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FIGURE 10 in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 10. Geographical distribution of the genus Amphithyris. A. seminula (■); A. buckmani (●); A. hallettensis (▲); A. richardsonae (+); A. parva (x); A. cavernicola n. sp. (*); A. comitodentis n. sp. (ο). Note that both collecting stations for A. hallettensis give only the longitudinal position, as they were found at lower latitudes in Antarctic waters not shown in the map.

FIGURE 8. Amphithyris cavernicola n in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 8. Amphithyris cavernicola n. sp., Coral Sea, Australia; A. Paratype ZMB Bra 2185. Lateral view showing ventribiconvex shells. B. Paratype QM G333508. Smooth dorsal valve exterior. C–E. Holotype QM G333507. C. Dorsal valve interior. D. Detail of punctae. E. Close-up of amphithyrid foramen. F. Paratype ZMB Bra 2175. Dorsal valve interior showing (dried) schizolophous lophophore and gonads. Scale bars: A, B, C, E and F = 200µm; D = 50µm.

FIGURE 9. Amphithyris cavernicola n in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 9. Amphithyris cavernicola n. sp., Coral Sea, Australia; A–C. Paratype ZMB Bra 2180. A. Ventral valve interior, showing low median septum and muscle impressions visible. B. Close-up of posterior region of ventral valve interior. C. Lateral view of ventral median septum and hinge teeth. D. Holotype QM G333507. Ventral valve exterior, with tubercles. E. Paratype ZMB Bra 2178. Broken ventral valve, exterior view, exposing secondary shell layer. F–H. Paratype ZMB Bra 2179. F. Protegulum with one middle and two lateral ridges. G–H. Tubercles on ventral valve exterior. I–L. Paratype ZMB Bra 2187. SEM backscatter images in environmental mode. I. Ventral valve exterior showing weak capillae. J–L. Ventral valve exterior showing exterior end of brushes with tubercles. Scale bars: A–E = 200µm; F, H and J = 50µm; G, I, K, L = 10µm.

FIGURE 5 in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 5. Amphithyris seminula (Philippi, 1836). Sicily, Mediterranean Sea. A–B. Paralectotype ZMB Bra 1675. A. Dorsal valve interior with low median septum. B. Lateral view of dorsal valve. C–F. Lectotype ZMB Bra 2146. C. Close-up of dorsal valve interior with short socket ridges. D. Ventral valve interior. E. Close-up of ventral valve interior showing beak-like hinge teeth. F. Lateral view of ventral valve, showing smooth surface. Scale bars = 200µm.

FIGURE 7. Amphithyris cavernicola n in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 7. Amphithyris cavernicola n. sp., Coral Sea, Australia; A. Paratype ZMB Bra 2186 Ventral view showing attachment to coral rock; B. Paratype ZMB Bra 2175. Ventral view, showing schizolophous lophophore (L) and gonads (G). Scale bar = 200µm.

FIGURE 6. Amphithyris comitodentis n in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 6. Amphithyris comitodentis n. sp. A–C. Holotype NIWA 92391. A. Dorsal valve interior, showing low median septum. B. Ventral valve interior. C. Detail of B showing teeth in parallel orientation to hinge line highlighted by dashed lines. D. Paratype ZMB Bra 2054, ventral valve interior showing imprints of capillae and tooth orientation. E–F. Paratype ZMB Bra 2353. E. Ventral valve exterior with concentric growth lines. F. Close-up of ventral protegulum showing a wrinkled surface. Scale bars: A–E = 200µm; F = 20µm.

FIGURE 4 in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 4. Amphithyris parva MacKinnon, Hiller, Long & Marshall, 2008. A–F. Paratype NMNZ Br 1069. A. Dorsal valve interior showing absence of median septum. B. Close-up of dorsal interior with large amphithyrid foramen. C. Dorsal valve exterior with weak capillae. D. Ventral valve interior. E. Close-up ventral valve interior showing long straight hinge line. F. Ventral exterior with weak capillae. Scale bars = 200µm.

FIGURE 2. Amphithyris hallettensis Foster, 1974. A–F. Paratype USNM I 550094C. A. Dorsal valve interior showing median septum. B in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 2. Amphithyris hallettensis Foster, 1974. A–F. Paratype USNM I 550094C. A. Dorsal valve interior showing median septum. B. Close-up of dorsal median septum. C. Close-up of dorsal valve interior. D. Ventral valve interior showing slight imprints of capillae. E. Close-up of ventral valve interior. F. Ventral valve exterior with endopunctae visible. Samples not sputter coated and SEM back-scatter images in environmental mode. Scale bars = 200µm.

FIGURE 3 in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 3. Amphithyris richardsonae Campbell and Fleming, 1981; Holotype NZGS BR 2277. A. Ventral valve exterior with faint capillae and growth lines. Note the unusual width of the shell. B. Close-up of the ventral valve showing punctae and two tubercles ("hollow spinules"). C. Ventral valve interior showing small teeth and mid-valve muscle scars. Samples not sputter coated and SEM back-scatter images in environmental mode. Scale bars = 200 µm.

