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Babblers, Biogeography and Bayesian Reasoning
Stockholm University, Faculty of Science, Department of Zoology.
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.
Keyword [en]
Africa, Asia, Bayesian inference, biogeography, Cettidae, dispersal, extinction, Middle East, persistence, Sylvioidea, Sylviidae, Timaliidae, vicariance
National Category
Biological Systematics
Research subject
Systematic Zoology
Identifiers
URN: urn:nbn:se:su:diva-71321ISBN: 978-91-7447-438-1 (print)OAI: oai:DiVA.org:su-71321DiVA: diva2:484628
Public defence
2012-03-01, Lilla Hörsalen, Naturhistoriska Riksmuseet, Frescativägen 40, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
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
List of papers
1. Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification
Open this publication in new window or tab >>Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification
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2009 (English)In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 38, no 3, 225-236 p.Article in journal (Refereed) Published
Abstract [en]

Babblers, family Timaliidae, have long been subject to debate on systematic position, family limits and internal taxonomy. In this study, we use five molecular regions to estimate the relationships among a large proportion of genera traditionally placed in Timaliidae. We find good support for five main clades within this radiation, and propose a new classification, dividing the babblers into the families Sylviidae and Timaliidae. Within the latter family, four subfamilies are recognized: Zosteropinae, Timaliinae, Pellorneinae and Leiothrichinae. Several taxa, previously not studied with molecular data, are phylogenetically placed within Sylviidae or Timaliidae. This is, however, not the case for the genus Pnoepyga, for which we propose the family name Pnoepygidae fam. n.

National Category
Zoology
Research subject
Zoology
Identifiers
urn:nbn:se:su:diva-35281 (URN)10.1111/j.1463-6409.2008.00374.x (DOI)000265041500001 ()
Available from: 2010-01-15 Created: 2010-01-15 Last updated: 2017-12-12Bibliographically approved
2. Neumann’s Warbler Hemitesia neumanni (Sylvioidea): the sole African member of a Palaeotropic Miocene avifauna
Open this publication in new window or tab >>Neumann’s Warbler Hemitesia neumanni (Sylvioidea): the sole African member of a Palaeotropic Miocene avifauna
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2011 (English)In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 153, no 1, 78-86 p.Article in journal (Refereed) Published
Abstract [en]

We present molecular evidence that Neumann’s Warbler Hemitesia neumanni is deeply nested within the Cettiidae. The species’ distribution in the Albertine Rift of East Africa is intriguing, as the family Cettiidae is principally an Asian radiation. This disjunct distribution could be a result of colonization of Africa by long-distance dispersal, or the Cettiidae may at some point in the past have had a much larger geographical distribution that also covered parts of Africa.

Keyword
Africa, Albertine Rift, Asia, biogeography, Cettiidae, dispersal, phylogeny, vicariance, warbler
National Category
Biological Systematics
Research subject
evolutionär genetik
Identifiers
urn:nbn:se:su:diva-49655 (URN)10.1111/j.1474-919X.2010.01084.x (DOI)000285008400009 ()
Available from: 2010-12-16 Created: 2010-12-16 Last updated: 2017-12-11Bibliographically approved
3. Ancestral ranges concealed by local extinctions: the historical biogeography of the African and Asian Turdoides babblers and allies (Aves: Passeriformes)
Open this publication in new window or tab >>Ancestral ranges concealed by local extinctions: the historical biogeography of the African and Asian Turdoides babblers and allies (Aves: Passeriformes)
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Aim

To infer the historical biogeography of the genus Turdoides and allies, and to investigate the impact of the geological history of the Arabian Peninsula on the biogeographic interactions between Africa and Asia.

Location

Terrestrial Africa and Asia, with focus on the Middle East.

Methods

A five-loci molecular phylogeny was estimated by Bayesian inference and by maximum likelihood. Divergence times were approximated by Bayesian inference under a relaxed clock model, and non-parametrically by asmoothing algorithm between sister paths (PATHD8). Historical biogeography was reconstructed by maximum likelihood approach under the DEC-model, and by the parsimony-based Bayes-DIVA on the trees sampled from the target distribution from the Bayesian inference of the phylogeny.

Results

The clade comprising Turdoides and its close relatives originated in the end of the Miocene, and initially the Middle East region played an important role. The clade radiated into two subclades, one mainly distributed in Africa, and one distributed in southern Asia, the Middle East and northern and eastern Africa.

Main conclusions

We propose that local extinctions may have played a key role, in combination with dispersals and vicariance, in forming the present distribution pattern of the study group. The Middle East has been an important and dynamic area for the early evolution of the investigated babblers. Further, we conclude that constraints on biogeographical inference have stronger impact on the analysis than does the biogeographical model implied in the analysis.

Keyword
Arabian Peninsula, event-based biogeography, extinction, Middle East, Miocene, Pliocene, Tethys sea, Timaliidae, Turdoides
National Category
Biological Systematics
Identifiers
urn:nbn:se:su:diva-71320 (URN)
Available from: 2012-01-27 Created: 2012-01-27 Last updated: 2014-10-13Bibliographically approved
4. Bayesian inference of total biogeographic history under an event-based model
Open this publication in new window or tab >>Bayesian inference of total biogeographic history under an event-based model
(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
Biogeography, Bayesian inference, stochastic mapping, dispersal, vicariance, persistence, extinction
National Category
Biological Systematics
Identifiers
urn:nbn:se:su:diva-71308 (URN)
Available from: 2012-01-27 Created: 2012-01-27 Last updated: 2012-01-27Bibliographically approved

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