Data from: A protocol for species delineation of public DNA databases, applied to the Insecta

Chesters D, Zhu C

Date Published: May 14, 2014

DOI: http://dx.doi.org/10.5061/dryad.k7t50

 

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Title delineation matrix
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Description delineation matrix (LxS), 24 loci (columns), ~78,000 species units (rows). tab delimited, unix line breaks. spaces separate individual members of a single gene motu. members are representated by their originally designated taxonomy which is converted to species strings according to Hunt and Vogler (2008, MPE 47:289), followed by underscore and NCBI accession.
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Title insecta.taxkey
Downloaded 51 times
Description table giving full taxonomic information for each taxonomic string used later in the results files. taxonomic string is the first string in each row. strings are built from full heirachy up to given node, according to Hunt and Vogler (2008, MPE 47:289). 2nd column is full taxonomic name for that node, 3rd column is NCBI taxonomy number for that node.
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Title insecta.fas
Downloaded 44 times
Description processed insect fasta database. file is compressed. entries are represented by taxonomic string followed by NCBI accession number. some duplicate data is removed from original insect db. and some particularly long DNA sequences are also ommited.
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Title Supplemental figure 1
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Description Supplementary Fig. 1: Assessment of the protocol. A: Contrasting estimates of species numbers for assigned names (x axis) and clusters based on sequence similarity (y axis). ~20 of the species dense homologs are plotted, based on species counts made only for the 26 model genera given in the methods. Upper gray point indicates COI locus, lower gray 18S. B: Contrasting the number of MOTU for each family in the dataset, where the species clustering parameters are inferred insect-wide (x-axis), or locally for each family (y-axis). Linear regression line is shown on A and B.
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When using this data, please cite the original publication:

Chesters D, Zhu C (2014) A protocol for species delineation of public DNA databases, applied to the Insecta. Systematic Biology 63(5): 712-725. http://dx.doi.org/10.1093/sysbio/syu038

Additionally, please cite the Dryad data package:

Chesters D, Zhu C (2014) Data from: A protocol for species delineation of public DNA databases, applied to the Insecta. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.k7t50
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