Presented at the biology seminar series, UBC okangan campus

1. Adaption to Climate Change: A Genetic Perspective
from a Small Mammal in the Coast Mountains of BC.
Philippe Henry & Michael Russello

2. Talk Outline
• Conservation Biology
• Population genetics
• Population genomics
• Application to American pikas

3. Conservation Biology
• C
Intro
• Scientific study of the nature and status of
the Earth’s biodiversity
• Aim to preserve ecosystems, species and
evolutionary potential (genetics)
• Termed coined in 1978 at UCSD by Michael
Soulé and others

4. Conservation Biology
• C
Intro
• Scientific study of the nature and status of
the Earth’s biodiversity
• Aim to preserve ecosystems, species and
evolutionary potential (genetics)
• Termed coined in 1978 at UCSD by Michael
Soulé and others

5. Conservation Biology
• C
Intro
• Scientific study of the nature and status of
the Earth’s biodiversity
• Aim to preserve ecosystems, species and
evolutionary potential (genetics)
• Termed coined in 1978 at UCSD by Michael
Soulé and others

6. Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change

7. Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change

8. Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change

9. Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change

10. Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change

11. Why conservation ?
• C
Intro
• Sixth mass extinction crisis
- 1 in 4 mammal
- 1 in 4 conifer
- 1 in 3 amphibian
- 1 in 8 birds are threatened
- extinction rates are 1000 times the norm
- at this pace, mass extinction will occur in 200 - 500
years

12. Why conservation ?
• C
Intro
• Sixth mass extinction crisis
- 1 in 4 mammal
- 1 in 4 conifer
- 1 in 3 amphibian
- 1 in 8 birds are threatened
- extinction rates are 1000 times the norm
- at this pace, mass extinction will occur in 200 - 500
years

13. Why conservation ?
• C
Intro
• Sixth mass extinction crisis
- 1 in 4 mammal
- 1 in 4 conifer
- 1 in 3 amphibian
- 1 in 8 birds are threatened
- extinction rates are 1000 times the norm
- at this pace, mass extinction will occur in 200 - 500
years

14. Why conservation ?
• C
Intro
• Sixth mass extinction crisis
- 1 in 4 mammal
- 1 in 4 conifer
- 1 in 3 amphibian
- 1 in 8 birds are threatened
- extinction rates are 1000 times the norm
- at this pace, mass extinction will occur in 200 - 500
years

15. Why conservation ?
• C
Intro
• Sixth mass extinction crisis
- 1 in 4 mammal
- 1 in 4 conifer
- 1 in 3 amphibian
- 1 in 8 birds are threatened
- extinction rates are 1000 times the norm
- at this pace, mass extinction will occur in 200 - 500
years

16. Why conservation ?
• C
Intro
• Sixth mass extinction crisis
- 1 in 4 mammal
- 1 in 4 conifer
- 1 in 3 amphibian
- 1 in 8 birds are threatened
- extinction rates are 1000 times the norm
- at this pace, mass extinction will occur in 200 - 500
years

17. Why conservation ?
• C
Intro
• Sixth mass extinction crisis
- 1 in 4 mammal
- 1 in 4 conifer
- 1 in 3 amphibian
- 1 in 8 birds are threatened
- extinction rates are 1000 times the norm
- at this pace, mass extinction will occur in 200 - 500
years (Barnosky et al 2011, Nature)

18. Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics
- Biophilia
• Ecosystem services
- Clean water / air
- Economical benefits

19. Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics
- Biophilia
• Ecosystem services
- Clean water / air
- Economical benefits

20. Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics
- Biophilia
• Ecosystem services
- Clean water / air
- Economical benefits

21. Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics
- Biophilia
• Ecosystem services
- Clean water / air
- Economical benefits

22. Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics
- Biophilia
• Ecosystem services
- Clean water / air
- Economical benefits

23. Conservation Genetics
• Arose in the 1980’s as a crisis discipline
• With the aim to preserve species
evolutionary potential (genetic variation)
• Under the central tenet that small, isolated
populations are at risk of genetic erosion
Intro

