Adaption to Climate Change: A Genetic Perspective from a Small Mammal in the Coast Mountains of BC.
Philippe Henry & Michael Russello
Talk Outline
• Conservation Biology
• Population genetics
• Population genomics
• Application to American pikas
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
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
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
Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change
Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change
Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change
Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change
Why conservation ?
• C
Intro
• Habitat loss, degradation and fragmentation
• Invasive species
• Overexploitation of natural resources
• Pollution and diseases
• Climate change
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
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
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
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
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
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
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)
Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics- Biophilia
• Ecosystem services
- Clean water / air- Economical benefits
Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics- Biophilia
• Ecosystem services
- Clean water / air- Economical benefits
Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics- Biophilia
• Ecosystem services
- Clean water / air- Economical benefits
Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics- Biophilia
• Ecosystem services
- Clean water / air- Economical benefits
Why conservation ?
• C
Intro
• Philosophical / Ethical
- Estetics- Biophilia
• Ecosystem services
- Clean water / air- Economical benefits
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
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
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
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
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
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
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
Conservation Genetics
• Genetic drift and inbreeding:
- Inbreeding depression
- Reduction in individual fitness
- Compromised evolutionary potential
Intro
Conservation Genetics
• Genetic drift and inbreeding:
- Inbreeding depression
- Reduction in individual fitness
- Compromised evolutionary potential
Intro
Conservation Genetics
• Genetic drift and inbreeding:
- Inbreeding depression
- Reduction in individual fitness
- Compromised evolutionary potential
Intro
Conservation Genetics
• Genetic drift and inbreeding:
- Inbreeding depression
- Reduction in individual fitness
- Compromised evolutionary potential
Intro
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
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
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
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
• 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 GeneticsIntro
• 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 GeneticsIntro
• 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 GeneticsIntro
• 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 GeneticsIntro
• 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 GeneticsIntro
• 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 GeneticsIntro
Genetics -> GenomicsIntro
• 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 GenomicsIntro
• 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 GenomicsIntro
• 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 GenomicsIntro
• 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 GenomicsIntro
• Impact of habitat fragmentation or climate change on selectively important variation
• Mechanisms underlying inbreeding depression
• Role of gene-environment interaction
• Gene expression
Conservation GenomicsIntro
• Impact of habitat fragmentation or climate change on selectively important variation
• Mechanisms underlying inbreeding depression
• Role of gene-environment interaction
• Gene expression
Conservation GenomicsIntro
• Impact of habitat fragmentation or climate change on selectively important variation
• Mechanisms underlying inbreeding depression
• Role of gene-environment interaction
• Gene expression
Conservation GenomicsIntro
• Impact of habitat fragmentation or climate change on selectively important variation
• Mechanisms underlying inbreeding depression
• Role of gene-environment interaction
• Gene expression
Conservation GenomicsIntro
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
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
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
Study species
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)
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)
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)
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)
Study species
Distribution
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)
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)
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)
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)
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)
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
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
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
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
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
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
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
Objectives
• Shed light on population genetic structure and demographic history
• Identify genomic region under selection
Objectives
• Shed light on population genetic structure and demographic history
• Identify genomic region under selection
Study siteMethods
Study site
10 KM
The Hill~ 1500 m
~ 800 m
~ 300 m
2 km
Methods
Nusatsum~ 1500 m
~ 800 m
2 km
Methods
Clayton Falls – M. Gurr~ 1500 m
~ 0 m
2 km
Methods
Sampling design
25 m25 m
Methods
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
Sampling
Sampling
Sampling
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
Microsatellite genotypingMethods
- Popular marker in population genetics
- Neutral
- Highly variable
Microsatellite genotyping
-10 microsatellite loci amplified in our 270 DNA samples
- Resulting in a probability of identity of 0.00029
Methods
AFLP genotyping
- Markers distributed throughout the genome (genome scan)
- Anonymous bands
Methods
AFLP genotyping
- 20 selective primer pairs
- 1509 bands amplified in our 270 DNA samples
Methods
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
Analyses
• Identification of “outlier” loci (under selection)
• Identification of main driving force through which selection acts
Methods
AFLP
Natural History
25 m
- Up to 7 different individuals sampled in the same hair snare
Results
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
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
155 m
Population StructureResults
Population StructureResults
Genetic variabilityResults
* * *
InbreedingResults
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
~ 1500 m
~ 800 m
~ 300 m
2 km
Outliers HillResults
~ 1500 m
~ 800 m
~ 300 m
2 km
Outliers HillResults
Outliers Nusatsum
~ 1500 m
~ 800 m
2 km
Methods
Outliers Nusatsum
~ 1500 m
~ 800 m
2 km
Methods
Outliers Clayton – M. Gurr~ 1500 m
~ 0 m
2 km
Methods
Outliers Clayton – M. Gurr~ 1500 m
~ 0 m
2 km
Methods
Summary OutliersMethods
TTC________E33T37_58_________ACT
TCG________E38T37_289_______ACT
Summary OutliersMethods
6.4°C2183mm
2.2°C2863mm
2.4°C2889mm
3.8°C2571mm
4.7°C711mm
2.7°C706mm
0.3°C848mm
Next step
• Cloning of outlier AFLP fragments
• BLAST against rabbit genome to identify genomic region under selection
• Next generation transcriptome sequencing
- SNP discovery
Next step
• Cloning of outlier AFLP fragments
• BLAST against rabbit genome to identify genomic region under selection
• Next generation transcriptome sequencing
- SNP discovery
Next step
• Cloning of outlier AFLP fragments
• BLAST against rabbit genome to identify genomic region under selection
• Next generation transcriptome sequencing
- SNP discovery
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
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
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
Acknowledgements
- Russello Lab
- Mary Peacock
- Kurt Galbreath
- Tweedsmuir Provincial Park