Evolutionary History of the Marchantia polymorpha Complex

Area of Science:

• Evolutionary Biology
• Genomics
• Plant Science

Background:

• Hybridization and introgression are increasingly recognized as drivers of adaptive divergence.
• Limited genomic data exist for haploid-dominant species, hindering a comprehensive understanding of these processes.
• The liverwort *Marchantia polymorpha* offers a model system to study introgression in haploid organisms.

Purpose of the Study:

• To investigate the role of hybridization and introgression in the evolutionary divergence of three *Marchantia polymorpha* subspecies.
• To analyze genomic data to resolve the phylogenetic relationships and divergence history of *M. polymorpha* subspecies.
• To test a previous hypothesis regarding the hybrid origin of *M. polymorpha* subsp. *ruderalis*.

Main Methods:

• Whole-genome sequencing (PacBio) and Illumina resequencing of multiple individuals from three *Marchantia polymorpha* subspecies (*ruderalis*, *montivagans*, *polymorpha*).
• Comparative genomic analyses using *M. paleacea* as an outgroup.
• Species tree analyses and examination of chromosomal divergence patterns.

Main Results:

• Genomic analyses revealed complex phylogenetic signals, with evidence for frequent introgression among the three subspecies.
• Subspecies *montivagans* diverged first, with *ruderalis* and *polymorpha* forming sister lineages.
• Pseudo-chromosome 2 in subsp. *montivagans* showed high divergence, potentially due to introgression or conserved regions, with chromosomal rearrangements supporting the latter.
• Each subspecies possessed distinct chloroplast and mitochondrial haplotype groups.
• The hypothesis of subsp. *ruderalis* being a recent stabilized hybrid was refuted.

Conclusions:

• Introgression appears to be a significant factor shaping the evolutionary history and divergence of *Marchantia polymorpha* subspecies.
• The phylogenetic relationships are complex, likely due to rapid divergence and ongoing or intermittent gene flow.
• The study provides crucial genomic insights into introgression dynamics in a haploid-dominant plant system.