DOI: 10.5061/dryad.0p2ngf289
title: Mitochondrial phylogenomics of liverworts

description: Premise: Liverworts, with approximately 7,300 species worldwide, exhibit
 remarkable morphological diversity, in terms of growth form, ontogeny and
 architecture. Based on phylogenetic inferences drawn from DNA data,
 including recent genomic-scale data, the relationships among families and
 orders have been constantly revised and refined, although new topological
 incongruences have emerged. The liverwort mitochondrial genome exhibits
 lower average substitution rates compared to their nuclear and plastid
 genomes, and shows less structural variation, suggesting its suitability
 for inferring relationships at higher taxonomic levels. Methods: The
 mitochondrial genomes of 112 liverworts were sequenced, covering 105
 species, 52 families and 18 orders. We analysed the structures of the
 liverwort mitogenomes using Mauve alignment. Maximum likelihood and
 Bayesian inference methods were used to infer a family-level phylogeny of
 liverworts. Results: We assembled the complete mitochondrial genome for 23
 species and identified four new structural variants. Phylogenetic
 inferences from mitochondrial genome sequences confirmed the monophyly of
 most suprafamilial taxa, with the expectations of Porellales, Ptilidiales,
 and Pelliidae. Herzogianthus (Ptilidiales) was well-supported as a sister
 group to Jungermanniales sensu lato, rather than forming a monophyletic
 lineage with Ptilidium (Ptilidiales). Given its distinct morphological
 traits, this genus should be singled out and elevated to a new order.
 Conclusions: The overall architecture of liverwort mitogenomes remains
 highly conserved, with taxa that diverged over 470 Mya still having
 co-linear mitogenomes. This study provides a genetic resource for future
 evolutionary research across the liverworts and highlights the utility of
 mitogenome across lineages diversifying for 470 Mya, including for
 family‐level classification.
description: # Mitochondrial phylogenomics of liverworts
 [https://doi.org/10.5061/dryad.0p2ngf289](https://doi.org/10.5061/dryad.0p2ngf289) **Usage notes** * captured_genes.zip——Mitochondrial genes captured using Hybpiper pipeline v1.3.  * complete_assemblies.zip——23 complete liverwort mitochondrial genomes. Files are in .gb format and can be viewed and edited using Geneious Prime. * 1_MrBayes_trimmed.zip——Trimmed alignment files of 57 complete liverwort mitochondrial and two moss genomes used for Bayesian inference. * 1_MrBayes.nex.con.zip——The Bayesian inferred tree file of 57 complete liverwort mitochondrial and two moss genomes. * 1_RAxML_trimmed.zip——Trimmed alignment files of 57 complete liverwort mitochondrial and two moss genomes used for maximum likelihood. * 1_RAxML_bipartitions.zip——The maximum likelihood tree file of 57 complete liverwort mitochondrial and two moss genomes. * 3_MrBayes_trimmed.zip——Trimmed alignment files of 178 liverwort mitochondrial and two moss outgroup genomes used for Bayesian inference. * 3_MrBayes.nex.con.zip——The Bayesian inferred tree file of 178 liverwort mitochondrial and two moss outgroup genomes. * 3_RAxML_trimmed.zip——Trimmed alignment files of 178 liverwort mitochondrial and two moss outgroup genomes used for maximum likelihood. * 3_RAxML_bipartitions.zip——The maximum likelihood tree file of 178 liverwort mitochondrial and two moss outgroup genomes.