CSPs: Phylogenetic tree of woody species in the Gutianshan National Reserve

Usage Rights

This data is Free for members.

Permission is granted to anybody to access, use and publish all open for public data freely. The commercial use of any data is prohibited. The quality and completeness of data cannot be guaranteed. Users employ these data at their own risk. In order to make attribution of use for owners of the data possible, the identifier of ownership of data must be retained with every data record. Users must publicly acknowledge, in conjunction with the use of the data, the data owners. Cite the data as follows:
Michalski, S., and Durka, W. (2013): Phylogenetic tree of the tree species found in the CSPs. BEF-China data portal (Accessed through URL http://china.befdata.biow.uni-leipzig.de/datasets/240)

Dataset Abstract

The data file contains the corrected species names for the tip labels of the phylogenetic tree. The attached text file is the phylogenetic tree. Methods concerning the phylogenetic tree see below sampling description.

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)). Aligned sequences were concatenated for each species resulting in a total alignment of 3521 nucleotide positions. 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).

Four species occurring in the CSPs but without sequence information available (Table 1) were added manually to the obtained ML tree by the following procedure. Acer cordatum was added within Acer as a polytomy to the most recent common ancestor (MRCA) of a monophyletic clade formed by other members of Acer sect. Palmata (i.e. A. elegantulum, A. wilsonii, A. olivaceum). Its branch length was defined as the average distance from the MRCA of that clade to the tips. Styrax wuyuanensis, Symplocos oblongifolia and Vaccinium mandarinorum were added similarily as polytomy emerging from the MRCA for all other members of the respective genus included, with branch lengths equalling the average branch length from that MRCA to the tips of congeners.

Using the ML topology and branch lengths an ultrametric tree was created by non-parametric rate smoothing (nprs) as implemented in r8s (Sanderson 1997). Absolute node ages were obtained using 27 published fossils or dates as age constrains. A fixed age of 125 million years was applied to the crown node of the Eudicots (Table 2).

Spatial Extent

Gutianshan Nature Reserve, Comparative study sites, BEF China Main Experiment

Taxonomic Extent

Trees in the Comparative Study Sites and the BEF China Main experiment.

Data Analysis

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

Freeformat files (3)

Paper proposal submissions

Published

2014

2013

2012

2010

Data columns available in the raw data part of this dataset

tip_label
tip label used in the phylogenetic tree file; Datagroup description: Helper
Data group: Helper
Keywords: species
Values
Abelia_chinensis
Abutilon_theophrasti
Acer_buergerianum
Acer_amplum
Acanthopanax_trifoliatus
species
Species name, correcting typos and exchanging some names according to the species name reference list.; Datagroup description: Scientific plant species name
Data group: Scientific plant species name
Keywords: species
Values
Acanthopanax trifoliatus
Acer buergerianum
Abutilon theophrasti
Acer amplum
Abelia chinensis
* Nadrowski, K. also contributed to this column.