Speciation, evolution and phylogeny of some shallow-water octocorals (Cnidaria: Anthozoa)

Shallow-water octocorals are among the most abundant macro-benthic organisms inhabiting tropical subtropical and temperate communities. In spite of being worldwide distributed and highly diverse, the systematics of many octocorals remains controversial and the understanding of the processes who led to their diversification is largely unexplored. This study includes five chapters, each dealing with different aspects of the systematics, phylogeny and evolution of six soft coral genera such as Lobophytum, Sarcophyton, Paramuricea, Leptogorgia, Muricea and Pacifigorgia. One of the main goals of the study was to explore, through the use of molecular methods, the genetic variation within species notoriously difficult to identify. Besides the use of standard molecular methods for phylogenetic reconstruction and species delimitation, the effectiveness of Next Generation Sequencing (NGS) technologies was tested for mitogenomic and genotyping analyses. In the first chapter the use of single-locus markers (e.g. COI, mtMutS and 28S rDNA) was investigated and different automated species delimitation methods (e.g. ABGD, bPTP) were employed to assess species richness among soft coral genera from Western Australia. The methods used appeared suitable for preliminary and rapid diversity assessments especially in the presence of species-rich genera such as Lobophytum and Sarcophyton where morphological identification is particularly difficult and time consuming. In the second chapter, along with the sequencing of complete mitogenomes of Mediterranean Paramuricea species (P. clavata and P. macrospina), the biogeography of the genus was investigated. The results revealed nucleotide and genome size polymorphisms, while the biogeographic predictions suggested that the Mediterranean species have resulted from independent speciation events, explaining in part the high phylogenetic divergence detected. In the third chapter, the sequencing of complete mitogenomes of five Leptogorgia species from different geographic areas (eastern Pacific, eastern Atlantic and Mediterranean) was followed by phylogenetic reconstructions based on an extended mtMutS dataset. The phylogenetic tree recovered Leptogorgia polyphyletic with a clear segregation between the eastern Pacific and eastern Atlantic forms. A time calibrated phylogeny provided insights into the evolution of the genus. In chapter four, using NGS approaches, the complete mitochondrial genome of two eastern Pacific Muricea species (M. crassa and M. purpurea) has been sequenced. The recovery of complete mitogenomes allowed to evaluate the presence of variable and informative regions and to infer a more robust phylogeny. Overall, the results showed high nucleotide diversity in the intergenic spacers, making these regions new potential molecular markers for species-level identifications. In the last chapter a genome-wide Single Nucleotide Polymorphisms (SNPs) and a Bayes Factor Delimitation method were used to infer the genetic relationships within species of the genus Pacifigorgia. The data obtained showed incongruence between molecular and morphological investigations suggesting the possibility of alternative taxonomic assignments for these species. This study provides information on the evolution and speciation of ecologically important soft corals, which distribution range from the littoral and sublittoral zones of the Mediterranean to the tropical and subtropical reefs of Western Australia (WA) and eastern Pacific (EP). The use of mitochondrial markers such as MutS allowed to shed some light on the biogeography and evolutionary history of widespread gorgonians with special emphasis on the Mediterranean endemics and the Atlantic species. Concerning the Western Australia, the obtained results will support the management and conservation of under-investigated marine biodiversity hotspots and potentially species-rich localities such as the Kimberley. In terms of species delimitation, the application of genome-wide SNPs and the use of NGS technologies showed a higher resolution when compared with the traditional methods based on DNA barcoding and single-locus phylogenies. The data generated have been used to clarify the systematics of the species investigated and will be considered as a baseline for future studies on population genetics with a closer look on the adaptive processes

Speciation, evolution and phylogeny of some shallow-water octocorals (Cnidaria: Anthozoa)

