454 sequencer datasets of Mengsong

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

The Operational Taxonomic Unit (OTU) representative sequences in Yinggeling

After denoising and deconvoluting, we clustered the reads into 97%-similarity Operational Taxonomic Units (OTUs), which should approximate or somewhat underestimate biological species. We further assigned taxonomic information to the OTUs. The data here shows the OTU representative sequences in Yinggeling

The Operational Taxonomic Unit (OTU) representative sequences in Mengsong

After denoising and deconvoluting, we clustered the reads into 97%-similarity Operational Taxonomic Units (OTUs), which should approximate or somewhat underestimate biological species. We further assigned taxonomic information to the OTUs. The data here shows the OTU representative sequences in Mengsong

R scripts

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

The Operational Taxonomic Unit (OTU) table with assigned taxonomies in Yinggeling

Arthropod community composition of each survey plot in Yinggeling. The rows are OTUs, and columns are survey plots together with taxonomies of each OTU. The formats of the dataset are slightly modified for input to R

The Operational Taxonomic Unit (OTU) table with assigned taxonomies in Mengsong

Arthropod community composition of each survey plot in both seasons of Mengsong. MS1 = November-December 2010 (the end of wet season), MS2 = May-June 2011 (the end of dry season). The rows are OTUs, and columns are survey plots together with taxonomies of each OTU. The formats of the dataset are slightly modified for input to 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)

Environmental variables in Mengsong

The data includes environmental variables in Mengsong. The row names are IDs of survey plots (i.e. 7, which corresponds to PLOT007 in the data of raw short reads). Abbreviations for column names are: HAB = habitat types (RF: regenerating forest, OL: open lands, MF: mature forest), UTM_E and UTM_N = geographic coordinates of each survey plot, F_NR = the survey plots inside the forests of Bulong Nature Reserve? (TRUE: yes, FALSE: no

Bioinformatic scripts of Mengsong

Command history (command_history_mengsong.txt) and related files, e.g. map files, reference data, programs written by perl language, etc

Raw Short Reads of Insects in Yinggeling National Nature Reserve

The data is for insect samples from Malaise traps in Yinggeling National Nature Reserve, Hainan 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 21 Yinggeling samples were sequenced on two 1/8 regions (one 1/8 region shared with other samples), producing 40 261 raw reads