DOI: 10.5061/dryad.msbcc2g1d
title: Data from: Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution

description: Flaveria (Asteraceae) is the prime model for the study of C4
 photosynthesis evolution and seems to support a stepwise acquisition of
 the pathway through C3-C4 intermediate phenotypes, still existing in
 Flaveria today. Molecular phylogenies of Flaveria based on concatenated
 data matrices are currently used to reconstruct the complex sequence of
 trait shifts during C4 evolution. To assess the possible role of
 hybridization in C4 evolution in Flaveria, we re-analyzed transcriptome
 data of 17 Flaveria species to infer the extent of gene tree discordance
 and possible reticulation events. We found massive gene tree discordance
 as well as reticulation along the backbone and within clades containing
 C3-C4 intermediate and C4-like species. An early hybridization event
 between two C3 species might have triggered C4 evolution in the genus. The
 clade containing all C4 species plus the C4-like species F. vaginata and
 F. palmeri is highly supported in our phylogenetic analyses, but it might
 be of hybrid origin involving F. angustifolia and F. sonorensis (both
 C3-C4 intermediate) as parental lineages. Hybridization seems to be a
 driver of C4 evolution in Flaveria and likely promoted the fast
 acquisition of C4 traits. This new insight can be used in further
 exploring C4 evolution and can inform C4 bioengineering efforts.
description: Data package from Morales-Briones and Kadereit
 Exploring the possible role of hybridization in the evolution of
 photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4
 photosynthesis evolution -
 https://doi.org/10.18061/bssb.v2i3.8992  This package
 contains the supplemental material and the data and software outputs (i.e.
 fasta files, alignments, trees, etc). - Supplemental
 material Table S1. Taxon sampling and source of
 data Table S2. HyDe significant hybridization tests for
 all species of Flaveria. Table S3. HyDe significant
 hybridization tests for all species of Flaveria excluding F. pringlei
 (C3). Fig. S1. a) Maximum likelihood phylogeny of
 Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene
 supermatrix. Numbers above branches represent bootstrap support (BS).
 Branch lengths as substitutions per site (scale bar on the bottom). b)
 ASTRAL tree of Flaveria inferred from the 2,127 nuclear gene trees. Local
 posterior probabilities (LPP) are shown next to nodes. Internal branch
 lengths are in coalescent units (scale bar on the
 bottom).<br> <br>Fig. S2. a) Maximum likelihood cladogram of
 Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene
 supermatrix. b) ASTRAL cladogram of Flaveria inferred from the 2,127
 nuclear gene trees. Pie charts represent the proportion of gene trees that
 support that clade (blue), the main alternative bifurcation (green), the
 remaining alternatives (red), and conflict or support that have
 &lt;50% bootstrap support (gray). Number above and below branches
 represent the number of concordant and discordant informative gene trees,
 respectively.<br> <br>Fig. S3. A. Maximum likelihood cladogram
 of Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene
 supermatrix. B. ASTRAL cladogram of Flaveria inferred from the 2,127
 nuclear gene trees. Quartet Sampling (QS) scores are shown above branches.
 QS scores: Quartet concordance/Quartet differential/Quartet
 informativeness. Circles at nodes are colored by quartet concordance
 support. Fig. S4. Distribution of tree-to-tree
 distances between empirical gene trees and the ASTRAL tree, compared to
 the distribution of tree-to-tree distances between simulated trees and the
 ASTRAL tree.<br> <br>Fig. S5. Maximum pseudo-likelihood scores
 for species networks inferred with PhyloNet using the a) 18-taxon, b) and
 16-taxon data sets. The x-axis notes the maximum number of reticulations
 for each of the network searches allowing up to ten reticulation
 events.<br> <br>Fig. S6. Maximum pseudo-likelihood species
 networks inferred with PhyloNet using the a) 18-taxon, b) and 17-taxon
 data sets and allowing up to 12 reticulation events. Red and blue curved
 branches indicate the minor and major edges, respectively of hybrid nodes.
 Numbers next to curved branches indicate inheritance probabilities for
 each hybrid node. Fig. S7. Maximum likelihood cladogram
 of Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene
 supermatrix. Numbers above branches are gene duplication counts and
 numbers below branches are gene duplication percentages.
