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EcoSystems Biology EcoSystems Biology
Justin Borevitz Ecology & Evolution University of Chicago Birds/insects in a cotton wood Fresh water and marine invasives Aquilegia, Arabidopsis, Mimulus? Deer mouse burrow 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 Temperate Grasslands, Savannas, & Shrublands NA0801 NA0802 NA0803 NA0804 NA0805 NA0806 NA0807 NA0808 NA0809 NA0810 NA0811 NA0812 NA0813 NA0814 NA0815 California Central Valley grasslands Canadian Aspen forests and parklands Central and Southern mixed grasslands Central forest-grasslands transition Central tall grasslands Edwards Plateau savanna Flint Hills tall grasslands Montana Valley and Foothill grasslands Nebraska Sand Hills mixed grasslands Northern mixed grasslands Northern short grasslands Northern tall grasslands Palouse grasslands Texas blackland prairies Western short grasslands
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Short, mixed, and Tall grass prairie
Fire maintains prairie-forest boundary
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Nielsen and Hole, 1963
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Lake Michigan sand dunes
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Are we getting to big for our house?
Footprint Dr. Mathis Wackernagel Eco-footprint helps us to understand that the impact of the human population on the planet is becoming increasingly large, or as the cartoon shows we are getting bigger and the planet is getting smaller! We are getting too big for our own house. Question for students Identify places on a world map where there is minimal evidence of human occupation? These are hard to find – some answers might include parts of Antarctica, the Arctic but even these most inhospitable parts of the globe have some human occupation.
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Who is getting what? Global equity Eco-footprint also helps us understand that a small proportion of the population is consuming a large amount of the resources. Approximately 20% of the global population consumes 80% of resources. Australia fits into the high-consuming category. Question for students: Can you identify 5 countries on a world map that each picture is referring to? Top picture: USA, Canada, Australia, New Zealand, United Kingdom. Bottom Picture: Mozambique, India, Ethiopia, Vietnam, Uganda
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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-Neutral Biofuels from
High-Diversity Low-Input Prairie Ecosystems by David Tilman University of Minnesota This has happened because of the incredible and recent dominance of humans on earth. Without ever planning for our impacts, we have come to dominate the earth – to own and determine the fate of every acre of land on its surface. This has occurred because of the dramatic recent rise in population and in per capita consumption. Why are humans now dominating global ecosystems? In essence, it comes from two major human needs: food and energy. I won’t talk today about energy use and global climate change because you are likely familiar with it and because many scientists working on global change believe that there is another issue that looms as large over humanity as climate change – and that is the impacts of global agricultural expansion. The best estimates are that. In 50 years, the earth will have 3 billion more people, each earning the projected 50% increase in global human population and increased per capita income during the coming 50 years will lead to at least a doubling in global demand for food by 2050. Photo credit: USDA, ARS, IS Photo Unit Image Number K1443-2; Ripening wheat on the Palouse hills of Washington. Photo by Doug Wilson.
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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.org/hapmap
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Local Population Structure
common haplotypes 149 Non singleton SNPs >6000 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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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 Sweden Spain
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Solar Calc II Kurt Spokas USDA-ARS Website Midwest Area (Morris,MN)
Version 2.0a June 2006 USDA-ARS Website Midwest Area (Morris,MN)
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Seasonal Flowering Time Response Seasonal Flowering Time Response
Kas/Col RILs Van/Col RILs 384 diverse Accessions Spain/Sweden Spring (early late) Fall (early late) * 10 Days 1000X
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Aquilegia (Columbines)
Recent adaptive radiation, 350Mb genome
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Genetics of Speciation along 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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Mediating the Environment
The Genomic Response Mediating the Environment ORFa Transcriptome Atlas ORFb start AAAAA deletion M M M M M M M M M M M M SFP 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 k SNPs, 1.6M tiling probes
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Universal Whole Genome Array
RNA DNA Gene/Exon Discovery Gene model correction Non-coding/ 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 CC*GG Methylome
Hpa msp Intensity Col Van * Hpa msp Col Van mSFP * * * Hpa msp Col Van Col Genomic DNA HpaII digestion Random labeling Col Genomic DNA MspI digestion Random labeling Van Genomic DNA 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 logLK20 AA 20198 AB 587 BB 13064
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NaturalVariation.org NaturalVariation.org Magnus Nordborg
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
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