The Experts below are selected from a list of 21414 Experts worldwide ranked by ideXlab platform
Paola Oliveri - One of the best experts on this subject based on the ideXlab platform.
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developmental transcriptomics of the brittle star amphiura filiformis reveals gene regulatory network rewiring in Echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the Echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other Echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model Echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ . We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different Echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in Echinoderms.
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developmental transcriptomics of the brittle star amphiura filiformis reveals gene regulatory network rewiring in Echinoderm larval skeleton evolution
bioRxiv, 2017Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the Echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other Echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model Echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different Echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of Echinoderm larval development.
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Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks
EvoDevo, 2016Co-Authors: David V. Dylus, Anna Czarkwiani, Josefine Stångberg, Olga Ortega-martinez, Sam Dupont, Paola OliveriAbstract:Background The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, Echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin. Results We show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformis pplx , the closest gene to the sea urchin double negative gate (DNG) repressor pmar1 , fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC , the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr , ets1/2 , and delta in A. filiformis . Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri , shows significantly different regulatory states. Conclusion Our data fill up an important gap in the picture of larval mesoderm in Echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of Echinoderm classes. In light of recent studies on other Echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of Echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis -regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of Echinoderms.
David V. Dylus - One of the best experts on this subject based on the ideXlab platform.
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Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in Echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paolo OliveriAbstract:BackgroundAmongst the Echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other Echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model Echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/.ResultsWe have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different Echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation.ConclusionsOur findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in Echinoderms.
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developmental transcriptomics of the brittle star amphiura filiformis reveals gene regulatory network rewiring in Echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the Echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other Echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model Echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ . We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different Echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in Echinoderms.
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developmental transcriptomics of the brittle star amphiura filiformis reveals gene regulatory network rewiring in Echinoderm larval skeleton evolution
bioRxiv, 2017Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the Echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other Echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model Echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different Echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of Echinoderm larval development.
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Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks
EvoDevo, 2016Co-Authors: David V. Dylus, Anna Czarkwiani, Josefine Stångberg, Olga Ortega-martinez, Sam Dupont, Paola OliveriAbstract:Background The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, Echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin. Results We show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformis pplx , the closest gene to the sea urchin double negative gate (DNG) repressor pmar1 , fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC , the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr , ets1/2 , and delta in A. filiformis . Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri , shows significantly different regulatory states. Conclusion Our data fill up an important gap in the picture of larval mesoderm in Echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of Echinoderm classes. In light of recent studies on other Echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of Echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis -regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of Echinoderms.
Imran A Rahman - One of the best experts on this subject based on the ideXlab platform.
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an edrioasteroid from the silurian herefordshire lagerstatte of england reveals the nature of the water vascular system in an extinct Echinoderm
Proceedings of The Royal Society B: Biological Sciences, 2017Co-Authors: Derek E G Briggs, Derek J Siveter, Mark D Sutton, Imran A RahmanAbstract:Echinoderms are unique in having a water vascular system with tube feet, which perform a variety of functions in living forms. Here, we report the first example of preserved tube feet in an extinct group of Echinoderms. The material, from the Silurian Herefordshire Lagerstatte, UK, is assigned to a new genus and species of rhenopyrgid edrioasteroid, Heropyrgus disterminus . The tube feet attach to the inner surface of compound interradial plates and form two sets, an upper and a lower, an arrangement never reported previously in an extant or extinct Echinoderm. Cover plates are absent and floor plates are separated creating a large permanent entrance to the interior of the oral area. The tube feet may have captured food particles that entered the oral area and/or enhanced respiration. The pentameral symmetry of the oral surface transitions to eight columns in which the plates are vertically offset resulting in a spiral appearance. This change in symmetry may reflect flexibility in the evolutionary development of the axial and extraxial zones in early Echinoderm evolution.