24. Conservation Genetics
• Arose in the 1980’s as a crisis discipline
• With the aim to preserve species
evolutionary potential (genetic variation)
• Under the central tenet that small, isolated
populations are at risk of genetic erosion
Intro

25. Conservation Genetics
• Arose in the 1980’s as a crisis discipline
• With the aim to preserve species
evolutionary potential (genetic variation)
• Under the central tenet that small, isolated
populations are at risk of genetic erosion
Intro

26. Conservation Genetics
• Small population size:
- Dominated by genetic drift and inbreeding
- Genetic drift: random fixation and loss of
alleles, whether adaptive or deleterious
- Inbreeding: increasing homozygosity
Intro

27. Conservation Genetics
• Small population size:
- Dominated by genetic drift and inbreeding
- Genetic drift: random fixation and loss of
alleles, whether adaptive or deleterious
- Inbreeding: increasing homozygosity
Intro

28. Conservation Genetics
• Small population size:
- Dominated by genetic drift and inbreeding
- Genetic drift: random fixation and loss of
alleles, whether adaptive or deleterious
- Inbreeding: increasing homozygosity
Intro

29. Conservation Genetics
• Small population size:
- Dominated by genetic drift and inbreeding
- Genetic drift: random fixation and loss of
alleles, whether adaptive or deleterious
- Inbreeding: increasing homozygosity
Intro

30. Conservation Genetics
• Genetic drift and inbreeding:
- Inbreeding depression
- Reduction in individual fitness
- Compromised evolutionary potential
Intro

31. Conservation Genetics
• Genetic drift and inbreeding:
- Inbreeding depression
- Reduction in individual fitness
- Compromised evolutionary potential
Intro

32. Conservation Genetics
• Genetic drift and inbreeding:
- Inbreeding depression
- Reduction in individual fitness
- Compromised evolutionary potential
Intro

33. Conservation Genetics
• Genetic drift and inbreeding:
- Inbreeding depression
- Reduction in individual fitness
- Compromised evolutionary potential
Intro

34. Conservation Genetics
• Genetic variation = evolutionary potential of
populations or species
• There are two principal types of genetic
variation:
- Neutral  (reflects demographic patterns)
- Adaptive  (reflects variation under natural
selection)
Intro

35. Conservation Genetics
• Genetic variation = evolutionary potential of
populations or species
• There are two principal types of genetic
variation:
- Neutral  (reflects demographic patterns)
- Adaptive  (reflects variation under natural
selection)
Intro

36. Conservation Genetics
• Genetic variation = evolutionary potential of
populations or species
• There are two principal types of genetic
variation:
- Neutral  (reflects demographic patterns)
- Adaptive  (reflects variation under natural
selection)
Intro

37. Conservation Genetics
• Genetic variation = evolutionary potential of
populations or species
• There are two principal types of genetic
variation:
- Neutral  (reflects demographic patterns)
- Adaptive  (reflects variation under natural
selection)
Intro

38. • Neutral genetic variation:
- population genetic structure
- demographic events, (bottlenecks and population
expansions)
- migration and gene flow
 Valuable information to help prioritize
populations for conservation efforts
X. Does not generally inform on long term
evolutionary potential of populations
Conservation Genetics
Intro

39. • Neutral genetic variation:
- population genetic structure
- demographic events, (bottlenecks and population
expansions)
- migration and gene flow
 Valuable information to help prioritize
populations for conservation efforts
X. Does not generally inform on long term
evolutionary potential of populations
Conservation Genetics
Intro

40. • Neutral genetic variation:
- population genetic structure
- demographic events, (bottlenecks and population
expansions)
- migration and gene flow
 Valuable information to help prioritize
populations for conservation efforts
X. Does not generally inform on long term
evolutionary potential of populations
Conservation Genetics
Intro

