Exploring Mitonuclear Discordance: Ghost Introgression From an Ancient Extinction Lineage in the Odorrana swinhoana...

Area of Science:

• Evolutionary Biology
• Genomics
• Amphibian Phylogenetics

Background:

• Mitonuclear discordance, incongruence between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA), presents evolutionary puzzles.
• Ghost introgression, involving genetic material from extinct or unsampled lineages, is a proposed explanation for such discordance.
• The Odorrana swinhoana frog complex exhibits unusual genetic patterns, including a population with highly divergent mtDNA.

Purpose of the Study:

• To investigate the evolutionary history of the Odorrana swinhoana complex.
• To test the ghost introgression hypothesis using genomic data and demographic modeling.
• To understand the origins of mitonuclear discordance in this amphibian group.

Main Methods:

• Phylogenetic analysis using mitochondrial DNA (mtDNA).
• Nuclear DNA sequencing via ddRADseq (double-digest restriction site-associated DNA sequencing).
• Demographic modeling to assess population history and introgression scenarios.

Main Results:

• Mitochondrial phylogeny indicated a basal lineage for the unidentified population, contrasting with nuclear data.
• Nuclear data revealed the unidentified population as a mix of derived O. swinhoana sequences and ancient mtDNA.
• Demographic models strongly supported ghost introgression, with models including a ghost population outperforming others.

Conclusions:

• The findings provide one of the first documented cases of ghost introgression in amphibians.
• An eastward expansion of western O. swinhoana likely replaced an ancient Odorrana lineage, leaving its mtDNA and nuclear fragments.
• The study highlights the importance of considering ghost introgression and the limitations of relying solely on mtDNA for evolutionary studies.