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Figure 3 in Checklist of Water mites in Mexico. Historical background and DNA barcoding perspectives

Figure 3 Neighbor joining tree based on all worldwideNeumaniaCOI sequences. The name is followed by the barcode index number (BIN). * Without data collection.

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Fig. 3 in New record of blunthead pufferfish, Sphoeroides pachygaster (Muller & Troschel, 1848) (Tetraodontiformes: Tetraodontidae) from Indian water along with DNA barcode and some biological aspects

Fig. 3 — Phylogenetic tree topology for Sphoeroides pachygaster (Müller & Troschel, 1848) with sister species based on 16S gene sequences using maximum likelihood method

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Fig. 2 in New record of blunthead pufferfish, Sphoeroides pachygaster (Muller & Troschel, 1848) (Tetraodontiformes: Tetraodontidae) from Indian water along with DNA barcode and some biological aspects

Fig. 2 — Histological section of gonad of S. pachygaster from the Indian water (10 µm thickness observed at 10X and 40X magnification). Fe: Follicular epithelium cells, Zr: Zona radiata, Yg: Yolk globules, Ysg: Egg yolk granules, and Af: Atretic follicle

Fig. 6 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 6: ML phylogenetic tree of the genus Polyclinum (sequences abbreviation: Pln) based on COI nucleotide sequences (1560 aligned nucleotide sites; best-fit substitution model GTR+I+G; bootstrap on 100 replicates). Eudistoma and Pseudodistoma species were used as outgroups. The sequence list and species abbreviations are reported in Supplementary table S1. Black dots: bootstrap values ≥ 70 %; red: P. constellatum sequences; blue: P. indicum sequences; yellow background: our sequences.

Fig. 4 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 4: A, C) Colonies of Polyclinum constellatum with different colours photographed and collected in the Heraklion marina (Crete) (A: colony K11 and C: colony K12); B) Transversal section of the colonies, joined only at the surface layer (upper white arrow); D) Zooid extracted from the red-orange colony (K11), with magnification of the 6-lobed anus; E) Zooid extracted from the dark blue colony (K12) with magnification of the 6-lobed anus. Both K11 and K12 have the same COI haplotype (sequence AC number: MT873559).

Fig. 5 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 5: A) Larva of P. constellatum, showing the ocellus, four long narrow ampullae, three adhesive papillae and a group of a few small ventral vesicles (red arrow). am, ampullae; ap, adhesive papillae; oc, ocellus; B) Larva of P. constellatum, red arrow pointing out the calcite crystal in the middle of the body.

Fig. 2 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 2: A) Orange colony of Polyclinum constellatum from Taranto harbour (colony P1); B) Magnification of the oral (arrow pointing put the oral tentacles of different size) and cloacal aperture (asterisk); C) P. constellatum collected in Heraklion (colony K19) with zooids arranged in systems around the cloacal apertures; D) Section of the colony showing the zooids located only around the outer edge (arrow).

Fig. 3 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 3: A) Whole zooid of Polyclinum constellatum, showing a clear division into thorax, abdomen and post-abdomen with a long vascular stolon. ab, abdomen; pa, post-abdomen; th, thorax; vs, vascular stolon; B) Zooid with evident pharynx, rectum, anus and four embryos incubated in the atrial cavity. The funnel-shaped oesophagus, the smooth stomach and the twisted gut loop are visible in the abdomen. The post-abdomen shows the heart at its terminal end, as well as several rounded testicular follicles and the ovary, with the gonoducts running parallel to the rectum. an, anus; e, embryos; gd, gonoducts; gl, gut loop; oe, oesophagus; ov, ovary; h, heart; r, rectum; st, stomach; tf, testicular follicles; C) Magnification of the oral siphon with six pointed lobes (arrows) and six longitudinal muscle bands (indicated with numbers 1-6); D) Branchial sac with 18 rows of stigmata and narrow languets of the dorsal lamina (arrows); E) Magnification of the pharynx, with minute papillae (arrows) at the level of the transverse vessels; F) Magnification of the six-lobed anus (lobes indicated with numbers 1-6).

