Biodiverse - Rosauer talk @ iEvoBio conference June 2010


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Biodiverse - Rosauer talk @ iEvoBio conference June 2010

  1. 1. Biodiverse A tool for spatial analysis of biological and other diversity Dan Rosauer Shawn Laffan June 2010
  2. 2. Biodiverse – a tool for spatial analysis of biodiversity <ul><li>indices of richness, endemism, compositional dissimilarity, sampling redundancy </li></ul><ul><li>phylogenetic indices of diversity, endemism & dissimilarity </li></ul><ul><li>spatial clustering </li></ul><ul><li>Monte Carlo randomisations </li></ul>Mean genetic similarity in Pultenaea Bickford et al (2004) <ul><li>So far, Biodiverse has been used to investigate: </li></ul><ul><ul><li>Endemism in the Australian Flora - Crisp et al (2001), Laffan & Crisp (2003) </li></ul></ul><ul><ul><li>Taxonomic and genetic patterns in Pultenaea (Fabaceae) - Bickford et al (2004) </li></ul></ul><ul><ul><li>Scale dependence of relationships between climate and fern species richness </li></ul></ul><ul><ul><li>Bickford & Laffan (2006) </li></ul></ul><ul><ul><li>Endemism of words in Australian Aboriginal languages (Jones and Laffan 2009) </li></ul></ul><ul><ul><li>Phylogenetic endemism - Rosauer et al (2009) </li></ul></ul>
  3. 3. Who is behind Biodiverse <ul><li>Shawn Laffan </li></ul><ul><ul><li>geographer and spatial scientist at UNSW. </li></ul></ul><ul><ul><li>lots of collaborations with biologists </li></ul></ul><ul><ul><li>developed Biodiverse </li></ul></ul><ul><li>Eugene Lubarsky </li></ul><ul><ul><li>computer science student & programming hotshot </li></ul></ul><ul><ul><li>built the user interface </li></ul></ul><ul><li>Dan Rosauer </li></ul><ul><ul><li>developed the phylogenetic components </li></ul></ul>
  4. 4. What does Biodiverse do? Species Phylogeny Visualise & Explore Calculate Where is each species found? check data List species in an area Which areas share species Where is each clade found? Which parts of the phylogeny are represented in an area? Species richness Endemism Turnover (beta diversity) Sampling redundancy Phylogenetic diversity Phylogenetic endemism Phylogenetic beta diversity Cluster similar areas Randomise locations Monte Carlo significance tests Extensible: use existing platform to program new analyses
  5. 5. Demonstration
  6. 6. Phylogenetic Diversity - Hylids <ul><li>Compared to species count </li></ul><ul><li>PD shows: </li></ul><ul><li>tropics more diverse </li></ul><ul><li> Central east coast less diverse </li></ul>
  7. 7. Sechrest et al 2002 Primates in global biodiversity hotspots Only in hotspots Hotspots & elsewhere Not in hotspots
  8. 8. Phylogenetic Endemism - Hylids Rosauer, Laffan, Crisp, Donnellan & Cook (2009) Molecular Ecology Litoria nanotis species group, Litoria dayi . All 5 spp. on the IUCN Red List Litoria andiirrmalin long distinct lineage. Known from tiny range on Cape Melville
  9. 9. Clustering on biological similarity
  10. 10. Monte Carlo randomisation tests <ul><li>For example: can centres of endemism be explained as simple a chance consequence of species richness? </li></ul><ul><li>After running a spatial analysis: </li></ul><ul><ul><li>shuffle the location data and repeat </li></ul></ul><ul><ul><li>for each grid cell – how often would a random value exceed the observed </li></ul></ul><ul><ul><li>null hypothesis epressed thourgh constraints on randomisation </li></ul></ul>
  11. 11. Frog Endemism Slatyer, Rosauer & Lemckert (2007) Journal of Biogeography
  12. 12. How does phylogenetic uncertainty affect spatial analysis? <ul><li>Phylogenetic uncertainty has typically been ignored in spatial PD analyses </li></ul><ul><ul><li>some exceptions </li></ul></ul><ul><ul><ul><li>Forest et al. (2007) showed their results were robust to the choice of phylogenetic inference method </li></ul></ul></ul><ul><ul><ul><li>Isaac et al. (2007) calculated node ages from the geometeric mean of the 95% confidence interval on node ages </li></ul></ul></ul><ul><ul><li>collapsing poorly supported nodes doesn’t help </li></ul></ul><ul><li>To assess the full effect of uncertainty, consider topology, branch lengths and their interactions </li></ul>
  13. 13. Drawn with DensiTree Bouckaert, R. (2010)
  14. 14. Placing confidence intervals on claims about significant areas Mean (solid line) and 95% confidence limits (dotted lines) for phylogenetic endemism from 1000 Bayesian trees. Areas ranking in the top 5% for phylogenetic endemism. Red and pink areas are robust to phylogenetic uncertainty. Cells outside the top 5% are not plotted.
  15. 15. Biodiverse is available on a GNU Lesser GeneralPublic License from: <ul><li>See Laffan, Lubarsky and Rosauer (2010) Ecography </li></ul><ul><li>Funding: </li></ul><ul><ul><li>Australian Research Council </li></ul></ul><ul><li>Partners: </li></ul>Data: Australian museums and conservation agencies (species locations) Mike Crisp & Lyn Cook – Daviesia phylogenies