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. 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:


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


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


• 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.


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. 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

Retrieving Data


1. Focus on ensuring resiliency across a range of future conditions/reduce risks from fire and biotic stress (competition, herbivory, insects & disease)



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


1. Focus on ensuring resiliency across a range of future conditions: reduce risks from fire and biotic stress (competition, herbivory, insects & disease)



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


1. Focus on ensuring resiliency across a range of future conditions: reduce risks from fire and biotic stress (competition, herbivory, insects & disease)



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



– Seed zones: adjusting for future climates

– Assisted migration: how/when/where?


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



– Seed zones

– Assisted migration


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



3. What can we do to help plants adapt to future climates?

4. How does this affect USFS genetic program activities & priorities?

Questions?

[email protected]

responding to climate change: genetic options€¦ · potentilla glandulosa from three different...

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