The new phylogeny of eukaryotes.

Area of Science:

• * Eukaryotic evolution and molecular phylogenetics.
• * Protist diversity and evolutionary relationships.

Background:

• * Morphological data presents challenges for interpreting evolutionary relationships among eukaryotes.
• * Ribosomal RNA (rRNA) molecular phylogenetics initially resolved eukaryotic trees, supporting early-emerging lineages.

Purpose of the Study:

• * To re-evaluate early eukaryotic evolution hypotheses challenged by new molecular data.
• * To investigate the placement of putative early-emerging, amitochondriate lineages.

Main Methods:

• * Analysis of alternative protein markers in molecular phylogenetics.
• * Identification and correction of molecular phylogeny reconstruction artifacts.
• * Reconstruction of eukaryotic phylogenies using updated methods.

Main Results:

• * Early hypotheses of early-emerging eukaryotic lineages are challenged.
• * Putative early lineages are identified as late-emerging, misplaced due to artifacts.
• * Eukaryotic evolution is better described by rapid diversification (multifurcation) aligning with the 'big bang' hypothesis.

Conclusions:

• * Molecular phylogenetics requires careful artifact identification for accurate evolutionary reconstruction.
• * Eukaryotic diversification was likely rapid, not a slow emergence from a few lineages.
• * Genomic data and improved phylogenetic methods are crucial for further resolving eukaryotic evolution.