Plant Life In Water
- Aquatic Botanist Yu Ito's Home Page -


-MISCELLANEOUS-

[Sponsors]

  • School of Science, The University of Tokyo [東京大学 大学院 理学系研究科] (JP: 2006-2010)

  • Inoue Foundation for Science [井上科学振興財団] (JP: 2008)

  • European Weed Research Society (EU: 2009)

  • Hungarian Scholarship Board (HU: 2010-2011)

  • Yamada Science Foundation [山田科学振興財団] (JP: 2011-2012)

  • Scandinavia-Japan Sasakawa Foundation [スカンジナビア･ニッポン ササカワ財団] (SW: 2012)

  • Royal Society of New Zealand (NZ: 2013-2014)

  • Chinese Academy of Science [中国科学院] (CN: 2015-2017)

  • Xishuangbanna Tropical Botanical Garden [シーサンバンナ熱帯植物園] (CN: 2015-2017)

[Colleagues]

  • Dr. Norio Tanaka (JP: 2004-): Tsukuba Botanical Garden

  • Dr. Jin Murata (JP: 2006-): Botanical Gardens, The University of Tokyo

  • Dr. Tetsuo Ohi-Toma (JP: 2006-): Botanical Gardens, The University of Tokyo

  • Dr. Nobuyuki Tanaka (JP: 2007-): Tsukuba Botanical Garden

  • Dr. Surrey W. L. Jacobs (AU: 2007-): Sydney Botanical Garden

  • Dr. Anna V. Skriptsova (RU: 2008-): Russian Academy of Sciences

  • Dr. Changkyun Kim (KR: 2010-): Ajou University

  • Dr. Attila Mesterhagy (HU: 2010-): University of West Hungary

  • Dr. Pablo Garcia-Murillo (SP: 2011-): Universidad de Sevilla

  • Dr. J. Hugo Cota-Sanchez (CA: 2011-): University of Saskatchewan

  • Dr. Anders S. Barfod (DK: 2012-): Aarhus University

  • Dr. Pieter B. Pelser (NZ: 2012-): University of Canterbury

  • Dr. Robert B. Kaul (US: 2013-): University of Nebraska-Lincoln

  • Dr. Okihito Yano (JP: 2013-): Okayama University of Science

  • Dr. Dirk C. Albach (DE: 2013-): Carl von Ossietzky Universitat Oldenburg

  • Dr. A. Muthama Muasya (SA: 2014-): University of Cape Town

  • Dr. Bengt Oxelman (SW: 2014-): University of Gothenburg

  • Dr. Natasha de Vere (UK: 2014-): National Botanic Garden of Wales

  • Dr. Brigitta Duyfjes (HL: 2014-): Nationaal Herbarium Nederland

  • Dr. Jie Li (CN: 2015-): Xishuangbanna Tropical Botanical Garden

  • Dr. Stephan Gale (CN: 2016-): Kadoorie Farm & Botanic Garden, Hong Kong

  • Dr. Chiara Nepi (IT: 2016-): Universita di Firenze

  • Dr. Annalisa Santangelo (IT: 2016-): Universita degli Studi di Napoli Federico II

  • Dr. Adriano Stinca (IT: 2016-): Universita degli Studi di Napoli Federico II

[List of Botanical Journals]

[Technical notes]

  • STACEY
    *open BEAUti 2.4.4. and download "Stacey"

  • BEAUti 2.4.4 (creating BEAST data)
    "with all ingroup species and exclude outgroup species to avoid rate differences and hidden substitutions between ingroup and outgroup species (B. Oxelman, personal communication, November 22, 2016)."
    @Partitions: File => Templete => Stacey
    @Partitions: Import one or more data sets using "+"
    @Taxon sets: Rename here, e.g., ecuadriensisYI1924 (not E_ecuadriensis_YI1924)
    use defaut setting (no need to change anything)
    save the xml file (to be used for BEAST 2 analysis)

  • BEAST 2.4.4
    Import the xml file generated with BEAUti 2.4.4 by clicking "choose file"
    RUN (I confirm if analysis is successfully run on my pc and then use CIPRES website and run BEAST)
    Download "species.trees" from CIPRES to "SpeciesDA" folder

  • TreeAnnotator 2.4.4
    set "Burnin percentate" to 10%
    @Input tree file: choose "species.trees"
    @Output tree: type "species.tre" and RUN

