Change search
ReferencesLink to record
Permanent link

Direct link
Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes
Stockholm University, Faculty of Science, Department of Mathematics.
2013 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 29, no 11, 1367-1374 p.Article in journal (Refereed) Published
Abstract [en]

Motivation: Diversification rates and patterns may be inferred from reconstructed phylogenies. Both the time-dependent and the diversity-dependent birthdeath process can produce the same observed patterns of diversity over time. To develop and test new models describing the macro-evolutionary process of diversification, generic and fast algorithms to simulate under these models are necessary. Simulations are not only important for testing and developing models but play an influential role in the assessment of model fit.

Results: In the present article, I consider as the model a global time-dependent birthdeath process where each species has the same rates but rates may vary over time. For this model, I derive the likelihood of the speciation times from a reconstructed phylogenetic tree and show that each speciation event is independent and identically distributed. This fact can be used to simulate efficiently reconstructed phylogenetic trees when conditioning on the number of species, the time of the process or both. I show the usability of the simulation by approximating the posterior predictive distribution of a birthdeath process with decreasing diversification rates applied on a published bird phylogeny (family Cettiidae).

Availability: The methods described in this manuscript are implemented in the R package TESS, available from the repository CRAN (

Place, publisher, year, edition, pages
2013. Vol. 29, no 11, 1367-1374 p.
Keyword [en]
Simulations, Birth-Death Process, Phylogenetics
National Category
Biochemistry and Molecular Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Bioinformatics (Computational Biology)
Research subject
Mathematical Statistics
URN: urn:nbn:se:su:diva-91828DOI: 10.1093/bioinformatics/btt153ISI: 000319428600002OAI: diva2:636060
Available from: 2013-07-08 Created: 2013-07-04 Last updated: 2013-10-28Bibliographically approved
In thesis
1. Bayesian Phylogenetic Inference: Estimating Diversification Rates from Reconstructed Phylogenies
Open this publication in new window or tab >>Bayesian Phylogenetic Inference: Estimating Diversification Rates from Reconstructed Phylogenies
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Place, publisher, year, edition, pages
Stockholm: Department of Mathematics, Stockholm University, 2013. 26 p.
Phylogenetics, Bayesian inference, Graphical Models, Birth-Death Process, Diversification
National Category
Evolutionary Biology Mathematics
Research subject
Mathematical Statistics
urn:nbn:se:su:diva-95361 (URN)978-91-7447-771-9 (ISBN)
Public defence
2013-11-29, sal 14, hus 5, Kräftriket, Roslagsvägen 101, Stockholm, 10:00 (English)

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Accepted.

Available from: 2013-11-07 Created: 2013-10-25 Last updated: 2015-03-10Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Search in DiVA

By author/editor
Höhna, Sebastian
By organisation
Department of Mathematics
In the same journal
Biochemistry and Molecular BiologyMedical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)Bioinformatics (Computational Biology)

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 112 hits
ReferencesLink to record
Permanent link

Direct link