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an edrioasteroid from the silurian herefordshire lagerstatte of england reveals the nature of the water vascular system in an extinct Echinoderm
Proceedings of The Royal Society B: Biological Sciences, 2017Co-Authors: Derek E G Briggs, Derek J Siveter, Mark D Sutton, Imran A RahmanAbstract:Echinoderms are unique in having a water vascular system with tube feet, which perform a variety of functions in living forms. Here, we report the first example of preserved tube feet in an extinct group of Echinoderms. The material, from the Silurian Herefordshire Lagerstatte, UK, is assigned to a new genus and species of rhenopyrgid edrioasteroid, Heropyrgus disterminus . The tube feet attach to the inner surface of compound interradial plates and form two sets, an upper and a lower, an arrangement never reported previously in an extant or extinct Echinoderm. Cover plates are absent and floor plates are separated creating a large permanent entrance to the interior of the oral area. The tube feet may have captured food particles that entered the oral area and/or enhanced respiration. The pentameral symmetry of the oral surface transitions to eight columns in which the plates are vertically offset resulting in a spiral appearance. This change in symmetry may reflect flexibility in the evolutionary development of the axial and extraxial zones in early Echinoderm evolution.
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progress in Echinoderm paleobiology
Journal of Paleontology, 2017Co-Authors: Samuel Zamora, Imran A RahmanAbstract:Echinoderms are a diverse and successful phylum of exclusively marine invertebrates that have an extensive fossil record dating back to Cambrian Stage 3 (Zamora and Rahman, 2014). There are five extant classes of Echinoderms (asteroids, crinoids, echinoids, holothurians, and ophiuroids), but more than 20 extinct groups, all of which are restricted to the Paleozoic (Sumrall and Wray, 2007). As a result, to fully appreciate the modern diversity of Echinoderms, it is necessary to study their rich fossil record. Throughout their existence, Echinoderms have been an important component of marine ecosystems. Because of their relatively good fossil record, researchers have been able to reconstruct Echinoderm diversity through geological time (e.g., Smith and Benson, 2013). Moreover, the Echinoderm skeleton is rich in characters for rigorous analyses of disparity, functional morphology, and phylogeny, providing the means to tackle large-scale evolutionary questions (e.g., Ausich and Peters, 2005; Gahn and Baumiller, 2010; Kroh and Smith, 2010; Deline and Ausich, 2011). Echinoderms are known to modify their physiology, ecology, and distribution in response to fluctuations in salinity, pH, or temperature, so fossil forms may be useful indicators of past and future environmental change (Aronson et al., 2009). Taken together, these aspects make Echinoderms an ideal group for addressing fundamental questions about the history of life on Earth. On June 15–16, 2015, around 50 Echinodermologists (Fig. 1) from 12 different countries attended the Progress in Echinoderm Palaeobiology meeting in Zaragoza, Spain, which was hosted by the Geological Survey of Spain and the University of Zaragoza. This meeting was followed by a five-day field trip (June 17–21, 2015) that included stops at the most remarkable Paleozoic …
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The Cambrian Substrate Revolution and the early evolution of attachment in suspension-feeding Echinoderms
Earth-Science Reviews, 2017Co-Authors: Samuel Zamora, Bradley Deline, J. Javier Álvaro, Imran A RahmanAbstract:Abstract The Cambrian, characterized by the global appearance of diverse biomineralized metazoans in the fossil record for the first time, represents a pivotal point in the history of life. This period also documents a major change in the nature of the sea floor: Neoproterozoic-type substrates stabilized by microbial mats were replaced by unconsolidated soft substrates with a well-developed mixed layer. The effect of this transition on the ecology and evolution of benthic metazoans is termed the Cambrian Substrate Revolution (CSR), and this is thought to have impacted greatly on early suspension-feeding Echinoderms in particular. According to this paradigm, most Echinoderms rested directly on non-bioturbated soft substrates as sediment attachers and stickers during the Cambrian Epoch 2. As the substrates became increasingly disturbed by burrowing, forming a progressively thickening mixed layer, Echinoderms developed new strategies for attaching to firm and hard substrates. To test this model, we evaluated the mode of attachment of 83 Cambrian suspension-feeding Echinoderm species; attachment mode was inferred based on direct evidence in fossil specimens and interpretations of functional morphology. These data were analyzed quantitatively to explore trends in attachment throughout the Cambrian. In contrast to previous studies, the majority of Cambrian clades (eocrinoids, helicoplacoids, helicocystoids, isorophid edrioasteroids, and solutes) are now interpreted as hard (shelly) substrate attachers. Only early edrioasteroids attached directly to firm substrates stabilized by microbially induced sedimentary structures. Contrary to the predictions of the CSR paradigm, our study demonstrates that Cambrian Echinoderms were morphologically pre-adapted to the substrate changes that occurred during the Cambrian, allowing them to fully exploit the appearance of hardgrounds in the Furongian. We find no support for the claim that the CSR explains the peak in Echinoderm diversity during Cambrian Epochs 2–3, or that it caused the extinction of helicoplacoids.
