Responding to Climate Change: Genetic Options€¦ · Potentilla glandulosa from three different...
Transcript of Responding to Climate Change: Genetic Options€¦ · Potentilla glandulosa from three different...
Brad St.ClairUSDA Forest Service, Pacific Northwest Research Station
Glenn HoweOregon State University
Vicky EricksonUSDA Forest Service, Region 6
Responding to Climate Change: Genetic Options
USDA Forest Service Genetic Resource ManagementClimate Change Workshop
Corvallis, OR, March 2, 2010
When considering ecosystem and management responses to climate change, it is important to consider genetics of adaptation and genetic variation in adaptive traits.
Three reasons:1. Plants are genetically adapted to their local climates
– The climatic tolerances of populations are considerably lower than the tolerances of the species as a whole
– Populations, not species, are the important biological unit of interest
2. Evolutionary adaptation will determine what happens to plant populations given climate change
3. Management of genetic variation may positively influence how plants respond and adapt to climate change
1. Are forests adapted to current and future climates?
2. Will forests naturally adapt to future climates?
3. What can we do to help forests adapt to future climates?
4. How does this affect USFS genetic program activities and priorities?
Outline
1. Are forests adapted to current and future climates?
1. Correlation between a character and environmental factors - the same form occurs in similar environments
2. Comparisons of naturally-occurring variants in environments where they are hypothesized to function as adaptations
3. Direct evidence from altering a character to see how it affects function in a given environment
Evidence for adaptation comes from common garden (provenance) studies
Evidence for adaptation:
from West-Eberhard 1992
Collect seed from many trees
Grow families in a common environment
Measure many adaptive traits
Traits vs source
environment
Douglas-Fir of Western OR and WA
December Minimum Temperature
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Evidence for adaptation: Correlations between traits and source environments - Douglas-fir Genecology Study
1. Populations differ2. Traits are correlated with source environments3. Different traits show different patterns and scales of adaptation
• Ultimately interested in survival, growth and reproduction
Bud-set
r = 0.76
Qst = 0.29
Biomass
r = 0.52
Qst = 0.13
Bud-burst
r = 0.60
Qst = 0.21
Fall cold damage
r = 0.79
Qst = 0.68
Douglas-Fir Genecology Study
Nati
ve
to
Grown at
Timberline
El. 3,030 m
Stanford
El. 35 m
Mather
El. 1,400 m
Sta
nfo
rd
El. 3
5 m
Math
er
El. 1
,400 m
Tim
berl
ine
El. 3
,030 m
Potentilla glandulosa from three
different elevations planted at
three different elevations
(Clausen, Keck & Hiesey 1940)
Evidence for adaptation: Comparisons of naturally-occurring variants in native environments – reciprocal transplant studies
Response functions derived from lodgepole pine provenance tests in British Columbia
from Wang et al. 2006. Use of response functions in
selecting lodgepole pine populations for future climate.
Global Change Biology 12: 2404-2416.
New provenance tests established for Douglas-fir in Oregon & Washington
Primary objective: to build transfer functions that look at tree growth and survival (and components) as a function of the differences between source and planting environments
Reciprocal transplant study:120 Douglas-fir families (from previous study)from 60 locations in 12 regionsplanted back into 9 of the regions
Some general findings:• Most forest tree spp. show significant geographic variation for:
timing of bud set, bud flushcold hardinessgrowth
• Traits correlate most strongly with: minimum winter temperaturemean annual temperature# of frost free daysdrought indices
• Patterns reflect adaptation of annual growth &dormancy cycle to local temperature regimes
Douglas-fir
variation in budset
St. Clair, 2008
Differences among species: distance needed to detect genetic differences in
Northern Rockies (Rehfeldt 1994)
Species
Elev.
(m)
Frost-
free days
Evolutionary
mode
Douglas-fir 200 18 Specialist
Lodgepole pine 220 20 Specialist
Engelmann spruce 370 33 Intermediate
Ponderosa pine 420 38 Intermediate
Western larch 450 40 Intermediate
Western redcedar 600 54 Generalist
Western white pine none 90 Generalist
Seed zones and breeding zones are used to ensure adaptability
Seed zones have been developed for most major tree species in the PNW and elsewhere
Randall (1996) OR Dept of Forestry
Randall and Berrang
(2002) WA Dept Nat
Resources
Adaptation in other forest species?
