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- Anderson, Cajsa Lisa,1972-Uppsala universitet,Institutionen för evolution, genomik och systematik (author)
Dating Divergence Times in Phylogenies
- BookEnglish2007
Publisher, publication year, extent ...
- Uppsala :Universitetsbiblioteket,2007
- 79 s.
- electronicrdacarrier
Numbers
- LIBRIS-ID:oai:DiVA.org:uu-8155
- ISBN:9789155469375
- https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8155URI
Supplementary language notes
- Language:English
- Summary in:English
Part of subdatabase
- SwePubSwePub
Classification
Series
- Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology,1651-6214 ;322
Notes
- 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.
Subject headings and genre
- NATURVETENSKAP Biologi hsv//swe
- NATURAL SCIENCES Biological Sciences hsv//eng
- systematic biology
- divergence time
- nonprametric rate smoothing
- Bayesian
- multidivtime
- eudicots
- Neoaves
- monocots
- dating
- molecular clock
- relaxed clock
- age constraint
- fossil
- calibration
- PATHd8
- penalized likelihood
- Biology
- Biologi
Added entries (persons, corporate bodies, meetings, titles ...)
- Bremer, Kåre (thesis advisor)
- Pryer, Katleen M.,ProfessorDepartment of Biology, Duke University (opponent)
- Uppsala universitetInstitutionen för evolution, genomik och systematik (creator_code:org_t)
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