Maximum likelihood estimates of pairwise rearrangement distances

Area of Science:

• Computational Biology
• Phylogenetics
• Genomics

Background:

• Accurate estimation of evolutionary distances is crucial for phylogenetic reconstruction.
• Genome rearrangement distances are corrected using empirical, Bayesian/MCMC, or combinatorial approaches.
• Existing methods may not fully account for inversion interactions or circular genome symmetries.

Purpose of the Study:

• To introduce a maximum likelihood estimator (MLE) for inversion distance between genomes.
• To address the complexities of inversion sequence interactions in distance estimation.
• To incorporate symmetries of circular arrangements into distance calculations.

Main Methods:

• Utilizing a group-theoretic approach to model genome inversions.
• Developing a maximum likelihood estimator for inversion distance.
• Incorporating the dihedral group to account for circular arrangement symmetries.

Main Results:

• The proposed MLE provides a corrected distance measure for genome inversions.
• Demonstrated that minimal and MLE distances can result in different phylogenetic orderings due to inversion interactions.
• Developed a method to estimate distances free from a priori frame of reference by accounting for symmetries.

Conclusions:

• The new MLE offers a more accurate way to estimate evolutionary distances considering inversion complexities.
• Accounting for symmetries is a valuable addition applicable to existing distance correction methods.
• This work advances phylogenetic reconstruction by improving genome rearrangement distance estimation.