• Growing evidence for local adaptation
• Different species show different patterns and scales of adaptation
• Moderate degree of adaptation (generalists)
• More work is needed
Patterns of Adaptive Molecular Genetic Diversity
Neutral GenotypePhenotype Genotype - Non-neutral and associated with phenotype
What about genetic variation at the level of DNA?
From Eckhart, Neale, et al. 2009
Variation in gene expressionDouglas-Fir Transcriptome Observatory
Ecodormancy
Shoot elongation
Bbreak
Bud set
Endodormancy
Onset of dormancy
Annual cycle of growth in Douglas-fir. Timing of key developmental stages is shown next to their approximate timing in western Oregon. Red points show sampling points being collected for a larger study.
• Which expressed genes show a correlated response with: weather or seasonal factors (temperature, precip, aridity, day length) phenotypic variation (budburst, growth/elongation, budset, dormancy)
• Which expressed genes and what portion of the transcriptome show significant variation in transcript abundance: among seasons among provenances
Fig. 1: left, Illumina Genome Analyzer, the MPS platform proposed for this study; right, microscopic image showing a field of ‘clusters’ (growing DNA chains), and the DNA sequence for each chain (indicated by color). The Illumina GA produces 15 billion bases of DNA per run.
Cronn, Denver, Dolan, Knaus, Wilhelm, St.Clair
Will current populations be adapted to future climates?
Risk of maladaptation from climate change and location of adapted populations
St.Clair and Howe. 2007. Genetic maladaptation of coastal
Douglas-fir seedlings to future climates. Global Change
Biology 13: 1441-1454.
Genetic variation in bud-set Risk of maladaptation from climate change
Risk = 0.20
Risk = 0.90
Seed movement guidelines for climate change
Current risk in seed
zones
Trait means expected to be adapted to future climates Risk in future climates
Trait Current trait
mean Mean Maximum CGCM2
B2 CSIRO
A2 CGCM2
B2 CSIRO
A2
Trait 1 0.00 0.20 0.43 0.90 2.24 0.50 0.90
Trait 2 0.00 0.12 0.27 -0.64 -1.74 0.30 0.70
Fall cold damage (%)
25.5 0.22 0.45 34.6 38.8 0.51 0.67
Bud-set (days) 273.6 0.15 0.32 279.3 283.6 0.36 0.59
Emergence (probits d-1)
0.0466 0.11 0.25 0.0458 0.0454 0.08 0.14
Total weight (g) 12.7 0.07 0.16 14.3 15.9 0.20 0.40
Root:shoot ratio 0.397 0.09 0.20 0.375 0.347 0.24 0.53
Bud burst (days) 106.3 0.09 0.21 105.4 103.0 0.09 0.31
Taper (mm cm-1) 0.188 0.14 0.29 0.184 0.187 0.12 0.10
Relative risks of maladaptation for different traits in Douglas-fir
Locations of seed sources adapted to future climates
1. Move• Migrate to new habitats
2. Stay• Acclimate by modifying individuals to
new environment (phenotypic plasticity)• Evolve through natural selection
3. Disappear• Extinction of local population
Three possibilities when environments change:
2. Will forests naturally adapt to future climates?
Aitken et al. 2008. Evolutionary Applications 1: 95-111.
• Evidence for range expansion northward and up in elevation
• Estimates of past migration rates vary– Davis and Shaw 2001: 200-400 m per yr
– Aitken et al 2007: 100- 200 m per yr
• But current rates of climate change might require 3000-5000 m per yr
What is the potential for migration?
Important factors include:• Phenotypic variation• Heritabilities/genetic variation• Intensity of selection• Fecundity• Population size
What is the potential for adaptation via natural selection?
Important factors include:• Generation turnover
What is the potential for adaptation via natural selection?
Optimum elevation = maximum
probability of presence
Avg optimum elevation shift =
29 m per decade
Much quicker for grassy species
compared to woody species:
grassy species: ~ 90 m shift
between 1986-2005 compared to
1905-1985
woody species: ~30 m shift
Important factors include:• Phenotypic variation• Heritabilities/genetic variation• Intensity of selection• Fecundity• Population size
What is the potential for adaptation via natural selection?
