Adaptation to climage change: a genetic perspective
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This document outlines a talk on applying genetics and genomics approaches to study the American pika's adaptation to climate change. It discusses conservation biology and genetics concepts, and how population genomics can help characterize adaptive genetic variation and evolutionary potential. The study species, the American pika, is introduced as sensitive to high temperatures and a good model to study local adaptation across altitudinal gradients. The talk will use pikas in coastal British Columbia to examine climate change impacts on selectively important genetic variation.
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Adaptation to climage change: a genetic perspective
- 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
- 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)
- 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
- 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
- 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
- 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