| 1. |
- Vondrák, Jan, et al.
(författare)
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Martin7 : a reference database of DNA barcodes for European epiphytic lichens and its taxonomic implications
- 2023
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Ingår i: Preslia. - : Czech Botanical Society. - 0032-7786. ; 95:3, s. 311-345
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Tidskriftsartikel (refereegranskat)abstract
- Molecular identification of organisms is now a common practice and, increasingly, species are identified from environmental samples. However, for most organisms, we still lack comprehensive reference databases of DNA barcodes to identify the sequences produced. We present a near-complete database of ITS and mtSSU barcodes, named Martin7, for accurate molecular identification of epiphytic lichens (mycobionts) of central Europe. New data were obtained by Sanger and PacBio sequencing. We obtained 907 ITS sequences from 603 species and 844 mtSSU sequences from 546 species and supplemented our dataset with sequences from other reliable sources. In total, 1,172 species are included in the database, 1,004 for the ITS barcode and 906 for mtSSU. ITS was newly sequenced for 224 species and mtSSU for 234 species. For 45 genera these are the first ITS or mtSSU (or both) barcodes ever obtained. In most cases, these barcodes distinguish species as currently circumscribed, but we detected 82 groups or pairs of species where at least one of the barcodes (mostly mtSSU) does not clearly discriminate between species. We revealed diverging genotypes, possibly representing cryptic taxa, within 37 traditionally conceived species. By sequencing phenotypically unidentifiable lichens, we detected numerous “known-unknowns” (presumed undescribed species), especially in the genera Bacidina and Micarea. Five species of sorediate crustose lichens are newly described in the genera Bacidina (two species), Chrysothrix, Japewia and Lecanora. We provide a number of taxonomic novelties, for example that Lecidea betulicola and L. coriacea are teleomorphs of Cheiromycina, and Dictyocatenulata is an anamorph of Thelenella.
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| 2. |
- Cuni-Sanchez, Aida, et al.
(författare)
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High aboveground carbon stock of African tropical montane forests
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 596:7873, s. 536-542
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Tidskriftsartikel (refereegranskat)abstract
- Tropical forests store 40–50per cent of terrestrial vegetation carbon. However, spatial variations in aboveground live tree biomass carbon (AGC) stocks remain poorly understood, in particular in tropical montane forests. Owing to climatic and soil changes with increasing elevation, AGC stocks are lower in tropical montane forests compared with lowland forests. Here we assemble and analyse a dataset of structurally intact old-growth forests (AfriMont) spanning 44 montane sites in 12 African countries. We find that montane sites in the AfriMont plot network have a mean AGC stock of 149.4megagrams of carbon per hectare (95% confidence interval 137.1–164.2), which is comparable to lowland forests in the African Tropical Rainforest Observation Network4 and about 70per cent and 32per cent higher than averages from plot networks in montane and lowland forests in the Neotropics, respectively. Notably, our results are two-thirds higher than the Intergovernmental Panel on Climate Change default values for these forests in Africa8. We find that the low stem density and high abundance of large trees of African lowland forests is mirrored in the montane forests sampled. This carbon store is endangered: we estimate that 0.8 million hectares of old-growth African montane forest have been lost since 2000. We provide country-specific montane forest AGC stock estimates modelled from our plot network to helpto guide forest conservation and reforestation interventions. Our findings highlight the need for conserving these biodiverse and carbon-rich ecosystems.
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| 3. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 4. |
- Lembrechts, Jonas J., et al.
(författare)
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SoilTemp : A global database of near-surface temperature
- 2020
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 26:11, s. 6616-6629
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Tidskriftsartikel (refereegranskat)abstract
- Current analyses and predictions of spatially explicit patterns and processes in ecology most often rely on climate data interpolated from standardized weather stations. This interpolated climate data represents long-term average thermal conditions at coarse spatial resolutions only. Hence, many climate-forcing factors that operate at fine spatiotemporal resolutions are overlooked. This is particularly important in relation to effects of observation height (e.g. vegetation, snow and soil characteristics) and in habitats varying in their exposure to radiation, moisture and wind (e.g. topography, radiative forcing or cold-air pooling). Since organisms living close to the ground relate more strongly to these microclimatic conditions than to free-air temperatures, microclimatic ground and near-surface data are needed to provide realistic forecasts of the fate of such organisms under anthropogenic climate change, as well as of the functioning of the ecosystems they live in. To fill this critical gap, we highlight a call for temperature time series submissions to SoilTemp, a geospatial database initiative compiling soil and near-surface temperature data from all over the world. Currently, this database contains time series from 7,538 temperature sensors from 51 countries across all key biomes. The database will pave the way toward an improved global understanding of microclimate and bridge the gap between the available climate data and the climate at fine spatiotemporal resolutions relevant to most organisms and ecosystem processes.
