Using genomics to understand and manage adaptation to climate

change in forest trees

Sally Aitken

Department of Forest and Conservation Sciences & Centre for Forest Conservation Genetics

Faculty of Forestry

University of British Columbia

Climate change is creating a mismatch between trees and

their environments

Insect and disease outbreaks

Some forests remain healthy

cold

warm

Tem

pe

ratu

re g

rad

ien

tPopulations are genetically adapted to historic climate

hot

warm

And mismatched with future climate

• Understand adaptation of tree populations to old and new climates

• Match germplasm with new climates

• Quantify risks from changes in climate averages and extremes

• Screen germplasm for climate-related biotic and abiotic risks

• Manage and conserve genetic diversity

Needs

California 12oC Oregon

11oC----British Columbia----

--------Alaska-------------

Local adaptation to climate: Growth of trees from different populations planted in a common

garden reflects provenance climate

10oC

8oC 7oC

5oC4oC

4oC3oC

Climate change is decoupling match between genetics and climate resulting in maladaptation

Sitka spruce planted in Vancouver

Using population genomics to select populations/seed sources for new climates

--------Alaska-----------------British Columbia-----

CaliforniaOregon

Assisted gene flow (AGF): Intentional translocation of individuals within a species range to facilitate adaptation to anticipated local conditions.

Aitken and Whitlock. 2013. Ann. Rev. Ecol. Evol. Syst.

Genetic variation provides some insurance against climatic uncertainty

Variation within a single Sitka spruce population from southern BC

Seed collected from many populations

Experiments planted in many locations

Field experiments traditionally used to understand adaptation to climate

Advantages of genomic approaches

Faster results than field trials

Can isolate effects of specific climatic factors

Can identify candidate genes, e.g., for susceptibility to specific climatic events, for screening breeding populations

Genomic selection for climate traits can be used for breeding within populations

Better matching natural populations with new climates can increase productivity substantially

LodgepolePineRange

2050s

PresentDay

Wang et al.2006

10 to 35% greater productivity

Phenotypic Data

Geospatial environmental data

Genomic data

POPULATION

GENOMICS

ECOLOGICAL

GENETICS

QUANTITATIVE

GENETICS

SPATIAL

ANALYSIS

Phenotype-Environment (PEA)

Use population genomic approaches to detect patterns of local adaptation

Sork et al. 2013. Tree Genetics and Genomes

Genomic approaches complement seedling tests of climate-related traits in

controlled environments• Heat, drought and cold tolerance

• Growth rates

• Timing of growth & dormancy

• Sample DNA to assess climate-related variation in genes

P. Smets, photos

Strongest signal of climatic adaptation in temperate and boreal tree species is to lowest

winter temperatures; little population variation for heat or drought stress response

Lodgepole pineCold injury 30-year extreme

minimum temp.

British Columbia

Alberta

Different species have similar patterns of adaptation to climate

Lodgepole pine Interior spruce

Liepe et al. 2016. Aitken and Bemmels. 2016. Evolutionary Applications

Genomic approaches in AdapTree

Sequence capture and resequencing: • ~25,000 genes• 4,500 non-coding regions• >250 populations/species• ~600 trees/species

• Pine: 10.9 million SNPs; 1.25 million after filters

• Spruce: 8.3 million SNPs; 1.1 million after filters

• Genetic-environment associations (GEA)

• Genotype-phenotype associations (GWAS)

• 50K SNP arrays

Lodgepole pine: Weak structure

Interior spruce: Strong structure (hybrid zone)

Detecting genomic signatures of adaptation requires adjusting for neutral population structure

due to history and demographics

AA

AG

GG

Identify genes and SNPs correlated with climatic variables

e.g., temperature, precipitation or elevation; no phenotypes required

131 genes, each row one gene with evidence of climate adaptation in spruce and pine

Temperature Precipitation

Frost

Genotype-environmentassociation

Comparative genomics identifies genes used by multiple species for climate adaptation

Yeaman et al. In prep.

AA

AC

CC

Can we identify individual genes and SNPs associated with climate-related traits?

Temperature Precipitation

FrostTraits

Genotype-environmentassociation

Genotype-traitassociation

Spruce and pine use many of the same genes to adapt to climate despite ~140MY of evolution

Yeaman et al. In prep.

131 genes, each row one gene with evidence of climate adaptation in spruce and pine

Use genomics or traditional common garden experiments to classify natural populations for climate adaptation

ForwardVelocity

ReverseVelocity

PresentDayto2050s

2050stoPresentDay

0 4 8+

km/year

0 4 8+

km/year

Hamannetal.2014.GlobalChangeBiol.

Use climate modeling to evaluate risks and needs

Genomics not the only technology for climate matching

Time to get moving

• Tree populations already lag well behind new climates in many places

• Genomic approaches can inform genetic choices for new climates more quickly than conventional field trials

• Need to recognize risk, climate uncertainty, local adaptation to non-climatic factors in strategy

• Genetic diversity should be used as a buffer against future climate uncertainty

• Scientific capacity is needed to translate knowledge to applications and to stakeholders

• FAO Symposium Organizers: ChittaranjanKole, John Ruane, Jarkko Koskela

• AdapTree team and collaborators: Sam Yeaman, Kay Hodgins, Katie Lotterhos, Loren Rieseberg, Michael Whitlock, Ian MacLachlan, Tongli Wang, Jon Degner, Andreas Hamann, Katharina Liepe, Laura Gray, Kristin Nurkowski, Jordan Bemmels

• AdapTree Scientific Advisory Board: Glenn Howe, Dominique Bachelet, Ed Buckler, Wolfgang Haider, Par Ingvarsson, OutiSavolainen

Acknowledgements