 Note: Supplemental files are compatible with the CC0 license are
 not included in the main text of the article. -
 Data 1_transcriptomes_and_genomes<br>   
  final_filtered_transcriptomes:<br>         - Coding sequence (CDS)
 fasta files (*.cds.fa)<br>        - Protein translated (PEP) fasta
 files (*.pep.fa)<br>     genomes:<br>         - CDS and PEP
 fasta files (*.fasta)<br>   
  original_transcriptome_assemblies:<br>         - Fasta files
 (*.fasta) of original Trinity transcriptome
 assemblies<br>2_final_homologs:<br>     - Tree files
 (*.subtre) of homologs in newick format inferred with RAxML after
 monophyletic clades and paraphyletic grades of same species were masked,
 and spurious tips removed with
 TreeShrink<br>3_MO_orthologs_min_10_taxa:<br>    - Tree files
 (*.tre) of final MO orthologs in newick format. Orthologs were obtained
 from final homologs
 (2_final_homologs)<br>4_MO_min_21_taxa_aln_fasta_files:<br>   
 - Ortholog DNA alignments (*.aln) obtained with MAFFT in fasta
 format<br>    - Clean ortholog DNA alignmentsalignments (*aln-cln)
 from pxclsq in fasta format.<br>5_concatenated_matrices
     - flaveria_21tx_500bp_concat.fa - alignment in nexus
 format<br>    - flaveria_21tx_500bp_concat.model - partition file in
 RAxML format<br>    - flaveria_21tx_500bp_concat.nex - alignment in
 nexus format<br>    - flaveria_21tx_500bp_concat.phy - alignment in
 phylip format<br>    -
 flaveria_21tx_500bp_concat_taxon_occupancy_stats - taxon occupancy
 stats 6_phylogenetic_analyses<br>   
  ASTRAL:<br>     <br>     -
 ASTRAL_flaveria_2124_gene_trees_concat.tre - Species tree output from
 ASTRAL<br>     - flaveria_2124_gene_trees_concat.tre - Input file
 containing all ortholog trees<br>     <br>   
  IQtree<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>     QS<br>       
  QS_ASTRAL_flaveria_2115_gene_trees_genetree_part - QuartetSampling output
 files from the analysis using the ASTRAL tree<br>       
  QS_IQtree2_flaveria_21taxa_500bp_concat_genetree_part - QuartetSampling
 output files from the analysis using the IQtree tree<br>       
 Note: "NA" values in Quartet Sampling scores means that a node
 has full suport (e.g., 1/NA/1) and there is no skew for an alternative
 topology.<br>     <br>     coalescent_simulations<br>   
      paup - input and out files from PAUP analyses enforcing a strict
 molecular clock <br>        input_output_code - input and output
 trees from coalescent simulations, also includes R code to run
 simulations<br>     <br>     hyde<br>        - Input and
 output files from HyDe analyses using the 18-taxa dataset (all species)
 and the 17-taxa dataset (F. pringlei removed).<br>     <br>   
  map_wgd<br>         orthogroups_min_15_taxa - orthogroup tree files
 (*.ortho) prune from 2_final_homologs<br>        mapping - output
 files from othrogroup mapping<br>     <br>   
  phylonet<br>         reduced_trees - unrooted ortholog trees (*red)
 in newick format after pruning all outgroup but Helianthus<br>     
    runs - Phylonet input (*.nex) and output (*.txt) files<br>   
  <br>     phyparts<br>     <br>         ASTRAL - output
 files from Phyparts from the analysis using the ASTRAL tree<br>     
    IQtree - output files from Phyparts from the analysis using the IQtree
 tree <br>     <br>     treePL<br>            dated_tees
 - tree files (*.tre) in newick format of dated trees with
 treePL<br>        fasta_files - fasta files (*.red) from
 reduced_trees<br>        reduced_trees - unrooted ortholog trees
 (*red) in newick format after pruning all outgroup but
 Helianthus <br>        reduced_trees_rr - rooted ortholog trees
 (*red) in newick format after pruning all outgroup but
 Helianthus<br>        <br>If you have any questions about the
 data, please do not hesitate to contact Diego F. Morales-Briones at
 dfmoralesb@gmail.com
description: # Data from: Exploring the possible role of hybridization in the evolution
 of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4
 photosynthesis evolution
 [https://doi.org/10.5061/dryad.msbcc2g1d](https://doi.org/10.5061/dryad.msbcc2g1d) ## Description of the data and file structure DATA PACKAGE FROM MORALES-BRIONES AND KADEREIT Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution - https://doi.org/10.18061/bssb.v2i3.8992 This package contains the supplemental material and the data and software outputs (i.e. fasta files, alignments, trees, etc). \- Supplemental material Table S1. Taxon sampling and source of data Table S2. HyDe significant hybridization tests for all species of Flaveria. Table S3. HyDe significant hybridization tests for all species of Flaveria excluding F. pringlei (C3). Fig. S1. a) Maximum likelihood phylogeny of Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene supermatrix. Numbers above branches represent bootstrap support (BS). Branch lengths as substitutions per site (scale bar on the bottom). b) ASTRAL tree of Flaveria inferred from the 2,127 nuclear gene trees. Local posterior probabilities (LPP) are shown next to nodes. Internal branch lengths are in coalescent units (scale bar on the bottom). Fig. S2. a) Maximum likelihood cladogram of Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene supermatrix. b) ASTRAL cladogram of Flaveria inferred from the 2,127 nuclear gene trees. Pie charts