FIGURE 1. Coral rock with attached brachiopod specimens, ZMB Bra 2235 in Revision of the brachiopod genus Amphithyris (Rhynchonelliformea: Platidiidae) with descriptions of two new species

FIGURE 1. Coral rock with attached brachiopod specimens, ZMB Bra 2235. White crosses indicate the position of specimens of A. cavernicola n. sp. Scale bar = 5 cm.

Figure 7 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 7. Ebiscothyris bellonensis gen. et sp. nov., cruise EBISCO, Coral Sea, South-West Pacific: A–H, ventral, dorsal, lateral, and anterior views of complete specimens, CP 2616, 786–836 m depth; A–D, paratype, IB-2013-2; E–H, holotype, IB-2013-1. I, dorsal view of complete specimen, with very long, thin pedicle, paratype, CP 2616, 786–836 m depth, IB- 2013-3. Scale bars: 5 mm.

Figure 6 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 6. rDNA tree of taxa with modified long loops. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2694 nucleotides of aligned sequences from SSU and LSU nuclear-encoded genes of 15 in-group and three rhynchonellide out-group taxa. Potentially misaligned and gapped sites (5%) were pruned by GBlocks. Several backbone nodes received very low bootstrap support and the tree has been redrawn by hand to remove them, leaving no effective resolution of relationships between the in-group superfamilies represented in this alignment. The sequence for Argyrotheca (JH97) was used with the permission of Dr J. Hoffman.

Figure 2. Case 2 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 2. Case 2: Cancellothyridoid gene tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2810 nucleotides of aligned sequences from up to four genes (12S and 16S mitochondrial, and SSU and LSU nuclear) from 30 in-group and three rhynchonellide out-group taxa. Gblocks was used to prune potentially misaligned and gap sites (18% were discarded). In-group backbone nodes with no bootstrap support value attached are considered to be unsupported (may be collapsed; boostrap <50%). Four taxa, marked (LSU), are represented by LSU sequence data alone, and in each case this sequence clusters with the cognate multiple sequences, indicating that the LSU fragment alone can accurately place the taxon.

Figure 5 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 5. Laqueoidea rDNA tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2882 nucleotides of aligned sequences from SSU and LSU nuclear-encoded genes of seven laqueoid in-group and six terebratulide out-group taxa. The small number of potentially misaligned and gap sites were not removed. The failure of the two Kingenoids to form a clade may be caused by limited sequence data rather than by misclassification.

Figure 9 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 9. Ebiscothyris bellonensis gen. et sp. nov., cruise EBISCO, Coral Sea, South-West Pacific, SEM micrographs; A, B, ventral valve, station CP 2556, 741–791 m depth, IB-2013-7; A, transverse section of the entire shell showing the primary layer (pri) underlain by the fibrous secondary layer (sec), passing into the prismatic tertiary layer (ter); B, section of the shell showing primary (pri), secondary (sec), and tertiary (ter) layers; a puncta with a radiating brush is also visible; C, D, dorsal valve, CP 2557, 800–923 m depth, IB-2013-5; C, latero-oblique view of internal surface, showing the incurved valve margin built of densely arranged sheets of secondary fibres (left) and prisms of tertiary layer (right); D, internal surface showing discrete units of prisms and very small punctae (arrows). E, F, Kanakythyris pachyrhynchos Laurin, 1997, cruise NORFOLK 2, Norfolk Ridge, station DW 2136, 402–410 m depth; E, transverse section of the entire shell; F, internal surface with discrete units of prisms. Scale bars: A, C, D, E, F, 50 μm, B, 20 μm.

Figure 4. Laqueoidea cox1 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 4. Laqueoidea cox1 tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 1218 nucleotides of aligned sequences of the cox1 mitochondrial gene from 14 laqueoid in-group and six terebratulide out-group taxa. The sequences were aligned with no gaps. Nodes with no bootstrap support value attached are considered to be unsupported (bootstrap <50%) and may be collapsed.

Figure 3. Case 3 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 3. Case 3: Dyscolioid and Terebratuloid gene tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 3427 nucleotides of aligned sequences from up to four genes (12S and 16S mitochondrial, and SSU and LSU nuclear) from 19 in-group and three rhynchonellide out-group taxa. Pruned of potentially misaligned and gap sites by hand (7% discarded). In-group backbone nodes with no bootstrap support value attached are considered to be unsupported (may be collapsed; boostrap <50%). Nine taxa, marked (LSU), are represented by LSU sequence data alone, and in each case this sequence clusters with the cognate multiple sequences, indicating that the LSU fragment alone can accurately place the taxon. These results validate the placement of Ebiscothyris, Dallithyris, and Dyscolia, each of which is represented by LSU alone.

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Figure 1 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 1. Locality map.

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Figure 8 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 8. Ebiscothyris bellonensis gen. et sp. nov., cruise EBISCO, Coral Sea, South-West Pacific, SEM micrographs: A, inner view of ventral valve to show symphytium with a weak line of junction, and small teeth, paratype, CP 2616, 786–836 m depth, IB-2013-4; B–E, inner, tilted, posterior, and side views of dorsal valve to show brachidium and cardinalia, paratype, CP 2557, 800–923 m depth, IB-2013-5; F, inner view of posterior part of complete specimen to show tubular pedicle collar and cardinal process, paratype, CP 2616, 786–836 m depth, IB-2013-6. Scale bars: 1 mm.