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| 2. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 4. |
- Kiefer, M., et al.
(författare)
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The SPARC water vapour assessment II: biases and drifts of water vapour satellite data records with respect to frost point hygrometer records
- 2023
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Ingår i: Atmospheric Measurement Techniques. - 1867-1381 .- 1867-8548. ; 16:19, s. 4589-4642
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Tidskriftsartikel (refereegranskat)abstract
- Satellite data records of stratospheric water vapour have been compared to balloon-borne frost point hygrometer (FP) profiles that are coincident in space and time. The satellite data records of 15 different instruments cover water vapour data available from January 2000 through December 2016. The hygrometer data are from 27 stations all over the world in the same period. For the comparison, real or constructed averaging kernels have been applied to the hygrometer profiles to adjust them to the measurement characteristics of the satellite instruments. For bias evaluation, we have compared satellite profiles averaged over the available temporal coverage to the means of coincident FP profiles for individual stations. For drift determinations, we analysed time series of relative differences between spatiotemporally coincident satellite and hygrometer profiles at individual stations. In a synopsis we have also calculated the mean biases and drifts (and their respective uncertainties) for each satellite record over all applicable hygrometer stations in three altitude ranges (10-30 hPa, 30-100 hPa, and 100 hPa to tropopause). Most of the satellite data have biases <10 % and average drifts <1 % yr-1 in at least one of the respective altitude ranges. Virtually all biases are significant in the sense that their uncertainty range in terms of twice the standard error of the mean does not include zero. Statistically significant drifts (95 % confidence) are detected for 35 % of the ≈ 1200 time series of relative differences between satellites and hygrometers.
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| 6. |
- Read, William G., et al.
(författare)
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The SPARC Water Vapor Assessment II: assessment of satellite measurements of upper tropospheric humidity
- 2022
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 15:11, s. 3377-3400
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Tidskriftsartikel (refereegranskat)abstract
- Nineteen limb-viewing data sets (occultation, passive thermal, and UV scattering) and two nadir upper tropospheric humidity (UTH) data sets are intercompared and also compared to frost-point hygrometer balloon sondes. The upper troposphere considered here covers the pressure range from 300-100 hPa. UTH is a challenging measurement, because concentrations vary between 2-1000 ppmv (parts per million by volume), with sharp changes in vertical gradients near the tropopause. Cloudiness in this region also makes the measurement challenging. The atmospheric temperature is also highly variable ranging from 180-250 K. The assessment of satellite-measured UTH is based on coincident comparisons with balloon frost-point hygrometer sondes, multi-month mapped comparisons, zonal mean time series comparisons, and coincident satellite-to-satellite comparisons. While the satellite fields show similar features in maps and time series, quantitatively they can differ by a factor of 2 in concentration, with strong dependencies on the amount of UTH. Additionally, time-lag response-corrected Vaisala RS92 radiosondes are compared to satellites and the frost-point hygrometer measurements. In summary, most satellite data sets reviewed here show on average similar to 30 % agreement amongst themselves and frost-point data but with an additional similar to 30 % variability about the mean bias. The Vaisala RS92 sonde, even with a time-lag correction, shows poor behavior for pressures less than 200 hPa.
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| 7. |
- Stiller, J., et al.
(författare)
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Spaghetti to a Tree: A Robust Phylogeny for Terebelliformia (Annelida) Based on Transcriptomes, Molecular and Morphological Data
- 2020
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Ingår i: Biology-Basel. - : MDPI AG. - 2079-7737. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- Terebelliformia-"spaghetti worms" and their allies-are speciose and ubiquitous marine annelids but our understanding of how their morphological and ecological diversity evolved is hampered by an uncertain delineation of lineages and their phylogenetic relationships. Here, we analyzed transcriptomes of 20 terebelliforms and an outgroup to build a robust phylogeny of the main lineages grounded on 12,674 orthologous genes. We then supplemented this backbone phylogeny with a denser sampling of 121 species using five genes and 90 morphological characters to elucidate fine-scale relationships. The monophyly of six major taxa was supported: Pectinariidae, Ampharetinae, Alvinellidae, Trichobranchidae, Terebellidae and Melinninae. The latter, traditionally a subfamily of Ampharetidae, was unexpectedly the sister to Terebellidae, and hence becomes Melinnidae, and Ampharetinae becomes Ampharetidae. We found no support for the recently proposed separation of Telothelepodidae, Polycirridae and Thelepodidae from Terebellidae. Telothelepodidae was nested within Thelepodinae and is accordingly made its junior synonym. Terebellidae contained the subfamily-ranked taxa Terebellinae and Thelepodinae. The placement of the simplified Polycirridae within Terebellinae differed from previous hypotheses, warranting the division of Terebellinae into Lanicini, Procleini, Terebellini and Polycirrini. Ampharetidae (excluding Melinnidae) were well-supported as the sister group to Alvinellidae and we recognize three clades: Ampharetinae, Amaginae and Amphicteinae. Our analysis found several paraphyletic genera and undescribed species. Morphological transformations on the phylogeny supported the hypothesis of an ancestor that possessed both branchiae and chaetae, which is at odds with proposals of a "naked" ancestor. Our study demonstrates how a robust backbone phylogeny can be combined with dense taxon coverage and morphological traits to give insights into the evolutionary history and transformation of traits.
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| 8. |
- Tilic, E., et al.
(författare)
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Phylogenomics resolves ambiguous relationships within Aciculata (Errantia, Annelida)
- 2022
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903. ; 166
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Tidskriftsartikel (refereegranskat)abstract
- Aciculata (Eunicida + Phyllodocida) is among the largest clades of annelids, comprising almost half of the known diversity of all marine annelids. Despite the group's large size and biological importance, most phylogenomic studies on Annelida to date have had a limited sampling of this clade. The phylogenetic placement of many clades within Phyllodocida in particular has remained poorly understood. To resolve the relationships within Aciculata we conducted a large-scale phylogenomic analysis based on 24 transcriptomes (13 new), chosen to represent many family-ranked taxa that have never been included in a broad phylogenomic study. Our sampling also includes several enigmatic taxa with challenging phylogenetic placement, such as Histriobdella, Struwela, Lacydonia, Pilargis and the holopelagic worms Lopadorrhynchus, Travisiopsis and Tomopteris. Our robust phylogeny allows us to name and place some of these problematic clades and has significant implications on the systematics of the group. Within Eunicida we reinstate the names Eunicoidea and Oenonoidea. Within Phyllodocida we delineate Phyllodociformia, Glyceriformia, Nereidiformia, Nephtyiformia and Aphroditiformia. Phyllodociformia now includes: Lacydonia, Typhloscolecidae, Lopadorrhynchidae and Phyllodocidae. Nephtyiformia includes Nephtyidae and Pilargidae. We also broaden the delineation of Glyceriformia to include Sphaerodoridae, Tomopteridae and Glyceroidea (Glyceridae + Goniadidae). Furthermore, our study demonstrates and explores how conflicting, yet highly supported topologies can result from confounding signals in gene trees. © 2021 The Author(s)
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