Fig. 1 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 1: Map of the Mediterranean Sea showing the literature records (black rhombuses) of P. constellatum and the new findings (red dots). performed in a final reaction volume of 25 μl contain- nus was reconstructed with the online software PHYML ing: 1X reaction buffer with 1 mM final concentration of v3.0 (http://www.atgc-montpellier.fr/phyml-sms/) (Guin- MgCl 2 (Takara Bio Inc.), 0.2 mM of each dNTP, 0.3 μM don & Gascuel, 2003), which also includes the automatof each primer and 1.25 Units of PrimeStar HS (Takara ic model selection algorithm SMS (Smart Model Selec- Bio Inc.). Amplification conditions were: 30 cycles with tion). The best-fit substitution model was selected using denaturation for 10 s at 98°C, annealing for 15 s at 46°C the Akaike Information Criterion (AIC). Bootstrap val- or 50°C, extension for 1 min 30 s at 72°C; a final elonga- ues, indicating node reliability, were based on 100 reption step of 5 min at 72°C. licates. The sequence dataset used for this phylogenetic PCRs with the DreamTaq polymerase were performed reconstruction is reported in Supplementary Table S1 and in a final volume of 25 μl containing: 1X reaction buffer was extracted from the phylogenetic dataset published in with 2 mM final concentration of MgCl 2 (Thermo Fish- Tabudravu et al. (2019). It includes representative species er Scientific), 0.2 mM of each dNTP, 0.4 μM of each of of the Polyclinidae family plus Eudistoma and Pseudodithe two primers, and 1.25 Units of DreamTaq polymerase stoma species chosen as outgroups for their morphologi- (Thermo Fisher Scientific). The amplification conditions cal similarities with Polyclinidae. were as follows: an initial denaturation for 3 min at 95°C, then 34 amplification cycles (denaturation for 30 s at 95°C; annealing for 30 s at 46-50°C; extension for 1 min Results 30 s at 72°C) followed by a final elongation step of 5 min at 72°C. Morphological analyses The obtained amplicons were purified with the DNA Clean&Concentrator kit (Zymo Research) and directly The colonies collected in Taranto harbour and Hersequenced according to the Sanger method by Microsynth aklion marina were all morphologically identified as P. AG (Switzerland). The sequence quality check, compar- constellatum based on the following features: colonies isons and alignment were carried out with Geneious ver. without sand in/outside, zooids arranged in systems, 5.5.7.2 (Kearse et al., 2012). The sequences obtained post-abdomen (without vascular stolon) shorter than the were deposited in the GenBank database (see Accession thorax and abdomen combined, pharynx with 16-18 rows numbers MT873559 and OL597608). For comparative of stigmata, more than 15 stigmata per row, and a 6-lobed analyses, homologous sequences of the genus Polycli- anus. These characteristics are in accordance with the key num were searched for in the non-redundant nucleotide of Polyclinum species edited by Kott (1963) and they are database (nr-nt db, on 21st September 2021) of the NCBI also reported in the description of the species made by (National Center for Biotechnology Information) by En- Van Name (1945). trez text search, and by BLASTn (Altschul et al., 1990) using our P. constellatum sequences as the query. Uncorrected pairwise distances were calculated with PAUP 4.0a (Swofford, 2002), while a Maximum Likelihood (ML) phylogenetic tree of the genus Polyclinum ge-

Figs 22–34 in MORPHOLOGICAL REDESCRIPTION AND DNA BARCODING OF TORLEYA PADUNICA KAZLAUSKAS, 1963 (EPHEMEROPTERA, EPHEMERELLIDAE) FROM THE EAST PALAEARCTIC REGION

Figs 22–34. Larvae of Torleya padunica. 22 – pro- and mesonotum; 23–25 – legs (23 – fore, 24 – mid, 25 – hind); 26–28 claws (26 – fore leg, 27 – mid leg, 28 – hind leg); 29 – abdomen, dorsal view; 30– gill I pair; 31–34 gills, sketchily (31 – II pair, 32 – III pair, 33 – IV pair, 34 – V pair). 9

Figs 6–10 in MORPHOLOGICAL REDESCRIPTION AND DNA BARCODING OF TORLEYA PADUNICA KAZLAUSKAS, 1963 (EPHEMEROPTERA, EPHEMERELLIDAE) FROM THE EAST PALAEARCTIC REGION

Figs 6–10. Torleya padunica: 6–11 male imago; 12 – female imago. 6 – genitalia; 7 – styliger and gonostyli; 8 – 3rd segment of gonostyli; 9 – genitalia; 10, 11 – penis; 12 – subanal plate. 6 – lateral view, 7, 10–12 – ventral view; 8, 9 – dorsal view.

