| 1. |
- Johansson, Ulf S, et al.
(författare)
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Build-up of the Himalayan avifauna through immigration : A biogeographical analysis of the Phylloscopus and Seicercus warblers
- 2007
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 61:2, s. 324-333
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Tidskriftsartikel (refereegranskat)abstract
- The Himalayan mountain range is one of the most species-rich areas in the world, harboring about 8% of the world's bird species. In this study, we compare the relative importance of immigration versus in situ speciation to the build-up of the Himalayan avifauna, by evaluating the biogeographic history of the Phylloscopus/Seicercus warblers, a speciose clade that is well represented in Himalayan forests. We use a comprehensive, multigene phylogeny in conjunction with dispersal-vicariance analysis to discern patterns of speciation and dispersal within this clade. The results indicate that virtually no speciation has occurred within the Himalayas. Instead, several speciation events are attributed to dispersal into the Himalayas followed by vicariance between the Himalayas and China/Southeast Asia. Most, perhaps all, of these events appear to be pre-Pleistocene. The apparent lack of speciation within the Himalayas stands in contrast to the mountain-driven Pleistocene speciation suggested for the Andes and the East African mountains.
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| 2. |
- Bachmann, L., et al.
(författare)
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The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022
- 2023
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 52:3, s. 187-214
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Tidskriftsartikel (refereegranskat)abstract
- On 25 August 2022, the Zoologica Scripta - An International Journal of Systematic Zoology and the Norwegian Academy of Sciences and Letters arranged a symposium entitled 'The role of systematics for understanding ecosystem functions' in the Academy's premises in Oslo, Norway. The symposium aimed at offering a forum for exploring and discussing trends and future developments in the field of systematics. Eleven international experts contributed expertise on various issues related to global challenges, such as biodiversity assessments, databases, cutting-edge analysis tools, and the consequences of the taxonomic impediment. Here, we compiled a multi-author proceedings paper of the symposium contributions that are arranged in chapters and presents the content and the key conclusions of the majority of the presentations.
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| 3. |
- Alström, P., et al.
(författare)
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Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves: Cettiidae)
- 2007
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Ingår i: Zoological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4082 .- 1096-3642. ; 149:3, s. 437-452
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Tidskriftsartikel (refereegranskat)abstract
- We used morphological, vocal and molecular (one mitochondrial and two nuclear loci) data to re-evaluate the taxonomic status of the taxa acanthizoides, concolor, and brunnescens in the Cettia acanthizoides (J. Verreaux, 1871) complex. We conclude that all three are valid taxa, and that acanthizoides of China and concolor of Taiwan are best treated as conspecific, whereas brunnescens of the Himalayas is better considered as a separate species. The degree of morphological, vocal, and genetic differentiation is variably congruent among all taxa; the recently separated acanthizoides and concolor differ slightly in plumage and structure but are indistinguishable in vocalizations, whereas the earlier diverged brunnescens and acanthizoides/concolor differ only slightly more in morphology but to a much greater degree in vocalizations. We stress the essential nature of taxonomic revisions as a prerequisite for the biodiversity estimates required for conservation planning.
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| 4. |
- Gilbert, M. Thomas P., et al.
(författare)
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Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
- 2008
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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. - 0027-8424 .- 1091-6490. ; 105:24, s. 8327-8332
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Tidskriftsartikel (refereegranskat)abstract
- We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximate to 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the C-14 ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.
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| 5. |
- Gilbert, M. Thomas P., et al.
(författare)
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Whole-genome shotgun sequencing of mitochondria from ancient hair shafts
- 2007
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 317:5846, s. 1927-1930
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Tidskriftsartikel (refereegranskat)abstract
- Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.
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| 6. |
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| 7. |
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| 8. |
- 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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| 9. |
- Bakker, F. T., et al.
(författare)
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The Global Museum: natural history collections and the future of evolutionary science and public education
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the 'Global Museum') is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow's technologies and hence further increasing the relevance of natural history museums.
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| 10. |
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| 11. |
- 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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| 12. |
- Miller, Webb, et al.
(författare)
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The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).
- 2009
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 19:2, s. 213-20
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Tidskriftsartikel (refereegranskat)abstract
- We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.
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| 13. |
- 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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| 14. |
- 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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| 15. |
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| 16. |
- Alström, Per, et al.
(författare)
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Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation
- 2018
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 126, s. 141-152
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Tidskriftsartikel (refereegranskat)abstract
- The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment, and we argue against proliferation of taxonomic names, and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.
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| 17. |
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| 18. |
- 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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| 19. |
- Alström, Per, et al.
(författare)
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Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae.
