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Fig. 17 in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 17 Palaeobiogeographic relations of the cyathaxonid coral fauna of the Aheimer Formation (asterisk) showing its rooting in the western Palaeotethys (red dots) and the strong relations to the cool-water Cordilleran–Arctic–Uralian realm (yellow dots). The fauna is a precursor of the Lower Permian cyathaxonid cool-water fauna of the eastern Cimmerian peri-Gondwana terranes (E´pGT). Base map from Abd-Elhameed et al. (2021) as modified from Kiessling et al. (1999)

Fig. 13 A in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 13 A Ufimia sp. A1 External view of the specimen RAh (101), showing a straight conical corallite with eroded calice rim and apex. Positions of thin-sections indicated. A2–A3 Two successive transverse thin-sections in the mature part of the corallite show the thick, rhopaloid major septa meet in the corallite centre. Scale bars: A1: 5 mm; A2, A3: 2 mm. B Bothrophyllum okense Kossovaya, 2001. B1 External view of the partly preserved corallite (RAh 37), with partly eroded wall. Positions of thin-sections indicated. Successive transverse thin-sections from the lower less mature part in B2 up to the more mature section below the calice in B4, the transverse sections show the axial septum and a very narrow dissepimentarium. Scale bars: 5mm

Fig. 12 in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 12 Relation between number of major septa and coralla alar diameters for: A Lytvolasma paraaucta n. sp., L aucta Fedorowski, 1987, L. asymetrica Soshkina, 1925 described by Chwieduk (2013), L. canadense Fedorowski and Bamber, 2001 and the current studied L. cf. canadense Fedorowski and Bamber, 2001. B Monophyllum galalaensis n. sp. and M. parvum Fomichev, 1953. C Rotiphyllum exile de Groot, 1963. D Zaphrentites cf. parallela (Carruthers, 1910) and Zaphrentites sp

Fig. 10 in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 10 Rotiphyllum exile de Groot, 1963. A1 External lateral view of the corallite RAh (116), showing a slightly curved corallite with a calice largely preserved but compressed. Positions of thin-sections indicated. A2 Transverse thin section at the immature part of the corallite, showing a stereocolumn in the centre. A3–A4 Two successive transverse thin-sections at the early and latest mature stages, showing a long cardinal septum with thin axial end (diagenetically broken in A4). B1 External lateral view of the corallite RAh (117), with partly eroded calice. B2–B4 Successive transverse thin-sections marked in B1, showing the radial to sub-radial arrangement of major septa, the central stereocolumn and the long cardinal septum with a thin axial end. C1–C2 Two successive transverse thin-sections in the mature part of the corallite RAh (21). D1 Transverse thin-section in the immature part of the specimen RAh (46) showing a zaphrentoid arrangement of major septa. D2 Transverse thin-section in the mature part of the corallite, showing a deformed long cardinal septum in a triangular fossula. Black dots indicate the positions of cardinal septum (below), counter septum (above) and the two alar septa

Fig. 3 in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 3 Field aspects of the Aheimer Formation; A General view of the studied succession of the lower member exposed in a faulted block to the north of Porto Sukhna; the shales mudstones close to the base (rectangle) are interbedded with thin, hard dolomitic bands. B Close up view on of the lower fossiliferous shale mudstone beds of A. C, D Close-up view on of two rugose corals entombed in the shale mudstone beds. E Close-up view on of a rugose coral species with diagenetically compressed calyx. Note strong ferrugination of corallite and surrounding matrix within the fossiliferous shale. F Fossiliferous shales mudstone with thin bands of ferruginous dolomitic limestone and secondary evaporite veinlets; Cr = crinoidal stems. G Crinoid columnals (Cr) and rugose corals (RC) are embedded in the shale mudstone. H Close-up view on of a spiriferid valve shell within the shale (arrow). Diameter of coins in C–E, G: 25 mm

Fig. 8 A Lytvolasma paraaucta n in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 8 A Lytvolasma paraaucta n. sp. A1 Lateral external view of the holotype specimen (RAh 54). Note that, calice is compressed due to compaction. A2 Transverse thin-section in the immature part, showing major septa with irregular zaphrentoid arrangement. A3 Transverse thin section in the early mature part of the corallite, showing radially arranged major septa with rhopaloid ends. A4 Laterally compressed section in the calice base, showing a deformed fossula. A5 Transverse thin-section in the compressed calice, with calcareous mud filling. B1 Lateral external view of the paratype specimen (RAh 19). B2–B5 Successive transverse thin-sections from the immature part near the apex (B2) to the last mature part in the calice (B5)

Fig. 4 in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 4 Effects of diagenesis on some coral specimens: A Thin-section in the calice of the specimen RAh (44) shows a completely compressed calice filled with fossiliferous mud. B Thin-section below the calice of the Bothrophyllum okense (RAh 37) shows beginning of compression and breakage of septa. C Thin-section below the calice of the specimen RAh (79), shows completely broken and altered septa, probable outer dissepimentarium and axial structure, filled with ferruginous mud. D Thin-section of a completely compressed specimen RAh (200) shows high alteration, breakage and ferrugination of skeletal elements. E Thin-section in the early mature part of the Actinophrentis crassithecata n. sp. (RAh 11), shows ferrugination affects a large part of the interior skeleton. F Mature thin-section of Rotiphyllum exile (RAh 29), shows ferrugination and dolomitization of skeletal elements. G, H Thin-sections of mature part of the specimen (RAh 81) in G and the immature part of the specimen RAh (99) in H show extensive dolomitization and ferrugination of the internal skeletal elements

