Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae

Figueroa, Diego F.; Baco, Amy R.

doi:10.1016/j.dsr2.2013.06.001

Cited by 25 publications

(37 citation statements)

References 41 publications

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“…The three new species in Pleurocorallium described here are supported by both morphological and molecular evidence. While previous studies indicated that species within Hemicorallium could not be delimited by mitochondrial markers (Ardila et al 2012;Figueroa & Baco 2014;Tu et al 2015b), morphometric measurements coupled with MFA can be used to separate most Hemicorallium species. Thus, by applying statistical comparisons of morphological features, the current study has succeeded in delimiting coralliids.…”

Section: Discussionmentioning

confidence: 99%

“…Current evidence has revealed that due to the recent diversification times and low mitochondrial DNA divergence, the widely used mitochondrial gene cannot delimit species in Hemicorallium (Ardila et al 2012;Figueroa & Baco 2014;Tu et al 2015b). The molecular resolution is inconsistent with morphological characters in Hemicorallium (Ardila et al 2012).…”

Section: Introductionmentioning

confidence: 99%

“…In order to accurately identify the harvested species, several studies have reviewed the taxonomy of corallid corals by molecular information coupled with morphological characters. Based on the results, a three-genera scheme of classification proposed by Gray (1867) was resurrected and redescribed (Ardila et al 2012;Figueroa & Baco 2014;Tu et al 2015b). Furthermore, the results revealed the existence of potential new species from New Caledonia.…”

Section: Introductionmentioning

confidence: 99%

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Taxonomic revision of Coralliidae with descriptions of new species from New Caledonia and the Hawaiian Archipelago

Dai

Jeng

2016

Marine Biology Research

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The systematics of Coralliidae has been revised based on molecular phylogenetic analysis and detailed morphological studies. This revision has also revealed the existence of new species. In order to fully accomplish this revision, five new species including Hemicorallium aurantiacum sp. nov., Pleurocorallium bonsaiarborum sp. nov., P. clavatum sp. nov., and P. norfolkicum sp. nov. from New Caledonia, and H. guttatum sp. nov. from the Hawaiian Archipelago are described by integrating the phylogenetic inference and morphological comparisons. Moreover, the type specimens of Corallium tortuosum, H. reginae, H. halmaheirense, P. porcellanum and P. kishinouyei as well as non-type specimens of C. stylasteroides are redescribed. The sclerites of H. reginae, H. halmaheirense, P. porcellanum and C. stylasteroides were first depicted by scanning electron microcopy. A thorough comparison between P. porcellanum and P. kishinouyei indicated that they should be regarded as one species and the former was adopted as the senior synonym. The two new species of Hemicorallium can be separated by morphological features based on the result of multiple factor analysis. A key is proposed for the identification of all existing species of Coralliidae.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Taxonomic revision of Coralliidae with descriptions of new species from New Caledonia and the Hawaiian Archipelago

Dai

Jeng

2016

Marine Biology Research

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“…Moreover, this study, together with the work by Pante et al (2014) in the octocoral genus Chrysogorgia, constitute the first applications of RADsequencing for phylogenetics and species delimitation in cnidarians. Only a handful of previous studies, using traditional mitochondrial data and the ITS2 and 28S nuclear markers, have attempted to evaluate phylogenetic relationships in the octocoral AC clade (Herrera et al 2010;Ardila et al 2012;Brockman & McFadden 2012;Herrera et al 2012;McFadden & van Ofwegen 2013;Uda et al 2013;Figueroa & Baco 2014). These studies find support for the monophyly of the genus Paragorgia, the family Coralliidae, and the sister relationship between the Paragorgiidae and Coralliidae.…”

