Responding to Climate Change:
Genetic Options
Brad St.Clair
USDA Forest Service, Pacific Northwest Research Station
Glenn Howe
Oregon State University
Vicky Erickson
USDA Forest Service, Region 6
USDA Forest Service Genetic Resource Management
Climate 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
–
–
2.
3.
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
Evolutionary adaptation will determine what happens
to plant populations given climate change
Management of genetic variation may positively
influence how plants respond and adapt to climate
change
Outline
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?
1. Are forests adapted to current and
future climates?
Evidence for adaptation:
1.
2.
3.
Correlation between a character and environmental
factors - the same form occurs in similar environments
Comparisons of naturally-occurring variants in
environments where they are hypothesized to function
as adaptations
Direct evidence from altering a character to see how it
affects function in a given environment
from West-Eberhard 1992
Evidence for adaptation comes from
common garden (provenance) studies
Evidence for adaptation: Correlations between traits and
source environments - Douglas-fir Genecology Study
Grow families in a
common environment
Measure many
adaptive traits
Collect
seed
from
many
trees
GIS
Combination of Variables, Primarily Growth
Douglas-Fir of Western OR and WA
3
2
1
0
Traits vs
source
environment
-1
-2
-3
-4
-5
-10
-8
-6
-4
-2
0
2
December Minimum Temperature
4
6
Douglas-Fir Genecology Study
Fall cold damage
r = 0.79
Qst = 0.68
Bud-set
r = 0.76
Qst = 0.29
Biomass
r = 0.52
Qst = 0.13
Bud-burst
r = 0.60
Qst = 0.21
1. Populations differ
2. Traits are correlated with source environments
3. Different traits show different patterns and scales of adaptation
•
Ultimately interested in survival, growth and reproduction
Mather
El. 1,400 m
Potentilla glandulosa from three
different elevations planted at
three different elevations
(Clausen, Keck & Hiesey 1940)
Stanford
El. 35 m
Native to
Timberline
El. 3,030 m
Evidence for adaptation: Comparisons of naturally-occurring
variants in native environments – reciprocal transplant studies
Stanford
El. 35 m
Mather
Timberline
El. 1,400 m El. 3,030 m
Grown at
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 regions
planted back into 9 of the regions
Some general findings:
• Most forest tree spp. show significant
geographic variation for:
timing of bud set, bud flush
cold hardiness
growth
• Traits correlate most strongly with:
 minimum winter temperature
mean annual temperature
# of frost free days
drought indices
•
Douglas-fir
variation in budset
St. Clair, 2008
Patterns reflect adaptation of annual growth &
dormancy cycle to local temperature regimes
Differences among species:
distance needed to detect genetic differences in
Northern Rockies (Rehfeldt 1994)
Species
Elev.
(m)
Frost- Evolutionary
free days
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 and Berrang
(2002) WA Dept Nat
Resources
Randall (1996) OR Dept of Forestry
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
What about genetic variation at the level of DNA?
Patterns of Adaptive Molecular Genetic Diversity
From Eckhart, Neale, et al. 2009
Phenotype
Neutral Genotype
Genotype - Non-neutral and
associated with phenotype
Variation in gene expression
Douglas-Fir Transcriptome Observatory
Cronn, Denver, Dolan, Knaus, Wilhelm, St.Clair
Ecodormancy
Bbreak
Shoot
elongation
Bud set
Onset of
dormancy
Endodormancy
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.
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.
•
Which expressed genes and what portion of the transcriptome show
significant variation in transcript abundance:
 among seasons
 among provenances
•
Which expressed genes show a correlated response with:
 weather or seasonal factors (temperature, precip, aridity, day length)
 phenotypic variation (budburst, growth/elongation, budset, dormancy)
Will current populations be adapted to
future climates?
Risk of maladaptation from climate change and
location of adapted populations
Risk = 0.90
Risk = 0.20
Genetic variation in bud-set
Risk of maladaptation from climate change
St.Clair and Howe. 2007. Genetic maladaptation of coastal
Douglas-fir seedlings to future climates. Global Change
Biology 13: 1441-1454.
Seed movement guidelines for climate change
Relative risks of maladaptation for
different traits in Douglas-fir
Current risk in seed
zones
Trait means expected
to be adapted to
future climates
Risk in future climates
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
25.5
0.22
0.45
34.6
38.8
0.51
0.67
273.6
0.15
0.32
279.3
283.6
0.36
0.59
Emergence (probits
d-1)
Total weight (g)
0.0466
0.11
0.25
0.0458
0.0454
0.08
0.14
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
Trait
Fall cold damage
(%)
Bud-set (days)
Locations of seed sources adapted
to future climates
2. Will forests naturally adapt to
future climates?
