DOI: 10.5061/dryad.02v6wwqbm
title: Data from: Genomic data provide insights into the classification of extant termites

description: The higher classification of termites requires substantial revision as the
 Neoisoptera, the most diverse termite lineage, comprise many paraphyletic
 and polyphyletic higher taxa. Here, we produced an updated termite
 classification using genomic-scale analyses. We reconstructed phylogenies
 under diverse substitution models with ultraconserved elements analyzed as
 concatenated matrices or within the multi-species coalescence framework.
 Our classification is further supported by analyses controlling for rogue
 loci and taxa, and topological tests. We show that the Neoisoptera are
 composed of seven family-level monophyletic lineages, including the
 Heterotermitidae Froggatt, Psammotermitidae Holmgren, and Termitogetonidae
 Holmgren, raised from subfamilial rank. The species-rich Termitidae are
 composed of 18 subfamily-level monophyletic lineages, including the new
 subfamilies Crepititermitinae, Cylindrotermitinae, Forficulitermitinae,
 Neocapritermitinae, Protohamitermitinae, and Promirotermitinae, and the
 revived Amitermitinae Kemner, Microcerotermitinae Holmgren, and
 Mirocapritermitinae Kemner. Building an updated taxonomic classification
 on the foundation of unambiguously supported monophyletic lineages makes
 it highly resilient to potential destabilization caused by the future
 availability of novel phylogenetic markers and methods. The taxonomic
 stability is further guaranteed by the modularity of the new termite
 classification, designed to accommodate as-yet undescribed species with
 uncertain affinities to the herein delimited monophyletic lineages in the
 form of new families or subfamilies.
description: # Supplementary Data from: Genomic data provide insights into the
 classification of extant termites Authors: Simon Hellemans, Mauricio M.
 Rocha, Menglin Wang, Johanna Romero Arias, Duur K. Aanen, Anne-Geneviève
 Bagnères, Aleš Buček, Tiago F. Carrijo, Thomas Chouvenc, Carolina Cuezzo,
 Joice Paulo Constantini, Reginaldo Constantino, Franck Dedeine, Jean
 Deligne, Paul Eggleton, Theodore A. Evans, Robert Hanus, Mark C. Harrison,
 Myriam Harry, Guy Josens, Corentin Jouault, Chicknayakanahalli M.
 Kalleshwaraswamy, Esra Kaymak, Judith Korb, Chow-Yang Lee, Frédéric
 Legendre, Hou-Feng Li, Nathan Lo, Tomer Lu, Kenji Matsuura, Kiyoto
 Maekawa, Dino McMahon, Nobuaki Mizumoto, Danilo E. Oliveira, Michael
 Poulsen, David Sillam-Dussès, Nan-Yao Su, Gaku Tokuda, Edward Vargo,
 Jessica L. Ware, Jan Šobotník , Rudolf H. Scheffrahn, Eliana Cancello,
 Yves Roisin, Michael S. Engel, and Thomas Bourguignon ### File 1:
 "ids\_to\_species.txt" Specimens and corresponding
 identification codes in the database (TER-X-UCEDB). ### File 2:
 "TER\_UCE\_DB\_CONTRIB\_4.fasta.gz" New UCE dataset presented in
 this study. Extracted UCEs from all samples using the bait set produced by
 Hellemans et al. (2022; doi: 10.1016/j.ympev.2022.107520). This is
 contribution #4 for the Termite UCE Database. Each sample was assigned a
 unique identification code (TER-X-UCEDB). The database is maintained at:
