| 1. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 2. |
- Zintzen, Vincent, et al.
(författare)
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Review and phylogeny of the New Zealand hagfishes (Myxiniformes: Myxinidae), with a description of three new species
- 2015
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Ingår i: Zoological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4082 .- 1096-3642. ; 174:2, s. 363-393
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Tidskriftsartikel (refereegranskat)abstract
- Hagfishes from New Zealand are reviewed and a phylogeny proposed using morphological and genetic data (DNA sequences of cytochrome c oxidase subunit I gene, COI, and the small subunit RNA, 16S). Eptatretus cryptus sp. nov. was previously confused with Eptatretus cirrhatus (Forster in Bloch & Schneider, 1801) because of their similar morphology, and is found from the Three Kings Islands to Stewart Island and in the eastern part of the Chatham Rise (at depths of 96–922 m). Eptatretus poicilus sp. nov. is endemic to the Three Kings Islands, where it is common and associated with soft sediment and deep-sea coral-sponge habitats (114–842 m). Neomyxine caesiovitta sp. nov. is a slender hagfish found along the east coast of the North Island south to the Chatham Rise (430–1083 m). A neotype is erected for E. cirrhatus (type locality: Breaksea Sound, Fiordland), occurring widely in New Zealand coastal, shelf, and slope waters (1–922 m), but not at the Three Kings Islands. Eptatetrus goliath Mincarone & Stewart, 2006, Neomyxine biniplicata (Richardson & Jowett, 1951), and Nemamyxine elongata Richardson, 1958 are further described using additional material. Rubicundus eos (Fernholm, 1991) is still only known from the holotype (type locality: Challenger Plateau). Genetic results showed that the New Zealand Eptatretus species form a monophyletic group within the subfamily Eptatretinae, indicating likely speciation from a single common ancestor within the area. Eptatretus poicilus sp. nov. is the sister species of E. cirrhatus, and E. cryptus sp. nov. is closely associated with the clade formed by these two species. Eptatretus goliath is most closely associated with Eptatretus minor Fernholm & Hubbs, 1981 (Gulf of Mexico), these two species basally diverging within New Zealand hagfishes. The endemic genus Neomyxine forms a well-supported monophyletic group of as yet uncertain position within the phylogenetic tree. A key to the New Zealand hagfishes, fresh colour photographs, distribution maps, and in situ video recordings are presented
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| 3. |
- Fernholm, Bo, et al.
(författare)
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Hagfish phylogeny and taxonomy, with description of the new genus Rubicundus (Craniata, Myxinidae)
- 2013
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Ingår i: Journal of Zoological Systematics and Evolutionary Research. - : Hindawi Limited. - 0947-5745 .- 1439-0469. ; 51:4, s. 296-307
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Tidskriftsartikel (refereegranskat)abstract
- A recent phylogenetic analysis of the Myxinidae based on the 16S rRNA gene resulted in synonymization of Paramyxine with Eptatretus. This created homonymy of Paramyxine fernholmi with Eptatretus fernholmi and Paramyxine wisneri with Eptatretus wisneri. In order to resolve this nomenclatural dilemma, we made a more extensive phylogenetic assessment of the Myxinidae and examined the nomenclature of the family. We used 75 sequences (37 of which new for this study) of a 561 bp fragment of the 16S rRNA gene, representing 33 species, and 72 sequences (37 of which new for this study) of a 687 bp fragment of the cytochrome c oxidase subunit I (COI) gene, representing 23 species, to reconstruct the phylogeny of Myxinidae. The monophyly of the subfamily Myxininae, traditionally characterized by having a single pair of external gill openings, was rejected (0.50 Bayesian posterior probability) by the 16S analysis, but supported by the COI and combined COI+16S analyses (0.99 and 0.81 Bpp, respectively). The monophyly of the subfamily Eptatretinae, characterized by having several pairs of external gill openings, was not supported by the 16S analysis and rejected by the COI and combined COI+16S analysis due to the placement of Eptatretus lopheliae as the earliest branch of Myxinidae (0.71 and 0.57 Bpp, respectively). Eptatretus lopheliae and Eptatretus rubicundus formed a monophyletic group and were allocated to a new genus, Rubicundus, characterized by the presence of an elongated tubular nostril and reddish coloration. A new monotypic subfamily, Rubicundinae, was proposed for Rubicundus. The synonymy of the genera Paramyxine and Quadratus with Eptatretus was confirmed. E. fernholmi is renamed Eptatretus luzonicus. Eptatretus wisneri was renamed Eptatretus bobwisneri. Petromyzon cirrhatus Forster, 1801, Homea banksii Fleming, 1822, and Bdellostoma forsteri Müller, 1836 are synonyms, but no type specimens are known to exist. Petromyzon cirrhatus was designated as type species of Eptatretus, conserving present usage. Gastrobranchus dombeyi Shaw, 1804 has priority over other names for Chilean myxinids. Bdellostoma stoutii was designated as type species of Polistotrema Gill. The validity of the Western Atlantic Myxine limosa as distinct from the Eastern Atlantic Myxine glutinosa was confirmed.
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| 4. |
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| 5. |
- van de Kamp, Thomas, et al.
(författare)
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Parasitoid biology preserved in mineralized fossils
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723.
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Tidskriftsartikel (refereegranskat)abstract
- About 50% of all animal species are considered parasites. The linkage of species diversity to a parasitic lifestyle is especially evident in the insect order Hymenoptera. However, fossil evidence for host–parasitoid interactions is extremely rare, rendering hypotheses on the evolution of parasitism assumptive. Here, using high-throughput synchrotron X-ray microtomography, we examine 1510 phosphatized fly pupae from the Paleogene of France and identify 55 parasitation events by four wasp species, providing morphological and ecological data. All species developed as solitary endoparasitoids inside their hosts and exhibit different morphological adaptations for exploiting the same hosts in one habitat. Our results allow systematic and ecological placement of four distinct endoparasitoids in the Paleogene and highlight the need to investigate ecological data preserved in the fossil record.
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