Amborella not a "basal angiosperm"? Not so fast.

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Genomics

Background:

• The plastid genome sequence of Amborella trichopoda, a key species in angiosperm phylogeny, was recently published.
• A study by Goremykin et al. proposed a basal position for monocots, challenging the widely accepted sister status of Amborella to all other angiosperms.
• This discrepancy was attributed by Goremykin et al. to increased character sampling (nucleotide data) in their phylogenetic analysis.

Purpose of the Study:

• To investigate whether limited taxon sampling, rather than limited character sampling, caused the artifactual "monocots basal" topology.
• To test the robustness of phylogenetic results to variations in taxon and character sampling.
• To clarify the basal relationships within angiosperms using plastid genome data.

Main Methods:

• Conducted phylogenetic analyses using a three-gene, multi-taxon dataset.
• Evaluated the impact of varying gene numbers (3 vs. 61), codon positions, and basal lineage taxa (Amborella, Nymphaea, Austrobaileya).
• Assessed the effect of different monocot representatives and the addition of other basal taxa on the resulting topology.

Main Results:

• The "monocots basal" topology is not an artifact of increased character sampling; it can be recovered with as few as two plastid genes.
• This topology is retained when Amborella is substituted with other basal lineages like Nymphaea or Austrobaileya, suggesting it arises from insufficient taxon representation.
• The "monocots basal" topology is unstable and sensitive to taxon sampling, with the addition of a single monocot (Oncidium) restoring Amborella as sister to angiosperms.

Conclusions:

• Limited taxon sampling, particularly when focusing on taxa with complete genome sequences, can lead to artifactual phylogenetic results.
• Amborella trichopoda is confirmed as sister to all other extant angiosperms, refuting the "monocots basal" hypothesis.
• Careful consideration of taxon sampling is crucial for accurate reconstruction of deep evolutionary relationships.