Bioinformatic command script

An example bioinformatic scrip

S1 fungus_uclust_R_script_nonrarefied

The HTML outputs of the R scripts using the non-rarefied UCLUST dataset

otutable_first200_tax

Top 200 most reads OTUs with their taxonomy assignment and reads numbe

S1 fungus_CROP_R_script_nonrarefied

The HTML outputs of the R scripts using the non-rarefied CROP dataset

S1 fungus_uclust_R_script_rarefied

The HTML outputs of the R scripts using the rarefied UCLUST dataset

454 sequencer datasets of Mengsong

The datasets are output of 454 sequencer, and input of the bioinformatic analyses

Tree community composition of survey plots in the forests of Bulong Nature Reserve

The dataset is a subset of plant community composition data in Mengsong. For cross-site predictions, we used only the Mengsong plots (n = 16) located within the forest of Bulong Nature Reserve (~60 km2) and only included trees > 5cm DBH in each plot, to maximum comparability between the two landscapes. The rows are survey plots and columns are tree species. This is an input file for R

Environmental variables in Yinggeling

The data includes environmental variables in Yinggeling. The row names are IDs of survey plots. Abbreviations for column names are: UTM_E and UTM_N = geographic coordinates of each survey plot, Time = the time when survey plots were established and trees were surveyed (2009 or 2011)

Raw Short Reads of Insects in Mengsong

The data is for insect samples from Malaise traps in Mengsong, Xishuangbanna, Yunnan Province, China. Samples were prepared by using one leg from all specimens equal to or larger than a large fly (~5 mm length) and whole bodies of everything smaller. Following the protocol of Ji et al. (2013), samples were homogenized, and DNA was extracted, quality-checked, PCR-amplified with indexed, degenerate primers for the standard mtCOI barcode region, and gel-purified. The PCR products were A-amplicon-sequenced on a Roche GS FLX at the Kunming Institute of Zoology. The 28 Mengsong samples were sequenced on one whole run (four 1/4 regions, November-December 2010: wet season) and two 1/4 regions (May-June 2011: dry season), producing 519 865 and 253 025 raw reads, respectively

R scripts

The file includes all R scripts used, and is of R Markdown format. You may need to open it in RStudio