Article https://doi.org/10.1038/s41586-019-1693-2 Supplementary information
One thousand plant transcriptomes and the phylogenomics of green plants
In the format provided by the One Thousand Plant Transcriptomes Initiative authors and unedited
Nature | www.nature.com/nature Supplemental Methods
Transcriptome data generation Sample acquisition: The 1000 plants initiative (1KP or onekp) analyzed 1342 RNA seq libraries from 1147 species including 1112 green plant species representing all of the major taxa within the Viridiplantae, including angiosperms, conifers, ferns, mosses, streptophytic algae and chlorophyte green algae (Supplementary Table 1). Because of the diversity of species, no one source could be used. Samples were provided by a global network of more than a hundred tissue and RNA providers (see author contributions) who obtained materials from a variety of sources, including field collection of wild plants, botanical gardens, greenhouses, laboratory specimens, and culture collections. Typically, samples were fast growing tissues such as young leaves or shoots, because these are expected to be largely comprised of live cells and therefore rich in RNA. However, some RNAs were derived from a mix of vegetative and reproductive tissues and we did not attempt to define specific standards on growth conditions, time of collection, or age of tissue. Vouchering system: The majority of the samples have corresponding vouchers deposited at various institutions, as convenient for the sample providers (http://www.onekp.com/samples/list.php). For the algal species, material from culture collections was sourced and the relevant collection identifiers are reported. Species names were validated with the Taxonomic Name Resolution Service1(http://tnrs.iplantcollaborative.org) or checked against other plant name databases such as Tropicos (http://www.tropicos.org). Numerous minor issues in species names were resolved in this way. RNA extraction: Because RNA is expected to degrade rapidly after a sample is taken, RNA extractions were either performed immediately after tissue collection, or tissue was flash frozen in liquid nitrogen and stored at or below -80˚C until extraction. Given the biochemical diversity of our samples, no one RNA extraction protocol was appropriate for every instance. Most of the samples were extracted with common extraction protocols such as CTAB, TRIzol, hot acid-phenol, or with commercial products such as Invitrogen Purelink or Qiagen RNeasy kits and variants thereof. For complete details of specific protocols please see Appendix S1 of Johnson et al.2 and Jordon-Thaden et al.3. Depending on the sample, the RNA extraction might have been done at the sequencing lab or by one of the sample providers. RNA was either shipped on dry ice or (for 36% of cases) at ambient temperatures in GenTegra. Sequencing at BGI: Before library construction, RNA quality was assessed by a Bioanalyzer spectrogram (typically requiring RIN scores of greater than 6) and basic photometery for obvious low-quality outliers. BGI used either in house protocols or TruSeq chemistry (low-mass cases) to create sequencing libraries of ~200 bp insert sizes. Initially, paired-end sequencing was done with Illumina GAII machines, but later samples were run on the HiSeq platform. Associated with this change was a shift from a ~72 bp read length to a 90 bp read length at each end. Libraries were barcoded and multiplexed on the sequencer lanes to a target sequencing depth of at least 2 Gbp of Q20 data per sample.
Percentile Dataset Size
5th 1.3 Gbp
25th 1.9 Gbp
50th 2.2 Gbp
75th 2.5 Gbp
95th 3.0 Gbp
After removal of read-pairs with various low-quality indications, and demultiplexing, the sequence was provided to the rest of the consortium for further analysis. De novo assembly: Quality filtered reads were assembled de novo using the SOAPdenovo-Trans assembler (version of 2012-04-05)4. No additional pre-processing of the data was performed. The assembly was done by running both the main assembler and the GapCloser post-processor programs. Options were the program defaults, except that the k-mer length was increased to 25 bp. Assembly qualities: We assessed the quality of each assembled scaffold using TransRate5 which maps reads to assemblies to assign a quality score to each scaffold as an assessment of accuracy, fragmentation and completeness5. Overall TransRate scores are the geometric mean of all contig scores multiplied by the proportion of reads mapping to the assembly. Scores ranged between 0.012 and 0.393 (median = 0.103; Supplementary Table 1), in line with the range of scores reported for NCBI SRA assemblies assessed in the TransRate publication (range 0-0.523, median = 0.217)5. The representation of conserved genes was assesses for each assembled transcriptome using CEGMA6 and BUSCO7 with both an all-plant reference (embryophyta_odb9) and an all-eukaryote reference (eukaryota_odb9). The table below shows the percentages of complete genes found for each of the three references.at several percentiles of the whole dataset.
Percentile CEGMA 248 BUSCO - Embryophyta* BUSCO - Eukaryota*
5 79.03 11.2 (8.5) 66.0 (37.3)
25 89.92 44.1 (29.8) 84.9 (64.4)
50 92.34 62.5 (48.2) 90.4 (75.9)
75 93.55 75.2 (59.6) 93.7 (84.1)
95 94.76 82.6 (73.2) 96.1 (91.0) *Complete+fragment assemblies reported with complete sequences in parentheses. Sample purity and contamination: The diversity of sample sources ensures that there will be some contamination of the plant tissue by other environmental nucleic acids. These contaminants can reasonably be expected to include bacterial, fungal, and insect species that live in and on the plant tissues, and more rarely, from contact with larger species such as frogs, mice, birds, and humans. For most analyses these minor contaminants are not expected to have an impact, as only the most abundant of such contaminants will be present in sufficient quantities to be assembled or in many cases they were sufficiently diverged from the intended species to be easily recognized as non-plant genes. Unfortunately, this is not always the case and unfiltered contaminants were identified as long branches in the gene trees for the single copy genes (see phylogenetics section of Methods). In general, users of RNAseq data sets, including those generated for this study, should be wary of contaminant reads and assemblies derived from endogenous microbes or other sources.
We guarded against these various problems by employing several analyses, the largest of which compared the assembled sequences by Blastn to a reference set of 18S rRNA sequences from the SILVA SSU rRNA database (http://www.arb-silva.de/)8. For most samples we were able to establish that an 18S rDNA sequence taxonomically close to the intended species was present. In a few cases, additional 18S sequences more- closely matched to other plants were found, suggesting that these might have been contaminated by other plants. We found that 560 samples have non-plant contaminants while 108 samples had unexpected matches with other plants. Contaminant sequences were filtered and 18 samples with multiple plant contaminant sequences (18S, plastid genes and protein-coding nuclear genes) were excluded from further analyses. Possible remaining contaminant sequences identified as highly divergent either when mapping reads to plastid gene assemblies or as exceedingly long branches in gene tree phylogenies. These reads and assemblies were filtered as described below.
For the chloroplast DNA sequence analyses, contaminating chloroplast sequences proved to be common—likely due to the high copy number per cell—and appropriate steps were taken to remove contaminants which was facilitated by the large number of chloroplast reference genes and genomes already available9. On average, 13.4% of sequences identified as a chloroplast gene from a particular sample were discarded as too divergent to represent the true sequence of that taxon.
Protein translation: To identify proteins within the assembled transcripts, they were passed through TransPipe10. The reading frame and protein translation for each sequence is identified by comparison to protein sequences from 25 sequenced and annotated plant genomes from Phytozome11. Using BLASTX12, best hit proteins are paired with each gene at a minimum cutoff of 30% sequence similarity over at least 150 sites. Genes that did not have a best hit protein at this level are removed. To determine reading frame and generate estimated amino acid sequences, each gene is aligned against its best hit protein by Genewise 2.2.213. Using the highest scoring Genewise DNA-protein alignments, custom Perl scripts are used to remove stop and 'N' containing codons and produce estimated amino acid sequences for each gene. Output includes paired DNA and protein sequences with the DNA sequence reading frame corresponding to each protein sequence.
Phylogenetic Analyses
Phylogenetic methods are described in the Methods section of the main text. Below are the command-line calls for the scripts and programs used for each phylogenetic analysis. All scripts used to perform analyses on the nuclear gene data are available at https://github.com/smirarab/1kp. Sequence alignment and filtering To build the combined PASTA and UPP alignments, we used the following script:
runupp.sh
We then used scripts mask-gt.sh to mask gappy sites and sequences from alignments and used remove-long-branch.sh to mask long branches. The last script uses Dendropy15 internally. Gene tree estimation: We used the following scripts to estimate gene trees:
● runraxml-rapidboot.sh upp-masked.fasta.mask10sites.mask33taxa FAA 4 [gene id] main 10 100 mp slow ● runraxml-rapidboot.sh upp-masked.fasta.mask10sites.mask33taxa FNA2AA 4 [gene id] main 10 100 mp slow
These scripts internally run the following RAxML commands: ● raxmlHPC-PTHREADS -m
Species tree estimation: To estimate species trees with no contraction of polytomies, we use: java -jar astral.5.0.3.jar -i Best -o
Estimation of supermatrix trees: alltaxa FAA-upp-masked.fasta.mask10sites.mask33taxa.bootstrap.tre FNA2AA-upp-masked-c12.fasta.mask10sites.mask33taxa.bootstrap.tree eudicots eudicot.FAA-upp-masked.fasta.mask10sites.mask33taxa.bootstrap.tree eudicot.FNA2AA-upp-masked-c12.fasta.mask10sites.mask33taxa.bootstrap.tree remove-rogue filtered_FAA-upp-masked.fasta.mask10sites.mask33taxa.bootstrap.tree filtered_FNA2AA-upp-masked-c12.fasta.mask10sites.mask33taxa.bootstrap.tree
The commands used to reproduce the results are given below.
Convert the supermatrix alignment to the ExaML input format parse-examl -s
Compute the RAxML MP starting tree raxmlHPC-PTHREADS-SSE3 -T 12 -s
Compute the FastTree-2 ML starting tree FastTreeMP (if DNA: -nt -gtr) -nosupport -out
Compute GTR matrix and alpha parameter for codon position raxmlHPC-PTHREADS-SSE3 -T 12 -s
Generate bootstrap replicate alignments raxmlHPC-PTHREADS-SSE3 -T 12 -s
Compute the ExaML final/replicate tree examl-OMP -s
Inferring and Placing Whole-Genome Duplications on the Phylogeny We used a total evidence approach to infer and place ancient WGDs across the 1KP phylogeny. WGDs were inferred from age distributions of gene duplications by analyzing transcriptomes of single species with the DupPipe pipeline10. To place inferred WGDs from Ks plots onto the phylogeny, we compared the median Ks of these peaks to the divergence of orthologs among species across the phylogeny10. Finally, we employed MAPS analyses14,15 to confirm the inference and phylogenetic placement of the ancient WGDs inferred in the preceding analyses. The detailed descriptions for each approach are provided in the methods section and results of all analyses are available in Supplementary Tables 2–5. Supplementary Table 2 provides an integrated guide to all of the results used to infer and place WGDs in the 1KP phylogeny (Fig. 4, Supplementary Fig. 8).
For each transcriptome, we used the DupPipe pipeline to construct gene families and estimate the age of gene duplications. The age distribution of gene duplications was plotted on two sets of histograms with x-axis scales of Ks = 2 and Ks = 5 to assess WGDs at different scales (Supplementary Table 2, https://bitbucket.org/barkerlab/1kp). To identify significant features in the paralog age distributions, two statistical tests were employed (K-S goodness of fit tests, and mixture models). A bootstrapped K-S goodness of fit test16 was used to assess if the overall age distributions deviated from a simulated null without paleopolyploidizations. Taxa that significantly deviated from the null were then further explored with mixture models and manual curation to infer peaks of gene duplication consistent with WGDs. We used a mixture model implemented in the mixtools R package17 to identify significant peaks and estimate their median Ks values (Supplementary Table 3). Although we examined Ks plots out to Ks = 5, we did not consider peaks with Ks > 2 as potential WGDs without other data available. This is because beyond Ks = 2, mixture models may identify peaks due to error rather than biological signal18. We also mitigated error in WGD inference from Ks plots by estimating the Ks of gene duplications from gene trees, rather pairwise comparisons19. Consistent with this practice, 99.6% of all inferred WGDs in our analyses had a median paralog divergence of Ks < 2 and should not be subject to significant error in their inference or be false positives from mixture model overfitting.
For many species with evidence of WGDs, Ks plots of their sister lineages did not contain evidence of the putative WGD. We inferred that these WGDs occurred independently in their lineage’s history and did not occur in the ancestry of their sister lineages in the 1kp phylogeny. We further confirmed the placement of these independent WGDs with analyses of ortholog divergence (Supplementary Table 4). We expected the median Ks of the signature peak of this independent WGD should be younger than the ortholog divergence between the species with evidence of the WGD and its sister taxa that did not. By calculating the ortholog divergence between two species from sister lineages, we estimated the expected upper bound of Ks for an independent WGD and confirmed the placement of each putative independent WGD. Comparisons of ortholog divergence and the median Ks values of peaks inferred as WGDs may be found in Supplementary Tables 2–4.
For any WGDs that may be shared by at least 3 species, we further used MAPS14,15 to confirm the placement of the shared WGD(s) (Supplementary Tables 2, 5-6). We circumscribed and constructed nuclear gene family phylogenies from multiple species for each MAPS analysis. MAPS requires nuclear gene families to contain at least one gene copy from each taxon in a given MAPS analysis and discards the remaining gene family clusters. To maintain sufficient gene tree numbers for each MAPS analysis, we used collections of gene family phylogenies for six to eight taxa to infer ancient WGDs. MAPS identifies and records nodes with a gene duplication shared by descendant taxa.
Errors in transcriptome or genome assembly, gene family clustering, and the construction of gene family phylogenies can result in topological errors in gene trees20. Previous studies have suggested that errors in gene trees can lead to bias placements of duplicates towards the root of the tree and losses towards the tips of the tree21. For this reason, we aim to put focal nodes for a particular MAPS analysis test in the middle of the phylogeny. To further decrease potential error in our inferences of gene duplications, we required at least 45% of the ingroup taxa to be present in all subtrees analyzed by MAPS. If this minimum ingroup taxa number requirement is not met, the gene subtree will be filtered out and excluded from our analysis. Increasing taxon occupancy should lead to more accurate duplication inference and reduce some of the biases in mapping duplications onto a species tree21,22.
We expect that the number of gene duplications on each branch will vary with branch length. We also expect that changes in species composition among our MAPS analyses will impact the number of shared gene duplications observed at a particular branch in different analyses. To account for this variation in our comparisons, all MAPS analyses were first compared to a null simulation of the number of gene duplications we expect on each branch from background gene birth and death. A Fisher’s exact test, implemented in R was used to identify locations with significant increases of gene duplication compared with a null simulation (Supplementary Table 5). For all MAPS analyses with significant bursts of gene duplication detected with the Fisher’s exact test, we simulated an additional distribution of gene trees with a WGD at the location of the significant burst of duplication. If these increases in gene duplications are due to WGDs, we expect the number of shared gene duplication in the observed MAPS result to be consistent with these positive simulations. A second Fisher’s exact test was then used to characterize bursts of duplication as WGDs if the observed data was not significantly less than the percentage of duplications in a positive simulation (Supplementary Table 6).
For the null simulations, we first estimated the mean background gene duplication rate (λ) and gene loss rate (μ) with WGDgc23. Gene count data were obtained from OrthoFinder24 clusters associated with each species tree (SupplementaryTable 11). λ and μ were estimated using only gene clusters that spanned the root of their respective species trees, which has been shown to reduce biases in the maximum likelihood estimates of λ and μ23. We chose a maximum gene family size of 100 for parameter estimation, which was necessary to provide an upper bound for numerical integration of node states23. We provided a prior probability distribution on the number of genes at the root of each species tree, such that ancestral gene family sizes followed a shifted geometric distribution with mean equal to the average number of genes per gene family across species (Supplementary Table 11).
Gene trees were then simulated within each MAPS species trees using the GuestTreeGen program from GenPhyloData25. For each species tree, we simulated 3000 gene trees with at least one tip per species: 1000 gene trees at the λ and μ maximum likelihood estimates, 1000 gene trees at half the estimated λ and μ, 1000 trees at three times λ and μ. For all simulations, we applied the same empirical prior used for estimation of λ and μ. We then randomly resampled 1000 trees without replacement from the total pool of gene trees 100 times to provide a measure of uncertainty on the percentage of subtrees at each node. Given that natural gene tree discordance and errors from methodological sources are an inescapable part of our analyses, we also introduced error into our gene tree simulations. For each set of 1000 gene trees, each gene tree had a 50% of chance that three pairs of genes would randomly swap positions. We selected to randomize three pairs of genes to introduce a range of errors in our gene trees similar to other studies26.
For positive simulations, we simulated gene trees using the same methods described above. However, we incorporated a WGD at the location in each of the MAPS phylogenies with significantly larger numbers of gene duplications compared to the null simulation. Previous empirical estimates of paralogs retained following a plant WGD are approximately 10% on average27. To be conservative for inferring WGDs in our MAPS analyses, we allowed at least 20% of the genes to be retained following the simulated WGD to account for biased gene retention and loss. To assess power for WGDs with lower gene retention rates, we ran an additional simulation using 15% gene retention (Supplementary Table 6).
To place ancestrally shared WGDs on species phylogenies, we used simulated gene family phylogenies with and without WGDs to identify significant bursts of gene duplication that are consistent with WGDs. A WGD will produce a large burst of shared duplications across taxa and gene trees. This burst of duplication will appear as an increase in the percentage of shared gene duplications at a particular branch in our MAPS analyses. We interpreted an episodic burst of shared gene duplication that had significantly more shared duplications than expected compared to the null simulations and statistically consistent with our positive simulations of WGDs as evidence of a shared WGD. Combined with evidence from Ks plots and ortholog divergence analyses, the MAPS analyses provided phylogenomic tests for evidence of ancient, shared genome duplication events (Supplementary Table 2). In the few cases where our data conflicted, we used a total evidence approach to infer duplication events. These were mostly cases where inferences from Ks plots, ortholog comparisons, and the previous literature agreed, but MAPS did not. In these instances where MAPS inferred a significant burst of gene duplication not clearly apparent in other analyses, we indicated this in Supplementary Tables 6 and as blue squares on the ED WGD Phylogeny Figure.
All datasets used for the WGD analyses are available at https://bitbucket.org/barkerlab/1kp and scripts used for the MAPS analyses are at https://bitbucket.org/barkerlab/maps . Gene Family Evolution
Transcriptome completeness for gene family analyses We used the BUSCO7 assessments described above for the eukaryote data set (eukaryota_odb9) with conditional reciprocal best BLAST (CRBB) hits calculated using CRB-BLAST 28 with default parameters for 248 core eukaryotic genes (CEGs) distributed with the CEGMA software (Core Eukaryotic Genes Mapping Approach)29. CRBB hits were produced for each library individually which accounts for species specific threshold determination.
Percentage BUSCO abundance was calculated as 100% minus missing percentage. Percentage CEG abundance was calculated as number of CEGs with a CRBB hit divided by the total number of used CEGs. All libraries that showed less than 57.5% BUSCO abundance were removed from further analysis to account for possible transcriptome incompleteness due to library preparation or sample quality.
Pfam detection is not unduly biased by the prevalence of angiosperm exemplars PFAM HMMs30 constructed from manually validated seed sequences in the UniProt database. Unfortunately, these seed sequences are highly biased towards angiosperms, since A. thaliana is a popular model in plant genetics. For example, the validated sequence collection for the F-box, a domain found across plants, animals, and fungi, has 158 sequences from Viridiplantae of which all come from angiosperms and 155 alone from A. thaliana.
To check whether the sequence composition biases the results of this study towards angiosperms and is the reason for the trends observed in Fig 4b we compared the results of: a) the PFAM database, b) the PFAM database without sequences from streptophytes. Default settings of HMMER v3.1b231 were used to screen for domain hits. Some gene families have been identified with using custom HMMs and therefore were not included in this study. Further, HMMs with less than 6 sequences left after eliminating streptophyte sequences have also been removed from this study. For the following 15 remaining gene families we re-evaluated family sizes: “F-box”, “AP2_EREBP”, “bHLH”, “bZIP”, “C2H2”, “C3H”, “WRKY”, “ABC”, “PP2C”, “Receptor-like Kinases”, “P450s”, “MYB”, “NAC”, “PHD”, and “GRAS”. Results from both approaches show a high Pearson correlation (r=0.997). We therefore conclude that angiosperm bias for PFAM sequence alignments cannot be responsible for the effects observed in Fig. 5b.
Evolution of MADS-box gene evolution
Identification of MADS-box genes: 1KP transcripts were translated in all six possible reading frames and searched using the HMMer program31 and the HMM of the MADS domain as described by Gramzow and Theißen32. As some of the transcripts are incomplete and as the K domain is a second characteristic protein domain of MIKC-type MADS domain proteins33, we also conducted HMMer searches using a customized HMM of the K domain. An alignment of exemplary K domains from MIKC-type MADS-domain proteins was used to identify transcript assemblies including only the K- domain (Extended Data Fig. 1). The alignment was used to construct an HMM for the K domain.
Phylogeny of MADS-box genes: MIKCC-group MADS-domain proteins from non-algae and non-seed-plant species as found in the 1kp data, known MADS-domain proteins from land plants, and CgMADS1 from Chara globularis were aligned using Probalign34. The alignment was checked manually, and poorly conserved positions were deleted. The MADS-box gene phylogeny (Extended Data Fig. 2) was constructed using RAxML where the protein substitution model LG35 was chosen, the maximum likelihood phylogeny and 1000 bootstrap replicates were calculated in one program run (option “-f a”), and CgMADS1 was set as representative of the outgroup.
Supplemental Results
Species Tree Estimations
As described above, species trees were estimated using the ASTRAL gene tree summary method (Supplementary Fig. 1), and RAxML analyses of concatenated supermatrices (Supplementary Fig. 2) for the 410 single-copy nuclear genes for 1147 accessions included in Supplementary Table 1. A tree was also estimated from plastid gene sequences extracted from the RNA seq data (see methods above; Supplementary Fig. 3). Occupancy in the data matrices was high with a across species median of 339 of the 410 genes included in the ASTRAL and supermatrix analyses (Supplementary Figures 4-5). Estimated species relationships were generally robust and consistent among analyses, but resolution of some historically problematic relationships (e.g. bryophytes (Supplementary Fig. 6b) or conifer lineages and gnetales (Supplementary Fig. 6c) did vary among between ASTAL and supermatrix analyses or between amino acid and nucleotide analyses (Supplementary Fig. 6). Differences between amino acid and nucleotide analyses may be due to variation in codon usage and GC content at 1st and 3rd codon positions (Supplementary Fig. 7)
Inferred WGDs
Overall, we inferred a total of 244 potential WGD events throughout the green plant phylogeny (Fig. 4, Supplementary Fig. 8). These putative WGDs were inferred using a total evidence approach that combined inferences of WGDs from gene age distributions (Ks plots) and their phylogenetic placement based on pairwise comparisons of ortholog divergence 10,16,19. These results were compared with simultaneous inference and phylogenetic placement of putative WGDs in MAPS15,36. We also compared our results to the large body of literature on WGDs during plant evolution16,19,37–84. We found that 106 of the 244 WGDs we inferred were previously reported in the literature (Supplementary Table 2). Almost all of the 138 newly inferred WGDs were inferred in lineages newly sampled by the 1KP project. All of the inferred WGDs were detected in Ks plots of species (Supplementary Table 3), and 63 WGDs on internal branches were also supported by MAPS analyses (Supplementary Table 2, 5-6). Nearly all of the putative WGDs were inferred with paralog peak medians of Ks < 2. These inferences should not be subject to significant error in their inference from saturation effects16,18,81. We found that 237 of the 244 inferred WGDs had a median peak paralog divergence of Ks < 2 in all species surveyed. Only seven of the inferred WGDs, or 2.9% of our results, had a median paralog divergence of Ks > 2 in some species. Of these seven WGDs, only 1 of the WGD inferences was higher than Ks = 2 in all species analyzed. In this case, CHROα, the WGD had an inferred median Ks ~ 2.1 in the Chloromonas algae and support from MAPS. In the other seven cases, the WGD had a Ks peak < 2 in one or more species. Two of these WGDs are also well described from previous studies using synteny (the eudicot hexaploidy ARTHγ46,52,85,86 and the τ WGD of the monocots ORSAγ64), one is described with support from synteny from the first sequenced fern genomes (CYATγ in Li et al. 2018 Nature Plants), and one is well known from previous analyses and well debated (the seed plant WGD GINKα15,44,45,87). Only three of these very ancient WGD inferences were not previously observed. All three of these WGDs— CHROα, OSMNβ, and LYCOβ— are from newly sequenced lineages in the 1KP project. We believe these three inferences of deep WGDs from combined MAPS, Ks plots, and orthologous divergence are robust, but as with any inference future analyses with new data and/or approaches may revise the nature of the duplications or their phylogenetic placements.
