visualizing evolution
DESCRIPTION
This talk describes the history of biodiversity and evolution visualizations and the current capabilities. It discusses the visualization needs of the research and education communities. It was presented at Bentley University during the MetroWest Boston Data Visualization Meetup in August of 2013.TRANSCRIPT
Visualizing Evolution
Anne [email protected]
Nothing in biology makes sense except in the light of evolution.
- Theodosius Dobzhansky(1900-1975)
Aristotle’s “Chain of Being”
Blooded
Humans Live Bearing Egg Layers
Bloodless
Insects Crustacea Molluscs
• Hierarchical “Ladder of Life” according to complexity of structure and function
• Final causes drove natural processes• Graded scale of perfection rising from plants
to humans• Eleven grades arranged according to “the
degree to which they are infected with potentiality”
Aristotle 384 BC to 322 BC
Drawing by Franciscan missionary, Didacus Valades published in Rhetorica Christiana.
Great Chain of Being 1579
• Order imparted by omnipotent Christian deity
• Included inanimate objects• Humans are at the top, under
supernatural beings
• God created the world perfectly, “Whatever is, is right”• To try to be something
we are not is to break the chain
Ladder of LifeHumans
Viviparous Quadrupeds
Birds
Egg-laying Quadrupeds
CetaceansFishMollusks (Cephalopods)
Crustaceans
Mollusks (Bivalves)
Jellyfish & Sponges
Higher Plants
Lower Plants
Inanimate Objects Alexander Pope (1688-1744)
God
Technology Check - Microscope• First detailed account of living
tissue based on use of microscope was in 1644
• The word “cell” is coined by Robert Hooke 1665
• Anton van Leeuwenhoek describes “animalcules” in 1674-1676
Technology Check - Taxonomy• Carolus Linnaeus published a comprehensive account
of all known species • First edition 1735• Starting point for zoological nomenclature• Contains about 10,000 species
Carolus Linnaeus (1707-1778)
Technology Check - Taxonomy• Carolus Linnaeus published a comprehensive account
of all known species • First edition 1735• Starting point for zoological nomenclature• Contains about 10,000 species
Carolus Linnaeus (1707-1778)
Philosophy Check - Enlightenment• Europe 1600s-1700s• Lincean Academy founded 1603• Reform society using reason• Challenge ideas grounded in tradition and faith• Scientific method
Evolution of Species by Natural Selection
Charles Darwin (1809-1882)
On the Origin of Species by Means of Natural Selection - 1859
• Species were not created by a supernatural being in their current state
• Species derive from other species
• Humans are not the best thing since sliced bread
Haeckel’s tree of life published in Generelle Morphologie der Organismen (1866) with the three branches Plantae, Protista, Animalia
Early Phylogenetic Trees
Ernst Haeckel (1834-1919)
Tree from Haeckel’s Anthropogenie oder Entwicklungsgeschichte des Menschen published in 1874
Early Phylogenetic Trees
Ernst Haeckel (1834-1919)
• Grouping species based on shared characters• Term “clade” coined in 1940• Imply relationship based on shared character states• A tree is a hypothesis
Technology Check - Cladistics
• Digital computers invented 1940-1945• First computer algorithms for cladistics written in
1965• First software package for phylogenetic analysis 1980
Technology Check - Computers
• DNA first isolated 1869• Frederick Griffith demonstrated that DNA carried
genetic information 1928• Watson and Crick publish structure of DNA using
Rosalind Franklin’s images 1953• DNA sequencing methods first developed in 1977
Technology Check - DNA
Trees contain information on the relative timing of nodes only when the nodes are on the same path from the root (i.e., when one node is a descendant of another).
These trees depict equivalent relationships despite being different in style.
How to Read a Phylogenetic Tree
Baum. 2008. Reading a phylogenetic tree: the meaning of monophyletic groups. Nature Education
How to Read a Phylogenetic Tree
Baum. 2008. Reading a phylogenetic tree: the meaning of monophyletic groups. Nature Education
The information on patterns of evolutionary descent is the same regardless of the lengths of branches.
"Evolution of patterns on Conus shells." By Zhenqiang Gong, Nicholas J. Matzke, Bard Ermentrout, Dawn Song, Jann E. Vendetti, Montgomery Slatkin, and George Oster. Proceedings of the National Academy of Sciences, 4 January 2012.
Page 2012. Space, time, form: viewing the tree of life. Trends Ecol & Evol 27(2):113-120.
• Non-directed web shape• Humans not at apex (there is no apex)• Supernatural and mythological beings not included• Mostly contains microscopic organisms• Much more complicated, more content• Trees are hypotheses that change due to type of
analysis
Dendrobatidae in Amazon http://fr.academic.ru/dic.nsf/frwiki/1328251
Geophylogeny of Hawaiian katydids constructed using GenGIS.http://lter.limnology.wisc.edu/cidimensions/node/56
Phylogeny Mapping Tools
Salamanders, GeoPhyloBuilderhttp://iphylo.blogspot.com/2007/06/earth-not-flat-official.html
Phylogeny Mapping Tools
Evolution EducationAbout half of Americans do not accept the reality of evolution
Common Evolution Misconceptions
• Everything wants to be human• Individuals evolve• Evolution is random• Less complex organisms have evolved less than
more complex organisms• Humans came from monkeys• Microevolution is different from macroevolution• Linnaean taxonomy = genetics
http://darwinbookcats.wordpress.com/2011/04/18/phylogenies-and-evolution-tree-thinking/
How Can Visualizations Help?
TimeMisconceptions• Everything wants to be
human• Less complex organisms
have evolved less than more complex organisms
Legacy• Reading from left to right• Humans at apex
http://darwinbookcats.wordpress.com/2011/04/18/phylogenies-and-evolution-tree-thinking/
How Can Visualizations Help?
Tim
e
Misconceptions• Everything wants to be
human• Less complex organisms
have evolved less than more complex organisms
Legacy• Reading from left to right• Humans at apex
How Can Visualizations Help?Misconceptions• Modern species evolved
from other modern species
Legacy• Reading from left to right
How Can Visualizations Help?• Research– Show lots of information in proper context over
space and time– Communicate uncertainty– Quantitative and Qualitative
• Education– More transparency– Directly address popular misconceptions– Design around legacy thinking
https://www.facebook.com/OpenTreeOfLife?hc_location=timeline
Questions?