Abstract
Whitebark pine (Pinus albicaulis) inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats – climate change, white pine blister rust, mountain pine beetle, and fire exclusion – and it is suffering significant mortality range-wide, prompting the tree to be listed as ‘globally endangered’ by the International Union for Conservation of Nature and ‘endangered’ by the Canadian government. Conservation collections (in situ and ex situ) are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 27 GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp), and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits), targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect. Quinquefolia) due to their limited genetic divergence.
Highlights
Whitebark pine (Pinus albicaulis) has an expansive range occurring across ∼340,000 square kilometers in the western U.S and Canada (Figure 1; Wilson, 2007; COSEWIC, 2010)
Our study shows that target enrichment generates high quality codominant genotypes, even when enrichment is low and repetitive loci are included in the bait pool, and that the resulting data are relevant to management and gene conservation activities
Coverage in P. albicaulis was highly correlated with repetitiveness in P. lambertiana (R2 = 0.16; p < 10−15; Figure 2), indicating that a small set of probes captured an inordinate number of reads because they match highly repetitive sequences
Summary
Whitebark pine (Pinus albicaulis) has an expansive range occurring across ∼340,000 square kilometers in the western U.S and Canada (Figure 1; Wilson, 2007; COSEWIC, 2010). There are an estimated 200 million individuals of whitebark pine in Canada (COSEWIC, 2010), with a potential 300–400 million individuals range-wide. This species has proven susceptible to an interconnected suite of threats that include anthropogenic climate change, white pine blister rust (Cronartium ribicola), mountain pine beetle outbreaks (Dendroctonus ponderosae), and fire exclusion; as a consequence, the species is suffering tremendous mortality across its range (Kendall and Keane, 2001; Warwell et al, 2007; Aubry et al, 2008; Gibson et al, 2008; Bockino and Tinker, 2012). As a result of these reported declines, whitebark pine is globally assessed as endangered by the IUCN (2015), regionally endangered by the Canadian government (COSEWIC, 2010), and has been determined to be “warranted” for listing under the U.S Endangered Species Act (currently withheld due to funding limitations; US Fish and Wildlife Service, 2011)
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