Phylogenetic data for construction of bryophyte tree using published sanger data

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 mos..., Phylogenetic data collection - Pyphlawd
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. 
 Phylogenetic analysis
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 replic..., , # 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.
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