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Supplementary material 1 from: Kise H, Fujii T, Masucci GD, Biondi P, Reimer JD (2017) Three new species and the molecular phylogeny of Antipathozoanthus from the Indo-Pacific Ocean (Anthozoa, Hexacorallia, Zoantharia). ZooKeys 725: 97-122. https://doi.org/10.3897/zookeys.725.21006
List of GenBank accesion number : Explanation note: GenBank accession numbers, names and details of the sequences used in phylogenetic analyses of COI, 16S-rDNA and ITS-rDNA in this study. Sequences that were concatenated are indicated by bold text.
Molecular phylogeny of North European Geometridae (Lepidoptera, Geometroidea)
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Fig. 2. Bayesian 50 in A molecular phylogeny of Boronia (Rutaceae): placement of enigmatic taxa and a revised infrageneric classification
Fig. 2. Bayesian 50% majority-rule consensus tree from the combined analysis of two nuclear (ITS, ETS) and three plastid markers (psbA–trnH, trnL–trnF and rbcL) showing the expanded section Boronia clade from Fig. 1. Thick lines show supported clades (≥0.95 PP). Jackknife percentages from MP analysis are indicated with symbols above branches: 100% JK (closed triangle); 90–99% JK (closed circle); (75–89% JK (open triangl)e; 50–74% JK (open circle). New or revised series assignments are indicated in bold.
Figure 6 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 6. Living individuals of four Elysia species from European waters used in this study. A, Elysia azorica sp. nov. (MNCN15.05/47823); B, E. flava (MNCN15.05/90931); C, E. rubeni (MNCN15.05/200080); D, E. timida (MNCN15.05/90934). Photos taken by Manuel Malaquías (A); Jakov Prkic (B); Fabio Vitale (C) and Giulia Furfaro (D). Scale bars = 1 mm.
Figure 5 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 5. Living individuals of the species Elysia viridis (A–F) and Elysia evelinae (G–H) used in this study. A, MNCN15.05/90901; B, MNCN15.05/90894; C, MNCN15.05/90910; D, MNCN15.05/90898; E, MNCN15.05/90906; F, MNCN15.05/90889; G, MNCN15.05/90924; H, MNCN15.05/90923. Photos taken by Peter H. van Bragt (A); Leila Carmona (B); Gianni Colucci (C); Marina Poddubetskaia (D, G–H); Alen Petani (E) and D'Onofrio (F). Scale bars = 1 mm.
Figure 7 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 7. Scanning electron micrographs of Elysia spp. radular teeth. A, E. azorica sp. nov. (MNCN15.05/47823); B, E. rubeni (MNCN15.05/200080); C, D, E. viridis: C, MNCN15.05/90903; D, MNCN15.05/90912; E, E. flava (MNCN15.05/90929); F, E. timida (MNCN15.05/90933); G, E. gordanae (MNCN15.05/90843); H, E. gordanae (MNCN15.05/90836); I, J, K, E. margaritae: I, J, MNCN15.05/90817; K, MNCN15.05/94854; L, E. evelinae (MNCN15.05/90924). Scale bars = 10 μm.
Figure 8 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 8. Elysia azorica sp. nov. reproductive system (MNCN 15.05/47823), scale bar = 100 μm. Abbreviations: ag, albumen gland; am, ampulla; fmgc, female gland complex; fp, female pore; hf, hermaphroditic follicle; gr, genital receptacle; p, penis; sr, seminal receptacle; vd, vas deferens.
Figure 4 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 4. Living individuals of the species Elysia gordanae (A–F) and Elysia margaritae (G–H) used in this study. A, MNCN15.05/90861; B, MNCN15.05/90854; C, MNCN15.05/90855; D, MNCN15.05/90829; E, MNCN15.05/90841; F, MNCN15.05/90839; G, MNCN15.05/90816; H, MNCN15.05/90817. Photos taken by Fabio Vitale (A, G–H); Marina Poddubetskaia (B–C, E) and Alen Petani (D). Scale bars = 1 mm.
Figure 3 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 3. Molecular phylogeny of Atlantic and Mediterranean Elysia species rooted on genus Bosellia (not shown), based on the combined dataset (H3 + COI + 16S) inferred by Bayesian inference analysis. Numerals in parentheses indicate the number of specimens from the same locality. Bold branches represent the Elysia species present in European waters arranged in four subclades labelled from A to D. Significant support values are given as ML bootstrap percentages (below branch) and BI posterior probabilities (above branch). Not supported branches are not labelled. Abbreviations: EA, eastern Atlantic Ocean; MED, Mediterranean Sea; WA, western Atlantic Ocean.
Figure 1 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 1. Molecular phylogeny of worldwide Elysia species rooted on genus Bosellia (not shown). Topology is based on Bayesian inference analysis of concatenated dataset (H3 + COI + 16S + 28S). Only one specimen per species is shown according to species delimitation analyses. Bold red species names indicate the species sequenced in this study that are present in European waters. Significant support values are given as ML bootstrap percentages (BS, below branch) and BI posterior probabilities (PP, above branch). Asterisks indicate complete support (PP = 1.0, BS = 100%). Vertical grey bars indicate specimens grouped as species entities by ABGD, GMYC and bPTP methods based on the COI gene. Unfilled vertical bars indicate the specimens grouped as species based on the 16S gene.
