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Bayesian inference of total biogeographic history under an event-based model
Stockholm University, Faculty of Science, Department of Zoology.
(English)Manuscript (preprint) (Other academic)
Abstract [en]


We propose a Bayesian approach to infer the historical biogeography under an event-based model, where the total biogeographic histories are sampled from its posterior probability distribution using Metropolis-coupled Markov chain Monte Carlo. Total histories are stochastically mapped on a phylogeny followed by invoking a biogeographical model, which defines the biogeographical events dispersal, vicariance, persistence and extinction. A hypothetic order of probabilities for these events to happen is applied in the priors of the analysis, where a stick-breaking process is used to pick variables from a flat Dirichlet distribution. In comparison to the two most commonly used methods, the proposed method delivers relatively similar reconstructions, albeit with some differences such as favouring extinctions more. These differences are linked to either the treatment of total histories, or to the fundamental statistical differences of the three approaches. In conculsion, this method favours extinctions more than the compared methods, but the main difference is more complex and is instead linked to the treatment of total histories.

Keyword [en]
Biogeography, Bayesian inference, stochastic mapping, dispersal, vicariance, persistence, extinction
National Category
Biological Systematics
URN: urn:nbn:se:su:diva-71308OAI: diva2:484567
Available from: 2012-01-27 Created: 2012-01-27 Last updated: 2012-01-27Bibliographically approved
In thesis
1. Babblers, Biogeography and Bayesian Reasoning
Open this publication in new window or tab >>Babblers, Biogeography and Bayesian Reasoning
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis, I try to proceed one step further towards an understanding of the biogeographic processes forming the distribution patterns of organisms that we see today. Babblers and warblers are diverse groups of passerines that are phylogenetically intermixed with other groups in the superfamily Sylvioidea.

First, the gross phylogeny of the babblers and associated groups was estimated. Five major lineages of a well-supported monophyletic babbler radiation were recovered, and we proposed a new classification at family and subfamily level. Further, the genus Pnoepyga was excluded from Timaliidae, and we proposed the new family Pnoepygidae fam. nov.

Second, the systematic position was investigated for the Albertine Rift taxon Hemitesia neumanni, which was found to be nested within the almost entirely Asian family Cettidae, and possible biogeographical scenarios were discussed. We concluded that the most plausible explanation involved late Miocene vicariance in combination with local extinctions.

Third, the historical biogeography of a Leiothrichinae subclade, the Turdoides babblers and allies, was inferred. We concluded that the Middle East region probably played an important role in the early history of this clade, followed by local extinctions in this region.

Fourth, a Bayesian method to reconstruct the historical biogeography under an event-based model was proposed, where the total biogeographic histories are sampled from its posterior probability distribution using Markov chains.

In conclusion, I believe that, especially with more sophisticated methods available, we will see an increasing number of studies inferring biogeographic histories that lead to distribution patterns built up by a combination of dispersals and vicariance, but where these distributions have been extensively reshaped, or litterally demolished, by local extinctions. Therefore, my answer to the frequently asked question dispersal or vicariance? is both, but not the least: extinctions.

Place, publisher, year, edition, pages
Stockholm: Department of Zoology, Stockholm University, 2012. 15 p.
Africa, Asia, Bayesian inference, biogeography, Cettidae, dispersal, extinction, Middle East, persistence, Sylvioidea, Sylviidae, Timaliidae, vicariance
National Category
Biological Systematics
Research subject
Systematic Zoology
urn:nbn:se:su:diva-71321 (URN)978-91-7447-438-1 (ISBN)
Public defence
2012-03-01, Lilla Hörsalen, Naturhistoriska Riksmuseet, Frescativägen 40, Stockholm, 10:00 (English)
At the time of the doctoral defence the following papers were unpublished and had a status as follows; Papers 3 and 4: ManuscriptsAvailable from: 2012-02-08 Created: 2012-01-27 Last updated: 2014-10-13Bibliographically approved

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