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The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
<p><strong>Datasets</strong>: The trimmed data matrices and partition files as shown in Table 2.</p> <ol> <li>P1P2R_Phylip.phy: 1<sup>st</sup> and 2<sup>nd</sup> positions of PCG nucleotides and rRNAs.</li> <li>P1P2R_partition.txt: Partition scheme for P1P2R_Phylip.phy.</li> <li>P12R_Phylip.phy: the united first two positions of PCG nucleotides plus rRNAs.</li> <li>P12R_partition.txt: Partition scheme for P12R_Phylip.phy.</li> <li>P2R_Phylip.phy: 2<sup>nd</sup> position of PCG nucleotides and rRNAs.</li> <li>P2R_partition.txt: Partition scheme for P2R_Phylip.phy.</li> <li>AA_Phylip.phy: PCG amino acids.</li> <li>AA_partition.txt: Partition scheme for AA_Phylip.phy.</li> </ol> <p><strong>Trees: </strong>The expanded consensus trees constructed by all data compositions, partition schemes, and models shown in Table 2.</p> <ol> <li>P1P2R_FP.tree: edge-unlinked and full partitioned (FP) dataset of PCG positions 1 & 2 + rRNAs.</li> <li>P1P2R_MP.tree: edge-unlinked and merged partitioned (MP) dataset of PCG positions 1 & 2 + rRNAs.</li> <li>P1P2R_NP.tree: unpartitioned (NP) dataset of PCG positions 1 & 2 + rRNAs.</li> <li>P1P2R_NPH4.tree: NP dataset of PCG positions 1 & 2 + rRNAs under +H4 heterotachy model.</li> <li>P12R_FP.tree: FP dataset of united PCG positions 1 & 2 + rRNAs.</li> <li>P12R_MP.tree: MP dataset of united PCG positions 1 & 2 + rRNAs.</li> <li>P12R_NP.tree: NP dataset of united PCG positions 1 & 2 + rRNAs.</li> <li>P12R_NPH4.tree: NP dataset of united PCG positions 1 & 2 + rRNAs under +H4 heterotachy model.</li> <li>P2R_FP.tree: FP dataset of PCG position 2 + rRNAs.</li> <li>P2R_MP.tree: MP dataset of PCG position 2 + rRNAs.</li> <li>P2R_NP.tree: NP dataset of PCG position 2 + rRNAs.</li> <li>P2R_NPH4.tree: NP dataset of PCG position 2 + rRNAs under +H4 heterotachy model.</li> <li>AA_FP.tree: FP dataset of PCG amino acids.</li> <li>AA_MP.tree: MP dataset of PCG amino acids.</li> <li>AA_NP.tree: NP dataset of PCG amino acids.</li> <li>AA_NPC60.tree: NP dataset of PCG amino acids under +C60 mixture model.</li> </ol> <p><strong>Tables S1-2.xlsx:</strong></p> <ol> <li>Table S1: Pairwise similarity of nucleotide alignments between <em>Creophilus maxillosus</em> and the 92 sampled species in the Staphylinoidea.</li> <li>Table S2: Percentage of conserved sites in amino acid alignments between <em>Creophilus maxillosus</em> and the 92 sampled species in the Staphylinoidea.</li> </ol> <p>Data Use Statement. Data on genetic material contained in this paper are published for non-commercial use only. Utilization by third parties for purposes other than non-commercial scientific research may infringe the conditions under which the genetic resources were originally accessed, and should not be undertaken without obtaining consent from the corresponding author of the paper and/or obtaining permission from the original provider of the genetic material.</p> <p> </p>
Fig. 3. Creophilus maxillosus pupae. A in Survival and Time of Development forCreophilus maxillosus(L.) (Coleoptera: Staphylinidae) at Three Constant Temperatures
Fig. 3. Creophilus maxillosus pupae. A) Reared at 32°C, third-instar exuvia partially attached ventrally, lateral view, B) Reared at 24°C, ventral view.
