| 1. |
- Jønsson, Knud A., et al.
(författare)
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Biogeographical history of cuckoo‐shrikes (Aves: Passeriformes) : transoceanic colonization of Africa from Australo-Papua
- 2010
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 37:9, s. 1767-1781
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Tidskriftsartikel (refereegranskat)abstract
- Aim Cuckoo-shrikes and allies (Campephagidae) form a radiation of birds widely distributed in the Indo-Pacific and Africa. Recent studies on the group have been hampered by poor taxon sampling, causing inferences about systematics and biogeography to be rather speculative. With improved taxon sampling and analyses within an explicit spatiotemporal framework, we elucidate biogeographical patterns of dispersal and diversification within this diverse clade of passerine birds. Location Africa, Asia, Australo-Papua, the Pacific, the Philippines and Wallacea. Methods We use model-based phylogenetic methods (MrBayes and garli) to construct a phylogenetic hypothesis of the core Campephagidae (Campephagidae with the exclusion of Pericrocotus). The phylogeny is used to assess the biogeographical history of the group with a newly developed Bayesian approach to dispersal-vicariance analysis (Bayes-diva). We also made use of a partitioned beast analysis, with several calibration points taken from island ages, passerine mitochondrial substitution rates and secondary calibration points for passerine birds, to assess the timing of diversification and dispersal. Results We present a robust molecular phylogeny that includes all genera and 84% of the species within the core Campephagidae. Furthermore, we estimate divergence dates and ancestral area relationships. We demonstrate that Campephagidae originated in Australo-Papua with a single lineage (Pericrocotus) dispersing to Asia early. Later, there was further extensive transoceanic dispersal from Australo-Papua to Africa involving lineages within the core Campephagidae radiation. Main conclusions The phylogenetic relationships, along with the results of the ancestral area analysis and the timing of dispersal events, support a transoceanic dispersal scenario from Australo-Papua to Africa by the core Campephagidae. The sister group to core Campephagidae, Pericrocotus, dispersed to mainland Asia in the late Oligocene. Asia remained uncolonized by the core Campephagidae until the Pliocene. Transoceanic dispersal is by no means an unknown phenomenon, but our results represent a convincing case of colonization over a significant water gap of thousands of kilometres from Australo-Papua to Africa.
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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
- 2012
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
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Tidskriftsartikel (refereegranskat)abstract
- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
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| 3. |
- Buckley, Thomas R., et al.
(författare)
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The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea)
- 2010
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Ingår i: Systematic Entomology. - : Wiley. - 0307-6970 .- 1365-3113. ; 35:2, s. 207-225
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Forskningsöversikt (refereegranskat)abstract
- The Lanceocercata are a clade of stick insects (Phasmatodea) that have undergone an impressive evolutionary radiation in Australia, New Caledonia, the Mascarene Islands and areas of the Pacific. Previous research showed that this clade also contained at least two of the nine New Zealand stick insect genera. We have constructed a phylogeny of the Lanceocercata using 2277 bp of mitochondrial and nuclear DNA sequence data to determine whether all nine New Zealand genera are indeed Lanceocercata and whether the New Zealand fauna is monophyletic. DNA sequence data were obtained from mitochondrial cytochrome oxidase subunits I and II and the nuclear large subunit ribosomal RNA and histone subunit 3. These data were subjected to Bayesian phylogenetic inference under a partitioned model and maximum parsimony. The resulting trees show that all the New Zealand genera are nested within a large New Caledonian radiation. The New Zealand genera do not form a monophyletic group, with the genus Spinotectarchus Salmon forming an independent lineage from the remaining eight genera. We analysed Lanceocercata apomorphies to confirm the molecular placement of the New Zealand genera and to identify characters that confirm the polyphyly of the fauna. Molecular dating analyses under a relaxed clock coupled with a Bayesian extension to dispersal-vicariance analysis was used to reconstruct the biogeographical history for the Lanceocercata. These analyses show that Lanceocercata and their sister group, the Stephanacridini, probably diverged from their South American relatives, the Cladomorphinae, as a result of the separation of Australia, Antarctica and South America. The radiation of the New Caledonian and New Zealand clade began 41.06 million years ago (mya, 29.05-55.40 mya), which corresponds to a period of uplift in New Caledonia. The main New Zealand lineage and Spinotectarchus split from their New Caledonian sister groups 33.72 (23.9-45.62 mya) and 29.9 mya (19.79-41.16 mya) and began to radiate during the late Oligocene and early Miocene, probably in response to a reduction in land area and subsequent uplift in the late Oligocene and early Miocene. We discuss briefly shared host plant patterns between New Zealand and New Caledonia. Because Acrophylla sensu Brock & Hasenpusch is polyphyletic, we have removed Vetilia Stal from synonymy with Acrophylla Gray.
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| 4. |
- Buerki, Sven, et al.
