investigating the genetic basis of adapation
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Investigating the genetic basis of adaptation in a climate change sensitive species: the American pika
Philippe Henry, November 21st 2011
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The Anthropocene
Crutzen, P.J. (2002) Nature
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[CO2 ]
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“Unequivocal” warming
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Predictions
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Biotic responses ?
Move Adapt Disappear
M. Bedart
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Biotic responses ?
M. Bedart L. Gooch
Move Adapt Disappear
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Biotic responses ?
M. Bedart L. Gooch C. Guthier
Move Adapt Disappear
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Disappear = Extinction
Monteverde golden toad (Bufo periglenes) 1966 - 1989
Pound et al. (1999) Nature; Thomas et al. (2004) Nature; Barnosky et al. (2011) NatureE. Monk
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Move = Range shifts
Upward movement of Alpine plants
Walther et al. (2005) TREE; Frei et al. (2010) Botanica Helvetica
10 m shift in elevation per
decade
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Move = Range shifts
Pole-ward movement of AnimalsParmesan (1996) Nature, Parmesan & Yohe (2003) Nature B. Bouton
6 km northward range shift, 6 m
shifts in elevation per decade
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Move = Range shifts
Fungi are also moving !Amanita ovoidea is a Mediterranean species now found in the UK C. Gregg
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Adapt = Evolution
Réale et al (2003) Proc R Soc B A. De la Cruz
Advanced breeding time by
18 days per decade
(6 days per generations)
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The American Pika
Harbinger of climate changeBeever et al. (2003) Journal of Mammalogy; Beever et al. (2011) Global Change Biology;
Smith et al. (2004) SpeciesR. Howie
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The American Pika
Small relative of Rabbits
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Specialized Habitat
Talus slopes throughout North American Mountains
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Evidence of susceptibility
Low tolerance towarm diurnaltemperaturesabove 27° C
Mac Arthur & Wang (1974) Canadian Journal of Zoology
Map with permission from David Hafner
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Evidence of susceptibility
30% of populations
have becomeextirpated in lastcentury
Beever et al. (2003) Journal of Mammalogy; Beever et al. (2011) Global Change Biology;
Map with permission from David Hafner
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Evidence of susceptibility
30% of populations
have becomeextirpated in lastcentury
145 m upsloperange retraction inthe last decadeBeever et al. (2003) Journal of Mammalogy;
Beever et al. (2011) Global Change Biology; Map with permission from David Hafner
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Ideal system
Pikasinhabitsharpelevationgradients
Henry et al. (Submitted) Northwest Science
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Temperature loggers along elevation gradietn
Average of7°C differencefrom top tobottom oftransect.
Henry et al. (Submitted) Northwest Science
Tem
pera
ture
°C
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Natural experimentThree elevation transectsas surrogates for
predictedclimate change
Tem
pera
ture
°C
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Hair Snares
Henry & Russello (2011) European Journal of Wildlife Research; Henry et al. (2011) Journal of
Visualized Experiments
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Noninvasive sampling
Henry & Russello (2011) European Journal of Wildlife Research; Henry et al. (2011) Journal of Visualized ExperimentsA. Henry
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Hair Samples
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168 individuals
156
17
2632
21
10
30
5
6
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Lab Work
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The QuestionAre pikas more likely to disperse to more favorable conditions or adapt in situ?
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Objectives
1. Assess whether upslope migration may represent a mitigation strategy to cope with climate change
2. Investigate the genetic basis of adaptation. Specifically detect genomic regions under selection and identify the environmental drivers
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Objectives
1. Assess whether upslope migration may represent a mitigation strategy to cope with climate change
2. Investigate the genetic basis of adaptation. Specifically detecting genomic regions under selection and identifying the environmental drivers
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10 Microsatellite Loci
Neutral genetic variation (not under selection)
Reflect demographic patterns
Used to investigate population genetic structure and gene flow
1. Migration across elevationsMETHODS
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1. Migration across elevationsRESULTS: Isolated populations
Henr
y et
al.
(Sub
mitt
ed) P
LoS
One
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1. Migration across elevationsRESULTS: No Evidence for upslope
migration
Henr
y et
al.
(Sub
mitt
ed) P
LoS
One
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Henr
y et
al.
(Sub
mitt
ed) P
LoS
One
1. Migration across elevationsCONCLUSION
Upslope dispersal will likely not
be a good mitigation strategy
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2. Genetic basis of adaptation across elevation gradients
METHODS1509 Amplified Fragment Length Polymorphism (AFLP) Loci
Generates a large number of markers
“Genomic scan”
Doesn’t require sequence information
Ideal for non-model organisms
Anonymous
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2. Genetic basis of adaptation across elevation gradients
METHODSEnvironmental variables
CLIMATEBC:
Altitude (ALT)Mean annual temperature (MAT)Mean annual precipitation (MAP)Precipitation as Snow (PAS)Summer mean maximum temperature (Tmax)Winter mean minimum temperature (Tmin)
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Loci with unusually high divergence Signature of selection
1.5 % of the genome showed outlier behaviour
2. Genetic basis of adaptation across elevation gradients
RESULTS
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Mean annual precipitation (R2adj = 0.82, F-test, F=24.6, DF=5, p=0.008)
High frequency of allele at low elevations may confer adaptation to drier conditions
2. Genetic basis of adaptation across elevation gradients
RESULTS
LowMid
High
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Summer mean maximum temperature (R2adj = 0.81, F-test, F=23, DF=5, p=0.009)
High frequency of allele at low elevations may confer adaptation to warmer conditions
2. Genetic basis of adaptation across elevation gradients
RESULTS
Low
Mid
High
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Summer mean maximum temperature (R2adj = 0.79, F-test, F=20.28, DF=5, p=0.01)
Low frequency at low elevation, may confer adaptation to colder temperatures
2. Genetic basis of adaptation across elevation gradients
RESULTS
LowMid
High
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2. Genetic basis of adaptation across elevation gradients
CONCLUSION
LowMid
HighEvidence for local adaptation, driven
by temperature and precipitation
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SummaryUpslope migrations will likely not represent a viable strategy to cope with anticipated climate change
20 loci were identified as under selection and may thus confer an advantage in the face of climate change.
MAP and Tmax were identified as potential selective forces
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Next stepsIsolate and Clone outlier AFLP fragments
Sanger sequencing of clones to identify genes under selection
Next Generation Sequencing of pika transcriptome and SNP discovery
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Upslope dispersal will likely not be a good mitigation strategy
Henr
y et
al.
(Sub
mitt
ed) P
LoS
One
1. Migration across elevationsRESULTS: No Evidence for upslope
migration
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Luikart et al. (2003) Nature Reviews Genetics
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Ouborg et al. (2010) Trends in Genetics
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Barret & Hoekstra (2011) Nature Reviews Genetics
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Chevin et al. (2010) PLoS Biology
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Chevin et al. (2010) PLoS Biology