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- Britton, Tom, et al.
(author)
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Bayesian support is larger than bootstrap support in phylogenetic inference : a mathematical argument.
- 2007
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In: Mathematical Medicine and Biology. - : Oxford University Press (OUP). - 1477-8599 .- 1477-8602. ; 24:4, s. 401-411
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Journal article (peer-reviewed)abstract
- In phylogenetic inference, the support of an estimated phylogenetic tree topology and its interior branches is usually measured either with non-parametric bootstrap support (BS) values or with Bayesian posterior probabilities (BPPs). Extensive empirical evidence indicates that BPP values are systematically larger than BS when measured on the same data set, but there are no theoretical results supporting such a systematic difference. In the present note, we give a heuristic mathematical argument supporting the empirically observed phenomenon. The argument uses properties of the marginal and profile likelihoods of the normal distribution. The heuristic arguments are supported in a simulation study evaluating different steps in the argument.
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- Brysting, A. K., et al.
(author)
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Untangling complex histories of genome mergings in high polyploids
- 2007
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In: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 56:3, s. 467-476
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Journal article (peer-reviewed)abstract
- Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated network-like histories, and the evolutionary history of many plant groups cannot be adequately represented by phylogenetic trees because of such reticulate events. The history of complex genome mergings within a high-polyploid species complex in the genus Cerastium (Caryophyllaceae) is here untangled by the use of a network algorithm and noncoding sequences of a low-copy number gene. The resulting network illustrates how hybridization and polyploidization have acted as key evolutionary processes in creating a plant group where high-level allopolyploids clearly outnumber extant parental genomes.
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- Eggens, Frida, 1975-
(author)
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Systematics in Sileneae (Caryophyllaceae) – Taxonomy and Phylogenetic patterns
- 2006
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Doctoral thesis (other academic/artistic)abstract
- The focus for the first part of the thesis is on the systematics of species belonging to Silene subgenus Silene. Phylogenetic relationships are inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ITS, intron of the RPB2 gene) genomes. Silene section Rigidulae is shown to be non-monophyletic in its previous circumscription, but instead consisting of six separate clades, each correlated to the geographical distribution of the included species. The taxonomic consequences for each clade are discussed. One of the clades is recognized as a new section and described as Silene sect. Arenosae sect. nov. The morphological descriptions of the species are formalized using a novel implementation of the Prometheus Description Model. Two proposals are included in the thesis, one to reject the name Silene polyphylla L., which is a senior synonym to S. portensis L. Silene linearis Decne. is proposed for conservation against the rarely used S. linearis Sweet. Silene antirrhina, a weedy American annual, is strongly supported as sister to the Hawaiian endemic species of Silene, suggesting an American origin for these. Two of the endemics have evolved woodiness after introduction to Hawaii. In the second part of the thesis we use four nuclear DNA regions, (introns from RPA2, RPB2, RPD2a, RPD2b), and the chloroplast psbE-petG spacer. A framework is developed to evaluate different phylogenetic explanations for conflicting gene trees, where divergence times are used to discriminate among inter- and intralineage processes. The incongruences observed regarding the relationships among the three major lineages of Heliosperma are best explained by homoploid hybridization. The pattern regarding the origin of Heliosperma itself is more complicated and is likely to include several reticulate events. Two lineages have probably been involved in the origin of Heliosperma, one leading to Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.
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| 7. |
- Eggens, F., et al.
(author)
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The origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)
- 2007
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In: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 94:2, s. 210-218
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Journal article (peer-reviewed)abstract
- The Hawaiian endemic Silene are a small group of woody or semiwoody representatives from a large, predominantly herbaceous, species-rich genus. We here investigated the origin and number of introductions of the endemic Hawaiian Silene based on phylogenetic relationships inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ribosomal internal transcribed sequences, ITS, and intron 23 of the RPB2 gene) genomes. Silene antirrhina, a widespread weedy American annual, is strongly supported as sister to a monophyletic group consisting of the Hawaiian Silene, indicating a single colonization event. There are no obvious morphological similarities between S. antirrhina and any of the species of Hawaiian Silene. Our results suggest an American origin for the Hawaiian endemics because that would require only a single trans-ocean dispersal. Two of the Hawaiian endemics (S. struthioloides and S. hawaiiensis) that form a subclade in the analyses have evolved woodiness after introduction to the Hawaiian Islands. Our results contribute to other recent results based on molecular phylogenetics that emphasize the American continent as a source area for the Hawaiian flora and support a striking morphological radiation and evolution of woodiness from a single introduction to the archipelago.