Our analyses with MAPS also found evidence of 24 significant bursts of gene duplication that were not clearly associated with a WGD from the literature or our analyses of Ks plots. These are indicated in the Supplementary Fig. 8 as blue squares and noted in the associated MAPS analyses as significant duplications without a WGD designation (Supplementary Table 6). Among all of these bursts of duplication, most occur among the mosses, monocots, and the Lamiales (Supplementary Fig. 8). It may be that our species tree has more error in these regions of the phylogeny and or that gene birth/death rates are highly heterogeneous among these taxa. Both issues could interfere with our MAPS inferences. Further analyses are needed to better resolve the nature of these significant duplications in MAPS and the placements of inferred WGDs in these regions of the phylogeny.
Aulacomnium heterostichum
Pseudotaxiphyllum elegans
Rhynchostegium serrulatum
Pseudolycopodiella caroliniana
Loeskeobryum brevirostre
Stereodon subimponens
Phylloglossum drummondii Selaginella selaginoides Selaginella cf. pallescens Selaginella moellendorffii Selaginella moellendorffii Selaginella acanthonota Fontinalis antipyretica
Calliergon cordifolium
Climacium dendroides Anomodon attenuatus Dendrolycopodium obscurum Selaginella kraussiana Claopodium rostratum Selaginella willdenowii Thuidium delicatulum
Leucodon brachypus
Lycopodium deuterodensum Isoetes tegetiformans
Orthotrichum lyellii
Leucodon julaceus
Selaginella wallacei
Neckera douglasii
Diphasiastrum digitatum Osmundastrum cinnamomeum Lycopodium annotinum Lycopodiella appressa
Huperzia myrsinites Huperzia squarrosa Selaginella apoda
Ophioglossum petiolatum Huperzia lucidula
Equisetum diffusum Huperzia selago Supplementary Fig. 1 Phylogenetic inferences based on Equisetum hyemale
Sceptridium dissectum Isoetes sp. Angiopteris evecta Hymenophyllum bivalve Botrypus virginianus Marattia attenuata Tmesipteris parva Danaea nodosa
Psilotum nudum Osmunda javanica
Lygodium japonicum Azolla cf. caroliniana Anemia Dipteristomentosa conjugata Cryptogramma acrostichoides Pilularia globulifera
Rosulabryum cf. capillare Bryum argenteum Plagiomnium insigne Philonotis fontana Thyrsopteris elegans Hedwigia ciliata Ceratodon purpureus Syntrichia princeps Dicranum scoparium Leucobryum albidum Ceratopteris thalictroides Leucobryum glaucum Racomitrium elongatum Racomitrium varium Scouleria aquatica Alsophila pinulosa Timmia austriaca ASTRAL analysis of 410 single-copy nuclear gene families Physcomitrium sp. Plagiogyria japonica Physcomitrella patens Encalypta streptocarpa Osmunda sp. Diphyscium foliosum Culcita macrocarpa Buxbaumia aphylla Polytrichum commune Atrichum angustatum Tetraphis pellucida Andreaea rupestris Lindsaea microphylla Sphagnum palustre Pityrogramma trifoliata Sphagnum recurvum Sphagnum lescurii Takakia lepidozioides Scapania nemorosa Barbilophozia barbata Odontoschisma prostratum Bazzania trilobata Calypogeia fissa LindsaeaLonchitis linearis hirsuta Schistochila sp. Porella navicularis Porella pinnata Radula lindenbergiana Frullania sp. Ptilidium pulcherrimum Metzgeria crassipilis AdiantumAdiantum raddianum aleuticum Pallavicinia lyellii Pellia cf. epiphylla Pteris ensiformis Pellia neesiana Vittaria appalachiana Marchantia polymorpha Dennstaedtia davallioides Marchantia paleacea Notholaena montieliae Marchantia emarginata extracted from genome and transcriptome data from 1178 Didymochlaena truncatula Conocephalum conicum Argyrochosma nivea Ricciocarpos natans Parahemionitis cordata Pteris vittata Lunularia cruciata Polystichum acrostichoides Sphaerocarpos texanus Nothoceros vincentianus Nothoceros aenigmaticus Vittaria lineata Megaceros flagellaris Phaeomegaceros coriaceus Myriopteris rufa Phaeoceros carolinianus Leucostegia immersa Phaeoceros carolinianus Paraphymatoceros hallii Anthoceros agrestis Phlebodium pseudoaureum Gaga arizonica Anthoceros agrestis Pleopeltis polypodioides Leiosporoceros dussii Phymatosorus grossus Xanthidium antilopaeum Nephrolepis exaltata Pleurotaenium trabecula Cosmarium ochthodes
Bolbitis repanda 0.45 Cosmarium subtumidum species, including 1112 green plant (Viridiplantae) species. Polypodium amorphum Micrasterias fimbriata Davallia fejeensis 0.41 Cosmarium tinctum Polypodium hesperium Staurodesmus omearii Polypodium hesperium Staurodesmus convergens Polypodium glycyrrhiza Desmidium aptogonum Onychonema laeve AspleniumAsplenium cf. x lucrosum platyneuron 0.99 Bambusina borreri Cosmarium granatum Gymnocarpium dryopteris Staurastrum sebaldi Euastrum affine Cosmocladium cf. constrictum 0.81 Cosmarium broomei Phymatodocis nordstedtiana Cystopteris utahensis 0.9 Penium exiguum Branches with BS support below 33% were removed from the Asplenium nidus Penium margaritaceum Homalosorus pycnocarpos Cystopteris reevesiana 0.99 Closterium lunula Gonatozygon kinahanii CystopterisCystopteris protrusa fragilis Planotaenium ohtanii Roya obtusa 0.56 Netrium digitus 0.52 Thelypteris acuminata 0.62 Nucleotaenium eifelense Cystopteris fragilis Mesotaenium kramstae 0.76 Zygnemopsis sp. 0.99 Cylindrocystis cushleckae Woodsia scopulina Mesotaenium caldariorum 0.94 Mougeotia sp. gene trees before estimating the ASTRAL tree. Branch support Deparia lobato-crenata Cylindrocystis sp. Woodsia ilvensis Blechnum spicant Cylindrocystis brebissonii Onoclea sensibilis Cylindrocystis brebissonii Diplazium wichurae Mesotaenium braunii Mesotaenium endlicherianum Athyrium filix-femina Spirogyra sp. Spirotaenia sp. Coleochaete irregularis 0.37 0.98 0.69 Coleochaete scutata 0.94 Chaetosphaeridium globosum Cycas micholitziiAthyrium sp. measured using local posterior probability (localPP) is shown on Encephalartos barteri Chara braunii Ginkgo biloba Chara vulgaris Stangeria eriopus Klebsormidium flaccidum 0.68 Klebsormidium subtile Welwitschia mirabilis Interfilum paradoxum Gnetum montanumDioon edule Entransia fimbriata Keteleeria evelynianaEphedra sinica 0.99 Spirotaenia minuta Nothotsuga longibracteata 0.99 Chlorokybus atmophyticus Mesostigma viride Pseudolarix amabilis Prasinoderma coloniale Pseudotsuga wilsoniana branches with support less than 1.0. Nodes with support less Abies lasiocarpaCedrus libani coccoid-prasinophyte Prasinococcus capsulatus Dunaliella primolecta Tsuga heterophylla Dunaliella tertiolecta Dunaliella salina Cathaya argyrophylla Dunaliella salina Dunaliella salina Picea engelmanniiLarix speciosa Asteromonas gracilis 0.73 Pleurastrum insigne Chloromonas perforata than 1.0 are marked with a circle. Supplementary Table 1 0.8 Pinus parviflora Stephanosphaera pluvialis 0.89 Haematococcus pluvialis Brachiomonas submarina Pinus taeda Chlamydomonas noctigama Pinus ponderosaPinus radiata Chlamydomonas bilatus Pinus jeffreyi Chlamydomonas moewusii WollemiaAraucaria nobilis rulei Chlamydomonas sp. Sundacarpus amarus Chloromonas subdivisa 0.62 0.8 Pteromonas angulosa includes taxonomy for each species and mapping of binomial 0.99 PhyllocladusMicrostrobosPrumnopitys hypophyllus fitzgeraldiiAgathis andinaAraucaria robusta sp. Pteromonas sp. Halocarpus bidwillii 0.75 Phacotus lenticularis Volvox aureus Volvox aureus Volvox carteri SaxegothaeaLagarostrobos conspicua franklinii Eudorina elegans Parasitaxus usta 0.84 Pandorina morum 0.83 species names to four letter codes. This information and major MicrocachrysManoao tetragona colensoi Volvox globator Gonium pectorale
0.25
0.96 Chloromonas oogama Acmopyle pancheri 0.96 Chlamydomonas reinhardtii Retrophyllum minus Chlamydomonas cribrum Lobomonas rostrata DacrycarpusPodocarpusPodocarpus compactus coriaceus rubens 0.64 Vitreochlamys sp. 0.99 Neochlorosarcina sp. group names (colors; see columns “Code” and “Brief Heterochlamydomonas inaequalis Dacrydium balansaeNageia nagi Oogamochlamys gigantea Falcatifolium taxoides 0.77 Lobochlamys segnis Falcatifolium taxoides Sciadopitys verticillata Chloromonas reticulata Amentotaxus argotaenia Chloromonas rosae Chlamydomonas sp. Chloromonas tughillensis Classification” in misc/names.csv), and data used to build the Cephalotaxus harringtonia Hafniomonas reticulata Carteria crucifera Torreya nucifera 0.98 0.72 Carteria obtusa Torreya taxifolia Pediastrum duplex Pediastrum duplex Pseudotaxus chienii 0.87 Botryosphaerella sudetica CunninghamiaTaxus lanceolataTaxus cuspidata baccata 0.35 TaiwaniaAustrotaxus cryptomerioides spicata Neodesmus pupukensis figure, available at doi.org/10.5281/zenodo.3255100 Metasequoia glyptostroboides Acutodesmus dimorphus Athrotaxis cupressoides 0.87 Ankistrodesmus sp. Golenkinia longispicula Sequoiadendron giganteum Microspora cf. tumidula Sequoia sempervirens Spermatozopsis exsultans Spermatozopsis similis 0.6 Cylindrocapsa geminella Cryptomeria japonica Uronema belkae GlyptostrobusTaxodium distichumpensilis Uronema sp. Pilgerodendron uviferum Fritschiella tuberosa Papuacedrus papuana Stigeoclonium helveticum WiddringtoniaAustrocedrus cedarbergensis chilensis Aphanochaete repens 0.99 Oedogonium cardiacum Oedogonium foveolatum Chaetopeltis orbicularis NeocallitropsisDiselma pancheri archeri Codium fragile 0.6 Bryopsis plumosa Callitris gracilis Percursaria percursa Callitris macleayana Ochlochaete sp. ChamaecyparisThujopsis lawsoniana dolabrata Entocladia endozoica 0.4 Bolbocoleon piliferum 0.89 Pirula salina Cupressus duprezianaThuja plicata Desmochloris halophila Fokienia hodginsii Pseudoneochloris marina Juniperus scopulorum 0.69 0.95 Planophila sp Calocedrus decurrens Planophila laetevirens 0.22 0.97 Helicodictyon planctonicum Platycladus orientalis Acrosiphonia sp. 0.99 0.49 MicrobiotaTetraclinis decussata sp. 0.84 Ignatius tetrasporus Amborella_trichopoda Halochlorococcum marinum Amborella trichopoda Oltmannsiellopsis viridis Trentepohlia annulata Cephaleuros virescens AustrobaileyaNuphar scandens advena Blastophysa cf. rhizopus Nymphaea sp. Cladophora glomerata Kadsura heteroclita 0.99 Chlorella variabilis Illicium floridanum Ettlia(?) oleoabundans Acorus americanus Parachlorella kessleri Prototheca wickerhamii Spirodela polyrhiza 0.98 0.99 Typhonium blumei Picochlorum atomus 0.91 0.99 Nannochloris atomus Pistia stratiotes 0.14 Eremosphaera viridis Sagittaria latifolia Posidonia australis Geminella sp. Botryococcus terribilis Triglochin maritima Botryococcus braunii Dioscorea villosa 0.96 Coccomyxa pringsheimii Talbotia elegans 0.85 Trebouxia arboricola Xerophyta villosa Microthamnion kuetzingianum Stemona tuberosa Leptosira obovata Prasiola crispa Freycinetia multiflora 0.89 Stichococcus bacillaris Ludovia sp. Tetraselmis chui 0.99 ElaeisNypa guineensis fruticans 0.7 Tetraselmis striata 0.34 Tetraselmis cordiformis Serenoa repens 0.41 Sabal bermudana Scherffelia dubia Pedinomonas minor Maranta leuconeura Chlorochytridion tuberculata Canna sp. unidentified sp CCMP 1205 Zingiber officinale Picocystis salinarum Curcuma longa Nephroselmis pyriformis OrchidanthaMusa maxillarioides acuminata Nephroselmis olivacea 0.26 Micromonas pusilla Heliconia sp. Mantoniella squamata 0.68 Strelitzia reginae 0.35 0.95 Ostreococcus lucimarinus Brocchinia reducta Bathycoccus prasinos Dolichomastix tenuilepis TyphaTypha angustifolia latifolia Monomastix opisthostigma Juncus inflexus Pyramimonas parkeae LepidospermaMapania palustrisgibsonii 0.97 Cymbomonas sp. 0.44 Pseudoscourfieldia marina ChondropetalumCyperus tectorumpapyrus Scourfieldia sp. 0.98 Glaucocystis cf. nostochinearum Joinvillea ascendens Gloeochaete wittrockiana 0.6 Cyanoptyche gloeocystis DeschampsiaOryza cespitosa sativa Cyanophora paradoxa Avena fatua 0.75 Gracilaria blodgettii 0.61 0.68 Gracilaria vermiculophylla Aristida stricta 0.72 Gracilaria sp. Uniola paniculata Gracilaria chouae Uniola paniculata Eleusine coracana 0.97 Gracilaria lemaneiformis Grateloupia livida MicrostegiumTriodia aff.vimineum bynoei Grateloupia filicina Grateloupia turuturu 0.98 CymbopogonSorghum nardusbicolor Grateloupia catenata Mazzaella japonica ThyridolepisPanicum mitchelliana miliaceum Chondrus crispus Thyridolepis multiculmis Gloiopeltis furcata 0.99 Ahnfeltiopsis flabelliformis Neurachne annularis Dumontia simplex Neurachne munroi Betaphycus philippinensis Neurachne tenuifolia Kappaphycus alvarezii Neurachne minor 0.84 0.83 Eucheuma denticulatum Paraneurachne muelleri 0.96 0.99 Neurachne alopecuroidea Symphyocladia latiuscula Neosiphonia japonica Neurachne lanigera Heterosiphonia pulchra XerophyllumHelonias asphodeloides bullata 0.86 Ceramium kondoi Pyropia yezoensis 0.8 Glaucosphaera vacuolata Lilium sargentiae 0.77 Smilax bona-nox Rhodella violacea Gloriosa superba Porphyridium purpureum 0.97 Porphyridium cruentum Colchicum autumnale 0.45 0.54 Colchicum autumnale Rhodochaete parvula Chroodactylon ornatum Vanilla planifolia 0.64 Oncidium sphacelatum Cyanidioschyzon_merolae Masdevallia yuangensis 0.93 0.84 Petalonia fascia Platanthera clavellata 0.49 Scytosiphon dotyi Scytosiphon lomentaria Drakaea elastica 0.97 Colpomenia sinuosa Goodyera pubescens Punctaria latifolia Haemaria discolor Saccharina sculpera Curculigo sp. Saccharina japonica Borya sphaerocephala Undaria pinnatifida Cyanastrum cordifolium Desmarestia viridis Cyanella orchidiformis Sargassum muticum Sisyrinchium angustifolium Sargassum hemiphyllum Xeronema callistemon Sargassum thunbergii Aloe vera Sargassum fusiforme Phormium tenax Sargassum horneri Johnsonia pubescens Sargassum vachellianum Hemerocallis sp. Sargassum henslowianum Hemerocallis spp. Sargassum integerrimum Agapanthus africanus Dictyopteris undulata Allium commutatum 0.67 Ishige okamurae Allium sativum Synura sp. Narcissus viridiflorus Synura petersenii Mallomonas sp. Traubia modesta Phycella aff. cyrtanthoides Pavlova lutheri Amaryllis belladonna Pavlova lutheri 0.85 Pavlova lutheri Zephyranthes treatiae 0.79 Pavlova lutheri Rhodophiala pratensis Rebecca salina Brodiaea sierrae Isochrysis sp. Urginea maritima Prymnesium parvum Drimia altissima 0.55 Chroomonas sp. 0.95 Hesperaloe parviflora 0.76 0.95 Cryptomonas curvata Chlorogalum pomeridianum Proteomonas sulcata Agave tequilana 0.81 Rhodomonas sp. Yucca brevifolia Micromeria fruticosa Yucca filamentosa Poliomintha bustamanta Thymus vulgaris Lomandra longifolia 0.6 Asparagus densiflorus 0.47 Agastache rugosa Eriospermum lancifolia Nepeta cataria Sansevieria trifasciata Prunella vulgaris Ruscus sp. 0.99 Rosmarinus officinalis Peliosanthes minor 0.85 Salvia spp. Nolina atopocarpa 0.99 Melissa officinalis Solenostemon scutellarioides Nolina bigelovii 0.98 0.7 Disporopsis pernyi Lavandula angustifolia 0.88 Marrubium vulgare Maianthemum sp. Leonurus japonicus Maianthemum canadense 0.93 Sarcandra glabra Pogostemon sp. 0.49 Scutellaria montana Ascarina rubricaulis Ajuga reptans Drimys winteri Teucrium chamaedrys Canella winterana Oxera neriifolia Saruma henryi Oxera pulchella Aristolochia elegans 0.79 Vitex agnus-castus Peperomia fraseri 0.83 Conopholis americana Piper auritum 0.97 Epifagus virginiana Saururus cernuus Orobanche fasciculata Houttuynia cordata Lindenbergia philippensis Myristica fragrans 0.92 Rehmannia glutinosa Michelia maudiae Paulownia fargesii Magnolia grandiflora Mimulus guttatus Eupomatia bennettii Lantana camara Annona muricata Phyla dulcis Uvaria microcarpa Verbena hastata 0.13 Tabebuia umbellata Idiospermum australiense Calycanthus floridus 0.98 Kigelia africana 0.44 0.68 Mansoa alliacea Laurelia sempervirens Gomortega keule Sanchezia sp. Strobilanthes dyeriana GyrocarpusPeumus americanus boldus 0.99 Ruellia brittoniana Anisacanthus quadrifidus Cassytha filiformis 0.96 Persea borbonia Pinguicula agnata Lindera benzoin 0.34 Pinguicula caudata Utricularia sp. Cinnamomum camphora Uncarina grandidieri Sassafras albidum 0.94 0.61 Schlegelia parasitica Ceratophyllum demersum Schlegelia violacea Euptelea pleiosperma Verbascum sp. Akebia trifoliata Celsia arcturus Nandina domestica Buddleja sp. Podophyllum peltatum Buddleja lindleyana Hydrastis canadensis Anticharis glandulosa Aquilegia coerulea 0.6 0.44 0.97 Byblis gigantea Plantago virginica Thalictrum thalictroides 0.99 Plantago maritima Anemone hupehensis 0.51 Anemone pulsatilla Digitalis purpurea Antirrhinum braun-blanquetii Hypecoum procumbens Antirrhinum majus Capnoides sempervirens Bacopa caroliniana Ceratocapnos vesicaria Saintpaulia ionantha Corydalis linstowiana 0.78 Sinningia tuberosa Eschscholzia californica Calceolaria pinifolia Chelidonium majus 0.42 Chionanthus retusus Sanguinaria canadensis unknown Argemone mexicana Olea europaea PapaverPapaver bracteatum rhoeas Ligustrum sinense 0.99 Polypremum procumbens Papaver setigerum 0.58 Apocynum androsaemifolium Papaver somniferum Apocynum androsaemifolium Meliosma cuneifolia Asclepias syriaca NelumboNelumbo nucifera sp. Asclepias curassavica Holarrhena pubescens 0.88 Wrightia natalensis PlatanusGrevillea occidentalis robusta Allamanda cathartica Hakea drupacea Catharanthus roseus Hakea prostrata 0.99 Rauvolfia tetraphylla Strychnos spinosa Trochodendron aralioides Exacum affine Buxus Dilleniasempervirens indica Gentiana acaulis Gunnera manicata 0.99 Gelsemium sempervirens 0.51 unknown Ximenia americana Psychotria marginata Daenikera sp. Psychotria ipecacuanha Dendropemon caribaeus 0.94 0.72 Galium boreale Heliotropium mendocinum Phoradendron serotinum Santalum acuminatum Heliotropium greggii Heliotropium tenuifolium Vitis vinifera ExocarposCissus cupressiformisquadrangularis Heliotropium texanum 0.99 Heliotropium racemosum Tetrastigma obtectum Heliotropium convolvulaceum 0.82 Heliotropium filiforme TetrastigmaPaeonia voinierianum lactiflora Heliotropium karwinskyi Heliotropium tenellum 0.82 Heliotropium calcicola Daphniphyllum macropodum 0.88 Lennoa madreporoides CercidiphyllumHamamelis japonicum virginiana Pholisma arenarium Loropetalum chinense Ehretia acuminata Loropetalum chinense 0.9 Phacelia campanularia Mertensia paniculata Solanum dulcamara AphanopetalumMyriophyllumCrassulaRhodiola resinosum aquaticum perforata rosea 0.49 Solanum ptychanthum Itea virginica Solanum lycopersicum 0.99 Solanum lasiophyllum Ribes aff. giraldii 0.99 0.69 Solanum sisymbriifolium 0.76 Solanum xanthocarpum 0.97 Kalanchoe crenato-diagremontianaSaxifraga Bergeniastolonifera sp. Lycopersicon cheesmanii 0.7 Brugmansia sanguinea Peltoboykinia watanabei 0.92 Datura metel 0.99 Lycium sp. OresitropheAstilbe chinensis rupifraga Lycium barbarum Boykinia jamesii 0.47 0.57 Atropa belladonna 0.95 Nicotiana sylvestris HeucheraTiarella sanguinea polyphylla 0.98 Ipomoea purpurea Tellima breviflora Ipomoea purpurea Mitella pentandra Ipomoea pubescens Ipomoea lindheimeri Geranium maculatum Ipomoea hederacea Staphylea trifolia Ipomoea nil Francoa appendiculata 0.95 Ipomoea indica Stachyurus praecox Ipomoea lobata ThladianthaBegonia villosula sp. Ipomoea coccinea Coriaria nepalensis Ipomoea quamoclit 0.94 Convolvulus arvensis Ziziphus jujuba Elaeagnus pungens 0.65 0.38 Cuscuta pentagona Pyrenacantha malvifolia RhamnusUlmus japonica alata 0.82 Ilex vomitoria 0.8 Ilex paraguariensis Rhamnus caroliniana 0.43 Ilex