| 1. |
- 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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| 2. |
- Olsson, Urban, 1954, et al.
(författare)
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Non-monophyletic taxa and cryptic species - Evidence from a molecular phylogeny of leaf-warblers (Phylloscopus, Aves)
- 2005
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Ingår i: Molecular Phylogenetics and Evolution. - Univ Gothenburg, Dept Zool, SE-40530 Gothenburg, Sweden. Uppsala Univ, Evolutionary Biol Ctr, Dept Systemat Zool, SE-75236 Uppsala, Sweden. Swedish Museum Nat Hist, Dept Vertebrate Zool, SE-10405 Stockholm, Sweden. Swedish Museum Nat Hist, Mol Systemat Lab, SE-10405 Stockholm, Sweden. : Elsevier BV. - 1055-7903 .- 1095-9513. ; 36:2, s. 261-276
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Tidskriftsartikel (refereegranskat)abstract
- The avian taxa Cryptigata and Aeanthopneuste have been treated either as subgenera within Phylloscopus (leaf-warblers), or as a distinct genus and an informal group, respectively. The circumscriptions of these taxa have varied between authors. We estimated the phylogeny, based on the mitochondrial cytochrome b and 12S genes and the nuclear myoglobin intron 11, of all except two of the species placed in the Cryptigata and Acanthopneuste groups, as well as two recently described species and representatives of all subgenera and major clades in Phylloscopus and Seicercus recognized by previous studies. Neither Cryptigata nor Acanthopneuste is found to be monophyletic. The polytypic species P. reguloides and P. davisoni show deep divergences between some of their respective subspecies, and the latter species is non-monophyletic. We propose that the former be split into three species and the latter into two species. Seicercus xanthoschistos is nested in a clade that includes only Phylloscopus, and we recommend that it be placed in Phylloscopus. The rate of morphological divergence varies considerably among the taxa in this study. Our results emphasize the importance of dense taxon sampling in intrageneric phylogenetic studies. (c) 2005 Elsevier Inc. All rights reserved.
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| 3. |
- Olsson, Urban, 1954, et al.
(författare)
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Phylogeography of Indonesian and Sino-Himalayan region bush warblers (Cettia, Aves)
- 2006
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 41:3, s. 556-565
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Tidskriftsartikel (refereegranskat)abstract
- We present a hypothesis for the phylogeny and phylogeography of a group of bush warblers in the genus Cettia, based on parts of the mitochondrial Cytochrome b gene and the nuclear myoglobin intron II (in all similar to 1.7 kb). Ancestral areas were reconstructed by dispersal-vicariance analysis and constrained Bayesian inference. The results suggest that the insular taxa in the Cettia vulcania group are most closely related to Cettia flavolivacea, and originated from a dispersal by an ancestral population in the Himalayas towards the south, to the Sunda region. From this population, a second dispersal along a different route colonized China and northern Vietnam. Hence, the Chinese taxon intricata and Vietnamese oblita, currently allocated to C. flavoliuacea, are more closely related to the vulcania group than to the other taxa in the flavolivacea group, and we propose that they be treated as conspecific with C vulcania, restricting C. flavolivacea to Myanmar and the Himalayas.
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| 4. |
- Cai, Tianlong, et al.
(författare)
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Near-complete phylogeny and taxonomic revision of the world's babblers (Aves: Passeriformes)
- 2019
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 130, s. 346-356
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Tidskriftsartikel (refereegranskat)abstract
- The babblers are a diverse group of passerine birds comprising 452 species. The group was long regarded as a "scrap basket" in taxonomic classification schemes. Although several studies have assessed the phylogenetic relationships for subsets of babblers during the past two decades, a comprehensive phylogeny of this group has been lacking. In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18-20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 genera of babblers, and a new linear sequence of names.
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| 5. |
- Fjeldså, Jon, et al.
(författare)
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An updated classification of passerine birds
- 2020
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Ingår i: <em>The Largest Avian Radiation</em>. - Barcelona : Lynx Edicions. - 9788416728336 ; , s. 45-63
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Hart Reeve, Andrew, et al.
(författare)
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The formation of the Indo-Pacific montane avifauna
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The processes generating the earth’s montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species’ ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region’s montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.
