| 1. |
- Abalde, Samuel, et al.
(författare)
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The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes
- 2023
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Ingår i: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group’s main clades and whose origin has been dated more than 400 million years ago.Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades.Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system.Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.
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| 2. |
- Alström, Per, et al.
(författare)
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Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification
- 2018
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 127, s. 367-375
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Tidskriftsartikel (refereegranskat)abstract
- The widespread Old World avian family Locustellidae ('grassbirds and allies') comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a Glade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.
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| 3. |
- Alström, Per, et al.
(författare)
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Dramatic niche shifts and morphological change in two insular bird species
- 2015
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Ingår i: Royal Society Open Science. - : The Royal Society. - 2054-5703. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla's niche change has led to divergence in both structure and plumage.
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| 4. |
- Alström, Per, et al.
(författare)
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Multiple species within the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex revealed through an integrative taxonomic approach
- 2020
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Ingår i: Ibis. - : Wiley. - 0019-1019 .- 1474-919X. ; 162:3, s. 936-967
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Tidskriftsartikel (refereegranskat)abstract
- We re-evaluated the taxonomy of the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex using molecular, morphological and vocal analyses. The extensive seasonal, sexual, age-related, geographical and taxon-specific variation in this complex has never before been adequately studied. As no previous genetic or vocal analyses have focused on this group, misinterpretation of taxonomic signals from limited conventional morphological study alone was likely. Using mitochondrial and nuclear DNA, we found that P. crinigera sensu lato (s.l.) comprises two non-sister groups of taxa (Himalayan crinigera and Chinese striata groups) that differ substantially morphologically and vocally and that are broadly sympatric in Yunnan Province, China. Prinia polychroa cooki (Myanmar) and P. p. rocki (southern Vietnam) are each morphologically, vocally and genetically distinct. Thai, Cambodian and Laotian populations formerly ascribed to P. p. cooki are morphologically and vocally most similar to and most closely related to Javan P. p. polychroa, and require a new name, proposed here. Prinia p. bangsi of Yunnan is part of the crinigera group rather than of P. polychroa, and hence there is no evidence for sympatry between P. polychroa s.l. and P. crinigera s.l., nor of the occurrence of P. polychroa in mainland China or Taiwan. We recommend the recognition of five species in the complex, with the following suggestions for new English names: Himalayan Prinia P. crinigera sensu stricto (s.s.; with subspecies striatula, crinigera, yunnanensis and bangsi); Chinese Prinia P. striata (subspecies catharia, parumstriata and striata); Burmese Prinia P. cooki (monotypic); Annam Prinia P. rocki (monotypic) and Deignan's Prinia P. polychroa s.s. (subspecies Javan polychroa and the new Southeast Asian taxon). This study underlines the importance of using multiple datasets for the elucidation of diversity of cryptic bird species and their evolutionary history and biogeography.
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| 5. |
- Alström, Per, Professor, et al.
(författare)
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Phylogeny and classification of the avian superfamily Sylvioidea
- 2006
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Ingår i: Molecular Phylogenetics and Evolution. - Swedish Museum Nat Hist, Dept Vertebrate Zool, SE-10405 Stockholm, Sweden. Swedish Museum Nat Hist, Mol Systemat Lab, SE-10405 Stockholm, Sweden. Uppsala Univ, Evolutionary Biol Ctr, Dept Systemat Zool, SE-75236 Uppsala, Sweden. Univ Gothenburg, Dept Zool, SE-40530 Gothenburg, Sweden. : Elsevier BV. - 1055-7903 .- 1095-9513. ; 38:2, s. 381-397
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Tidskriftsartikel (refereegranskat)abstract
- Sylvioidea is one of the three superfamilies recognized within the largest avian radiation, the parvorder Passerida. In the present study, which is the first taxon-dense analysis of the Sylvioidea based on sequence data (nuclear myoglobin intron II and mitochondrial cytochrome b gene), we investigate the interrelationships among the four "sylvioid" clades found by previous workers, as well as the relationships within the largest of these clades. The nuclear and mitochondrial loci estimate basically the same phylogeny, with minor differences in resolution. The trees based on myoglobin and the combined data identify a strongly supported clade that includes the taxa previously allocated to Sylvioidea, except for Sitta (nuthatches), Certhia (treecreepers), Parus (tits), Remiz (penduline tits), Troglodytes and Campylorhynchus (wrens), Polioptila (gnatcatchers), and Regulus (crests/kinglets); this clade also comprises larks, which have previously been placed in the superfamily Passeroidea. We refer to this clade as Sylvioidea. This clade is further divided into 10 main, well-supported clades, which we suggest form the basis for a revised classification. (c) 2005 Elsevier Inc. All rights reserved.
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| 6. |
- Alström, Per, Professor, et al.
