• 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. They are a climate-change sensitive species that displays limited dispersal.1

• 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.

Adapting to climate change: using genomic scans to detect signatures of selection in American pika populations

Philippe Henry and Michael A. RusselloDepartment of Biology, University of British Columbia, Okanagan campus, Kelowna, British Columbia, Canada.

Correspondence: phenry@alumni.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.

•The development of population genomics has enabled the investigation of the genetic basis of adaptation in natural populations of non-model organisms. By screening large numbers of loci distributed throughout the genome, researchers are able to tease apart neutral (genome-wide) and adaptive (locus-specific or “outlier”) effects

Study System

• We have previously shown that pika populations in our study area display restricted gene flow along elevation transects1, suggesting that pikas may have to rely on local adaptation to persist in a warmer world. • Here we identify a small fraction of loci that are potentially under natural selection, and may confer adaptive advantages to local environmental conditions. • Outlier loci that were also correlated with environmental variables may be good candidate markers to assess the evolutionary potential of the species in the face of climate change. • 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.• Current efforts are directed towards SNP identification and screening in order to uncover the functional basis of adaptation in this climate change sensitive mammal.

Methods

Figure 1: Map of the location of the study site: the Bella Coola Valley, British Columbia, Canada

• We used population and landscape genomics to investigate the genetic basis of adaptation in populations of O. princeps found along three elevation gradients in the central Coast Mountains of BC, Canada, ranging from sea level to 1500 m.

• 168 Pikas were sampled from ten populations along three elevation gradients using non-invasive hair snares2,3.• DNA was extracted from 25 hairs using the Promega DNA IQ system.• An AFLP genomic scan was used to screen for loci under selection. The protocol included digestion of 50ng of DNA with EcoRI and TaqI followed by ligation of adapters, pre-selective amplification and selective amplification with 20 primer combinations.• ScanAFLP3 was used to select the most repeatable and informative AFLP fragments. Furthermore, loci with less than 5% and more than 95% presence were removed from the dataset.• We used a combination of softwares including Bayescan4, Mcheza5, Arlequin6 to evaluate the probability of each locus being under positive selection. Candidate loci were designated only if they were identified by at least two independent methods.• Additionally we used SAM7 and logistic regression to identify the main drivers of natural selection in this system.

Figure 3: Graphical representation of outlier loci (red area) for the entire study area. Black circles indicate loci that are significantly associated with Mean Annual Precipitation.

1. Henry et al. 2012 (PLoS One) 5. Antao & Beaumont 2011 (Bioinformatics)2. Henry et al., 2011 (JoVE) 6. Excoffier et al. 2009 (Heredity)3. Henry & Russello 2011 (EJWR) 7. Joost et al. 2008 (MER)4. Foll & Gagiotti, 2008 (Genetics)

Acknowledgements We would like to thank the UBCO students that provided

assistance in the field and lab. Kurt Galbreath and Mary Peacock for kindly providing samples.

• A total of 1509 informative and repeatable loci were retained for analyzes.• Our combination of approaches identified that 23 of the 1509 loci (1.5%) showed strong evidence for natural selection in our populations sampled along three altitudinal gradients (Fig. 3).• Additionally, six loci displayed significant associations with environmental variables such as mean annual precipitation and maximum summer temperatures.

Funding

Figure 2: An American pika emerging from the rocks in the Bella Coola valley, British Columbia (Philippe Henry Photo)