32 +0100 (Mon, 19 Dec 2011)
New Revision: 980
Modified:
www/literature.html
Log:
+2ref
Modified: www/literature.html
===================================================================
--- www/literature.html 2011-12-15 11:04:13 UTC (rev 979)
+++ www/literature.html 2011-12-19 13:35:32 UTC (rev 980)
@@ -50,7 +50,9 @@
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>
+to
+the
+bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
<img style="width: 80px; height: 37px;" alt="" src="images/new.png"><br
style="color: rgb(0, 153, 0);">
<br>
@@ -68,30 +70,29 @@
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>),
-
+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>
+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
+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>
@@ -99,7 +100,6 @@
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>),
@@ -111,25 +111,27 @@
of
genealoies
-of haplotypes (<span
- style="font-family: monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
+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>
+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>):<img
style="width: 80px; height: 37px;" alt="" src="images/new.png"><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>
@@ -143,9 +145,7 @@
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,
@@ -159,7 +159,6 @@
[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
@@ -215,8 +214,8 @@
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>
+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
@@ -228,15 +227,12 @@
[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
@@ -252,7 +248,6 @@
<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
@@ -277,8 +272,8 @@
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>
+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
@@ -308,8 +303,8 @@
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
+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
@@ -331,7 +326,6 @@
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
@@ -339,7 +333,9 @@
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
+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>
@@ -365,7 +361,9 @@
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
+Lepidoptera,
+Notodontidae).
+<span style="font-style: italic;">Journal
of Evolutionary Biology</span>, no.
doi: 10.1111/j.1420-9101.2010.02147.x<br>
</p>
@@ -379,7 +377,9 @@
<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
+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
@@ -389,7 +389,9 @@
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.
+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
@@ -424,7 +426,6 @@
CASTONGUAY, M., RIEMANN, L., AARESTRUP, K., MUNK, P., SPARHOLT, H.,
HANEL, R. and BERNATCHEZ, L. , All roads lead to home: panmixia of
European eel in the Sargasso Sea. <span style="font-style: italic;">Molecular
-
Ecology</span>. doi: 10.1111/j.1365-294X.2011.05011.x<br>
</p>
<p class="intro"> <span class="citation_author">[33] Balmer O, </span>
@@ -433,7 +434,9 @@
class="citation_author">Caccone A, </span> <span
class="citation_date">2011</span> <span class="citation_article_title">Phylogeography
-and Taxonomy of <i>Trypanosoma brucei</i>. </span> <span
+and
+Taxonomy
+of <i>Trypanosoma brucei</i>. </span> <span
class="citation_journal_title">PLoS Negl Trop Dis</span><span
class="citation_issue"> 5(2):</span> <span class="citation_start_page">e961.</span>
<span class="citation_doi">doi:10.1371/journal.pntd.0000961<br>
@@ -441,7 +444,6 @@
<p class="intro">[34] THIERRY, M., BECKER, N., HAJRI, A., REYNAUD, B.,
LETT, J.-M. and DELATTE, H. (2011), Symbiont diversity and non-random
hybridization among indigenous (Ms) and invasive (B) biotypes of <em>Bemisia
-
tabaci</em>. Molecular Ecology, 20: no.
doi: 10.1111/j.1365-294X.2011.05087.x<br>
</p>
@@ -478,7 +480,9 @@
style="font-style: italic;">in press</span>) Human impact on genetic
diversity of <span style="font-style: italic;">Toxoplasma gondii</span>:
-Example of the anthropized environment from French Guiana. <br>
+Example
+of
+the anthropized environment from French Guiana. <br>
Infection, Genetics and Evolution.<br>
</p>
<p class="intro">[39] MONTANO, V., FERRI, G., MARCARI, V., BATINI, C.,
@@ -508,7 +512,9 @@
HUGHES, J. M. (2011), Cytonuclear evidence for hybridogenetic
reproduction in natural populations of the Australian carp gudgeon (<em>Hypseleotris</em>:
-Eleotridae). Molecular Ecology.
+Eleotridae).
+Molecular
+Ecology.
doi: 10.1111/j.1365-294X.2011.05206.x<br>
</p>
<p class="intro">[44] Kinziger, A. P., Nakamoto, R. J., Anderson, E. C.
@@ -560,7 +566,9 @@
and overfishing on the population genetic structure of the European
spiny lobster (<span style="font-style: italic;">Palinurus elephas</span>).
-Biological Journal of the Linnean Society. doi:
+Biological
+Journal
+of the Linnean Society. doi:
10.1111/j.1095-8312.2011.01728.x<br>
</p>
[52]* Farjadian S, Sazzini M, Tofanelli S, Castrì L, Taglioli L,
@@ -629,11 +637,22 @@
escapees. AQUACULTURE ENVIRONMENT INTERACTIONS Vol. 2: 75–86, 2011 doi:
10.3354/aei00032<br>
<br>
+[65] Montanari, S. R., van Herwerden, L., Pratchett, M. S., Hobbs,
+J.-P. A. and Fugedi, A. (2011), Reef fish hybridization: lessons learnt
+from butterflyfishes (genus Chaetodon). Ecology and Evolution. doi:
+10.1002/ece3.83<br>
<br>
+[66] Andrés García-Lor, François Luro, Luis
+Navarro and Patrick Ollitrault (2011). Comparative use of InDel
+and SSR markers in deciphering the interspecific structure of
+cultivated citrus genetic diversity: a perspective for genetic
+association studies. MOLECULAR GENETICS AND GENOMICS DOI:
+10.1007/s00438-011-0658-4<br>
<br>
<br>
<br>
<br>
+<br>
<p class="intro">* adegenet not or wrongly cited, but actually used in
the paper. <br>
</p>
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