sp. Helwingia japonica CeltisHumulus occidentalis lupulus Cannabis sativa Aucuba japonica Urtica dioica 0.98 Eucommia ulmoides BoehmeriaMorus nivea nigra 0.89 Flaveria kochiana Flaveria vaginata Ficus religiosa Flaveria trinervia Geum quellyon 0.67 Flaveria bidentis Flaveria palmeri Flaveria brownii Rosa palustris 0.76 Sanguisorba minor Flaveria sonorensis Flaveria pubescens Dryas octopetala Flaveria pringlei Cercocarpus ledifolius Flaveria angustifolia Kerria japonica 0.82 Flaveria cronquistii Prunus prostrata Xanthium strumarium Physocarpus opulifoliusPrunus persica Helenium autumnale Inula helenium Aruncus dioicus Erigeron canadensis Malus baccata Conyza canadensis Solidago canadensis Aster tataricus Sorbus koehneana Leontopodium alpinum Matricaria matricarioides Cotoneaster transcaucasicusNothofagusFagus obliquasylvatica Anthemis tinctoria Tanacetum parthenium Amelanchier canadensis 0.55 0.51 Quercus shumardii Senecio rowleyanus Castanea crenata 0.6 0.77 Juglans nigra 0.99 Tragopogon castellanus Castanea pumila Tragopogon porrifolius Myrica cerifera Tragopogon pratensis Tragopogon dubius Betula pendula Cicerbita plumieri Alnus serrulata 0.77 0.38 0.61 Lactuca graminifolia Polygala lutea Carthamus lanatus Casuarina equisetifolia Silybum marianum Scaevola mossambicensis 0.38 Quillaja saponaria 0.9 Menyanthes trifoliata Platyspermation crassifolium Copaifera officinalis 0.99 Cercis canadensis 0.41 Corokia cotoneaster Phelline lucida Bauhinia tomentosa 0.4 Stylidium adnatum 0.73 Platycodon grandiflorus 0.96 GymnocladusGleditsiaGleditsia triacanthos dioicus sinensis 0.98 Lobelia siphilitica Senna hebecarpa Heracleum lanatum Angelica archangelica Centella asiatica Acacia pycnantha 0.23 Myodocarpus sp. Hedera helix DesmanthusAcacia illinoensis argyrophyllaCladrastis lutea Polyscias fruticosa Hydrocotyle umbellata Pittosporum sahnianum 0.74 Pittosporum resiniferum XanthocercisLupinus Lupinuszambesiaca angustifolius polyphyllus 0.58 Griselinia racemosa Apios americana 0.7 Griselinia littoralis Pennantia corymbosa Glycine soja Symphoricarpos sp. Phaseolus vulgaris 0.23 Lonicera japonica Codariocalyx motorius Dipsacus asper 0.64 Valeriana officinalis Gompholobium polymorphum Sambucus canadensis BituminariaWisteria bituminosa floribunda Glycyrrhiza glabra 0.68 Viburnum odoratissimum Lathyrus sativus Escallonia sp. cv. Newport Escallonia rubra Glycyrrhiza lepidota 0.53 0.62 0.84 Ledum palustre 0.66 0.8 Rhododendron scopulorum Cavendishia cuatrecasasii Astragalus propinquusLarrea tridentata 0.29 Monotropa uniflora Krameria lanceolata Sarcodes sanguinea Actinidia chinensis Tribulus eichlerianus 0.9 Roridula gorgonias Astragalus membranaceus Galax urceolata TerminaliaMedinillaTetrazygia neotaliala magnifica bicolor Galax urceolata Sinojackia xylocarpa Symplocos tinctoria Ternstroemia gymnanthera Eucalyptus grandis Ardisia humilis 0.97 0.99 Ardisia revoluta Eucalyptus leucoxylonPunica granatumEpilobium sp. Jacquinia sp. Maesa lanceolata Syzygium paniculatum Diospyros malabarica Syzygium micranthum 0.41 Manilkara zapota LagerstroemiaOenothera indica rosea Synsepalum dulcificum Sideroxylon reclinatum Oenothera speciosaOenothera gaura Phlox sp. 0.97 0.38 0.99 Phlox drummondii Fouquieria macdougalii 0.54 Souroubea exauriculata Oenothera filiformis Impatiens balsamifera 0.29 Oenothera affinis Hydrangea quercifolia Dichroa febrifuga Oenothera serrulata 0.64 Oenothera berlandieriOenothera nana Caiophora chuquitensis Oenothera suffulta suffulta Cornus florida Oenothera picensis 0.94 Alangium chinense Nyssa ogeche Aextoxicon punctatum Oenothera villaricae Berberidopsis beckleri 0.99 Boerhavia coccinea OenotheraOenothera clelandii grandis Boerhavia dominii 0.36 Allionia incarnata Oenothera elata Allionia incarnata Oenothera rhombipetalaOenotheraOenothera laciniata biennis Mirabilis jalapa Oenothera elata 0.54 Bougainvillea spectabilis Petiveria alliacea Hilleria latifolia Oenothera grandiflora 0.56 Phytolacca bogotensis Phytolacca americana Croton tiglium Sarcobatus vermiculatus 0.7 Sesuvium portulacastrum Sesuvium verrucosum Cypselea humifusa Zaleya pentandra
Ricinus communis 0.99 Trianthema portulacastrum StackhousiaEuphorbia spathulata pekinensis Delosperma echinatum ManihotManihot esculenta grahamii 0.59 Portulaca pilosa Crossopetalum rhacoma Phyllanthus sp. Portulaca suffruticosa Viola tricolor Portulaca amilis Portulaca grandiflora Bischofia javanica Portulaca umbraticola Portulaca umbraticola Portulaca cryptopetala Portulaca molokiniensis RhizophoraErythroxylum mangle coca Portulaca oleracea Passiflora_sp Lophophora williamsii Pereskia aculeata Viola canadensis Talinum sp. Basella alba Drypetes deplanchei Passiflora edulis Mollugo cerviana Salix fargesii Mollugo nudicaulis Mollugo verticillata Salix acutifolia Mollugo pentaphylla Alternanthera sessilis Alternanthera brasiliana Euphorbia mesembryanthemifolia Salix purpurea Alternanthera tenella Alternanthera caracasana Passiflora caerulea Blutaparon vermiculare Aerva lanata Aerva persica Malesherbia fasciculata Populus trichocarpa Salix viminalis Amaranthus retroflexus Amaranthus cruentus Atriplex prostrata Atriplex hortensis Salix eriocephala Atriplex rosea Chenopodium quinoa Beta maritima Salix sachalinensis Beta_vulgaris Kochia scoparia Salix dasyclados Saponaria officinalis Ochna serrulata Dianthus caryophyllus Schiedea membranacea Silene latifolia Spergularia media Galphimia gracilis Polycarpaea repens Microtea debilis Physena madagascariensis Simmondsia chinensis Polygonum convolvulus Limonium spectabile Linum flavum Nepenthes alata Draba sachalinensis Draba magellanica Draba oligosperma Draba ossetica Draba aizoides Draba hispida Arabis alpina Sinapis alba Brassica nigra Cochlearia officinalis Arabidopsis_thaliana Polanisia trachysperma Cleome violacea Linum macraei Cleome viscosa Linum leonii Mammea americana Licania michauxii Linum strictum Oxalis sp. Linum hirsutumLinum perenne Linum lewisii Garcinia livingstonei Linum bienne Ochna mossambicensisHypericum perforatumGarcinia oblongifolia Linum tenuifolium
Chrysobalanus icaco
Linum grandiflorum Acer negundo Kirkia wilmsii Litchi chinensis Cunonia capensis Aesculus pavia Rhus radicans Tapiscia sinensis Linum usitatissimum Bixa orellana Peganum harmala Quassia amara Boswellia sacra Citrus x paradisi Bursera simaruba Daphne giraldii Cistus inflatus Melia azedarach
Salvadora sp.
Akania lucens
Batis maritima Schizolaena sp. Carica_papaya ElaeocarpusCephalotus sylvestris follicularis
Moringa oleifera
Reseda odorata Ailanthus altissima Azadirachta indica Theobroma cacao
Muntingia calabura
Cleome gynandra
Hoheria angustifolia
Koeberlinia spinosa Dombeya burgessiae Edgeworthia papyrifera Hibiscus cannabinus
Limnanthes douglasii
Tropaeolum peregrinum
Gyrostemon ramulosus Aulacomnium heterostichum
Pseudotaxiphyllum elegans
Rhynchostegium serrulatum
Pseudolycopodiella caroliniana
Loeskeobryum brevirostre
Stereodon subimponens
Phylloglossum drummondii Selaginella selaginoides Selaginella cf. pallescens
Dendrolycopodium obscurum Climacium dendroides Selaginella acanthonota Fontinalis antipyretica
Selaginella moellendorffii Calliergon cordifolium Selaginella moellendorffii Claopodium rostratum
Selaginella kraussiana Thuidium delicatulum Selaginella willdenowii Lycopodium deuterodensum Anomodon attenuatus Leucodon brachypus
Isoetes tegetiformans
Orthotrichum lyellii
Leucodon julaceus
Selaginella wallacei
Neckera douglasii Diphasiastrum digitatum Osmundastrum cinnamomeum Lycopodiella appressa
Huperzia myrsinites Selaginella apoda Ophioglossum petiolatum Lycopodium annotinum Huperzia squarrosa
Sceptridium dissectum Huperzia lucidula Equisetum hyemale Equisetum diffusum Huperzia selago
Isoetes sp. Botrypus virginianus Hymenophyllum bivalve Tmesipteris parva Psilotum nudum
Angiopteris evecta Marattia attenuata Osmunda javanica Lygodium japonicum Danaea nodosa
Azolla cf. caroliniana Dipteris conjugata Cryptogramma acrostichoides PilulariaAnemia globulifera tomentosa
Bryum argenteum Rosulabryum cf. capillare Plagiomnium insigne Philonotis fontana Thyrsopteris elegans Hedwigia ciliata Ceratodon purpureus Syntrichia princeps Dicranum scoparium Leucobryum glaucum Ceratopteris thalictroides Leucobryum albidum Racomitrium elongatum Plagiogyria japonica Racomitrium varium Scouleria aquatica Alsophila pinulosa Timmia austriaca Physcomitrella patens Physcomitrium sp. Encalypta streptocarpa Osmunda sp. Diphyscium foliosum Buxbaumia aphylla Polytrichum commune Lindsaea microphylla Atrichum angustatum Culcita macrocarpa Tetraphis pellucida Andreaea rupestris Sphagnum palustre Pityrogramma trifoliata Sphagnum lescurii Sphagnum recurvum Takakia lepidozioides Scapania nemorosa Barbilophozia barbata Odontoschisma prostratum Bazzania trilobata Calypogeia fissa Supplementary Fig. 2 Phylogenetic inferences Lonchitis hirsuta Schistochila sp. Ptilidium pulcherrimum Lindsaea linearis Porella navicularis Porella pinnata Frullania sp. Radula lindenbergiana Metzgeria crassipilis AdiantumAdiantum raddianum aleuticum Pallavicinia lyellii Pellia neesiana Pteris ensiformis Pellia cf. epiphylla Vittaria appalachiana Marchantia paleacea Dennstaedtia davallioides Marchantia polymorpha Polystichum acrostichoides Notholaena Argyrochosmamontieliae nivea Marchantia emarginata Parahemionitis cordata Conocephalum conicum Ricciocarpos natans Pteris vittata Lunularia cruciata Sphaerocarpos texanus Nothoceros aenigmaticus Didymochlaena truncatula Nothoceros vincentianus Vittaria lineata Megaceros flagellaris Phaeomegaceros coriaceus Leucostegia immersa Phaeoceros carolinianus in a concatenated analysis of 410 single-copy Myriopteris rufa Phaeoceros carolinianus Paraphymatoceros hallii Anthoceros agrestis Phlebodium pseudoaureum Anthoceros agrestis Leiosporoceros dussii
Pleopeltis polypodioides Gaga arizonica 73 PhymatosorusNephrolepis grossus exaltata Desmidium aptogonum 69 Bambusina borreri Onychonema laeve Bolbitis repanda Staurastrum sebaldi Cosmarium granatum Polypodium amorphumDavallia fejeensis Euastrum affine Polypodium hesperium 80 Xanthidium antilopaeum
99 Pleurotaenium trabecula
Polypodium hesperium 96 Polypodium glycyrrhiza Cosmarium ochthodes Cosmarium subtumidum AspleniumAsplenium cf. x lucrosum platyneuron Micrasterias fimbriata nuclear gene families extracted from genome Staurodesmus convergens Gymnocarpium dryopteris Cosmarium tinctum Staurodesmus omearii Cosmocladium cf. constrictum 86 Cosmarium broomei Phymatodocis nordstedtiana Asplenium nidus 98 82 Penium exiguum Cystopteris protrusa Penium margaritaceum Cystopteris reevesiana Closterium lunula Gonatozygon kinahanii Cystopteris fragilis Planotaenium ohtanii CystopterisCystopteris utahensis fragilis 54 39 Roya obtusa 86 Netrium digitus and transcriptome data from 1178 species, Nucleotaenium eifelense Woodsia scopulina Spirogyra sp. 99 Zygnemopsis sp. Homalosorus pycnocarpos Mesotaenium kramstae DiplaziumWoodsia wichurae ilvensis Cylindrocystis cushleckae Athyrium Blechnumfilix-femina spicant Mesotaenium caldariorum Mougeotia sp. Deparia lobato-crenata 59 Cylindrocystis brebissonii Cylindrocystis sp. Thelypteris acuminata Cylindrocystis brebissonii 99 Mesotaenium endlicherianum Mesotaenium braunii including 1112 green plant (Viridiplantae) 68 Spirotaenia sp. Onoclea sensibilis Athyrium sp. Coleochaete irregularis 86 Coleochaete scutata Chaetosphaeridium globosum Cycas micholitzii Encephalartos barteri Chara braunii Ginkgo biloba Chara vulgaris Welwitschia mirabilisStangeria eriopus Klebsormidium subtile 75 97 Klebsormidium flaccidum
90 Interfilum paradoxum species. Trees were inferred using ExaML. Dioon edule Entransia fimbriata Gnetum montanumEphedra sinica Chlorokybus atmophyticus Keteleeria evelyniana Spirotaenia minuta Nothotsuga longibracteata 27 Mesostigma viride PseudolarixAbies amabilis lasiocarpa Dunaliella primolecta Dunaliella tertiolecta Cedrus libani 54 Pseudotsuga wilsonianaTsuga heterophylla Dunaliella salina 96 47 Dunaliella salina Dunaliella salina Branch support measured using bootstrap support Cathaya argyrophylla Asteromonas gracilis 54 Pleurastrum insigne Larix speciosa Chloromonas perforata Picea engelmannii Stephanosphaera pluvialis 63 54 Brachiomonas submarina Haematococcus pluvialis Pinus parviflora 37 Chlamydomonas bilatus Chlamydomonas noctigama 78 Chlamydomonas moewusii Pinus ponderosa Chloromonas subdivisa (100 replicates) is shown on branches with Pinus taeda 74 Pinus radiata Chlamydomonas sp. Pteromonas sp. 66 98 WollemiaAraucariaPinus nobilis jeffreyirulei Pteromonas angulosa Sundacarpus amarus Phacotus lenticularis Agathis robusta 69 Volvox aureus PhyllocladusMicrostrobosPrumnopitys hypophyllus fitzgeraldii andina Volvox aureus Halocarpus bidwilliiAraucaria sp. Volvox carteri support less than 100%. Supplementary Table 1 69 98 Pandorina morum Eudorina elegans Lagarostrobos franklinii Volvox globator 93 Saxegothaea conspicua 98 Gonium pectorale Parasitaxus usta 99 Chloromonas oogama 98 Microcachrys tetragona Chlamydomonas reinhardtii Manoao colensoi Chlamydomonas cribrum Dacrycarpus compactus Lobomonas rostrata includes taxonomy for each species and mapping Acmopyle pancheri 67 Vitreochlamys sp. 98 Neochlorosarcina sp. FalcatifoliumDacrydium taxoides balansae Heterochlamydomonas inaequalis Falcatifolium taxoides Lobochlamys segnis Oogamochlamys gigantea Podocarpus coriaceus 74 Chloromonas rosae Podocarpus rubens Chloromonas reticulata Retrophyllum minus Chlamydomonas sp. of binomial species names to four letter codes. Cephalotaxus harringtonia 95 Chloromonas tughillensis Sciadopitys verticillata Carteria obtusa Amentotaxus argotaenia 93 59 Hafniomonas reticulata Carteria crucifera Nageia nagi 74 Pediastrum duplex Pediastrum duplex 90 Botryosphaerella sudetica This information and major group names (colors; Torreya nucifera Neodesmus pupukensis Torreya taxifolia Acutodesmus dimorphus Taxus cuspidata CunninghamiaPseudotaxus lanceolata chienii 99 Ankistrodesmus sp. TaiwaniaAustrotaxus cryptomerioidesTaxus spicata baccata Golenkinia longispicula Metasequoia glyptostroboides Spermatozopsis similis Athrotaxis cupressoides Spermatozopsis exsultans Sequoiadendron giganteum Microspora cf. tumidula Cylindrocapsa geminella see columns “Code” and “Brief Classification” in 98 Uronema sp. Sequoia sempervirens Uronema belkae Cryptomeria japonica Stigeoclonium helveticum Glyptostrobus pensilis Fritschiella tuberosa Aphanochaete repens PilgerodendronTaxodium uviferumdistichum 86 52 Oedogonium cardiacum misc/names.csv), and data used to build the Austrocedrus chilensis Oedogonium foveolatum Widdringtonia cedarbergensis 96 Chaetopeltis orbicularis Papuacedrus papuana Ochlochaete sp. Percursaria percursa Neocallitropsis pancheri Entocladia endozoica Diselma archeri 68 28 Pirula salina Bolbocoleon piliferum figure, available at doi.org/10.5281/ Callitris macleayana 50 Desmochloris halophila Pseudoneochloris marina Planophila laetevirens Chamaecyparis lawsonianaCallitris gracilis 97 Thujopsis dolabrata 90 79 Planophila sp FokieniaThuja hodginsii plicata Helicodictyon planctonicum Juniperus scopulorum Acrosiphonia sp. zenodo.3255100. Cupressus dupreziana Ignatius tetrasporus 92 Halochlorococcum marinum Calocedrus decurrens Oltmannsiellopsis viridis Cladophora glomerata Microbiota decussata Blastophysa cf. rhizopus PlatycladusTetraclinis orientalis sp. 93 69 Trentepohlia annulata Amborella trichopoda Cephaleuros virescens Amborella_trichopoda Codium fragile 99 Bryopsis plumosa 90 Botryococcus braunii AustrobaileyaNuphar scandens advena Botryococcus terribilis Nymphaea sp. Coccomyxa pringsheimii Illicium floridanum Microthamnion kuetzingianum CeratophyllumKadsura demersum heteroclita Trebouxia arboricola Leptosira obovata Acorus americanus Prasiola crispa Stichococcus bacillaris Sagittaria latifolia 78 Triglochin maritima 97 90 Chlorella variabilis Posidonia australis Ettlia(?) oleoabundans Spirodela polyrhiza Parachlorella kessleri 34 Prototheca wickerhamii Typhonium blumei Picochlorum atomus Pistia stratiotes Nannochloris atomus Dioscorea villosa Eremosphaera viridis Talbotia elegans Geminella sp. Xerophyta villosa Tetraselmis striata Stemona tuberosa Tetraselmis chui Tetraselmis cordiformis Freycinetia multiflora Scherffelia dubia Ludovia sp. Chlorochytridion tuberculata 98 ElaeisNypa guineensis fruticans Pedinomonas minor Picocystis salinarum Serenoa repens unidentified sp CCMP 1205 Sabal bermudana Nephroselmis pyriformis Maranta leuconeura Nephroselmis olivacea Canna sp. Micromonas pusilla Curcuma longa Mantoniella squamata Zingiber officinale Ostreococcus lucimarinus OrchidanthaMusa maxillarioides acuminata Bathycoccus prasinos Monomastix opisthostigma Heliconia sp. Dolichomastix tenuilepis Strelitzia reginae Pseudoscourfieldia marina Typha angustifolia 98 Pyramimonas parkeae 80 Cymbomonas sp. BrocchiniaTypha reducta latifolia Scourfieldia sp. Juncus inflexus Prasinoderma coloniale coccoid-prasinophyte Mapania palustris 74 66 LepidospermaCyperus papyrusgibsonii Prasinococcus capsulatus Chondropetalum tectorum Glaucocystis cf. nostochinearum 95 Gloeochaete wittrockiana Joinvillea ascendens Cyanoptyche gloeocystis 71 Cyanophora paradoxa DeschampsiaOryza cespitosa sativa Gracilaria blodgettii Avena fatua 95 Gracilaria vermiculophylla Gracilaria chouae Aristida stricta Gracilaria sp. Triodia aff. bynoei 98 Eleusine coracana Gracilaria lemaneiformis Grateloupia livida Uniola paniculata Grateloupia filicina Uniola paniculata Microstegium vimineum 95 Grateloupia turuturu Cymbopogon nardus Grateloupia catenata Chondrus crispus Sorghum bicolor 40 Mazzaella japonica ThyridolepisPanicum mitchelliana miliaceum Gloiopeltis furcata Thyridolepis multiculmis Ahnfeltiopsis flabelliformis 84 71 Dumontia simplex Neurachne annularis Betaphycus philippinensis Neurachne munroi Kappaphycus alvarezii Neurachne tenuifolia 67 Eucheuma denticulatum Symphyocladia latiuscula ParaneurachneNeurachne muelleri minor Neurachne alopecuroidea Neosiphonia japonica 99 Heterosiphonia pulchra Neurachne lanigera 57 Ceramium kondoi XerophyllumHelonias asphodeloides bullata Pyropia yezoensis 77 Porphyridium cruentum Lilium sargentiae Porphyridium purpureum Smilax bona-nox Chroodactylon ornatum 65 Glaucosphaera vacuolata Gloriosa superba Rhodella violacea Colchicum autumnale 95 Colchicum autumnale Rhodochaete parvula 63 Cyanidioschyzon_merolae MasdevalliaVanilla yuangensis planifolia 98 Scytosiphon lomentaria Oncidium sphacelatum 60 Petalonia fascia Scytosiphon dotyi Platanthera clavellata Colpomenia sinuosa Drakaea elastica Punctaria latifolia Goodyera pubescens Saccharina sculpera Haemaria discolor Saccharina japonica Curculigo sp. 85 Undaria pinnatifida Borya sphaerocephala Desmarestia viridis Cyanastrum cordifolium Sargassum hemiphyllum Cyanella orchidiformis Sargassum muticum Sisyrinchium angustifolium 92 Sargassum thunbergii Xeronema callistemon Sargassum fusiforme Sargassum horneri Aloe vera Phormium tenax Sargassum henslowianum Johnsonia pubescens