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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

Visualizing Evolution in Space and Time

David M. Kidd

National Evolutionary Synthesis Center

2024 West Main Street, Suite A200, Durham, NC27705

[email protected]


Evolution
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



  • "Nothing in biology makes sense except in the light of evolution."

    Theodosius Dobzhansky (1900 - 1975)

    The American Biology Teacher, March 1973


    Kevin W. Boyack, Sandia National Labs evolution."

    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


    Connecting the Dots evolution."


    Space place time
    Space, Place & Time evolution."


    Goodeidae
    Goodeidae evolution."


    Species
    Species evolution."

    Endemics

    Widespread

    Pacific

    Vicariant


    Tribes
    Tribes evolution."


    Catchment history
    Catchment History evolution."

    Miocene 14.5 – 5 Mya

    Pliocene 2- 2.4 Mya

    Modern


    A complex and incomplete history
    A Complex and Incomplete History evolution."

    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



    Matthew chapter 1 evolution." King 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:


    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)


    Charles Darwin's 1837 sketch, (1809) First Notebook on Transmutation of Species.

    Charles Darwin (1809-1882)

    painted by George Richmond in the late 1830s.


    Charles Darwin 1859. Chapter IV, The Divergence of Character.

    On The Origin of Species by Natural Selection.


    Tree thinking
    Tree-Thinking Character.

    • 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


    Rooting

    B Character.

    D

    A

    C

    Unrooted

    Rooting

    Temporaldirection

    D

    A

    B

    C

    Rooted


    Branch lengths
    Branch Lengths Character.

    continuous

    time

    ordered

    time

    Unequal branch lengths

    Equal branch lengths

    Additive Tree

    Ultrametric Tree


    Up or down

    t Character.

    t

    Up or Down?

    Deep-time

    Mirrors stratigraphy

    Tree metaphor

    Shallow-time

    Mirrors family tree

    More suitable for map metaphor


    Extinction
    Extinction Character.

    Stephen J. Gould

    1942-2002

    Chapter 1. The Iconography of Expectation in Wonderful Life (1989)


    Gene trees and the species tree
    Gene Trees and the Species Tree Character.

    Reticulation

    Bifurcation

    Speciation


    Geospatial Revolution Character.

    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.


    Island Character.

    Biogeography

    and Migration

    Phylogeography:

    Genes in space


    Coalescent Character.

    Entity Attributes


    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.


    Geophylogenies
    Geophylogenies paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail


    Phylogeographer 1 0
    Phylogeographer 1.0 paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail

    Buckler, Edward S., IV. 1999. Phylogeographer: Software for the analysis of phylogeographic hypotheses.

    http://www.maizegenetics.net/bioinformatics/phylogeographer/index.htm


    Mesquite cartographer
    Mesquite Cartographer paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail

    David R. Maddison, University of Arizona

    Wayne P. Maddison, University of British Columbia

    http://mesquiteproject.org/mesquite/mesquite.html


    Data entities
    Data Entities paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail

    • 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


    Visualization issues
    Visualization Issues paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail

    • 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


    3d geophylogeny
    3D Geophylogeny paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail


    3d visualization
    3D Visualization paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail


    Google earth
    Google Earth paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail


    Arcgis
    ArcGIS paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail


    Cetartiodactyla paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail


    Cetartiodactyla supertree
    Cetartiodactyla Supertree paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail

    Hippopotamidae

    Antilocapridae

    Tayassuidae

    Moschidae

    Camelidae

    Bovidae

    Giraffidae

    Tragulidae

    Cervidae

    CETACEA

    Suidae

    31:9

    10:11

    10:1

    30:13

    33:15

    36:25

    53:7

    47:7

    35:25


    Geophylobuilder the movie
    GeoPhyloBuilder - The Movie paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail


    With thanks
    With Thanks… paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail

    • NSF #EF-0423641

    • Xianhua Lui

    • Michael Lavantucksin

  • Data

    • Constantino Marcias-Garcia (UNAM), Michael Ritchie (St. Andrews), John Wiens & Sarah Smith (Stony Brook), Kyle Dexter (Duke), Sam Price (NESCent) & others.

  • Google Maps

    • Bill Piel (Yale), Declan Butler (Science), Daniel Janies, Andrew Hill (Univ. Colorado) & Eric Waltari (AMNH).

  • GeoPhyloBuilder – The Movie

    • Rachel Brady

    • Zachary Pogue

  • http://www.evoviz.org


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