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| 7. |
- Jiang, Zhiyong, et al.
(författare)
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Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)
- 2024
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Ingår i: BMC Biology. - : BioMed Central (BMC). - 1741-7007. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundResolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary.ResultsHere we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression.ConclusionsCollectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.
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| 8. |
- Olsson, Urban, 1954, et al.
(författare)
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Non-monophyly of the avian genus Seicercus (Aves : Sylviidae) revealed by mitochondrial DNA
- 2004
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Ingår i: Zoologica Scripta. - Gothenburg Univ, Dept Zool, SE-40530 Gothenburg, Sweden. Uppsala Univ, Evolutionary Biol Ctr, Dept Systemat Zool, SE-75236 Uppsala, Sweden. : Wiley. - 0300-3256 .- 1463-6409. ; 33:6, s. 501-510
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Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of all species and nearly all subspecies of Seicercus and representatives of all subgenera in Phylloscopus was estimated based on two mitochondrial genes. According to the gene tree, and supported by non-molecular data, Seicercus belongs in three separate clades. Two of these include only taxa currently classified as Seicercus, while the third comprises S. xanthoschistos and P. occipitalis. These results suggest that both Seicercus and Phylloscopus are paraphyletic. The gene tree suggests two more cases of non-monophyly: (1) the 'S. burkii complex' is separated into two different clades, one of which also includes S. affinis and S. poliogenys; (2) two populations of S. affinis intermedius are more closely related to S. affinis ocularis than to a third population of intermedius. A recent proposal to split the 'S. burkii complex' into six species is corroborated, as is the recognition of the taxon cognitus as a colour morph of S. affinis intermedius. Our study also revealed unexpectedly large genetic divergences between three different populations of the monotypic S. poliogenys, indicating the presence of cryptic species. Our results underscore the importance of dense sampling at the specific and infraspecific levels in intrageneric phylogenetic studies.
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| 9. |
- Song, Gang, et al.
(författare)
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Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late-Pleistocene demographic expansion across the Northern Hemisphere
- 2018
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Ingår i: Journal of Avian Biology. - : WILEY. - 0908-8857 .- 1600-048X. ; 49:2
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.
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| 10. |
- Song, Gang, et al.
(författare)
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Great journey of Great Tits (Parus major group) : Origin, diversification and historical demographics of a broadly distributed bird lineage
- 2020
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Ingår i: Journal of Biogeography. - : WILEY. - 0305-0270 .- 1365-2699. ; 47:7, s. 1585-1598
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Tidskriftsartikel (refereegranskat)abstract
- Aim The Pleistocene glacial cycles play a prominent role in shaping phylogeographical patterns of organisms, while few studies have focused on the regional difference of glacial effects. By acquiring comprehensive knowledge of the origin, diversification and historical demography of an intensively studied passerine species complex, Great Tit, we aim to test the regional variation of the Late Pleistocene glaciation impacts on this widely distributed bird lineage. Location Eurasia and associated peninsulas and archipelagos. Taxa Parus major species complex. Methods Phylogeny, divergence times and demographic dynamics were estimated with Bayesian methods. Population structure, genetic diversity and correlation between genetic and physical distances were estimated based on mtDNA variation. Glacial-to-present distributional changes were assessed via ecological niche modelling (ENM). Results Five major clades (Central Asia, Eastern Asia, Eastern Himalaya, Northern and Western Eurasia and Southern Asia) were detected, with divergence times ranging 1.57-0.50 million years ago. Genetic diversity values and Bayesian skyline plots suggest that the three eastern clades had a deeper population history. A more complex geographic structure was observed in East Asia. Demographic expansion during the last glacial cycle was indicated for all five clades. ENM results showed broad conservatism of traits related to climate tolerances, and generally broader and more continuous distributional patterns under glacial conditions. Main Conclusions The Great Tit complex probably originated in Southeast Asia. Geographic barriers, such as the deserts of Central Asia and the Qinghai-Tibet Plateau appear to be related to the lineage divergence. Late Pleistocene climate cycles influenced both demographic dynamics and divergence, especially in terms of east-west differences in relation to geographic complexity.
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