Shallow-water octocorals are among the most abundant macro-benthic organisms inhabiting tropical subtropical and temperate communities. In spite of being worldwide distributed and highly diverse, the systematics of many octocorals remains controversial and the understanding of the processes who led to their diversification is largely unexplored. This study includes five chapters, each dealing with different aspects of the systematics, phylogeny and evolution of six soft coral genera such as Lobophytum, Sarcophyton, Paramuricea, Leptogorgia, Muricea and Pacifigorgia. One of the main goals of the study was to explore, through the use of molecular methods, the genetic variation within species notoriously difficult to identify. Besides the use of standard molecular methods for phylogenetic reconstruction and species delimitation, the effectiveness of Next Generation Sequencing (NGS) technologies was tested for mitogenomic and genotyping analyses. In the first chapter the use of single-locus markers (e.g. COI, mtMutS and 28S rDNA) was investigated and different automated species delimitation methods (e.g. ABGD, bPTP) were employed to assess species richness among soft coral genera from Western Australia. The methods used appeared suitable for preliminary and rapid diversity assessments especially in the presence of species-rich genera such as Lobophytum and Sarcophyton where morphological identification is particularly difficult and time consuming. In the second chapter, along with the sequencing of complete mitogenomes of Mediterranean Paramuricea species (P. clavata and P. macrospina), the biogeography of the genus was investigated. The results revealed nucleotide and genome size polymorphisms, while the biogeographic predictions suggested that the Mediterranean species have resulted from independent speciation events, explaining in part the high phylogenetic divergence detected. In the third chapter, the sequencing of complete mitogenomes of five Leptogorgia species from different geographic areas (eastern Pacific, eastern Atlantic and Mediterranean) was followed by phylogenetic reconstructions based on an extended mtMutS dataset. The phylogenetic tree recovered Leptogorgia polyphyletic with a clear segregation between the eastern Pacific and eastern Atlantic forms. A time calibrated phylogeny provided insights into the evolution of the genus. In chapter four, using NGS approaches, the complete mitochondrial genome of two eastern Pacific Muricea species (M. crassa and M. purpurea) has been sequenced. The recovery of complete mitogenomes allowed to evaluate the presence of variable and informative regions and to infer a more robust phylogeny. Overall, the results showed high nucleotide diversity in the intergenic spacers, making these regions new potential molecular markers for species-level identifications. In the last chapter a genome-wide Single Nucleotide Polymorphisms (SNPs) and a Bayes Factor Delimitation method were used to infer the genetic relationships within species of the genus Pacifigorgia. The data obtained showed incongruence between molecular and morphological investigations suggesting the possibility of alternative taxonomic assignments for these species. This study provides information on the evolution and speciation of ecologically important soft corals, which distribution range from the littoral and sublittoral zones of the Mediterranean to the tropical and subtropical reefs of Western Australia (WA) and eastern Pacific (EP). The use of mitochondrial markers such as MutS allowed to shed some light on the biogeography and evolutionary history of widespread gorgonians with special emphasis on the Mediterranean endemics and the Atlantic species. Concerning the Western Australia, the obtained results will support the management and conservation of under-investigated marine biodiversity hotspots and potentially species-rich localities such as the Kimberley. In terms of species delimitation, the application of genome-wide SNPs and the use of NGS technologies showed a higher resolution when compared with the traditional methods based on DNA barcoding and single-locus phylogenies. The data generated have been used to clarify the systematics of the species investigated and will be considered as a baseline for future studies on population genetics with a closer look on the adaptive processes

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Background: Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. Results: We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, the mtMutS, was found to undergo alternative polyadenylation, and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected. Conclusions: Mt-mRNA processing in octocorals possessing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represent a first step towards understanding its functional and evolutionary implications

Nothing in (sponge) biology makes sense - except when based on holotypes

Sponge species are infamously difficult to identify for non-experts due to their high morphological plasticity and the paucity of informative morphological characters. The use of molecular techniques certainly helps with species identification, but unfortunately it requires prior reference sequences. Holotypes constitute the best reference material for species identification, however their usage in molecular systematics and taxonomy is scarce and frequently not even attempted, mostly due to their antiquity and preservation history. Here we provide case studies in which we demonstrate the importance of using holo-type material to answer phylogenetic and taxonomic questions. We also demonstrate the possibility of sequencing DNA fragments out of century-old holotypes. Furthermore we propose the deposition of DNA sequences in conjunction with new species descriptions

Shallow-water zoantharians (Cnidaria, Hexacorallia) from the Central Indo-Pacific