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Deciphering The Early Evolution of Echinoderms with Cambrian Fossils
Palaeontology, 2014Co-Authors: Samuel Zamora, Imran A RahmanAbstract:Echinoderms are a major group of invertebrate deuterostomes that have been an important component of marine ecosystems throughout the Phanerozoic. Their fossil record extends back to the Cambrian, when several disparate groups appear in different palaeocontinents at about the same time. Many of these early forms exhibit character combinations that differ radically from extant taxa, and thus their anatomy and phylogeny have long been controversial. Deciphering the earliest evolution of Echinoderms therefore requires a detailed understanding of the morphology of Cambrian fossils, as well as the selection of an appropriate root and the identification of homologies for use in phylogenetic analysis. Based on the sister-group relationships and ontogeny of modern species and new fossil discoveries, we now know that the first Echinoderms were bilaterally symmetrical, represented in the fossil record by Ctenoimbricata and some early ctenocystoids. The next branch in Echinoderm phylogeny is represented by the asymmetrical cinctans and solutes, with an Echinoderm-type ambulacral system originating in the more crownward of these groups (solutes). The first radial Echinoderms are the helicoplacoids, which possess a triradial body plan with three ambulacra radiating from a lateral mouth. Helicocystoids represent the first pentaradial Echinoderms and have the mouth facing upwards with five radiating recumbent ambulacra. Pentaradial Echinoderms diversified rapidly from the beginning of their history, and the most significant differences between groups are recorded in the construction of the oral area and ambulacra, as well as the nature of their feeding appendages. Taken together, this provides a clear narrative of the early evolution of the Echinoderm body plan.
Samuel Zamora - One of the best experts on this subject based on the ideXlab platform.
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Re-evaluating the phylogenetic position of the enigmatic early Cambrian deuterostome Yanjiahella.
Nature Communications, 2020Co-Authors: Samuel Zamora, Bertrand Lefebvre, Thomas E. Guensburg, Rich Mooi, Bruno David, Przemysław Gorzelak, Colin D Sumrall, David F. Wright, Selina R. Cole, Aaron W HunterAbstract:Deuterostomes are a morphologically disparate clade, encompassing the chordates (including vertebrates), the hemichordates (the vermiform enteropneusts and the colonial tube-dwelling pterobranchs) and the Echinoderms (including starfish). Although deuterostomes are considered monophyletic, the interrelationships between the three clades remain highly contentious. Here we report, Yanjiahella biscarpa, a bilaterally symmetrical, solitary metazoan from the early Cambrian (Fortunian) of China with a characteristic Echinoderm-like plated theca, a muscular stalk reminiscent of the hemichordates and a pair of feeding appendages. Our phylogenetic analysis indicates that Y. biscarpa is a stemEchinoderm and not only is this species the oldest and most basal Echinoderm, but it also predates all known hemichordates, and is among the earliest deuterostomes. This taxon confirms that Echinoderms acquired plating before pentaradial symmetry and that their history is rooted in bilateral forms. Yanjiahella biscarpa shares morphological similarities with both enteropneusts and Echinoderms, indicating that the enteropneust body plan is ancestral within hemichordates.