Section: Rad Sequencing Enables Unprecedented Phylogenetic Resolutionmentioning

confidence: 99%

Evolutionary and ecological genomics in deep-sea organisms

Monroy¹

2015

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Hydrothermal vents and coral ecosystems are conspicuous biological hot spots in the deep-sea. These ecosystems face increasing threats from human activities. Having thorough taxonomic inventories as well as understanding species' relatedness, genetic diversity, connectivity patterns, and adaptive potential is fundamental for the implementation of conservation strategies that help mitigate these threats. This thesis provides fundamental high-priority knowledge in taxonomic, evolutionary, and ecological aspects of deep-sea coral and vent species, by harnessing the power of genomic tools and overcoming long-standing methodological barriers. First, I develop bioinformatic tools that help guide the design of studies aiming to characterize eukaryotic genome diversity using restriction-site associated DNA sequencing. Using these tools I find that the predictability of restriction site frequencies in eukaryotic genomes is chiefly determined by the phylogenetic position of the target species and the recognition sequence of the selected restriction enzyme. These tools are then applied to test global-scale historical biogeographic hypotheses of vent fauna using barnacles as model. Phylogeographic inferences suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastward along the southern hemisphere during the Neogene. I suggest that the geological processes and dispersal mechanisms discussed here can explain distribution patterns of many other marine taxa in addition to barnacles. Regional-scale analyses indicate that vent barnacle populations are well connected within basins and ridge systems, and that their diversity patterns do not conform to the predictions from the hypothesis that seamounts are centers of endemism. I then move on to resolve long-standing questions regarding species definitions in recalcitrant deep-sea coral taxa, by unambiguously resolving evolutionary relationships and objectively inferring species boundaries. Finally, I explore the adaptive potential of deep-sea coral species to environmental changes by examining a case of adaptation to shallow water from the deep sea. Candidate positive-selection markers shared between pairs of shallow and deep populations are identified as likely makers for genomic regions involved in adaptation. Overall, the results from this thesis constitute critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems. AKNOWLEDGEMENTSThis degree is the fulfillment of a lifelong dream. I am infinitely grateful to Tim Shank, for taking a chance with me, for challenging me constantly, for honest advising, for providing limitless opportunities to pursue my interests and develop my skills, for unconditional support and trust, and for making me feel more like a colleague than a student since the first day. I could not imagine a better place to have done my PhD. I look forward to many more ventures to come. I am extremely grateful to my committee ...

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“…Species from the cnidarian class Anthozoa (the clade containing reef-building corals, sea anemones, soft corals, and their relatives) possess relatively large, circular mitochondrial genomes in which protein-coding genes are interspaced with intergenic regions (IGRs) that might play a role in mitochondrial mRNA maturation (e.g. 18,19 ). The mt genome in the cnidarian subphylum Medusozoa (e.g.…”

Section: Introductionmentioning

confidence: 99%

Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa)

2016

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Background: In most animals, the mitochondrial genome is characterized by its small size, organization into a single circular molecule, and a relative conservation of the number of encoded genes. In box jellyfish (Cubozoa, Cnidaria), the mitochondrial genome is organized into 8 linear mito-chromosomes harboring between one and 4 genes each, including 2 extra protein-coding genes: mt-polB and orf314. Such an organization challenges the traditional view of mitochondrial DNA (mtDNA) expression in animals. In this study, we investigate the pattern of mitochondrial gene expression in the box jellyfish Alatina alata, as well as several key nuclear-encoded molecular pathways involved in the processing of mitochondrial gene transcription. Results: Read coverage of DNA-seq data is relatively uniform for all 8 mito-chromosomes, suggesting that each mito-chromosome is present in equimolar proportion in the mitochondrion. Comparison of DNA and RNA-seq based assemblies indicates that mito-chromosomes are transcribed into individual transcripts in which the beginning and ending are highly conserved. Expression levels for mt-polB and orf314 are similar to those of other mitochondrialencoded genes, which provides further evidence for them having functional roles in the mitochondrion. Survey of the transcriptome suggests recognition of the mitochondrial tRNA-Met by the cytoplasmic aminoacyl-tRNA synthetase counterpart and C-to-U editing of the cytoplasmic tRNA-Trp after import into the mitochondrion. Moreover, several mitochondrial ribosomal proteins appear to be lost. Conclusions: This study represents the first survey of mitochondrial gene expression of the linear multi-chromosomal mtDNA in box jellyfish (Cubozoa). Future exploration of small RNAs and the proteome of the mitochondrion will test the hypotheses presented herein.

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Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae

Cited by 25 publications

References 41 publications

Taxonomic revision of Coralliidae with descriptions of new species from New Caledonia and the Hawaiian Archipelago

Taxonomic revision of Coralliidae with descriptions of new species from New Caledonia and the Hawaiian Archipelago

Evolutionary and ecological genomics in deep-sea organisms

Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa)

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