41. • Neutral genetic variation:
- population genetic structure
- demographic events, (bottlenecks and population
expansions)
- migration and gene flow
 Valuable information to help prioritize
populations for conservation efforts
X. Does not generally inform on long term
evolutionary potential of populations
Conservation Genetics
Intro

42. • Neutral genetic variation:
- population genetic structure
- demographic events, (bottlenecks and population
expansions)
- migration and gene flow
 Valuable information to help prioritize
populations for conservation efforts
X. Does not generally inform on long term
evolutionary potential of populations
Conservation Genetics
Intro

43. • Neutral genetic variation:
- population genetic structure
- demographic events, (bottlenecks and population
expansions)
- migration and gene flow
 Valuable information to help prioritize
populations for conservation efforts
X. Does not generally inform on long term
evolutionary potential of populations
Conservation Genetics
Intro

44. Genetics -> Genomics
Intro

45. • Complement conservation genetics with the use of
a large number of molecular markers
• Concerned with the characterization of adaptive
genetic variation
- shed light on the evolutionary potential of
populations
- assist management decisions, especially with
regard to adaptation to environmental changes
Conservation Genomics
Intro

46. • Complement conservation genetics with the use of
a large number of molecular markers
• Concerned with the characterization of adaptive
genetic variation
- shed light on the evolutionary potential of
populations
- assist management decisions, especially with
regard to adaptation to environmental changes
Conservation Genomics
Intro

47. • Complement conservation genetics with the use of
a large number of molecular markers
• Concerned with the characterization of adaptive
genetic variation
- shed light on the evolutionary potential of
populations
- assist management decisions, especially with
regard to adaptation to environmental changes
Conservation Genomics
Intro

48. • Complement conservation genetics with the use of
a large number of molecular markers
• Concerned with the characterization of adaptive
genetic variation
- shed light on the evolutionary potential of
populations
- assist management decisions, especially with
regard to adaptation to environmental changes
Conservation Genomics
Intro

49. • Impact of habitat fragmentation or climate change
on selectively important variation
• Mechanisms underlying inbreeding depression
• Role of gene-environment interaction
• Gene expression
Conservation Genomics
Intro

50. • Impact of habitat fragmentation or climate change
on selectively important variation
• Mechanisms underlying inbreeding depression
• Role of gene-environment interaction
• Gene expression
Conservation Genomics
Intro

51. • Impact of habitat fragmentation or climate change
on selectively important variation
• Mechanisms underlying inbreeding depression
• Role of gene-environment interaction
• Gene expression
Conservation Genomics
Intro

52. • Impact of habitat fragmentation or climate change
on selectively important variation
• Mechanisms underlying inbreeding depression
• Role of gene-environment interaction
• Gene expression
Conservation Genomics
Intro

53. Climate change and the
American pika
• Species sensitive to high ambient temperatures
• Contemporary climate warming may be partly
responsible for extirpation of its southern
populations
• Good candidate to study the genetic basis of
local adaptation since it is distributed along
altitudinal gradients in BC

54. Climate change and the
American pika
• Species sensitive to high ambient temperatures
• Contemporary climate warming may be partly
responsible for extirpation of its southern
populations
• Good candidate to study the genetic basis of
local adaptation since it is distributed along
altitudinal gradients in BC

55. Climate change and the
American pika
• Species sensitive to high ambient temperatures
• Contemporary climate warming may be partly
responsible for extirpation of its southern
populations
• Good candidate to study the genetic basis of
local adaptation since it is distributed along
altitudinal gradients in BC

56. Study species

57. Study species
Taxonomy
• American Pika: Ochotona princeps
• 5 ssp found throughout western NA
• 2 ssp described in BC
• Taxonomy based on morphology, mitochondrial DNA
lineage and call dialects (Hafner & Smith, 2010)

58. Study species
Taxonomy
• American Pika: Ochotona princeps
• 5 ssp found throughout western NA
• 2 ssp described in BC
• Taxonomy based on morphology, mitochondrial DNA
lineage and call dialects (Hafner & Smith, 2010)

