DOI: 10.5061/dryad.0p2ngf23f
title: Data from: Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes

description: Polyploids represent a new frontier in species discovery among
 embryophytes. Within mosses, polyploid discovery is challenged by low
 morphological complexity. The rapid expansion of sub-genome sequencing
 approaches in addition to computational approaches to identifying whole
 genome duplication using allelic variation among nuclear markers has
 allowed for increased polyploid discovery among mosses. We confirm the
 intergeneric hybrid nature of E. hungaricus, and the allopolyploid origin
 of P. eurystomum and of one population of P. collenchymatum. We also
 reveal that hybridization gave rise to P. immersum, as well as to yet
 unrecognized lineages sharing the phenotype of P. pyriforme, P. sphaericum
 and P. collenchymatum. Our findings and methods demonstrate the utility of
 a novel approach to allele phasing and subgenome assignment, called
 homologizer, when working with polyploid genomes, and its value in
 identifying progenitor species using target capture data.
description: # Frequent allopolyploidy with distant progenitors in the moss genera
 Physcomitrium and Entosthodon (Funariaceae) identified via subgenome
 phasing of targeted nuclear genes.
 [https://doi.org/10.5061/dryad.0p2ngf23f](https://doi.org/10.5061/dryad.0p2ngf23f) Give a brief summary of dataset contents, contextualized in experimental procedures and results. ## Description of the data and file structure Raw target capture data is published in Sequence Read Archive (SRA) at [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA674709](https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fbioproject%2FPRJNA674709&data=05%7C01%7C%7C099e9a28680b41de4c4608da3510dc7c%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637880643777556861%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=fdX9YrJbzdKa0%2BnOTUQ17yUHJcqlnpM053RS43aEro8%3D&reserved=0) ### Folder 1: Alignments for each of 50 genes sampled for all taxa including individual sequences for each phased allele labeled as `h1` or `h2` ### Folder 2: Trimmed alignments for each of 50 genes sampled for all taxa including individual sequences for each phased allele labeled as `h1` or `h2` ### Folder 3: Gene trees for each of 50 genes sampled. Each gene tree is generated using RAxML and rerooted using the *Physcomitrellopsis* clade as an outgroup. ### Folder 4: Homologizer output * `genelist.txt` is a list of the 50 genes used in the Homologizer analysis * `InitialPhase.rev` and `Phasemoves.rev` are files used to direct Homologizer within the RevBayes script `revbayes_template.txt` * `physco.50genes_geneNN_phase.log` for each gene the Homologizer phase information output, one line per generation sampled * `physco.50genes.log` RevBayes output for substitution model parameters, one line per generation * `physco.50genes.trees` RevBayes phylogeny output for each generation * `physco.50genes.tree` Maximum clade credibility tree summarized from RevBayes output with 10% discarded as burnin * `physco_genecopymap.csv` file used to generate Phase moves used by Revbayes logfiles indicating each iteration of subgenome phasing for each of 50 genes indicated in genelist.txt. Includes homologizing.sh batch file. ### Folder 5: Phased subgenomes for each of 50 genes indicated as “h1” or “h2” for each allodiploid genome, respectively. As determined by the Homologizer output from RevBayes if the posterior probability of phase was greater than 80% ### Folder 6: rerooted homologizer trees Gene trees with haploid samples and allopolyploids with phased subgenome sequences ### Folder 7: Log files and output from TreeShrink. Output trees collapse unrealistically long branches. `subgenomePhased_genetrees_rerooted_collapsed_RS_0.05.txt` contains a summary of removed sequences Also contains node-by-node output from Phyparts on the ASTRAL species tree generated from TreeShrink gene trees, used to generate the PieCharts in pies.svg ### Folder 8: Phyparts input * `subgenomePhased_genetrees_rerooted_collapsed.tre` \- gene trees collapsed to remove nodes with low bootstrap support * `subgenomePhased_astral_collapsed.tre` \- astral tree from collapsed gene trees * `subgenomePhased_astral_rerooted.tre` \- astral tree rerooted from the outgroup PhyParts output can be found in Folder7 ### Folder 9: Triploid Homologizer "Iteration Two" from the manuscript RevBayes log files for 10 independent runs where two putatively triploid samples were coded as having three subgenomes while the subgenome phase from "Iteration one" (only allodiploids) were fixed. The astral subfolder contains: * gene trees where sequences are phased to subgenomes according to the RevBayes output * astral tree inferred from these gene trees * phyparts output summarizing bipartition conflict among gene trees * results of the "minority report" for alternative bipartitions at node 15 and node 34 (see tree\_nodes.pdf for numbered nodes) *Collenchymatum\_7379.fasta* \- FASTA format Sanger sequence for three Physcomitrium collenchymatum accessions\. Contains forward and reverse Sanger sequencing reads for approximately 360bp of gene 7379\. *Collenchymatum\_4780.fasta* \- FASTA format Sanger sequence for three Physcomitrium collenchymatum accessions\. Contains forward and reverse Sanger sequencing reads for approximately 360bp of gene 4780\. *Collenchymatum\_5274\_plastid\_rps4\_psba* \- FASTA format Sanger sequence for one Physcomitrium collenchymatum accession\. Contains consensus sequences for plastid markers psba and rsp4\. *Funariaceae4loci\_reduced.nex.con.tre* \- Contains a bayesian phylogeny based on plastid markers incorporating Physcomitrium collenchymatum 5274 to discern the maternal genome position among the Funariaceae\. ## Code/Software *homologizing.sh* \- example command lines run to collect sequences and add polyploid samples to the existing alignments\, conduct subgenome phasing in homologizer\, recover phased subgenome sequences\, and infer ASTRAL species trees *best.models.iqtree.txt* \- list of best models inferred by BIC for each gene tree