Sargassum vachellianum Hemerocallis sp. Sargassum integerrimum Hemerocallis spp. Dictyopteris undulata Agapanthus africanus Ishige okamurae Allium commutatum Synura petersenii Synura sp. Allium sativum Narcissus viridiflorus 95 Mallomonas sp. Pavlova lutheri Traubia modesta 93 Phycella aff. cyrtanthoides Pavlova lutheri 95 Pavlova lutheri Amaryllis belladonna Pavlova lutheri Rhodophiala pratensis 88 Rebecca salina Zephyranthes treatiae Isochrysis sp. Brodiaea sierrae Prymnesium parvum Drimia altissima Rhodomonas sp. Urginea maritima Proteomonas sulcata Chlorogalum pomeridianum 87 Chroomonas sp. Hesperaloe parviflora Cryptomonas curvata Agave tequilana 99 Micromeria fruticosa Yucca brevifolia 89 Poliomintha bustamanta Yucca filamentosa 93 Thymus vulgaris Asparagus densiflorus Prunella vulgaris Lomandra longifolia Nepeta cataria Eriospermum lancifolia Agastache rugosa Sansevieria trifasciata Salvia spp. Ruscus sp. Rosmarinus officinalis 82 Peliosanthes minor Melissa officinalis Nolina bigelovii 83 Solenostemon scutellarioides Nolina atopocarpa Lavandula angustifolia 59 Oxera neriifolia Disporopsis pernyi Oxera pulchella Maianthemum canadense 99 Ajuga reptans Maianthemum sp. 90 Teucrium chamaedrys Ascarina rubricaulis Marrubium vulgare Sarcandra glabra 99 Leonurus japonicus Drimys winteri 66 Pogostemon sp. Canella winterana Scutellaria montana Saruma henryi Vitex agnus-castus Aristolochia elegans 65 Mimulus guttatus Saururus cernuus Conopholis americana Houttuynia cordata Epifagus virginiana Peperomia fraseri 77 Orobanche fasciculata Piper auritum Lindenbergia philippensis Myristica fragrans Rehmannia glutinosa Michelia maudiae Paulownia fargesii 65 99 Magnolia grandiflora Tabebuia umbellata Eupomatia bennettii Kigelia africana Annona muricata 83 Mansoa alliacea Uvaria microcarpa Phyla dulcis Lantana camara Idiospermum australiense 61 Verbena hastata Calycanthus floridus Schlegelia violacea Laurelia sempervirens Gomortega keule Schlegelia parasitica 90 Uncarina grandidieri GyrocarpusPeumus americanus boldus Sanchezia sp. Strobilanthes dyeriana Cassytha filiformis 92 Persea borbonia 84 Ruellia brittoniana Lindera benzoin Anisacanthus quadrifidus 48 Pinguicula caudata Cinnamomum camphora Pinguicula agnata Sassafras albidum Utricularia sp. Euptelea pleiosperma Celsia arcturus Akebia trifoliata Verbascum sp. Nandina domestica Buddleja sp. Podophyllum peltatum Buddleja lindleyana Hydrastis canadensis Anticharis glandulosa Byblis gigantea Anemone hupehensis Plantago virginica Anemone pulsatilla 87 92 Plantago maritima ThalictrumAquilegia thalictroides coerulea Digitalis purpurea Antirrhinum majus Hypecoum procumbens Antirrhinum braun-blanquetii Capnoides sempervirens Bacopa caroliniana Corydalis linstowiana Sinningia tuberosa Ceratocapnos vesicaria 89 Saintpaulia ionantha Calceolaria pinifolia EschscholziaChelidonium californica majus 83 Polypremum procumbens Sanguinaria canadensis Chionanthus retusus Argemone mexicana unknown PapaverPapaver bracteatum rhoeas Olea europaea 70 Ligustrum sinense Papaver somniferum Asclepias curassavica Papaver setigerum Asclepias syriaca Meliosma cuneifolia 98 75 Apocynum androsaemifolium NelumboNelumbo nucifera sp. 80 Apocynum androsaemifolium 88 Holarrhena pubescens Wrightia natalensis PlatanusGrevillea occidentalis robusta Allamanda cathartica Hakea drupacea Rauvolfia tetraphylla Hakea prostrata Catharanthus roseus Strychnos spinosa Gentiana acaulis TrochodendronBuxus sempervirens aralioides Gunnera manicata Exacum affine 44 Gelsemium sempervirens Aextoxicon punctatum 42 unknown BerberidopsisVitis beckleri vinifera Psychotria marginata Cissus quadrangularis Psychotria ipecacuanha 44 Galium boreale 92 Heliotropium tenuifolium TetrastigmaTetrastigma voinierianum obtectum Heliotropium mendocinum Ximenia americana Heliotropium greggii 98 Heliotropium racemosum DendropemonDaenikera caribaeus sp. Heliotropium convolvulaceum Phoradendron serotinum Heliotropium texanum Heliotropium filiforme Heliotropium karwinskyi ExocarposSantalumPaeonia cupressiformis acuminatum lactiflora Heliotropium tenellum Heliotropium calcicola Pholisma arenarium Lennoa madreporoides Daphniphyllum macropodum 84 71 CercidiphyllumHamamelis japonicum virginiana Ehretia acuminata Loropetalum chinense Phacelia campanularia Loropetalum chinense 75 Mertensia paniculata Solanum lasiophyllum Solanum lycopersicum AphanopetalumMyriophyllumCrassulaRhodiola resinosum aquaticum perforata rosea 50 Solanum ptychanthum Itea virginica 98 Solanum dulcamara 85 Solanum xanthocarpum Ribes aff. giraldii 98 Solanum sisymbriifolium Lycopersicon cheesmanii Brugmansia sanguinea Kalanchoe crenato-diagremontianaSaxifraga stolonifera Bergenia sp. 94 Datura metel Lycium barbarum PeltoboykiniaOresitrophe watanabei rupifraga 46 Lycium sp. Boykinia jamesii Atropa belladonna Astilbe chinensis 92 Nicotiana sylvestris 91 Ipomoea purpurea HeucheraTiarella sanguinea polyphylla Ipomoea purpurea Tellima breviflora 87 Ipomoea pubescens Mitella pentandra Ipomoea lindheimeri Ipomoea hederacea StachyurusStaphylea praecox trifolia 56 Ipomoea nil 93 Ipomoea indica Geranium maculatum Ipomoea coccinea Begonia sp. 95 97 Ipomoea lobata FrancoaCoriaria appendiculata nepalensis 98 Ipomoea quamoclit Convolvulus arvensis Cuscuta pentagona Thladiantha villosula 97 ElaeagnusZiziphus pungens jujuba 89 94 98 85 Pyrenacantha malvifolia Ilex vomitoria Ulmus alata Ilex paraguariensis RhamnusRhamnus caroliniana japonica Ilex sp. Helwingia japonica CeltisCannabis occidentalis sativa Aucuba japonica Urtica dioica Eucommia ulmoides Humulus lupulus Flaveria bidentis Morus nigra 97 Flaveria trinervia Boehmeria nivea Flaveria vaginata Ficus religiosa Flaveria kochiana 77 99 Flaveria palmeri Geum quellyon Flaveria brownii Rosa palustris Flaveria sonorensis Sanguisorba minor Flaveria pubescens Flaveria pringlei Flaveria angustifolia Dryas octopetala Flaveria cronquistii CercocarpusKerria ledifolius japonica Xanthium strumarium Prunus persica 65 Helenium autumnale Physocarpus opulifolius Inula helenium Prunus prostrata Erigeron canadensis Aruncus dioicus Conyza canadensis Solidago canadensis Aster tataricus Sorbus koehneanaMalus baccata 83 Leontopodium alpinum Amelanchier canadensis Anthemis tinctoria Matricaria matricarioides NothofagusFagus obliquasylvatica Tanacetum parthenium Senecio rowleyanus 84 Tragopogon pratensis Cotoneaster transcaucasicusQuercusCastanea shumardii pumila 95 98 Tragopogon porrifolius CastaneaMyricaJuglans crenata cerifera nigra Tragopogon castellanus Tragopogon dubius Cicerbita plumieri Alnus serrulata 26 Lactuca graminifolia Betula pendula 99 Carthamus lanatus 48 Silybum marianum Casuarina equisetifolia Polygala lutea 28 Scaevola mossambicensis Quillaja saponaria Menyanthes trifoliata Stylidium adnatum Corokia cotoneaster CopaiferaCercis canadensisofficinalis Platyspermation crassifolium Phelline lucida Bauhinia tomentosa 54 Platycodon grandiflorus Gleditsia sinensis 32 Lobelia siphilitica 54 Gymnocladus dioicus 20 Heracleum lanatum Senna hebecarpa Angelica archangelica Gleditsia triacanthos Centella asiatica Myodocarpus sp.
84 Polyscias fruticosa AcaciaAcacia argyrophylla pycnantha Hedera helix Desmanthus illinoensisCladrastis lutea Hydrocotyle umbellata 52 Pittosporum sahnianum Pittosporum resiniferum 94 Griselinia littoralis LupinusLupinus angustifolius polyphyllus Griselinia racemosa Xanthocercis zambesiacaApios americana Pennantia corymbosa Symphoricarpos sp. Glycine soja Lonicera japonica 33 Phaseolus vulgaris 88 Dipsacus asper Codariocalyx motorius Valeriana officinalis Viburnum odoratissimum Gompholobium polymorphumWisteria floribunda Sambucus canadensis Bituminaria bituminosaGlycyrrhiza glabra Escallonia rubra Lathyrus sativus Escallonia sp. cv. Newport Rhododendron scopulorum Glycyrrhiza lepidota 32 11 Ledum palustre 36 Cavendishia cuatrecasasii Monotropa uniflora Larrea tridentata 97 Sarcodes sanguinea Astragalus propinquus 93 Krameria lanceolata 88 Roridula gorgonias 34 Actinidia chinensis Galax urceolata Tribulus eichlerianus Galax urceolata Astragalus membranaceusTerminaliaTetrazygia neotaliala bicolor 99 Sinojackia xylocarpa Medinilla magnifica Symplocos tinctoria Ternstroemia gymnanthera Eucalyptus grandis Ardisia revoluta Ardisia humilis
93 Jacquinia sp. Punica granatumEpilobium sp. 64 Maesa lanceolata Eucalyptus leucoxylon Diospyros malabarica Syzygium micranthum Synsepalum dulcificum Oenothera rosea 93 Sideroxylon reclinatum Syzygium paniculatum 99 Lagerstroemia indica Manilkara zapota
99 Phlox sp. Oenothera gaura Phlox drummondii Oenothera speciosa Fouquieria macdougalii Souroubea exauriculata Impatiens balsamifera Oenothera filiformis 61 Dichroa febrifuga OenotheraOenothera serrulata affinis Hydrangea quercifolia 73 Caiophora chuquitensis Oenothera suffulta suffulta Cornus florida Oenothera berlandieriOenothera nana 99 Alangium chinense Oenothera picensisOenothera elata Nyssa ogeche 97 Allionia incarnata Oenothera villaricaeOenothera elata Allionia incarnata Boerhavia dominii Boerhavia coccinea Mirabilis jalapa
58 Bougainvillea spectabilis Oenothera biennis Petiveria alliacea 99 Hilleria latifolia Oenothera grandiflora Phytolacca americana 54 Phytolacca bogotensis Oenothera grandis 86 Oenothera clelandii Sarcobatus vermiculatus Sesuvium verrucosum Oenothera laciniata Sesuvium portulacastrum Oenothera rhombipetala Cypselea humifusa Zaleya pentandra Croton tiglium Trianthema portulacastrum Delosperma echinatum Ricinus communis Portulaca suffruticosa Drypetes deplanchei Viola tricolor Portulaca pilosa Stackhousia spathulata Portulaca amilis Manihot grahamii Portulaca grandiflora Crossopetalum rhacoma 73 Portulaca umbraticola Portulaca umbraticola Manihot esculenta Portulaca cryptopetala Euphorbia pekinensis Viola canadensis Passiflora_sp Portulaca oleracea Portulaca molokiniensis Lophophora williamsii Passiflora edulis Pereskia aculeata Talinum sp. Salix fargesii Basella alba Salix acutifolia Mollugo nudicaulis Mollugo cerviana Mollugo verticillata Mollugo pentaphylla Salix purpurea Alternanthera sessilis Passiflora caerulea Alternanthera brasiliana Alternanthera tenella Malesherbia fasciculata Alternanthera caracasana Populus trichocarpa Salix viminalis Blutaparon vermiculare Aerva persica Aerva lanata Amaranthus retroflexus Salix eriocephala Amaranthus cruentus Euphorbia mesembryanthemifolia Salix sachalinensis Phyllanthus sp. Atriplex prostrata Atriplex hortensis Salix dasyclados Atriplex rosea Chenopodium quinoa Kochia scoparia Beta_vulgaris Beta maritima Dianthus caryophyllus Saponaria officinalis Schiedea membranacea Silene latifolia Bischofia javanica Spergularia media Polycarpaea repens Microtea debilis Physena madagascariensis Simmondsia chinensis RhizophoraErythroxylum mangle coca Polygonum convolvulus Galphimia gracilis Limonium spectabile Nepenthes alata Dillenia indica Draba sachalinensis Licania michauxii Draba magellanica Draba oligosperma Linum flavum Draba hispida Draba ossetica Draba aizoides Arabis alpina Brassica nigra Sinapis alba Cochlearia officinalis Arabidopsis_thaliana Cleome violacea Polanisia trachysperma Cleome viscosa Cleome gynandra Ochna serrulata Linum macraei Chrysobalanus icaco Mammea americana Linum strictum Oxalis sp. Linum hirsutum Linum bienne Linum leonii Garcinia livingstonei Hypericum perforatum Linum lewisii Garcinia oblongifolia Linum tenuifolium Linum perenne
Linum grandiflorum
Ochna mossambicensis Acer negundo Tapiscia sinensis Kirkia wilmsii Linum usitatissimum Litchi chinensis Rhus radicans Cunonia capensis Aesculus pavia Bixa orellana
Peganum harmala Quassia amara Boswellia sacra Cistus inflatus
Bursera simaruba Citrus x paradisi Melia azedarach Daphne giraldii Salvadora sp.
Schizolaena sp. Akania lucens
Batis maritima Carica_papaya Cephalotus follicularis Moringa oleifera
Ailanthus altissima Reseda odorata Elaeocarpus sylvestris Azadirachta indica Theobroma cacao
Muntingia calabura
Hoheria angustifolia
Koeberlinia spinosa
Dombeya burgessiae Hibiscus cannabinus
Limnanthes douglasii
Edgeworthia papyrifera
Tropaeolum peregrinum
Gyrostemon ramulosus Pseudolycopodiella caroliniana
Dendrolycopodium obscurum Phylloglossum drummondii
Lycopodium deuterodensum
Selaginella cf. pallescens
Selaginella moellendorffii
Selaginella selaginoides
Osmundastrum cinnamomeum Selaginella acanthonota
Selaginella willdenowii
Selaginella kraussiana
Diphasiastrum digitatum
Ophioglossum petiolatum
Lycopodiella appressa Lycopodium annotinum
Huperzia myrsinites
Sceptridium dissectum Huperzia squarrosa
Selaginella apoda
Equisetum hyemale Hymenophyllum bivalve Equisetum diffusum Huperzia lucidula Botrypus virginianus
Huperzia selago
Tmesipteris parva Angiopteris evecta Psilotum nudum Cryptogramma acrostichoides Lygodium japonicum Azolla cf. caroliniana Osmunda javanica Marattia attenuata
Danaea nodosa Isoetes sp. Ceratopteris thalictroides Dipteris conjugata Anemia tomentosa Thyrsopteris elegansPilularia globulifera Plagiogyria japonica Alsophila pinulosa Lindsaea microphylla Pityrogramma trifoliata Culcita macrocarpa Osmunda sp.
Lonchitis hirsuta Supplementary Fig. 3 Phylogenetic inferences derived from Lindsaea linearis Vittaria appalachianaAdiantumAdiantum raddianum aleuticum Dennstaedtia davallioides Pteris ensiformis Notholaena montieliaeArgyrochosma nivea
Isoetes tegetiformans Thuidium delicatulum Polystichum acrostichoidesDidymochlaena truncatula Stereodon subimponens Calliergon cordifolium Rhynchostegium serrulatum Loeskeobryum brevirostre Climacium dendroides Claopodium rostratum Parahemionitis cordata Anomodon attenuatus Neckera douglasii Leucodon brachypus Leucodon julaceus Pseudotaxiphyllum elegans Fontinalis antipyretica Aulacomnium heterostichum Orthotrichum lyellii Rosulabryum cf. capillare Bryum argenteum Plagiomnium insigne Hedwigia ciliata Philonotis fontana Timmia austriaca Pteris vittata Selaginella wallacei Dicranum scoparium Leucostegia immersa Syntrichia princeps Phlebodium pseudoaureum Ceratodon purpureus Leucobryum albidum Vittaria lineata Leucobryum glaucum Racomitrium elongatum Pleopeltis polypodioides Myriopteris rufa Racomitrium varium Scouleria aquatica Physcomitrella patens Physcomitrium sp. Gaga arizonica Encalypta streptocarpa Nephrolepis exaltata Diphyscium foliosum Buxbaumia aphylla ExaML analyses of a concatenated supermatrix of amino Phymatosorus grossus Atrichum angustatum Polytrichum commune Polypodium glycyrrhiza Tetraphis pellucida Bolbitis repanda Andreaea rupestris Polypodium amorphum Davallia fejeensis Sphagnum palustre Sphagnum recurvum Polypodium hesperium Sphagnum lescurii Takakia lepidozioides Scapania nemorosa Barbilophozia barbata Thelypteris acuminata Odontoschisma prostratum Bazzania trilobata Calypogeia fissa Schistochila sp. Porella pinnata Woodsia scopulina Porella navicularis Homalosorus pycnocarpos 99 Frullania sp.
67 Radula lindenbergiana
92 Deparia lobato-crenataAthyrium filix-femina 20 Ptilidium pulcherrimum BlechnumWoodsia spicant ilvensis Pellia cf. epiphylla acid alignments for 78 shared protein-coding genes as 99 Pellia neesiana Metzgeria crassipilis Asplenium cf.Asplenium x lucrosum platyneuronOnoclea sensibilis Pallavicinia lyellii Gymnocarpium dryopteris Diplazium wichurae Marchantia polymorpha Marchantia paleacea Marchantia emarginata Ricciocarpos natans
95 Conocephalum conicum
6
12 Lunularia cruciata 72 Cystopteris utahensis Sphaerocarpos texanus Asplenium nidus Nothoceros vincentianus 98 Nothoceros aenigmaticus CystopterisCystopteris reevesiana protrusa 95 Megaceros flagellaris
86 84 Phaeomegaceros coriaceus Bootstrap support (100 58 Phaeoceros carolinianus described by Gitzendanner et al. . Cystopteris fragilis 85 99 Paraphymatoceros hallii Anthoceros agrestis 93
11 Anthoceros agrestis 99 70 Leiosporoceros dussii 77 Bambusina borreri Encephalartos barteriCycas micholitzii Desmidium aptogonum Stangeria eriopus Onychonema laeve 96 Ginkgo biloba 99 48 Staurastrum sebaldi 67 Cosmarium granatum 99 99 Euastrum affine
34 88 Xanthidium antilopaeum replicates) is shown on branches with support less than 100% Staurodesmus convergens Dioon edule Pinus parviflora 48 Staurodesmus omearii Pseudotsuga wilsoniana Cedrus libani Netrium digitus Cathaya argyrophylla Cosmarium subtumidum Pinus radiata 66 Micrasterias fimbriata Nothotsuga longibracteata Pinus ponderosa 81 Pleurotaenium trabecula Picea engelmannii Cosmarium tinctum Pseudolarix amabilis Pinus taeda 22 Pinus jeffreyi Cosmocladium cf. constrictum 49 99 Cosmarium broomei Phymatodocis nordstedtiana Tsuga heterophylla 97 86 13 93 Penium exiguum and associated have widths proportional to the support values (if 14 88 99 Gonatozygon kinahanii 99 90 Keteleeria evelyniana 51 Closterium lunula 79 Nucleotaenium eifelense 47 Roya obtusa Abies lasiocarpa 75 Larix speciosa 26 98 Welwitschia mirabilis Planotaenium ohtanii Gnetum montanum 3 64 Cylindrocystis brebissonii 43 Cylindrocystis sp. Ephedra sinica Spirogyra sp. 96 Mesotaenium caldariorum 91 72 Zygnemopsis sp. < 100%). Major groups are differentiated by tip colors, identically 55 Phyllocladus hypophyllusWollemiaAraucaria nobilis rulei 18 Mesotaenium kramstae 44 55 92 Cylindrocystis cushleckae Agathis robusta 99 55 94 Mougeotia sp. Halocarpus bidwillii Parasitaxus usta 51 Spirotaenia sp. Mesotaenium braunii Araucaria sp. 83 MicrostrobosPrumnopitys fitzgeraldii andina 38 99 Mesotaenium endlicherianum Sundacarpus amarus 85 78 95 Coleochaete irregularis Chaetosphaeridium globosum Lagarostrobos franklinii 74 to Supplementary Figs 1& 2. Supplementary Table 1 includes Saxegothaea conspicua 74 57 Chara vulgaris Klebsormidium flaccidum Microcachrys Manoaotetragona colensoi Klebsormidium subtile 97 45 97 Interfilum paradoxum Dacrycarpus compactus 18 Entransia fimbriata 50 Chlorokybus atmophyticus Acmopyle pancheri 42 33 32 Spirotaenia minuta Dacrydium balansae 33 66 Mesostigma viride 64 Haematococcus pluvialis Podocarpus coriaceus 83 taxonomy for each species and mapping of bionomial species Podocarpus rubens Brachiomonas submarina 97 46 68 Chloromonas perforata Cephalotaxus harringtonia 97 Pleurastrum insigne SciadopitysRetrophyllum verticillata minus 96 43 Stephanosphaera pluvialis 66 Amentotaxus argotaenia 92 Dunaliella primolecta
83 Nageia nagi Dunaliella tertiolecta 85 Dunaliella salina 62 33 names to four letter codes. This information and major group 47 80 Asteromonas gracilis Chlamydomonas bilatus 79 AustrotaxusTorreya spicata taxifolia 68 Chlamydomonas noctigama PseudotaxusTorreya chienii nucifera 70 40 60 Chlamydomonas moewusii 95 Chloromonas subdivisa Cunninghamia lanceolata 47 66 Pteromonas sp. MetasequoiaTaiwania glyptostroboides cryptomerioides 95 94 Pteromonas angulosa 99 37 Athrotaxis cupressoidesTaxusTaxus cuspidata baccata 31 Phacotus lenticularis 98 names (colors; see columns “Code” and “Brief Classification” in Sequoiadendron giganteum 89 Lobochlamys segnis Oogamochlamys gigantea 42 87 90 99 Chloromonas rosae Sequoia sempervirens 91 Chloromonas reticulata 88 Chlamydomonas sp.