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progress in Echinoderm paleobiology
Journal of Paleontology, 2017Co-Authors: Samuel Zamora, Imran A RahmanAbstract:Echinoderms are a diverse and successful phylum of exclusively marine invertebrates that have an extensive fossil record dating back to Cambrian Stage 3 (Zamora and Rahman, 2014). There are five extant classes of Echinoderms (asteroids, crinoids, echinoids, holothurians, and ophiuroids), but more than 20 extinct groups, all of which are restricted to the Paleozoic (Sumrall and Wray, 2007). As a result, to fully appreciate the modern diversity of Echinoderms, it is necessary to study their rich fossil record. Throughout their existence, Echinoderms have been an important component of marine ecosystems. Because of their relatively good fossil record, researchers have been able to reconstruct Echinoderm diversity through geological time (e.g., Smith and Benson, 2013). Moreover, the Echinoderm skeleton is rich in characters for rigorous analyses of disparity, functional morphology, and phylogeny, providing the means to tackle large-scale evolutionary questions (e.g., Ausich and Peters, 2005; Gahn and Baumiller, 2010; Kroh and Smith, 2010; Deline and Ausich, 2011). Echinoderms are known to modify their physiology, ecology, and distribution in response to fluctuations in salinity, pH, or temperature, so fossil forms may be useful indicators of past and future environmental change (Aronson et al., 2009). Taken together, these aspects make Echinoderms an ideal group for addressing fundamental questions about the history of life on Earth. On June 15–16, 2015, around 50 Echinodermologists (Fig. 1) from 12 different countries attended the Progress in Echinoderm Palaeobiology meeting in Zaragoza, Spain, which was hosted by the Geological Survey of Spain and the University of Zaragoza. This meeting was followed by a five-day field trip (June 17–21, 2015) that included stops at the most remarkable Paleozoic …
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The Cambrian Substrate Revolution and the early evolution of attachment in suspension-feeding Echinoderms
Earth-Science Reviews, 2017Co-Authors: Samuel Zamora, Bradley Deline, J. Javier Álvaro, Imran A RahmanAbstract:Abstract The Cambrian, characterized by the global appearance of diverse biomineralized metazoans in the fossil record for the first time, represents a pivotal point in the history of life. This period also documents a major change in the nature of the sea floor: Neoproterozoic-type substrates stabilized by microbial mats were replaced by unconsolidated soft substrates with a well-developed mixed layer. The effect of this transition on the ecology and evolution of benthic metazoans is termed the Cambrian Substrate Revolution (CSR), and this is thought to have impacted greatly on early suspension-feeding Echinoderms in particular. According to this paradigm, most Echinoderms rested directly on non-bioturbated soft substrates as sediment attachers and stickers during the Cambrian Epoch 2. As the substrates became increasingly disturbed by burrowing, forming a progressively thickening mixed layer, Echinoderms developed new strategies for attaching to firm and hard substrates. To test this model, we evaluated the mode of attachment of 83 Cambrian suspension-feeding Echinoderm species; attachment mode was inferred based on direct evidence in fossil specimens and interpretations of functional morphology. These data were analyzed quantitatively to explore trends in attachment throughout the Cambrian. In contrast to previous studies, the majority of Cambrian clades (eocrinoids, helicoplacoids, helicocystoids, isorophid edrioasteroids, and solutes) are now interpreted as hard (shelly) substrate attachers. Only early edrioasteroids attached directly to firm substrates stabilized by microbially induced sedimentary structures. Contrary to the predictions of the CSR paradigm, our study demonstrates that Cambrian Echinoderms were morphologically pre-adapted to the substrate changes that occurred during the Cambrian, allowing them to fully exploit the appearance of hardgrounds in the Furongian. We find no support for the claim that the CSR explains the peak in Echinoderm diversity during Cambrian Epochs 2–3, or that it caused the extinction of helicoplacoids.
