adaptation to climage change: a genetic perspective

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

• 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 ?

• Habitat loss, degradation and fragmentation

• Invasive species

• Overexploitation of natural resources

• Pollution and diseases

• Climate change

Why conservation ?

• Climate change

Why conservation ?

• Climate change

Why conservation ?

• Climate change

Why conservation ?

• Climate change

Why conservation ?

• 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 ?

- at this pace, mass extinction will occur in 200 - 500 years (Barnosky et al 2011, Nature)

Why conservation ?

• Philosophical / Ethical

- Estetics- Biophilia

• Ecosystem services

- Clean water / air- Economical benefits

Why conservation ?

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

• Small population size:

- Dominated by genetic drift and inbreeding

- Genetic drift: random fixation and loss of alleles, whether adaptive or deleterious

- Inbreeding: increasing homozygosity

• Genetic drift and inbreeding:

- Inbreeding depression

- Reduction in individual fitness

- Compromised evolutionary potential

• 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)

• 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

• Impact of habitat fragmentation or climate change on selectively important variation

• Mechanisms underlying inbreeding depression

• Role of gene-environment interaction

• Gene expression

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

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

Study species

Taxonomy

Study species

Taxonomy

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

Study species

Life History

Study species

Life History

Study species

Life History

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

Study species

Dispersal

Study species

Dispersal

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

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

The Hill~ 1500 m

~ 800 m

~ 300 m

Methods

Nusatsum~ 1500 m

~ 800 m

Methods

Clayton Falls – M. Gurr~ 1500 m

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

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

Natural History

- Up to 7 different individuals sampled in the same hair snare

Results

Natural History

- Up to 7 different individuals sampled In the same hair snare

- Neighboring hair snares recovered the same individuals in 4 cases

Results

Natural History

- 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

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

Outliers HillResults

~ 1500 m

~ 800 m

~ 300 m

Outliers HillResults

Outliers Nusatsum

~ 1500 m

~ 800 m

Methods

Outliers Nusatsum

~ 1500 m

~ 800 m

Methods

Outliers Clayton – M. Gurr~ 1500 m

Methods

Outliers Clayton – M. Gurr~ 1500 m

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

- SNP discovery

Next step

- 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

Acknowledgements

- Russello Lab

- Mary Peacock

- Kurt Galbreath

- Tweedsmuir Provincial Park

adaptation to climage change: a genetic perspective

Environment