investigating the genetic basis of adapation

Investigating the genetic basis of adaptation in a climate change sensitive species: the American pika

Philippe Henry, November 21st 2011

The Anthropocene

Crutzen, P.J. (2002) Nature

[CO2 ]

http

://ww

w.ip

cc.c

h/gr

aphi

cs/a

r4-w

g1/jp

g/sp

m4.

jpg

“Unequivocal” warming

http

://ww

w.ip

cc.c

h/gr

aphi

cs/a

r4-w

g1/jp

g/sp

m5.

jpg

Predictions

Biotic responses ?

Move Adapt Disappear

M. Bedart

Biotic responses ?

M. Bedart L. Gooch

Move Adapt Disappear

Biotic responses ?

M. Bedart L. Gooch C. Guthier

Move Adapt Disappear

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

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

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

Move = Range shifts

Fungi are also moving !Amanita ovoidea is a Mediterranean species now found in the UK C. Gregg

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)

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

The American Pika

Small relative of Rabbits

Specialized Habitat

Talus slopes throughout North American Mountains

Evidence of susceptibility

Low tolerance towarm diurnaltemperaturesabove 27° C

Mac Arthur & Wang (1974) Canadian Journal of Zoology

Map with permission from David Hafner

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

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

Ideal system

Pikasinhabitsharpelevationgradients

Henry et al. (Submitted) Northwest Science

Temperature loggers along elevation gradietn

Average of7°C differencefrom top tobottom oftransect.

Henry et al. (Submitted) Northwest Science

Tem

pera

ture

°C

Natural experimentThree elevation transectsas surrogates for

predictedclimate change

Tem

pera

ture

°C

Hair Snares

Henry & Russello (2011) European Journal of Wildlife Research; Henry et al. (2011) Journal of

Visualized Experiments

Noninvasive sampling

Henry & Russello (2011) European Journal of Wildlife Research; Henry et al. (2011) Journal of Visualized ExperimentsA. Henry

Hair Samples

168 individuals

156

17

2632

21

10

30

5

6

Lab Work

The QuestionAre pikas more likely to disperse to more favorable conditions or adapt in situ?

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

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

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

1. Migration across elevationsRESULTS: Isolated populations

Henr

y et

al.

(Sub

mitt

ed) P

LoS

One

1. Migration across elevationsRESULTS: No Evidence for upslope

migration

Henr

y et

al.

(Sub

mitt

ed) P

LoS

One

Henr

y et

al.

(Sub

mitt

ed) P

LoS

One

1. Migration across elevationsCONCLUSION

Upslope dispersal will likely not

be a good mitigation strategy

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

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)

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

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

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

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

2. Genetic basis of adaptation across elevation gradients

CONCLUSION

LowMid

HighEvidence for local adaptation, driven

by temperature and precipitation

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

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

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

Luikart et al. (2003) Nature Reviews Genetics

Ouborg et al. (2010) Trends in Genetics

Barret & Hoekstra (2011) Nature Reviews Genetics

Chevin et al. (2010) PLoS Biology

Chevin et al. (2010) PLoS Biology