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Research Article DOI: 10.2110/palo.2010.p10-052r PELMATOZOAN EchinodermS AS COLONIZERS OF CARBONATE FIRMGROUNDS IN MID- CAMBRIAN HIGH ENERGY ENVIRONMENTS
2016Co-Authors: Samuel Zamora, Javier J. Álvaro, Andrew B. SmithAbstract:New Echinoderm holdfast discoveries from Gondwana demonstrate that pelmatozoans have been cementers able to attach to carbonate firm-grounds since the basal middle Cambrian. Echinoderms were thus colonizing shallow, high-energy environments well before the appearance of the first true carbonate hardgrounds in the Furongian. Morphological innovations and adaptations to firmground media (5substrates) were first developed in softground, clayey, offshore environments where echino-derms cemented to shell fragments. This preadaption allowed Echinoderms to quickly and effectively exploit the newly emerging hardground habitats in the Furongian to Early Ordovician
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Deciphering The Early Evolution of Echinoderms with Cambrian Fossils
Palaeontology, 2014Co-Authors: Samuel Zamora, Imran A RahmanAbstract:Echinoderms are a major group of invertebrate deuterostomes that have been an important component of marine ecosystems throughout the Phanerozoic. Their fossil record extends back to the Cambrian, when several disparate groups appear in different palaeocontinents at about the same time. Many of these early forms exhibit character combinations that differ radically from extant taxa, and thus their anatomy and phylogeny have long been controversial. Deciphering the earliest evolution of Echinoderms therefore requires a detailed understanding of the morphology of Cambrian fossils, as well as the selection of an appropriate root and the identification of homologies for use in phylogenetic analysis. Based on the sister-group relationships and ontogeny of modern species and new fossil discoveries, we now know that the first Echinoderms were bilaterally symmetrical, represented in the fossil record by Ctenoimbricata and some early ctenocystoids. The next branch in Echinoderm phylogeny is represented by the asymmetrical cinctans and solutes, with an Echinoderm-type ambulacral system originating in the more crownward of these groups (solutes). The first radial Echinoderms are the helicoplacoids, which possess a triradial body plan with three ambulacra radiating from a lateral mouth. Helicocystoids represent the first pentaradial Echinoderms and have the mouth facing upwards with five radiating recumbent ambulacra. Pentaradial Echinoderms diversified rapidly from the beginning of their history, and the most significant differences between groups are recorded in the construction of the oral area and ambulacra, as well as the nature of their feeding appendages. Taken together, this provides a clear narrative of the early evolution of the Echinoderm body plan.
Anna Czarkwiani - One of the best experts on this subject based on the ideXlab platform.
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Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in Echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paolo OliveriAbstract:BackgroundAmongst the Echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other Echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model Echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/.ResultsWe have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different Echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation.ConclusionsOur findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in Echinoderms.
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developmental transcriptomics of the brittle star amphiura filiformis reveals gene regulatory network rewiring in Echinoderm larval skeleton evolution
Genome Biology, 2018Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the Echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other Echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model Echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ . We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different Echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in Echinoderms.
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developmental transcriptomics of the brittle star amphiura filiformis reveals gene regulatory network rewiring in Echinoderm larval skeleton evolution
bioRxiv, 2017Co-Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R Elphick, Paola OliveriAbstract:Amongst the Echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other Echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model Echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different Echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of Echinoderm larval development.
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Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks
EvoDevo, 2016Co-Authors: David V. Dylus, Anna Czarkwiani, Josefine Stångberg, Olga Ortega-martinez, Sam Dupont, Paola OliveriAbstract:Background The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, Echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin. Results We show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformis pplx , the closest gene to the sea urchin double negative gate (DNG) repressor pmar1 , fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC , the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr , ets1/2 , and delta in A. filiformis . Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri , shows significantly different regulatory states. Conclusion Our data fill up an important gap in the picture of larval mesoderm in Echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of Echinoderm classes. In light of recent studies on other Echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of Echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis -regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of Echinoderms.