- 2011
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 58:3, s. 513-26
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Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of most of the species in the avian passerine family Locustellidae is inferred using a Bayesian species tree approach (Bayesian Estimation of Species Trees, BEST), as well as a traditional Bayesian gene tree method (MrBayes), based on a dataset comprising one mitochondrial and four nuclear loci. The trees inferred by the different methods agree fairly well in topology, although in a few cases there are marked differences. Some of these discrepancies might be due to convergence problems for BEST (despite up to 1×10(9) iterations). The phylogeny strongly disagrees with the current taxonomy at the generic level, and we propose a revised classification that recognizes four instead of seven genera. These results emphasize the well known but still often neglected problem of basing classifications on non-cladistic evaluations of morphological characters. An analysis of an extended mitochondrial dataset with multiple individuals from most species, including many subspecies, suggest that several taxa presently treated as subspecies or as monotypic species as well as a few taxa recognized as separate species are in need of further taxonomic work.
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| 20. |
- Alström, Per, et al.
(författare)
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Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset.
- 2011
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 352-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. The close relationship of most of these taxa was unexpected, and called for a comprehensive study based on multiple loci and dense taxon sampling. In the present study, we infer the relationships of all except one of the species in this family using one mitochondrial and three nuclear loci. We use traditional gene tree methods (Bayesian inference, maximum likelihood bootstrapping, parsimony bootstrapping), as well as a recently developed Bayesian species tree approach (*BEAST) that accounts for lineage sorting processes that might produce discordance between gene trees. We also analyse mitochondrial DNA for a larger sample, comprising multiple individuals and a large number of subspecies of polytypic species.RESULTS: There are many topological incongruences among the single-locus trees, although none of these is strongly supported. The multi-locus tree inferred using concatenated sequences and the species tree agree well with each other, and are overall well resolved and well supported by the data. The main discrepancy between these trees concerns the most basal split. Both methods infer the genus Cettia to be highly non-monophyletic, as it is scattered across the entire family tree. Deep intraspecific divergences are revealed, and one or two species and one subspecies are inferred to be non-monophyletic (differences between methods).CONCLUSIONS: The molecular phylogeny presented here is strongly inconsistent with the traditional, morphology-based classification. The remarkably high degree of non-monophyly in the genus Cettia is likely to be one of the most extraordinary examples of misconceived relationships in an avian genus. The phylogeny suggests instances of parallel evolution, as well as highly unequal rates of morphological divergence in different lineages. This complex morphological evolution apparently misled earlier taxonomists. These results underscore the well-known but still often neglected problem of basing classifications on overall morphological similarity. Based on the molecular data, a revised taxonomy is proposed. Although the traditional and species tree methods inferred much the same tree in the present study, the assumption by species tree methods that all species are monophyletic is a limitation in these methods, as some currently recognized species might have more complex histories.
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| 21. |
- Bachmann, L., et al.
(författare)
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Systematics and biodiversity research in the era of genomics
- 2016
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 45, s. 3-4
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Tidskriftsartikel (refereegranskat)abstract
- On 5 November 2015, The Norwegian Academy of Sciences and Letters (DNVA) and the editors of the Zoologica Scripta invited to the one-day symposium ‘Systematics and Biodiversity Research in the Era of Genomics’. Some 80 scientists gathered at the premises of the DNVA in Oslo, Norway, to explore and discuss the current trends and future developments in the field of Animal Systematics. © 2016 The Authors. Zoologica Scripta published by John Wiley & Sons Ltd on behalf of Royal Swedish Academy of Sciences.
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| 22. |
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| 23. |
- Cibois, A., et al.
(författare)
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Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiothrichidae) and a proposal for a revised taxonomy
- 2018
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 47:4, s. 428-440
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenies have gradually shed light on the phylogenetic relationships of the large babbler group. We focus in this study on the family Leiothrichidae (laughingthrushes and song babblers), which represents the largest clade of babblers in terms of species diversity. Our phylogeny includes all genera and 82% of the recognized species, using mitochondrial and nuclear loci. The sister group to Leiothrichidae is composed of the Pellorneidae (jungle babblers) plus the genus Alcippe. Within Leiothrichidae, four strongly supported primary clades (A-D) are recovered. Clade A includes Grammatoptila, Laniellus and Cutia. Clade B includes a large group of laughingthrushes, all of them classified in Trochalopteron. In Clade C, the two laughingthrushes endemic to southern India, T.fairbanki and T.cachinnans, which have recently been proposed to be placed in the newly erected genus Montecincla, form a sister clade to the group comprising the song babblers (Lioptila, Leiothrix, Heterophasia, Minla, Liocichla, Actinodura, Chrysominla, Siva, and Sibia). Clade D includes the African babblers (Turdoides, Phyllanthus, Kupeornis), Asian relatives (Argya, Acanthoptila, Chatarrhaea) and all remaining laughingthrushes (Garrulax). The time estimates suggest that the early diversification of the Leiothrichidae occurred in the mid-Miocene, a period that corresponds to the diversification of many passerine groups in Asia. A revised taxonomic classification of the family is proposed in the light of these results.
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| 25. |
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