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

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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 selectionP. 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

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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

−10

12

3

mean of normalized counts

log 2

fold

cha

nge

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

155

160

165

170

Na vs AQP2

AQP2 expression

Seru

m S

odiu

m

350 400 450 500

105

110

115

120

125

Cl vs AQP2

AQP2 expression

Seru

m C

hlor

ide

dry wet

350

400

450

500

Aquaporin 2

FPM

K

PEER

PEMA

Mus

Rattus

ω=NS

Combining Physiology, Expression, Nat. Selection

Combining Physiology, Expression, Nat. Selection

30 35 40 45

155

160

165

170

Na vs Slc2a9

Slc2a9 expression

Seru

m S

odiu

m

30 35 40 45

105

110

115

120

125

Cl vs Slc2a9

Slc2a9 expression

Seru

m C

hlor

ide

dry wet

3035

4045

Slc2a9

FPM

K

PEER

PEMA

Mus

Rattus

ω=254

10 20 30 40 50 60 70

155

160

165

170

Na vs Slc22a11

Slc22a11 expression

Seru

m S

odiu

m

10 20 30 40 50 60 70

105

110

115

120

125

Cl vs Slc22a11

Slc22a11 expression

Seru

m C

hlor

ide

dry wet

1020

3040

5060

70

Slc22a11

FPM

K

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

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