Indiana Dunes National Lakeshore

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EcoSystems Biology
EcoSystems Biology
Justin BorevitzEcology EvolutionUniversity of
Chicagohttp//naturalvariation.org/
Indiana Dunes National Lakeshore
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Release our pursuit of reductionism

• Green your lawn, Chem.Green.com ??
• Food production, fence our wildlife/birds to
  prevent contamination of our salad greens.

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EcoZones/ Biomes/ Realms

• Australasia Antarctic Afrotropic
  Indo-Malayan Nearctic Neotropic Oceania
  Palearctic

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Short, mixed, and Tall grass prairie
http//climate.konza.ksu.edu/
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Nielsen and Hole, 1963
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Lake Michigan sand dunes
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House
Are we getting to big for our house?
Footprint
Dr. Mathis Wackernagel
www.FootprintNetwork.org
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Global equity
Who is getting what?
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The Energy Problem

• How will society meet growing energy demands in a
  sustainable manner?
• Fossil-fuels currently supply 80 of world
  energy demand.

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Are Biofuels the Answer?...
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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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Burgeoning real estate market in Greenland
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Talk Outline
Talk Outline

• Genetic Diversity biodiverisity
• Population structure, migration, admixture
• Phenotyping in Natural environments
• Seasonal Variation in the Lab
• Next Species/ Ecological plant communities
• Aquilegia
• SNP/Tiling microarrays
• Methylation
• Deletions

• Genetic Diversity biodiverisity
• Population structure, migration, admixture
• Phenotyping in Natural environments
• Seasonal Variation in the Lab
• Next Species/ Ecological plant communities
• Aquilegia
• SNP/Tiling microarrays
• Methylation
• Deletions

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Global and Local Population Structure
Olivier Loudet
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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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Local Population Structure
common haplotypes
149 Non singleton SNPs gt6000 accessions Global,
Midwest, and UK
Megan Dunning, Yan Li
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Diversity within and between populations
80 Major Haplotypes
Google Earth Fly By
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Diversity within and between populations
17 Major Haplotypes
80 Major Haplotypes
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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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Aquilegia (Columbines)
Recent adaptive radiation, 350Mb genome
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Genetics of Speciationalong a Hybrid Zone
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Aquilegia (Columbine) NSF Genome Complexity

• Microarray floral 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 2007)

Scott Hodges (UCSB) Elena Kramer (Harvard) Magnus
Nordborg (USC) Justin Borevitz (U Chicago) Jeff
Tompkins (Clemson)
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Next Species.
Next Species.
Virtual Ecological Observatory
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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The Genomic Response Mediating the Environment
ORFa
Transcriptome Atlas
ORFb
start
AAAAA
deletion
M
M
M
M
M
M
SFP
M
M
M
M
M
M
SNP
SNP
SFP
SFP
conservation
Chromosome (bp)
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Which arrays should be used?
BAC array
cDNA array
Long oligo array
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Which arrays should be used?
Gene array
Exon array
Tiling array
35bp tile, 25mers 10bp gaps
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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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Universal Whole Genome Array
DNA
RNA
Gene/Exon Discovery Gene model correction Non-codi
ng/ micro-RNA
Chromatin Immunoprecipitation ChIP chip
Alternative Splicing
Methylation
Antisense transcription
Polymorphism SFPs Discovery/Genotyping
Transcriptome Atlas Expression levels Tissues
specificity
Comparative Genome Hybridization
(CGH) Insertion/Deletions Copy Number
Polymorphisms
RNA Immunoprecipitation RIP chip
Allele Specific Expression
Control for hybridization/genetic
polymorphisms to understand TRUE expression
variation
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Potential Deletions
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SFPs and CCGG Methylome
Genomic DNA
Col
HpaII digestion
Random labeling
Col
Genomic DNA
MspI digestion
Random labeling
Genomic DNA
Van
HpaII digestion
Random labeling
Van
Genomic DNA
MspI digestion
Random labeling
Full model Intensity genotype enzyme
genotype x enzyme
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Natural Copy Variation on Tiling Arrays
Segregating self seed from wild ME isolate (Early
Late)
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Chip genotyping of a Recombinant Inbred Line
Van x Col RIL 23
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http//www.plosone.org/
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NaturalVariation.org
NaturalVariation.org
USC Magnus Nordborg Paul Marjoram Max
Planck Detlef Weigel Scripps Sam
Hazen University of Michigan Sebastian Zoellner
USC Magnus Nordborg Paul Marjoram Max
Planck Detlef Weigel Scripps Sam
Hazen University of Michigan Sebastian Zoellner
University of Chicago Xu Zhang Yan Li Peter
Roycewicz Evadne Smith Megan Dunning Joy
Bergelson Michigan State Shinhan
Shiu Purdue Ivan Baxter
University of Chicago Xu Zhang Yan Li Peter
Roycewicz Evadne Smith Megan Dunning Joy
Bergelson Michigan State Shinhan
Shiu Purdue Ivan Baxter