Parallel Mitogenome Sequencing Alleviates Random Rooting Effect in Phylogeography

Area of Science:

• Evolutionary Biology
• Genomics
• Phylogenetics

Background:

• Reliably rooted phylogenetic trees are crucial for understanding species diversification but are often lacking in phylogeographic studies, especially for rapidly expanding populations with star-like phylogenies.
• The random rooting effect, caused by distant outgroups, poses a significant challenge in accurately rooting unrooted trees.

Purpose of the Study:

• To investigate if parallel mitochondrial genome (mitogenome) sequencing can overcome the random rooting effect in phylogeography.
• To reliably root the Sea of Japan lineage of *Chaenogobius annularis*, which exhibits a star-like phylogeny.

Main Methods:

• High-throughput and low-cost parallel sequencing was used to determine the mitogenomes of 83 *Chaenogobius annularis* individuals.
• Phylogenetic analysis of the obtained mitogenome sequences was performed to root the Sea of Japan lineage.
• Bootstrap tree topologies were analyzed to assess the alleviation of the random rooting effect.

Main Results:

• Parallel mitogenome sequencing successfully rooted the Sea of Japan lineage, overcoming limitations encountered with specific gene sequences.
• A novel, northern lineage was discovered with high bootstrap support, indicating expansion during an interglacial period.
• The study provided a new recent calibration point, revising divergence time estimates between Sea of Japan and Pacific Ocean lineages.

Conclusions:

• Parallel mitogenome sequencing is effective in resolving the random rooting problem in phylogeographic studies.
• This approach facilitates the discovery of new lineages and improves the accuracy of divergence time estimations.
• The findings enhance our understanding of population expansion patterns and glacial refugia.