• Generation turnover• Levels of gene flow• Mating system• Structure of genetic variation/
steepness of clines• Central vs peripheral populations• Trailing edge vs leading edge• Biotic interactions
What about phenotypic plasticity?
• Phenotypic plasticity = the ability of an individual to change its characteristics (phenotype) in response to changes in the environment
• Phenotypic plasticity is common in plants– Plants modify their phenology, physiology and growth in
response to changes in environments• Bud-set• Bud-burst• Flowering• Acclimation to drought
• However, patterns of genetic variation in adaptive characteristics associated with environmental variation suggest that phenotypic plasticity is insufficient– No single phenotypically plastic genotype is optimal in all
environments
Determined “possibility line” to predict date of
budburst
Effects of Winter Environment on BudburstHarrington, Gould and St.Clair 2009
Recording budburst
Model predicts budburst well for WA site
Provenances variation in date of budburst observed at two WA sites in 2009
…as well as earlier studies
Douglas-fir budburst model adjusted for population effects
Population coefficient was most strongly correlated with precipitation and summer maximum temperatures supporting a summer drought avoidance hypothesis
Predicted date of spring budburst is earlier with warmer winters
But experimental evidence indicates that more warming will delay budburst as chilling is not satisfied.
3. What can we do to help forests adapt to future climates?
3. What can we do to help forests adapt to future climates?
1. Focus on ensuring resistance and resiliency across a range of future conditions/reduce risks from fire and biotic stress (competition, herbivory, insects & disease)
3. What can we do to help forests adapt to future climates?
1. Focus on ensuring resistance and resiliency across a range of future conditions/reduce risks from fire and biotic stress (competition, herbivory, insects & disease)
2. Promote natural migration and gene flow
Avoid fragmentation and maintain corridors for gene flow
But, • Seed migration may not be
sufficient• Pollen flow may be limited
by temperature-associatedflowering phenology
3. What can we do to help forests adapt to future climates?
1. Focus on ensuring resistance and resiliency across a range of future conditions/reduce risks from fire and biotic stress (competition, herbivory, insects & disease)
2. Promote natural migration and gene flow
3. Gradually change species and seed sources for reforestation in anticipation of warming (assisted migration)
What to plant for future climates?
Seedlot Selection Tool
Ron Beloin, Glenn Howe, Brad St.Clair,
Lauren Magalska, Greg DeVeer
Funded by the USFS Climate Change
Research Program
But…Which future climate do we aim for?
Plants must be adapted to the next decade as well as the next century.
- the Red Queen to Alice in Through the Looking Glass
“Now here you see, it takes all the running you can do, to keep in the same place.”
Selection, whether natural or human, requires generation turnover.
Center for Forest Provenance Data
Objectives:
1. Archive data from long-term provenance tests and seedling genecology tests
2. Make datasets available to researchers through the web
Denise Cooper, Brad St.Clair, Glenn Howe,
Jessica Wright, Greg DeVeer
Funded by USFS Climate Change
Research Program
Submitting Data
Submitting Data
Retrieving Data
Retrieving Data
3. What can we do to help forests adapt to future climates?
1. Focus on ensuring resiliency across a range of future conditions/reduce risks from fire and biotic stress (competition, herbivory, insects & disease)
2. Promote natural migration and gene flow
3. Gradually change species and seed sources for reforestation in anticipation of warming (assisted migration)
4. Enhance genetic diversity – “bet hedging”• Deploy species and/or provenance mixtures within sites or
across landscapes
• Allow for selection with higher planting densities, thinning
• Maintain diversity within provenances
• Establish genetic outposts for facilitating gene flow into adjacent native stands – small number may be effective
3. What can we do to help forests adapt to future climates?
1. Focus on ensuring resiliency across a range of future conditions: reduce risks from fire and biotic stress (competition, herbivory, insects & disease)
2. Promote natural migration and gene flow
3. Gradually change species and seed sources for reforestation in anticipation of warming (assisted migration)
4. Enhance genetic diversity – “bet hedging”
5. Practice selection and breeding for adaptive characteristics
Breed for drought/cold hardiness and growth phenology• Tests have been developed to assess cold and drought hardiness.• But breeding per se may not be needed – rely on assisted migrationinstead?
Breed for resistance or tolerance to pests• A long-term, expensive, difficult prospect.• Key pests are being addressed – which others will become problematic?• Biotech approaches may be the most effective (e.g., Bt insect toxins).
