Phylogenomics, divergence time estimation and trait evolution provide a new look into the Gracilariales (Rhodophyta)

Area of Science:

• Marine Biology
• Phycology
• Genomics

Background:

• The order Gracilariales (red algae) is ecologically important and a source of valuable compounds.
• Previous phylogenetic studies using limited genes had unresolved relationships within this clade.
• Understanding Gracilariales evolution is crucial for taxonomy and resource utilization.

Purpose of the Study:

• To construct a fully-resolved phylogeny of the Gracilariales using a comprehensive phylogenomic dataset.
• To clarify evolutionary relationships within Gracilaria sensu lato and Gracilariopsis.
• To inform taxonomic treatment and classification of Gracilariales.

Main Methods:

• Assembly of a phylogenomic dataset with 79 nuclear, 195 plastid, and 24 mitochondrial genes.
• Phylogenetic analyses across all major Gracilariales lineages (Melanthalia, Gracilariopsis, Gracilaria s.l.).
• Divergence time estimation, organellar genome architecture analysis, and ancestral character evolution.

Main Results:

• A fully-resolved and consistent phylogeny of Gracilariales was achieved across genomic compartments.
• Melanthalia obtusata confirmed as sister to Gracilaria s.l. and Gracilariopsis, with both latter clades well-supported.
• Uncertainty in Gracilaria s.l. relationships was resolved; Gracilariopsis and Gracilaria s.l. show comparable divergence times and overlapping morphological characters.

Conclusions:

• The phylogenomic data provides a robust framework for Gracilariales taxonomy.
• Proposed taxonomic classification aligns with monophyly and stability, addressing long-standing issues in Gracilaria s.l.
• Genomic and morphological data support revised taxonomic treatments for Gracilariales.