Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)

Mol Biol Evol. 2017 Jul 1;34(7):1689-1701. doi: 10.1093/molbev/msx111.


Plastid sequences are a cornerstone in plant systematic studies and 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 tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.

Keywords: chloroplast genomes; hybridization; phylogenetic incongruence; recombination; reticulate evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Evolution
  • DNA, Plant / genetics
  • Evolution, Molecular
  • Gene Transfer, Horizontal*
  • Genes, Plant
  • Genome, Plastid
  • High-Throughput Nucleotide Sequencing / methods
  • Hybridization, Genetic
  • Phylogeny
  • Picea / genetics*
  • Plastids / genetics
  • Sequence Analysis, DNA / methods*


  • DNA, Plant