(författare)
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Systematics of the avian family Alaudidae using multilocus and genomic data
- 2023
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Ingår i: Avian Research. - : Elsevier BV. - 2053-7166. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The family Alaudidae, larks, comprises 93–100 species (depending on taxonomy) that are widely distributed across Africa and Eurasia, with single species extending their ranges to North and northernmost South America and Australia. A decade-old molecular phylogeny, comprising ∼80% of the species, revealed multiple cases of parallel evolution and large variation in rates of morphological evolution, which had misled taxonomists into creating many non-monophyletic genera. Here, we reconstruct the phylogeny of the larks, using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species (in total 133 taxa; not all loci available for all species). We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling (in total 51 samples of 44 taxa across 40 species). Our results confirm the previous findings of rampant morphological convergence and divergence, and reveal new cases of paraphyletic genera. We propose a new subfamily classification, and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae. Our study supports recently proposed species splits as well as some recent lumps, while also questioning some of the latter. This comprehensive phylogeny will form an important basis for future studies, such as comparative studies of lark natural history, ecology, evolution and conservation.
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| 7. |
- Andersson, Stefan S., et al.
(författare)
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Apatite as a tracer of the source, chemistry and evolution of ore-forming fluids : The case of the Olserum-Djupedal REE-phosphate mineralisation, SE Sweden
- 2019
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Ingår i: Geochimica et Cosmochimica Acta. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0016-7037 .- 1872-9533. ; 255, s. 163-187
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Tidskriftsartikel (refereegranskat)abstract
- This study explores the suitability of apatite as a tracer of the source(s), chemistry, and evolution of ore-forming hydrothermal fluids. This is tested by analysing the halogen (F, Cl, Br, and I), stable Cl isotopic, and trace element compositions of fluorapatite from the regional-scale Olserum-Djupedal rare earth element (REE) phosphate mineralisation in SE Sweden, which is dominated by monazite-(Ce), xenotime-(Y), and fluorapatite. The primary hydrothermal fluid flow system is recorded in a sequence from proximal granite-hosted to distal metasediment-hosted fluorapatite. Along this sequence, primary fluorapatite shows a gradual increase of Cl and Br concentrations and in (Gd/Yb)N, a decrease of F and I concentrations, a decrease in δ37Cl values, in (La/Sm)N, and partly in (La/Yb)N and (Y/Ho)N. Local compositional differences of halogen and trace element concentrations have developed along rims and in domains adjacent to fractures of fluorapatite due to late-stage partial reaction with fracture fluids. These differences are insignificant compared to the larger deposit-scale zoning. This suggests that apatite can retain the primary record of the original ore-forming fluid despite later overprinting fluid events. The agreement between Br/Cl and I/Cl ratios of apatite and those of co-existing fluid inclusions at lower temperatures indicates that only a minor fractionation of Br from I occurs during apatite precipitation. The halogen ratios of apatite can thus be used as a first-order estimate for the composition of the ore-forming fluid. Taking the small fractionation factors for Cl isotopes between apatite and co-existing fluid at high temperatures into account, we propose that the Cl isotopic composition of apatite and the halogen ratios derived from the apatite composition can be used jointly to trace the source(s) of ore-forming fluids. By contrast, most trace elements incorporated in apatite are affected by the host rock environment and by fluid-mineral partitioning due to growth competition between co-crystallising minerals. Collectively, apatite is sensitive to changing fluid compositions, yet it is also able to record the character of primary ore-forming fluids. Thus, apatite is suitable for tracing the origin, chemistry, and evolution of fluids in hydrothermal ore-forming settings.
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| 8. |
- Baiao, Guilherme Costa, et al.
(författare)
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Revision of the West Palaearctic species of Rhoptromeris Forster, 1869 (Hymenoptera: Figitidae: Eucoilinae)
- 2018
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Ingår i: Journal of Natural History. - : TAYLOR & FRANCIS LTD. - 0022-2933 .- 1464-5262. ; 52:17-18, s. 1201-1224
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Tidskriftsartikel (refereegranskat)abstract
- The West Palearctic species of Rhoptromeris are revised. A total of 11 species are recognised as valid in this region, including four newly described species: Rhoptromeris dichromata sp. nov., Rhoptromeris koponeni sp. nov., Rhoptromeris leptocornis sp. nov. and Rhoptromeris macaronesiensis sp. nov. Eucoila luteicornis Ionescu, 1959 is synonymised with Rhoptromeris heptoma (Hartig, 1840) syn. nov. A checklist of the Holarctic Rhoptromeris is presented and an identification key to the West Palearctic species is provided.www.zoobank.org/urn:lsid:zoobank.org:pub:8164332C-93E2-4E3F-A408-F5FF5DFB366E
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| 9. |
- Barnes, Christopher, et al.
