Zenodo (CERN European Organization for Nuclear Research), Dec 31, 2008
Brissalius vannoordenburgi gen. nov., sp. nov. occurs at depths of 200 meters off Siquijor Island... more Brissalius vannoordenburgi gen. nov., sp. nov. occurs at depths of 200 meters off Siquijor Island in the Philippines and is typical of the family Brissopsidae in having specialised aboral tube feet in ambulacra III within the peripetalous fasciole used for funnel building. It is distinct from species of Brissopsis and Metalia in having a shield-shaped subanal fasciole in conjunction with confluent posterior petals. This species has a particularly diverse array of highly localised pedicellariae, with three distinct forms of globiferous pedicellaria (simple fistulate, fanged fistulate and fanged open-bladed), three forms of straight bladed tridentate (narrow-valved, spatulate and terminal-toothed) as well as typical spatangoid rostrate, ophicephalous and triphyllous pedicellariae. Brissopsis persica is the only species in the genus that has a shield-shaped subanal fasciole. However, this species has divergent posterior petals, simple (non-lobed) anterior aboral tube feet, enlarged tubercles along the anterior ambulacrum, no anal fasciole, and lacks both globiferous and ophicephalous pedicellariae. These findings demonstrate that this Brissopsis persica does not belong in Brissopsis but should be placed in Metalia.
FIGURE 6. NHM 1962.8. 16.17, Brissopsis persica from the Persian Gulf: A, aboral view; B, oral vi... more FIGURE 6. NHM 1962.8. 16.17, Brissopsis persica from the Persian Gulf: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
<i>Echinothrix calamaris</i> (Pallas, 1774) Specimens were collected from Ryuka Is. (... more <i>Echinothrix calamaris</i> (Pallas, 1774) Specimens were collected from Ryuka Is. (Japan), Red Sea (Egypt), Mariana Is. (Guam), Ignoitijala (Maldives), Luzon (Philippines), Dravuni Is., Taveuni Is., Yanuca Is., Suva (Fiji), and Nouméa (New Caledonia). This species is reported to have the broadest range of colour morphs of any species in the family Diadematidae (H. L. Clark 1925). The most commonly found colour morphs throughout the Indo-Pacific were the white (interambulacral spines) and brown (test and ambulacral spines) and the completely brown colour morph. These were commonly found together throughout the Pacific, and were therefore closely studied in this investigation. Test diameters varied significantly between colour morphs. Adult specimens of the white colour morph had a mean horizontal test diameter of 108 mm (SD ± 8.2 mm) and a mean vertical diameter of 45 mm (SD ± 5.4 mm). Adults of the brown colour morph typically grew to a significantly larger size, with mean test diameters of 120 mm (h.d.) (SD ± 8.7 mm) and 60 mm (v.d.) (SD ± 5.5 mm). Mortensen (1940) reported that the largest recorded specimen of <i>E. calamaris</i> measured 130 mm (h.d.) from the old collection of the "Royal Museum", Copenhagen. The largest specimen recorded in this study, from 200 specimens of each colour morph measured 143 mm (h.d.) by 68mm (v.d.) and was of the brown colour variety. In comparison, the largest white colour morph only measured 119 mm (h.d.) by 52 mm (v.d.). The ambulacra in both colour morphs measured 24-28% of the interambulacra measured at the ambitus and widened distinctly towards the periproct, narrowing beneath the ambitus then widening towards the peristome. Many authors including Clark &amp; Rowe (1971) have differentiated this species from <i>Echinothrix diadema</i> by the ambulacra which are distinctly raised aborally in <i>E. calamaris.</i> This feature was, however, not constant, and as Mortensen (1940) reported, "considerable variation occurs in the elevation aborally of the ambulacra". Such variat [...]
Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitocho... more Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.
The sea urchins Echinothrix calamaris and E. diadema have sympatric distributions throughout the ... more The sea urchins Echinothrix calamaris and E. diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discreet clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and central Pacific ...
<i>Coelopleurus</i> L. Agassiz, 1840 <i>Catalogus systematicus Ectyporum Echino... more <i>Coelopleurus</i> L. Agassiz, 1840 <i>Catalogus systematicus Ectyporum Echinodermatum fossilium Musei Neocomensis</i>. p. 12 and p. 19. Type species: <i>Cidaris coronalis</i> Leske, 1778 (= <i>Coelopleurus equis</i> L. Agassiz, 1840) by monotypy. <i>Assigned species</i>: see Mortensen (1935) for the additional 11 species/subspecies
FIG. 1. — Drawings of the apical systems, showing species specific characters of the periproct an... more FIG. 1. — Drawings of the apical systems, showing species specific characters of the periproct and genital plates: A, Diadema antillarum; B, D. ascensionis; C, D. mexicanum; D, D. palmeri; E, D. paucispinum; F, D. savignyi; G, D. setosum; H, Echinothrix calamaris (brown colour morph); I, E. calamaris (white colour morph); J, E. diadema. Scale bars: 5 mm.
