DOI: 10.5061/dryad.xsj3tx9hh
title: On the hybrid origin of the C2 Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages

description: C2 photosynthesis is characterized by recapturing photorespiratory CO2 by
 RuBisCO in Kranz-like cells and is therefore physiologically intermediate
 between C3 and C4 photosynthesis. C2 can be interpreted as an evolutionary
 precursor of C4 and/or as the result of hybridization between a C3 and C4
 lineage. We compared the expression of photosynthetic traits among
 populations of the Salsola divaricata agg. (C2) from humid subtropical to
 arid habitats on the coasts of the Canary Islands and Morocco and
 subjected them to salt and drought treatments. We screened for enhanced
 C4-like expression of traits related to habitat or treatment. We estimated
 species trees with a transcriptome dataset of Salsoleae and explored
 patterns of gene tree discordance. With phylogenetic networks and
 hybridization analyses we tested for hybrid origin of the Salsola
 divaricata agg. We observed distinct independent variation of
 photosynthetic traits within and among populations and no clear evidence
 for selection towards C4-like trait expression in more stressful habitats
 or treatments. We found reticulation and gene tree incongruence in
 Salsoleae supporting a putative hybrid origin of the Salsola divaricata
 agg. C2 photosynthesis in the Salsola divaricata agg. combines traits
 inherited from its C3 and C4 parental lineages and seems evolutionarily
 stable, possibly well adapted to a wide climatic amplitude.
description: DATA PACKAGE FROM TEFARIKIS ET AL (New
 Phytologist)<br><br>On the hybrid origin of the C2 Salsola
 divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages
 <br><br>This package contains the data and software outputs
 (i.e. fasta files, alignments, trees,
 etc).<br><br>1_transcriptomes_and_genomes:
 - final_filtered_transcriptomes: <br>Coding sequence (CDS)
 fasta files (*.cds.fa)<br>Coding sequence (CDS) fasta files
 clustered with CD-HIT (*cdhitest)<br>Protein translated (PEP) fasta
 files (*.pep.fa)      - genomes: <br>CDS and PEP
 fasta files (*.fasta) of Beta vulgaris genome -
 original_transcriptome_assemblies:<br>Fasta files of original
 Trinity transcriptome assemblies<br>            
 <br>2_final_homologs: - Tree files (*.tre) 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:
 - Tree files (*.tre) of final MO orthologs in newick format.
 Orthologs were obtained from final homologs
 (2_final_homologs)<br><br>4_MO_fasta_files_17tx_aln:
 - Ortholog DNA alignments (*.aln) obtained with MAFFT in fasta
 format<br>- Clean ortholog DNA alignmentsalignments (*aln-cln) from
 pxclsq in fasta format.<br><br>5_concatenated_matrices:
 Concatenated alignment from 4_MO_fasta_files_17tx_aln -
 concatenate_MO_orthologs_300_17_taxon_occupancy_stats - taxon occupancy
 stats<br>- concatenate_MO_orthologs_300_17.fa - alignment in fasta
 format<br>- concatenate_MO_orthologs_300_17.model - partition file
 in RAxML format<br>- concatenate_MO_orthologs_300_17.nex - alignment
 in nexus format<br>- concatenate_MO_orthologs_300_17.phy - alignment
 in phylip format<br><br>6_phylogenetic_analyses
 - ASTRAL: <br>all_orthologs_trees.tre - Input tree
 containing all ortholog trees<br>astral_all_orthologs_trees_lpp.tre
 - Species tree output from ASTRAL - HyDe:
 <br>run_hyde_individuals.sh - command used to run
 HyDe<br>ind_level_all_sites-out-filtered.txt - filtered output of
 HyDe<br>ind_level_all_sites-out.txt - raw output of
 HyDe<br>map_ind_level.txt - map file at individual
 label<br>concatenate_MO_orthologs_300_17_for_hyde.phy - concatenated
 alignment of ortholog alignments in phylip format.<br>  
  <br>- Phylonet:<br>    <br>1(3)-5_hyb.nex - best
 networks from each analyses (see Table 2)<br>astral_fit.nex - nexus
 file to calculate the ML score of the ASTRAL tree with CalGTProb in
 PhyloNet<br>astral_fit.out - ML score of the ASTRAL tree with
 CalGTProb in PhyloNet<br>cpdna_fit.nex - nexus file to calculate the
 ML score of the cpDNA tree<br>cpdna_fit.out - ML score of the cpDNA
 tree tree with CalGTProb in PhyloNet<br>raxml_fit.nex - nexus file
 to calculate the ML score of the RAxML tree with CalGTProb in
 PhyloNet<br>raxml_fit.out - ML score of the RAxML tree with
 CalGTProb in PhyloNet<br>phylonet_mpl_(1-5)hyb.nex - PhyloNet nexus
 input files for searches with 1 to 5 reticulation
 events.<br>phylonet_mpl_(1-5)hyb.out - Phylogenetic networks output
 from PhyloNet for searches with 1 to 5 reticulation events.
 - Phyparts: <br>ASTRAL: output files from Phyparts from the
 analysis using the ASTRAL
 tree<br>directory_of_ortholog_MO_trees_rooted: rerooted orthologs
 trees in newick format (*.rr)<br>RAxML: output files from Phyparts
 from the analysis using the RAxML tree -
 QuartetSampling:   <br>raxml_quartet_sampling: QuartetSampling
 output files from the analysis using the RAxML
 tree<br>astral_quartet_sampling: QuartetSampling output files from
 the analysis using the ASTRAL tree<br>    <br>-
 RAxML_concatenated Output files from RAxML for the
 concatenated alignment.<br>    <br>-
 RAxML_invidivual_gene_trees Tree files in newick format
 (*.tre) from RAxML for the individual MO ortholog alignments.
 - cpDNA: Input and output files from plastome data
 set.<br>IQtree - Input and output files from IQ-Tree for the
 contiguous cpDNA alignment.<br>QuartetSampling: Input and output
 files from Quartet Sampling<br>aln: Contiguous cpDNA alignment with
 MAFFT (*aln) and also masked alignment with GBlocks
 (*.aln-cln)<br>filtered_contigs_from_cp_assemblies: filtered contigs
 form partial assemblies in fasta format (*.fasta) for five species of
 Salsola -
 photosynthetic_gene_trees<br>gene_trees: unrooted (*.ur) and rooted
 (*reroot) baited gene trees in newick format<br>AT_baits:
 Arabidopsis references for baited homology of C4 genes of
 interest<br>        <br>If you have any questions about the
 data, please do not hesitate to contact Diego F. Morales-Briones at
 dfmoralesb@gmail.com