Biomimicry

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Genetics of AdaptationFrom Model Organism to
Model Ecosystems
Genetics of AdaptationFrom Model Organism to
Model Ecosystems
Justin BorevitzEcology EvolutionUniversity of
Chicagohttp//borevitzlab.uchicago.edu/
Indiana Dunes National Lakeshore
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Genetics of Adaptation

• Transgenetics 1
• Mutants 10
• Families 100
• Ancestral Populations 1000
• Compatible Species 10000
• Communities 100000
• Ecosystems 1000000000
• Biosphere 1000000000000

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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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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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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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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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Genetic Variation within aMidwest Field (PNA)

• Haplotype frequency differs across collection
  dates

Yan Li
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• Genetic tree (overall histogram, shared haplotyes
  within and across regions)

Cluster of 5810 lines
Histogram of haplotype sizes 2108
haplotypes/unique haplotypes in total among 5810
lines
Biggest Clone
Haplotype sizes
Singletons
Non-singleton groups(clones) at h0
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Geoff Morris
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Genetic diversity within and between eco-regions
Appalachian-Blue Ridge forests Atlantic
coastal pine barrens
2 42
Central forest-grasslands transition
Central U.S. hardwood forests
286
28 Lake
New England-Acadian forests
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9 Northeastern coastal forests
Southern Great Lakes forests
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1172
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Haplotype sharing/distribution among sites 5810
lines
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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
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Kas/Col floweringtime QTL
FLM
FRI
Yan Li
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Kas/Col flowering time QTL GxE
Chr4 FRI
Chr1 FLM Chr4 FRI
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Environment and Epistasis
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Seasonal Flowering Time Response
Seasonal Flowering Time Response
Hybrid dwarf
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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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Whole Genome Association MappingFlowering Time
Chromosome 1
Chromosome 2
Chromosome 3
Chromosome 4
Chromosome 5
Magnus Nordborg
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Disease Resistance (HR) LD mapping
Data from Aranzana, PLoS 2006 Brian Traw, Katrin
Jakob
RPS5
RPT2
250k SNP array, Yan Li, Susi
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Comparing Association Mapping with BSA Mapping
0.4
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Chromosome
Zhao et al., 2006
Ivan Baxter
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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
• 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 Remnant, restored,
reconstructed, prairies savannahs Comparative
population structure, in species assemblages
Differential effects on annuals, perennials,
selfers, outcrossers Categorize existing genetic
diversity- Conservation Genetics Restore with
maximal regional diversity samples to allow
natural selection breeding.
Eco region diversity plant community population
genomics. Genetic variation within and between
species and locations Remnant, restored,
reconstructed, prairies savannahs Comparative
population structure, in species assemblages
Differential effects on annuals, perennials,
selfers, outcrossers Categorize existing genetic
diversity- Conservation Genetics Restore with
maximal regional diversity samples to allow
natural selection breeding.
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Aquilegia (Columbines)
Recent adaptive radiation, 350Mb genome
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Species withgt 20k ESTs 11/14/2003
Animal lineage good coverage
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Aquilegia and pollinators
Humming Bird Hawkmouth
Bumble Bee
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Christos Noutsos
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Genetics of Speciationalong a Hybrid Zone
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Indiana Dunes Collection site
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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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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Water Scarcity
Comprehensive Assessment of Water Management in
Agriculture Stockholm World Water Week, 2006
www.iwmi.org/assessment
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Global Soil Degradation
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Total Carbon (LPJ)
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Carbon in Vegetation (LPJ)
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Carbon in Soil (LPJ)
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Nielsen and Hole, 1963
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Environmental Shakeup

• Specialists can
• Migrate
• Adapt
• or Go Extinct
• Generalists
• are Advantaged
• Invasive species
• Bioclimatic mapping
• 32 of the European plant species in a given cell
  in 1990 would disappear by 2050
• Bakkenes et al. (2002)

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Breeding for Natural Selection

• 1) Target Foundation Prairie Species
• Next Gen expressed gene sequencing
• 250k sequences, 10,000s SNPs
• Macro and Micro evolutionary importance
• 2) Landscape Genetics
• Sample 1000s of genotypes across tallgrass region
• Identify population structure and diversity mix
• 3) Use Diversity Mix for Restoration
• Monitor local adaptation, genetic/community level

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Succession Lake Michigan sand dunes
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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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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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Remote Sensing (micro NEON)
Real time sensing 100s of cameras Temperature Humi
dity Light spectrum/intensity Wind speed
direction Air quality (CO2, NOX..) Water levels,
quality (salts etc) Soil temp, moisture
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http//borevitzlab.uchicago.edu
http//borevitzlab.uchicago.edu
Arabidopsis Yan Li Megan Dunning Joy
Bergelson Magnus Nordborg Paul Marjoram Aquilegia
Christos Noutsos Scott Hodges Tall Grass
Prairie Geoff Morris Mike Miller
Arabidopsis Yan Li Megan Dunning Joy
Bergelson Magnus Nordborg Paul Marjoram Aquilegia
Christos Noutsos Scott Hodges Tall Grass
Prairie Geoff Morris Mike Miller
Arrays Xu Zhang Shinhan Shiu Ivan Baxter
Arrays Xu Zhang Shinhan Shiu Ivan Baxter