Biomimicry

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Conservation and Restoration Geneticsin the
Chicago Wilderness
Conservation and Restoration Geneticsin the
Chicago Wilderness
Justin BorevitzEcology EvolutionUniversity of
Chicagohttp//borevitzlab.uchicago.edu/
Indiana Dunes National Lakeshore
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Short Mixed
Tall Grassland Prairie
Prairie Model Ecosystem
Breed for Natural Selection Farm Ecosystems
Services
Tall Grass Prairies. 99.9 plowed under long term
survival is in danger
http//climate.konza.ksu.edu/
464 species declined 328 (71) endemic
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People Cause 10X More Soil Erosion Than All
Natural Processes Combined...
Human activity causes 10 times more erosion of
continental surfaces than all natural processes
combined, an analysis by a University of Michigan
geologist shows. "If you ask how fast erosion
takes place over geologic timesay over the last
500 million yearson average, you get about 60
feet every million years," Wilkinson said. In
those parts of the United States where soil is
being eroded by human agricultural activity,
however, the rate averages around 1,500 feet per
million years,
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www.uni.edu/ceee/foodproject/mud.jpg
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Fossil Water Ogallala Aquifer 2 to 6 million
old 2/3 Lake Michigan volume Draining the flow of
18 Colorado Rivers Dry up in 25 years.
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Nielsen and Hole, 1963
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Total Carbon (LPJ)
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Conservation and Restoration
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Scientific Questions
Mapping Genetic Diversity on the
Landscape Remnants Diversity Hotspots Species
Range limits Fragmentation Invasive or
Dominant types Genetic Diversity controls
Phenotype Diversity new mutations
(slow) evolutionary significant units new
allelic combinations (fast) cryptic subspecies
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Genotype
Environment
Phenotype
http//farm1.static.flickr.com/7/9927631_aa10584e0
a.jpg
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Talk Outline
Talk Outline
Genetic Diversity biodiverisity Population
structure, migration, admixture Phenotyping in
Natural environments Seasonal Variation in the
Lab Whole Genome Association Mapping Next
Species Aquilegia, Switchgrass Ecological plant
communities Indiana Dunes, Tall Grass Prairies
Genetic Diversity biodiverisity Population
structure, migration, admixture Phenotyping in
Natural environments Seasonal Variation in the
Lab Whole Genome Association Mapping Next
Species Aquilegia, Switchgrass Ecological plant
communities Indiana Dunes, Tall Grass Prairies
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Local adaptation under strong selection
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Seasonal Variation
Matt Horton
Megan Dunning
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Variation within a field http//naturalvariation.o
rg/hapmap
Variation within a field http//naturalvariation.o
rg/hapmap
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Genetic Structure

• Family Structure
• 100-1000 SNPs
• Deep racial historical population structure
• 10,000 SNPs
• Genetic Association
• causative gene
• 100k, 1M SNPs

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Which genotyping tool should be used?
Yan Li
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Geoff Morris
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Probability of a Divergent Haplotype
Alex Platt
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Diversity among 5707 lines
Random alleles (unique) Random alleles (all) All
pairs North America Europe
American Family structure
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Diversitywithin andbetween populations
80 Major Haplotypes
Google Earth Fly By
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Distribution of the common haplotype in USA
43/6368 of the sites in USA has this most
common haplotypeAmong big sites(nlinesgt10)
36/4286
Common haplotype sharing across sites in USA
Yan Li
of colors 629
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Seasonal Variation in Genotype Frequency
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Selecting mapping population
All data 5309 lines at 142 SNPs
1841 lines at 142 SNPs after removing clones
384 diverse lines (1 line from each of the 384
group)
Redundancy randomly chosen 25 lines from the
1680 unique lines (data1_5) will have 282
alleles141 SNPs x 2
Final 360 lines in seasonal flowering time
Yan Li
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Summary

• Genetic Diversity
• Within and between populations
• Local, regional, global
• Phenotypic Diversity Adaptation
• New mutations
• New genetic combinations of existing alleles
• Evolution
• Colonization, expansion, and collapse
• In migration, recombination, diversity

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Begin with regions spanning the Native Geographic
range
Lund Sweden
Nordborg et al PLoS Biology 2005 Li et al PLoS
ONE 2007
Tossa Del Mar Spain
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Sweden Spain
Seasons in the Growth Chamber
Seasons in the Growth Chamber

• Changing Day length
• Cycle Light Intensity
• Cycle Light Colors
• Cycle Temperature

• Changing Day length
• Cycle Light Intensity
• Cycle Light Colors
• Cycle Temperature