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| 5. |
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| 6. |
- Svoboda, Jiří, et al.
(författare)
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Dramatic Drop in the X-Ray Polarization of Swift J1727.8–1613 in the Soft Spectral State
- 2024
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Ingår i: Astrophysical Journal Letters. - 2041-8205 .- 2041-8213. ; 966:2
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Tidskriftsartikel (refereegranskat)abstract
- Black hole X-ray binaries exhibit different spectral and timing properties in different accretion states. The X-ray outburst of a recently discovered and extraordinarily bright source, Swift J1727.8–1613, has enabled the first investigation of how the X-ray polarization properties of a source evolve with spectral state. The 2–8 keV polarization degree was previously measured by the Imaging X-ray Polarimetry Explorer (IXPE) to be ≈4% in the hard and hard intermediate states. Here we present new IXPE results taken in the soft state, with the X-ray flux dominated by the thermal accretion disk emission. We find that the polarization degree has dropped dramatically to ≲1%. This result indicates that the measured X-ray polarization is largely sensitive to the accretion state and the polarization fraction is significantly higher in the hard state when the X-ray emission is dominated by upscattered radiation in the X-ray corona. The combined polarization measurements in the soft and hard states disfavor a very high or low inclination of the system.
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| 7. |
- Svoboda, Jiří, et al.
(författare)
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First X-Ray Polarization Measurement Confirms the Low Black Hole Spin in LMC X-3
- 2024
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Ingår i: Astrophysical Journal. - : Institute of Physics. - 0004-637X .- 1538-4357. ; 960:1
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Tidskriftsartikel (refereegranskat)abstract
- X-ray polarization is a powerful tool to investigate the geometry of accreting material around black holes, allowing independent measurements of the black hole spin and orientation of the innermost parts of the accretion disk. We perform X-ray spectropolarimetric analysis of an X-ray binary system in the Large Magellanic Cloud, LMC X-3, that hosts a stellar-mass black hole, known to be persistently accreting since its discovery. We report the first detection of the X-ray polarization in LMC X-3 with the Imaging X-ray Polarimetry Explorer, and find the average polarization degree (PD) of 3.2% ± 0.6% and a constant polarization angle of −42° ± 6° over the 2-8 keV range. Using accompanying spectroscopic observations by NICER, NuSTAR, and the Neil Gehrels Swift observatories, we confirm previous measurements of the black hole spin via the X-ray continuum method, a ≈ 0.2. From polarization analysis only, we found consistent results with low black hole spin, with an upper limit of a < 0.7 at a 90% confidence level. A slight increase in the PD with energy, similar to other black hole X-ray binaries in the soft state, is suggested from the data but with a low statistical significance.
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| 8. |
- Yang, Xiaolong, et al.
(författare)
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Unveiling the Small-scale Jets in the Rapidly Growing Supermassive Black Hole IZw1
- 2024
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Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 966:2
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Tidskriftsartikel (refereegranskat)abstract
- Accretion of black holes at near-Eddington or super-Eddington rates represents the most powerful episode driving black hole growth, potentially occurring across various types of objects. However, the physics governing accretion and jet-disk coupling in such states remains unclear, primarily due to the difficulty in detecting associated jets, which may emit extremely weakly or exhibit episodic behavior. Only a few near/super-Eddington systems have demonstrated radio activity, and it remains uncertain whether jets exist and what their properties are in super-Eddington active galactic nuclei (AGNs) and ultraluminous X-ray sources. This uncertainty stems mainly from the complex radio emission mix, which includes contributions from jets, star formation activity, photoionized gas, accretion disk wind, and coronal activity. In this work, we conducted high-resolution, very long baseline interferometry observations to investigate jets in the highly accreting narrow-line Seyfert I system I Zw 1. Our observations successfully revealed small-scale jets (with a linear size of ∼45 pc) at both 1.5 and 5 GHz, based on the high radio brightness temperature, radio morphology, and spectral index distribution. Additionally, the parsec-scale jet observed in I Zw 1 displays a knotted morphology reminiscent of other sources accreting at similar rates. In summary, the high accretion rates and jet properties observed in the AGN I Zw 1 may support the AGN/X-ray binary analogy in this extreme state.
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| 9. |
- 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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