Transcript The Scale of Evolution - Duke Univ. Visualization Technology Group

Visualizing Evolution in
Space and Time
David M. Kidd
National Evolutionary Synthesis Center
2024 West Main Street, Suite A200, Durham, NC27705
[email protected]
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
"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
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
Space, Place & Time
Goodeidae
Species
Endemics
Pacific
Widespread
Vicariant
Tribes
Catchment History
Miocene 14.5 – 5 Mya
Modern
Pliocene 2- 2.4 Mya
A Complex and Incomplete History
OR
Lake
MtDNA ultrametric tree
Tectonic Uplift
Miocene
14.9MY
Pliocene
5MY
Chapenc
Chappar
Alloorob
Amspl
Xenvar
Xeneis
Xenmel
Xenocapt
Zoogquit
Zoogteq
Gooatr
Allotcat
Allotdia
Allotdug
Allotgos
Allotmac
Allotreg
Ataentow
Skiffran
Skifmult
Skiflerm
Skifbil
Girmult
Girviv
Hubtur
Allodtam
Allodzon
Allodpoly
Allodhub
Ilyfur
Ilywhi
Xenres
Charaud
Charlat
Emplat
Proflab
M. Lerma & Pacific
Balsas (restricted)
Widespread
Pacific
Widespread
Pacific
Pacific
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
Pleistocene
2.4MY
Holocene
Trees and Tree-Thinking
Matthew chapter 1
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:
Lamarck (1774 – 1829)
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
Charles Darwin (1809-1882)
painted by George Richmond in the late 1830s.
Charles Darwin's 1837 sketch, First Notebook on
Transmutation of Species.
Charles Darwin 1859. Chapter IV, The Divergence of Character.
On The Origin of Species by Natural Selection.
Tree-Thinking
•
•
•
•
(Fish,(Frog,(Lizard,(Mouse,Human))))
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
Rooting
Temporal
direction
B
D
D
A
C
A
B
Unrooted
C
Rooted
Branch Lengths
continuous
time
ordered
time
Unequal branch lengths
Additive Tree
Equal branch lengths
Ultrametric Tree
Up or Down?
t
t
Deep-time
Mirrors stratigraphy
Tree metaphor
Shallow-time
Mirrors 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)
Extinction
Stephen J. Gould
1942-2002
Chapter 1. The Iconography of Expectation in Wonderful Life (1989)
Gene Trees and the Species Tree
Reticulation
Bifurcation
Speciation
Geospatial Revolution
Phylogeography:
Genes in space
Island
Biogeography
and Migration
Entity
Attributes
Reticulate
Networks
Coalescent:
Gene trees
embedded in
species trees
Molecular Revolution
Modern Synthesis
Simple Tree
Hewitt, G. M. (2001). Speciation, hybrid zones and
phylogeography - or seeing genes in space and time.
Molecular Ecology 10: 537-549.
Island
Biogeography
and 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 Arizona
Wayne 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
31:9
10:11
47:7
30:13
33:15
36:25
53:7
35:25
10:1
Camelidae
Tayassuidae
Suidae
Hippopotamidae
CETACEA
Tragulidae
Antilocapridae
Giraffidae
Moschidae
Cervidae
Bovidae
Cetartiodactyla Supertree
GeoPhyloBuilder - The
Movie
With Thanks…
– NSF #EF-0423641
– Xianhua Lui
– Michael Lavantucksin
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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
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http://www.evoviz.org