| 1. |
- Adl, Sina M., et al.
(författare)
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Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
- 2019
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Ingår i: Journal of Eukaryotic Microbiology. - : WILEY. - 1066-5234 .- 1550-7408. ; 66:1, s. 4-119
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Tidskriftsartikel (refereegranskat)abstract
- This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.
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| 2. |
- Cárdenas, Paco, 1976-, et al.
(författare)
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First records of Geodia demosponges from the New England seamounts, an opportunity to test the use of DNA mini-barcodes on museum specimens
- 2019
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Ingår i: Marine Biodiversity. - : Springer Science and Business Media LLC. - 1867-1616 .- 1867-1624. ; 49:1, s. 163-174
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Tidskriftsartikel (refereegranskat)abstract
- We report the first records of the sponge genus Geodia (Demospongiae, Tetractinellida, Geodiidae) from the New England Seamounts and Muir Seamount, at lower bathyal depths. Nine specimens collected between 2000 and 2005 belong to two boreal species (Geodia macandrewii and Geodia barretti) and a temperate species (Geodia megastrella). These records extend the distributions of these deep-sea amphi-Atlantic species to the west. Most of these specimens were originally fixed in formalin, which substantially degraded the DNA. We nonetheless managed to sequence two cytochrome c oxidase subunit I (COI) mini-barcodes: the universal mini-barcode at the 5′ end of the Folmer barcode (130 bp) and a newly proposed mini-barcode at the 3′ end of the Folmer barcode (296 bp). These mini-barcodes unambiguously confirmed our identifications. As an additional test, we also successfully sequenced these two mini-barcodes from the holotype of G. barretti, collected in 1855. We conclude by advocating the use of mini-barcodes on formalin-fixed or old specimens with degraded DNA.
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| 3. |
- Cárdenas, Paco, 1976-, et al.
(författare)
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From marine caves to the deep sea, a new look at Caminella (Demospongiae, Geodiidae) in the Atlanto-Mediterranean region
- 2018
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Ingår i: Zootaxa. - : Magnolia Press. - 1175-5326 .- 1175-5334. ; 4466:1, s. 174-196
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Tidskriftsartikel (refereegranskat)abstract
- Caminella Lendenfeld, 1894 is a poorly known Geodiidae genus with unclear phylogenetic relationships. In order to find new lines of evidence that could shed light on the evolutionary history of Caminella, we decided to revise type material and museum material, as well as examine new material from underwater caves and deep-sea ecosystems. In doing so, we formally show that Isops maculosus Vosmaer, 1894 and Caminella loricata Lendenfeld, 1894 are junior synonyms of Caminella intuta (Topsent, 1892). We discuss different spicule morphological phenotypes in C. intuta, which may be linked to silica availability. We also discovered two new species of deep-sea Caminella: 1) from Cape Verde (Caminella caboverdensis sp. nov.) and 2) from seamounts located south of the Azores archipelago and the North of Spain (Caminella pustula sp. nov.). We reveal that Caminella sterrasters have complex surface microstructures, unique amongst the Geodiidae, where actin tips are linked to each other. Molecular markers (COI, 28S (C1-D2) and 18S) sequenced for some specimens led to new phylogenetic analyses, which continue to suggest a close relationship of Caminella with the Erylinae and Calthropella; these affinities are discussed in light of morphological characters.
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| 4. |
- Kelly, Michelle, et al.
(författare)
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Molecular study supports the position of the New Zealand endemic genus Lamellomorpha in the family Vulcanellidae (Porifera, Demospongiae, Tetractinellida), with the description of three new species
- 2019
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Ingår i: European journal of taxonomy. - : Museum National D'Histoire Naturelle. - 2118-9773. ; 506, s. 1-25
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Tidskriftsartikel (refereegranskat)abstract
- Due to the possession of huge contort strongyles, and a lack of triaenes in an otherwise 'astrophorine' spicule complement, the phylogenetic position of the endemic, monospecific New Zealand sponge genus, Lamellomorpha Bergquist, 1968, has remained enigmatic. The genus was established within Jaspidae de Laubenfels, 1968 (in the abandoned order Epipolasida Sollas, 1888), but it was not until 2002 that the genus was transferred formally to Astrophorina Sollas, 1887, albeit incertae sedis, by Hooper & Maldonado (2002). In this study, we recognise specimens of Lamellomorpha from the Subantarctic New Zealand region and Chatham Rise, considered by Bergquist to be conspecific with the type species, L. strongylata Bergquist, 1968, first described from the Three Kings-Spirits Bay region of Northland, as the new species, L. australis Kelly & Cardenas sp. nov. These two species of Lamellomorpha have differences in external morphology and colour, skeletal architecture and spicules, natural products, geographical distribution, and depth ranges. Sequencing of the COI Folmer barcode/mini-barcode and of 28S (C1-C2 domains) of these two species suggests phylogenetic affinities of Lamellomorpha with the tetractinellid suborder Astrophorina and the family Vulcanellidae Cardenas et al., 2011. Two Subantarctic New Zealand species of the vulcanellid genus Poecillastra Sollas, 1888, P. ducitriaena Kelly & Cardenas sp. nov. and P. macquariensis Kelly & Cardenas sp. nov., provide further support for the close relationship of Lamellomorpha and Poecillastra.