represent the proportion of gene trees that support that clade (blue), the main alternative bifurcation (green), the remaining alternatives (red), and conflict or support that have &lt;50% bootstrap support (gray). Number above and below branches represent the number of concordant and discordant informative gene trees, respectively. Fig. S3. A. Maximum likelihood cladogram of Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene supermatrix. B. ASTRAL cladogram of Flaveria inferred from the 2,127 nuclear gene trees. Quartet Sampling (QS) scores are shown above branches. QS scores: Quartet concordance/Quartet differential/Quartet informativeness. Circles at nodes are colored by quartet concordance support. Fig. S4. Distribution of tree-to-tree distances between empirical gene trees and the ASTRAL tree, compared to the distribution of tree-to-tree distances between simulated trees and the ASTRAL tree. Fig. S5. Maximum pseudo-likelihood scores for species networks inferred with PhyloNet using the a) 18-taxon, b) and 16-taxon data sets. The x-axis notes the maximum number of reticulations for each of the network searches allowing up to ten reticulation events. Fig. S6. Maximum pseudo-likelihood species networks inferred with PhyloNet using the a) 18-taxon, b) and 17-taxon data sets and allowing up to 12 reticulation events. Red and blue curved branches indicate the minor and major edges, respectively of hybrid nodes. Numbers next to curved branches indicate inheritance probabilities for each hybrid node. Fig. S7. Maximum likelihood cladogram of Flaveria inferred with IQ-TREE from the concatenated 2124-nuclear gene supermatrix. Numbers above branches are gene duplication counts and numbers below branches are gene duplication percentages. Note: Supplemental files are compatible with the CC0 license are not included in the main text of the article. \- Data 1_transcriptomes_and_genomes final_filtered_transcriptomes: \- Coding sequence (CDS) fasta files (*.cds.fa) \- Protein translated (PEP) fasta files (*.pep.fa) genomes: \- CDS and PEP fasta files (*.fasta) original_transcriptome_assemblies: \- Fasta files (*.fasta) of original Trinity transcriptome assemblies 2_final_homologs: \- Tree files (*.subtre) of homologs in newick format inferred with RAxML after monophyletic clades and paraphyletic grades of same species were masked, and spurious tips removed with TreeShrink 3_MO_orthologs_min_10_taxa: \- Tree files (*.tre) of final MO orthologs in newick format. Orthologs were obtained from final homologs (2_final_homologs) 4_MO_min_21_taxa_aln_fasta_files: \- Ortholog DNA alignments (*.aln) obtained with MAFFT in fasta format \- Clean ortholog DNA alignmentsalignments (*aln-cln) from pxclsq in fasta format. 5_concatenated_matrices \- flaveria_21tx_500bp_concat.fa - alignment in nexus format \- flaveria_21tx_500bp_concat.model - partition file in RAxML format \- flaveria_21tx_500bp_concat.nex - alignment in nexus format \- flaveria_21tx_500bp_concat.phy - alignment in phylip format \- flaveria_21tx_500bp_concat_taxon_occupancy_stats - taxon occupancy stats 6_phylogenetic_analyses ASTRAL: \- ASTRAL_flaveria_2124_gene_trees_concat.tre - Species tree output from ASTRAL \- flaveria_2124_gene_trees_concat.tre - Input file containing all ortholog trees IQtree    IQtree_concatenated - Input and output files from IQ-Tree for the concatenated alignment.    IQtree_invidivual_gene_trees - Input and output files from IQ-Tree for the individual MO ortholog alignments.    IQtree_invidivual_gene_trees_rooted - Rooted trees in newick format from IQtree_invidivual_gene_trees QS    QS_ASTRAL_flaveria_2115_gene_trees_genetree_part - QuartetSampling output files from the analysis using the ASTRAL tree    QS_IQtree2_flaveria_21taxa_500bp_concat_genetree_part - QuartetSampling output files from the analysis using the IQtree tree Note: "NA" values in Quartet Sampling scores means that a node has full suport (e.g., 1/NA/1) and there is no skew for an alternative topology. coalescent_simulations    paup - input and out files from PAUP analyses enforcing a strict molecular clock input_output_code - input and output trees from coalescent simulations, also includes R code to run simulations hyde \- Input and output files from HyDe analyses using the 18-taxa dataset (all species) and the 17-taxa dataset (F. pringlei removed). map_wgd    orthogroups_min_15_taxa - orthogroup tree files (*.ortho) prune from 2_final_homologs mapping - output files from othrogroup mapping phylonet    reduced_trees - unrooted ortholog trees (*red) in newick format after pruning all outgroup but Helianthus    runs - Phylonet input (*.nex) and output (*.txt) files phyparts ASTRAL - output files from Phyparts from the analysis using the ASTRAL tree IQtree - output files from Phyparts from the analysis using the IQtree tree treePL dated_tees - tree files (*.tre) in newick format of dated trees with treePL fasta_files - fasta files (*.red) from reduced_trees reduced_trees - unrooted ortholog trees (*red) in newick format after pruning all outgroup but Helianthus reduced_trees_rr - rooted ortholog trees (*red) in newick format after pruning all outgroup but Helianthus If you have any question about the data, please do not hesitate to contact Diego F. Morales-Briones at dfmoralesb@gmail.com