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Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling
Stockholm University, Faculty of Science, Department of Mathematics.
2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 1, e84184Article in journal (Refereed) Published
Abstract [en]

Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e. g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e. g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models - ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models - on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be violated.

Place, publisher, year, edition, pages
2014. Vol. 9, no 1, e84184
National Category
Evolutionary Biology Mathematics
Research subject
Mathematical Statistics
Identifiers
URN: urn:nbn:se:su:diva-100655DOI: 10.1371/journal.pone.0084184ISI: 000329462700016OAI: oai:DiVA.org:su-100655DiVA: diva2:696041
Note

AuthorCount:1;

Available from: 2014-02-12 Created: 2014-02-10 Last updated: 2017-12-06Bibliographically 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.
Keyword
Phylogenetics, Bayesian inference, Graphical Models, Birth-Death Process, Diversification
National Category
Evolutionary Biology Mathematics
Research subject
Mathematical Statistics
Identifiers
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)
Opponent
Supervisors
Note

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

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