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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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| 3. |
- Jonsson, Knud Andreas, et al.
(författare)
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Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return
- 2019
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 137, s. 200-209
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Tidskriftsartikel (refereegranskat)abstract
- Old World orioles (Oriolidae) are medium-sized passerine birds confined largely to forested areas of Africa, Eurasia and Australasia. We present a new complete molecular (mtDNA) subspecies level phylogeny of the Oriolidae including all 113 taxa (35 species) together with a backbone phylogeny of 19 taxa from the main Oriolus clades based on (i) 21 nuclear genes, (ii) whole mito-genomes, and (iii) genome-wide ultraconserved elements. We use this phylogeny to assess systematic relationships and the biogeographical history of this avian family. Furthermore, we use morphological measurements to investigate the relationship between size and shape axes and upstream or back-colonization of this extensive island region from Asia. We show that several subspecies or groups of subspecies may warrant species rank and we find a continental example of two morphologically distinct species (O. mellianus/O. traillii) being genetically (mtDNA) very similar. Biogeographically, we confirm previous findings that members of the Oriolidae originated in Australo-Papua. Dispersal out of this area took place around 15 Mya to southeast Asia and Africa, and from Africa to the Palearctic followed by recolonization of the Indonesian and Philippine island region during the Plio-Pleistocene. Recolonisation of the Indonesian and Philippine islands coincided with an increase in body size, which may have facilitated the ability to co-exist with other congenerics.
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| 4. |
- Reeve, A. H., et al.
(författare)
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The Sulawesi Thrush (Cataponera turdoides; Aves: Passeriformes) belongs to the genus Turdus
- 2022
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 51:1, s. 32-40
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Tidskriftsartikel (refereegranskat)abstract
- The Asian and Australo-Papuan faunas meet and intermix across the islands of Wallacea. Untangling the origins and relationships of the species inhabiting these archipelagos is an ongoing project that has lasted for well over a century. In recent years, molecular phylogenetic studies have made considerable progress in clarifying the affinities of enigmatic Wallacean taxa, but taxonomic riddles remain, even in groups as well studied as birds. Such is the case with Sulawesi Thrush Cataponera turdoides, a scarce and elusive montane songbird whose taxonomic placement has remained controversial since its description. To determine the evolutionary relationships of this monotypic genus, we obtained a museum specimen and employed whole-genome resequencing to generate a multi-locus dataset. Phylogenetic analyses were performed using UCEs, and individual mitochondrial and nuclear genes. We show that Cataponera is a true thrush of the large and geographically widespread genus Turdus. It belongs to a clade predominantly composed of migratory Palearctic species, but has no close relatives within that group. Sulawesi Thrush is one of only two members of the genus Turdus known to have crossed Wallace's Line to form resident populations.
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| 5. |
- Ericson, Per G P, 1956-, et al.
(författare)
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The earliest record of house sparrows (Passer domesticus) in northern Europe
- 1997
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Ingår i: Journal of Archaeological Science. - : Elsevier BV. - 0305-4403 .- 1095-9238. ; 24:2, s. 183-190
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Tidskriftsartikel (refereegranskat)abstract
- Remains of the house sparrow (Passer domesticus) recovered from a late Bronze Age (1200-800 sc) settlement in central Sweden are described. The house sparrow is conspicuously rare in prehistoric Europe, and this record constitutes the earliest from the northern part. The find predates the introduction of domestic fowl (Gallus gallus) to Sweden, a species with which the house sparrow has been assumed to be spread simultaneously. Instead, it is here suggested that house sparrows most likely spread over Europe along with the horse Equus caballus. (C) 1997 Academic Press Limited
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| 8. |
- Jonsson, Knud Andreas, et al.
(författare)
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Unrecognised (species) diversity in New Guinean passerine birds
- 2019
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Ingår i: Emu (Print). - : TAYLOR & FRANCIS AUSTRALASIA. - 0158-4197 .- 1448-5540. ; 119:3, SI, s. 233-241
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Tidskriftsartikel (refereegranskat)abstract
- Species represent an important unit for the study of diversity, but may not always be delimited consistently across regions and clades. Many of these taxonomic inconsistencies are due to the variable views of taxonomists. In recent years, however, new methodologies have attempted to circumvent this problem by assigning more objective criteria for the delimitation of species, drawing on a wide range of data such as DNA, morphology, vocalisation and ecology. Here, we apply a genetic screening approach in which we sequence the mitochondrial gene ND2 for all recognised subspecies of 16 species in eight genera (a mix of lowland and montane species) from the geologically complex tropical island of New Guinea. We show that populations within some species are genetically highly divergent despite little morphological differentiation, but we also find an example in which populations from five morphologically distinct species are genetically very similar. Overall, our data show higher levels of genetic differentiation than expected, but also highlight the difficulty of predicting which groups contain unrecognised diversity. These results are interesting in their own right, but also have implications for further analyses that focus on increasing our understanding of how diversity builds up over time.
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| 9. |
- Troll, Valentin R., et al.
(författare)
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Global Fe–O isotope correlation reveals magmatic origin of Kiruna-type apatite-iron-oxide ores
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Kiruna-type apatite-iron-oxide ores are key iron sources for modern industry, yet their origin remains controversial. Diverse ore-forming processes have been discussed, comprising low-temperature hydrothermal processes versus a high-temperature origin from magma or magmatic fluids. We present an extensive set of new and combined iron and oxygen isotope data from magnetite of Kiruna-type ores from Sweden, Chile and Iran, and compare them with new global reference data from layered intrusions, active volcanic provinces, and established low-temperature and hydrothermal iron ores. We show that approximately 80% of the magnetite from the investigated Kiruna-type ores exhibit δ56Fe and δ18O ratios that overlap with the volcanic and plutonic reference materials (> 800 °C), whereas ~20%, mainly vein-hosted and disseminated magnetite, match the low-temperature reference samples (≤400 °C). Thus, Kiruna-type ores are dominantly magmatic in origin, but may contain late-stage hydrothermal magnetite populations that can locally overprint primary high-temperature magmatic signatures.
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