Despite the Central Indo-Pacific (CIP) and the Indonesian Archipelago being a well-known region of coral reef biodiversity, particularly in the ‘Coral Triangle’, little published information is available on its zoantharians (Cnidaria: Hexacorallia: Zoantharia). In order to provide a basis for future research on the Indo-Pacific zoantharian fauna and facilitate comparisons between more well-studied regions such as Japan and the Great Barrier Reef, this report deals with CIP zoantharian specimens in the Naturalis collection in Leiden, the Netherlands; 106 specimens were placed into 24 morpho-species and were supplemented with 88 in situ photographic records from Indonesia, the Philippines, and Papua New Guinea. At least nine morpho-species are likely to be undescribed species, indicating that the region needs more research in order to properly understand zoantharian diversity within the CIP. The Naturalis’ zoantharian specimens are listed by species, as well as all relevant collection information, and in situ images are provided to aid in future studies on zoantharians in the CIP

Additional Files: Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Background: Mitogenome diversity is staggering among early branching animals with respect to size, gene density and content, gene orders, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. Results: We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions (UTRs) of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, mtMutS, was found to undergo alternative polyadenylation (APA), and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected. Conclusions: Mt-mRNA processing in octocorals bearing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represents a first step towards understanding its functional and evolutionary implications

Digitate and capitate soft corals (Cnidaria: Octocorallia: Alcyoniidae) from Western Australia with reports on new species and new Australian geographical records

Bryce, Monika, Poliseno, Angelo, Alderslade, Philip, Vargas, Sergio (2015): Digitate and capitate soft corals (Cnidaria: Octocorallia: Alcyoniidae) from Western Australia with reports on new species and new Australian geographical records. Zootaxa 3963 (2): 160-200, DOI: http://dx.doi.org/10.11646/zootaxa.3963.2.

Historical biogeography and mitogenomics of two endemic Mediterranean gorgonians (Holaxonia, Plexauridae)

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Historical biogeography and mitogenomics of two endemic Mediterranean gorgonians (Holaxonia, Plexauridae)

Among the Mediterranean plexaurids, four species are endemics and despite their ecological importance comprehensive studies on the evolution and biogeography of these organisms are lacking. Here we explore the mitogenomic variability of two endemic, ecologically important Mediterranean Paramuricea species. We assess their phylogenetic relationships and provide first insights into their evolution and biogeography. Complete mitogenome sequences of Paramuricea clavata and Paramuricea macrospina were obtained using long range PCR, primer-walking and Sanger sequencing. For an enlarge sample of Paramuricea species, maximum likelihood and Bayesian phylogenetic trees of the mitochondrial gene mtMutS were obtained and used to study the biogeographic history of Paramuricea through a statistical Dispersal-Vicariance method (S-DIVA). Divergence time was estimated under a strict molecular clock model in BEAST using published octocoral mutation rates. Our results revealed high nucleotide diversity (2.6%) among the two Mediterranean endemics; the highest mutation rates were found in the mtMutS, Nad4 and Nad5. In addition, we found length polymorphisms in several intergenic regions and diversity in mitochondrial genome size. The red gorgonian Paramuricea clavata was closely related to the Eastern Atlantic P. grayi rather than its Mediterranean congener, P. macrospina. Our biogeographic results provide evidence for the independent speciation of the Mediterranean species and point to a Miocene origin of the two endemics, highlighting the role played by the Messinian Salinity Crisis in the evolutionary history of Mediterranean Paramuricea

Pixel-Bit

Resumen tomado de la publicaciónSe ha desarrollado un instrumento válido y fiable para evaluar la competencia digital del profesorado. El Cuestionario sobre la Competencia Digital del profesorado de la Educación Superior Española fue construido a partir de la revisión bibliográfica de estudios e investigaciones referentes a la temática. Dicho instrumento está compuesto de 112 ítems, distribuidos en cuatro dimensiones. Se ofrecen los diferentes resultados obtenidos de los valores de alfa de Cronbach, así como una serie de estadísticos descriptivos. La población ha estado formada por 8.013 docentes, obteniendo 1.145, la validez de contenido fue evaluada mediante juicio de expertos.ES