| 1. |
- Erixon, Per, et al.
(författare)
-
Reliability of Bayesian Posterior Probabilities and Bootstrap Frequencies in Phylogenetics
- 2003
-
Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 52:5, s. 665-673
-
Tidskriftsartikel (refereegranskat)abstract
- Many empirical studies have revealed considerable differences between nonparametric bootstrapping and Bayesian posterior probabilities in terms of the support values for branches, despite claimed predictions about their approximate equivalence. We investigated this problem by simulating data, which were then analyzed by maximum likelihood bootstrapping and Bayesian phylogenetic analysis using identical models and reoptimization of parameter values. We show that Bayesian posterior probabilities are significantly higher than corresponding nonparametric bootstrap frequencies for true clades, but also that erroneous conclusions will be made more often. These errors are strongly accentuated when the models used for analyses are underparameterized. When data are analyzed under the correct model, nonparametric bootstrapping is conservative. Bayesian posterior probabilities are also conservative in this respect, but less so.
|
|
| 2. |
- Svennblad, Bodil, et al.
(författare)
-
Fundamental differences between the Methods of Maximum Likelihood and Maximum Posterior Probabilities in Phylogenetics
- 2006
-
Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 55:1, s. 116-121
-
Tidskriftsartikel (refereegranskat)abstract
- Using a four-taxon example under a simple model of evolution, we show that the methods of maximum likelihood and maximum posterior probability (which is a Bayesian method of inference) may not arrive at the same optimal tree topology. Some patterns that are separately uninformative under the maximum likelihood method are separately informative under the Bayesian method. We also show that this difference has impact on the bootstrap frequencies and the posterior probabilities of topologies, which therefore are not necessarily approximately equal. Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434, 1996) stated that bootstrap frequencies can, under certain circumstances, be interpreted as posterior probabilities. This is true only if one includes a noninformative prior distribution of the possible data patterns, and most often the prior distributions are instead specified in terms of topology and branch lengths.
|
|
| 3. |
|
|
| 4. |
- Rautenberg, Anja, 1976-, et al.
(författare)
-
Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene
- 2008
-
Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8:1, s. 299-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Increasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (SlX1/Y1) show conflicting phylogenies within Silene (Caryophyllaceae). SlX1 and SlY1 are sex-linked genes on the sex chromosomes of dioecious members of Silene sect. Elisanthe. Results: We sequenced the homologues of the SlX1/Y1 genes in several Sileneae species. We demonstrate that different parts of the SlX1/Y1 region give different phylogenetic signals. The major discrepancy is that Silene vulgaris and S. sect. Conoimorpha (S. conica and relatives) exchange positions. To determine whether gene duplication followed by recombination (an intralineage process) may explain the phylogenetic conflict in the Silene SlX1/Y1 gene, we use a novel probabilistic, multiple primer-pair PCR approach. We did not find any evidence supporting gene duplication/loss as explanation to the phylogenetic conflict. Conclusion: The phylogenetic conflict in the Silene SlX1/Y1 gene cannot be explained by paralogy or artefacts, such as in vitro recombination during PCR. The support for the conflict is strong enough to exclude methodological or stochastic errors as likely sources. Instead, the phylogenetic incongruence may have been caused by recombination of two divergent alleles following ancient interspecific hybridization or incomplete lineage sorting. These events probably took place several million years ago. This example clearly demonstrates that different parts of the genome may have different evolutionary histories and stresses the importance of using multiple genes in reconstruction of taxonomic relationships.
|
|
| 5. |
- Britton, Tom, et al.
(författare)
-
Bayesian support is larger than bootstrap support in phylogenetic inference : a mathematical argument.
- 2007
-
Ingår i: Mathematical Medicine and Biology. - : Oxford University Press (OUP). - 1477-8599 .- 1477-8602. ; 24:4, s. 401-411
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 6. |
|
|
| 7. |
- Svennblad, Bodil, et al.
(författare)
-
Improving divergence time estimation in phylogenetics : More taxa vs. longer sequences
- 2007
-
Ingår i: Statistical Applications in Genetics and Molecular Biology. - : Walter de Gruyter GmbH. - 1544-6115 .- 1544-6115 .- 2194-6302. ; 6, s. 35-
-
Tidskriftsartikel (refereegranskat)abstract
- Maximum Likelihood (ML) is used as a standard method for estimating divergence times in phylogenetic trees. The method is consistent and hence the precision can be improved by analyzing longer sequences. In this paper we show that the precision can be improved also by including more taxa to the existing tree. It is a theoretical study, complemented with simulations, showing that the gain in precision is faster with increasing sequence length than with increasing number of taxa. We further compare the results of estimating divergence times using Maximum Likelihood with the much faster and less complex estimation method of Mean Path Length (MPL), which works with the evolution model of Jukes-Cantor (1969). It is shown that MPL is as good as ML in estimating divergence times of nodes that are located near the root in the tree, but ML is better in estimating the divergence times of nodes lower down.
|
|
| 8. |
- Svennblad, Bodil, 1966-
(författare)
-
On Estimating Topology and Divergence Times in Phylogenetics
- 2008
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This PhD thesis consists of an introduction and five papers, dealing with statistical methods in phylogenetics.A phylogenetic tree describes the evolutionary relationships among species assuming that they share a common ancestor and that evolution takes place in a tree like manner. Our aim is to reconstruct the evolutionary relationships from aligned DNA sequences.In the first two papers we investigate two measures of confidence for likelihood based methods, bootstrap frequencies with Maximum Likelihood (ML) and Bayesian posterior probabilities. We show that an earlier claimed approximate equivalence between them holds under certain conditions, but not in the current implementations of the two methods.In the following two papers the divergence times of the internal nodes are considered. The ML estimate of the divergence time of the root is improved if longer sequences are analyzed or if more taxa are added. We show that the gain in precision is faster with longer sequences than with more taxa. We also show that the algorithm of the software package PATHd8 may give biased estimates if the global molecular clock is violated. A change of the algorithm to obtain unbiased estimates is therefore suggested.The last paper deals with non-informative priors when using the Bayesian approach in phylogenetics. The term is not uniquely defined in the literature. We adopt the idea of data translated likelihoods and derive the so called Jeffreys' prior for branch lengths using Jukes Cantor model of evolution.
|
|