Cryptomeria japonica 67 62 Chloromonas tughillensis GlyptostrobusTaxodium pensilisdistichum 99 95 Eudorina elegans 99 Vitreochlamys sp. misc/names.csv), and data used to build the figure, available at Papuacedrus papuana 49 Austrocedrus chilensis Volvox carteri WiddringtoniaPilgerodendron cedarbergensis uviferum 96 Volvox aureus 99 89 Pandorina morum 83 93 Volvox globator 34 96 Neocallitropsis pancheri Gonium pectorale Diselma archeri 19 Chlamydomonas reinhardtii 98 90 Chloromonas oogama doi.org/10.5281/zenodo.3255100.. 20 89 86 Chlamydomonas cribrum 91 96 Callitris macleayana 63 99 Lobomonas rostrata Callitris gracilis Neochlorosarcina sp. Chamaecyparis lawsoniana 32 Heterochlamydomonas inaequalis Thujopsis dolabrata Hafniomonas reticulata 33 Fokienia Thujahodginsii plicata 89 Carteria obtusa Cupressus dupreziana 70 71 Acutodesmus dimorphus Juniperus scopulorum 54 97 Neodesmus pupukensis Calocedrus decurrens Botryosphaerella sudetica 73 Ankistrodesmus sp. 84 33 Cylindrocapsa geminella Microbiota decussata Platycladus orientalis 51 87 Spermatozopsis similis Tetraclinis sp. Spermatozopsis exsultans Amborella trichopoda Microspora cf. tumidula Amborella_trichopoda 88 87 34 Golenkinia longispicula 97 63 Carteria crucifera Austrobaileya scandens 16 86 Fritschiella tuberosa Nymphaea sp. Stigeoclonium helveticum Nuphar advena Uronema sp. 87 Illicium floridanum 69 51 Aphanochaete repens Kadsura heteroclita 66 Oedogonium foveolatum 94 Oedogonium cardiacum AscarinaSarcandra rubricaulis glabra 94 Chaetopeltis orbicularis 86 26 98 41 Ochlochaete sp. CanellaDrimys winterana winteri 94 Entocladia endozoica 62 Percursaria percursa Aristolochia elegans 5 12 Bolbocoleon piliferum Saruma henryi 93 19 Pirula salina Saururus cernuus 86 Houttuynia cordata 96 77 85 Pseudoneochloris marina Acrosiphonia sp. 91 43 Peperomia fraseri 76 Planophila laetevirens 99 97 Planophila sp MyristicaPiper fragrans auritum 42 Helicodictyon planctonicum Michelia maudiae Halochlorococcum marinum Magnolia grandiflora 22 84 Oltmannsiellopsis viridis Eupomatia bennettii Ignatius tetrasporus 25 Tetraselmis chui IdiospermumAnnona australiense muricata 16 Uvaria microcarpa Tetraselmis striata 72 Scherffelia dubia Calycanthus floridus Tetraselmis cordiformis Laurelia sempervirens 44 97 96 Chlorella variabilis 96 85 Ettlia(?) oleoabundans Gomortega keule Gyrocarpus americanus 92 Parachlorella kessleri Peumus boldus 37 Picochlorum atomus Chlorochytridion tuberculata Cassytha filiformis 84 68 Pedinomonas minor Lindera benzoin 40 Codium fragile Cinnamomum camphora 92 99 98 Persea borbonia 89 Bryopsis plumosa Cephaleuros virescens Sassafras albidum 90 44 Trentepohlia annulata Acorus americanus 81 97 Cladophora glomerata Spirodela polyrhiza Eremosphaera viridis 66 33 Nannochloris atomus Pistia stratiotes 57 Typhonium blumei 30 Botryococcus terribilis Sagittaria latifolia 99 27 Botryococcus braunii Triglochin maritima 87 Coccomyxa pringsheimii 19 92 Posidonia australis 99 Microthamnion kuetzingianum 99 Dioscorea villosa Prasiola crispa Xerophyta villosa 4 Stichococcus bacillaris 85 Trebouxia arboricola Talbotia elegans 12 Stemona tuberosa 96 Geminella sp. 5 Freycinetia multiflora 74 42 unidentified sp CCMP 1205 Xerophyllum asphodeloides 34 Picocystis salinarum Pseudoscourfieldia marina Ludovia sp. 60 47 62 Cymbomonas sp. Helonias bullata Pyramimonas parkeae Smilax bona-nox 20 coccoid-prasinophyte Lilium sargentiae Prasinoderma coloniale 64 ColchicumGloriosa autumnale superba 12 Prasinococcus capsulatus Colchicum autumnale 97 Micromonas pusilla 18 43 Mantoniella squamata Nypa fruticans 99 Bathycoccus prasinos Elaeis guineensis 19 98 Monomastix opisthostigma Serenoa repens 37 31 Dolichomastix tenuilepis Orchidantha maxillarioides Sabal bermudana 60 Scourfieldia sp. Nephroselmis olivacea 54 Strelitzia reginae 11 Nephroselmis pyriformis 96 Cyanophora paradoxa Heliconia sp. 59 31 Musa acuminata 99 31 Glaucocystis cf. nostochinearum Maranta leuconeura 28 45 Gloeochaete wittrockiana 95 Cyanoptyche gloeocystis ZingiberCanna officinale sp. 92 Mazzaella japonica 48 Chondrus crispus Curcuma longa Brocchinia reducta 57 Gloiopeltis furcata Typha angustifolia Ahnfeltiopsis flabelliformis 85 Betaphycus philippinensis Typha latifolia Eucheuma denticulatum Juncus inflexus 24 96 26 Kappaphycus alvarezii Mapania palustris Lepidosperma gibsonii Dumontia simplex 69 Grateloupia filicina ChondropetalumCyperus tectorumpapyrus 47 Grateloupia livida 74 Joinvillea ascendens Grateloupia turuturu 70 Grateloupia catenata Oryza sativa 37 Gracilaria chouae DeschampsiaAvena cespitosa fatua Gracilaria sp. 99 Gracilaria blodgettii 84 Gracilaria vermiculophylla Aristida stricta 77 96 Uniola paniculata 64 Gracilaria lemaneiformis Eleusine coracana Symphyocladia latiuscula Triodia aff. bynoei 70 67 Neosiphonia japonica Cymbopogon nardus 74 Heterosiphonia pulchra Microstegium vimineum 49 98 Ceramium kondoi 55 Sorghum bicolor Pyropia yezoensis Panicum miliaceum 98 89 Porphyridium cruentum Thyridolepis mitchelliana 73 Chroodactylon ornatum 48 60 Thyridolepis multiculmis 98 68 97 Rhodochaete parvula 98 84 Neurachne annularis 78 Glaucosphaera vacuolata Neurachne tenuifolia 98 Rhodella violacea 99 Cryptomonas curvata Neurachne minor 77 98 83 Neurachne alopecuroidea 76 Punctaria latifolia 50 Colpomenia sinuosa Neurachne lanigera 99 94 28 Petalonia fascia Neurachne munroi 35 Scytosiphon lomentaria Paraneurachne muelleri 67 51 61 97 Scytosiphon dotyi Vanilla planifolia 32 58 Saccharina japonica Masdevallia yuangensis 59 Saccharina sculpera Oncidium sphacelatum 91 91 97 Undaria pinnatifida Platanthera clavellata 52 Desmarestia viridis Drakaea elastica Sargassum hemiphyllum Goodyera pubescens 84 63 88 5 Sargassum thunbergii Haemaria discolor 80 Sargassum horneri Borya sphaerocephala 73 38 Sargassum muticum Curculigo sp. 44 88 Sargassum vachellianum 75 Cyanastrum cordifolium 94 Sargassum henslowianum Cyanella orchidiformis 91 Sargassum integerrimum Sisyrinchium angustifolium Sargassum fusiforme 92 Xeronema callistemon 24 Dictyopteris undulata Aloe vera Synura petersenii Phormium tenax Synura sp. 98 Mallomonas sp. Johnsonia pubescens 82 Hemerocallis spp. 70 87 87 Isochrysis sp. Hemerocallis sp. Prymnesium parvum Pavlova lutheri Agapanthus africanus 75 62 Allium sativum Poliomintha bustamanta 75 Micromeria fruticosa Allium commutatum Thymus vulgaris Narcissus viridiflorus Prunella vulgaris Phycella aff. cyrtanthoides 97 Agastache rugosa Traubia modesta Nepeta cataria Zephyranthes treatiae 80 99 Salvia spp. Rhodophiala pratensis Rosmarinus officinalis Amaryllis belladonna Melissa officinalis Brodiaea sierrae Solenostemon scutellarioides Drimia altissima 88 Lavandula angustifolia Urginea maritima Leonurus japonicus 92 93 Chlorogalum pomeridianum Marrubium vulgare Agave tequilana 40 88 Pogostemon sp. Hesperaloe parviflora 33 87 74 Scutellaria montana Yucca filamentosa 95 Oxera neriifolia Yucca brevifolia 44 Oxera pulchella Asparagus densiflorus Ajuga reptans Lomandra longifolia 75 Teucrium chamaedrys 98 Vitex agnus-castus Eriospermum lancifolia 69 Ruscus sp. 87 82 Conopholis americana 51 57 71 Epifagus virginiana Sansevieria trifasciata 83 Disporopsis pernyi Rehmannia glutinosa 73 Lindenbergia philippensis Peliosanthes minor Orobanche fasciculata Nolina atopocarpa Paulownia fargesii Nolina bigelovii 88 89 73 Phyla dulcis Maianthemum canadense 96 14 Lantana camara Maianthemum sp. 54 86 Verbena hastata Ceratophyllum demersum 48 Mansoa alliacea Euptelea pleiosperma 97 19 Kigelia africana Akebia trifoliata Tabebuia umbellata Nandina domestica 43 Schlegelia parasitica 87 Schlegelia violacea Podophyllum peltatum 52 Hydrastis canadensis 30 Uncarina grandidieri Thalictrum thalictroides 51 Strobilanthes dyeriana 69 98 99 Sanchezia sp. Anemone hupehensis 99 Anemone pulsatilla Ruellia brittoniana 38 70 61 99 Anisacanthus quadrifidus Hypecoum procumbens Pinguicula caudata Capnoides sempervirens Pinguicula agnata Corydalis linstowiana Utricularia sp. Ceratocapnos vesicaria 84 Byblis gigantea Eschscholzia californica 66 28 Buddleja lindleyana Sanguinaria canadensis 99 Buddleja sp. Chelidonium majus 98 Celsia arcturus Argemone mexicana 99 Verbascum sp. Papaver bracteatum Papaver rhoeas Anticharis glandulosa Plantago maritima Papaver setigerum Plantago virginica Papaver somniferum Digitalis purpurea Meliosma cuneifolia 98 Antirrhinum majus NelumboNelumbo nucifera sp. Antirrhinum braun-blanquetii 98 Bacopa caroliniana Platanus occidentalis Sinningia tuberosa Grevillea robusta Saintpaulia ionantha Hakea drupacea Calceolaria pinifolia Hakea prostrata 43 88 Polypremum procumbens 94 Chionanthus retusus 94 67 49 93 Trochodendron aralioides 55 98 Buxus sempervirens 48 Olea europaea Gunnera manicata 67 89 Ligustrum sinense Dillenia indica 52 94 Heliotropium tenuifolium Vitis vinifera 85 Heliotropium mendocinum Cissus quadrangularis Heliotropium greggii 49 Heliotropium texanum Tetrastigma voinierianum Heliotropium filiforme Tetrastigma obtectum Heliotropium convolvulaceum Heliotropium racemosum Cercidiphyllum japonicum Heliotropium karwinskyi DaphniphyllumHamamelis macropodum virginiana Heliotropium calcicola Heliotropium tenellum LoropetalumPaeonia chinenselactiflora 84 21 99 90 68 Pholisma arenarium 98 52 48 Lennoa madreporoides Aphanopetalum resinosum 69 Ehretia acuminata MyriophyllumCrassulaRhodiola aquaticum perforata rosea 75 89 Phacelia campanularia 59 19 Mertensia paniculata 84 Itea virginica 94 Solanum xanthocarpum 14 99 Solanum sisymbriifolium Ribes aff. giraldii Lycopersicon cheesmanii Kalanchoe crenato-diagremontianaAstilbe chinensis Solanum lycopersicum Tellima breviflora 29 Solanum lasiophyllum Solanum dulcamara Heuchera sanguinea 93 Tiarella polyphylla 81 73 30 Solanum ptychanthum Mitella pentandra Datura metel Bergenia sp. 60 Brugmansia sanguinea Oresitrophe rupifraga Lycium sp. 98 39 Lycium barbarum 91 99 99 Atropa belladonna PeltoboykiniaSaxifragaBoykinia watanabei stolonifera jamesii 73 95 Nicotiana sylvestris 60 69 99 Ipomoea lobata 92 33 Ipomoea coccinea Francoa appendiculata 97 Geranium maculatum 71 Ipomoea quamoclit Tetrazygia bicolor 97 41 96 Ipomoea purpurea Medinilla magnifica Ipomoea hederacea 98 67 Ipomoea nil Syzygium paniculatum Ipomoea pubescens 88 SyzygiumEucalyptus micranthum grandis 50 98 94 Ipomoea lindheimeri 96 42 Ipomoea indica Eucalyptus leucoxylon 76 Convolvulus arvensis Terminalia neotaliala 62 Cuscuta pentagona LagerstroemiaPunicaEpilobium granatum indica sp. 94 Asclepias syriaca Asclepias curassavica 49 99 Holarrhena pubescens OenotheraOenothera speciosa rosea 68 Apocynum androsaemifolium 52 Wrightia natalensis Oenothera gaura Allamanda cathartica 21 Rauvolfia tetraphylla Oenothera suffulta suffulta Oenothera filiformis 60 66 Catharanthus roseus Oenothera berlandieri Gentiana acaulis OenotheraOenothera serrulata nana 96 Exacum affine 73 Oenothera affinis 83 Gelsemium sempervirens 23 Strychnos spinosa Oenothera picensis 40 88 40 unknown 65 Psychotria marginata OenotheraOenothera villaricae elata 50 96 Oenothera elata Psychotria ipecacuanha 98 Galium boreale 87 Eucommia ulmoides 98 OenotheraOenothera grandiflora biennis 52 Aucuba japonica Oenothera grandis 10 Pyrenacantha malvifolia Flaveria kochiana Oenothera laciniata 88 42 39 Flaveria vaginata Oenothera clelandii 58 32 93 Flaveria bidentis 79 Flaveria trinervia OenotheraStachyurusStaphylea rhombipetala praecox trifolia Flaveria angustifolia Flaveria sonorensis PeganumQuassia harmala amara 88 80 Flaveria brownii 83 Flaveria pubescens AilanthusCitrus altissima x paradisi 68 Flaveria palmeri Flaveria cronquistii AzadirachtaMelia azedarach indica Flaveria pringlei 99 45 Xanthium strumarium LitchiAcer chinensis negundo 67 Helenium autumnale Aesculus pavia Inula helenium Kirkia wilmsii Matricaria matricarioides Rhus radicans 45 Anthemis tinctoria 22 Tanacetum parthenium Bursera simaruba Leontopodium alpinum Boswellia sacra Erigeron canadensis
96 Tapiscia sinensis Conyza canadensis Solidago canadensis MuntingiaDaphne calabura giraldii Aster tataricus Bixa orellana Senecio rowleyanus 81 82 53 Tragopogon dubius Schizolaena sp. 3 51 Tragopogon castellanus Edgeworthia papyriferaCistus inflatus 32 Tragopogon porrifolius 11 21 Tragopogon pratensis Theobroma cacao 91 Lactuca graminifolia 59 98 Cicerbita plumieri Carthamus lanatus Dombeya burgessiae 45 Hoheria angustifolia 98 Silybum marianum 50 Akania lucens 90 88 Scaevola mossambicensis Hibiscus cannabinusCarica_papaya Menyanthes trifoliata 73 Phelline lucida Tropaeolum peregrinumMoringa oleifera 20 Platyspermation crassifolium Batis maritima Stylidium adnatum 3 Corokia cotoneaster 80 99 Platycodon grandiflorus Limnanthes douglasii 12 Lobelia siphilitica 55 Koeberlinia spinosa 98 Escallonia sp. cv. Newport ResedaSalvadora odorata sp. 97 81 Escallonia rubra Hedera helix Gyrostemon ramulosusCleome violacea 22 Polyscias fruticosa 38 90 20 Hydrocotyle umbellata Cleome viscosa 73 11 Myodocarpus sp. Sinapis alba 44 78 52 79 Heracleum lanatum Cleome gynandra Angelica archangelica Polanisia trachysperma 37 Brassica nigra 74 Centella asiatica 32 67 Pittosporum sahnianum Arabidopsis_thalianaArabis alpina 85 Pittosporum resiniferum 33 Griselinia littoralis Draba hispida 68 29 87 79 Griselinia racemosa Draba ossetica 35 Pennantia corymbosa Cochlearia officinalis 80 82 78 Valeriana officinalis 78 35 Draba aizoides 49 Dipsacus asper Draba magellanica 10 Lonicera japonica Symphoricarpos sp. Sambucus canadensis Draba oligosperma Oxalis sp. 18 Viburnum odoratissimum 41 66 Ilex paraguariensis Draba sachalinensisLarrea tridentata 92 Ilex vomitoria Krameria lanceolata 55 Ilex sp. Helwingia japonica Tribulus eichlerianus 63 Manilkara zapota 16 Synsepalum dulcificum Cunonia capensis 65 Sideroxylon reclinatum Sinojackia xylocarpa Elaeocarpus sylvestris 99 Symplocos tinctoria Phlox sp. Cephalotus follicularis 42 37 Phlox drummondii Fouquieria macdougalii Ricinus communisCroton tiglium 23 57 ManihotManihot esculenta grahamii 83 Ternstroemia gymnanthera Crossopetalum rhacoma 77 Rhododendron scopulorum Stackhousia spathulata Ledum palustre Cavendishia cuatrecasasii Phyllanthus sp. Sarcodes sanguinea Galax urceolata 95 Roridula gorgonias Euphorbia pekinensis 42 Actinidia chinensis Bischofia javanica 60 Ardisia humilis Rhizophora mangle Ardisia revoluta Erythroxylum coca 76 Jacquinia sp. 94 Maesa lanceolata Viola tricolor Diospyros malabarica Drypetes deplanchei 99 Mammea americana Souroubea exauriculata 65 Impatiens balsamifera Hydrangea quercifolia Dichroa febrifuga Hypericum perforatum 28 Garcinia oblongifolia 69 Caiophora chuquitensis Euphorbia mesembryanthemifolia Garcinia livingstoneiViola canadensisPassiflora_sp Nyssa ogeche Cornus florida Passiflora edulis 45 91 Alangium chinense Boerhavia coccinea Boerhavia dominii Salix acutifolia Allionia incarnata Allionia incarnata Salix fargesii 93 Malesherbia fasciculataPassiflora caerulea Mirabilis jalapa Populus trichocarpaSalix eriocephala Sarcobatus vermiculatus 49 Bougainvillea spectabilis Salix purpurea 99 Petiveria alliacea Hilleria latifolia Salix sachalinensisSalix dasycladosSalix viminalis Phytolacca americana Phytolacca bogotensis Sesuvium portulacastrum 57 Sesuvium verrucosum Cypselea humifusa Galphimia gracilisOchna serrulata Zaleya pentandra Linum flavum 54 Trianthema portulacastrum Delosperma echinatum 99 Portulaca suffruticosa
66 Linum macraei 62 Portulaca pilosa Licania michauxii Linum strictum Portulaca amilis Portulaca grandiflora 96 Portulaca cryptopetala Portulaca oleracea Chrysobalanus icaco Linum hirsutumLinum bienne Portulaca molokiniensis Ochna mossambicensis Portulaca umbraticola Linum tenuifolium Portulaca umbraticola Linum leonii Pereskia aculeata Linum perenneLinum lewisii Lophophora williamsii Talinum sp. Basella alba Linum grandiflorum Mollugo cerviana Mollugo pentaphylla Polygala lutea Mollugo verticillata Mollugo nudicaulis Microtea debilis Alternanthera brasiliana Alternanthera sessilis Linum usitatissimum Alternanthera tenella Alternanthera caracasana Blutaparon vermiculare Aerva lanata Aerva persica Quillaja saponaria Amaranthus cruentus Amaranthus retroflexus Atriplex prostrata Atriplex hortensis Atriplex rosea Chenopodium quinoa Cercis canadensis Beta maritima Bauhinia tomentosa Kochia scoparia Dianthus caryophyllus Saponaria officinalis Silene latifolia Schiedea membranacea Gleditsia sinensis Spergularia media Copaifera officinalis Polycarpaea repens Physena madagascariensis Simmondsia chinensis Senna hebecarpa Limonium spectabile Polygonum convolvulus Nepenthes alata Aextoxicon punctatum Berberidopsis beckleri Daenikera sp. Phoradendron serotinum Exocarpos cupressiformis Santalum acuminatum Dendropemon caribaeus Ximenia americana Cotoneaster transcaucasicus Sorbus koehneana Cladrastis lutea Malus baccata Amelanchier canadensis Gymnocladus dioicusGleditsia triacanthos Acacia pycnantha Glycine soja
Acacia argyrophylla Apios americana Desmanthus illinoensis Begonia sp. Lupinus polyphyllus Lupinus angustifolius
Phaseolus vulgaris Lathyrus sativus Wisteria floribundaGlycyrrhiza glabra
Juglans nigra Xanthocercis zambesiaca Codariocalyx motorius Fagus sylvatica Myrica cerifera Ulmus alata Glycyrrhiza lepidota Morus nigra
