| 1. |
- Anderson, Cajsa Lisa
(författare)
-
All we need now is fossils; a new phylogenetic dating method (PATHd8) allowing thousands of taxa and multiple fossil constraints.
- 2006
-
Ingår i: Ancient life and modern approaches. - 7312019560 ; , s. 45-
-
Konferensbidrag (refereegranskat)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.
|
|
| 2. |
- Anderson, Cajsa Lisa, 1972-
(författare)
-
Dating Divergence Times in Phylogenies
- 2007
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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.
|
|
| 3. |
|
|
| 4. |
- Anderson, Cajsa Lisa, et al.
(författare)
-
Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points
- 2005
-
Ingår i: American Journal of Botany. ; 92, s. 1737-1748
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 5. |
|
|
| 6. |
- Anderson, Cajsa Lisa, et al.
(författare)
-
Divergence times of phylogenetically basal eudicots
- 2005
-
Ingår i: XVII International Botanical Congress. ; , s. 728-
-
Konferensbidrag (refereegranskat)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.
|
|
| 7. |
- Anderson, Cajsa Lisa, et al.
(författare)
-
Monocots
- 2009
-
Ingår i: Timetree of life. - : Oxford University Press. - 9780199535033
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)
|
|
| 8. |
- Anderson, Cajsa Lisa
(författare)
-
PATHd8 - a new phylogenetic dating method allowing thousands of taxa and multiple fossil constraints
- 2006
-
Ingår i: 7th european paleobotany-palynology. - 8070361980 ; , s. 6-
-
Konferensbidrag (refereegranskat)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.
|
|
| 9. |
- Arrigo, N., et al.
(författare)
-
A TOTAL EVIDENCE APPROACH TO UNDERSTANDING PHYLOGENETIC RELATIONSHIPS AND ECOLOGICAL DIVERSITY IN SELAGINELLA SUBG. TETRAGONOSTACHYS
- 2013
-
Ingår i: American Journal of Botany. - : Wiley. - 0002-9122. ; 100:8, s. 1672-1682
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 10. |
- Barres, L., et al.
(författare)
-
RECONSTRUCTING THE EVOLUTION AND BIOGEOGRAPHIC HISTORY OF TRIBE CARDUEAE (COMPOSITAE)
- 2013
-
Ingår i: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 100:5, s. 867-882
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 11. |
- Britton, Tom, et al.
(författare)
-
Estimating divergence times in large phylogenetic trees
- 2007
-
Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 56:5, s. 741-752
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 12. |
- Ericson, Per G. P., et al.
(författare)
-
Diversification of Neoaves through time : Integration of molecular sequence data and fossils
- 2006
-
Ingår i: Biology Letters. - : The Royal Society. - 1744-9561 .- 1744-957X. ; 2:4, s. 543-547
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 13. |
- Jones, M. E. H., et al.
(författare)
-
Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara)
- 2013
-
Ingår i: Bmc Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 13:208
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Lepidosauria (lizards, snakes, tuatara) is a globally distributed and ecologically important group of over 9,000 reptile species. The earliest fossil records are currently restricted to the Late Triassic and often dated to 227 million years ago (Mya). As these early records include taxa that are relatively derived in their morphology (e. g. Brachyrhinodon), an earlier unknown history of Lepidosauria is implied. However, molecular age estimates for Lepidosauria have been problematic; dates for the most recent common ancestor of all lepidosaurs range between approximately 226 and 289 Mya whereas estimates for crown-group Squamata (lizards and snakes) vary more dramatically: 179 to 294 Mya. This uncertainty restricts inferences regarding the patterns of diversification and evolution of Lepidosauria as a whole. Results: Here we report on a rhynchocephalian fossil from the Middle Triassic of Germany (Vellberg) that represents the oldest known record of a lepidosaur from anywhere in the world. Reliably dated to 238-240 Mya, this material is about 12 million years older than previously known lepidosaur records and is older than some but not all molecular clock estimates for the origin of lepidosaurs. Using RAG1 sequence data from 76 extant taxa and the new fossil specimens two of several calibrations, we estimate that the most recent common ancestor of Lepidosauria lived at least 242 Mya (238-249.5), and crown-group Squamata originated around 193 Mya (176-213). Conclusion: A Early/Middle Triassic date for the origin of Lepidosauria disagrees with previous estimates deep within the Permian and suggests the group evolved as part of the faunal recovery after the end-Permain mass extinction as the climate became more humid. Our origin time for crown-group Squamata coincides with shifts towards warmer climates and dramatic changes in fauna and flora. Most major subclades within Squamata originated in the Cretaceous postdating major continental fragmentation. The Vellberg fossil locality is expected to become an important resource for providing a more balanced picture of the Triassic and for bridging gaps in the fossil record of several other major vertebrate groups.
|
|
| 14. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
-
Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
-
Tidskriftsartikel (refereegranskat)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
|
|
| 15. |
- Sauquet, Herve, et al.
(författare)
-
Contrasted patterns of hyperdiversification in Mediterranean hotspots
- 2009
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 106:1, s. 221-225
-
Tidskriftsartikel (refereegranskat)abstract
- Dating the Tree of Life has now become central to relating patterns of biodiversity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of divergence times for each of their components. A critical aspect of dating by using molecular sequence divergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn, stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, diversified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically diverse but include numerous lineages with low diversification rates.
|
|
| 16. |
- Sauquet, Herve, et al.
(författare)
-
Using fossils and molecular data to reveal the origins of the Cape proteas (subfamily Proteoideae)
- 2009
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 51:1, s. 31-43
-
Tidskriftsartikel (refereegranskat)abstract
- The angiosperm family Proteaceae is a distinct component of the Cape Floristic Region biodiversity hot-spot with 330 endemic species. Phylogenetic analyses of subfamily Proteoideae using sequence data from one nuclear and six plastid loci show that most of this diversity is contained in two distinct Cape floral clades. Molecular dating analyses, using Bayesian and penalized likelihood methods and four phylogenetically supported fossil age constraints. reveal contrasting histories for these two clades. The genus Protea belongs to a lineage that may have been in Africa since the Late Cretaceous but began to diversify in the Cape only 5-18 Myr ago. In contrast, the Leucadendrinae clade presumably arrived in the region no earlier than 46 Myr ago by long-distance dispersal from an Australian ancestor and the extant members of this clade began to diversify in the Cape 22-39 Myr ago. These results join a growing number of case studies that challenge the commonly accepted view that most of the Cape flora radiated synchronously in the Late Miocene and Early Pliocene when a Mediterranean climate settled in the region. (C) 2008 Elsevier Inc. All rights reserved.
|
|
