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| 2. |
- Schoch, CL, et al.
(författare)
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
- 2012
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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. - 1091-6490. ; 109:16, s. 6241-6246
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Tidskriftsartikel (refereegranskat)abstract
- Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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| 3. |
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| 4. |
- 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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| 5. |
- Catalan, Jordi, et al.
(författare)
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Global change revealed by palaeolimnological records from remote lakes : a review
- 2013
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Ingår i: Journal of Paleolimnology. - : Springer Netherlands. - 0921-2728 .- 1573-0417. ; 49:3, s. 513-535
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Tidskriftsartikel (refereegranskat)abstract
- Over recent decades, palaeolimnological records from remote sites have provided convincing evidence for the onset and development of several facets of global environmental change. Remote lakes, defined here as those occurring in high latitude or high altitude regions, have the advantage of not being overprinted by local anthropogenic processes. As such, many of these sites record broad-scale environmental changes, frequently driven by regime shifts in the Earth system. Here, we review a selection of studies from North America and Europe and discuss their broader implications. The history of investigation has evolved synchronously with the scope and awareness of environmental problems. An initial focus on acid deposition switched to metal and other types of pollutants, then climate change and eventually to atmospheric deposition-fertilising effects. However, none of these topics is independent of the other, and all of them affect ecosystem function and biodiversity in profound ways. Currently, remote lake palaeolimnology is developing unique datasets for each region investigated that benchmark current trends with respect to past, purely natural variability in lake systems. Fostering conceptual and methodological bridges with other environmental disciplines will upturn contribution of remote lake palaeolimnology in solving existing and emerging questions in global change science and planetary stewardship.
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| 6. |
- Holtgrieve, Gordon W., et al.
(författare)
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A Coherent Signature of Anthropogenic Nitrogen Deposition to Remote Watersheds of the Northern Hemisphere
- 2011
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 334:6062, s. 1545-1548
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Tidskriftsartikel (refereegranskat)abstract
- Humans have more than doubled the amount of reactive nitrogen (Nr) added to the biosphere, yet most of what is known about its accumulation and ecological effects is derived from studies of heavily populated regions. Nitrogen (N) stable isotope ratios (N-15:N-14) in dated sediments from 25 remote Northern Hemisphere lakes show a coherent signal of an isotopically distinct source of N to ecosystems beginning in 1895 +/- 10 years (+/- 1 standard deviation). Initial shifts in N isotope composition recorded in lake sediments coincide with anthropogenic CO2 emissions but accelerate with widespread industrial Nr production during the past half century. Although current atmospheric Nr deposition rates in remote regions are relatively low, anthropogenic N has probably influenced watershed N budgets across the Northern Hemisphere for over a century.
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| 7. |
- Liu, Yu, et al.
(författare)
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Individual and pooled tree-ring stable-carbon isotope series in Chinese pine from the Nan Wutai region, China: Common signal and climate relationships
- 2012
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Ingår i: Chemical Geology. - : Elsevier BV. - 0009-2541. ; 330-331, s. 17-26
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Tidskriftsartikel (refereegranskat)abstract
- To investigate the differences in the climatic signals in stable-carbon isotopic composition captured by averaging series from individual trees versus raw wood of trees pooled prior to analysis, we analyzed two groups of Chinese pine (Pinus tabulaeformis Carr.) from the Nan Wutai region of the Qinling Mountains, China. One group included three trees that were analyzed separately, and the other group comprised four other trees that were pooled prior to preparation and analysis. All δ13C series were positively correlated (r= 0.50–0.58, pb0.0001) for the period AD 1901–2003. After removing the effects of changing δ13C of atmospheric CO2, correlations between the meteorological data and all individual and pooled discrimination (Δ13C) series revealed significant negative responses to temperature for several specific months and for mean January to September (TJ–S) temperature. We used a “numerical mix method” (NMM, equivalent to unweighted mean), by averaging individual Δ13C series (NPS1+NPS2+NPS3), to generate a new series that more strongly correlated to climate series TJ–S (r=−0.67, pb0.0001). This time interval from January through September (J–S) includes the growing season and months prior to the growing season, but the temperature prior to the growing season may provide energy necessary for timely initiation of growth. Thus, the mean TJ–S is significant for plant growth and is consistent with the tree physiology in this region. Our results suggest that the numerical mix method with tree-ring stable isotope data from three trees provides a series quite satisfactory for climatic reconstruction. The relationship of the numerical mix model Δ13C with temperature was stronger than for the pooled series, suggesting numerical mixing of series can be more effective than raw wood sample pooling at least according to the trees in this study.
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| 8. |
- Reuss, Nina, et al.
