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| 2. |
- Anderson, Frank E., et al.
(författare)
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Bilaterian phylogeny based on analyses of a region of the sodium-potassium ATPase alpha-subunit gene
- 2004
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 58:3, s. 252-268
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Tidskriftsartikel (refereegranskat)abstract
- Molecular investigations of deep-level relationships within and among the animal phyla have been hampered by a lack of slowly evolving genes that are amenable to study by molecular systematists. To provide new data for use in deep-level metazoan phylogenetic studies, primers were developed to amplify a 1.3-kb region of the subunit of the nuclear-encoded sodium–potassium ATPase gene from 31 bilaterians representing several phyla. Maximum parsimony, maximum likelihood, and Bayesian analyses of these sequences (combined with ATPase sequences for 23 taxa downloaded from GenBank) yield congruent trees that corroborate recent findings based on analyses of other data sets (e.g., the 18S ribosomal RNA gene). The ATPase-based trees support monophyly for several clades (including Lophotrochozoa, a form of Ecdysozoa, Vertebrata, Mollusca, Bivalvia, Gastropoda, Arachnida, Hexapoda, Coleoptera, and Diptera) but do not support monophyly for Deuterostomia, Arthropoda, or Nemertea. Parametric bootstrapping tests reject monophyly for Arthropoda and Nemertea but are unable to reject deuterostome monophyly. Overall, the sodium–potassium ATPase -subunit gene appears to be useful for deep-level studies of metazoan phylogeny.
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| 3. |
- Brindefalk, Björn, et al.
(författare)
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A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:9, s. e24457-
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Tidskriftsartikel (refereegranskat)abstract
- Background: According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria. Methodology/Principal Findings: We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade. Conclusions/Significance: Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria.
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| 4. |
- Brindefalk, Björn, et al.
(författare)
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Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases
- 2007
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 24:3, s. 743-756
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Tidskriftsartikel (refereegranskat)abstract
- Many theories favor a fusion of 2 prokaryotic genomes for the origin of the Eukaryotes, but there are disagreements on the origin, timing, and cellular structures of the cells involved. Equally controversial is the source of the nuclear genes for mitochondrial proteins, although the α-proteobacterial contribution to the mitochondrial genome is well established. Phylogenetic inferences show that the nuclearly encoded mitochondrial aminoacyl-tRNA synthetases (aaRSs) occupy a position in the tree that is not close to any of the currently sequenced α-proteobacterial genomes, despite cohesive and remarkably well-resolved α-proteobacterial clades in 12 of the 20 trees. Two or more α-proteobacterial clusters were observed in 8 cases, indicative of differential loss of paralogous genes or horizontal gene transfer. Replacement and retargeting events within the nuclear genomes of the Eukaryotes was indicated in 10 trees, 4 of which also show split α-proteobacterial groups. A majority of the mitochondrial aaRSs originate from within the bacterial domain, but none specifically from the α-Proteobacteria. For some aaRS, the endosymbiotic origin may have been erased by ongoing gene replacements on the bacterial as well as the eukaryotic side. For others that accurately resolve the α-proteobacterial divergence patterns, the lack of affiliation with mitochondria is more surprising. We hypothesize that the ancestral eukaryotic gene pool hosted primordial "bacterial-like" genes, to which a limited set of α-proteobacterial genes, mostly coding for components of the respiratory chain complexes, were added and selectively maintained.
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| 5. |
- Cárdenas, Paco, et al.
(författare)
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A new Hymedesmia (Demospongiae, Poecilosclerida) with large sigmas off western Sweden
- 2016
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Ingår i: Journal of the Marine Biological Association of the United Kingdom. - 0025-3154 .- 1469-7769. ; 96:6, s. 1305-1312
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Tidskriftsartikel (refereegranskat)abstract
- Hymedesmia (Hymedesmia) lindstroemae sp. nov. collected at 178–210 m depth off the western Swedish coast is described. This encrusting sponge is notably characterized by its unusually large sigmas. This new species brings the number of Hymedesmia (Hymedesmia) species in Swedish waters to 30. A key for all the North Atlantic Hymedesmia (Hymedesmia) species with sigmas (32 species) is included.
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| 6. |
- Cardenas, Paco, et al.
