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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

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Phyloclimatic Modelling:

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  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

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