Fig. 40 in MORPHOLOGICAL REDESCRIPTION AND DNA BARCODING OF TORLEYA PADUNICA KAZLAUSKAS, 1963 (EPHEMEROPTERA, EPHEMERELLIDAE) FROM THE EAST PALAEARCTIC REGION

Fig. 40. Ultrametric Bayesian inference (BI) tree based on the cytochrome c oxidase I (COI) nucleotide sequence data of the genus Torleya Lestage. Bayesian posterior probabilities (higher than 0.7) are given above tree nodes. Specimens obtained in this study are in bold.

Figs 15–21 in MORPHOLOGICAL REDESCRIPTION AND DNA BARCODING OF TORLEYA PADUNICA KAZLAUSKAS, 1963 (EPHEMEROPTERA, EPHEMERELLIDAE) FROM THE EAST PALAEARCTIC REGION

Figs 15–21. Larvae of Torleya padunica. 15 – head; 16 – labrum; 17 –hypopharynx and superlinguas; 18, 19 – mandibles, ventral view (18 – right, 19 – left); 20 – maxilla; 21 – labium.

Figs 36–39. Torleya mikhaili, genitalia. 36 in MORPHOLOGICAL REDESCRIPTION AND DNA BARCODING OF TORLEYA PADUNICA KAZLAUSKAS, 1963 (EPHEMEROPTERA, EPHEMERELLIDAE) FROM THE EAST PALAEARCTIC REGION

Figs 36–39. Torleya mikhaili, genitalia. 36 – styliger and gonostyli; 37 – penis; 38 – penis and gonostyli; 39 – penis lobes. 36, 38–39 – ventral view; 37 – dorsal view.

Fig. 1 in Polyclinum constellatum (Tunicata, Ascidiacea), an emerging non-indigenous species of the Mediterranean Sea: integrated taxonomy and the importance of reliable DNA barcode data Abstract

Fig. 1: Map of the Mediterranean Sea showing the literature records (black rhombuses) of P. constellatum and the new findings (red dots).

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Fig. 3 in Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River

Fig. 3. Phylogenetic trees of Hoplias malabaricus haplotypes based on COI mitochondrial gene sequences. a) Neighbor-Joining; b) Maximum likelihood and c) Maximum Parsimony. Values in the nodes indicate the statistical support from bootstrap test.

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Fig. 2. C in Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River

Fig. 2. C-banded karyotype of karyomorph C of Hoplias malabaricus, from lower Amazonas River. M - metacentric, SM - submetacentric. Bar = 10µm.

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Fig. 1 in Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River

Fig. 1. Map of collection sites of Hoplias malabaricus in the lower Amazonas River. Localities: 1 - Sapucuá lake; 2 - Óbidos; 3 - Juá lake; 4 - Urumari stream; 5 - Maicá lake; 6 - Almeirim. A map of Brazil (box on left corner) with the Pará State shaded in gray indicates the studied area by a white rectangle.

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Fig. 1 in DNA barcode of Parodontidae species from the La Plata river basin - applying new data to clarify taxonomic problems

Fig. 1. Map of the La Plata River basin showing the localities of Parodontidae samples used in this study. Empty pentagon: P. nasus; full pentagon: A. affinis; empty star: P. moreirai; full star: A. affinis; empty square: A. vittatus; full square: A. piracicabae; empty lozenge: Apareiodon sp.; full lozenge: A. vladii; empty triangle: A. affinis; full triangle: A. ibitiensis. The Iguaçu Falls and the Itaipu hydroelectric Power Plant are located in the city of Foz do Iguaçu, PR and the old Seven Falls in the city of Guaíra, PR - shown on the map.