59. Study species
Taxonomy
• American Pika: Ochotona princeps
• 5 ssp found throughout western NA
• 2 ssp described in BC
• Taxonomy based on morphology, mitochondrial DNA
lineage and call dialects (Hafner & Smith, 2010)

60. Study species
Taxonomy
• American Pika: Ochotona princeps
• 5 ssp found throughout western NA
• 2 ssp described in BC
• Taxonomy based on morphology, mitochondrial DNA
lineage and call dialects (Hafner & Smith, 2010)

61. Study species
Distribution

62. Study species
Life History
• Habitat specific to Talus slopes
• Do not hibernate and make hay-piles
• Defend individual territories
• 2-3 young successfully weaned per year
• Relatively long-lived (5-7 years)

63. Study species
Life History
• Habitat specific to Talus slopes
• Do not hibernate and make hay-piles
• Defend individual territories
• 2-3 young successfully weaned per year
• Relatively long-lived (5-7 years)

64. Study species
Life History
• Habitat specific to Talus slopes
• Do not hibernate and make hay-piles
• Defend individual territories
• 2-3 young successfully weaned per year
• Relatively long-lived (5-7 years)

65. Study species
Life History
• Habitat specific to Talus slopes
• Do not hibernate and make hay-piles
• Defend individual territories
• 2-3 young successfully weaned per year
• Relatively long-lived (5-7 years)

66. Study species
Life History
• Habitat specific to Talus slopes
• Do not hibernate and make hay-piles
• Defend individual territories
• 2-3 young successfully weaned per year
• Relatively long-lived (5-7 years)

67. Study species
Dispersal
• Young are generally philopatric
• If no territories are available, young will disperse
• Mortality during dispersal is high
• Evidence for gene-flow up to 3km

68. Study species
Dispersal
• Young are generally philopatric
• If no territories are available, young will disperse
• Mortality during dispersal is high
• Evidence for gene-flow up to 3km

69. Study species
Dispersal
• Young are generally philopatric
• If no territories are available, young will disperse
• Mortality during dispersal is high
• Evidence for gene-flow up to 3km

70. Study species
Dispersal
• Young are generally philopatric
• If no territories are available, young will disperse
• Mortality during dispersal is high
• Evidence for gene-flow up to 3km

71. Study species
Susceptibility to climate change
• Widespread distribution during Pleistocene
• Contemporary climate warming may be responsible
for the extirpation of one quarter of Pika
populations in the Great Basin USA
• Their distribution has shifted 100m upslope per
decade

72. Study species
Susceptibility to climate change
• Widespread distribution during Pleistocene
• Contemporary climate warming may be responsible
for the extirpation of one quarter of Pika
populations in the Great Basin USA
• Their distribution has shifted 100m upslope per
decade

73. Study species
Susceptibility to climate change
• Widespread distribution during Pleistocene
• Contemporary climate warming may be responsible
for the extirpation of one quarter of Pika
populations in the Great Basin USA
• Their distribution has shifted 100m upslope per
decade

74. Objectives
• Shed light on population genetic
structure and demographic history
• Identify genomic region under
selection

75. Objectives
• Shed light on population genetic
structure and demographic history
• Identify genomic region under
selection

76. Study site
Methods

77. Study site
10 KM

78. The Hill
~ 1500 m
~ 800 m
~ 300 m
2 km
Methods

79. Nusatsum
~ 1500 m
~ 800 m
2 km
Methods

80. Clayton Falls – M. Gurr
~ 1500 m
~ 0 m
2 km
Methods

81. Sampling design
25 m25 m
Methods

82. Sampling design
25 m25 m
- 15 - 30 hair snares set up at each site
- Collected 300 individual hair samples
- 270 high quality DNA samples
Methods

83. Sampling

84. Sampling

85. Sampling

86. Labwork
• DNA extracted from 300 hair samples
collected in the summers 2008, 2009 and
2010
• 2 types of genetic markers amplified by
PCR:
- microsatellites
- AFLP