Betula pendula Urtica dioica Bituminaria bituminosa Castanea pumila Alnus serrulata Coriaria nepalensis Ziziphus jujuba Castanea crenata Nothofagus obliqua Quercus shumardii Astragalus propinquus Thladiantha villosula Ficus religiosa Rosa palustris
Geum quellyon Cannabis sativa
Prunus persica Gompholobium polymorphum Kerria japonica Humulus lupulus
Boehmeria nivea
Prunus prostrata Rhamnus japonica Dryas octopetala Aruncus dioicus
Elaeagnus pungens Celtis occidentalis
Astragalus membranaceus Rhamnus caroliniana Sanguisorba minor
Cercocarpus ledifolius
Physocarpus opulifolius Supplementary Fig. 4 Frequency of species with x number of genes in the ASTRAL and supermatrix 100 analyses (min = 75, max = 398, median = 338 out of 410 genes)
50 Number of genes
0 100 200 300 400 Occupancy (out of 410) Supplementary Fig. 5 Species (X-axis) occupancy in single copy gene alignments (Y-axis). Species names corresponding to the x-axis numbered taxon codes and data are included in Supplementary Table 1 and posted at doi.org/10.5281/zenodo.3255100 Supplementary Fig. 6 Support for alternative resolutions for problematic portions of the green plant phylogeny. Rows represent hypothesized branching orders, and columns correspond to various analyses, including ASTRAL trees with various levels of contraction g. within gene trees, ("full for no contraction or polytomies contracting clades with less than 33%, 20%, 10%, 5% bootstrap support), Spirotaenia sp+Zygnemophyceae Spirotaenia sp+Zygnemophyceae+LandPlants ASTRAL on binned gene trees, and concatenation using ExaML (CAML), applied to both amino acid data (AA) and DNA sequences, with Spirotaenia sp+Zygnemophyceae+ third codon position removed (C12). Also shown are trees with rogue taxa (Dillenia indica, Tetrastigma obtectum, Tetrastigma LandPlants+Coleochaetales voinierianum, Vitis vinifera, Cissus quadrangularis, Ceratophyllum demersum, "Spirotaenia" sp., and Prasinococcus capsulatus) removed LandPlants+Chara and with only eudicots included. Shades of blue correspond to clades that have been recovered in an analysis, and the light to dark LandPlants+Coleochaetales+Chara shade indicates strength of support (local posterior probability for ASTRAL and bootstrap for CAML). Yellow indicates a clade was not h. recovered, but light (dark) yellow corresponds to branches that were (were not) compatible with that clades if branches below 90% Chlorophyceae+Bryopsidales support were contracted. Missing tiles (e.g., those in white) represent hypotheses that could not be tested because relevant taxa were OtherUlvophyceae+Trent/Clado 88 Chlorophyceae+Bryopsidales+ missing. The figures are created using DiscoVista . For data used to build the figure, refer to doi.org/10.5281/zenodo.3255100 OtherUlvophyceae+Trent/Clado a. Bryopsidales+OtherUlvophyceae+Trent/Clado Green Plants+Glaucophyta Bryopsidales+Trent/Clado Green Plants+Glaucophyta+Red Algae i. b. Gunnera+Dillenia Hornworts+Mosses/Liverworts Saxifragales+CoreRosids Mosses/Liverworts+Vascs Saxifragales+CoreRosids+Vitales c. Saxifragales+CoreRosids+Vitales+Santalales Gnetales+Pinaceae Asterids+Berberidopsidales Pinaceae+Other Pinales Asterids+Berberidopsidales+Caryophyllales d. Eudicots − Gunnera/Dillenia Waterlilies+Other Angios Dillenia+Caryophyllales Waterlilies+Amborella Asterids+Dillenia+Caryophyllales Other Angios+Amborella Vitales+Santalales e. Eudicots − Gunnera/Berberidopsidales OtherPrasinococcales+Prasinococcus capsulatus Asterids+Caryophyllales Strept+Prasinococcales Asterids+Santalales+Caryophyllales Strept+Chloro j. Chloro+Prasinococcales Palms+Zings f. Palms+Poales Ophio. + Psilotales+Marattiales Zings+Poales Ophio. + Psilotales+Marattiales+Polypodiidae Marattiales+Polypodiidae C12 C12 C12 C12 C12 C12 C12 FAA FAA FAA FAA FAA FAA FAA FAA FAA FAA FAA − − − − Plastid full full − C12 − C12 − F AA − F AA only − only − − only − only − − − C12 − F AA 05% − 10% − 20% − 33% − − − − − Plastid rogue − rogue − rogue − rogue − − − − − CAML CAML − − − − binning − binning − − − CAML − C12 CAML − F AA Rejected ASTRAL Weakly Strongly ASTRAL Eudicots Eudicots Eudicots Eudicots remove remove remove remove ASTRAL ASTRAL ASTRAL ASTRAL − − − − − − − (<90%) (>90%) − ASTRAL − full C12 ASTRAL − full F AA ASTRAL ASTRAL ASTRAL − 20% F AA ASTRAL − 10% F AA ASTRAL − 05% F AA ASTRAL − 33% FAA ASTRAL − binning ASTRAL − binning CAML CAML CAML Support CAML ASTRAL ASTRAL ASTRAL ASTRAL CAML − remove rogue CAML − remove rogue ASTRAL − remove rogue ASTRAL − remove rogue Full amino acid Full DNA Filtered rogue 0 50 100 Full amino acid Full DNA Filtered rogue Eudicots only 0.8 Supplementary Fig. 7 Distribution of the GC content across all single-copy genes for each species (x-axis). The distributions are shown for all codon positions (top row), and each also separately for
● each of the codon positions (rows 2-4). The GC content of the first and the second codon position are on average similar across all species, whereas, the GC content of the third codon varies dramatically, ● ●●●● ●●● ●●●● ●●● ●●●●●●● ●●●●●●●●●●●● rendering assumptions of the GTR model invalid. The x-axis is labeled by numbers with four letter taxon codes and species names posted at doi.org/10.5281/zenodo.3255100 ●●●●●● ●●●●● ●●●●●●●●● ●●●●●●●●●● ●●●●●●●● ●●●●●●●●●●●● ●●●●●●●●●●●●●●● ●●●●●●●●●●●●●● 0.6 ●●●●●●●●●● ●●●●●●●●●●●●● ●●●●●●●●●●●●●●●● ●●●●●●● ●●●●●●●●●●●●●●● ●●●●●●●●●● ●●●●●●●●●● ●●● ALL ●●●●●●●●●●●●● ●●●●●●●●●●● ●●●●●●●●● ●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●● ●● 0.4 ● ●●
0.2
0.8
● ●● ● ●● 0.7 ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ●● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● C1 ●● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ●● ● ●● ●● ●● ● ● ● ● 0.6 ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●●●● ●●● ● ●●● ● ●●●● ●● ● ●● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ●● ● ● ● ● ● ●●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ●●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●●●● ● ●● ●● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ●●● ● ●● ● ● ● ● ●●● ● ●●●● ●●●● ● ●● ●●●●● ●● ●●●● ● ●●● ●● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ●●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ●● ● ● ● ● ● ●●● ●● ● ● ● ●●● ● ● ● ● ● ●● ●●●●● ● ●●●● ● ● ● ●●●● ●●● ●● ●●● ●●●●●● ●● ● ●●●●●●●● ● ●● ● ● ● ● ● ●● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ●●●● ● ● ●●● ●● ●●● ●● ●● ●● ●● ● ● ● ●●●●● ●●● ● ● ● ●● ●● ● ● ●●● ●● ● ● ●● ● ● ● ● ● ● ● ●●● ● ● ●● ● ● ● ●● ● ● ● ● ●●●● ● ● ● ●●● ● ● ● ● ●●●● ● ●● ● ● ●● ●●● ●● ●●●●●● ● ●●●●●● ● ●●●● ●● ● ●● ●●● ● ● ●● ●●●● ●● ● ● ● ●●●●●● ● ● ● ●●●●●●●●● ● ● ● ●●●●●●●● ● ●● ●● ●● ●●● ●● ●●●● ● ●●● ●● ● ● ● ●● ● ● ● ● ●●●● ● ●● ●●● ● ● ● ● ● ● ● ● ● ●●● ● ● ●●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ●● ● ●●● ●●● ● ● ● ● ● ●● ● ● ●●● ●●●● ● ●●●● ●●● ● ●● ● ● ●●● ●●●● ●●● ● ●● ● ● ●● ● ●●●●● ● ● ●● ● ●● ●● ●● ●● ● ●●● ● ●●●●●●● ●●●● ● ●● ● ● ● ●● ● ●●●● ● ● ● ● ● ● ● ● ●● ●● ● ●●● ● ●● ●●● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ●● ● ● ● ● ● ●● ●●●●● ● ● ● ●● ● ●● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ●●●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● 0.5 ●●● ● ● ● ● ● ●
0.4
0.3
GC content 0.6
●
0.5 ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ●● C2 ● ● ●●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●●● ●● ● ● ● ●●●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ●●● ●●●● ● ●●● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ● ●● ●●●●● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ● ● ● ● ● ●● ●●● ● ● ● ●●● ●●● ●● ●● ● ●●●● ●● ●● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ●●● ● ● ● ● ● ● ● ●● ●● ● ●● ● ● ● ● ● ● ●●● ● ● ●●● ● ● ● ● ●●● ● ● ● ● ●● ● ● ● ● ● ● ● ●●● ● ●●● ● ● ● ● ●●● ●●●●●● ●● ●● ●●● ●● ● ●● ●●●● ● ●● ●● ●● ●●● ●●● ●● ● ●●●●● ● ●● ●●●●● ●●●● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ●● ● ●●● ●● ● ● ● ● ● ● ● ● ●● ●●●● ●●● ● ● ●● ●●● ● ●● ●● ● ● ● ●● ●● ●● ●●● ●● ● ● ●● ●● ●●● ●● ● ●●● ● ●● ●●●● ● ● ● ● ● ●● ●●● ●●● ●● ● ● ● ● ● ● ● ●●●●●●● ●●●● ●●● ●●●●● ●● ●●●● ●●●● ●● ●●●●●●●● ● ● ● ●● ●●●● ●● ● ●● ● ● ●●●● ● ● ●●● ●●●●● ● ●●●●● ●● ●●● ●●● ● ● ●● ●● ●●●●● ●● ●●●● ● ●● ● ●●● ●● ●● ●● ●● ● ● ●● ● ●●●●● ● ● ●● ●●●●● ● ● ●● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ●● ●● ●● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ●●●●● ● ● ● ●●● ●● ● ●● ●● ●● ● ● ●●●●● ● ● ● ● ● ●● ● ● ● ●●● ● ●●●●● ●● ● ●● ● ● ●● ● ●●● ●● ● ● ● ●●● ● ● ● ● ●● ● ● ● ●● ●● ●● ●● ●●● ● ●● ● ●●●● ● ●●●● ●● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ●● ● ● ● ● ●● ● ● ● ●● ● ● ● ●● ●●● ● ●● ●●● ● ●● ● ● ●●● ● ● ● ●● ● ● ● ● ● ●●● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ●●● ●● ● ● ●●●●●●●●● ● ● ●●● ●● ●●● ● ● ●● ● ● ● ● ● ● ● ● ● ●●●●● ● ●● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● 0.4 ●● ● ● ●●● ●●● ●●●● ●● ●●●● ● ●●● ●● ●●● ● ● ● ● ● ● ●● ●●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●
0.3
1.2
● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ●● ● ● ● ●● ●● ● ● ● ● ● ● ●●●● ● ● ● ● ● ●● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ●● ● ● ● ●●● ● ● 0.8 ●● ● ● ● ●● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ●●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ●● ● ● ● ● ●●●● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ●● ● ●● ● ● ● C3 ● ● ● ● ● ●● ● ●● ● ● ● ● ●●●●● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ●●●●● ● ●●● ● ●●●● ●●●● ● ● ● ● ● ● ● ● ● ●● ●●● ●●● ● ● ● ● ● ● ● ●● ● ●● ●● ●● ●●●● ●●● ● ● ● ●● ● ●● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●●●● ● ● ● ● ● ● ●● ● ● ● ●● ●●● ● ● ● ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ●●●● ● ●● ●●●●●●● ●● ●●●● ● ●●●●●●●●● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ● ●● ● ● ● ● ●●●● ● ● ●● ●● ● ●● ● ●●●● ● ● ● ● ● ●● ●●● ● ● ● ● ●● ● ●●● ● ●● ●● ●● ● ●●●● ● ● ● ● ● ● ●● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●●●● ●● ●● ● ● ● ●● ● ● ●●●● ● ● ●●● ●●● ●●●●●●●●●● ●●●●●●●●● ● ●● ●●●●● ●●●●●●●●● ●● ● ● ● ●●● ● ● ● ● ● ●● ● ●● ● ●●● ●● ● ● ● ●● ● ●● ● ● ● ● ● ●● ●● ● ● ● ● ●● ●● ●●● ● ● ●●●●● ●● ●● ●●●●● ●●●●●●●●●● ●● ●●● ●●●●●●●●●●●●●● ●●●●●● ●●●●●●●●●● ●●●●●●●● ●●●●●●●●●●● ●●● ●●●● ●● ●●● ● ●●● ●● ● ● ●●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ●● ● ● ●●● ●●● ●● ●● ● ●● ●●●● ●●●●●●●● ●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●● ●●●● ●●● ●●●●●●● ● ●●●●●● ●● ●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ●● ●●● ●●●● ●●●● ●●●●● ●●●●●●●●●●●●●●●●●●●● ● ●●●● ●●●●● ●● ●●●●● ●● ● ●●●● ● ● ● ● ●● ● ●●● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●●●● ● ● ●●● ●●● ●●●●●●●●● ●●●●●●●● ●●●●●● ●●●●●● ●●●●●● ●●●●●●●●●●●●● ●● ●●●●● ●● ● ● ● ● ● ● ● ● ● ● ● 0.4 ●● ●● ● ●● ● ●● ● ● ●● ●● ● ●● ●●●●●●●●●●●●● ●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ●● ● ●●● ●● ● ●●● ●● ● ● ● ● ● ● ● ● ●●●●●●●●● ●●● ● ● ● ●●●● ● ● ● ●● ●●● ● ●●●●
● ●
0.0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 Physcomitrella patens_Phypa_v3.0
Rosulabryum cf. capillare_XWHK
Racomitrium elongatum_ABCD
Odontoschisma prostratum_YBQN
Encalypta streptocarpa_KEFD
Plagiomnium insigne_BGXB Ceratodon purpureus_FFPD
Dicranum scoparium_NGTD Leucobryum glaucum_RGKI Leucobryum albidum_VMXJ Racomitrium varium_RDOO Polytrichum commune_SZYG
Syntrichia princeps_GRKU Orthotrichum lyellii_CMEQ
Atrichum angustatum_ZTHV
Diphyscium foliosum_AWOI Bryum argenteum_JMXW
Philonotis fontana_ORKS Buxbaumia aphylla_HRWG Scouleria aquatica_BPSG Barbilophozia barbata_OFTVTakakia lepidozioides_SKQD Andreaea rupestris_WOGB Physcomitrium sp._YEPO Sphagnum recurvum_UHLI
Tetraphis pellucida_HVBQ Hedwigia ciliata_YWNF Sphagnum palustre_RCBT Sphagnum lescurii_GOWD Radula lindenbergiana_BNCU Timmia austriaca_ZQRI Ptilidium pulcherrimum_HPXA Scapania nemorosa_IRBN
Bazzania trilobata_WZYK Marchantia polymorpha_JPYU Metzgeria crassipilis_NRWZ Porella navicularis_KRUQ Phaeomegaceros coriaceus_AKXBNothoceros aenigmaticus_DXOU Calypogeia fissa_RTMU Marchantia paleacea_HMHL Conocephalum conicum_ILBQMarchantia emarginata_TFYI Schistochila sp._LGOW Nothoceros vincentianus_TCBCSphaerocarpos texanus_HERT Porella pinnata_UUHD Phaeoceros carolinianus_WEEQ Ricciocarpos natans_WJLO Phaeoceros carolinianus_WCZB Pallavicinia lyellii_YFGP Pellia cf. epiphylla_PIUF Megaceros flagellaris_UCRN Paraphymatoceros hallii_FAJB Frullania sp._TGKW Cosmarium subtumidum_WDGV Lunularia cruciata_TXVB Pellia neesiana_JHFI
Pleurotaenium trabecula_MOYY LeiosporocerosAnthoceros dussii_ANON agrestis_TWUW Staurodesmus convergens_WCQUXanthidium antilopaeum_GBGT Cosmarium ochthodes_STKJ Anthoceros agrestis_BSNI Staurodesmus omearii_RPRU Cosmocladium cf. constrictum_RQFE Micrasterias fimbriata_MCHJ
Desmidium aptogonum_DFDS Phymatodocis nordstedtiana_RPQV Cosmarium tinctum_BHBK Onychonema laeve_GGWH
Aulacomnium heterostichum_WNGH Fontinalis antipyretica_DHWX Pseudotaxiphyllum elegans_QKQO Leucodon julaceus_IGUH Leucodon brachypus_ZACW Calliergon cordifolium_TAVP Thuidium delicatulum_EEMJ Stereodon subimponens_LNSF Anomodon attenuatus_QMWB Cosmarium granatum_MNNM Neckera douglasii_TMAJ Climacium dendroides_MIRS Loeskeobryum brevirostre_WSPM Rhynchostegium serrulatum_JADL Claopodium rostratum_VBMM Phylloglossum drummondii_ZZEI Huperzia myrsinites_CBAE Huperzia squarrosa_GAON Huperzia selago_YHZW Huperzia lucidula_GKAG Bambusina borreri_QWFV Pseudolycopodiella caroliniana_UPMJ Lycopodiella appressa_ULKT Lycopodium deuterodensum_PQTO Staurastrum sebaldi_ISHC Dendrolycopodium obscurum_XNXF Diphasiastrum digitatum_WAFT Lycopodium annotinum_ENQF Isoetes tegetiformans_PKOX Isoetes sp._PYHZ Selaginella selaginoides_KUXM Selaginella kraussiana_ZFGK Selaginella wallacei_JKAA Penium margaritaceum_AEKF Selaginella acanthonota_ZYCD Cosmarium broomei_HIDG Selaginella willdenowii_KJYC Selaginella apoda_LGDQ Selaginella cf. pallescens_ABIJ Gonatozygon kinahanii_KEYW Selaginella moellendorffii_Selmo_v1.0 Selaginella moellendorffii_ZZOL Euastrum affine_GYRP Equisetum hyemale_JVSZ Equisetum diffusum_CAPN Nucleotaenium eifelense_KMNX ENSTα Danaea nodosa_DFHO Marattia attenuata_UGNK Angiopteris evecta_NHCM Psilotum nudum_QVMR Penium exiguum_YSQT Tmesipteris parva_ALVQ Planotaenium ohtanii_SNOX Ophioglossum petiolatum_DJSE Closterium lunula_DRFX Sceptridium dissectum_EEAQ PHPAα Botrypus virginianus_BEGM Cylindrocystis cushleckae_JOJQ Osmundastrum cinnamomeum_RFMZ Mesotaenium kramstae_NBYP Osmunda sp._UOMY Mesotaenium endlicherianum_WDCWMesotaenium caldariorum_HKZW Osmunda javanica_VIBO Dipteris conjugata_MEKP Supplementary Fig. 8 Phylogenetic placement of ancient WGDs inferred in the phylogeny of green plants. Yellow stars Hymenophyllum bivalve_QIAD Cylindrocystis brebissonii_RPGL Lygodium japonicum_PBUU Anemia tomentosa_CQPW Azolla cf. caroliniana_CVEG Pilularia globulifera_KIIX represent WGDs inferred from Ks plots and synonymous ortholog divergence analyses; Red stars represent WGDs inferred by Ks Zygnemopsis sp._MFZO SEKRα Alsophila pinulosa_GANB FRULα Thyrsopteris elegans_EWXK Cylindrocystis brebissonii_YOXI PHYDα Netrium digitus_FFGRRoya obtusa_XRTZ Plagiogyria japonica_UWOD Culcita macrocarpa_PNZO Lonchitis hirsuta_VVRN plots, synonymous ortholog divergence analyses and MAPS analyses; Blue squares represent significant increases in gene Chaetosphaeridium globosum_DRGY Lindsaea microphylla_YIXP Lindsaea linearis_NOKI Ceratopteris thalictroides_PIVW STOMβ STOMα COSUα Mesotaenium braunii_WSJO LYAPα Pityrogramma trifoliata_UJTT Cylindrocystis sp._VAZEMougeotia sp._ZRMT Pteris ensiformis_FLTD duplications inferred by MAPS analyses; The WGD identification labels correspond to WGD ID codes in Supplementary Table 2. SCHLα Pteris vittata_POPJ AZOLα Cryptogramma acrostichoides_WQML Coleochaete irregularis_QPDY Vittaria appalachiana_NDUV Vittaria lineata_SKYV HUSQα Klebsormidium flaccidum_Klefl_v1.0 COTIα Adiantum raddianum_BMJR Coleochaete scutata_VQBJ LYCOα SCEPα Adiantum aleuticum_WCLG Argyrochosma nivea_XDDT Myriopteris rufa_GSXD Notholaena montieliae_YCKE SpirotaeniaSpirogyra sp._TPHT sp._HAOX Parahemionitis cordata_ZXJO Klebsormidium subtile_FQLP LONCα Gaga arizonica_DCDT Chlorokybus atmophyticus_AZZW PSILβ PSILα Dennstaedtia davallioides_MTGC Chara braunii_Chabr_v0.1 CYATα MIFIα VILIα Leucostegia immersa_WGTU HUSQβ Didymochlaena truncatula_RFRB Interfilum paradoxum_FPCO OPHIα Chara vulgaris_MWXT ADIAα Polystichum acrostichoides_FQGQ LINDα Bolbitis repanda_JBLI MARAα Nephrolepis exaltata_NWWI CERAα Davallia fejeensis_OQWW Prasinococcus capsulatus_XMCLEntransia fimbriata_BFIK ISTEβ ISTEα Phymatosorus grossus_ORJE Prasinoderma Spirotaeniacoloniale_HYHN minuta_NNHQ Pleopeltis polypodioides_UJWU coccoid-prasinophyte_XJGM NUEIα Phlebodium pseudoaureum_ZQYU LEIAα Polypodium amorphum_YLJA Polypodium hesperium_GYFU Mesostigma viride_KYIO Polypodium glycyrrhiza_CJNT Polypodium hesperium_IXLH Dunaliella primolecta_WDWX Asplenium platyneuron_KJZG Dunaliella tertiolecta_ZDIZ Asplenium cf. x lucrosum_BMIF Asplenium nidus_PSKY CYBRα Gymnocarpium dryopteris_HEGQ Cystopteris utahensis_HNDZ Chloromonas perforata_QRTH LYCOβ Cystopteris fragilis_LHLE StephanosphaeraAsteromonas pluvialis_ZLQEDunaliella gracilis_ZFXU salina_RHVC MEBRα Cystopteris reevesiana_RICC Brachiomonas submarina_GUBDDunaliella salina_UKUC Cystopteris protrusa_YOWV Cystopteris fragilis_XXHP Dunaliella salina_SYJM Homalosorus pycnocarpos_OCZL ChlamydomonasHaematococcus noctigama_VALZPleurastrum pluvialis_KFEB insigne_PRIQ Thelypteris acuminata_MROH Chlamydomonas bilatus_MULF Woodsia ilvensis_YQEC Chlamydomonas moewusii_JRGZ LEIAβ Woodsia scopulina_YJJY Onoclea sensibilis_HTFH Blechnum spicant_VITX Chloromonas subdivisa_GFUR ASNIα Deparia lobato-crenata_FCHS Diplazium wichurae_UFJN Athyrium filix-femina_URCP Athyrium sp._AFPO Chlamydomonas sp._TSBQ Ginkgo biloba_SGTW B1 Cycas micholitzii_XZUY Pteromonas angulosa_LNIL Dioon edule_WLIC Encephalartos barteri_GNQG Stangeria eriopus_KAWQ PhacotusPteromonas lenticularis_ZIVZ sp._ACRY BUAPα Ephedra sinica_VDAO Welwitschia mirabilis_TOXE Chlamydomonas reinhardtii_Chlre_v5.5 Gnetum montanum_GTHK Volvox carteri_Volca_v2.0 Cedrus libani_GGEA Volvox aureus_WRSL Abies lasiocarpa_VSRH PandorinaVolvox morum_RYJX aureus_JWGT Keteleeria evelyniana_JUWL Pseudolarix amabilis_AQFM Eudorina elegans_RNAT WELMα Tsuga heterophylla_GAMH HeterochlamydomonasChlamydomonas inaequalis_IRYHChloromonas cribrum_BCYF oogama_IHOI RLINβ Nothotsuga longibracteata_AREG Gonium pectorale_KUJU Volvox globator_ISPU Larix speciosa_WVWN Pseudotsuga wilsoniana_IOVS Chloromonas rosae v. psychrophila_AJUW Cathaya argyrophylla_NPRL Picea engelmannii_AWQB NeochlorosarcinaLobomonas rostrata_JKKI sp._USIX LYGOα Pinus parviflora_IIOL