(författare)
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An evaluation of new parsimony-based versus parametric inference methods in biogeography : a case study using the globally distributed plant family Sapindaceae
- 2011
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 38:3, s. 531-550
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Tidskriftsartikel (refereegranskat)abstract
- Aim Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersal-extinction-cladogenesis (DEC), against a parsimony-based method, dispersal-vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study. Location World-wide. Methods Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years. Results Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events - which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node. Main conclusions By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.
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| 5. |
- Dupont, Chris L., et al.
(författare)
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Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:2, s. e89549-
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
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| 6. |
- Ericson, Per G P, 1956-, et al.
(författare)
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Dating the diversification of the major lineages of Passeriformes (Aves)
- 2014
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 14:8, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Background: The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% ofall living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the lateCretaceous. However, previous molecular dating studies have relied heavily on the geological split between NewZealand and Antarctica, assumed to have occurred 85–82 Mya, for calibrating the molecular clock and might thusbe circular in their argument.Results: This study provides a time-scale for the evolution of the major clades of passerines using seven nuclearmarkers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealandsplit from Antarctica 85–52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretationsof the New Zealand–Antarctica vicariance event influence our age estimates. Our results suggest that thediversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration forthe New Zealand–Antarctica vicariance event (85–52 Mya) dramatically increases the 95% credibility intervals andleads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genesanalyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines,which can be used as secondary calibration points in future molecular studies.Conclusions: Our analysis takes recent paleontological and geological findings into account and provides the bestestimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporalframework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, andadds to the growing support for a Cretaceous origin of Passeriformes.
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| 7. |
- Larsson, John, et al.
(författare)
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Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits
- 2011
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 187-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. Results: A total of 404 protein families, present in all cyanobacterial genomes, were identified. Two of these are unique to the phylum, corresponding to an AbrB family transcriptional regulator and a gene that escapes functional annotation although its genomic neighbourhood is conserved among the organisms examined. The evolution of cyanobacterial genome sizes involves a mix of gains and losses in the clade encompassing complex cyanobacteria, while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. Orthologs unique to cyanobacteria exhibiting specific characteristics, such as filament formation, heterocyst differentiation, diazotrophy and symbiotic competence, were also identified. An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genes, 4%-6% of which are unique to cyanobacteria today. Conclusions: The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the history of cyanobacteria. The expansion strategy is driven by gene-family enlargment and generates a broad adaptive potential; while the genome streamlining strategy imposes adaptations to highly specific niches, also reflected in their different functional capacities. A few genomes display extreme proliferation of non-coding nucleotides which is likely to be the result of initial expansion of genomes/gene copy number to gain adaptive potential, followed by a shift to a life-style in a highly specific niche (e. g. symbiosis). This transition results in redundancy of genes and gene families, leading to an increase in junk DNA and eventually to gene loss. A few orthologs can be correlated with specific phenotypes in cyanobacteria, such as filament formation and symbiotic competence; these constitute exciting exploratory targets.
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| 8. |
- Ran, Liang, et al.
(författare)
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Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium
- 2010
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 5:7
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Tidskriftsartikel (refereegranskat)abstract
- Background: An ancient cyanobacterial incorporation into a eukaryotic organism led to the evolution of plastids (chloroplasts) and subsequently to the origin of the plant kingdom. The underlying mechanism and the identities of the partners in this monophyletic event remain elusive.Methodology/Principal Findings: To shed light on this evolutionary process, we sequenced the genome of a cyanobacterium residing extracellularly in an endosymbiosis with a plant, the water-fern Azolla filiculoides Lam. This symbiosis was selected as it has characters which make it unique among extant cyanobacterial plant symbioses: the cyanobacterium lacks autonomous growth and is vertically transmitted between plant generations. Our results reveal features of evolutionary significance. The genome is in an eroding state, evidenced by a large proportion of pseudogenes (31.2%) and a high frequency of transposable elements (,600) scattered throughout the genome. Pseudogenization is found in genes such as the replication initiator dnaA and DNA repair genes, considered essential to free-living cyanobacteria. For some functional categories of genes pseudogenes are more prevalent than functional genes. Loss of function is apparent even within the ‘core’ gene categories of bacteria, such as genes involved in glycolysis and nutrient uptake. In contrast, serving as a critical source of nitrogen for the host, genes related to metabolic processes such as cell differentiation and nitrogen-fixation are well preserved.Conclusions/Significance: This is the first finding of genome degradation in a plant symbiont and phenotypically complex cyanobacterium and one of only a few extracellular endosymbionts described showing signs of reductive genome evolution. Our findings suggest an ongoing selective streamlining of this cyanobacterial genome which has resulted in an organism devoted to nitrogen fixation and devoid of autonomous growth. The cyanobacterial symbiont of Azolla can thus be considered at the initial phase of a transition from free-living organism to a nitrogen-fixing plant entity, a transition process which may mimic what drove the evolution of chloroplasts from a cyanobacterial ancestor.
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