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- Höhna, Sebastian, 1983-
(författare)
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Bayesian Phylogenetic Inference : Estimating Diversification Rates from Reconstructed Phylogenies
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Phylogenetics is the study of the evolutionary relationship between species. Inference of phylogeny relies heavily on statistical models that have been extended and refined tremendously over the past years into very complex hierarchical models. Paper I introduces probabilistic graphical models to statistical phylogenetics and elaborates on the potential advantages a unified graphical model representation could have for the community, e.g., by facilitating communication and improving reproducibility of statistical analyses of phylogeny and evolution.Once the phylogeny is reconstructed it is possible to infer the rates of diversification (speciation and extinction). In this thesis I extend the birth-death process model, so that it can be applied to incompletely sampled phylogenies, that is, phylogenies of only a subsample of the presently living species from one group. Previous work only considered the case when every species had the same probability to be included and here I examine two alternative sampling schemes: diversified taxon sampling and cluster sampling. Paper II introduces these sampling schemes under a constant rate birth-death process and gives the probability density for reconstructed phylogenies. These models are extended in Paper IV to time-dependent diversification rates, again, under different sampling schemes and applied to empirical phylogenies. Paper III focuses on fast and unbiased simulations of reconstructed phylogenies. The efficiency is achieved by deriving the analytical distribution and density function of the speciation times in the reconstructed phylogeny.
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| 2. |
- Höhna, Sebastian, 1983-
(författare)
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Bayesian Phylogenetic Inference
- 2011
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis we consider two very different topics in Bayesian phylogenetic inference. The first paper, "Inferring speciation and extinction rates under different sampling schemes" by Sebastian Höhna, Tanja Stadler, Fredrik Ronquist and Tom Britton, focuses on estimating the rates of speciation and extinction of species when only a subsample of the present day species is available. The second paper "Burnin Estimation and Convergence Assessment" by Sebastian Höhna and Kristoffer Sahlin focuses on how to analyze the output of Markov chain Monte Carlo (MCMC) runs with respect to convergence to the stationary distribution and approximation of the posterior probability distribution.The birth-death process is used to describe the evolution of species diversity. Previous work enabled the estimation of speciation and extinction rates under the assumption of a constant rate birth-death process and complete sampling of all extant species. We extend the complete sampled birth-death process to incomplete sampling with three different types of sampling schemes: random sampling, diversified sampling and clustered sampling. On a set of empirical phylogenies with known sampling fraction we observe that taking the sampling fraction into account gives better fitting models, either by random sampling or diversified sampling.The current trend in Bayesian phylogenetic inference is to extend the available models by using more complex models and/or hierarchical models. This renders Bayesian inference by means of the MCMC algorithm very intricate. Performance of single or multiple MCMC runs need to be assessed. We investigate which methods are used in Bayesian phylogenetics to assess the performance of MCMC runs, which methods are available from other research areas and compile a strategy on how to assess convergence and how to estimate the burnin automatically in a statistically sound framework.
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| 3. |
- Stigenberg, Julia, 1975-
(författare)
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Hidden Creatures – systematics of the Euphorinae (Hymenoptera)
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Parasitic wasps constitute one of the last remaining frontiers in the charting of animal diversity. The Braconidae is the second most species-rich family of parasitic wasps; the world fauna has been estimated at 40 000 species and the Swedish fauna is believed to include a little more than 2 000 species, 1 200 of which are currently documented. This thesis is a contribution to the rapidly increasing knowledge of braconid diversity. In paper I, a new gregarious parasitoid, Meteorus acerbiavorus sp. nov. (Braconidae: Eupohrinae), is described from specimens reared from the cocoons of the butterfly Acerbia alpina (Quensel) (Lepidoptera, Arctiidae) in northwestern Finnish Lapland. Based on a molecular phylogenetic analysis, the new species is shown to belong to the M. rubens species group. In the second paper, the Western Palearctic fauna of the tribe is revised, seven new species are described and a key to the Western Palearctic species is presented. Two molecular markers, 28S and COI, are used to study phylogenetic relationships in the tribe. The molecular results showed that the Meteorini fall into four well supported clades. The results also reveal a considerable cryptic species diversity. The third paper deals with distributional, phenological and in many cases rearing data from nearly 2 500 specimens (44 species) of the Meteorini in the collection of the National Museums of Scotland (NMS), Edinburgh. Patterns in the breadth of host ranges are discussed in relation to a reiterated speciation hypothesis. Paper IV examines the phylogenetic relationships of the entire subfamily Euphorinae based upon four gene regions (18S, CAD, 28S D2, and COI). A revised classification of the Euphorinae is proposed that recognizes 55 genera and 14 tribes. Our study shows that early members of the Euphorinae were parasitoids of coleopteran larvae, with a host shift to larval Lepidoptera, adult or immature hosts in the Hemiptera, Hymenoptera, Neuroptera, Orthoptera and Psocoptera.
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