Evolution2014 desert mouse talk

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Information about Evolution2014 desert mouse talk
Technology

Published on June 23, 2014

Author: macmanes

Source: slideshare.net

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This is the talk I gave at the 2014 Evolution conferences about the desert mouse project.

Understanding Adaptation to Deserts in Peromyscus eremicus Matthew MacManes University of New Hampshire ! Twitter: @PeroMHC macmanes@gmail.com

How do desert animals survive???

Climate Change ! ! ! It’s getting hotter It’s getting drier IPCC 2007 Report on Climate Change

Peromyscus eremicus: model species for the study of adaptation

Adaptation • Anatomy/Physiology/Metabolism/Behavior • Genetics • Allelic diffs • Expression diffs • Pathway diffs • Epigenetics

Peromyscus eremicus as a model organism • Genome sequence • 2.6Gb - Illumina short insert + mate pair + PacBio • 89k scaffolds, CEGMA 85% core genes NG50 max 30kb 610kb

Peromyscus eremicus as a model organism • Annotation • Automated + manual curation • Informatics, RNAseq CpGi liver brain testes kidney CpGiZbt20 Slc27a5

Branch-site model of positive selection P. eremicus P. maniculatus Mus Rattus

Branch-site model of positive selection Prostaglandin R3 ω=237 Best1 ω=999 Slc36a1 ω=1.2 Slc38a8 ω=999 Slc2a9 ω=254 ABC9A ω=123 (80 others) P. eremicus P. maniculatus Mus Rattus

Branch-site model of positive selection Prostaglandin R3 ω=237 Best1 ω=999 Slc36a1 ω=1.2 Slc38a8 ω=999 Slc2a9 ω=254 ABC9A ω=123 (80 others) P. eremicus P. maniculatus Mus Rattus Aquaporins absent

Captive animals - Experimental Genomics

Experimental Genomics Cool - water Cool + water Hot - water Hot + water ]Cool + RH Hot + RH

Experimental Genomics Cool - water Cool + water Hot - water Hot + water ] ! •RNAseq •ChIPseq •BiSeq Cool + RH Hot + RH

Experimental Genomics Cool - water Cool + water Hot - water Hot + water ] ! •RNAseq •ChIPseq •BiSeq RNAi CRISPR-Cas9 Cool + RH Hot + RH

Winter: ± water Cool - water ! Weight: -35% Na: 165 K: 7.0 BUN: 55 Cr: 0.3 Cool + water ! Weight: ~20gm Na: 151 K: 8.1 BUN: 46 Cr: 0.2 !

RNAseq - kidneys • RNAseq • 10-20M reads per sample • Mapped reads to genome using STAR • eXpress -> filter low abundance transcripts • DESeq2

RNAseq - kidneys wet dry 1e−01 1e+01 1e+03 1e+05 −3−2−10123 mean of normalized counts log2foldchange

Number of genes GO:0004872 GO:0005488 GO:0005576 GO:0022610 GO:0031012 PC00102 0 20 40 60 80 Gene Ontology Enrichment Extracellular Matrix Protein Extracellular Matrix Biological Adhesion Extracellular Region Binding Receptor Activity

Number of genes GO:0004872 GO:0005488 GO:0005576 GO:0022610 GO:0031012 PC00102 0 20 40 60 80 Gene Ontology Enrichment Extracellular Matrix Protein Extracellular Matrix Biological Adhesion Extracellular Region Binding Receptor Activity

350 400 450 500 155160165170 Na vs AQP2 AQP2 expression SerumSodium 350 400 450 500 105110115120125 Cl vs AQP2 AQP2 expression SerumChloride dry wet 350400450500 Aquaporin 2 FPMK PEER PEMA Mus Rattus ω=NS Combining Physiology, Expression, Nat. Selection

Combining Physiology, Expression, Nat. Selection 30 35 40 45 155160165170 Na vs Slc2a9 Slc2a9 expression SerumSodium 30 35 40 45 105110115120125 Cl vs Slc2a9 Slc2a9 expression SerumChloride dry wet 30354045 Slc2a9 FPMK PEER PEMA Mus Rattus ω=254

10 20 30 40 50 60 70 155160165170 Na vs Slc22a11 Slc22a11 expression SerumSodium 10 20 30 40 50 60 70 105110115120125 Cl vs Slc22a11 Slc22a11 expression SerumChloride dry wet 10203040506070 Slc22a11 FPMK PEER PEMA Mus Rattus ω=NS Combining Physiology, Expression, Nat. Selection

Summary • Summary • Strong signal of lineage-specific positive selection. • Physiological differences with water deprivation • Differential gene expression • Solute carriers seem important • Aquaporins might be boring…

Questions? @PeroMHC macmanes@gmail.com Poster Tonight #120 Lindsay Havens:Ladybugs www.spotaladybug.com Lightning talk: Rm 304 9:10AM

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