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- Britton, Tom, et al.
(författare)
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Estimating divergence times in large phylogenetic trees
- 2007
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 56:5, s. 741-752
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Tidskriftsartikel (refereegranskat)abstract
- A new method, PATHd8, for estimating ultrametric trees from trees with edge (branch) lengths proportional to the number of substitutions is proposed. The method allows for an arbitrary number of reference nodes for time calibration, each defined either as absolute age, minimum age, or maximum age, and the tree need not be fully resolved. The method is based on estimating node ages by mean path lengths from the node to the leaves but correcting for deviations from a molecular clock suggested by reference nodes. As opposed to most existing methods allowing substitution rate variation, the new method smoothes substitution rates locally, rather than simultaneously over the whole tree, thus allowing for analysis of very large trees. The performance of PATHd8 is compared with other frequently used methods for estimating divergence times. In analyses of three separate data sets, PATHd8 gives similar divergence times to other methods, the largest difference being between crown group ages, where unconstrained nodes get younger ages when analyzed with PATHd8. Overall, chronograms obtained from other methods appear smoother, whereas PATHd8 preserves more of the heterogeneity seen in the original edge lengths. Divergence times are most evenly spread over the chronograms obtained from the Bayesian implementation and the clock-based Langley-Fitch method, and these two methods produce very similar ages for most nodes. Evaluations of PATHd8 using simulated data suggest that PATHd8 is slightly less precise compared with penalized likelihood, but it gives more sensible answers for extreme data sets. A clear advantage with PATHd8 is that it is more or less instantaneous even with trees having several thousand leaves, whereas other programs often run into problems when analyzing trees with hundreds of leaves. PATHd8 is implemented in freely available software.
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- Brysting, A. K., et al.
(författare)
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Untangling complex histories of genome mergings in high polyploids
- 2007
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 56:3, s. 467-476
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Tidskriftsartikel (refereegranskat)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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- Ekman, Stefan, 1965-, et al.
(författare)
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The Limitations of Ancestral State Reconstruction and the Evolution of the Ascus in the Lecanorales (Lichenized Ascomycota)
- 2008
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Ingår i: Systematic Biology. - London : Taylor & Francis. - 1063-5157 .- 1076-836X. ; 57:1, s. 141-156
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Forskningsöversikt (refereegranskat)abstract
- Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasinglyfrequent. They rely on constancy of character state change rates over trees, a correlation between neutral geneticchange and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions.This investigation explored the outcomes of a variety of methods for reconstructing discrete ancestral state in the ascus apexof the Lecanorales, a group containing the majority of lichen-forming ascomycetes. Evolution of this character complex hasbeen highly controversial in lichen systematics for more than two decades. The phylogeny was estimated using BayesianMarkov chain Monte Carlo inference on DNA sequence alignments of three genes (small subunit of the mitochondrialrDNA, large subunit of the nuclear rDNA, and largest subunit of RNA polymerase II). We designed a novel method forassessing the suitable number of discrete gamma categories, which relies on the effect on phylogeny estimates rather thanon likelihoods. Ancestral state reconstructions were performed using maximum parsimony and maximum likelihood ona posterior tree sample as well as two fully Bayesian methods. Resulting reconstructions were often strikingly differentdepending on the method used; different methods often assign high confidence to different states at a given node. Thetwo fully Bayesian methods disagree about the most probable reconstruction in about half of the nodes, even when similarlikelihood models and similar priors are used. We suggest that similar studies should use several methods, awaiting animproved understanding of the statistical properties of the methods. A Lecanora-type ascus may have been ancestral in theLecanorales. State transformations counts, obtained using stochastic mapping, indicate that the number of state changes is12 to 24, which is considerably greater than the minimum three changes needed to explain the four observed ascus apextypes. Apparently, the ascus in the Lecanorales is far more apt to change than has been recognized. Phylogeny correspondswell with morphology, although it partly contradicts currently used delimitations of the Crocyniaceae, Haematommataceae,Lecanoraceae, Megalariaceae, Mycoblastaceae, Pilocarpaceae, Psoraceae, Ramalinaceae, Scoliciosporaceae, and Squamarinaceae.
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- Frajman, Bozo, et al.
(författare)
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Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) – a multigene phylogenetic approach with Relative Dating
- 2009
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 58:3, s. 328-345
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Tidskriftsartikel (refereegranskat)abstract
- We used four potentially unlinked nuclear DNA regions from the gene family encoding the second largest subunit of the RNA polymerases, as well as the psbE-petG spacer and the rps16 intron from the chloroplast genome, to evaluate the origin of and relationships within Heliosperma (Sileneae, Caryophyllaceae). Relative dates of divergence times are used to discriminate between hybridization and gene duplication/loss as alternative explanations for topological conflicts between gene trees. The observed incongruent relationships among the three major lineages of Heliosperma are better explained by homoploid hybridization than by gene duplication/losses because species branching events exceed gene coalescence times under biologically reasonable population sizes and generation times, making lineage sorting an unlikely explanation. The origin of Heliosperma is complex and the gene trees likely reflect both reticulate evolution and sorting events. At least two lineages have been involved in the origin of Heliosperma, one most closely related to the ancestor of Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.
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