Visualizing evolution in space and time
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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

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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


  • The scale of evolution

    The Scale of Evolution


    Visualizing evolution in space and time

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

    Theodosius Dobzhansky (1900 - 1975)

    The American Biology Teacher, March 1973


    Visualizing evolution in space and time

    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


    Visualizing evolution in space and time

    Connecting the Dots


    Space place time

    Space, Place & Time


    Goodeidae

    Goodeidae


    Species

    Species

    Endemics

    Widespread

    Pacific

    Vicariant


    Tribes

    Tribes


    Catchment history

    Catchment History

    Miocene 14.5 – 5 Mya

    Pliocene 2- 2.4 Mya

    Modern


    A complex and incomplete history

    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


    Trees and tree thinking

    Trees and Tree-Thinking


    Visualizing evolution in space and time

    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:


    Visualizing evolution in space and time

    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)


    Visualizing evolution in space and time

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

    Charles Darwin (1809-1882)

    painted by George Richmond in the late 1830s.


    Visualizing evolution in space and time

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

    On The Origin of Species by Natural Selection.


    Tree thinking

    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


    Rooting

    B

    D

    A

    C

    Unrooted

    Rooting

    Temporaldirection

    D

    A

    B

    C

    Rooted


    Branch lengths

    Branch Lengths

    continuous

    time

    ordered

    time

    Unequal branch lengths

    Equal branch lengths

    Additive Tree

    Ultrametric Tree


    Up or down

    t

    t

    Up or Down?

    Deep-time

    Mirrors stratigraphy

    Tree metaphor

    Shallow-time

    Mirrors family tree

    More suitable for map metaphor


    Extinction

    Extinction

    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

    Reticulation

    Bifurcation

    Speciation


    Visualizing evolution in space and time

    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.


    Visualizing evolution in space and time

    Island

    Biogeography

    and Migration

    Phylogeography:

    Genes in space


    Visualizing evolution in space and time

    Coalescent

    Entity Attributes


    Visualizing evolution in space and time

    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


    Phylogeographer 1 0

    Phylogeographer 1.0

    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

    David R. Maddison, University of Arizona

    Wayne P. Maddison, University of British Columbia

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


    Data entities

    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


    Visualization issues

    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


    3d geophylogeny

    3D Geophylogeny


    3d visualization

    3D Visualization


    Google earth

    Google Earth


    Arcgis

    ArcGIS


    Visualizing evolution in space and time

    Cetartiodactyla


    Cetartiodactyla supertree

    Cetartiodactyla Supertree

    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


    With thanks

    With Thanks…

    • 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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