(författare)
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Taxonomy, biogeography and DNA barcodes of Geodia species (Porifera, Demospongiae, Tetractinellida) in the Atlantic boreo-arctic region
- 2013
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Ingår i: Zoological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4082 .- 1096-3642. ; 169:2, s. 251-311
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Tidskriftsartikel (refereegranskat)abstract
- Geodia species north of 60 degrees N in the Atlantic appeared in the literature for the first time when Bowerbank described Geodia barretti and G.macandrewii in 1858 from western Norway. Since then, a number of species have been based on material from various parts of the region: G.simplex, Isops phlegraei, I.pallida, I.sphaeroides, Synops pyriformis, G.parva, G.normani, G.atlantica, Sidonops mesotriaena (now called G.hentscheli), and G.simplicissima. In addition to these 12 nominal species, four species described from elsewhere are claimed to have been identified in material from the northeast Atlantic, namely G.nodastrella and G.cydonium (and its synonyms Cydonium muelleri and Geodia gigas). In this paper, we revise the boreo-arctic Geodia species using morphological, molecular, and biogeographical data. We notably compare northwest and northeast Atlantic specimens. Biological data (reproduction, biochemistry, microbiology, epibionts) for each species are also reviewed. Our results show that there are six valid species of boreo-arctic Atlantic Geodia while other names are synonyms or mis-identifications. Geodia barretti, G.atlantica, G.macandrewii, and G.hentscheli are well established and widely distributed. The same goes for Geodia phlegraei, but this species shows a striking geographical and bathymetric variation, which led us to recognize two species, G.phlegraei and G.parva (here resurrected). Some Geodia are arctic species (G.hentscheli, G.parva), while others are typically boreal (G.atlantica, G.barretti, G.phlegraei, G.macandrewii). No morphological differences were found between specimens from the northeast and northwest Atlantic, except for G.parva. The Folmer cytochrome oxidase subunit I (COI) fragment is unique for every species and invariable over their whole distribution range, except for G.barretti which had two haplotypes. 18S is unique for four species but cannot discriminate G.phlegraei and G.parva. Two keys to the boreo-arctic Geodia are included, one based on external morphology, the other based on spicule morphology.
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| 7. |
- Christerson, Linus, et al.
(författare)
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A novel Chlamydiaceae-like bacterium found in faecal specimens from sea birds from the Bering Sea
- 2010
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229 .- 1758-2229. ; 2:4, s. 605-610
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Tidskriftsartikel (refereegranskat)abstract
- The family Chlamydiaceae contains several bacterial pathogens of important human and veterinary medical concern, such as Chlamydia trachomatis and Chlamydophila psittaci. Within the order Chlamydiales there are also an increasing number of chlamydia-like bacteria whose biodiversity, host range and environmental spread seem to have been largely underestimated, and which are currently being investigated for their potential medical relevance. In this study we present 16S rRNA, rnpB and ompA gene sequence data congruently indicating a novel chlamydia-like bacterium found in faecal specimens from opportunistic fish-eating sea birds, belonging to the Laridae and Alcidae families, from the Bering Sea. This novel bacterium appears to be closer to the Chlamydiaceae than other chlamydia-like bacteria and is most likely a novel genus within the Chlamydiaceae family.
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| 8. |
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| 9. |
- Eggens, Frida, et al.
(författare)
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Phylogeny and species delimitation in Silene sect. Arenosae (Caryophyllaceae): a new section
- 2020
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Ingår i: Phytokeys. - : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; :159, s. 1-34
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Tidskriftsartikel (refereegranskat)abstract
- A putatively monophyletic group of annual Silene species is revised taxonomically and described as the new section S. sect. Arenosae. The species of this section were previously treated as a part of a widely circumscribed and polyphyletic S. sect. Rigidulae. Silene sect. Arenosae as circumscribed here consists of nine species. Members of the section show a predominantly E Mediterranean to SW Asian distribution pattern from Turkey southward to Egypt and eastward to Iran and Pakistan, although most of the species have a limited distribution range. The species of S. sect. Arenosae are characterized by narrowly lanceolate calyx teeth, which are often highly polymorphic, and lanceolate to oblanceolate (non-spathulate) basal leaves. The provided taxonomic revision is based on morphological characters and supported by phylogenetic analyses of two nuclear loci (nrITS and an intron of the RPB2 gene) and one chloroplast locus (the intron of the rps16 gene). The species descriptions are formalized using a novel implementation of the Prometheus Description Model.
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| 10. |
- Frajman, B., et al.
(författare)
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Taxonomic revision of Atocion and Viscaria (Sileneae, Caryophyllaceae)
- 2013
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Ingår i: Botanical Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 173:2, s. 194-210
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Tidskriftsartikel (refereegranskat)abstract
- A species-level taxonomic revision of Atocion and Viscaria, based on a recent phylogenetic study, is presented. Atocion includes six species (A. armeria, A. compactum, A. lerchenfeldianum, A. reuterianum, A. rupestre and A. scythicinum), and Viscaria includes three species (V. alpina, V. asterias and V. vulgaris). The highest species diversity is found on the Balkan Peninsula. Species descriptions based on a study of morphological characters and generated using the Prometheus description model are provided and are also available in the Sileneae online database. Complete synonymy, notes on the ecology and geographical distribution of the taxa and an identification key are provided. Lectotypes for nine names (Lychnis helvetica, L. suecica, Silene armeria var. angustifolia, S. berdaui, S. lituanica, S. compacta, S. orientalis, S. reuteriana and Viscaria media) and a neotype for one name (S. lerchenfeldiana) are assigned. (C) 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 194-210.
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