(författare)
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High-spatial resolution dating of monazite and zircon reveals the timing of subduction–exhumation of the Vaimok Lens in the SeveNappe Complex (Scandinavian Caledonides)
- 2019
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Ingår i: Contributions to Mineralogy and Petrology. - : Springer Berlin/Heidelberg. - 0010-7999 .- 1432-0967. ; 174:1
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Tidskriftsartikel (refereegranskat)abstract
- In-situ monazite Th–U–total Pb dating and zircon LA–ICP–MS depth-profiling was applied to metasedimentary rocks from the Vaimok Lens in the Seve Nappe Complex (SNC), Scandinavian Caledonides. Results of monazite Th–U–total Pb dating, coupled with major and trace element mapping of monazite, revealed 603 ± 16 Ma Neoproterozoic cores surrounded byrims that formed at 498 ± 10 Ma. Monazite rim formation was facilitated via dissolution–reprecipitation of Neoproterozoic monazite. The monazite rims record garnet growth as they are depleted in Y2O3 with respect to the Neoproterozoic cores. Rims are also characterized by relatively high SrO with respect to the cores. Results of the zircon depth-profiling revealed igneous zircon cores with crystallization ages typical for SNC metasediments. Multiple zircon grains also exhibit rims formedby dissolution–reprecipitation that are defined by enrichment of light rare earth elements, U, Th, P, ± Y, and ± Sr. Rims also have subdued Eu anomalies (Eu/Eu* ≈ 0.6–1.2) with respect to the cores. The age of zircon rim formation was calculated from three metasedimentary rocks: 480 ± 22 Ma; 475 ± 26 Ma; and 479 ± 38 Ma. These results show that both monazite and zircon experienced dissolution–reprecipitation under high-pressure conditions. Caledonian monazite formed coeval with garnet growth during subduction of the Vaimok Lens, whereas zircon rim formation coincided with monazite breakdown to apatite, allanite and clinozoisite during initial exhumation.
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| 10. |
- Barnes, C. J., et al.
(författare)
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Using Th-U-Pb geochronology to extract crystallization ages of Paleozoic metamorphic monazite contaminated by initial Pb
- 2021
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Ingår i: Chemical Geology. - : Elsevier. - 0009-2541 .- 1872-6836. ; 582
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Tidskriftsartikel (refereegranskat)abstract
- Geochronology of Th-rich minerals is advantageous as it allows use of three isotopic systems (i.e., Pb-206/U-238, Pb-207/U-235, and Pb-208/Th-232) for accurate data assessment. The Pb-208/Th-232 system is especially advantageous in cases where the dated mineral includes an initial Pb component, as Pb-208/Th-232 is the least sensitive to the effects of initial Pb amongst the three systems. This benefit is demonstrated with monazite from a white mica schist of the Tsakkok Lens, Scandinavian Caledonides, where three distinct generations of Paleozoic monazite (Mnzsingle bondI, Mnz-II, Mnz-III) are recognized and dated using laser ablation inductively coupled mass spectrometry. The generations are interpreted to represent monazite crystallization in high-pressure conditions (Mnzsingle bondI), followed by lower-pressure monazite growth (Mnz-II), and likely dissolution-reprecipitation of the pre-existing monazite (Mnz-III). The results are compared in Tera-Wasserburg, Wetherill, and Th-U-Pb concordia space for each monazite generation. In both Tera-Wasserburg and Wetherill space, the data are all discordant and indicate an initial Pb component in the monazite. The trend and magnitude of discordance due to initial Pb in Mnz-I and Mnz-II is generally controlled by UO2 content of the monazite, with higher UO2 equating to greater radiogenic Pb and a dampening of the initial Pb effect, which is most prominent in the Pb-207/U-235 system. For the same generations, initial Pb discordance of Pb-206/U-238 versus Pb-208/Th-232 is less apparent due to the insensitivity of Pb-208/Th-232. Mnz-III does not follow the initial Pb trends, likely due to disturbance of the chemical and isotopic systems during recrystallization. Additional discordance in Mnz-I and Mnz-II, which is not related to initial Pb, is recognized and increases with actinide content. The additional discordance may be due to Pb-mobilization in Mnz-I and Mnz-II domains and is revealed when utilizing the( 208)Pb/Th-232 system due to its insensitivity to initial Pb effects. Consequently, relying only on the U-Pb systems can lead to significant initial Pb overcorrections in Tera-Wasserburg or Wetherill concordia space and to calculations of erroneously young concordia dates. The Th-U-Pb concordia method, incorporating all three systems, does not require an initial Pb correction and, therefore, can account for the additional discordance. The Th-U-Pb concordia dates are interpretated as accurate crystallization ages for Mnz-I (484.7 +/- 1.1 Ma, MSWD: 1.4) and Mnz-II (474.7 +/- 1.2 Ma, MSWD: 1.9). The timing for Mnz-III formation is not well-resolved as it formed via result of dissolution-reprecipitation of the pre-existing monazite, likely under lower amphibolite- to greenschist-facies conditions.
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