DOI: 10.5061/dryad.9m5h0
title: Data from: Gene duplication and the evolution of phenotypic diversity in insect societies

description: Gene duplication is an important evolutionary process thought to
 facilitate the evolution of phenotypic diversity. We investigated if gene
 duplication was associated with the evolution of phenotypic differences in
 a highly social insect, the honeybee Apis mellifera. We hypothesized that
 the genetic redundancy provided by gene duplication could promote the
 evolution of social and sexual phenotypes associated with advanced
 societies. We found a positive correlation between sociality and rate of
 gene duplications across the Apoidea, indicating that gene duplication may
 be associated with sociality. We also discovered that genes showing biased
 expression between A. mellifera alternative phenotypes tended to be found
 more frequently than expected among duplicated genes than singletons.
 Moreover, duplicated genes had higher levels of caste-, sex-, behavior-,
 and tissue-biased expression compared to singletons, as expected if gene
 duplication facilitated phenotypic differentiation. We also found that
 duplicated genes were maintained in the A. mellifera genome through the
 processes of conservation, neofunctionalization, and specialization, but
 not subfunctionalization. Overall, we conclude that gene duplication may
 have facilitated the evolution of social and sexual phenotypes, as well as
 tissue differentiation. Thus this study further supports the idea that
 gene duplication allows species to evolve an increased range of phenotypic
 diversity.
description: Amell_Ashby_casteFPKMColumn 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.Amell_SingleCopyGenes.txtFIle 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.Amell_DupPairs.txtFile 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.Amell_DupsPairs.txtAmell_Bterr_EvoProc.txtFile 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.Bterr_caste_FPKM.txtColumn 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.Bterr_casteFPKM.txtAmell_Expression.txtFile 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 DatasetAmell_Expression.csvParseDups_ODBv9.1.plPerl 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.ParseDups_ODBv9.plApoidea_DupRates.txtText 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).READMERead me text.