| 1. |
- Anderson, Cajsa Lisa
(author)
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All we need now is fossils; a new phylogenetic dating method (PATHd8) allowing thousands of taxa and multiple fossil constraints.
- 2006
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In: Ancient life and modern approaches. - 7312019560 ; , s. 45-
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Conference paper (peer-reviewed)abstract
- Estimation of divergence times in phylogenetic trees using sequence databecomes increasingly popular, but so far dating studies have given widely different results,and especially datings of the lower nodes within the angiosperms and metazoans, have givenmuch older ages than those obtained from the fossil record. It has been concluded in differentstudies that more taxa, and more fossils are needed for more reliable age estimates. For thisreason, a dating method that can handle very large data sets with multiple fossil constraints isnecessary.Chronograms obtained by e.g. penalized likelihood and Bayesian methods, oftenadds a large "ghost range" to the fossil record, and produces chronograms with a more or lesssmooth appearance, even if the corresponding phylograms have apparently veryheterogeneous rates. Compared to the other methods, our recently developed method,PATHd8, gives the results with the best agreement with the fossil record, which coincideswith the least smooth appearance of the chronograms. When other programs often run intocomputational problems when analysing trees with hundreds of leaves, PATHd8 has noproblems analysing thousands of taxa instantaneously. An arbitrary number of fossil ageconstraints can be specified, either as fixed-, minimum or maximum age.With our new method, the biggest problem in dating studies is that we needmore fossils, and these fossils must be well dated and assigned to the correct branches of thephylogeny. Therefore, to accomplish divergence time estimates, which hopefully approximatethe real ages, biologists now need to cooperate with palaeontologists.
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| 2. |
- Anderson, Cajsa Lisa, 1972-
(author)
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Dating Divergence Times in Phylogenies
- 2007
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Doctoral thesis (other academic/artistic)abstract
- 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.
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| 3. |
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| 4. |
- Anderson, Cajsa Lisa, et al.
(author)
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Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points
- 2005
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In: American Journal of Botany. ; 92, s. 1737-1748
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Journal article (peer-reviewed)abstract
- A molecular dating of the phylogenetically basal eudicots (Ranunculales, Proteales, Sabiales, Buxales and Trochodendrales sensuAngiosperm Phylogeny Group II) has been performed using several fossils as minimum age constraints. All rbcL sequences availablein GenBank were sampled for the taxa in focus. Dating was performed using penalized likelihood, and results were compared withnonparametric rate smoothing. Fourteen eudicot fossils, all with a Cretaceous record, were included in this study for age constraints.Nine of these are assigned to basal eudicots and the remaining five taxa represent core eudicots. Our study shows that the choice ofmethods and fossil constraints has a great impact on the age estimates, and that removing one single fossil change the results in themagnitude of tens of million years. The use of several fossil constraints increase the probability of approaching the true ages. Ourresults suggest a rapid diversification during the late Early Cretaceous, with all the lineages of basal eudicots emerging during thelatest part of the Early Cretaceous. The age of Ranunculales was estimated to 120 my, Proteales to 119 my, Sabiales to 118 my,Buxales to 117 my, and Trochodendrales to 116 my.
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| 5. |
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| 6. |
- Anderson, Cajsa Lisa, et al.
(author)
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Divergence times of phylogenetically basal eudicots
- 2005
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In: XVII International Botanical Congress. ; , s. 728-
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Conference paper (peer-reviewed)abstract
- A molecular dating of the phylogenetically basal eudicots (Ranunculales, Proteales, Sabiales, Buxales and Trochodendrales sensu APGII) has been performed using several fossils as minimum age constraints. We have sampled all rbcL sequences available in GenBank for the taxa in focus. Dating was done using Penalized Likelihood, and compared with NonParametric Rate Smoothing. We show that choice of method and fossil constraints has a great impact on the age estimates, and that it is important to use several fossil constraints to yield good age estimates. We discuss the 14 fossils we have chosen to include in this study and present a critical review of other fossils potentially useful in dating studies within the basal eudicots. Our results suggest a rapid diversification during the Early-mid Cretaceous, with all the lineages of basal eudicots emerging during the latest part of the Early Cretaceous. The age of Ranunculales was estimated to 120 myr, Proteales to 119 myr, Sabiales to 118 myr, Buxales to 117 myr and Trochodendrales to 116 myr.
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| 7. |
- Anderson, Cajsa Lisa, et al.
