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Visualizing Evolution in Space and Time

Visualizing Evolution in Space and Time. David M. Kidd National Evolutionary Synthesis Center 2024 West Main Street, Suite A200, Durham, NC27705 dk @nescent.org. Evolution & …. Scale Space, Place and Time Trees and Tree-Thinking Evolution of evolutionary trees Geophylogenies

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Visualizing Evolution in Space and Time

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  1. Visualizing Evolution in Space and Time David M. Kidd National Evolutionary Synthesis Center 2024 West Main Street, Suite A200, Durham, NC27705 dk@nescent.org

  2. Evolution & … • Scale • Space, Place and Time • Trees and Tree-Thinking • Evolution of evolutionary trees • Geophylogenies • 3D Visualization • Google Earth • Geographical Information Systems (GIS) • GeoPhyloBuilder - The Movie

  3. The Scale of Evolution

  4. "Nothing in biology makes sense except in the light of evolution." Theodosius Dobzhansky (1900 - 1975) The American Biology Teacher, March 1973

  5. Kevin W. Boyack, Sandia National Labs Richard Klavans, SciTech Strategies Mathematics Physics and Chemistry Life Sciences Medical Sciences Social Sciences Image created with the VxOrd graph layout routine from the citation patterns in 800,000 scientific papers published in 2002. A research group is a group of papers (9 on average) that are written on the same research topic. Over time, communities can be born, continue, split, merge, or die

  6. Connecting the Dots

  7. Space, Place & Time

  8. Goodeidae

  9. Species Endemics Widespread Pacific Vicariant

  10. Tribes

  11. Catchment History Miocene 14.5 – 5 Mya Pliocene 2- 2.4 Mya Modern

  12. A Complex and Incomplete History OR Lake M. Lerma & Pacific Balsas (restricted) MtDNA ultrametric tree Widespread Pacific Widespread Pacific Pacific Tectonic Uplift Panuco & adjacent Widespread Pacific Widespread Balsas (restricted) U. Balsas & adj. closed Widespread Pacific Pacific Balsas (restricted) Panuco Pacific M. Lerma & Pacific U. Lerma & adj. closed M. Lerma & closed U. Lerma & U. Balsas Mexico City U. Lerma & adj. closed Pacific Pacific Pacific Pacific Pacific Balsas Vicariant Pacific San Pedro San Pedro Miocene Pliocene Pleistocene 14.9MY 5MY 2.4MY Holocene

  13. Trees and Tree-Thinking

  14. Matthew chapter 1King James Version 1 The book of the generation of Jesus Christ, the son of David, the son of Abraham. 2 Abraham begat Isaac; and Isaac begat Jacob; and Jacob begat Judas and his brethren; 3 And Judas begat Phares and Zara of Thamar; and Phares begat Esrom; and Esrom begat Aram; 4 And Aram begat Aminadab; and Aminadab begat Naasson; and Naasson begat Salmon; 5 And Salmon begat Booz of Rachab; and Booz begat Obed of Ruth; and Obed begat Jesse; 6 And Jesse begat David the king; and David the king begat Solomon of her that had been the wife of Urias; 7 And Solomon begat Roboam; and Roboam begat Abia; and Abia begat Asa; 8 And Asa begat Josaphat; and Josaphat begat Joram; and Joram begat Ozias; 9 And Ozias begat Joatham; and Joatham begat Achaz; and Achaz begat Ezekias; 10 And Ezekias begat Manasses; and Manasses begat Amon; and Amon begat Josias; 11 And Josias begat Jechonias and his brethren, about the time they were carried away to Babylon:

  15. Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck (1809) Zoological Philosophy: An Exposition with Regard to the Natural History of Animals, H. Elliot, transl. (Macmillan, London, 1914), p. 179 Lamarck (1774 – 1829)

  16. Charles Darwin's 1837 sketch, First Notebook on Transmutation of Species. Charles Darwin (1809-1882) painted by George Richmond in the late 1830s.

  17. Charles Darwin 1859. Chapter IV, The Divergence of Character. On The Origin of Species by Natural Selection.

  18. Tree-Thinking • Topology isomers • Proximity or left-to-right • Evolution only at nodes • Backward projection of living species (Fish,(Frog,(Lizard,(Mouse,Human)))) Baum, D.A. et al. 2005. The Tree-Thinking Challenge. Science 310: 979-980

  19. B D A C Unrooted Rooting Temporaldirection D A B C Rooted

  20. Branch Lengths continuous time ordered time Unequal branch lengths Equal branch lengths Additive Tree Ultrametric Tree

  21. t t Up or Down? Deep-time Mirrors stratigraphy Tree metaphor Shallow-time Mirrors family tree More suitable for map metaphor

  22. Extinction Stephen J. Gould 1942-2002 Chapter 1. The Iconography of Expectation in Wonderful Life (1989)

  23. Gene Trees and the Species Tree Reticulation Bifurcation Speciation

  24. Geospatial Revolution Entity Attributes Phylogeography: Genes in space Coalescent: Gene trees embedded in species trees Island Biogeography and Migration Reticulate Networks Molecular Revolution Modern Synthesis Simple Tree Hewitt, G. M. (2001). Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Molecular Ecology10: 537-549.

  25. Island Biogeography and Migration Phylogeography: Genes in space

  26. Coalescent Entity Attributes

  27. Hugall, A., C. Moritz, et al. (2003). Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proceedings of the National Academy of Science99(9): 6112-6117.

  28. Geophylogenies

  29. Phylogeographer 1.0 Buckler, Edward S., IV. 1999. Phylogeographer: Software for the analysis of phylogeographic hypotheses. http://www.maizegenetics.net/bioinformatics/phylogeographer/index.htm

  30. Mesquite Cartographer David R. Maddison, University of Arizona Wayne P. Maddison, University of British Columbia http://mesquiteproject.org/mesquite/mesquite.html

  31. Data Entities • One or more trees • size • quasi-fractal • nodes • Observed and inferred • Spatial footprint (point, line, polygon) • Attributes (SNPs, body size, colour, sounds) • branches • Network topology between nodes • Spatial path • Attributes (time, depth, attribute change, geographical context) • Biological context • ranges, attributes from other studies • Geographical context • elevation, climate, drainage, places, land cover • present, past and future • Uncertainty in all of above

  32. Visualization Issues • Media • paper, screen, virtual reality • Audience and Message • What organism am I looking at? • Where am I looking at? • What’s so interesting? • Compression of dimensions • x, y, z, t to 2D or 3D • Data fidelity verses cartographic license • Geographic projection • equal area, equal distance, orthogonal • Furniture • legend, scale bars, grid/graticule, orientation • Design • symbols, colour, multiple phylogenies • Interaction • zooming, 3D-rotation, selection, adding own data

  33. 3D Geophylogeny

  34. 3D Visualization

  35. Google Earth

  36. ArcGIS

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