evolution2014 desert mouse talk
DESCRIPTION
This is the talk I gave at the 2014 Evolution conferences about the desert mouse project.TRANSCRIPT
Understanding Adaptation to Deserts in Peromyscus eremicus
Matthew MacManes University of New Hampshire !
Twitter: @PeroMHC [email protected]
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 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
!
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
Poster Tonight #120 Lindsay Havens:Ladybugs www.spotaladybug.com Lightning talk: Rm 304 9:10AM