 [https://github.com/sihellem/TER-UCE-DB/](https://github.com/sihellem/TER-UCE-DB/). ### File 3: "supermatrices.tar" Supermatrices used in this study. Refer to the Supplementary Data 4 published alongside the main text for relevant metrics. The tar archive contains the following supermatrices and partitions: 1_internal_unfiltered.charsets 1_internal_unfiltered.nexus 2_internal_cogenic.charsets 2_internal_cogenic.nexus 3_internal_intergenic.charsets 3_internal_intergenic.nexus 4_edge_no_stop_nuc.charsets 4_edge_no_stop_nuc.nexus 4_edge_no_stop_nuc_no3rd.charsets 5_edge_two_stops_nuc.charsets 5_edge_two_stops_nuc.nexus 5_edge_two_stops_nuc_no3rd.charsets 6_edge_no_stop_codon.charsets 6_edge_no_stop_codon.nexus 7_edge_two_stops_codon.charsets 7_edge_two_stops_codon.nexus 8_edge_no_stop_prot.charsets 8_edge_no_stop_prot.fasta 9_edge_two_stops_prot.charsets 9_edge_two_stops_prot.fasta ### File 4: "trees.tar" Phylogenetic trees reconstructed in this study. Prefix of treefiles is as follows: tree#*software_analysis#*... Refer to the Supplementary Data 5 published alongside the main text for more information on analysis#. Trees 1-30 were reconstructed with IQ-TREE (30 trees), while trees 31-72 were reconstructed with ASTRAL-III (21 trees: #31-51), or with TreeShrink followed by ASTRAL-III (21 trees: #52-72). The tar archive contains the following trees: *# Trees from IQ-TREE* 01_iqtree_01_DNA_70_unfilt_GTR_aln.nexus.treefile.tree 02_iqtree_02_DNA_70_unfilt_TESTMERGE_aln.nexus.treefile.tree 03_iqtree_03_DNA_70_cogenic_GTR_aln.nexus.treefile.tree 04_iqtree_04_DNA_70_cogenic_TESTMERGE_aln.nexus.treefile.tree 05_iqtree_05_DNA_70_intergenic_GTR_aln.nexus.treefile.tree 06_iqtree_06_DNA_70_intergenic_TESTMERGE_aln.nexus.treefile.tree 07_iqtree_07_DNA_70_no-stop-pal_NUCLEO_no_3rd_GTR+I+G_bb_aln.nexus.treefile.tree 08_iqtree_08_DNA_70_no-stop-pal_NUCLEO_no_3rd_TESTMERGE_rcluster_aln.nexus.treefile.tree 09_iqtree_09_DNA_70_max-two-stops-pal_NUCLEO_no_3rd_GTR+I+G_bb_aln.nexus.treefile.tree 10_iqtree_10_DNA_70_max-two-stops-pal_NUCLEO_no_3rd_TESTMERGE_rcluster_aln.nexus.treefile.tree 11_iqtree_11_COD_70_no-stop-pal_NUCLEO_all_partitions_GTR+I+G_bb_aln.nexus.treefile.tree 12_iqtree_12_COD_70_no-stop-pal_NUCLEO_all_partitions_TESTMERGE_rcluster_aln.nexus.treefile.tree 13_iqtree_13_COD_70_max-two-stops-pal_NUCLEO_all_partitions_GTR+I+G_bb_aln.nexus.treefile.tree 14_iqtree_14_COD_70_max-two-stops-pal_NUCLEO_all_partitions_TESTMERGE_rcluster_aln.nexus.treefile.tree 15_iqtree_15_COD_70_no-stop-pal_NUCLEO_coding_ECMK07_rcluster_aln.nexus.treefile.tree 16_iqtree_16_COD_70_no-stop-pal_NUCLEO_coding_GY2K_rcluster_aln.nexus.treefile.tree 17_iqtree_17_COD_70_no-stop-pal_NUCLEO_coding_MG2K_rcluster_aln.nexus.treefile.tree 18_iqtree_18_COD_70_max-two-stops-pal_NUCLEO_coding_ECMK07_rcluster_aln.nexus.treefile.tree 19_iqtree_19_COD_70_max-two-stops-pal_NUCLEO_coding_GY2K_rcluster_aln.nexus.treefile.tree 20_iqtree_20_COD_70_max-two-stops-pal_NUCLEO_coding_MG2K_rcluster_aln.nexus.treefile.tree 21_iqtree_21_COD_70_no-stops-aln_PROT_LG+F+G_rcluster_aln.fasta.treefile.tree 22_iqtree_22_COD_70_no-stops-aln_PROT_LG+C20+F+G_rcluster_aln.fasta.treefile.tree 