Abstract
Plastid sequences are a cornerstone in plant systematic studies but key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using 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 deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for plastomes generated by interspecific hybridization and 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 reconcile conflicting plastid-based phylogenies reported in previous studies and strengthen the mounting evidence 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.