Geneva Scientific/ Percival
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Solar Calc II
Kurt Spokas Version 2.0a June 2006
USDA-ARS Website Midwest Area (Morris,MN) http//
www.ars.usda.gov/mwa/ncscrl
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\
Seasonal Flowering Time Response
Seasonal Flowering Time Response
Hybrid dwarf
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\
Seasonal Flowering Time Response
Seasonal Flowering Time Response
Kas/Col RILs Van/Col RILs 360 Diverse
Accessions Spain/Sweden Spring (early late)
Fall (early late)
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Sweden
Spain
Spring
Summer
Yan Li
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Which arrays should be used?
SNP array
How about multiple species? Microbial
communities?
Pst,Psm,Psy,Psx, Agro, Xanthomonas, H parasitica,
15 virus,
Ressequencing array
Tiling/SNP array 2007 250k SNPs, 1.6M
tiling probes
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WGA seasonal Flowering time
Spain Spring
Sweden Spring
Chromosome 1
Chromosome 2
Spain Summer
Sweden Summer
Yan Li
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Association Mapping of 107 Traits across 192 lines
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Summary Arabidopsis

• Simulating Seasons in the lab
• Changing day length, end of day FR, temp
• Video phenotyping, growth rate and rhythm
• QTL mapping (Yan Li, et al PLoS ONE)
• G x E, suggests adaptive importance
• Epistasis, genetic background importance
• Whole Genome Association mapping
• Complex traits, complex genetic architecture
• Mendelian traits, simple to resolve

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Next Species.
Next Species.
Eco region diversity plant community population
genomics. Genetic variation within and between
species and locations Conservation
Genetics Restoration with high diversity
genotypes
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Aquilegia (Columbines)
Recent adaptive radiation, 350Mb genome
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Aquilegia and pollinators
Justen Wittall Scott Hodges
Humming Bird Hawkmouth
Bumble Bee
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Genetics of Speciationalong a Hybrid Zone
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Christos Noutsos
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Christos Noutsos
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NSF Genome Complexity

• Microarray development
• QTL candidates
• Physical Map (BAC tiling path)
• Physical assignment of ESTs
• QTL for pollinator preference
• 400 RILs, map abiotic stress
• QTL fine mapping/ LD mapping
• Develop transformation techniques
• VIGS
• Whole Genome Sequencing (JGI?)

Scott Hodges (UCSB) Elena Kramer (Harvard) Magnus
Nordborg (USC) Justin Borevitz (U Chicago) Jeff
Tompkins (Clemson)
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The Next Generation of Biofuels Greenhouse-Neutra
l Biofuels from High-Diversity Low-Input
Prairie Ecosystems by David Tilman University
of Minnesota
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Sustainable Bioenergy Crop Production Research
Facility

• New 5.4-ha facility at Fermilab
• Argonne Ecology Group (Julie Jastrow Mike
  Miller)

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Genetic variation in growth
Cave-in-Rock (S. Illinois)
Dacotah (ND)

• Genetic differences affect growth
• But does increase genetic diversity improve
  productivity?

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Productivity and genetic diversity

• Cultivar mixes had a mean yield excess of 32
  (26) g/m2 over mono-cultivar expectations

Cultivar diversity plots (164 X 6m2)
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Real Time Ecosystem Monitoring

• HPWREN
• San Diego wireless ecological data sensing.

Fermilab AmeriFlux site, provided by Timothy J.
Martin (ANL-EVS)
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Succession Lake Michigan sand dunes
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Habitats of the Indiana Dunes
Lakeshore Dune
Dune Flats
Blowout
Tallgrass Prairie
Oak flatwoods
Ruderal land
Black Oak Savanna
Geoff Morris
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Microclimate stations

• 4 weather stations on ecotones
• 8 microclimate modules (2 per station)

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1
Backdune
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Foredune
Blowout
Flatwoods
Lake
SG
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2
Panne
Interdune flats
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Backdune ridge
SG
Geoff Morris
Interdune trough
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Microclimate and plant community

• How, when, and where are plants stressed?
• How does this vary over the landscape?

• How do plants shape their own environment?
• Are particular grass genotypes found in
  particular environments?

Geoff Morris
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Microclimates determined byplant communities
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Wild population collections

• Hierarchical, georeferenced sample of 100s of
  individuals from extremely variable environments
• Interdunal flats
• troughs (sand) and swales (sandy loam)
• Wet mesic prairies
• Sandy Black Oak savanna
• Waste ground - Utility and transportation
  corridors

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Not emerged Tiller only One leaf Two leaves
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Google Earth

• Gigapan.org

Gigavision.org Tim Brown www.time-science.com
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http//borevitzlab.uchicago.edu
http//borevitzlab.uchicago.edu
Arabidopsis Yan Li Alex Platt Yu Huang Andy
Cal Xu Zhang Joy Bergelson Magnus Nordborg Paul
Marjoram Sabasian Zoellner
Arabidopsis Yan Li Alex Platt Yu Huang Andy
Cal Xu Zhang Joy Bergelson Magnus Nordborg Paul
Marjoram Sabasian Zoellner
Aquilegia Christos Noutsos Scott Hodges Tall
Grass Prairie Traci Viinanen Geoff Morris Paul
Grabowski Mike Miller
Aquilegia Christos Noutsos Scott Hodges Tall
Grass Prairie Traci Viinanen Geoff Morris Paul
Grabowski Mike Miller