Breed for broad adaptation
Selection and Breeding
Imposed drought
3-cm
stem
section
Cavitated cell
Xylem
cavitation
Testing for
drought
hardiness
3. What can we do to help forests adapt to future climates?
1. Focus on ensuring resiliency across a range of future conditions: reduce risks from fire and biotic stress (competition, herbivory, insects & disease)
2. Promote natural migration and gene flow
3. Gradually change species and seed sources for reforestation in anticipation of warming (assisted migration)
4. Enhance genetic diversity – “bet hedging”
5. Practice selection and breeding for adaptive characteristics
6. Ensure that gene conservation strategies are robust in the face of climate change
Conserving Genetic Diversity
In situ conservation• Locate reserves in areas of high environmental and
genetic diversity• Reduce disturbance probability and intensity
– thinning, prescribed fire, fuels reduction, insect traps
• Supplement existing variation with genetic outposts
Ex situ conservation• Seed collections becomes more
important with increasing threats to in situ reserves
• Assisted migration (plantings) may also be considered a form of ex situ conservation
Species and populations most threatened by climate change:
• Long-lived species• Genetic specialists• Species or populations with low dispersal potential• Species or populations with low genetic variation
– Inbreeding species – Small populations
• Fragmented, disjunct populations• Populations at the trailing edge of climate change• Species or populations with “nowhere to go”• Rare species• Populations threatened from habitat loss, fire,
disease, insects
Tree Species of Concern
Western regions: • 5-needle pines: white pine, sugar pine, whitebark, bristlecone, limber, pinyon, foxtail
• Port-orford cedar
• Western red cedar
• Subalpine fir
• Mountain & western hemlock
• Englemann spruce
• Tanoak
• Monterey pine, knobcone pine
• Cupressus spp.
• Torrey pine
• Brewer spruce
• Coast redwood
• Alder spp., cottonwood, aspen, birch
Eastern regions:
• butternut
• oak spp. (>50)
• ash
• eastern hemlock
Research Needs• Monitor health, phenology, regeneration, and productivity in natural
populations and in plantations
• Revisit old species and provenance trials for knowledge to guide changes to reforestation
• Establish new field experiments to test species distribution model predictions and to evaluate species and populations in a wider range of climates over time (i.e., test facilitated migration of spp. and seed sources)
• Establish controlled-environment experiments to study species and provenance responses to temperature and CO2 increases
• Establish studies to evaluate effective pollen flow in natural stands
• Establish studies to consider epigenetic effects in major species
4. How does this affect USFS genetic program activities & priorities?
USFS Climate Change Strategic Framework
• Science Integration
• Monitoring
• Adaptation
• Mitigation
• Sustainable Operations
• Education
• Alliances
Adaptation Investment Priorities:Genetic Resource Management
1) Expand efforts to develop native seed supplies & production capabilities
2) Develop solutions for seed deployment
– Seed zones: adjusting for future climates
– Assisted migration: how, when, where?
3) Expand gene conservation efforts
Seed Supplies: Conifer spp. Concerns:•Existing supplies are aging & losing viability
• Wildfires & other disturbances are depleting supplies
• Many spp. & sources are absent or poorly represented
• Inadequate funding• Loss of expertise
• Managed locally
R6 Conifer Seed Orchards
• 1860 acres, 12 species• high value seed sources• critical for reforestation • irreplaceable geneticrepositories & storehouses
Needs:• maintenance & protection• funding & personnel• regional/national maps &databases
• additional facilities?
USDA Forest Service National Forest System
Genetic Resource Programs
Disease Resistance Breeding• Blister rust in 5-needle pines
• Port-Orford-cedar root rot
• Fusiform rust in loblolly pine
• American chestnut blight
• Butternut, dogwood fungal diseases
Blister rust resistance trial
Collecting rust resistant whitebark pine seed
Phytophthora resistance screening
in Port-orford-cedar
Seed Supplies:Other Native Plants
Building a PNWNative Plant Restoration Program
Priority 1: Species & seed need projections
Priority 2: Plant material development/production
Priority 3: Funding & partnerships
Priority 4: Education, technology transfer
Priority 5: R&D
Adaptation Investment Strategy
1) Expand efforts to develop native seed supplies & production capabilities
2) Develop solutions for seed deployment
– Seed zones: adjusting for future climates
– Assisted migration: how/when/where?
