Visualizing Evolution in Space and Time

David M. KiddNational Evolutionary Synthesis Center

2024 West Main Street, Suite A200, Durham, NC27705dk@nescent.org

Scale

Space, Place and Time

Trees and Tree-ThinkingEvolution of evolutionary trees

Geophylogenies

3D VisualizationGoogle Earth

Geographical Information Systems (GIS)

GeoPhyloBuilder - The Movie

Evolution & …

The Scale of Evolution

"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

Richard Klavans, SciTech Strategies

MathematicsPhysics and ChemistryLife SciencesMedical SciencesSocial 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

Space, Place & Time

Goodeidae

SpeciesEndemics Widespread

Pacific Vicariant

Tribes

Catchment History

Miocene 14.5 – 5 Mya Pliocene 2- 2.4 Mya

Modern

A Complex and Incomplete HistoryChapencChapparAlloorobAmsplXenvarXeneisXenmelXenocaptZoogquitZoogteqGooatrAllotcatAllotdiaAllotdugAllotgosAllotmacAllotregAtaentowSkiffranSkifmultSkiflermSkifbilGirmultGirvivHubturAllodtamAllodzonAllodpolyAllodhubIlyfurIlywhiXenresCharaudCharlatEmplatProflab

PleistoceneMiocene Pliocene

Holocene

San Pedro

San Pedro

Pacific

Balsas Vicariant

Pacific

Pacific

Pacific

Pacific

Pacific

U. Lerma & adj. closed

Mexico City

U. Lerma & U. Balsas

M. Lerma & closed

M. Lerma & Pacific

Pacific

U. Lerma & adj. closed

Panuco

14.9MY 5MY 2.4MY

Balsas (restricted)

Pacific

Pacific

Widespread

U. Balsas & adj. closed

Balsas (restricted)

Widespread

Pacific

Widespread

Panuco & adjacent

Pacific

Pacific

Widespread

Pacific

Widespread

Balsas (restricted)

M. Lerma & PacificLake

Tectonic Uplift

OR

MtDNA ultrametric tree

Trees and Tree-Thinking

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:

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, 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

• Topology isomers• Proximity or left-to-right• Evolution only at nodes• Backward projection of living species

Baum, D.A. et al. 2005. The Tree-Thinking Challenge. Science 310: 979-980

(Fish,(Frog,(Lizard,(Mouse,Human))))

Rooting

A

B C

D

Temporaldirection

Rooted

B

AC

D

Unrooted

Branch Lengths

orderedtime

continuoustime

Unequal branch lengths Equal branch lengths

Additive Tree Ultrametric Tree

Up or Down?

Deep-timeMirrors stratigraphy

Tree metaphor

Shallow-timeMirrors family tree

More suitable for map metaphor

‘When a "family tree" chart is used, I am used to seeing the passage of time, and successive generations, move down the page. In this chart, it moves upward. I found it easier to view when I inverted it, rotating the tree pattern to a root pattern’.

Ask T. E. (Tufte)

t

t

Extinction

Stephen J. Gould1942-2002

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

Gene Trees and the Species Tree

Reticulation

Bifurcation

Speciation

Hewitt, G. M. (2001). Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Molecular Ecology 10: 537-549.

IslandBiogeographyand Migration

Phylogeography:Genes in space

ReticulateNetworks

EntityAttributes

Coalescent:Gene trees

embedded inspecies trees

Simple Tree

Modern Synthesis

Molecular Revolution

Geospatial Revolution

IslandBiogeographyand Migration

Phylogeography:Genes in space

Entity Attributes Coalescent

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 Science 99(9): 6112-6117.

Geophylogenies

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

David R. Maddison, University of ArizonaWayne P. Maddison, University of British Columbia

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

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• 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 Visualization

Google Earth

ArcGIS

Cetartiodactyla

Cetartiodactyla SupertreeB

ovi

dae

Cer

vid

ae

Mo

sch

idae

Gir

affi

dae

An

tilo

cap

rid

ae

Tra

gu

lidae

CE

TA

CE

A

Hip

po

po

tam

idae

Su

idae

Tay

assu

idae

Cam

elid

ae

35:2547:7

53:736:25

33:1531:9 10:11 30:13 10:1

GeoPhyloBuilder - The Movie

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