Phylogenomic insights into the origin of primary plastids

The origin of plastids was a major evolutionary event that paved the way
for an astonishing diversification of photosynthetic eukaryotes. Plastids
originated by endosymbiosis between a heterotrophic eukaryotic host and
cyanobacteria, presumably in a common ancestor of the primary
photosynthetic eukaryotes (Archaeplastida). A single origin of primary
plastids is well supported by plastid evidence but not by nuclear
phylogenomic analyses, which have consistently failed to recover the
monophyly of Archaeplastida hosts. Importantly, plastid monophyly and
nonmonophyletic hosts could be explained under scenarios of independent or
serial eukaryote-to-eukaryote endosymbioses. Here, we assessed the
strength of the signal for the monophyly of Archaeplastida hosts in four
available phylogenomic data sets. The effect of phylogenetic methodology,
data quality, alignment trimming strategy, gene and taxon sampling, and
the presence of outlier genes were investigated. Our analyses revealed a
lack of support for host monophyly in the shorter individual data sets.
However, when analyzed together under rigorous data curation and complex
mixture models, the combined nuclear data sets supported the monophyly of
primary photosynthetic eukaryotes (Archaeplastida) and recovered a
putative association with plastid-lacking Picozoa. This study represents
an important step toward better understanding deep eukaryotic evolution
and the origin of plastids.