(författare)
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Development and application of sedimentary pigments for assessing effects of climatic and environmental changes on subarctic lakes in northern Sweden
- 2010
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Ingår i: Journal of Paleolimnology. - : Springer Science and Business Media LLC. - 0921-2728 .- 1573-0417. ; 43:1, s. 149-169
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Tidskriftsartikel (refereegranskat)abstract
- A surface-sediment survey of pigments in 100 lakes in the Scandes Mountains, northern Sweden, was combined with a reconstruction of Holocene sedimentary pigments from Lake Seukokjaure to assess the major factors regulating phototrophic communities, and how these controls may have changed during the period from the deglaciation (similar to 9700 cal. years BP) to the present. The study area covers a pronounced gradient of temperature and precipitation, and encompasses the subarctic tree line, an important ecotonal boundary in this region. Lake Seukokjaure is located in a presently treeless basin close to the modern tree line. The spatial survey of sedimentary pigments was analyzed using principle components analysis (PCA) and redundancy analysis (RDA). PCA explained 73-83% of variance in pigment abundance and composition, whereas RDA explained 22-32% of variation in fossil assemblages. Dissolved organic carbon (DOC) content of lake water, sediment delta C-13, maximum lake depth, elevation and lake-water conductivity were all identified as environmental variables with significant association with pigment abundances in the spatial survey, although phototrophic communities of lakes situated in different vegetation zones (alpine, birch, conifer/birch) were incompletely distinguished by the ordinations. In the RDAs, the primary pigment variability occurred along a production gradient that was correlated negatively to water-column DOC content and delta C-13 signature of sediments. This pattern suggested that the important controls of primary production were light regime and terrestrial supplies of C-13-depleted carbon. In contrast, depth, elevation and conductivity were found to be more important for the differentiation of the phototrophic community composition. Application of these spatial survey results to the Holocene sediment record of Lake Seukokjaure demonstrated the importance of DOC for the temporal development of the lake, from an early state of high production to a period of slight oligotrophication. In general, the algal changes were regulated by the interaction of DOC and conductivity, although transitions in the phototrophic community during the late Holocene were less easily interpreted. Terrestrial vegetation development thus appears to be of utmost importance for the regulation of primary production in oligotrophic alpine and subarctic lakes and climate impacts on lakes, whereas other basin-specific factors may control the ontogeny of algal community composition.
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| 9. |
- Savage, Candida, et al.
(författare)
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Effects of land use, urbanization, and climate variability on coastal eutrophication in the Baltic Sea
- 2010
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 55:3, s. 1033-1046
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Tidskriftsartikel (refereegranskat)abstract
- Sedimentary records of organic matter inputs (stable nitrogen isotopes [delta N-15], nitrogen [N], and carbon [C] content), phytoplankton abundance (pigments, stable carbon isotopes [delta C-13]), and community composition (pigments) were used to reconstruct the history and pathway to water-quality degradation in a Swedish Baltic coastal bay. Changes in nutrient sources and cycling began in the 1800s, but eutrophication intensified only after the 1950s, coincident with intensified agricultural practices. Specifically, sedimentary N and C content doubled, delta 13C increased, and concentrations of pigments indicative of total algal biomass (beta-carotene, Chlorophyll a), diatoms (fucoxanthin, diatoxanthin), chlorophytes (lutein-zeaxanthin, Chlorophyll b), and cyanobacteria (canthaxanthin) increased significantly after 1950. Enhanced algal abundance was most strongly related to total N influx and secondly to total P influx. In particular, historical change in algae was related to agricultural N influx and only weakly to agricultural P. In recent decades, wastewater N influx has further stimulated algal biomass, particularly diatoms. In contrast, colonial cyanobacteria were more correlated to total P than total N inputs. Variance-partitioning analysis explained 60% of the changes in algal abundance and community composition since 1880, with diffuse and point nutrients jointly explaining 36% of the long-term change in algal biomass. Climate variability has become more important as a factor influencing coastal eutrophication in recent decades, explaining 14% of the variance in the algal data since 1975. Both urban and agricultural sources of nutrients have degraded water quality, illustrating the need for cooperation between stakeholders at regional levels to achieve ""good ecological status'' in the Baltic coastal environment.
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| 10. |
- Thell, Arne, et al.
(författare)
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A review of the lichen family Parmeliaceae - history, phylogeny and current taxonomy.
- 2012
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Ingår i: Nordic Journal of Botany. - : Wiley. - 0107-055X. ; 30:6, s. 641-664
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Tidskriftsartikel (refereegranskat)abstract
- The largest family of lichen-forming fungi, the Parmeliaceae, is reviewed. It includes 79 genera in current use and ca 2726 species, a large majority of which belong to one of five main clades: the parmelioid, cetrarioid, usneoid, alectorioid and hypogymnioid. However, 21 genera are positioned outside these clades, and four genera in current use still lack DNA- data. The family has been shown to be monophyletic and the generic classification is relatively well-settled compared with other lecanoralean families. Each clade and its genera are presented here with the latest results from phylogenetic analyses and current taxonomy. In addition, a historical outline of the family and its most prominent researchers is provided.
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