IInvestigation of the genetic basis of adaptation
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This document summarizes a study investigating genetic variation in American pika populations along an elevational gradient in British Columbia. Preliminary results show neutral genetic markers detect population structure corresponding to sampling locations, with 17% of variation among populations. Genomic scans identified 9.3% of loci under selection. Ongoing work includes further genotyping individuals to refine estimates of population structure and demography, and identifying genes linked to markers under selection to understand local adaptation and survival under climate change. The study aims to assess genetic health and evolutionary potential of pika populations to inform conservation.
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IInvestigation of the genetic basis of adaptation
- 1. Investigating the genetic basis of adaptation in American pikas Philippe Henry & Michael Russello Ecological and Conservation Genomics Lab
- 2. • Introduction and background • Methods and analyzes used • Preliminary results and anticipated significance Outline
- 3. • 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
- 4. • 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
- 5. • 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
- 6. 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
- 7. 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
- 8. Study site
- 9. Study site: The Hill ~ 1500 m ~ 800 m ~ 300 m 2 km
- 10. Study site: The Hill ~ 1500 m ~ 800 m ~ 300 m 2 km
- 16. 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?
- 17. Neutral genetic variation Analyzes • 8 microsatellite loci • Estimates of genetic diversity • Estimates of population genetic structure
- 18. Neutral genetic variation Preliminary results • 5 of 8 loci are polymorphic in this sample • Pop n He Ho Na High 5 0.55 0.50 3.00 Med 5 0.62 0.68 3.80 Low1 4 0.50 0.50 2.80 Low2 4 0.62 0.60 3.60 Low3 4 0.60 0.65 3.60 Total/mean 22 0.58 0.59 3.36
- 19. 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
- 20. Neutral genetic variation Preliminary results • Pairwise Fst • No signal of population decline Pop Med Low1 Low2 Low3 High 0.17 0.17 0.18 0.07 Med 0.17 0.18 0.24 Low1 0.18 0.14 Low2 0.13
- 21. Adaptive genetic variation Questions • Can genomic scans identify regions underlying local adaptations in our samples? • Can these markers be used to provide additional information about population genetic structure?
- 22. Adaptive genetic variation Analyzes • AFLP genomic scans (20 primer combinations, 1177 bands) • Detection of loci under selection • Loci not under selection used to calculate: - Genetic diversity - Population structure
- 23. Adaptive genetic variation Preliminary results • Genomic scans detected 9.3% of loci potentially under selection (127/1177) Fst Genetic diversity
- 24. Adaptive genetic variation Preliminary results • Overall Genetic diversity • Genetic differentiation Med Low1 Low2 Low3 High 0.022 0.091 0.073 0.053 Med 0.035 0.035 0.019 Low1 0.032 0.029 Low2 0.012 Pop Hj High 0.20679 Med 0.27301 Low1 0.31964 Low2 0.33829 Low3 0.32404
- 25. 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
- 26. Work in progress Adaptive 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
- 27. 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
- 28. Acknowledgements - Mary Peacock and her lab - Kurt Galbreath - Russello Lab - Tweedsmuir Provincial Park Staff
Editor's Notes
- - INTRO: Go over some basic concepts of genetic variation in wild population and
- Genetic variation is necessary for the maintenance of evolutionary potential of populations and species There are two principal types of genetic variation, which are often not acknowledged
- Classically, Neutral genetic variation is widely used to investigate population genetic structure as well as past demographic events, (bottlenecks and population expansions) While this information is valuable to help prioritize populations for conservation efforts, it does not generally inform on long term evolutionary potential of populations
- On the other hand. Adaptive genetic variation can now be directly assessed in wildlife populations by screening the entire genome for signature of selection This information will help - shed light on the evolutionary potential of populations and - greatly assist management decisions, especially with regards to adaptation to changing environmental conditions
- Pikas have also been found to be susceptible to contemporary climate change as 28% of lower elevation population surveyed by Eric Beever and colleagues have become extirpated since their initial description in the early 20th century. Pikas are considered early warning systems for the negative effects of climate change on alpine species.
- Environmental gradients are ideal situations to study genetic basis of adaptation
- So here is a quick snap shot to give you an idea of the location of « the Hill »
- The hill is the section of highway 20 that descends from the chilcotin plateau at heckman pass (1524m) down to the bottom of the bella coola valley at an elevation of 300m. I explored the valley last summer and found population at 300, 800 and 1500m elevation along or close to the highway. Here i have represented an additional two populations per altitude that were remotely identified using googleearth shown in orange here!
- The hill is the section of highway 20 that descends from the chilcotin plateau at heckman pass (1524m) down to the bottom of the bella coola valley at an elevation of 300m. I explored the valley last summer and found population at 300, 800 and 1500m elevation along or close to the highway. Here i have represented an additional two populations per altitude that were remotely identified using googleearth shown in orange here!
- This is a satellite picture from one of talus slopes from the Bella Coola valley. Pikas generally establish their territories close to the talus-vegetation interface! Pikas are hard to life trap and can be sensitive to handling, so we are going to be setting up hair snags to collected genetic material (hair) from the animals
- Here i have shaded the areas with the most likely chance of hosting pika territories. With the darkest shades been the most hospitable. In a nutshell, the plan is to survey each talus slope upon arrival and flagging each territory.
- Once all territories have been identified and flagged (on the basis of haypiles and latrine sites) we will set up hair-snags around the centre of each territory and check it after leaving it out for a night
- This is what a successful hair snag should look like, the hair collected will be stored in tubes or paper envelopes and stored at -20 in a liquid nitrogen dewer until the samples are returned to the lab for molecular work.
- In chapter 2 i will use quantify population differentiation and shed light on past demographic events in our populations from the bella coola valley
- I will also calculate the genetic diversity, estimate of effective popuilation size and i will test for genetic signature of bottleneck in each population
- I will also calculate the genetic diversity, estimate of effective popuilation size and i will test for genetic signature of bottleneck in each population
- I will also calculate the genetic diversity, estimate of effective popuilation size and i will test for genetic signature of bottleneck in each population
- I will also calculate the genetic diversity, estimate of effective popuilation size and i will test for genetic signature of bottleneck in each population
- As only a limited number of genes have been identified in pikas Genomic scanswill be used to identify other areas of the genomes that are under selection Between 300 and 400 aflp loci distributed throughout the genome will be amplified
- A multiple univariate regressions will be used to test for correlation between the frequency of an allele and an environmental variable
- A multiple univariate regressions will be used to test for correlation between the frequency of an allele and an environmental variable
- 50 more sampled last year and an additional 150 from the next field season
- With specific mutations associated with populations at different altitudes Additional signal of selection from scans, leading to the identification of other (LESS OBVIOUS = OTHER FUNCTIONS) genes involved in adaptation Lastly the spatial analyses method will help identify the major selective forces acting on pikas
- All together, contribute valuable information relative to reconstructing Pika evolutionary history and taxonomy, identifying genes underlying ecologically important traits, and assessing the potential of Pikas to persist in the face of projected climate change
- All together, contribute valuable information relative to reconstructing Pika evolutionary history and taxonomy, identifying genes underlying ecologically important traits, and assessing the potential of Pikas to persist in the face of projected climate change