1 / 23

Phyloclimatic Modelling:

Phyloclimatic Modelling:. Reconstructing ancestral bioclimatic models on phylogenetic trees. - Chris Yesson. Drosera orbiculata. Introduction. Bioclimatic models have been used to examine distributions in the present, and to predict the near future

fritz
Télécharger la présentation

Phyloclimatic Modelling:

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. PhyloclimaticModelling: Reconstructing ancestral bioclimatic models on phylogenetic trees - Chris Yesson Drosera orbiculata BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  2. Introduction • Bioclimatic models have been used to examine distributions in the present, and to predict the near future • A few studies have looked at the recent past • Studies on evolutionary time-scales have been overlooked • … such studies could provide insight into evolutionary responses to climate change BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  3. Phyloclimatic modelling – the idea • There are long established phylogenetic techniques of ancestral state reconstruction • These have been applied to DNA sequences, morphological features & environmental preferences • These optimised preferences can be combined into an ancestral bioclimatic model T A T T T Parsimony optimisation on a phylogenetic tree BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  4. Phyloclimatic modelling – the idea • There are long established phylogenetic techniques of ancestral state reconstruction • These have been applied to DNA sequences, morphological features & environmental preferences • These optimised preferences can be combined into an ancestral bioclimatic model Parsimony optimisation of environmental character BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  5. Phyloclimatic modelling – the idea • There are long established phylogenetic techniques of ancestral state reconstruction • These have been applied to DNA sequences, morphological features & environmental preferences • These optimised preferences can be combined into an ancestral bioclimatic model With sufficient climate parameters we can build a BIOCLIM model BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  6. Projecting into the past • Temporal calibration of phylogenetic trees is a widely used technique • This establishes a time-period for the projection of the ancestral bioclimatic model 0 5 10 MYA Time calibrated phylogeny (a chronogram) BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  7. The study group – Sundews (Droseraceae) Sundews: • Carnivorous • c. 150 spp. • Global distribution • Main area of diversity is the Mediterranean-type climate of SW Australia (c.30% of species) Locality data for Droseraceae from GBIF (and other sources) BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005 Drosera rotundifolia

  8. Rivadavias’ phylogeny (c.60spp. rbcL) • Monophyletic (SW) Australian groups from Mediterranean-type climate • Similar pattern with African group Rivadavia, et. al. (2003): American Journal of Botany.90, 123-130 BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  9. Drosera in Mediterranean-type Climate • Hot-dry summer, wet winter • Include SW Australia & South African Cape • Med. Climates arose 15-10MYA • Are Drosera radiations linked with this climate change? BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  10. Tuberous Sundews Dating the Drosera Phylogeny 50 million years BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  11. Bioclimatic Models for Tuberous Sundews in Australia BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  12. Tortonian projection of bioclimatic model for ancestral tuberous sundew Model prediction: red-core; blue-marginal BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  13. Next Steps • Bigger data-set • More study groups • More time-slices of climate data • Automate in BiodiversityWorld BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  14. How can BDWorld help? • This analysis draws on taxonomic verification, molecular biology, phylogenetics and bioclimatic modelling BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  15. Workflow BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  16. How can BDWorld help? • This analysis draws on taxonomic verification, molecular biology, phylogenetics and bioclimatic modelling • Having all these tools in an integrated system would make my life much easier! BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  17. A BDWorld Workflow BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  18. A BDWorld Workflow Viewers Misc Input Real Tools Input Real Tools BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  19. A BDWorld Workflow Work in progress BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  20. Putting resources into BDWorld – An example MrBayes – an open-source project with a CLI to do Bayesian phylogenetic analysis • … use the same process for other CLI tools • … but MrBayes v3.0 cannot except path names with the input file MrBayes –b –f /bdworld/temp/myInput.nex MrBayes –b –f myInput.nex • New version 3.1 does! • New version creates different output files Old output: myInput.nex.t New output: myInput.nex.run1.t, myInput.nex.run2.t, etc. • Problems running on a 64bit server BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  21. Hurdles • Integrating new tools • New ideas often require new software • How can we incorporate new applications? • What new helper tools do we need? BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  22. Hurdles • Shifting sands • Relying on external web-sites can be problematic • GUIs • Phylogenetics software is often dependent on GUIs • BDWorld is more suited to Command Line applications • Long running processes • How do we deal with a process that takes several days? BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

  23. Acknowledgements • BBSRC • BiodiversityWorld • A. Culham • P. Valdes • P. Brewer, T.Sutton, N. Caithness D. erythrorhiza subsp. magna BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005

More Related