This document summarizes research investigating the genetic basis of adaptation in American pikas to climate change. Key findings include: 1) There was no evidence that pikas are migrating upslope to track warming temperatures, suggesting upslope migration is not a viable strategy for coping with climate change. 2) Genomic scans identified 20 loci under selection across elevation gradients that may confer adaptation to changing climate variables like precipitation and temperature. 3) Precipitation and maximum summer temperature were identified as potential selective forces shaping adaptation at these loci.

1. Investigating the genetic basis of adaptation in a
climate change sensitive species: the American pika
Philippe Henry, November 21st 2011

2. The Anthropocene
Crutzen, P.J. (2002) Nature

3.  [CO2 ]

4. http://www.ipcc.ch/graphics/ar4-wg1/jpg/spm4.jpg
“Unequivocal” warming

5. http://www.ipcc.ch/graphics/ar4-wg1/jpg/spm5.jpg
Predictions

6. Biotic responses ?
Move Adapt Disappear
M. Bedart

7. Biotic responses ?
M. Bedart L. Gooch
Move Adapt Disappear

8. Biotic responses ?
M. Bedart L. Gooch C. Guthier
Move Adapt Disappear

9. Disappear = Extinction
Monteverde golden toad
(Bufo periglenes) 1966 - 1989
Pound et al. (1999) Nature; Thomas et al. (2004) Nature; Barnosky et al. (2011)
Nature E. Monk

10. 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

11. Move = Range shifts
Pole-ward movement of Animals
Parmesan (1996) Nature, Parmesan & Yohe (2003) Nature B. Bouton
6 km northward
range shift, 6 m
shifts in
elevation per
decade

12. Move = Range shifts
Fungi are also moving !
Amanita ovoidea is a Mediterranean species now found in the UK C. Gregg

13. 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)

14. The American Pika
Harbinger of climate change
Beever et al. (2003) Journal of Mammalogy; Beever et al. (2011) Global Change Biology;
Smith et al. (2004) Species
R. Howie

15. The American Pika
Small relative of Rabbits

16. Specialized Habitat
Talus slopes throughout North
American Mountains

17. Evidence of susceptibility
Low tolerance to
warm diurnal
temperatures
above 27° C
Mac Arthur & Wang (1974) Canadian Journal
of Zoology
Map with permission from David Hafner

18. Evidence of susceptibility
30% of populations
have become
extirpated in last
century
Beever et al. (2003) Journal of Mammalogy;
Beever et al. (2011) Global Change Biology;
Map with permission from David Hafner

19. Evidence of susceptibility
30% of populations
have become
extirpated in last
century
145 m upslope
range retraction in
the last decade
Beever et al. (2003) Journal of Mammalogy;
Beever et al. (2011) Global Change Biology;
Map with permission from David Hafner

20. Ideal system
Pikas
inhabit
sharp
elevation
gradients
Henry et al. (Submitted)
Northwest Science

21. Temperature loggers along
elevation gradietn
Average of
7°C difference
from top to
bottom of
transect.
Henry et al. (Submitted)
Northwest Science
Temperature°C

22. Natural experiment
Three elevation transects
as surrogates for predicted
climate change
Temperature°C

23. Hair Snares
Henry & Russello (2011) European Journal
of Wildlife Research; Henry et al. (2011)
Journal of Visualized Experiments

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

25. Hair Samples

26. 168 individuals
15
6
17
26
32
21
10
30
5
6

27. Lab Work

28. The Question
Are pikas more likely to
disperse to more favorable
conditions or adapt in situ?

29. 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

30. 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

31. 10 Microsatellite Loci
Neutral genetic variation (not under selection)
Reflect demographic patterns
Used to investigate population genetic structure and
gene flow
1. Migration across elevations
METHODS

32. 1. Migration across elevations
RESULTS: Isolated populations
Henryetal.(Submitted)PLoSOne

33. 1. Migration across elevations
RESULTS: No Evidence for upslope migration
Henryetal.(Submitted)PLoSOne

34. Henryetal.(Submitted)PLoSOne
1. Migration across elevations
CONCLUSION

35. 2. Genetic basis of adaptation across
elevation gradients
METHODS
1509 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

36. 2. Genetic basis of adaptation across
elevation gradients
METHODS
Environmental 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)

37. Fst/He
Markers Candidate balancing selection Candidate neutral Candidate positive selection
0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60
He
-0.1
0.0
0.1
0.2
0.3
0.4
0.5
0.6
Fst
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

38. Mean annual precipitation (R2
adj = 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
Low
Mid
High

39. Summer mean maximum temperature (R2
adj = 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

40. Summer mean maximum temperature (R2
adj = 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
Low
Mid
High

41. 2. Genetic basis of adaptation across
elevation gradients
CONCLUSION
Low
Mid
High

42. Summary
720 740 760 780 800 820 840
0.40.50.60.70.8
Mean Annual Precipitation (mm)
FrequencyofE38_T32_136
Fst/He
Markers Candidate balancing selection Candidate neutral Candidate positive selection
0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.6
He
-0.100
-0.075
-0.050
-0.025
0.000
0.025
0.050
0.075
0.100
0.125
0.150
0.175
0.200
Fst
PIKA_E31T39_55.6
PIKA_E33T37_107.4
PIKA_E33T37_109.5
PIKA_E43T37_100.6
PIKA_E38T32_85.8
PIKA_E38T37_259.7
PIKA_E44T44_111.4
Upslope 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

43. Next steps
Isolate and Clone outlier
AFLP fragments
Sanger sequencing of
clones to identify genes
under selection
Next Generation
Sequencing of pika
transcriptome and SNP
discovery

45. Upslope dispersal will likely not be
a good mitigation strategy
Henryetal.(Submitted)PLoSOne
1. Migration across elevations
RESULTS: No Evidence for upslope migration

46. Luikart et al. (2003) Nature Reviews
Genetics

47. Ouborg et al. (2010) Trends in
Genetics

48. Barret & Hoekstra (2011) Nature
Reviews Genetics

50. Chevin et al. (2010) PLoS Biology

51. Chevin et al. (2010) PLoS Biology