87. Microsatellite genotyping
Methods
- Popular marker in population genetics
- Neutral
- Highly variable

88. Microsatellite genotyping
-10 microsatellite loci amplified in our 270 DNA samples
- Resulting in a probability of identity of 0.00029
Methods

89. AFLP genotyping
- Markers distributed throughout the genome (genome scan)
- Anonymous bands
Methods

90. AFLP genotyping
- 20 selective primer pairs
- 1509 bands amplified in our 270 DNA samples
Methods

91. Analyses
• Identify individuals based on multilocus
genotypes = DNA fingerprint
• Assessment of population genetic structure
• Calculations of genetic diversity indices
• Estimates of demographic history
Methods
Microsatellites

92. Analyses
• Identification of “outlier” loci (under
selection)
• Identification of main driving force through
which selection acts
Methods
AFLP

93. Natural History
25 m
- Up to 7 different individuals sampled
in the same hair snare
Results

94. Natural History
25 m
- Up to 7 different individuals sampled
In the same hair snare
- Neighboring hair snares recovered
the same individuals in 4 cases
Results

95. Natural History
25 m
- Up to 4 different individuals
sampled in the same hair snare
- Neighboring hair snares recovered
the same individuals in 4 cases
- In one case, the same individual
was sampled 155m apart
Results

96. Population Structure
Results

97. Population Structure
Results

98. Genetic variability
Results
* * * 

99. Inbreeding
Results

100. Bottleneck
Test High 1+2 Mid Low 1 Low 2
Wilcoxon * * * NS
Mode Shift * NS NS NS
M-ratio NS NS NS NS
Results
No evidence for reduction
in population size

101. ~ 1500 m
~ 800 m
~ 300 m
2 km
Outliers Hill
Results

102. ~ 1500 m
~ 800 m
~ 300 m
2 km
Outliers Hill
Results

103. Outliers Nusatsum
~ 1500 m
~ 800 m
2 km
Methods

104. Outliers Nusatsum
~ 1500 m
~ 800 m
2 km
Methods

105. Outliers Clayton – M. Gurr
~ 1500 m
~ 0 m
2 km
Methods

106. Outliers Clayton – M. Gurr
~ 1500 m
~ 0 m
2 km
Methods

107. Summary Outliers
Methods
TTC________E33T37_58_________ACT
TCG________E38T37_289_______ACT

108. Summary Outliers
Methods
6.4°C
2183mm
2.2°C
2863mm
2.4°C
2889mm
3.8°C
2571mm
4.7°C
711mm
2.7°C
706mm
0.3°C
848mm

109. Next step
• Cloning of outlier AFLP fragments
• BLAST against rabbit genome to identify genomic
region under selection
• Next generation transcriptome sequencing
- SNP discovery

110. Next step
• Cloning of outlier AFLP fragments
• BLAST against rabbit genome to identify genomic
region under selection
• Next generation transcriptome sequencing
- SNP discovery

111. Next step
• Cloning of outlier AFLP fragments
• BLAST against rabbit genome to identify genomic
region under selection
• Next generation transcriptome sequencing
- SNP discovery

112. Overall significance
• Hill and Nusatsum / Clayton- M.Gurr represent
two different “populations”
• Lowest genetic variability found at Clayton-
M.Gurr
-> Priority population
• Different outliers found in the different
transects. Need to investigate the effect of
environmental variables on genes

113. Overall significance
• Hill and Nusatsum / Clayton- M.Gurr represent
two different “populations”
• Lowest genetic variability found at Clayton-
M.Gurr
-> Priority population
• Different outliers found in the different
transects. Need to investigate the effect of
environmental variables on genes

114. Overall significance
• Hill and Nusatsum / Clayton- M.Gurr represent
two different “populations”
• Lowest genetic variability found at Clayton-
M.Gurr
-> Priority population
• Different outliers found in the different
transects. Need to investigate the effect of
environmental variables on genes

115. Acknowledgements
- Russello Lab
- Mary Peacock
- Kurt Galbreath
- Tweedsmuir Provincial Park