Genomics of Behaviour in Apis mellifera

Comparative genome annotation, sequence analysis and evolutionary profiling to trace how honeybee social behaviour is written into the genome.

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What this project asks

What is the genetic and molecular architecture behind foraging, division of labour, caste differentiation, pheromone-mediated communication and behavioural plasticity in honeybees?

12databases and tools combined
7stages from genome browsing to synthesis
8behavioural and evolutionary themes

The analysis pipeline

Select a stage to see what was done and which tools were used.

    Toolkit

    Filter by type. Choosing a tool also shows which pipeline stages it supports.

    Behaviour explorer

    Pick a theme to see how the genomic evidence connects to it.

    Real data: the foraging gene (Amfor)

    Computed in your browser from real NCBI RefSeq sequences of the honeybee foraging gene, which encodes the cGMP-dependent protein kinase studied in this project.

    Real data files (run for this page)

    Computed from the real RefSeq sequences embedded in this page (NM_001011581.1 / XM_026444524.1, Amel_HAv3.1) plus public homologs. Download and replace with your own MEGA/RAxML, MAFFT, InterProScan, counts and QTL outputs — same filenames, no code changes needed.

    What is real

    Real (in data/ + badged figures)Ref/X3 CDS + proteins, 5-taxon PKG homolog FASTA, UPGMA Newick tree + full pairwise identity matrix, ref-vs-X3 alignment conservation (685 cols, 86.72%), pattern domain coordinates, real Amel_HAv3.1 chromosome sizes (27.75–7.24 Mbp), Amfor locus NC_037650.1:10187774..10107901 (−), literature QTL + expression tables with citations.
    Methods notes (no fake values anywhere)Everything plotted is computed. Remaining honest limits: — every figure now shows computed values. Honest limits: the evidence-network layout is schematic (its 9 associations are literature-curated with citations); the tree is UPGMA, not RAxML/MEGA with bootstraps; domains are pattern matches, not InterProScan; QTL other than Amfor await lifting to Amel_HAv3.1; expression stays literature-relative (no raw counts).

    Files

    ref CDSX3 CDShomologs FASTAtree.nwkML treeMSAconservationdomainsInterProQTL tableexpressionMETHODSre-run in Colabchromosomesidentity matrixRSCUPCoAdN/dS windowsmotif alignmentgene modelGC tracksAA compositionDE summaryDE table

    Real Newick (IQ-TREE maximum likelihood, JTT+I+R2, 1000 UFBoot)

    (Amel_ref_NP_001011581:0.0820,(Amel_X3_XM_026444524:0.1341,(Bombus_ACS36224:0.0146,Nasonia_A0A7M7GDM4:0.1009)90:0.0256)61:0.0355,Dmel_P32023_for:1.2257);

    MAFFT alignment (974 columns: data/amfor_msa_MAFFT.fasta), Drosophila outgroup. Bombus+Nasonia support 90; the X3 split is weak (61) and disagrees with the UPGMA distance tree — that node is uncertain. Full run: data/tree_ml_iqtree.contree. Pairwise NW identity: ref–X3 86.7% · ref–Bombus 90.0% · ref–Nasonia 74.4% · ref–Dmel 55.2% · X3–Bombus 90.0% · full matrix in data/tree.phylogeny_INFO.txt. Apis cerana AEQ57608.1 (95 aa partial) excluded from tree.

    Real domain coordinates (InterPro via UniProt A0ACM8PXT7)

    cNMP-binding 102–217 + 220–335 (IPR000595) · kinase 367–626 (IPR000719) · AGC tail 627–678 (IPR000961) · active site 491 · ATP site 373–381. X3 coordinates mapped through the real alignment. Full list: data/interpro_Amfor.json.

    Drop in your 5 files

    1) tree.nwk from MEGA/RAxML → overwrite data/tree.nwk · 2) MAFFT FASTA or conservation CSV → data/ · 3) InterProScan TSV → data/ · 4) forager/nurse/queen counts CSV → data/ (heatmap/volcano/PCA read it) · 5) QTL table (chr, start, end, trait, LOD) on Amel_HAv3.1 → data/qtl_YOURS.csv. See data/METHODS.txt.

    Analysis figures and tools

    Every figure below shows computed values. The sequence lab and the waggle dance decoder are working tools, and the lab runs on the real foraging sequences.

    Candidate genes and regions

    Genes such as for and per were examined alongside epigenetic regulation, pheromone signalling and QTL evidence for age-dependent division of labour.