Investigating the genetic basis of adaptation in American pikas

Philippe Henry & Michael RusselloEcological and Conservation Genomics Lab

• Introduction and background

• Methods and analyzes used

• Preliminary results and anticipated significance

Outline

• 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)

Introduction

• Neutral genetic variation: - population genetic structure - demographic events, (bottlenecks and

population expansions)

Valuable information to help prioritize populations for conservation efforts

X. Does not generally inform on long term evolutionary potential of populations

Introduction

• Adaptive genetic variation can be assessed in wildlife populations

• This information will help

- shed light on the evolutionary potential of populations

- assist management decisions, especially with regard to adaptation to environmental changes

Introduction

The American pika as a model?

• Species sensitive to high ambient temperatures

• Contemporary climate warming may be partly responsible for the extirpation

• Good candidate to study the genetic basis of local adaptation

Study site

• Pikas can be found along elevation gradients spanning over 1000 m in the central Coast mountains of BC,

• I have sampled Pikas from 5 populations along an altitudinal gradient in the Bella Coola valley, BC, Canada

Study site

Study site: The Hill~ 1500 m

~ 800 m

~ 300 m

2 km

Study site: The Hill~ 1500 m

~ 800 m

~ 300 m

2 km

Methods: Sampling

Methods: Sampling

Methods: Sampling

Sampling: Hair snares

Sampling: Hair snares

Neutral genetic variation

Questions

• Is there evidence for gene flow between Pika populations sampled at different altitudes?

• Do populations from different elevations display signal of population declines?

Neutral genetic variationAnalyzes

• 8 microsatellite loci

• Estimates of genetic diversity

• Estimates of population genetic structure

• Estimates of demographic history

Neutral genetic variation

Preliminary results• 5 of 8 loci are polymorphic in this sample

• Pop n He Ho NaHigh 5 0.55 0.50 3.00Med 5 0.62 0.68 3.80Low1 4 0.50 0.50 2.80Low2 4 0.62 0.60 3.60Low3 4 0.60 0.65 3.60

Total/mean 22 0.58 0.59 3.36

Neutral genetic variation

Preliminary results• Two individuals sampled at 155m intervals

had matching genotypes (PI = 0.02)

• Population structure analyzes: 5 clusters corresponding to each sampled population

• AMOVA indicates that 17% variation is found among populations

Neutral genetic variation

Preliminary results

• Pairwise Fst

• No signal of population decline

Pop Med Low1 Low2 Low3High 0.17 0.17 0.18 0.07Med 0.17 0.18 0.24Low1 0.18 0.14Low2 0.13

Adaptive genetic variationQuestions

• Can genomic scans identify regions underlying local adaptations in our samples?

• Can these markers be used to provide additional information about population genetic structure?

Adaptive genetic variationAnalyzes

• AFLP genomic scans (20 primer combinations, 1177 bands)

• Detection of loci under selection

• Loci not under selection used to calculate:- Genetic diversity- Population structure

Adaptive genetic variationPreliminary results

• Genomic scans detected 9.3% of loci potentially under selection (127/1177)

Fst

Genetic diversity

Adaptive genetic variationPreliminary results

• Overall Genetic diversity

• Genetic differentiationMed Low1 Low2 Low3

High 0.022 0.091 0.073 0.053Med 0.035 0.035 0.019Low1 0.032 0.029Low2 0.012

Pop HjHigh 0.20679Med 0.27301Low1 0.31964Low2 0.33829Low3 0.32404

Work in progress

Neutral genetic variation

• Genotype a large number of individuals(to be sampled this field season)

• Genotype 12 or more microsatellite loci

• Re-analyzes this dataset to provide final estimates of population genetic structure, and

demography

Work in progressAdaptive genetic variation

• Identification of signature of selection in DNA sequences of targeted genes

• Identifying genes linked to outlier AFLPs detected

• Identification of the main selective forces driving Pika evolution

Overall significance

• Assessment of demography and overall genetic health of pika populations

• Identifying important genes for adaptation

• Provide an assessment of the potential of pikas to survive in the face of climate change

Acknowledgements

- Mary Peacock and her lab

- Kurt Galbreath

- Russello Lab

- Tweedsmuir Provincial Park Staff