FIGURE 3 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 3 Inferred secondary structures of 22 tRNAs of C. maxillosus. The red bases are anticodon. The tRNAs are labelled with the abbreviations of their corresponding amino acids according to the IUPAC-IUB code.
FIGURE 5 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 5 Consensus trees built with different datasets under the respective best-fitting partitioning scheme and substitution model selected by AIC (see Table 2). (A) FP scheme of P1P2R matrix; (B) FP scheme of P12R matrix; (C) FP scheme of P2R matrix; (D) NP scheme of AA matrix (C60). The branch lengths are proportional to the number of nucleotide or amino acid substitutions. The species followed by an asterisk (*) are sequenced for this study. Coloured circles indicate bootstrap support. Nodes with 90–94 bootstrap values are labelled by red; 95–99 by yellow; 100 by blue. The expanded trees and trees built with alternative models can be found in the supplementary files at Zenodo (10.5281/zenodo.5847830).
FIGURE 2 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 2 Relative synonymous codon usage (RSCU) of C. maxillosus and P. impotens. Codon families (in alphabetical order) are provided below the horizontal axis.
FIGURE 1 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 1 Gene map of the mitochondrial genome of C. maxillosus and P. impotens. Genes outside the map are transcribed counterclockwise (reverse strand), whereas those inside are transcribed clockwise (forward strand). The outermost circle shows the gene features, sandy brown for rRNAs, salmon for tRNAs, and light sea green for PCGs. The innermost circle shows the GC content calculated in every 50-site window.
FIGURE 4 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 4 Inferred secondary structures of 22 tRNAs of P. impotens. The red bases are anticodon. The tRNAs are labelled with the abbreviations of their corresponding amino acids according to the IUPAC-IUB code.
Figure 34 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 34. Distribution of all georeferenced specimens of C. oculatus (circles) on the New Zealand mainland (left) and Chatham Islands archipelago (right). This species is also known from several other offshore islands, including the subantarctic Auckland and Snares Islands in the south, and the Kermadec Islands in the north east. Rectangle at southern end of New Zealand indicates area shown in Figure 35.
Figure 28 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 28. Distribution of all georeferenced specimens of C. albertisi (circles), C. erythrocephalus (square) and C. imitator (triangles) in New Guinea.
Figure 33 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 33. New Zealand Creophilus species, details of morphology (setae of heads, pronota, mesoventrites, and legs omitted). C. oculatus (A, D, G, J, M, N); C. huttoni (B, E, H, O); C. rekohuensis, holotype (C, F, I, K, L, P). A–C, head, dorsal; D–F, pronotum; G–I, mesoventrite; J, K, protarsus, dorsal; L, M, right protibia, anterior; N–P, left wing, dorsal; Q, scatter plot of wing length vs. pronotum length as proxy for body size (circles = C. oculatus, squares = C. huttoni, triangles = C. rekohuensis; black symbols = males, white symbols = females). Abbreviations: CuA, MP3, MP4, wing veins mentioned in text. Scale bars = 1 mm.
Figure 37 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 37. Distribution of georeferenced specimens of C. rekohuensis in the Chatham Islands, New Zealand (circles). The four largest islands from west to east are Little Mangere, Mangere, Pitt, and Rangatira. The record off the north-west coast of Pitt Island is from the tiny Rabbit Island. This species is also known from Star Keys, 14.5 km east of Pitt Island. For location of Chatham Islands see Figure 34.
Figure 27 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 27. Creophilus imitator, details of morphology (setae of mandibles, antenna, and pronotum omitted). A, mandibles, dorsal (bases omitted); B, right antenna, dorsal (only apical setae shown); C, median lobe apex, ventral; D, aedeagus with details of inverted internal sac, right lateral (parameral setae omitted); E, pronotum (female); F, female internal genitalia, ventral – arrow indicates small sclerotic ridges of vaginal fold; G, paramere, dorsal; H, ventral sclerite of internal sac, ventral (lower) and apical (upper). Abbreviations: T2, T3, mandibular teeth. Additional abbreviations as in Figure 3 (male) and Figure 5 (female). Scale bars: H = 0.1 mm; rest = 1 mm.
