Cross-species outlier detection reveals different evolutionary pressures between sister species

• Published in: The New phytologist Vol. 204; no. 1; pp. 215 - 229
• Main Authors: Cullingham, Catherine I., Cooke, Janice E. K., Coltman, David W.
• Format: Journal Article
• Language: English
• Published: England New Phytologist Trust 01.10.2014; Wiley Subscription Services, Inc; BlackWell Publishing Ltd
• Subjects: Adaptation; Adaptation, Biological - genetics; adaptive variation; Beetles; Biological Evolution; Canada; Data analysis; Ecological genetics; Ecosystem; Environment; environmental correlation; Evolution; Evolutionary genetics; Families; Genetic diversity; Genetic loci; Genetic Variation; Genetics, Population; Genomes; Heterogeneity; Heterozygote; Hybridization, Genetic; Identification; Interspecific; jack pine (Pinus banksiana); Loci; lodgepole pine (Pinus contorta var. latifolia); Marine ecology; Models, Genetic; Mountains; Nucleotides; outlier detection; Outliers; Outliers (statistics); Pest outbreaks; Pine; Pine trees; Pinus - genetics; Pinus - physiology; Pinus banksiana; Pinus contorta; Polymorphism; Polymorphism, Single Nucleotide; Population ecology; Range extension; selection; Selection, Genetic; Sibling species; Single-nucleotide polymorphism; Species; Species diversity; Canada; lodgepole pine (Pinus contorta var. latifolia); adaptive variation; jack pine (Pinus banksiana); selection; environmental correlation; outlier detection
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.12896

Lodgepole pine (Pinus contorta var. latifolia) and jack pine (Pinus banksiana) hybridize in western Canada, an area of recent mountain pine beetle range expansion. Given the heterogeneity of the environment, and indications of local adaptation, there are many unknowns regarding the response of these forests to future outbreaks. To better understand this we aim to identify genetic regions that have adaptive potential. We used data collected on 472 single nucleotide polymorphism (SNP) loci from 576 tree samples collected across 13 lodgepole pine-dominated sites and four jack pine-dominated sites. We looked at the relationship of genetic diversity with the environment, and we identified candidate loci using both frequency-based (arlequin and bayescan) and correlation-based (matsam and bayenv) methods. We found contrasting relationships between environmental variation and genetic diversity for the species. While we identified a number of candidate outliers (34 in lodgepole pine, 25 in jack pine, and 43 interspecific loci), we did not find any loci in common between lodgepole and jack pine. Many of the outlier loci identified were correlated with environmental variation. Using rigorous criteria we have been able to identify potential outlier SNPs. We have also found evidence of contrasting environmental adaptations between lodgepole and jack pine which could have implications for beetle spread risk.