Interspecific plastome recombination in Picea (Pinaceae) reveals ancient reticulate evolution

Plastid sequences are a cornerstone in plant evolutionary inference and their interpretation is often guided by strong assumptions. Biparental inheritance, heteroplasmy, and sexual recombination appear rare, but detecting exceptions to these rules requires extensive taxon sampling and abundant sequence data. Utilizing advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of ~35 coniferous forest trees, to test for violations of canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for plastomes generated by interspecific hybridization and sexual recombination in the clade comprising Norway spruce (P. abies) and ten other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results resolve conflicting plastid-based phylogenies reported in previous studies and strengthen the inference of reticulate evolution in Picea. Given the relatively high frequency of biparental plastid inheritance and hybridization in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.