Data from: Plant diversity accurately predicts insect diversity in two tropical landscapes

Zhang K, Lin S, Ji Y, Yang C, Wang X, Yang C, Wang H, Jiang H, Harrison RD, Yu DW

Date Published: July 29, 2016

DOI: http://dx.doi.org/10.5061/dryad.37b53

 

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Title Raw Short Reads of Insects in Mengsong
Downloaded 21 times
Description 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.
Download submission_fastq_MS.tar.gz (293.6 Mb)
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Title Raw Short Reads of Insects in Yinggeling National Nature Reserve
Downloaded 7 times
Description 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.
Download submission_fastq_YGL.tar.gz (9.439 Mb)
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Title 454 sequencer datasets of Mengsong
Downloaded 5 times
Description The datasets are output of 454 sequencer, and input of the bioinformatic analyses.
Download 454sequencer_dataset_MS.tar.gz (350.9 Mb)
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Title 454 sequencer datasets of Yinggeling
Downloaded 5 times
Description The datasets are output of 454 sequencer, and input of the bioinformatic analyses.
Download 454sequencer_dataset_YGL.tar.gz (30.34 Mb)
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Title Bioinformatic scripts of Mengsong
Downloaded 5 times
Description Command history (command_history_mengsong.txt) and related files, e.g. map files, reference data, programs written by perl language, etc.
Download bioinformatic_script_MS.zip (1.166 Mb)
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Title Bioinformatic scripts of Yinggeling
Downloaded 5 times
Description Command history (command_history_yinggeling.txt) and related files, e.g. map files, reference data, programs written by perl language, etc.
Download bioinformatic_script_YGL.zip (1.159 Mb)
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Title R scripts
Downloaded 11 times
Description The file includes all R scripts used, and is of R Markdown format. You may need to open it in RStudio.
Download Plants_accurately_predict_insects.Rmd (508.5 Kb)
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Title Environmental variables in Mengsong
Downloaded 7 times
Description 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)
Download MSenv.csv (1.294 Kb)
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Title Environmental variables in Yinggeling
Downloaded 5 times
Description 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).
Download YGLenv.csv (871 bytes)
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Title Plant community composition in Mengsong
Downloaded 10 times
Description Plant community composition of each survey plot in Mengsong. The rows are survey plots and columns are plant species. This is an input file for R.
Download MS_Plant_output.csv (62.82 Kb)
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Title Tree community composition in Yinggeling
Downloaded 7 times
Description Tree community composition of each survey plot in Yinggeling. The rows are survey plots and columns are plant species. This is an input file for R.
Download YGL_treedensity.csv (30.24 Kb)
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Title Tree community composition of survey plots in the forests of Bulong Nature Reserve
Downloaded 8 times
Description 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.
Download MS_Tree_output_5cm.csv (26.28 Kb)
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Title The Operational Taxonomic Unit (OTU) representative sequences in Mengsong
Downloaded 10 times
Description 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.
Download MSall_CROP97_DNACLUST_otus_r0.cluster.fasta (1.786 Mb)
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Title The Operational Taxonomic Unit (OTU) representative sequences in Yinggeling
Downloaded 9 times
Description 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.
Download YGL_CROP97_otus_z5k.cluster.fasta (1.461 Mb)
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Title The Operational Taxonomic Unit (OTU) table with assigned taxonomies in Mengsong
Downloaded 5 times
Description 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.
Download MBCar_MS.rar (87.11 Kb)
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Title The Operational Taxonomic Unit (OTU) table with assigned taxonomies in Yinggeling
Downloaded 7 times
Description 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.
Download MBCar_YGL.csv (289.1 Kb)
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When using this data, please cite the original publication:

Zhang K, Lin S, Ji Y, Yang C, Wang X, Yang C, Wang H, Jiang H, Harrison RD, Yu DW (2016) Plant diversity accurately predicts insect diversity in two tropical landscapes. Molecular Ecology 25(17): 4407-4419. http://dx.doi.org/10.1111/mec.13770

Additionally, please cite the Dryad data package:

Zhang K, Lin S, Ji Y, Yang C, Wang X, Yang C, Wang H, Jiang H, Harrison RD, Yu DW (2016) Data from: Plant diversity accurately predicts insect diversity in two tropical landscapes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.37b53
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