DOI: 10.5061/dryad.31zcrjdwm
title: Phylogenetic data for construction of bryophyte tree using published sanger data

description: Genome size varies by orders of magnitude across land plants, and the
 factors driving evolutionary increases and decreases in genome size vary
 across lineages. Bryophytes have the smallest genomes relative to other
 land plants and there is growing evidence for frequent whole genome
 duplication (WGD) across the lineage. However, the broad scale patterns of
 genome size, chromosome number, and WGD have yet to be characterized
 across bryophytes in a phylogenetic context. In the present study, we use
 a phylogenetic comparative approach and leverage all published data on
 genome size, chromosome number, and WGD to reconstruct the evolutionary
 history of these traits across the three major bryophyte lineages:
 hornworts, liverworts, and mosses.  Each lineage of bryophytes
 exhibits a distinct pattern of genome size evolution and prevalence of
 WGD, with mosses having the most dynamic genome sizes and highest
 propensity for WGD. For the lineages with robust sampling, we found that
 21.3% of mosses and 13% of liverworts species have naturally occurring
 polyploids. In addition, haploid genome size (1C) is most dynamic in the
 mosses which includes 15 transitions to larger genomes and nine reversals
 largely in the orders Dicranles and Hypnales. Crucially, there is no
 correlation between genome size and WGD or chromosome number, potentially
 suggesting rapid genome downsizing following WGD. As bryophytes are
 poikilohydric, desiccation tolerant plants, having large genomes may be
 physiologically prohibitive given the cost to growth and metabolism
 associated with them. These findings emphasize the unique evolution of the
 bryophytes broadly and of the hornworts, liverworts, and mosses
 individually, and should therefore serve as impetus for more in-depth
 experimental study of genome size evolution and WGD in
 bryophytes. 
description: <em>Phylogenetic data collection -
 Pyphlawd</em> A DNA matrix of 3,890 taxa and 10
 concatenated loci (5.8S, 26S, atpb, nad5, psbA-trnH, psbA, rbcL,
 rps4-trnS, trnA, trnL-F) was assembled using PyPhlawd (Smith &
 Walker, 2018). PyPhlawd was run using “Embryophyte” as the taxonomic group
 and then narrowed to all  bryophyte species (hornworts, liverworts, and
 mosses) using a taxon list including all listed species available on
 genbank. The clustering function in PyPhlawd produced 311 clusters of
 which the ten with the largest taxonomic representation were selected for
 further analysis. 
 <em><strong> </strong>Phylogenetic
 analysis</em> Matrices for each locus were
 aligned using Mafft v7.419 with default settings. The loci were
 concatenated and each locus was assigned a separate partition.
 Phylogenetic inference was implemented in IQTREE v.2 (Minh et al., 2020)
 using Model Finder Plus (Kalyaanamoorthy et al., 2017) to find best fit
 models for each partition. IQTREE was implemented using 1000 bootstrap
 replicates. The concatenated matrix and phylogenetic tree are available on
 Dryad digital repository ()
description: # Phylogenetic data for construction of bryophyte tree using published
 sanger data
 [https://doi.org/10.5061/dryad.31zcrjdwm](https://doi.org/10.5061/dryad.31zcrjdwm) ## Description of the data and file structure ### Files and variables #### File: updated\_final.tre **Description:** Phylogenetic tree inferred from concatenated matrix using IQtree #### File: cocatenated\_it10.fasta **Description:** Concatenated matrix of 10 plastid and nuclear markers used for phylogenetic inference. #### File: ALL\_DATA\_Embryophyta\_3193.table Description: This table contains genbank IDs for sequences in original PyPhlawd matrix.