Fig. 2

Gene family evolutionary analysis and positive selection analysis in the red turpentine beetle. a Phylogenetic tree and orthologs in the red turpentine beetle and 15 other arthropod species. The intra- and interspecies orthologs and paralogs were assigned using the OrthoMCL. The phylogenetic tree was inferred from 952 strict single-copy orthologous genes among 16 arthropod species using the RAxML software with the maximum likelihood method employing LG+G+I model and 500 bootstrap replications. All the nodes have at least 90% bootstrap support. The divergence time was estimated using the MCMCtree program with several calibration time points adopted from the TimeTree database (https://www.timetree.org). Numbers on internal nodes indicate divergence time, and gray bars represent error ranges. The phylogenetic tree was rooted on the two-spotted spider mite Tetranychus urticae. MRCA is the abbreviation of most recent common ancestor. 1:1:1 represents universal single-copy genes across these species, allowing for absence in two beetles and duplication in one species. N:N:N stands for universal multiple-copy genes across these species. The genes that were specific in Hymenoptera, Lepidoptera, Diptera, and Coleoptera were also shown in the figure in corresponding colors. Meanwhile, lineage-specific genes were also displayed for each species. Other denotes genes that do not belong to these groups in these species. Expansion and contraction analysis of gene families was performed using CAFÉ 3. The number of expanded (red) and contracted (blue) gene families are marked in the corresponding branch. b KEGG pathway enrichment analysis result of rapidly expanded gene families. Gene families with P < 0.05 were defined as rapidly evolving families. Pathway with qvalue < 0.05 was considered significantly enriched. c Gene ontology (GO) enrichment analysis result of positively selected genes in D. valens. GO categories with P < 0.05 were considered significantly enriched