| 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. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 3. |
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| 4. |
- Gulick, Sean, P.S., et al.
(författare)
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The first day of the Cenozoic
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : US National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116, s. 19342-19351
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Tidskriftsartikel (refereegranskat)abstract
- Highly expanded Cretaceous–Paleogene (K-Pg) boundary section from the Chicxulub peak ring, recovered by International Ocean Discovery Program (IODP) –International Continental Scientific Drilling Program (ICDP) Expedition 364, provides an unprecedented window into the immediate aftermath of the impact. Site M0077 includes ∼130 m of impact melt rock and suevite deposited the first day of the Cenozoic covered by <1 m of micrite-rich carbonate deposite over subsequent weeks to years. We present an interpreted series of events based on analyses of these drill cores. Within minutes of the impact, centrally uplifted basement rock collapsed outward to forma peak ring capped in melt rock. Within tens of minutes, the peak ring was covered in ∼40 m of brecciated impact melt rock and coarsegrained suevite, including clasts possibly generated by melt–water interactions during ocean resurge. Within an hour, resurge crested the peak ring, depositing a 10-m-thick layer of suevite with increased particle roundness and sorting. Within hours, the full resurge deposit formed through settling and seiches, resulting in an 80-m-thick fining-upward, sorted suevite in the flooded crater. Within a day, the reflected rim-wave tsunami reached the crater, depositing a cross-bedded sand-to-fine gravel layer enriched in polycyclic aromatic hydrocarbons overlain by charcoal fragments. Generation of a deep crater open to the ocean allowed rapid flooding and sediment accumulation rates among the highest known in the geologic record. The high-resolution section provides insight into the impact environmental effects, including charcoal as evidence for impactinduced wildfires and a paucity of sulfur-rich evaporites from the target supporting rapid global cooling and darkness as extinction mechanisms.
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| 5. |
- Lyon, Ian C., et al.
(författare)
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Pb nanospheres in ancient zircon yield model ages for zircon formation and Pb mobilization
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Nanospheres of lead (Pb) have recently been identified in zircon (ZrSiO4) with the potential to compromise the veracity of U-Pb age determinations. The key assumption that the determined age is robust against the effects of Pb mobility, as long as Pb is not lost from the zircon during subsequent geological events, is now in question. To determine the effect of nanosphere formation on age determination, and whether analysis of nanospheres can yield additional information about the timing of both zircon growth and nanosphere formation, zircons from the Napier Complex in Enderby Land, East Antarctica, were investigated by high-spatial resolution NanoSIMS (Secondary Ion Mass Spectrometry) mapping. Conventional SIMS analyses with >µm resolution potentially mixes Pb from multiple nanospheres with the zircon host, yielding variable average values and therefore unreliable ages. NanoSIMS analyses were obtained of 207Pb/206Pb in nanospheres a few nanometres in diameter that were resolved from 207Pb/206Pb measurements in the zircon host. We demonstrate that analysis for 207Pb/206Pb in multiple individual Pb nanospheres, along with separate analysis of 207Pb/206Pb in the zircon host, can not only accurately yield the age of zircon crystallization, but also the time of nanosphere formation resulting from Pb mobilization during metamorphism. Model ages for both events can be derived that are correlated due to the limited range of possible solutions that can be satisfied by the measured 207Pb/206Pb ratios of nanospheres and zircon host. For the Napier Complex zircons, this yields a model age of ca 3110 Ma for zircon formation and a late Archean model age of 2610 Ma for the metamorphism that produced the nanospheres. The Nanosphere Model Age (NMA) method constrains both the crystallization age and age of the metamorphism to ~±135 Ma, a significant improvement on errors derived from counting statistics.
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| 6. |
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| 7. |
- Yates, James A. Fellows, et al.
(författare)
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The evolution and changing ecology of the African hominid oral microbiome
- 2021
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 118:20
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Tidskriftsartikel (refereegranskat)abstract
- The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.
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| 9. |
- Danise, Silvia, et al.
(författare)
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Land-sea ecological connectivity during a Jurassic warming event
- 2022
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Ingår i: Earth and Planetary Science Letters. - Amsterdam : Elsevier. - 0012-821X .- 1385-013X. ; 578, s. 117290-117290
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge on how climate change affects land-sea ecological connectivity in deep time is scarce. To fill this knowledge gap we have assembled a unique dataset through a Jurassic (early Toarcian) warming event that includes quantitative abundance data from pollen and spores, organic-walled marine plankton and benthic macro-invertebrates, in association with geochemical data derived from the same sampled horizons, from the Cleveland Basin, UK. Using this dataset we: (i) reconstruct the timing of degradation and recovery of land-plants, marine primary producers and benthic fauna in response to this event, and (ii) test for connectivity between changes in land and marine ecosystems. We find a discrepancy between the timing of the response of land-plant and marine ecosystems to the event. Land-plants were the first to be affected by initial warming, but also recovered relatively quickly after the peak of warmth to return to pre-event levels of richness and diversity. Plankton and benthic fauna instead experienced a delayed response to initial warming, but as warming peaked, they suffered a rapid and extreme turnover. Recovery in the shelf sea was also delayed (particularly for the benthos) compared to the vegetation. Ecological connectivity analyses show a strong link between changes in terrestrial and marine ecosystems. The loss of large trees on land contributed to changes in marine plankton, from dinoflagellate-to prasinophyte algal-dominated communities, by enhancing erosion, runoff and nutrient-supply into shallow seas. Eutrophication and changes in primary productivity contributed to the decrease of dissolved oxygen in the water column and in bottom waters, which in turn affected benthic communities. Such cause-effect mechanisms observed in the Cleveland Basin are likely to have occurred in other basins of the Boreal Realm, and in part also in basins of the Sub-Boreal and Tethyan realms. Although palaeolatitudinal and palaeoceanographic gradients may have controlled local and regional changes in land-plants and marine ecosystems during the Early Jurassic, the main climatic and environmental changes linked to rapid global warming, enhanced weathering and high primary productivity, are shared among all the examined realms.
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| 10. |
- Dean, W. Richard J., et al.
(författare)
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Avian type localities and the type specimens collected by Johan August Wahlberg in southern Africa
- 2022
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Ingår i: Zootaxa. - : Magnolia Press. - 1175-5326 .- 1175-5334. ; 5134:4, s. 521-560
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Tidskriftsartikel (refereegranskat)abstract
- Avian type specimens collected in southern Africa between 1839–1856 by J.A. Wahlberg for the Swedish Museum of Natural History, Stockholm (Naturhistoriska riksmuseet; NRM) are listed. Each species account discusses collection sites, nomenclature, and taxonomy, and as needed, gives notes from Wahlberg’s journal of travel routes and camp sites that correct or modify type localities.
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