CYATβ Pinus taeda_Pinta_v2.0 OogamochlamysVitreochlamys gigantea_XDLL sp._QWRA Pinus radiata_DZQM Lobochlamys segnis_OFUE PTANα SPPAα Pinus ponderosa_JBND Pinus jeffreyi_MFTM Araucaria rulei_XTZO Chloromonas reticulata_LBRP Wollemia nobilis_RSCE EQUIα Chloromonas tughillensis_UTRE CHMOα OSMNα Agathis robusta_MIXZ Chlamydomonas sp._AOUJ Agathis macrophylla_ACWS Hafniomonas reticulata_FXHG Prumnopitys andina_EGLZ Sundacarpus amarus_KLGF Halocarpus bidwillii_OWFC C6 PHFOα Phyllocladus hypophyllus_JRNA Microstrobos fitzgeraldii_BBDD Botryosphaerella sudetica_VJDZ Parasitaxus usta_JZVE PediastrumCarteriaCarteria duplex_XTON crucifera_VIAU obtusa_RUIF Pediastrum duplex_XKWQ Lagarostrobos franklinii_ZQWM NeodesmusAcutodesmus pupukensis_MWAN dimorphus_PZIF Manoao colensoi_CDFR Saxegothaea conspicua_QCGM Microcachrys tetragona_MHGD Acmopyle pancheri_HILW GolenkiniaAnkistrodesmus longispicula_BZSH sp._OTQG Microspora cf. tumidula_FOYQ Dacrycarpus compactus_FMWZ Spermatozopsis exsultans_MXDS Dacrydium balansae_IZGN Spermatozopsis similis_ENAU Falcatifolium taxoides_ROWR
DISCα Falcatifolium taxoides_QHBI Cylindrocapsa geminella_DZPJ Podocarpus coriaceus_SCEB Stigeoclonium helveticum_JMUI Podocarpus rubens_XLGK Nageia nagi_UUJS Retrophyllum minus_VGSX Fritschiella tuberosa_VFIV Sciadopitys verticillata_YFZK CHROα Amentotaxus argotaenia_IAJW Oedogonium foveolatum_SDPC B3 Torreya taxifolia_EFMS AphanochaeteUronema repens_IJMTbelkae_RAWF PTERα Torreya nucifera_HQOM Oedogonium cardiacum_DVYEUronema sp._ISGT Cephalotaxus harringtonia_NVGZ Chaetopeltis orbicularis_BAZF Austrotaxus spicata_BTTS Pseudotaxus chienii_YLPM Taxus cuspidata_ZYAX Taxus baccata_WWSS Bryopsis plumosa_JTIG Cunninghamia lanceolata_ZQVF Taiwania cryptomerioides_QSNJ PercursariaCodium percursa_OAEZ fragile_GYBH EntocladiaOchlochaete endozoica_OQON sp._CQQP CYATγ Athrotaxis cupressoides_XIRK Metasequoia glyptostroboides_NRXL Sequoiadendron giganteum_QFAE DesmochlorisBolbocoleon halophila_KSFK piliferum_LSHT Sequoia sempervirens_HBGV Pseudoneochloris marina_GJIY Cryptomeria japonica_GMHZ Pirula salina_NQYP Glyptostrobus pensilis_OXGJ Planophila laetevirens_CBNG Helicodictyon planctonicum_AJAU PINEα Taxodium distichum_FHST Pilgerodendron uviferum_ETCJ Austrocedrus chilensis_YYPE HYMEα PODOα Papuacedrus papuana_OVIJ Planophila sp_LETF Widdringtonia cedarbergensis_AUDE HalochlorococcumOltmannsiellopsisIgnatiusAcrosiphonia tetrasporus_KADG marinum_ALZF viridis_NSTT sp._JIWJ Diselma archeri_GKCZ Callitris gracilis_IFLI Callitris macleayana_RMMV Cladophora glomerata_VBLH Neocallitropsis pancheri_JDQB Blastophysa cf. rhizopus_VHIJ Thuja plicata_VFYZ Cephaleuros virescens_YDCQ Thujopsis dolabrata_NKIN Trentepohlia annulata_NATT Fokienia hodginsii_UEVI Botryococcus braunii_ETGN Chamaecyparis lawsoniana_AIGO Botryococcus terribilis_QYXY Juniperus scopulorum_XMGP Coccomyxa pringsheimii_GXBM B2 Cupressus dupreziana_QNGJ Calocedrus decurrens_FRPM MicrothamnionTrebouxia kuetzingianum_EATP arboricola_NKXU Tetraclinis sp._CGDN Microbiota decussata_XQSG Leptosira obovata_ZNUM Platycladus orientalis_BUWV Stichococcus bacillaris_WXRI Amborella trichopoda_URDJ Amborella_trichopoda_Ambtr_v1.0.27 Ettlia(?) oleoabundans_EEJO Nymphaea sp._PZRT Chlorella variabilis_Chlva_v1.0Prasiola crispa_WCLV BTERα Nuphar advena_WTKZ Parachlorella kessleri_AKCR Austrobaileya scandens_FZJL Prototheca wickerhamii_BILC Illicium floridanum_VZCI D4 Kadsura heteroclita_NWMY Picochlorum atomus_JQFK MIKUα AUSCα Acorus americanus_MTII Eremosphaera viridis_MNCB Sagittaria latifolia_DWZT Nannochloris atomus_MFYC ILFLα Triglochin maritima_COCP METAα Posidonia australis_BYQM Spirodela polyrhiza_Spipo_v2 TetraselmisGeminella striata_HHXJ sp._PFUD Pistia stratiotes_MFIN Tetraselmis cordiformis_DUMA Tetraselmis chui_HVNO Typhonium blumei_YMES Chlorophyta incertaeChlorochytridion sedis CCMP tuberculata_PUAN 1205_AYPS Dioscorea villosa_OCWZ SALAα Scherffelia dubia_FMVB ERISα Xerophyta villosa_QOXT Talbotia elegans_SILJ Pedinomonas minor_RRSV SPPOα Stemona tuberosa_VBHQ DIVIα Freycinetia multiflora_DGXS NephroselmisPicocystis olivacea_MMKUsalinarum_TGNL Ludovia sp._VVVV TAELα STTUαFRMUα Nypa fruticans_NSPR OstreococcusNephroselmis lucimarinus_Ostlu_v2.0 pyriformis_ISIM TECOα Elaeis guineensis_Elagu_v2.0 Bathycoccus prasinos_MCPK Sabal bermudana_HWUP FRMUβ Serenoa repens_HXJE MicromonasMantoniella pusilla_Micpu_v3.0 squamata_QXSZ Musa acuminata_Musac_v1.0 Monomastix opisthostigma_BTFM Heliconia sp._XHHU Strelitzia reginae_UOEL Dolichomastix tenuilepis_XOAL Orchidantha maxillarioides_LSKK OSMNβ NYFRα Curcuma longa_LEMW PyramimonasCymbomonas parkeae_TNAW sp._XIVI Zingiber officinale_BDJQ Pseudoscourfieldia marina_JMTE ACAMα Maranta leuconeura_JNUB MUACα ZINGα Canna sp._TZNS Brocchinia reducta_BYPY Scourfieldia sp._EGNB Typha angustifolia_PPQR Scytosiphon dotyi_ULXR Typha latifolia_BRUD ScytosiphonPetalonia lomentaria_JCXF fascia_VRGZ MALEα Juncus inflexus_CIEA Colpomenia sinuosa_QLMZ TYPHα Mapania palustris_XPAF JUINα Cyperus papyrus_PWSG SaccharinaPunctaria japonica_SRSQ latifolia_ASZK CYPAα Lepidosperma gibsonii_WBIB LEGIα Chondropetalum tectorum_BSTR Saccharina sculpera_RAPY Joinvillea ascendens_WXNT Undaria pinnatifida_FIDQ NUADα Oryza sativa_Orysa_v7.0 SargassumDesmarestia hemiphyllum_VYER viridis_FSQE Deschampsia cespitosa_IADP Avena fatua_RMVB Sargassum muticum_JGGD Aristida stricta_HATH Sargassum thunbergii_YRMA Triodia aff. bynoei_YXNR Sargassum fusiforme_LDRY Eleusine coracana_EFCZ SargassumSargassum henslowianum_FIKG horneri_RWXW Uniola paniculata_RCAH CHTEα Uniola paniculata_YLWW Sargassum vachellianum_HFIK SAJAα Microstegium vimineum_YPIC Sargassum integerrimum_FOMH Cymbopogon nardus_ROEI Sorghum bicolor_Sorbi_v2.1 Dictyopteris undulata_LIRF Panicum miliaceum_SOHV Ishige okamurae_APTP Thyridolepis multiculmis_WCOR Synura petersenii_DBYD Thyridolepis mitchelliana_XBKS Neurachne munroi_ZMGN MallomonasSynura sp._BOGTsp._VKVG Neurachne annularis_BPKH Pavlova lutheri_NMAK ORSAβ Neurachne tenuifolia_NNOK ORSAα Neurachne minor_BXAY Pavlova lutheri_VJED Paraneurachne muelleri_XUAB Pavlova lutheri_LLEN Neurachne lanigera_VQYB Pavlova lutheri_RFAD Neurachne alopecuroidea_ZENX Rebecca salina_EBWI Prymnesium parvum_LXRN ORSAγ Xerophyllum asphodeloides_AFLV Helonias bullata_OOSO Isochrysis sp._BAJW Smilax bona-nox_MWYQ Rhodomonas sp._IAYV HEBUα SMBOα Proteomonas sulcata_IRZA Lilium sargentiae_THEW Cryptomonas curvata_BAKF C4 D1 Gloriosa superba_GDKK Colchicum autumnale_QNPH Chroomonas sp._ROZZ Colchicum autumnale_NHIX Gracilaria chouae_FTRP GLSUα Vanilla planifolia_THDM Gracilaria vermiculophylla_VNALGracilaria sp._PWKQ E7 Masdevallia yuangensis_JSAG Oncidium sphacelatum_CNTZ Gracilaria blodgettii_LJPN Platanthera clavellata_MTHW Gracilaria lemaneiformis_IKWM GINKα Drakaea elastica_XZME Grateloupia filicina_ZJOJ Haemaria discolor_LELS Grateloupia livida_IKIZ Goodyera pubescens_VTUS Grateloupia turuturu_URSB Borya sphaerocephala_EMJJ Grateloupia catenata_PYDB VAPLα Curculigo sp._YJUG Chondrus crispus_UGPM Cyanella orchidiformis_KYNE Mazzaella japonica_WEJN AMBOα Cyanastrum cordifolium_RDYY Sisyrinchium angustifolium_LTZF Gloiopeltis furcata_SBLT Ahnfeltiopsis flabelliformis_CKXF Xeronema callistemon_SART E5 Aloe vera_JVBR Dumontia simplex_IEHF SIANα ALVEα Phormium tenax_FCEL Kappaphycus alvarezii_IHJY Johnsonia pubescens_WTDE Betaphycus philippinensis_BWVJ PHTEα Hemerocallis spp._BLAJ Eucheuma denticulatum_JEBK Hemerocallis sp._JHUL Neosiphonia japonica_XAXW Agapanthus africanus_PRFO Symphyocladia latiuscula_UYFR AGAFα Allium sativum_GJPF Heterosiphonia pulchra_YSBD ALCOα Allium commutatum_KBXS Ceramium kondoi_VZWX NAVIα Narcissus viridiflorus_TRRQ Pyropia yezoensis_ZULJ Phycella aff. cyrtanthoides_DMIN Porphyridium cruentum_OBUY NAVIβ Traubia modesta_ZKPF Porphyridium purpureum_PVGP E14 Amaryllis belladonna_LDME Rhodella violacea_RTLC Rhodophiala pratensis_JDTY Glaucosphaera vacuolata_RSOF Zephyranthes treatiae_DPFW BRSIα Brodiaea sierrae_IXEM Rhodochaete parvula_JJZR Drimia altissima_SVTS Chroodactylon ornatum_LLXJ Urginea maritima_KOFB 'Cyame v1.0' Chlorogalum pomeridianum_PLBZ Gloeochaete wittrockiana_PQED CHPOα Hesperaloe parviflora_CMCY Glaucocystis cf. nostochinearum_POOW Agave tequilana_KXSK Cyanoptyche gloeocystis_JKHA Yucca filamentosa_ICNN Cyanophora paradoxa_QFND LOLOα Yucca brevifolia_YBML Nepeta cataria_FUMQ Lomandra longifolia_MUMD Agastache rugosa_PUCW PRVUα Asparagus densiflorus_FGRF Prunella vulgaris_PHCE SATRα Eriospermum lancifolia_ONBE Poliomintha bustamanta_XMBA Sansevieria trifasciata_MVRF Micromeria fruticosa_WHNV Ruscus sp._LSJW Thymus vulgaris_IYDF Peliosanthes minor_TCYS Salvia spp._EQDA Nolina bigelovii_RQZP Nolina atopocarpa_HOKG Rosmarinus officinalis_FDMM E16 Disporopsis pernyi_UZXL Melissa officinalis_TAGM LAVAα SLSCα ASCAα Maianthemum canadense_XFJG Lavandula angustifolia_FYUH Maianthemum sp._RCUX Solenostemon scutellarioides_BAHE OXPUα Ascarina rubricaulis_WZFE Oxera pulchella_RTNA CANEα Sarcandra glabra_OSHQ Oxera neriifolia_GNPX DRWIα Canella winterana_SJEV Teucrium chamaedrys_LRRR Drimys winteri_WKSU Ajuga reptans_UCNM SAHEα Aristolochia elegans_PAWA Leonurus japonicus_SNNC Saruma henryi_QDVW Marrubium vulgare_EAAA PEPRα Houttuynia cordata_CSSK Pogostemon sp._GETL Saururus cernuus_OPDF Piper auritum_MUNP Scutellaria montana_ATYL SASSβ Vitex agnus-castus_DMLT Peperomia fraseri_XSZI ORFAα Myristica fragrans_OBPL Epifagus virginiana_FROP Magnolia grandiflora_WBOD Conopholis americana_FAMO Michelia maudiae_XQWC Orobanche fasciculata_VYDM PASOβ Eupomatia bennettii_DHPO Lindenbergia philippensis_EJCM Uvaria microcarpa_PSJT Rehmannia glutinosa_OWAS GOKEα Annona muricata_YZRI Paulownia fargesii_UMUL Calycanthus floridus_FALI Idiospermum australiense_WPHN Mimulus Kigeliaguttatus_Mimgu_v2.0 africana_XAYK PEBOα Gomortega keule_MAQO Laurelia sempervirens_WAIL Tabebuia umbellata_UTQR CASYα Mansoa alliacea_TKEK SASSα Gyrocarpus americanus_BSVG Phyla dulcis_MQIV Peumus boldus_KRJP Lantana camara_PSHB Cassytha filiformis_VYLQ Verbena hastata_GCFE Persea borbonia_WIGA Lindera benzoin_KAYP StrobilanthesSanchezia dyeriana_WEAC sp._NBMW PICAα Sassafras albidum_ABSS Ruellia brittoniana_AYIY ANMAα Cinnamomum camphora_BCGB UTRIα Ceratophyllum demersum_NPND Anisacanthus quadrifidus_PCGJ Euptelea pleiosperma_QTJY Pinguicula caudata_JCMU Akebia trifoliata_CCID Pinguicula agnata_MXFG Utricularia sp._HRUR Podophyllum peltatum_WFBF Nandina domestica_YHFG Uncarina grandidieri_ZRIN Hydrastis canadensis_VGHH Schlegelia violacea_EDXZ VERBα Anemone pulsatilla_UPOG Anemone hupehensis_ZUHO Schlegelia parasitica_WOHL BYGIα BuddlejaBuddleja lindleyana_XRLM sp._GRFT Thalictrum thalictroides_GBVZ Aquilegia coerulea_Aquco_v1.1 Celsia arcturus_SIBR ESCAα Hypecoum procumbens_NMGG Verbascum sp._XXYA Capnoides sempervirens_AUGV Corydalis linstowiana_ZGQD Anticharis glandulosa_EJBY Byblis gigantea_GDZS BACAα PASOα ARMEα Ceratocapnos vesicaria_UDHA Plantago maritima_YKZB Eschscholzia californica_EVOD Plantago virginica_PTBJ Sanguinaria canadensis_XHKT Chelidonium majus_XMVD Digitalis purpurea_GNRI Argemone mexicana_IRAF Antirrhinum majus_XISJ E50OLEUβ OLEUα MELIα Papaver bracteatum_SSDU ARTHγ NENUα Papaver rhoeas_BEKN AntirrhinumBacopa braun-blanquetii_YRHD caroliniana_CLRW Papaver somniferum_RQNK Sinningia tuberosa_DTNC POPRα Papaver setigerum_QCOU HAKEα PLOCα Saintpaulia ionantha_RWKR Meliosma cuneifolia_AALA Calceolariaunknown_YZGX pinifolia_DCCI Nelumbo sp._FAKD Nelumbo nucifera_Nelnu_v1.0 Platanus occidentalis_VQFW ChionanthusOlea europaea_TORX retusus_KTAR Grevillea robusta_GRRW BUSEα Hakea prostrata_RQUG Ligustrum sinense_MZLD TRARα STRSα EXCUα Hakea drupacea_SIIK Buxus sempervirens_IWMW PolypremumAsclepiasAsclepias procumbens_COBX curassavica_DSUV syriaca_YADI Trochodendron aralioides_SWOH Gunnera manicata_XMQO Dillenia indica_EHNF EXAFα Ximenia americana_XKPS Apocynum androsaemifolium_YFQX E49 MEPAβ Dendropemon caribaeus_VGVI ApocynumHolarrhena Wrightiaandrosaemifolium_JCLQ pubescens_JGYZ natalensis_EDEQ Exocarpos cupressiformis_XGFU Santalum acuminatum_RSPO Allamanda cathartica_MGVU Phoradendron serotinum_QKMG Rauvolfia tetraphylla_QEHE GABOα Daenikera sp._BSEY CatharanthusStrychnos roseus_UOYNspinosa_GGJD Cissus quadrangularis_BGZG Gentiana acaulis_ECTD Vitis vinifera_Vitvi_Genoscope.12X Exacum affine_KPUM Tetrastigma voinierianum_SZPD Tetrastigma obtectum_BBBA unknown_KTWL Paeonia lactiflora_HTIP GelsemiumPsychotria sempervirens_HGSM marginata_PCNH Daphniphyllum macropodum_FYTP CRAPα Cercidiphyllum japonicum_NUZN MEPAα Galium boreale_WQRD Hamamelis virginiana_YKQR Psychotria ipecacuanha_ZSGF SASTβ SASTα APREα Loropetalum chinense_HQRJ Heliotropium greggii_ABEH Loropetalum chinense_OMDH ORRPα Myriophyllum aquaticum_IUSR Aphanopetalum resinosum_TOKV Heliotropium mendocinum_MZOB Crassula perforata_KWGC HeliotropiumHeliotropium tenuifolium_JWEY texanum_MDJK LYBAα Kalanchoe crenato-diagremontiana_DRIL Rhodiola rosea_ZJUL Itea virginica_UWFU HeliotropiumHeliotropiumHeliotropium convolvulaceum_OUER racemosum_IDGE filiforme_OEKO Ribes aff. giraldii_SYHW Saxifraga stolonifera_FCBJ Heliotropium karwinskyi_NIGS Peltoboykinia watanabei_YKFU Heliotropium calcicola_XVRU Heliotropium tenellum_DIHD Oresitrophe rupifraga_UHBY Pholisma arenarium_HANM Bergenia sp._CIAC PYMAα Boykinia jamesii_OOVX LennoaEhretia madreporoides_SMUR acuminata_EMAL Astilbe chinensis_CKKR IPQUα Heuchera sanguinea_ERIA Phacelia campanularia_YQIJ Tiarella polyphylla_SLOI Mertensia paniculata_DKFZ STTRα Mitella pentandra_DAYQ Solanum lasiophyllum_DLAI FRAPα Tellima breviflora_CTSS GEMAα Stachyurus praecox_VYGG ELPUα Solanum ptychanthum_DLJZ BEGOα Staphylea trifolia_PTLU Solanum dulcamara_GHLP Francoa appendiculata_HDWF Solanum lycopersicum_Solly_iTAGv2.3 Geranium maculatum_YGCX Solanum xanthocarpum_LQJYDatura metel_JNVS Thladiantha villosula_AXAF XASTβ Begonia sp._OCTM Solanum sisymbriifolium_NMDZ Coriaria nepalensis_NNGU Lycopersicon cheesmanii_UGJILycium sp._OSMU CASAαCELTα Elaeagnus pungens_RBYC BrugmansiaLycium sanguinea_AIOU barbarum_LWCK Ziziphus jujuba_ZHEE XASTα Rhamnus caroliniana_WVEF Atropa belladonna_BOLZ Rhamnus japonica_EILE ILPAα Ulmus alata_CQMG Nicotiana sylvestris_MKZR Celtis occidentalis_KYAD Ipomoea lindheimeri_NAUM URDIα Cannabis sativa_BJSW Humulus lupulus_AQGE IpomoeaIpomoea pubescens_EMBR Ipomoeapurpurea_VXKB nil_NHAG Ficus religiosa_EDHN HEJAα POLUβ POLUα Ipomoea purpurea_XQRV GLSOβ MADOα Morus nigra_XVJB Urtica dioica_WKCY Ipomoea indica_OQBM Boehmeria nivea_ACFP Ipomoea hederacea_QSLH Geum quellyon_DHAW QUSAα IpomoeaIpomoea coccinea_ERWT lobata_IZNU AUJAα Rosa palustris_IANR GYDIα Sanguisorba minor_QNOC E26 Dryas octopetala_SQCF Ipomoea quamoclit_ALUC Cercocarpus ledifolius_XFFT Physocarpus opulifolius_SXCE Ilex sp._DFYF ConvolvulusCuscuta pentagona_AHRNarvensis_CPOC Kerria japonica_TJQY Ilex vomitoria_ASMV Prunus persica_Prupe_v1.0 Ilex paraguariensis_SXML Prunus prostrata_NCVK Pyrenacantha malvifolia_QZZU Aruncus dioicus_ZPKK STADα Cotoneaster transcaucasicus_QIEH Helwingia japonica_QACK Malus baccata_VCIN Aucuba japonica_GIPR Amelanchier canadensis_EAVM Eucommia ulmoides_SZUO Sorbus koehneana_BLVL Flaveria bidentis_JEPE Nothofagus obliqua_TJLC Flaveria trinervia_ZCUA Fagus sylvatica_SVVG JUNIα Quercus shumardii_HENI Flaveria vaginata_HXCD Castanea pumila_UZWG Flaveria kochiana_QXWF Castanea crenata_NHUA Flaveria palmeri_NVSO LUPOα BATOαCOPOα Myrica cerifera_INSP Juglans nigra_DXQW Flaveria brownii_JYMN ARTHβ Flaveria sonorensis_UYED Casuarina equisetifolia_LNER Alnus serrulata_LWDA Flaveria pubescens_LYPZ Betula pendula_CWZU Flaveria pringlei_AQZD HEHEα OEGRα Polygala lutea_OHAE Flaveria angustifolia_YRBQ Quillaja saponaria_OQHZ Flaveria cronquistii_BIDT Copaifera officinalis_RKLL Bauhinia tomentosa_JETM Inula helenium_AFQQ Xanthium strumarium_UBLN Cercis canadensis_RKFX Helenium autumnale_DUNJ Gymnocladus dioicus_QZXQ Gleditsia sinensis_VHZV Gleditsia triacanthos_GEHT Conyza canadensis_MHYGAster tataricus_XRCX Senna hebecarpa_KZED Erigeron canadensis_DESP E33 Desmanthus illinoensis_XOOE Solidago canadensis_TEZA Acacia argyrophylla_ZCDJ PHLUα LAINα Acacia pycnantha_PJSX Anthemis tinctoria_GUMF PLCRα ACCHβ Xanthocercis zambesiaca_ZSSR Leontopodium alpinum_DOVJ ANGRα Cladrastis lutea_SLYR GLSOα Lupinus polyphyllus_CMFF Lupinus angustifolius_TTRG BAALβ DIASβ Gompholobium polymorphum_VLNB MatricariaTanacetumSenecio matricarioides_OAGK parthenium_DUQG rowleyanus_BMSE TENEα Apios americana_NXOH MEMAα Codariocalyx motorius_SUAK Tragopogon porrifolius_KGJF DIOSα SYMIα Phaseolus vulgaris_Phavu_v1.0 Glycine soja_KEGA TragopogonTragopogonTragopogon castellanus_KFZY pratensis_FUPX dubius_DDRL Bituminaria bituminosa_TVSH Cicerbita plumieri_JNKW Wisteria floribunda_RMWJ Lactuca graminifolia_RFSD LATRα Glycyrrhiza lepidota_JTQQ Silybum marianum_EYKJ TREIα Glycyrrhiza glabra_PEZP Lathyrus sativus_KNMB Carthamus lanatus_CFRN Astragalus membranaceus_HJMP SAACα COFLα Astragalus propinquus_MYMP Menyanthes trifoliata_IXVJPhelline lucida_AUIP Krameria lanceolata_ZHMB Larrea tridentata_UDUT Corokia cotoneaster_GIOY DIASα Tribulus eichlerianus_KVAY Terminalia neotaliala_AJJE Scaevola mossambicensis_HUQCStylidiumLobelia adnatum_FXGI siphilitica_IZLO MOUNα Tetrazygia bicolor_SWGX Medinilla magnifica_WWQZ Syzygium micranthum_NEBM Syzygium paniculatum_FGDU MOPEα Eucalyptus grandis_Eucgr_v1.1 Platyspermation crassifolium_TPEM ARTHα Centella asiatica_WEQK DRDEα Eucalyptus leucoxylon_AYMT PlatycodonAngelicaHeracleum grandiflorus_IHPC archangelica_TQKZMyodocarpus lanatum_CWYJHedera sp._AJFN helix_SUVN Lagerstroemia indica_RJNQ ALINβ Punica granatum_YNUE Epilobium sp._FEDW Polyscias fruticosa_EDBB Oenothera rosea_UJGI
