| 1. |
- 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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| 2. |
- 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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| 3. |
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| 4. |
- Dalen, Love, et al.
(författare)
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Partial Genetic Turnover in Neandertals : Continuity in the East and Population Replacement in the West
- 2012
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 29:8, s. 1893-1897
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Tidskriftsartikel (refereegranskat)abstract
- Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mitochondrial DNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recent western European neandertals (< 48 kyr) constitute a tightly defined group with low mitochondrial genetic variation in comparison with both eastern and older (> 48 kyr) European neandertals. Using control region sequences, Bayesian demographic simulations provide higher support for a model of population fragmentation followed by separate demographic trajectories in subpopulations over a null model of a single stable population. The most parsimonious explanation for these results is that of a population turnover in western Europe during early Marine Isotope Stage 3, predating the arrival of anatomically modern humans in the region.
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| 5. |
- Delling, Bo, 1964-, et al.
(författare)
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Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring- and autumnspawners confined to early postglacial arrival
- 2014
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 4:22, s. 4346-4360
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Tidskriftsartikel (refereegranskat)abstract
- Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring- or winter-spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring- and autumn-spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring-spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized.
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| 6. |
- Forshage, Mattias, et al.
(författare)
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Eucoilinae of North America: a revised catalog of genera and described species
- 2013
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Ingår i: Proceedings of the Entomological Society of Washington. - : Entomological Society of Washington. - 0013-8797. ; 115:3, s. 225-255
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Tidskriftsartikel (refereegranskat)abstract
- We present an updated catalog of North American Eucoilinae, bearing little resemblance to previous regional catalogs, which have been lagging behind in the recent systematic work in the group. The current catalog comprises 34 genera, arranged in six tribes. Of these genera, 9 are represented wholly by unidentified or undescribed species in the region, while the other 25 include 108 species recorded from the region. In comparison with previous catalogs, 24 genera and 41 species are added, and 34 species-level names are recombined, while 7 genera, five subgenera and 11 species are removed from the list of North American taxa. A modern, phylogenetically stable and type-based classification is implemented, as well as a tribal classification. In terms of nomenclatural acts, 25 new combinations are made (one is a reinstatement of an old combination); four new genus-levels synonymies are made (Tetramerocera Ashmead junior synonym of Ganaspis Fo ̈rster, Bewelda Quinlan and Aporeucoela Kieffer junior synonyms of Hexacola Fo ̈rster, Pentaplastidia Weld junior synonym of Trybliographa Fo ̈rster); eight new species-level synonymies are made; two species names are removed from synonymy; one new replacement name given (Hexacola pennsylvanicus for Hexacola subaperta Kieffer 1907 nec (Kieffer 1901a)).
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| 7. |
- Lind, Ylva, 1954-, et al.
(författare)
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Stability of fatty acid composition in seal blubber during long-term storage
- 2012
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Ingår i: Marine Ecology Progress Series. - : Inter-Research Science Center. - 0171-8630 .- 1616-1599. ; 461, s. 283-291
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Tidskriftsartikel (refereegranskat)abstract
- This study was performed to evaluate the stability of the fatty acid (FA) composition of blubber from Baltic grey seals Halichoerus grypus archived at −25°C in the Swedish Environmental Specimen Bank (SESB). Possible alterations of FA compositions with storage time and temperature were evaluated. Blubber from 5 seals was kept at +2°C and at −20°C and sampled for up to 6 mo and 33 mo, respectively. Furthermore, FA profile stability was evaluated in blubber stored in the SESB for 4 and 6 yr. This was done by re-sampling and re-analyzing blubber samples from SESB. In both parts of the study, a principal component analysis was performed on 48 FAs comprising 98 to 99% of the total FAs in blubber of Baltic grey seals. We found no indication of a critically altered FA composition, neither in blubber stored at +2°C for 6 mo nor in blubber stored at −20°C for 33 mo. The re-analysis of samples stored in SESB for ~4 to 6 yr only differed for a few FAs in some samples. The most remarkable differences were a slight increase in some long-chain unsaturated FAs (18:2n-6, 20:3n-3, 20:4n-3, 22:4n-3). As an increase in long-chain polyunsaturated FAs due to storage is highly unlikely, we believe that this is probably more due to the sampling technique than to a critically altered FA composition due to storage. Our results suggest that archived seal blubber may be safely used in retrospective analyses of diet using an FA signature analysis technique.
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| 8. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
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Tidskriftsartikel (refereegranskat)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 9. |
- Norén, Karin, et al.
(författare)
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Arctic fox Vulpes lagopus population structure : circumpolar patterns and processes
- 2011
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Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 120:6, s. 873-885
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Tidskriftsartikel (refereegranskat)abstract
- Movement is a prominent process shaping genetic population structure. In many northern mammal species, population structure is formed by geographic distance, geographical barriers and various ecological factors that influence movement over the landscape. The Arctic fox Vulpes lagopus is a highly mobile, opportunistic carnivore of the Arctic that occurs in two main ecotypes with different ecological adaptations. We assembled microsatellite data in 7 loci for 1834 Arctic foxes sampled across their entire distribution to describe the circumpolar population structure and test the impact of (1) geographic distance, (2) geographical barriers and (3) ecotype designation on the population structure. Both Structure and Geneland demonstrated distinctiveness of Iceland and Scandinavia whereas low differentiation was observed between North America-northern Greenland, Svalbard and Siberia. Genetic differentiation was significantly correlated to presence of sea ice on a global scale, but not to geographical distance or ecotype designation. However, among areas connected by sea ice, we recorded a pattern of isolation by distance. The maximum likelihood approach in Migrate suggested that connectivity across North America-northern Greenland and Svalbard was particularly high. Our results demonstrate the importance of sea ice for maintaining connectivity between Arctic fox populations and we therefore predict that climate change will increase genetic divergence among populations in the future.
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| 10. |
- Olsson, Urban, 1954, et al.
(författare)
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Systematic revision of the avian family Cisticolidae based on a multi-locus phylogeny of all genera
- 2013
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 66:3, s. 790-799
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Tidskriftsartikel (refereegranskat)abstract
- The avian taxon Cisticolidae includes c. 110 species which are distributed throughout the tropical and subtropical parts of the Old World. We estimated the phylogeny of 47 species representing all genera assumed to be part of Cisticolidae based on sequence data from two mitochondrial and two nuclear markers, in total 3495 bp. Bayesian inference and maximum likelihood analyses resulted in a generally well-supported phylogeny which clarified the position of several previously poorly known taxa. The placement of Drymocichla, Malcorus, Micromacronus, Oreophilais, Phragmacia, Phyllolais, Poliolais and Urorhipis in Cisticolidae is corroborated, whereas Rhopophilus and Scotocerca are removed from Cisticolidae. Urorhipis and Heliolais are placed in the genus Prinia whereas Prinia burnesii is shown to be part of Timaliidae, and is placed in the genus Laticilla. Although not recovered by all single loci independently, four major clades were identified within Cisticolidae, and one of these is here described as a new taxon (Neomixinae).
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