Three possibilities when environments change:
1. Move
•
Migrate to new habitats
•
•
Acclimate by modifying individuals to
new environment (phenotypic plasticity)
Evolve through natural selection
•
Extinction of local population
2. Stay
3. Disappear
Aitken et al. 2008. Evolutionary Applications 1: 95-111.
What is the potential for migration?
• 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 adaptation
via natural selection?
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
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
What is the potential for adaptation
via natural selection?
Important factors include:
•
•
•
•
•
Phenotypic variation
Heritabilities/genetic variation
Intensity of selection
Fecundity
Population size
• 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
Effects of Winter Environment on Budburst
Harrington, Gould and St.Clair 2009
Determined “possibility
line” to predict date of
budburst
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.
2.
Focus on ensuring resistance and resiliency across a range
of future conditions/reduce risks from fire and biotic
stress (competition, herbivory, insects & disease)
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-associated
flowering phenology
3. What can we do to help forests
adapt to future climates?
1.
2.
3.
Focus on ensuring resistance and resiliency across a range
of future conditions/reduce risks from fire and biotic
stress (competition, herbivory, insects & disease)
Promote natural migration and gene flow
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.
“Now here you see, it
takes all the running
you can do, to keep in
the same place.”
- the Red Queen to Alice in Through the Looking Glass
Selection, whether natural or human, requires
generation turnover.
Center for Forest
Provenance Data
Objectives:
1. Archive data from longterm 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)
Promote natural migration and gene flow
Gradually change species and seed sources for
reforestation in anticipation of warming
(assisted migration)
Enhance genetic diversity – “bet hedging”
2.
3.
4.
•
•
•
•
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.
2.
3.
4.
5.
Focus on ensuring resiliency across a range of future
conditions: reduce risks from fire and biotic stress
(competition, herbivory, insects & disease)
Promote natural migration and gene flow
Gradually change species and seed sources for
reforestation in anticipation of warming
(assisted migration)
Enhance genetic diversity – “bet hedging”
Practice selection and breeding for adaptive
characteristics
Selection and Breeding
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 migration
instead?
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
Xylem
cavitation
Testing for
drought
hardiness
3-cm
stem
section
Imposed drought
Cavitated cell
3. What can we do to help forests
adapt to future climates?
1.
2.
3.
4.
5.
6.
Focus on ensuring resiliency across a range of future
conditions: reduce risks from fire and biotic stress
(competition, herbivory, insects & disease)
Promote natural migration and gene flow
Gradually change species and seed sources for
reforestation in anticipation of warming
(assisted migration)
Enhance genetic diversity – “bet hedging”
Practice selection and breeding for adaptive
characteristics
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
•
•
•
•
•
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
– Inbreeding species
– Small populations
Tree Species of Concern
Western regions:
Eastern regions:
• butternut
• oak spp. (>50)
• ash
• eastern hemlock
• 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
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 genetic
repositories & 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
Collecting rust resistant whitebark pine seed
Blister rust resistance trial
Phytophthora resistance screening
in Port-orford-cedar
Seed Supplies:
Other Native Plants
Building a PNW
Native Plant Restoration Program
Priority
Priority
Priority
Priority
Priority
1: Species & seed need projections
2: Plant material development/production
3: Funding & partnerships
4: Education, technology transfer
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
Adapted Germplasm for Restoration
Collaborative Seed Zone Studies
Brad St. Clair1, Randy Johnson1, Matt Horning1, Rich Cronn1, Nancy
Shaw1, Vicky Erickson1, RC Johnson2, Dale Darris3, Peggy Olwell4
1
2
3
4
Forest Service (PNW, RMRS, R6)
ARS Plant Genetic Resources
NRCS-Corvallis PMC
Bureau of Land Management
Native Plant Common Gardens
Species
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
PNW, PSW
Data collection
complete
Mountain brome (Bromus marginatus)
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 in
the meantime?
• Increase accessibility
and usability of climate
data
• Delineate areas of similar
climate for use as
surrogate seed zones
T:\FS\Reference\GIS\r06\Data
Provisional Seed Zones
for
Oregon and Washington
Andy Bower
Brad St. Clair
Vicky Erickson
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
1) 5-needle pines:
2) Ash
- white pine
- sugar pine
- whitebark
- bristlecone
- limber
- pinyon
- foxtail
3) Butternut
•
•
•
•
Partners & stakeholders
Threats & impacts
Current genetic knowledge
Conservation needs & priorities
•
•
•
•
•
•
Restoration needs
R&D needs
Policy actions
Communication plan
Resources needs
Monitoring & assessment
– In situ
– Ex situ
PNW Whitebark Pine Conservation Strategy
Carol Aubry, Don Goheen, Robin Shoal
Priority Actions:
• 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 situ
collections in priority
areas:
- 225 trees in OR
- 120 trees in WA
• FY-10 funds to complete
collection goals?
Plant Conservation and Climate Change:
An Action Plan for National Forests in Western
Washington
The 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?
bstclair@fs.fed.us