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| 5. |
- Luis Carballo, Jose, et al.
(författare)
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Molecular and morphological data from Thoosidae in favour of the creation of a new suborder of Tetractinellida
- 2018
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Ingår i: Systematics and Biodiversity. - : TAYLOR & FRANCIS LTD. - 1477-2000 .- 1478-0933. ; 16:5, s. 512-521
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Tidskriftsartikel (refereegranskat)abstract
- The Thoosidae (Porifera, Demospongiae, Tetractinellida) currently includes the genera Thoosa, Alectona, and Delectona. To this date, molecular data are only available for Alectona. In this study, the phylogenetic affinities of the genera Thoosa and Alectona have been investigated with the species T. mismalolli, T. calpulli, and T. purpurea from the Mexican Pacific using morphology and three molecular loci: the mitochondrial cytochrome oxidase subunit 1 (CO1 mtDNA), 28S rRNA (fragment D2), and 18S rRNA. Morphology and embryology showed that these genera are quite different from the rest of the tetractinellids because larvae of Alectona and Thoosa have unique features in sponges, such as the presence of monaxonic discs in Thoosa and tetraxonic discs in Alectona which disappear in the adult stages. A phylogenetic analysis using selected species from the order Tetractinellida revealed that Thoosa groups with Alectona thus confirming morphological studies. The peculiarities in spiculation and embryology of the Thoosa and Alectona larvae, which are markedly different from species belonging to the suborders Astrophorina and Spirophorina and their distant phylogenetic position (based on three molecular loci), suggest that Thoosidae could be placed in the new suborder Thoosina.
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| 6. |
- Morrow, Christine, et al.
(författare)
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Integrating morphological and molecular taxonomy with the revised concept of Stelligeridae (Porifera : Demospongiae)
- 2019
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Ingår i: Zoological Journal of the Linnean Society. - : OXFORD UNIV PRESS. - 0024-4082 .- 1096-3642. ; 187:1, s. 31-81
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Tidskriftsartikel (refereegranskat)abstract
- This study reinforces and extends the findings of previous molecular studies showing that there is a dose relationship between species assigned to the sponge genera Halicnemia, Higginsia, Paratimea and Stelligera and that the family Heteroxyidae is polyphyletic. The present study has led to the description of one new species of Halicnemia and six new species of Paratimea, the resurrection of Halicnemia gallica and a better understanding of the characters uniting Stelligeridae. A new species of Heteroxya is also described. We demonstrate that many of the taxa assigned to Heteroxyidae are more closely related to other families, and we propose several changes to the classification of Heteroscleromorpha. Desmoxyidae is resurrected from synonymy and transferred to Poecilosclerida; Higginsia anfractuosa is transferred to Hymedesmiidae, and a new genus, Hooperia, is erected for its reception; Higginsia durissima is returned to Bubaris (Bubaridae); Higginsia fragilis is transferred to Spanioplon (Hymedesmiidae); Hemiasterella camelus is transferred to Paratimea; and Raspailia (Parasyringella) australiensis and Ceratopsion axiferum are transferred to Adreus (Hemiasterellidae).
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| 7. |
- Pubill-Ulldemolins, Cristina, et al.
(författare)
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Heck Diversification of Indole-Based Substrates under Aqueous Conditions : From Indoles to Unprotected Halo-tryptophans and Halo-tryptophans in Natural Product Derivatives
- 2019
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 25:46, s. 10866-10875
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Tidskriftsartikel (refereegranskat)abstract
- The blending of synthetic chemistry with biosynthetic processes provides a powerful approach to synthesis. Biosynthetic halogenation and synthetic cross-coupling have great potential to be used together, for small molecule generation, access to natural product analogues and as a tool for chemical biology. However, to enable enhanced generality of this approach, further synthetic tools are needed. Though considerable research has been invested in the diversification of phenylalanine and tyrosine, functionalisation of tryptophans thorough cross-coupling has been largely neglected. Tryptophan is a key residue in many biologically active natural products and peptides; in proteins it is key to fluorescence and dominates protein folding. To this end, we have explored the Heck cross-coupling of halo-indoles and halo-tryptophans in water, showing broad reaction scope. We have demonstrated the ability to use this methodology in the functionalisation of a brominated antibiotic (bromo-pacidamycin), as well as a marine sponge metabolite, barettin.
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| 8. |
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| 9. |
- Rubin-Blum, Maxim, et al.
(författare)
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Fueled by methane : deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts
- 2019
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Ingår i: The ISME Journal. - : NATURE PUBLISHING GROUP. - 1751-7362 .- 1751-7370. ; 13:5, s. 1209-1225
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Tidskriftsartikel (refereegranskat)abstract
- Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 Glade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host-symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.
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| 10. |
- Schuster, Astrid, et al.
(författare)
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Evolution of group I introns in Porifera : new evidence for intron mobility and implications for DNA barcoding
- 2017
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Ingår i: BMC Evolutionary Biology. - : BIOMED CENTRAL LTD. - 1471-2148. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background: Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns. Results: For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated. Conclusion: This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.
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