FIG. 2. — A-I, photographs of the median areas of the interambulacra, showing the variation in ch... more FIG. 2. — A-I, photographs of the median areas of the interambulacra, showing the variation in characters that occur: A, Diadema antillarum; B, D. mexicanum; C, D, D. savignyi; E, D. setosum; F, Echinothrix calamaris (brown colour morph); G, E. calamaris (white colour morph); H, E. diadema; I, D. palmeri; J, D. palmeri (whole specimen). Scale bars: A-I, 5 mm; J, 50 mm.
FIGURE 7. NHM 1936.5. 13, denuded specimen (1 of 16) of Metalia sternalis from the Red Sea: A, ab... more FIGURE 7. NHM 1936.5. 13, denuded specimen (1 of 16) of Metalia sternalis from the Red Sea: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
Table S1. Extraction, library preparation and sequencing protocols for all newly sequenced sample... more Table S1. Extraction, library preparation and sequencing protocols for all newly sequenced samples, as well as statistics output by Agalma for all transcriptomes included. (DOCX 18 kb)
Figure S1. Visual representation of the occupancy of the matrix employed. Figure S2: Phylogenetic... more Figure S1. Visual representation of the occupancy of the matrix employed. Figure S2: Phylogenetic position of Arbacia punctulata and evidence for contamination. Figure S3. Residuals obtained from a linear regression of p-distances for each gene in the final alignment against its inferred orthologue in two other randomly selected taxa. Figure S4. Analyses excluding 345 outlier sequences detected by TreeShrink. (DOCX 5026 kb)
FIGURE 1. Timing of cladogenesis based on concatenated COI, 16S, and 28S data, as derived from an... more FIGURE 1. Timing of cladogenesis based on concatenated COI, 16S, and 28S data, as derived from analysis on BEAST calibrated using the fossil record and the final closure of the Panama Isthmus (adapted from Coppard et al. 2013). Ages of stages and epoch series are based on International Commission on Stratigraphy stratigraphic chart (Cohen et al. 2012). Error bars estimated by BEAST are shown in light blue. Colours of clades indicate geographic range (red = Atlantic and Caribbean, blue = eastern Pacific, green = Gulf of California).
FIGURE 1. NHM 2008.619, paratype of Brissalius vannoordenburgi gen. nov., sp. nov.: A, aboral vie... more FIGURE 1. NHM 2008.619, paratype of Brissalius vannoordenburgi gen. nov., sp. nov.: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throug... more The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discrete clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and centra...
Zenodo (CERN European Organization for Nuclear Research), Dec 31, 2008
Brissalius vannoordenburgi gen. nov., sp. nov. occurs at depths of 200 meters off Siquijor Island... more Brissalius vannoordenburgi gen. nov., sp. nov. occurs at depths of 200 meters off Siquijor Island in the Philippines and is typical of the family Brissopsidae in having specialised aboral tube feet in ambulacra III within the peripetalous fasciole used for funnel building. It is distinct from species of Brissopsis and Metalia in having a shield-shaped subanal fasciole in conjunction with confluent posterior petals. This species has a particularly diverse array of highly localised pedicellariae, with three distinct forms of globiferous pedicellaria (simple fistulate, fanged fistulate and fanged open-bladed), three forms of straight bladed tridentate (narrow-valved, spatulate and terminal-toothed) as well as typical spatangoid rostrate, ophicephalous and triphyllous pedicellariae. Brissopsis persica is the only species in the genus that has a shield-shaped subanal fasciole. However, this species has divergent posterior petals, simple (non-lobed) anterior aboral tube feet, enlarged tubercles along the anterior ambulacrum, no anal fasciole, and lacks both globiferous and ophicephalous pedicellariae. These findings demonstrate that this Brissopsis persica does not belong in Brissopsis but should be placed in Metalia.