(author)
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Monocots
- 2009
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In: Timetree of life. - : Oxford University Press. - 9780199535033
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Book chapter (other academic/artistic)
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| 8. |
- Anderson, Cajsa Lisa
(author)
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PATHd8 - a new phylogenetic dating method allowing thousands of taxa and multiple fossil constraints
- 2006
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In: 7th european paleobotany-palynology. - 8070361980 ; , s. 6-
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Conference paper (peer-reviewed)abstract
- Estimation of divergence times in phylogenetic trees using DNA sequence data becomes increasingly popular, but so far dating studies have given widely different results, and especially datings of the lower nodes within the angiosperms and metazoans, have given much older ages than those obtained from the fossil record. It has been concluded in different studies that more taxa, and more fossils are needed for more reliable age estimates. For this reason, a dating method that can handle very large data sets with multiple fossil constraints is necessary.Chronograms obtained by the currently most used methods often adds a large "ghost range" to the fossil record. Compared to the other methods, our recently developed method, PATHd8, gives the most reasonable results, with the best agreement with the fossil record, in all studies performed so far.The only way to improve the datings further, and hopefully obtain divergence time estimates which approximate the real ages, is to include more fossils. The combination of allowing an arbitrary number of fossil age constraints with the capability to analyse thousands of taxa instantaneously, makes PATHd8 a strong alternative to other methods. All we need now to accomplish better studies, is cooperation between biologists and paleontologists.
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| 9. |
- Arrigo, N., et al.
(author)
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A TOTAL EVIDENCE APPROACH TO UNDERSTANDING PHYLOGENETIC RELATIONSHIPS AND ECOLOGICAL DIVERSITY IN SELAGINELLA SUBG. TETRAGONOSTACHYS
- 2013
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In: American Journal of Botany. - : Wiley. - 0002-9122. ; 100:8, s. 1672-1682
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Journal article (peer-reviewed)abstract
- Premise of the Study: Several members of Selaginella are renowned for their ability to survive extreme drought and "resurrect" when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of similar to 45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade. Methods: Our study included most Tetragonostachys species, using plastid and nuclear sequences, fossil and herbarium records, and climate variables to describe the species diversity, phylogenetic relationships, divergence times, and climatic niche evolution in the subgenus. Key Results: We found that subgenus Tetragonostachys forms a monophyletic group sister to Selaginella lepidophylla and may have diverged from other Selaginella because of a Gondwanan-Laurasian vicariance event ca. 240 mya. The North American radiation of Tetragonostachys appears to be much more recent and to have occurred during the Early Cretaceous-late Paleocene interval. We identified two significant and nested ecological niche shifts during the evolution of Tetragonostachys associated with extreme drought tolerance and a more recent shift to cold climates. Our analyses suggest that drought tolerance evolved in the warm deserts of southwest North America and may have been advantageous for colonization of cold and dry boreal climates. Conclusions: Our investigation provides a foundation for future research addressing the genomics of ecological niche evolution and the potential role of reticulate evolution in Selaginella subgenus Tetragonostachys.
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| 10. |
- Barres, L., et al.
(author)
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RECONSTRUCTING THE EVOLUTION AND BIOGEOGRAPHIC HISTORY OF TRIBE CARDUEAE (COMPOSITAE)
- 2013
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In: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 100:5, s. 867-882
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Journal article (peer-reviewed)abstract
- • Premise of the study: Tribe Cardueae (thistles) forms one of the largest tribes in the family Compositae (2400 species), with representatives in almost every continent. The greatest species richness of Cardueae occurs in the Mediterranean region where it forms an important element of its flora. New fossil evidence and a nearly resolved phylogeny of Cardueae are used here to reconstruct the spatiotemporal evolution of this group. • Methods: We performed maximum parsimony and Bayesian phylogenetic inference based on nuclear ribosomal DNA and chloroplast DNA markers. Divergence times and ancestral area reconstructions for main lineages were estimated using penalized likelihood and dispersal–vicariance analyses, respectively, and integrated over the posterior distribution of the phylogeny from the Bayesian Markov chain Monte Carlo analysis to accommodate uncertainty in phylogenetic relationships. • Key results: The phylogeny shows that subtribe Cardopatiinae is sister to the remaining subtribes, and subtribes Carlininae and Echinopsinae appear as consecutive sister-clades to the Carduinae/Centaureinae. Tribe Cardueae is inferred to have originated around the Mid Eocene in West Asia, which is also the ancestral area of most subtribes within Cardueae. Diversification within each subtribe began during the Oligocene-Miocene period. • Conclusions: Most diversification events within Cardueae are related to the continuous cycles of area connection and division between the Anatolian microplate and the western Mediterranean Basin during the Oligocene-Miocene and with the uplift of the Himalayan range from the Miocene onward. From these two regions, thistles dispersed and colonized the rest of the continents (e.g., the New World, Africa, and Australia), most likely during the colder Pliocene-Pleistocene period.
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