Compositional shifts associated with major evolutionary transitions in plants.

Area of Science:

• * Evolutionary Biology
• * Genomics
• * Bioinformatics

Background:

• * Compositional heterogeneity is a known factor influencing phylogenetic analyses in major plant clades.
• * Previous studies have noted variations in gene trees, morphology, and composition across plant groups.
• * Understanding compositional shifts is crucial for accurate evolutionary reconstructions.

Purpose of the Study:

• * To investigate compositional heterogeneity across a large plant transcriptomic dataset.
• * To determine if shifts in composition occur in shared locations and directions across gene regions.
• * To explore the implications of compositional variation for understanding plant evolution.

Main Methods:

• * Analysis of a large-scale plant transcriptomic dataset.
• * Estimation of mixed models for nucleotide and amino acid composition.
• * Examination of compositional shifts across different gene regions and plant lineages.

Main Results:

• * Detected significant shifts in both nucleotide and amino acid composition, with more pronounced changes in nucleotides.
• * Identified Chlorophytes and early land plant lineages (land, vascular, seed plants) as experiencing the most compositional shifts.
• * Observed that while genes within these clades may not share identical composition, their shifts tend to follow a similar direction.

Conclusions:

• * Compositional heterogeneity is prevalent in plant transcriptomes and occurs at key evolutionary transitions.
• * The directional consistency of compositional shifts suggests underlying shared biological processes.
• * Further investigation into these patterns is necessary to fully understand their impact on phylogenetic inference and evolutionary signals.