Poster presented at the Society for the Study of Evoultion, University of Idaho, Moscow ID

1. • The American pika (Fig. 2; Ochotona princeps) is a small
lagomorph that inhabits talus slopes and rocky habitats throughout
mountainous regions of western North America.
• In the northern most part of their range, the central Coast
Mountains of BC (Fig. 1), pikas are present along altitudinal
gradients ranging from sea level to above 1500m, making them an
ideal system to investigate the genetic basis of local adaptation to
changing environmental conditions.
Investigating the genetic basis of local adaptation in American
pika using genomic scans
Philippe Henry and Michael A. Russello
Department of Biology and Centre for Species at Risk and Habitat Studies (SARAHS), University of British Columbia Okanagan, Kelowna, BC, Canada.
Correspondence: phenry@interchange.ubc.ca
ResultsContext
Objective
Discussion
References
• Alpine species are starting to show responses to global
environmental changes. One obvious example is the upslope
movement of species as they seek to retain their optimal niches.
• Besides the ability to migrate, species with special habitat
requirements may be constrained to stay put. These species will
have to respond to the environmental changes by adapting to the
changing conditions.
• Their responses to environmental changes will largely depend on
the underlying adaptive genetics variability present in its
populations.
• To date the task of identifying genomic regions under selection
from environmental changes has been a difficult one, mostly owing
to the lack of genetic markers for natural populations.
• Technical advances that have lead to the identification of a large
number of genetic markers along with statistical developments have
allowed researchers to tease apart adaptive from neutral genetic
variation by comparing levels of genetic differentiation between
loci, where outlier loci with high differentiation are interpreted as
been subject to natural selection.
Study Species
• The advent of molecular markers such as AFLP have enabled
researcher to study the adaptive genetic variation in wild, non‐model
species.
• In the present study we show that a small fraction of loci found in
pikas are potentially under natural selection, while most loci are
selectively neutral.
• These loci were only present in samples from high (A, C, E) and low
(B, D) elevations but absent from the mid elevation site.
• This point suggests that the outlier loci are responsible for the local
adaptation to environmental conditions that vary with altitude. Yet it
is important to bear in mind that these results are preliminary as
they were obtained from only 32 samples.
• Besides all advantages of using AFLPs, one drawback is that this
type of markers are anonymous and thus it is difficult to pinpoint the
genes or genomic regions under selection.
• Other complementary approaches (SAM) can also be used to shed
light on the association between loci and eco‐climatic variables.
• This latter approach will be implemented in the future on a larger
dataset, and will hopefully identify the main driver of selection in
American pikas from the Bella Coola valley.
Figure 2: An American pika emerging from the rocks in the Bella Coola valley, British Columbia
(Philippe Henry Photo)
Methods
Figure 1: Map of the
location of the study site:
the Bella Coola Valley,
British Columbia, Canada.
This site is of particular
interest since pikas are
distributed along an
altitudinal gradient
ranging from the bottom
of the valley at 300m, up
to 1500m over very short
geographical distances.
The highway descending
from the Chilcotin plateau
into the Bella Coola valley
offers ideal access to
populations at different
altitudes.
• Use a genomic scan approach to identify candidate loci under
natural selection that may be responsible for local adaptation in the
American pika.
A. Samples
• Pika populations were sampled from five populations at three
different elevations: 300m (N=3), 800m (N=1) and 1500m (N=1)
above sea level in the Bella Coola Valley, British Columbia, Canada.
• Non‐invasive snares1 were used to collect hair from 32 individuals.
B. Lab work
• DNA was extracted from 25 hairs using the Promega DNA IQ
system.
• A genomic scan was undertaken using AFLPs. The protocol
included digestion of 50ng of DNA with EcoRI and TaqI followed by
ligation of adapters, pre‐selective amplification and selective
amplification with a total of 64 primer combinations2.
• 44 primer combinations produced bands that were run onto an
ABI 3130XL genotyper and visualized using Genemapper 3.7.
C. Analyzes
• The software scanAFLP3 was used to select the most repeatable
and informative primer combinations. 15 primer combinations with
high signal to noise ratios and low error rates were thus retained.
Furthermore, loci with less than 5% and more than 95% presence
were removed from the dataset.
• The program Bayescan4 which uses a Bayesian approach to
directly calculate the probability of been under selection for each
locus was used to detect candidate loci potentially under natural
selection.
Figure 3: Bayescan
analysis graphic with,
on the x‐axis, the
posterior probability for
a locus to be under
natural selection. The
vertical line indicates
the threshold beyond
which there is strong
evidence for selection
to act. 5 out of 1238 loci
show strong evidence
for selection:
A ‐ E32T35_115,
B – E43T44_123,
C – E43T35_83,
D – E31T37_96,
E – E43T35_73.
1. Henry & Russello (Submitted)
2. Bonin et al., 2005
3. Herrmann et al., 2010
4. Foll & Gagiotti, 2008
Acknowledgements
We would like to thank the members of the ECGL for help
in the field and lab, Kurt Galbreath and Mary Peacock
for kindly providing samples. Sarka Jahodova is
thanked for providing guidance with AFLP.
• A total of 1238 loci were obtained with 15 selective primer
combinations that proved to be informative and repeatable.
• Bayescan analysis detected that 5 of the 1238 loci (0.4%) showed
strong evidence for natural selection in our populations sampled
along an altitudinal gradient (Fig. 3).
Funding