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Dating Divergence Times in Phylogenies
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis concerns different aspects of dating divergence times in phylogenetic trees, using molecular data and multiple fossil age constraints.

Datings of phylogenetically basal eudicots, monocots and modern birds (Neoaves) are presented. Large phylograms and multiple fossil constraints were used in all these studies. Eudicots and monocots are suggested to be part of a rapid divergence of angiosperms in the Early Cretaceous, with most families present at the Cretaceous/Tertiary boundary. Stem lineages of Neoaves were present in the Late Cretaceous, but the main divergence of extant families took place around the Cre-taceous/Tertiary boundary.

A novel method and computer software for dating large phylogenetic trees, PATHd8, is presented. PATHd8 is a nonparametric smoothing method that smoothes one pair of sister groups at a time, by taking the mean of the added branch lengths from a terminal taxon to a node. Because of the local smoothing, the algorithm is simple, hence providing stable and very fast analyses, allowing for thousands of taxa and an arbitrary number of age constraints.

The importance of fossil constraints and their placement are discussed, and concluded to be the most important factor for obtaining reasonable age estimates.

Different dating methods are compared, and it is concluded that differences in age estimates are obtained from penalized likelihood, PATHd8, and the Bayesian autocorrelation method implemented in the multidivtime program. In the Bayesian method, prior assumptions about evolutionary rate at the root, rate variance and the level of rate smoothing between internal edges, are suggested to influence the results.

Place, publisher, year, edition, pages
Uppsala: Universitetsbiblioteket , 2007. , 79 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 322
Keyword [en]
systematic biology, divergence time, nonprametric rate smoothing, Bayesian, multidivtime, eudicots, Neoaves, monocots, dating, molecular clock, relaxed clock, age constraint, fossil, calibration, PATHd8, penalized likelihood
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-8155ISBN: 978-91-554-6937-5 (print)OAI: oai:DiVA.org:uu-8155DiVA: diva2:170514
Public defence
2007-09-21, Zootissalen, Evolutionsmuseet, Zoologi, Evolutionsbiologiskt centrum, Villavägen 9, Uppsala, 10:00
Opponent
Supervisors
Available from: 2007-09-03 Created: 2007-09-03Bibliographically approved
List of papers
1. Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil constraints.
Open this publication in new window or tab >>Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil constraints.
2005 In: American Journal of Botany, Vol. 92, no 10, 1737–1748- p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-96058 (URN)
Available from: 2007-09-03 Created: 2007-09-03Bibliographically approved
2. Diversification of Neoaves through time: Integration of molecular sequence data and fossils
Open this publication in new window or tab >>Diversification of Neoaves through time: Integration of molecular sequence data and fossils
Show others...
2006 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 4, 543-547 p.Article in journal (Refereed) Published
Abstract [en]

Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.

Keyword
Divergence times, Fossils, Molecular clock, Neoaves, Nuclear DNA, Phylogeny
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-96059 (URN)10.1098/rsbl.2006.0523 (DOI)000242686500018 ()17148284 (PubMedID)
Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2017-12-14Bibliographically approved
3. Hangin’ on to our rocks ’n clocks: a reply to Brown et al.
Open this publication in new window or tab >>Hangin’ on to our rocks ’n clocks: a reply to Brown et al.
2007 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 3, no 3, 260-261 p.Article in journal (Refereed) Published
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-96060 (URN)10.1098/rsbl.2007.0103. (DOI)
Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2017-12-14Bibliographically approved
4. Estimating divergence times in large phylogenetic trees
Open this publication in new window or tab >>Estimating divergence times in large phylogenetic trees
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2007 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 5, 741-752 p.Article in journal (Refereed) Published
Abstract [en]

A new method, PATHd8, for estimating ultrametric trees from trees with edge (branch) lengths proportional to the number of substitutions is proposed. The method allows for an arbitrary number of reference nodes for time calibration, each defined either as absolute age, minimum age, or maximum age, and the tree need not be fully resolved. The method is based on estimating node ages by mean path lengths from the node to the leaves but correcting for deviations from a molecular clock suggested by reference nodes. As opposed to most existing methods allowing substitution rate variation, the new method smoothes substitution rates locally, rather than simultaneously over the whole tree, thus allowing for analysis of very large trees. The performance of PATHd8 is compared with other frequently used methods for estimating divergence times. In analyses of three separate data sets, PATHd8 gives similar divergence times to other methods, the largest difference being between crown group ages, where unconstrained nodes get younger ages when analyzed with PATHd8. Overall, chronograms obtained from other methods appear smoother, whereas PATHd8 preserves more of the heterogeneity seen in the original edge lengths. Divergence times are most evenly spread over the chronograms obtained from the Bayesian implementation and the clock-based Langley-Fitch method, and these two methods produce very similar ages for most nodes. Evaluations of PATHd8 using simulated data suggest that PATHd8 is slightly less precise compared with penalized likelihood, but it gives more sensible answers for extreme data sets. A clear advantage with PATHd8 is that it is more or less instantaneous even with trees having several thousand leaves, whereas other programs often run into problems when analyzing trees with hundreds of leaves. PATHd8 is implemented in freely available software.

Keyword
Divergence times, estimation, molecular clock, phylogenetic trees, substitution rates
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-96061 (URN)10.1080/10635150701613783 (DOI)000250959000004 ()17886144 (PubMedID)
Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2017-12-14Bibliographically approved
5. Monocots
Open this publication in new window or tab >>Monocots
2009 (English)In: Timetree of life / [ed] S. Blair Hedges and Sudhir Kumar, Oxford University Press, 2009Chapter in book (Other academic)
Place, publisher, year, edition, pages
Oxford University Press, 2009
Series
Oxford biology
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-96062 (URN)978-0-19-953503-3 (ISBN)
Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2013-06-18Bibliographically approved
6. Dating phylogenies: an evaluation of three methods based on the lycopod family Selaginellaceae.
Open this publication in new window or tab >>Dating phylogenies: an evaluation of three methods based on the lycopod family Selaginellaceae.
Manuscript (Other academic)
Identifiers
urn:nbn:se:uu:diva-96063 (URN)
Available from: 2007-09-03 Created: 2007-09-03 Last updated: 2010-01-13Bibliographically approved

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