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| 8. |
- Eggens, Frida, et al.
(author)
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The Origin of the Hawaiian endemic Silene species
- 2005
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In: Abstracts - XVII International Botanical Congress: Vienna, Austria.
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Conference paper (other academic/artistic)abstract
- Geographically, one could expect an Asian origin for species from the Hawaiian Islands. Despite this, a number of Hawaiian taxa have been shown to have their closest relatives on the North American continent. The seven species of Silene endemic to Hawaii were placed in a section with two Japanese Silene in the latest global revision of the genus. They were thought to be the result of two colonizations, one for the shrubby species and one for the remaining herbaceous ones. Our results, based on DNA sequences from the plastid genome, ITS, and the nuclear low copy number gene RPB2 of five of the seven species (representing both of the putative colonizations) instead strongly indicate a close relationship between the endemic Hawaiian species and the North American species S. antirrhina, which is sister to a monophyletic group of the Hawaiian Silene, indicating a single colonization event. S. antirrhina is a diploid North American species that is not related to other native North American Silene, of which the majority are polyploid and belong to other clades. There is no obvious morphological support for the relationship between the Hawaiian Silene and S. antirrhina.
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| 9. |
- Erixon, Per, 1972-
(author)
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Phylogenetic Support and Chloroplast Genome Evolution in Sileneae (Caryophyllaceae)
- 2006
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Doctoral thesis (other academic/artistic)abstract
- Evolutionary biology is dependent on accurate phylogenies. In this thesis two branch support methods, Bayesian posterior probablities and bootstrap frequencies, were evaluated with simulated data and empirical data from the chloroplast genome. Bayesian inference was found to be more powerful and less conservative than maximum likelihood bootstrapping, but considerably more sensitive to choice of parameters. Bayesian inference increased in power when data were underparameterized, but the associated increase in type I error was comparatively larger. The chloroplast DNA phylogeny of the tribe Sileneae (Caryophyllaceae) was inferred by analysis of 33,149 aligned nucleotide bases representing 24 taxa. The position of the SW Anatolian taxa Silene cryptoneura and S. sordida strongly disagreed with previous studies on nuclear DNA sequence data, and indicate a possible case of homoploid hybrid origin. Silene atocioides and S. aegyptiaca formed a sister group to Lychnis and remaining Silene, thus suggesting that Silene may be paraphyletic, despite recent revisions based on molecular data. Several nodes in the phylogeny remained poorly supported, despite large amounts of data. Additional sequence sampling is not expected to solve this problem. The main reason for poor resolution is probably a combination of rapid radiation and substitution rate hererogeneity. Apparent incongruent patterns between different regions of the chloroplast genome are evaluated with ancient interspecific chloroplast recombination as explanatory model. Extremely elevated substitution rates in the exons of the plastid clpP gene was documented in Oenothera and three separate lineages of Sileneae. Introns have been lost in some of the lineages, but where present, intron sequences have a markedly slower substitution rate, similar to the rates found in other introns of their genomes. Three branches in the phylogeny show significant whole gene positive selection. In two of the lineages multiple partial copies of the gene were found.
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| 10. |
- Erixon, Per, et al.
(author)
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Reticulate or treelike chloroplast DNA evolution in Sileneae (Caryophyllaceae)?
- 2008
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 48:1, s. 313-325
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Journal article (peer-reviewed)abstract
- Despite sampling of up to 25 kb of chloroplast DNA sequence from 24 species in Sileneae a number of nodes in the phylogeny remain poorly supported and it is not expected that additional sequence sampling will converge to a reliable phylogenetic hypothesis in these parts of the tree. The main reason for this is probably a combination of rapid radiation and substitution rate heterogeneity. Poor resolution among closely related species are often explained by low levels of variation in chloroplast data, but the problem with our data appear to be high levels of homoplasy. Tree-like cpDNA evolution cannot be rejected, but apparent incongruent patterns between different regions are evaluated with the possibility of ancient interspecific chloroplast recombination as explanatory model. However, several major phylogenetic relationships, previously not recognized, are confidently resolved, e.g. the grouping of the two SW Anatolian taxa S. cryptoneura and S. sordida strongly disagrees with previous studies on nuclear DNA sequence data, and indicate a possible case of homoploid hybrid origin. The closely related S. atocioides and S. aegyptiaca form a sister group to Lychnis and the rest of Silene, thus suggesting that Silene may be paraphyletic, despite recent revisions based on molecular data.
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