Main Experiment: Phylogenetic tree of the tree species (Site A & B)

Usage Rights

This data is Free for members.

Dataset Abstract

This dataset contains the phylogenetic tree for the tree species in the Main experiment. It is a subset of the extensive phylogenetic tree for the Flora in the Gutianshan National Nature Reserve available from the dataset 240 (http://china.befdata.biow.uni-leipzig.de/datasets/240). Please see the respective dataset for more information on the Materials and Methiods used to derive the phylogeny (c.f. freeformat file 'Materials_and_methods2_436taxa.doc' in dataset 240).

The relevant data to obtain the phylogenetic tree is stored in the freeformat file ('phy_main.tre') connected to this dataset.

Dataset Design

We gathered sequence information, i.e. matK, rbcL and the ITS region including the 5.8s gene for all woody species from Gutianshan National Reserve (Lou & Li 1998) or closely related species available in GenBank (http://www.ncbi.nlm.nih.gov/genbank/, accessed between May and June 2012). For some species of the CSPs, matK and rbcL were sequenced using standard barcoding protocols (Fazekas et al. 2012) (Accession numbers: KF569888-KF569899, Table 1). All sequences were aligned separately for the different markers using MAFFT v6 (Katoh et al. 2002). Sequences for matK and rbcL were aligned with the ‘Auto’ option in the online version of the program (http://mafft.cbrc.jp/alignment/server/). The ITS region was aligned with the ‘Q-INS-I’ option considering secondary structure of RNA using the MAFFT application at Bioportal (https://www.bioportal.uio.no/, Kumar et al. 2009)). A phylogenetic tree was inferred using a Maximum Likelihood (ML) method implemented in PhyML (Guindon & Gascuel 2003). For ML inference, the best fitting model (GTR+I+G) selected by Modeltest (Posada & Crandall 1998) was applied with the following options: tree topology search operation: best of NNI and SPR search, number of substitution rate categories =6, all other parameters were estimated (Gamma Distribution Parameter Alpha, Proportion of Invariable Sites, Transition/Transversion Ratio).

Spatial Extent

BEF China Experimental Site A (29°07'28.2"N 117°54'27.5"E)
BEF China Experimental Site B (29°05'06.8"N 117°55'44.4"E)

Taxonomic Extent

Castanea henryi
Schima superba
Choerospondia axillaris
Liquidambar formosana
Quercus serrata
Cyclobalanopsis myrsinifolia
Castanopsis carlesii
Cyclobalanopsis glauca
Lithocarpus glaber
Castanopsis sclerophylla
Diospyros japonica
Daphniphyllum oldhamii
Cinnamomum camphora
Koelreuteria bipinnata
Sapindus saponaria
Nyssa sinensis
Triadica sebifera
Triadica cochinchinensis
Rhus chinensis
Quercus fabri
Quercus acutissima
Melia azedarach
Acer davidii
Castanopsis fargesii
Ailanthus altissima
Alniphyllum fortunei
Betula luminifera
Celtis biondi
Elaeocarpus chinensis
Elaeocarpus glabripetalus
Elaeocarpus japonicus
Idesia polycarpa
Meliosma flexuosa
Machilus grijsii
Machilus thunbergii
Machilus leptophylla
Manglietia fordiana
Pheobe bournei
Quercus phillyreoides

Data Analysis

Use read.tree from package ape to read in the text file (phy_dat = read.tree("phy_main.tre")). Use the corrected species names of the tip labels to relate phylogenetic distances to trait or community data.

Freeformat files (1)

  • phy_main.tre (1.53 KB)
    Phylogenetic tree of 38 tree species in the Main experiment. Use read.tree() from R package 'ape' to read in the tree.