DOI: 10.5061/dryad.83bk3j9t6
title: Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades

description: • Premise of the study: Phylogenomic datasets using genomes and
 transcriptomes provide rich opportunities beyond resolving bifurcating
 phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system
 for evolutionary ecology. However, it lacks a well-supported phylogeny for
 a stable taxonomy and for macroevolutionary comparisons. • Methods: We
 sampled 24 genomes and transcriptomes in Phrymaceae and closely related
 families, including eight newly sequenced transcriptomes. We reconstructed
 the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance
 using PhyParts, Quartet Sampling, and cloudogram, and carried out
 phylogenetic network analyses using PhyloNet and HyDe. We searched for
 whole genome duplication (WGD) events using chromosome numbers, synonymous
 distance, and gene duplication events. • Key results: Most gene trees
 support the monophyly of Phrymaceae and each of its tribes. Most gene
 trees also support the tribe Mimuleae being sister to Phrymeae + Diplaceae
 + Leucocarpeae, with extensive gene tree discordance among the latter
 three. Despite the discordance, polyphyly of Mimulus s.l. is strongly
 supported, and no particular reticulation event among the Phrymaceae
 tribes is well supported. Reticulation likely occurred among Erythranthe
 bicolor and close relatives. No ancient WGD event was detected in
 Phrymaceae. Instead, small-scale duplications are among potential drivers
 of macroevolutionary diversification of Phrymaceae. • Conclusions: We show
 that analysis of reticulate evolution is sensitive to taxon sampling and
 methods used. We also demonstrate that genome-scale data do not always
 fully “resolve” phylogenetic relationships. They present rich
 opportunities to investigate reticulate evolution, and gene and genome
 evolution involved in lineage diversification and adaptation.
description: DATA PACKAGE FROM MORALES-BRIONES ET AL (American Journal of
 Botany)<br><br>Phylogenomic analyses using genomes and
 transcriptomes do not “resolve” relationships among major clades in
 Phrymaceae<br><br>This package contains the data and software
 outputs (i.e. fasta files, alignments, trees,
 etc).<br><br><br>1_transcriptomes_and_genomes:<br>     final_filtered_transcriptomes: CDS and PEP Fasta files of filtered transcriptomes<br>     genomes: Fasta files of CDS used genomes<br>     original_transcriptome_assemblies: Fasta files of original Trinity transcriptome assemblies<br>2_final_homologs: Tree files of final homologs in newick format<br>3_MO_orthologs: Tree files of final MO orthologs in newick format<br>4_MO_fasta_files_24tx_aln: Alignment and clean Alignments in fasta format from MO orthologs.<br>5_concatenated_matrices: Concatenated alignment from 4_MO_fasta_files_24tx_aln in fasta, nexus and phylyip formats.<br>6_phylogenetic_analyses<br>    ASTRAL: Input and output files from ASTRAL<br>    IQtree_concatenated: Input and output files from IQ-Tree for the concatenated alignment.<br>    IQtree_invidivual_gene_trees: Input and output files from IQ-Tree for the individual MO ortholog alignments.<br>    IQtree_invidivual_gene_trees_rooted: Rooted trees in newick format from IQtree_invidivual_gene_trees<br>    Phyparts: Input and output files Phyparts<br>    QS: Input and output files from Quartet Sampling<br>    cpDNA: Analises of the chloroplast data set.<br>         IQtree: Input and output files from IQ-Tree for the contiguous cpDNA alignment.<br>         QS: Input and output files from Quartet Sampling<br>         aln: Contiguous cpDNA alignment<br>         assemblies: cpDNA assemblies using FastPlast<br>             full_assemblies: Complete assemblies from 7 species.<br>             partial_assemblies: Partial assemblies from 7 species.<br>    hybridization_test: Hybridization analyses<br>         hyde: Input and output files from HyDe analyses.<br>         phylonet: Input and output files from PhyloNet analyses.<br>            mcmc_gt: Input and output files from MCMC_GT analyses.<br>            ml: Input and output files from InferNetworks_ML analyses.<br>    map_dup: Input and output files from the orthogroup mapping.<br>    treepl: Input and output files from individual time-calibrated ortholog trees for cloudogram<br>    wgd: Input and output files from analyses of distribution of Synonymous Distance among Gene Pairs (Ks plots)<br> <br> <br> If you have any question about the data, please do not hesitate to contact Diego F. Morales-Briones at dfmoralesb@gmail.com