Low Range-Wide Genetic Structure Inferred from Complete Chloroplast Genomes in Alaska Yellow-Cedar

Decline and mortality of yellow-cedar (Callitropsis nootkatensis; YC) is one of the most challenging problems facing coastal forests in SE Alaska. YC occupies habitats with extensive snow cover, but climate change has reduced late season snowpack levels across YC habitat in coastal Alaska, leaving fine and shallow roots exposed to freezing injury. Cumulative damage to root systems weakens and kills YC; aerial surveys have documented >200,000 ha of dying YC forests in SE Alaska, and mortality can reach 80% in affected stands. We are characterizing range-wide chloroplast genome diversity in YC to determine patterns of cytoplasmic variation, differentiation, and the degree of isolation in the highly fragmented landscape of SE Alaska. Chloroplast genomes from 70 YC individuals were sequenced from leaf tissue using a combination of targeted enrichment and single-end Illumina sequencing (101 bp). Hybridization capture probes spanned 121 kb of the predicted 128 kb genome, and were used to isolate the chloroplast from 48 individuals simultaneously. Initial results identify 142 variable SNPs across the 128 kb genome, with an average of 10.8 pairwise SNPs between these individuals (range = 0 – 21). YC chloroplast genomes show exceedingly low spatial differentiation range-wide, leading us to suggest that YC has a high migration rate, and that glaciated regions of SE Alaska were recolonized from local refugia, as opposed to distant sources. This information is being combined with information from nuclear markers to complement adaptive management for this ecologically, economically, and culturally important Pacific Northwest tree.