Dating ancient splits in phylogenetic trees, with application to the human-Neanderthal split

Area of Science:

• Genomics
• Evolutionary Biology
• Computational Biology

Background:

• Estimating species Time to Most Recent Common Ancestor (TMRCA) is crucial for understanding evolutionary history.
• Existing methods often require reconstructing complex phylogenetic trees for each analysis.
• Accurate TMRCA estimation relies on understanding genetic mutation rates and patterns.

Purpose of the Study:

• To develop novel, accurate, and efficient estimators for species TMRCAs.
• To leverage existing, large-scale phylogenetic trees for TMRCA estimation.
• To provide updated TMRCA estimates for hominin and great ape lineages.

Main Methods:

• Developed multiple estimators based on Poisson distributed transitions and observed parity.
• Utilized transition statistics from the human mitochondrial DNA (mtDNA) phylogenetic tree (Phylotree).
• Simulated data using mtDNA substitution statistics to mimic real-world rates.

Main Results:

• Proposed estimators demonstrated high accuracy across a wide range of TMRCAs.
• Outperformed the widely-used BEAST2 software in both accuracy and speed.
• Applied to Neanderthal, Denisovan, and Chimpanzee mtDNA, yielding later TMRCA estimates than previously reported.

Conclusions:

• The new methods offer a significant improvement over existing tools like BEAST2, especially for deep divergences.
• Eliminates the need for de novo tree reconstruction for TMRCA estimation.
• Updated TMRCA estimates suggest later divergence times for Neanderthals and chimpanzees relative to modern humans.