3) Expand gene conservation efforts
Brad St. Clair1, Randy Johnson1, Matt Horning1, Rich Cronn1, Nancy Shaw1, Vicky Erickson1, RC Johnson2, Dale Darris3, Peggy Olwell41 Forest Service (PNW, RMRS, R6)2 ARS Plant Genetic Resources3 NRCS-Corvallis PMC4 Bureau of Land Management
Adapted Germplasm for RestorationCollaborative Seed Zone Studies
Native Plant Common GardensSpecies Source Principals Status
Blue wildrye (Elymus glaucus Buckley) OR, CA PNW, PSW Erickson et al. 2004
Roemer’s fescue (Festuca idahoensis) OR, WA NRCS, PNWRS Wilson et al. 2008
Oceanspray (Holodiscus discolor) OR, WA NRCS, PNWRS Horning et al. 2008
Broadleaf lupine (Lupinus latifolius) OR, WA PNW Doede 1995
California brome (Bromus carinatus) OR, CA PNW, PSW Internal report
Mountain brome (Bromus marginatus) PNW, PSW Data collection
complete
Bluebunch wheatgrass (Pseudoroegneria
spicata)
OR, WA,
ID, NV, CA
PNWRS, ARS,
RMRS
Data collection
complete
Antelope bitterbrush (Purshia tridentata) OR, WA PNWRS Data collection
complete
Sanderg’s bluegrass (Poa secunda) OR, WA,
ID, NV, CA
PNWRS, ARS,
RMRS
Planted spring 2008
Prairie Junegrass (Koeleria macrantha) OR, WA,
ID, NV, CA
PNWRS, PNW,
NRCS
Planted fall 2008
Bottlebrush squirreltail (Elymus
elymoides)
OR, WA PNWRS Seed collected
What to do inthe meantime?
• Increase accessibility and usability of climate data
• Delineate areas of similarclimate for use assurrogate seed zones
T:\FS\Reference\GIS\r06\Data
Andy BowerBrad St. ClairVicky Erickson
Provisional Seed Zones for
Oregon and Washington
T:\FS\Reference\GIS\r06\Data\
Adaptation Investment Strategy
1) Expand efforts to develop native seed supplies & production capabilities
2) Develop solutions for seed deployment
– Seed zones
– Assisted migration
3) Expand gene conservation efforts
Framework for Gene Conservation• Partners & stakeholders• Threats & impacts• Current genetic knowledge• Conservation needs & priorities
– In situ– Ex situ
• Restoration needs• R&D needs• Policy actions• Communication plan• Resources needs• Monitoring & assessment
1) 5-needle pines: - white pine- sugar pine - whitebark- bristlecone- limber- pinyon- foxtail
2) Ash
3) Butternut
PNW Whitebark Pine Conservation Strategy
Priority Actions:
Carol Aubry, Don Goheen, Robin Shoal
• Continue inventory, monitoring,& assessment work
• Collect seed, fast!!!
• Expand/accelerate efforts to develop rust resistant planting stock
• Increase active restoration: (planting, thinning, pruning)
• Establish new populations
• widespread cone crop in 2009
• FY09 operational & ex situcollections in priority areas:
- 225 trees in OR- 120 trees in WA
• FY-10 funds to completecollection goals?
Plant Conservation and Climate Change:An Action Plan for National Forests in Western
WashingtonThe question: How can the 3 national
forests in western Washington conserve biodiversity and increase resiliency given the predicted changes in temperature and precipitation?
The focus:• Tree species, both
widespread and rare• Vulnerable habitats such
as wetlands and subalpine ecosystems
Topics include:• Species vulnerability assessments
• Plant material – needs & methods
• Gene conservation – needs & methods
• Assisted migration – if, how, when, where?
• A monitoring plan to measure changes important life history traits such as phenology
The result:• A 5-year action plan to implement in partnership
with the WDNR, NPS, and PNWRS
• A template for other national forests
Summary
1. Are forests adapted to current and future climates?
2. Will forests naturally adapt to future climates?
3. What can we do to help plants adapt to future climates?
4. How does this affect USFS genetic program activities & priorities?
Questions?