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

BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005 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 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 T T T A Parsimony optimisation on a phylogenetic tree

BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005 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 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 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 MYA Time calibrated phylogeny (a chronogram)

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

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

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

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

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

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

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

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

BiodiversityWorld GRID Workshop NeSC, Edinburgh – 30 June and 1 July 2005 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 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 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 Acknowledgements BBSRCBBSRC BiodiversityWorldBiodiversityWorld A. CulhamA. Culham P. ValdesP. Valdes P. Brewer, T.Sutton, N. CaithnessP. Brewer, T.Sutton, N. Caithness D. erythrorhiza subsp. magna