Figure 2 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 2. Histogram of pairwise genetic COI distances (Kimura parameter) among 638 sequences including all available National Center for Bioinformatics (NCBI) sequences for Elysia, showing barcoding gap; the arrow indicates the threshold that allows to distinguish intraspecific (left) and interspecific (right) distances for the COI region, based on ABGD analyses.
FIGURE 2. Molecular phylogeny estimated using IQTREE2 in A cautionary note on synonymization based on mitochondrial data in Orthoptera: a comment of Hochkirch et al. 2023
FIGURE 2. Molecular phylogeny estimated using IQTREE2 (Minh et al. 2020) and the complete mitochondrial genome showing the paraphyly of the species within the genus Omocestus and Gomphocerrippus. Node supports are ultra-fast bootstrap supports. The code to the right of the species name indicates SRA accession number. All data are from Hawlitschek et al. 2022 except Omocestus haemorrhoidalis accession SRR21022974. Abbreviation: O. = Omocestus, P. = Pseudochorthippus and G. = Gomphocerrippus.
FIGURE 1. Molecular phylogeny estimated using IQTREE2 in A cautionary note on synonymization based on mitochondrial data in Orthoptera: a comment of Hochkirch et al. 2023
FIGURE 1. Molecular phylogeny estimated using IQTREE2 (Minh et al. 2020) and ITS2 loci. Colours represent species according to Supplementary Table 1 of Hochkirch et al. 2023. Dotted lines indicate species not supported by the phylogenetic estima.
Fig. 2 50 in Molecular phylogeny of the endemic fern genera Cyrtomidictyum and Cyrtogonellum (Dryopteridaceae) from East Asia
Fig. 2 50% majority rule consensus tree from four Bayesian analyses of 1,000,000 generations each of the rbcL data set, excluding burn-in trees. Posterior probability support values ≥ 0.90 from Bayesian analyses shown above branches, bootstrap support values>50% from Maximum Likelihood analyses below branches
Fig. 5 in Molecular phylogeny of the endemic fern genera Cyrtomidictyum and Cyrtogonellum (Dryopteridaceae) from East Asia
Fig. 5 Consensus tree resulting from Bayesian analysis of the combined (rbcL, atpB, rps4-trnS, and trnL-trnF) data set. Numbers on branches are Bayesian (PP)/Maximum Likelihood (BS) support values
Fig. 4 50 in Molecular phylogeny of the endemic fern genera Cyrtomidictyum and Cyrtogonellum (Dryopteridaceae) from East Asia
Fig. 4 50% majority rule consensus tree from Bayesian analyses of the three-gene (rbcL, rps4-trnS, and trnL-trnF) data set. Numbered solid circles indicate nodes receiving good support in both Bayesian (PP ≥ 0.90) and Maximum Likelihood (BS ≥ 70) analyses; open circles indicate nodes not receiving good support from either mea- sure; see also Figure 3. Single letters in dark and light grey squares on branches refer to synapomorphic indels in the rps4-trnS and trnL-trnF alignments, respectively. "P" denotes polystichoid ferns; major groups also indicated at right
Fig. 3 in Molecular phylogeny of the endemic fern genera Cyrtomidictyum and Cyrtogonellum (Dryopteridaceae) from East Asia
Fig. 3 Support values for major clades. Each row corresponds to a clade receiving either Bayesian posterior probability (PP)≥ 0.50 or Maximum Likelihood bootstrap support (BS)≥ 50% from single- or multiple-gene data sets. Clades 01–14 were resolved in the three-gene combined analysis and correspond to the numbered nodes in Figure 4. The remaining clades were supported in different single-gene data sets; their composition is indicated in terms of nodes resolved in the combined
FIGURE 6 in The first zoeal stage morphology of Achelous spinimanus (Latreille), A. gibbesii (Stimpson), and Portunus sayi (Gibbes) (Decapoda, Brachyura) provides support for molecular phylogeny
FIGURE 6. Telson furcae, detail of spinulation. a. Achelous gibbesii (Stimpson, 1859); b. Portunus sayi (Gibbes, 1850) (Scale bar: 0.02 mm)
FIGURE 5. Maxillule. a in The first zoeal stage morphology of Achelous spinimanus (Latreille), A. gibbesii (Stimpson), and Portunus sayi (Gibbes) (Decapoda, Brachyura) provides support for molecular phylogeny
FIGURE 5. Maxillule. a. Achelous gibbesii (Stimpson, 1859); b. Portunus sayi (Gibbes, 1850). Maxilla. c. A. gibbesii; d. P. sayi. (Scale bar: 0.05 mm)
FIGURE 3. Cephalothorax, lateral view. a in The first zoeal stage morphology of Achelous spinimanus (Latreille), A. gibbesii (Stimpson), and Portunus sayi (Gibbes) (Decapoda, Brachyura) provides support for molecular phylogeny
FIGURE 3. Cephalothorax, lateral view. a. Achelous gibbesii (Stimpson, 1859); b. Portunus sayi (Gibbes, 1850). Magnification of lateroventral margin. c. A. gibbesii; d. P. sayi. (Scale bar: a, c = 0.1 mm; b, d = 0.05 mm)
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