23_iqtree_23_COD_70_no-stops-aln_PROT_Q.insect+F+G_rcluster_aln.fasta.treefile.tree 24_iqtree_24_COD_70_no-stops-aln_PROT_DCMut_rcluster_aln.fasta.treefile.tree 25_iqtree_25_COD_70_no-stops-aln_PROT_TESTMERGE_rcluster_aln.fasta.treefile.tree 26_iqtree_26_COD_70_max-two-stops-aln_PROT_LG+F+G_rcluster_aln.fasta.treefile.tree 27_iqtree_27_COD_70_max-two-stops-aln_PROT_LG+C20+F+G_rcluster_aln.fasta.treefile.tree 28_iqtree_28_COD_70_max-two-stops-aln_PROT_Q.insect+F+G_rcluster_aln.fasta.treefile.tree 29_iqtree_29_COD_70_max-two-stops-aln_PROT_DCMut_rcluster_aln.fasta.treefile.tree 30_iqtree_30_COD_70_max-two-stops-aln_PROT_TESTMERGE_rcluster_aln.fasta.treefile.tree *# Trees from ASTRAL without TreeShrink* 31_astral_01_sptree-renamed.tree 32_astral_03_sptree-renamed.tree 33_astral_05_sptree-renamed.tree 34_astral_07_sptree-renamed.tree 35_astral_09_sptree-renamed.tree 36_astral_11_sptree-renamed.tree 37_astral_13_sptree-renamed.tree 38_astral_15_sptree-renamed.tree 39_astral_16_sptree-renamed.tree 40_astral_17_sptree-renamed.tree 41_astral_18_sptree-renamed.tree 42_astral_19_sptree-renamed.tree 43_astral_20_sptree-renamed.tree 44_astral_21_sptree-renamed.tree 45_astral_22_sptree-renamed.tree 46_astral_23_sptree-renamed.tree 47_astral_24_sptree-renamed.tree 48_astral_26_sptree-renamed.tree 49_astral_27_sptree-renamed.tree 50_astral_28_sptree-renamed.tree 51_astral_29_sptree-renamed.tree *# Trees from ASTRAL with TreeShrink* 52_astral_treeshrink_01_sptree-renamed.tree 53_astral_treeshrink_03_sptree-renamed.tree 54_astral_treeshrink_05_sptree-renamed.tree 55_astral_treeshrink_07_sptree-renamed.tree 56_astral_treeshrink_09_sptree-renamed.tree 57_astral_treeshrink_11_sptree-renamed.tree 58_astral_treeshrink_13_sptree-renamed.tree 59_astral_treeshrink_15_sptree-renamed.tree 60_astral_treeshrink_16_sptree-renamed.tree 61_astral_treeshrink_17_sptree-renamed.tree 62_astral_treeshrink_18_sptree-renamed.tree 63_astral_treeshrink_19_sptree-renamed.tree 64_astral_treeshrink_20_sptree-renamed.tree 65_astral_treeshrink_21_sptree-renamed.tree 66_astral_treeshrink_22_sptree-renamed.tree 67_astral_treeshrink_23_sptree-renamed.tree 68_astral_treeshrink_24_sptree-renamed.tree 69_astral_treeshrink_26_sptree-renamed.tree 70_astral_treeshrink_27_sptree-renamed.tree 71_astral_treeshrink_28_sptree-renamed.tree 72_astral_treeshrink_29_sptree-renamed.tree *# Consensus trees* 73_iqtree_majority_rule_phytools_updated.tree 74_astral_majority_rule_phytools_updated.tree 75_astral_treeshrink_majority_rule_phytools_updated.tree ### File 5: "termitidae\_diagnosing\_database\_v1.fasta.gz" Database containing the top 20 UCE loci diagnostic of subfamilies of Termitidae. This file was designed with all samples of Termitidae available in the Termite UCE Database (Contributions 1-4; i.e., 227 samples). The database file will be updated with each new contribution (maintained at: [https://github.com/sihellem/TER-UCE-DB/](https://github.com/sihellem/TER-UCE-DB/)). The presently deposited file (version 1) is not diagnostic for subfamilies represented by only one sample (i.e., Crepititermitinae, Forficulitermitinae, and Protohamitermitinae).