  • SpeciesDA
    Download "SpeciesDelimitationAnalyser" from here and save in C drive (if use D drive change C to D in the following steps)
    Open command prompt and type: cd C:\Users\Yu\BEAST\2.4\speciesDA
    type: java -jar speciesDA.jar -burnin 200 -collapseheight .0001 -simcutoff 1 species.trees result_out.txt
    open result_out.txt with PAUP*

  • R
    Download R
    File => Change Directory => move to SpeciesDA folder
    type: ( x <- read.table("result_out.txt", header=T) )
    type: (renames <- matrix(c( + "YI1707", "YI1707", + "NT96", "NT96", + "YI2178", "YI2178", + "YI2112", "YI2112", + "YI2277", "YI2277", + "YI2255", "YI2255", + "NT16", "NT16", + "YI2111", "YI2111", + "TD139", "TD139", + "TD138", "TD138", + "NT100", "NT100", + "TD1118", "TD1118", + "TD3682", "TD3682", + "TD4630", "TD4630", + "Chen1", "Chen1", + "Chen2", "Chen2", + "TD5186", "TD5186", + "Chen3", "Chen3", + "NT85", "NT85", + "TD5185", "TD5185", + "YI2225", "YI2225", + "YI1157", "YI1157", + "M080636", "M080636", + "YI2223", "YI2223", + "YI2189", "YI2189", + "M080655", "M080655", + "HNL0922", "HNL0922", + "ovalifolia", "ovalifolia", + "YI2260", "YI2260", + "YI2280", "YI2280", + "TD4878", "TD4878", + "TD4877", "TD4877", + "TD1288", "TD1288", + "TD4875", "TD4875"), + nrow=34, ncol=2, byrow=TRUE))
    type: (mincl.names <- colnames(x)[-(1:4)])
    type: (displaynames <- renames[,2])
    type: (nmincls <- length(displaynames))
    type: (sim <- matrix(0, ncol=nmincls, nrow=nmincls, dimnames=list(displaynames, displaynames)))
    type: for (i in 1:nmincls) { for (j in 1:nmincls) { coli <- x[,mincl.names[i]] colj <- x[,mincl.names[j]] w <- coli == colj sim[i,j] <- sum(x[w,"fraction"]) } }
    type: (coli <- x[,mincl.names[i]])
    type: (colj <- x[,mincl.names[j]])
    type: (w <- coli == colj)
    type: (sim[i,j] <- sum(x[w,"fraction"]))
    type: (sim <- pmin(sim,1))

  • Excel
    import data to Excel
    use: "カンマやタブなどの区切り文字によってフィールドどとに区切られたデータ"
    @home: "条件付き書式" => "カラースケール" => "その他のルール" => "三色スケール" => "パーセント"

  • Illustrator
    Copy and paste the excel file data
    Select all => copy => paste => undo => remove table from PP numbers

  • RAxML constraint trees
    i. input data for RAxML
    ii. constraint file (.tre) <= include all OTUs
    1. visit RAxML on XSEDE and upload input data and constraint file
    2. obtain Best.tre

  • SH test
    i. input data for PAUP (.nex)
    ii. non-constraint RAxML tree
    iii. constraint RAxML tree(s)
    1. Open Paup and execute input data
    2. type "gettrees mode=7"
    3. get non-constraint RAxML tree by "get trees from file" (check "Ignore internal rootednedd directves" and "Interpret trees as rooted")
    4. get constraint RAxML tree(s) as is
    5. Tree scores => Likelihood => SH test and AU test

  • Diversification analysis with BAMM
    i. install bamm-2.5.0-windows.zip (available at here)
    ii. prepare calibrated phylogeny (e.g. BEAST tree)
    iii. create "myControlFile.txt"
    -use command prompt-
    1. type "cd /d D:\デスクトップ\BAMM\bamm-2.5.0-Windows\bamm-2.5.0-Windows"
    2. type "bamm -c myControlFile.txt"

  • Analyze BAMM data with BAMMtools
    i. install R
    ii. type "install.packages('BAMMtools')" to download BAMMtools
    -use R-
    1. File => Change Directory => move to BAMM folder
    2. type library(BAMMtools) tree <- read.tree("test.tre") plot(tree, cex = 0.35) events <- read.csv("event_data.txt") edata <- getEventData(tree, eventdata = "event_data.txt", burnin=0.1) head(edata$eventData) bamm.test <- plot.bammdata(edata, lwd=2, labels = T, cex = 0.5) addBAMMshifts(edata, cex=2) addBAMMlegend(bamm, corners = c(-1, -0.5, 40, 80), nTicks = 4, side = 4, las = 1)

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