DOI: 10.5061/dryad.b412jp5
title: Data from: Tandem-running and scouting behavior are characterized by up-regulation of learning and memory formation genes within the ant brain

description: Tandem-running is a recruitment behavior in ants that has been described
 as a form of teaching, where spatial information possessed by a leader is
 conveyed to following nestmates. Within Temnothorax ants, tandem-running
 is used within a variety of contexts, from foraging and nest relocation to
 – in the case of slavemaking species – slave raiding. Here, we elucidate
 the transcriptomic basis of scouting, tandem-leading, and tandem-following
 behavior across two species with divergent lifestyles: the slavemaking
 Temnothorax americanus and its primary, non-parasitic host T.
 longispinosus. Analysis of gene expression data from brains revealed that
 only a small number of unique differentially-expressed genes are
 responsible for scouting and tandem-running. Comparison of orthologous
 genes between T. americanus and T. longispinosus suggests that
 tandem-running is characterized by species-specific patterns of gene
 usage. However, within both species, tandem-leaders showed gene expression
 patterns median to those of scouts and tandem-followers, which was
 expected, as leaders can be recruited from either of the other two
 behavioral states. Most importantly, a number of differentially-expressed
 behavioral genes were found, with functions relating to learning and
 memory formation in other social and non-social insects. This includes a
 number of up-regulated receptor genes such as a glutamate and dopamine
 receptor, as well as serine/threonine protein phosphatases and kinases.
 Learning and memory genes were specifically up-regulated within scouts and
 tandem-followers, not only reinforcing previous behavioral studies into
 how Temnothorax navigate novel environments and share information, but
 also providing insight into the molecular underpinnings of teaching and
 learning within social insects.
description: Script_S1This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": DESeq2 analysis of T. americanus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEMScript_S2This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": DESeq2 analysis of T. longispinosus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEM.Script_S3This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": Weighted Gene Co-expression Analysis (WGCNA) of T. americanus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEM and filtered for contigs with at least 10 count in at least 4 samples and maximum Cook's distance below 38. Script modified from Tutorials provided on https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/Script_S4This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": Weighted Gene Co-expression Analysis (WGCNA) of T. longispinosus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEM and filtered for contigs with at least 10 count in at least 4 samples and maximum Cook's distance below 38. Script modified from Tutorials provided on https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/Script_S5This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": GO enrichment analysis of T. americanus, Transcriptome constructed using Trinity, Differentially expressed contigs obtained using DESeq2, Modules of contigs obtained using WGCNA.Script_S6This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": GO enrichment analysis of T. longispinosus, Transcriptome constructed using Trinity, Differentially expressed contigs obtained using DESeq2, Modules of contigs obtained using WGCNA.Script_S7This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": Homologue analysis between T. americanus and T. longispinosus, Transcriptomes constructed using Trinity, DEGs obtained by using DESeq2, Orthogroups created using Orthofinder.Table_S1Expression matrix of T. americanus, generated using RSEM v.1.3.0.Table_S2Expression matrix T. longispinosus generated using RSEM v.1.3.0.Table_S3Differentially expressed genes of T. americanus generated using R packages DESeq2 v.1.16.1. This table consists of six sub-tables, one for each pairwise comparison between behaviors with only over-expressed contigs with a adjusted p-value&lt;0.05 and Dunn p-value&lt;0.05 shown.Table_S4Differentially expressed genes of T. longispinosus generated using R packages DESeq2 v.1.16.1. This table consists of six sub-tables, one for each pairwise comparison between behaviors with only over-expressed contigs with a adjusted p-value&lt;0.05 and Dunn p-value&lt;0.05 shown.Table_S5Contigs in significant modules of WGCNA in T. americanus generated using R packages WGCNA v.1.64-1, ggpubr v.0.1.8, DESeq2 v.1.16.1.Table_S6Contigs in significant modules of WGCNA in T. longispinosus generated using R packages WGCNA v.1.64-1, ggpubr v.0.1.8, DESeq2 v.1.16.1.Table_S7Enriched GO terms in DEGs and modules of T. americanus generated using InterProScan v.5.25-64.0, R package topGO v.2.28.0.Table_S8Enriched GO terms in DEGs and modules of T. longispinosus generated using InterProScan v.5.25-64.0, R package topGO v.2.28.0.Table_S9Enriched KEGG pathways in DEGs and modules of T. americanus generated using InterProScan v.5.25-64.0.Table_S10Enriched KEGG pathways in DEGs and modules of T. longispinosus generated using InterProScan v.5.25-64.0.Table_S11Orthogroups found between transcriptomes of T. americanus and T. longispinosus generated using Orthofinder v.1.1.8.Table_S12Orthogroups found between DEGs of T. americanus and T. longispinosus generated using Orthofinder v.1.1.8.Table_S13Orthogroups found between DEGs of T. longispinosus and T. americanus generated using Orthofinder v.1.1.8.Tamer_BLAST_transcriptomeBLAST annotations of all contigs in the Trinity transcriptome of T. americanus generated using blastx, NCBI BLAST v2.6.0.Tamer_Interproscan_GOGene ontology annotations of all contigs of the transcriptome of T. americanus generated using InterProScan v.5.25-64.0.Tamer_Interproscan_KEGGKEGG pathways of all contigs of the transcriptome of T. americanus generated using InterProScan v.5.25-64.0.Tamer_transcriptome_filteredTranscriptome of T. americanus after all filtering steps prior to gene expression analysis generated using Trinity v.2.4.0, TransDecoder TransDecoder v.3.0.1, R package DESeq2 v.1.16.1.Tamer_Trinity_TranscriptomeTranscriptome of T. americanus created by Trinity without any filtering steps generated using Trinity v.2.4.0.Tlongi_BLAST_transcriptomeBLAST annotations of all contigs in the Trinity transcriptome of T. longispinosus generated using blastx, NCBI BLAST v2.6.0.Tlongi_Interproscan_GOGene ontology annotations of all contigs of the transcriptome of T. longispinosus generated using InterProScan v.5.25-64.0.Tlongi_Interproscan_KEGGKEGG pathways of all contigs of the transcriptome of T. longispinosus generated using InterProScan v.5.25-64.0.Tlongi_transcriptome_filteredTranscriptome of T. longispinosus after all filtering steps prior to gene expression analysis generated using Trinity v.2.4.0, TransDecoder TransDecoder v.3.0.1, R package DESeq2 v.1.16.1.Tlongi_Trinity_TranscriptomeTranscriptome of T. longispinosus created by Trinity without any filtering steps generated using Trinity v.2.4.0.ReadMeThis file describes all supplementary material provided alongside: Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain (A. Alleman, M. Stoldt, B. Feldmeyer, S. Foitzik) 2019