A phylogenetic foundation for comparative mammalian genomics.

Area of Science:

• Evolutionary Biology
• Genomics
• Mammalian Phylogenetics

Background:

• Ongoing efforts to sequence mammalian genomes necessitate robust phylogenetic frameworks.
• Resolving evolutionary relationships among the 18 orders of placental mammals is a key challenge.
• Previous classifications require refinement based on new molecular data.

Purpose of the Study:

• To construct and analyze the largest amino acid sequence alignments to date for placental mammals.
• To establish superordinal groups (clades) as hypotheses for further evolutionary testing.
• To estimate divergence times for major mammalian splits and revise placental mammal classification.

Main Methods:

• Construction and analysis of extensive amino acid sequence alignments.
• Molecular divergence-time estimations using sequence data.
• Statistical framework for clade testing using SINE (short interspersed nuclear element) data.

Main Results:

• Strong evidence supports the Supraprimates clade (Euarchonta + Glires), including primates, rodents, and tree shrews.
• Identified clades: Boreotheria (placental mammals excluding Xenarthra and Afrotheria), Laurasiatheria, and others.
• Estimated earliest superordinal divergences predate 65 million years ago (Cretaceous period); primate split at ~55 mybp.
• SINE data provides significant support for tarsier/anthropoid and other clades, while Bayesian methods show limitations.

Conclusions:

• Sequence analysis is crucial for hypothesizing clades, while SINE data is essential for testing them.
• Tree shrews are strongly supported as closer relatives to primates than rodents.
• Revised classification and divergence time estimates provide a framework for understanding mammalian evolution.