FIGURE 6. NHM 1962.8. 16.17, Brissopsis persica from the Persian Gulf: A, aboral view; B, oral vi... more FIGURE 6. NHM 1962.8. 16.17, Brissopsis persica from the Persian Gulf: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
<i>Echinothrix calamaris</i> (Pallas, 1774) Specimens were collected from Ryuka Is. (... more <i>Echinothrix calamaris</i> (Pallas, 1774) Specimens were collected from Ryuka Is. (Japan), Red Sea (Egypt), Mariana Is. (Guam), Ignoitijala (Maldives), Luzon (Philippines), Dravuni Is., Taveuni Is., Yanuca Is., Suva (Fiji), and Nouméa (New Caledonia). This species is reported to have the broadest range of colour morphs of any species in the family Diadematidae (H. L. Clark 1925). The most commonly found colour morphs throughout the Indo-Pacific were the white (interambulacral spines) and brown (test and ambulacral spines) and the completely brown colour morph. These were commonly found together throughout the Pacific, and were therefore closely studied in this investigation. Test diameters varied significantly between colour morphs. Adult specimens of the white colour morph had a mean horizontal test diameter of 108 mm (SD ± 8.2 mm) and a mean vertical diameter of 45 mm (SD ± 5.4 mm). Adults of the brown colour morph typically grew to a significantly larger size, with mean test diameters of 120 mm (h.d.) (SD ± 8.7 mm) and 60 mm (v.d.) (SD ± 5.5 mm). Mortensen (1940) reported that the largest recorded specimen of <i>E. calamaris</i> measured 130 mm (h.d.) from the old collection of the "Royal Museum", Copenhagen. The largest specimen recorded in this study, from 200 specimens of each colour morph measured 143 mm (h.d.) by 68mm (v.d.) and was of the brown colour variety. In comparison, the largest white colour morph only measured 119 mm (h.d.) by 52 mm (v.d.). The ambulacra in both colour morphs measured 24-28% of the interambulacra measured at the ambitus and widened distinctly towards the periproct, narrowing beneath the ambitus then widening towards the peristome. Many authors including Clark &amp; Rowe (1971) have differentiated this species from <i>Echinothrix diadema</i> by the ambulacra which are distinctly raised aborally in <i>E. calamaris.</i> This feature was, however, not constant, and as Mortensen (1940) reported, "considerable variation occurs in the elevation aborally of the ambulacra". Such variat [...]
Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitocho... more Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.
The sea urchins Echinothrix calamaris and E. diadema have sympatric distributions throughout the ... more The sea urchins Echinothrix calamaris and E. diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discreet clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and central Pacific ...
<i>Coelopleurus</i> L. Agassiz, 1840 <i>Catalogus systematicus Ectyporum Echino... more <i>Coelopleurus</i> L. Agassiz, 1840 <i>Catalogus systematicus Ectyporum Echinodermatum fossilium Musei Neocomensis</i>. p. 12 and p. 19. Type species: <i>Cidaris coronalis</i> Leske, 1778 (= <i>Coelopleurus equis</i> L. Agassiz, 1840) by monotypy. <i>Assigned species</i>: see Mortensen (1935) for the additional 11 species/subspecies
FIG. 1. — Drawings of the apical systems, showing species specific characters of the periproct an... more FIG. 1. — Drawings of the apical systems, showing species specific characters of the periproct and genital plates: A, Diadema antillarum; B, D. ascensionis; C, D. mexicanum; D, D. palmeri; E, D. paucispinum; F, D. savignyi; G, D. setosum; H, Echinothrix calamaris (brown colour morph); I, E. calamaris (white colour morph); J, E. diadema. Scale bars: 5 mm.
FIG. 2. — A-I, photographs of the median areas of the interambulacra, showing the variation in ch... more FIG. 2. — A-I, photographs of the median areas of the interambulacra, showing the variation in characters that occur: A, Diadema antillarum; B, D. mexicanum; C, D, D. savignyi; E, D. setosum; F, Echinothrix calamaris (brown colour morph); G, E. calamaris (white colour morph); H, E. diadema; I, D. palmeri; J, D. palmeri (whole specimen). Scale bars: A-I, 5 mm; J, 50 mm.
FIGURE 7. NHM 1936.5. 13, denuded specimen (1 of 16) of Metalia sternalis from the Red Sea: A, ab... more FIGURE 7. NHM 1936.5. 13, denuded specimen (1 of 16) of Metalia sternalis from the Red Sea: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
Table S1. Extraction, library preparation and sequencing protocols for all newly sequenced sample... more Table S1. Extraction, library preparation and sequencing protocols for all newly sequenced samples, as well as statistics output by Agalma for all transcriptomes included. (DOCX 18 kb)
Figure S1. Visual representation of the occupancy of the matrix employed. Figure S2: Phylogenetic... more Figure S1. Visual representation of the occupancy of the matrix employed. Figure S2: Phylogenetic position of Arbacia punctulata and evidence for contamination. Figure S3. Residuals obtained from a linear regression of p-distances for each gene in the final alignment against its inferred orthologue in two other randomly selected taxa. Figure S4. Analyses excluding 345 outlier sequences detected by TreeShrink. (DOCX 5026 kb)
FIGURE 1. Timing of cladogenesis based on concatenated COI, 16S, and 28S data, as derived from an... more FIGURE 1. Timing of cladogenesis based on concatenated COI, 16S, and 28S data, as derived from analysis on BEAST calibrated using the fossil record and the final closure of the Panama Isthmus (adapted from Coppard et al. 2013). Ages of stages and epoch series are based on International Commission on Stratigraphy stratigraphic chart (Cohen et al. 2012). Error bars estimated by BEAST are shown in light blue. Colours of clades indicate geographic range (red = Atlantic and Caribbean, blue = eastern Pacific, green = Gulf of California).
FIGURE 1. NHM 2008.619, paratype of Brissalius vannoordenburgi gen. nov., sp. nov.: A, aboral vie... more FIGURE 1. NHM 2008.619, paratype of Brissalius vannoordenburgi gen. nov., sp. nov.: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throug... more The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discrete clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and centra...
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