Data from: Gene duplication and the evolution of phenotypic diversity in insect societies

Chau LM, Goodisman MAD

Date Published: September 8, 2017

DOI: https://doi.org/10.5061/dryad.9m5h0

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Title Amell_Ashby_casteFPKM
Downloaded 2 times
Description Column 1 has the A. mellifera gene IDs. Column 2 through 4 represents average FPKM for the respective caste (drone, queen, worker), across all samples. These expression levels were derived from Ashby et al.
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Download Amell_Ashby_casteFPKM.txt (332.5 Kb)
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Title Amell_SingleCopyGenes.txt
Downloaded 7 times
Description FIle with all the single copy genes in A. mellifera. Column 1(EOG) has the EOG id from OrthoDB v9.1 in which the single copy genes were derivived from. Column 1 (A. mellifera) has the single copy gene in A. mellifera and column 2 (B. terrestris) represents the sinlge copy ortholog in B. terrestris.
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Title Amell_DupPairs.txt
Downloaded 6 times
Description File with all the duplicate genes in A. mellifera. Column 1(EOG) has the EOG id from OrthoDB v9.1 in which the gene duplicates were derivived from. Column 1 (Gene 1) and column 2 (Gene 2) represent the paralogs in A. mellifera in no particular order.
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Title Amell_Bterr_EvoProc.txt
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Description File that has the gene families used to identify the evolutionary processes maintaining paralogs in the A. mellifera genome. Column 1 (AMELL_D1) is the paralog with the highest sequence similarity to the single copy ortholog in B. terrestris, while column 2 (AMELL_D2) is the one with the lease sequence similarity. BTERR_ortho is the single copy ortholog of the duplicates in B. terrestris. Methods on how sequence similarity was measured can be found in the methods.
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Title Bterr_caste_FPKM.txt
Downloaded 7 times
Description Column 1 has the B. terrestris gene IDs. Column 2 through 4 represents average FPKM for the respective caste, across all samples. These expression levels were derived from Harrison et al.
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Title Amell_Expression.txt
Downloaded 8 times
Description File that includes expression and other evolutionary measures for duplicate and singletons in A. mellifera. column description Gene A. mellifera gene ID EOG OrthoDB v9.1 group ID Homology Duplicate gene or singleton Ashby_DQ_logFC Expression ratio (Drones/Queens) Ashby et al Dataset Ashby_DQ_FDR FDR (Drones/Queens) Ashby et al Dataset Ashby_DW_logFC Expression ratio (Drones/Workers) Ashby et al Dataset Ashby_DW_FDR FDR (Drones/Workers) Ashby et al Dataset Ashby_QW_logFC Expression ratio (Queens/Workers) Ashby et al Dataset Ashby_QW_FDR FDR (Queens/Workers) Ashby et al Dataset N_Tau Tissue Specificity, calculated across 10 tissues in Nurses; Jasper et al F_Tau Tissue Specificity, calculated across 10 tissues in Foragers; Jasper et al Jasper_NF_logFC Expression ratio (Nurse/Forager) in brains; Jasper et al Dataset Jasper_NF_FDR FDR (Nurse/Forager) in brains; Jasper et al Dataset V_DQ_logFC Expression ratio (Drones/Queens) Vleurinck et al Dataset V_DQ_FDR (Drones/Queens) Vleurinck et al Dataset V_DW_logFC Expression ratio (Drones/Workers) Vleurinck et al Dataset V_DW_FDR FDR (Drones/Workers) Vleurinck et al Dataset V_QW_logFC Expression ratio (Queens/Workers) Vleurinck et al Dataset V_QW_FDR FDR (Queens/Workers) Vleurinck et al Dataset C_QW_logFC Expression ratio (Queens/Workers) Cameron et al Dataset C_QW_FDR FDR (Queens/Workers) Cameron et al Dataset
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Title ParseDups_ODBv9.1.pl
Downloaded 28 times
Description Perl script that uses an OrthoDB v9.1 tab delimited file to identify EOGs with a certain number of genes per species, which was used to identify genes that were duplicated in A. mellifera but single copy in every other species in the Apoidea. ie. perl parse_full_orthodb9v1_byStuff.pl ODB_v9.1_input.txt 7460.1.1, 7461.1.1, 7462.1.1, 7463.1.1, 30195.1.1, 88501.1.1, 132113.1.1, 143995.1.1, 166423.1.1, 178035.1.1, 516756.1.1, 597456.1.1 ODB_v9.1_output.txt Further details on how to run the script can be found in the file.
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Title Apoidea_DupRates.txt
Downloaded 5 times
Description Text file with 10 bees in the Apoidea, along with the number of species-specific duplicates, divergence time, duplication rate, and social state. Divergence time was taken from Cardinal and Danforth (2013). Social State was determined from Kapheim et al. (2015).
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Title README
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Description Read me text.
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When using this data, please cite the original publication:

Chau LM, Goodisman MAD (2017) Gene duplication and the evolution of phenotypic diversity in insect societies. Evolution, online in advance of print. https://doi.org/10.1111/evo.13356

Additionally, please cite the Dryad data package:

Chau LM, Goodisman MAD (2017) Data from: Gene duplication and the evolution of phenotypic diversity in insect societies. Dryad Digital Repository. https://doi.org/10.5061/dryad.9m5h0
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