Mountains, climate change,
and conservation:
the role of landscape genomics
Brenna R. Forester, Dean L. Urban,
Thomas F. Schultz, Jennifer J. Wernegreen
Duke University
Species have four options in response
to climate change:
1. Persist in place
2. Track climate conditions
3. Go extinct
4. Adaptation
aa
Warmer, drier
AA
Aa
x
Cooler, wetter
Landscape genomics
Extension of landscape genetics:
Incorporates explicit tests of
landscape heterogeneity on
gene flow & spatial patterns of
genetic variation.
Landscape genomics:
Samples are collected
across selection gradients
and are genotyped at
100s-1000s of markers;
comparative.
Manel et al. 2010 Molecular Ecology
Why landscape genomics?
Genetic
Data
POPULATION
GENOMICS
Geospatial
Data
Weller’s Salamander photos: Katy Cain
SPATIAL
ANALYSIS
x
ECOLOGICAL
GENETICS
x
x
QUANTITATIVE
GENETICS
Phenotypic
Data
Sork et al. 2013 Tree Genetics & Genomes
Weller’s salamander
n = 32
n = 26
n = 27
n = 32
n = 11
Step 1: Sample within/across mountains
Step 2: Develop markers (SNPs)
• Double digest restriction site-associated DNA
sequencing (ddRAD-seq)
• “Reduced-representation” genome sequencing
• Replicable, requires no prior genomic information
• Dense sampling
• ~$45/sample
• Bioinformatics
Step 3: Detect outliers
• Migration and
genetic drift
are genomewide forces
that influence
all loci
• Selection is a
locus-specific
force that
results in
atypical
patterns of
variation
Redundancy Analysis:
-10
-5
PC2
0
5
Step 4: Assess gene flow
-5
0
5
PC1
10
Step 4: Integrate data sets
• Adaptive loci
• Neutral loci
• Environmental data
• Geographic distance
• Isolation by distance
• Local adaptation
• Interaction of gene flow (or lack of) & adaptation
In summary, landscape genomics…
• ...is applicable across all taxa.
• …is an excellent tool for understanding the response
of montane species to changing climate.
• …provides information of high conservation value:
• Conservation prioritization (neutral vs. adaptive)
• Build “evolutionary resilience”
• Identify evolutionary refugia
• Increase “adaptability”
Thank you…
• Andy Bunn, MtnClim Sponsors & Steering Committee
• Dean Urban, Tom Schultz, Jen Wernegreen, Rob Dunn
• Lori Williams, NC Wildlife Resources Commission
• Funding:
o Sigma Xi
o American Museum of Natural History
o Chopsticks for Salamanders
o Society for the Study of Amphibians and Reptiles
o Duke University Graduate School