Fig. 9 A Monophyllum galalaensis n in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 9 A Monophyllum galalaensis n. sp. (Holotype specimen, Rah 9). A1 Lateral external view of the corallite, positions of thin-sections indicated in A1. A2 A calice view of the paratype specimen (RAh 41), with eroded rim, shows an elongated counter septum that form a columella (arrow). A3–A5 Successive transverse thin-sections of the neanic stage, showing the pseudo-radial to pinnate arrangement of major septa, a long thin ended cardinal septum, and a longer counter septum with a swollen end in a dense stereocolumn. A6–7 Two successive mature sections, showing a short cardinal septum. A81, 2 Transverse thin-section in the late mature stage below the calice, showing radially arranged major septa that retreat a little leaving a narrow free axial area occupied by the elongated part of the counter septum. Note, A82 is a redrawing of section A81. Paratype specimen (RAh 13). External alar view of the corallite, positions of thin-sections are indicated in white lines. B2 Nepionic stage. B3 Early neanic stage. B4–5 Two partly compressed successive mature sections (ephebic stage), show a distinctly long counter septum. B6 Last mature section—more or less in the calice—showing a detached columella that is separated from the long counter septum. Black dots indicate the positions of cardinal septum (below), counter septum (above) and the two alar septa

Fig. 11 A, B in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 11 A, B Zaphrentites cf. parallela (Carruthers, 1910). A1–A3 Successive transverse sections in the specimen RAh (118), starting from the early immature stage with zaphrentoid arrangement of the septa in A1 to the last mature stage below the calice in A3. B1 External lateral view of the specimen RAh (109), showing strong longitudinal ribbing on the corallite wall. Positions of thin-sections indicated. B2–B4 Successive transverse sections represent the ontogenetic development, starting from the immature section in the apical part in B2 to the last mature section below the calice floor in B4. C Zaphrentites sp. C1 External view of the specimen RAh (84). C2–C4 Successive transverse sections; from the immature section in C2 to the last mature section below the calice floor in C4. Black dots indicate the positions of cardinal septum (below), counter septum (above) and the two alar septa

Fig. 2 A in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 2 A Lithostratigraphic succession of the Aheimer Formation studied along the eastern cliffs of the Northern Galala Plateau after Kora and Mansour (1992). B Enlargement of the mudstone dominated basal shale part of the lower member of the Aheimer Formation studied herein (see also Fig. 3A)

Fig. 1 in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 1 Geological map of the eastern cliffs of the Northern Galala Plateau, modified after Abdallah and El Adindani (1965)

Fig. 6 A Actinophrentis crassithecata n in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 6 A Actinophrentis crassithecata n. sp.: (Holotype specimen RAh (57). A1 External view showing a thick walled, slightly curved corallite with septal furrows ornamenting the external wall. Position of thin-sections indicated. A2 Transverse thin-section near the non-preserved apical part, shows thick major septa meeting in the centre and adaxially thinning cardinal septum. A3 Transverse thin-section in the middle part of the corallite, shows major septa meeting in the centre and noticeable fossular breaks. A4 Last adult transverse thin section just below the calice shows septa withdrawn a little from the centre. A5 Details of the external wall of A3. B1, B2 External lateral views of the specimen RAh (11) showing a thick walled, slightly curved corallite with septal furrows and concentric growth lines on the external wall. C Lytvolasma cf. canadense Fedorowski and Bamber, 2001, specimen RAh (66). C1, C2 Transverse thin-section in the middle mature part of the corallite, shows a short cardinal septum and a long counter septum with a rhopaloid axial end. C3 Transverse thin-section in the calice, shows a long counter septum. Scale bars: 2.5 mm, except A2–A5: 2 mm. Black dots indicate the positions of cardinal septum (below), counter septum (above) and the two alar septa

Fig. 7 Lytvolasma aheimerensis n in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 7 Lytvolasma aheimerensis n. sp. A External view of the specimen RA (2), showing a straight corallite with partly eroded calice and non-preserved apical part, positions of thin-sections indicated. B–D Successive transverse thin-sections in the early preserved growth stages, shows very thick major septa joining together near the centre. The cardinal septum is deformed in D. E–G Successive thin-sections in the early mature stages show the formation of a stereozone with a free axial area, shortening of the cardinal septum with maturity and the longest counter septum with a rhopaloid end. H–I Two transverse thin-sections below the calice, deformed due to rejuvenation in H and lateral compaction in I. Scale bars: 2.5 mm, except A: 5 mm. Black dots indicate the positions of cardinal septum (below), counter septum (above) and the two alar septa

Fig. 5 in Kasimovian (late Pennsylvanian) cornute rugose corals from Egypt: taxonomy, facies and palaeogeography of a cool-water fauna from northern Gondwana

Fig. 5 Internal morphological characters of the non-dissepimented rugose corals referred to in the systematic descriptions, after Denayer and Hoşgör (2014). A Transverse section. B Longitudinal section

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-