Figure 25 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 25. Creophilus erythrocephalus, details of morphology (setae of mandibles, antenna, and pronotum omitted). A, pronotum (large male); B, mandibles, dorsal (bases omitted); C, right antenna, dorsal (only apical setae shown); D, paramere, dorsal. Abbreviations: T2, T3, mandibular teeth. Scale bars = 1 mm.
Figure 24 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 24. Distribution of all georeferenced Creophilus specimens from South America. C. variegatus (triangles), C. erythrocephalus (squares), C. maxillosus maxillosus (circles).
Figure 21 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 21. Creophilus flavipennis, details of morphology (setae of head, mandibles, antenna, and pronotum omitted). A, head, dorsal (small male); B, mandibles, dorsal (bases omitted); C, right antenna, dorsal (only apical setae shown); D, paramere, dorsal; E, apical part of median lobe with fully everted internal sac, right lateral; F, aedeagus with details of internal sac, right lateral (parameral setae omitted); G, pronotum (small male); H, female internal genitalia, ventral – arrow indicates subsclerotized or pigmented regions; I, ventral sclerite of internal sac, ventral (lower) and apical (upper); J, median lobe apex, ventral – arrow indicates internal tooth flanking the groove of the median orifice. Abbreviations: T1, T2, T3, mandibular teeth. Additional abbreviations as in Figure 3 (male) and Figure 5 (female). Scale bars: I = 0.1 mm; rest = 1 mm.
Figure 26 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 26. Distribution of all georeferenced Australian specimens of C. erythrocephalus (circles). See Figure 24 for distribution in South America, and Figure 28 for New Guinea. This species is also known from Lord Howe Island, Fiji, French Polynesia, New Caledonia, Tonga, and Vanuatu.
Figure 32 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 32. Creophilus oculatus, details of morphology (setae of mandibles, antenna, and pronotum omitted). A, mandibles, dorsal (bases omitted); B, right antenna, dorsal (only apical setae shown); C, aedeagus with details of inverted internal sac, ventral; D, same, right lateral (parameral setae omitted); E, ventral sclerite of internal sac, ventral (lower) and apical (upper); F, pronotum (female); G, female internal genitalia, ventral; H, paramere, dorsal; I, median lobe apex, ventral. Abbreviations: T1, T2, T3, mandibular teeth. Additional abbreviations as in Figure 3 (male) and Figure 5 (female). Scale bars: E = 0.1 mm; rest = 1 mm.
Figure 29 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 29. Creophilus lanio, details of morphology (setae of mandibles, antenna, and pronotum omitted). A, mandibles, dorsal (bases omitted); B, right antenna, dorsal (only apical setae shown); C, female internal genitalia, ventral; D, paramere, dorsal; E, aedeagus with details of inverted internal sac, right lateral (parameral setae omitted); F, pronotum (female); G, ventral sclerite of internal sac, ventral (lower) and apical (upper); H, basal cap of internal sac; I, median lobe apex, ventral. Abbreviations: T1, T2, T3, mandibular teeth. Additional abbreviations as in Figure 3 (male) and Figure 5 (female). Scale bars: G and H = 0.1 mm; rest = 1 mm.
Figure 20 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 20. Distribution of all georeferenced specimens of C. galapagensis on Isla Isabela in the Galapagos Islands (circles). The species is also known from Fernandina, Santiago and San Cristóbal Islands.
Figure 17 in Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae)
Figure 17. Distribution of all georeferenced specimens of C. incanus in Madagascar and Mayotte (circles). This species is also known from Réunion and Mauritius islands.
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