SIMHα LIUSα Oenothera speciosa_TLCA ACCHα Oenothera suffulta suffulta_JKNQ Oenothera filiformis_AXNH Oenothera gaura_PMTB Hydrocotyle umbellata_OINMGriselinia littoralis_MVSE PHMAα Oenothera serrulata_SJAN BAALα Oenothera berlandieri_EQYT
Pittosporum resiniferum_SALZ KOSPα Oenothera villaricae_HKMQ Griselinia racemosa_QIKZ Oenothera nana_CJGZ Pittosporum sahnianum_NTEODipsacus asper_JTRM MAESα Oenothera picensis_DZLN Valeriana officinalis_FFFY PAEDα Oenothera affinis_GVCB Pennantia corymbosa_SBZH STSPα Oenothera elata_ROLB Lonicera japonica_GSZA EUMEα Oenothera elata_IDAU Oenothera grandiflora_ZINQ Oenothera biennis_BZDF Symphoricarpos sp._CAQZ Oenothera laciniata_ARYD Escallonia rubra_CLMX Oenothera grandis_IMZV PHYLα Oenothera clelandii_KBRW IMPAα ALINα Oenothera rhombipetala_YHLF ERCOαBIJAα Ledum palustre_WXVX SOURα AMREβ Crossopetalum rhacoma_IHCQ ViburnumSambucus odoratissimum_HLJG canadensis_ZJRC RHMAα Stackhousia spathulata_MFEA Euphorbia mesembryanthemifolia_RHAU Euphorbia pekinensis_PXYR VITRα Ricinus communis_PAZJ Croton tiglium_VVPY Monotropa uniflora_LRTN OCMOα Manihot grahamii_XNLP Escallonia sp. cv. Newport_CLNUSarcodes sanguinea_SERMGalax urceolata_UFHF DAGIα Manihot esculenta_Manes_v4.1 Roridula gorgonias_HUSX GRLIα Phyllanthus sp._YGAT Galax urceolata_ADHK Bischofia javanica_VNMY Rhododendron scopulorum_PPPZActinidia chinensis_QAUE GAGRα Erythroxylum coca_RPPC Cavendishia cuatrecasasii_AVJK Rhizophora mangle_ZTLR Drypetes deplanchei_RVGH Viola canadensis_NJLF Jacquinia sp._PTFA Viola tricolor_LPGY Ardisia revoluta_DAAD SCMEβ Symplocos tinctoria_JPDJArdisia humilis_ODDO AMREα Malesherbia fasciculata_COAQ Sinojackia xylocarpa_AXBO DLECα Passiflora edulis_EZZT Passiflora caerulea_SIZE
HICAα Passiflora_sp_ZIWB Phlox sp._FNEN OXALα MAAMαHYPEα Populus trichocarpa_Poptr_v3.0 Salix acutifolia_INQX Maesa lanceolata_VKJD Salix fargesii_RZTJ Salix purpurea_LFOG Salix sachalinensis_TDTF Salix eriocephala_GLVK Manilkara zapota_BEFC Salix dasyclados_IEPQ Salix viminalis_KKDQ Galphimia gracilis_XPBC Ternstroemia gymnanthera_NGRRDiospyros malabarica_KVFU Ochna serrulata_CKDK
RHRAα Ochna mossambicensis_TVCU Garcinia oblongifolia_FWCQ Phlox drummondii_WVMY Cornus florida_BFJL Garcinia livingstonei_OSIP Hypericum perforatum_BNDE Synsepalum dulcificum_WRPP Mammea americana_NFXV Nyssa ogeche_VUSY Chrysobalanus icaco_ZBVT Sideroxylon reclinatum_OXYP AESCα Licania michauxii_HBUQ Linum flavum_AXPJ Linum macraei_KCPT Linum strictum_TXMP Linum tenuifolium_VXOD Impatiens balsamifera_JEXAAlangium chinense_FWBF Linum hirsutum_HNCF Fouquieria macdougalii_YSRZ Linum grandiflorum_MYVH Dichroa febrifuga_QURC BRNIα Linum usitatissimum_POZS SCHIα CIINα Linum bienne_OODC
TRPRα HICAβ Linum perenne_BVOF
REODα GYRAα Linum lewisii_BHYC Souroubea exauriculata_BNTL SCMEα Linum leonii_AEPI Oxalis sp._JHCN Portulaca pilosa_IWIS Cunonia capensis_TIUZ Cephalotus follicularis_YZVJ NEPNα Elaeocarpus sylvestris_THHD Portulaca amilis_LDEL Tapiscia sinensis_WWKL
COOFα Peganum harmala_OBTI Hydrangea quercifolia_ZETY Litchi chinensis_WAXR Acer negundo_VFFP Aesculus pavia_HBHB Kirkia wilmsii_BCAA Rhus radicans_YUOM LISBα Boswellia sacra_FCCA Caiophora chuquitensis_VTLJ Bursera simaruba_JSZD Talinum sp._LKKX Citrus x paradisi_UHJR Berberidopsis beckleri_HAEU POCNα Azadirachta indica_UVDC Melia azedarach_RJIM Ailanthus altissima_QICX Quassia amara_IKFD Aextoxicon punctatum_QUTB CLGYα Daphne giraldii_PUDI Portulaca suffruticosa_GCYL Edgeworthia papyrifera_AWJM Basella alba_CTYH Bixa orellana_KPTE Cistus inflatus_PKMO Schizolaena sp._WMUK Muntingia calabura_ATFX Theobroma cacao_Theca_v1.1 Portulaca grandiflora_CPLT Dombeya burgessiae_WYIG Hibiscus cannabinus_OLXF Hoheria angustifolia_ZSAB Tropaeolum peregrinum_MYZV Akania lucens_HYZL Moringa oleifera_CZPV Carica_papaya_Carpa_ASGPBv0.4 Limnanthes douglasii_CRNC Batis maritima_DZTK Koeberlinia spinosa_JOIS Reseda odorata_SWPE Gyrostemon ramulosus_UAXP Salvadora sp._RTTY Polanisia trachysperma_QSKP Cleome violacea_LVUS Portulaca oleracea_EZGRPereskia aculeata_JLOV Portulaca umbraticola_KDCH Portulaca umbraticola_BYNZ Portulaca cryptopetala_LLQV Mollugo cerviana_RNBN Mollugo nudicaulis_SCAO Lophophora williamsii_CPKP Mollugo verticillata_NXTS Portulaca molokiniensis_UQCB Allionia incarnata_EGOS Mirabilis jalapa_JGAB Allionia incarnata_DVXD Hilleria latifolia_SFKQ Mollugo pentaphylla_KJAABoerhavia dominii_VJPU
Boerhavia coccinea_ZBTA Petiveria alliacea_AZBL
Aerva lanata_PDQH Zaleya pentandra_BERS Aerva persica_HDSY Bougainvillea spectabilis_JAFJ Cypselea humifusa_GJNX
Phytolacca americana_BKQU Atriplex rosea_CBJR Sesuvium verrucosum_EDIT Phytolacca bogotensis_MRKX Beta maritima_FVXD
Atriplex prostrata_AAXJ Silene latifolia_FZQN Sarcobatus vermiculatus_GIWN Alternanthera tenella_EYRD Atriplex hortensis_ONLQ
Delosperma echinatum_BJKT Sinapis alba_VMNH Kochia scoparia_WGET Sesuvium portulacastrum_HZTS Microtea debilis_YNFJ Arabis alpina_TZWR Draba hispida_GTSV
Brassica nigra_IPWB Alternanthera sessilis_BWRK Draba ossetica_LJQF Beta_vulgaris_Betvu_v1.1 Draba aizoides_HABV Alternanthera brasiliana_ZBPY Amaranthus cruentus_XSSD Spergularia media_TJES Blutaparon vermiculare_CUTE
Cleome viscosa_UPZX
Nepenthes alata_WQUF Trianthema portulacastrum_OMYKAlternanthera caracasana_OHKC Saponaria officinalis_SKNL Chenopodium quinoa_SMMC
Draba magellanica_UVQL Polycarpaea repens_RXEN Cleome gynandra_VDKG Amaranthus retroflexus_WMLW Draba oligosperma_LAPO Dianthus caryophyllus_SHEZ
Draba sachalinensis_BXBF
Limonium spectabile_WOBD
Cochlearia officinalis_CSUV Simmondsia chinensis_CVDF
Schiedea membranacea_OLES
Polygonum convolvulus_FYSJ
Physena madagascariensis_RUUB
Arabidopsis_thaliana_Arath_TAIR10 Supplemental References:
1. Boyle, B. et al. The taxonomic name resolution service: an online tool for automated
standardization of plant names. BMC Bioinformatics 14, 16 (2013).
2. Johnson, M. T. J. et al. Evaluating methods for isolating total RNA and predicting the
success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 7, e50226
(2012).
3. Jordon-Thaden, I. E., Chanderbali, A. S., Gitzendanner, M. A. & Soltis, D. E. Modified
CTAB and TRIzol protocols improve RNA extraction from chemically complex
Embryophyta. Appl. Plant Sci. 3, (2015).
4. Xie, Y. et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq
reads. Bioinformatics 30, 1660–1666 (2014).
5. Smith-Unna, R., Boursnell, C., Patro, R., Hibberd, J. M. & Kelly, S. TransRate: reference-
free quality assessment of de novo transcriptome assemblies. Genome Res. 26, 1134–
1144 (2016).
6. Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in
eukaryotic genomes. Bioinformatics 23, 1061–1067 (2007).
7. Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M.
BUSCO: assessing genome assembly and annotation completeness with single-copy
orthologs. Bioinformatics 31, 3210–3212 (2015).
8. Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data
processing and web-based tools. Nucleic Acids Res. 41, D590–6 (2013).
9. Gitzendanner, M. A., Soltis, P. S., Wong, G. K.-S., Ruhfel, B. R. & Soltis, D. E. Plastid
phylogenomic analysis of green plants: A billion years of evolutionary history. Am. J. Bot.
105, 291–301 (2018).
10. Barker, M. S. et al. EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary
Genomics. Evol. Bioinform. Online 6, 143–149 (2010). 11. Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics.
Nucleic Acids Res. 40, D1178–86 (2012).
12. Wheeler, D. L. et al. Database resources of the National Center for Biotechnology
Information. Nucleic Acids Res. 36, D13–21 (2008).
13. Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–
995 (2004).
14. Li, Z. et al. Multiple large-scale gene and genome duplications during the evolution of
hexapods. Proc. Natl. Acad. Sci. U. S. A. 115, 4713–4718 (2018).
15. Li, Z. et al. Early genome duplications in conifers and other seed plants. Sci Adv 1,
e1501084 (2015).
16. Cui, L. et al. Widespread genome duplications throughout the history of flowering plants.
Genome Res. 16, 738–749 (2006).
17. Benaglia, T., Chauveau, D., Hunter, D. R. & Young, D. mixtools: AnRPackage for Analyzing
Finite Mixture Models. Journal of Statistical Software 32, (2009).
18. Vanneste, K., Van de Peer, Y. & Maere, S. Inference of genome duplications from age
distributions revisited. Mol. Biol. Evol. 30, 177–190 (2013).
19. Barker, M. S. et al. Multiple paleopolyploidizations during the evolution of the Compositae
reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol.
25, 2445–2455 (2008).
20. Yang, Y. & Smith, S. A. Orthology inference in nonmodel organisms using transcriptomes
and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.
Mol. Biol. Evol. 31, 3081–3092 (2014).
21. Hahn, M. W. Bias in phylogenetic tree reconciliation methods: implications for vertebrate
genome evolution. Genome Biol. 8, R141 (2007).
22. Smith, S. A., Moore, M. J., Brown, J. W. & Yang, Y. Analysis of phylogenomic datasets
reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evol. Biol. 15, 150 (2015).
23. Rabier, C.-E., Ta, T. & Ané, C. Detecting and locating whole genome duplications on a
phylogeny: a probabilistic approach. Mol. Biol. Evol. 31, 750–762 (2014).
24. Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome
comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157
(2015).
25. Sjöstrand, J., Arvestad, L., Lagergren, J. & Sennblad, B. GenPhyloData: realistic simulation
of gene family evolution. BMC Bioinformatics 14, 209 (2013).
26. Wu, D., Jospin, G. & Eisen, J. A. Systematic Identification of Gene Families for Use as
‘Markers’ for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and
Archaea and Their Major Subgroups. PLoS One 8, e77033 (2013).
27. Tiley, G. P., Ané, C. & Burleigh, J. G. Evaluating and Characterizing Ancient Whole-
Genome Duplications in Plants with Gene Count Data. Genome Biol. Evol. 8, 1023–1037
(2016).
28. Aubry, S., Kelly, S., Kümpers, B. M. C., Smith-Unna, R. D. & Hibberd, J. M. Correction:
Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of
Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLoS Genet. 12,
e1006087 (2016).
29. Parra, G., Bradnam, K., Ning, Z., Keane, T. & Korf, I. Assessing the gene space in draft
genomes. Nucleic Acids Res. 37, 289–297 (2009).
30. Finn, R. D. et al. The Pfam protein families database: towards a more sustainable future.
Nucleic Acids Res. 44, D279–85 (2016).
31. Eddy, S. R. Accelerated Profile HMM Searches. PLoS Comput. Biol. 7, e1002195 (2011).
32. Gramzow, L. & Theißen, G. Phylogenomics of MADS-Box Genes in Plants - Two Opposing
Life Styles in One Gene Family. Biology 2, 1150–1164 (2013).
33. Ma, H., Yanofsky, M. F. & Meyerowitz, E. M. AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes. Genes Dev. 5, 484–495 (1991).
34. Roshan, U. & Livesay, D. R. Probalign: multiple sequence alignment using partition function
posterior probabilities. Bioinformatics 22, 2715–2721 (2006).
35. Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol.
Evol. 25, 1307–1320 (2008).
36. Li, Z. et al. Multiple large-scale gene and genome duplications during the evolution of
hexapods. Proc. Natl. Acad. Sci. U. S. A. 115, 4713–4718 (2018).
37. Landis, J. B. et al. Impact of whole-genome duplication events on diversification rates in
angiosperms. Am. J. Bot. 105, 348–363 (2018).
38. Shi, T., Huang, H. & Barker, M. S. Ancient genome duplications during the evolution of
kiwifruit (Actinidia) and related Ericales. Ann. Bot. 106, 497–504 (2010).
39. Banks, J. A. et al. The Selaginella genome identifies genetic changes associated with the
evolution of vascular plants. Science 332, 960–963 (2011).
40. Yang, Y. et al. Dissecting Molecular Evolution in the Highly Diverse Plant Clade
Caryophyllales Using Transcriptome Sequencing. Mol. Biol. Evol. 32, 2001–2014 (2015).
41. Ibarra-Laclette, E. et al. Architecture and evolution of a minute plant genome. Nature 498,
94–98 (2013).
42. Barker, M. S., Vogel, H. & Schranz, M. E. Paleopolyploidy in the Brassicales: analyses of
the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and
other Brassicales. Genome Biol. Evol. 1, 391–399 (2009).
43. Edger, P. P. et al. The butterfly plant arms-race escalated by gene and genome
duplications. Proc. Natl. Acad. Sci. U. S. A. 112, 8362–8366 (2015).
44. Ruprecht, C. et al. Revisiting ancestral polyploidy in plants. Sci Adv 3, e1603195 (2017).
45. Jiao, Y. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100
(2011).
46. Jiao, Y. et al. A genome triplication associated with early diversification of the core eudicots. Genome Biol. 13, R3 (2012).
47. Rensing, S. A. et al. An ancient genome duplication contributed to the abundance of
metabolic genes in the moss Physcomitrella patens. BMC Evol. Biol. 7, 130 (2007).
48. Rensing, S. A. et al. The Physcomitrella genome reveals evolutionary insights into the
conquest of land by plants. Science 319, 64–69 (2008).
49. Myburg, A. A. et al. The genome of Eucalyptus grandis. Nature 510, 356–362 (2014).
50. Velasco, R. et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nat.
Genet. 42, 833–839 (2010).
51. Tuskan, G. A. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Science 313, 1596–1604 (2006).
52. Vekemans, D. et al. Gamma paleohexaploidy in the stem lineage of core eudicots:
significance for MADS-box gene and species diversification. Mol. Biol. Evol. 29, 3793–3806
(2012).
53. Ren, R. et al. Widespread Whole Genome Duplications Contribute to Genome Complexity
and Species Diversity in Angiosperms. Mol. Plant 11, 414–428 (2018).
54. Cannon, S. B. et al. Multiple polyploidy events in the early radiation of nodulating and
nonnodulating legumes. Mol. Biol. Evol. 32, 193–210 (2015).
55. Barker, M. S., Husband, B. C. & Pires, J. C. Spreading Winge and flying high: The
evolutionary importance of polyploidy after a century of study. Am. J. Bot. 103, 1139–1145
(2016).
56. Barker, M. S. et al. Most Compositae (Asteraceae) are descendants of a paleohexaploid
and all share a paleotetraploid ancestor with the Calyceraceae. Am. J. Bot. 103, 1203–
1211 (2016).
57. Wan, T. et al. A genome for gnetophytes and early evolution of seed plants. Nat Plants 4,
82–89 (2018).
58. Xiang, Y. et al. Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication. Mol. Biol. Evol. 34, 262–281 (2017).
59. Huang, C.-H. et al. Multiple Polyploidization Events across Asteraceae with Two Nested
Events in the Early History Revealed by Nuclear Phylogenomics. Mol. Biol. Evol. 33, 2820–
2835 (2016).
60. Mandáková, T., Li, Z., Barker, M. S. & Lysak, M. A. Diverse genome organization following
13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns
of gene retention. Plant J. 91, 3–21 (2017).
61. Kagale, S. et al. Polyploid evolution of the Brassicaceae during the Cenozoic era. Plant Cell
26, 2777–2791 (2014).
62. Unruh, S. A. et al. Phylotranscriptomic analysis and genome evolution of the
Cypripedioideae (Orchidaceae). Am. J. Bot. 105, 631–640 (2018).
63. McKain, M. R. et al. A Phylogenomic Assessment of Ancient Polyploidy and Genome
Evolution across the Poales. Genome Biol. Evol. 8, 1150–1164 (2016).
64. Jiao, Y., Li, J., Tang, H. & Paterson, A. H. Integrated syntenic and phylogenomic analyses
reveal an ancient genome duplication in monocots. Plant Cell 26, 2792–2802 (2014).
65. D’Hont, A. et al. The banana (Musa acuminata) genome and the evolution of
monocotyledonous plants. Nature 488, 213–217 (2012).
66. McKain, M. R. et al. Phylogenomic analysis of transcriptome data elucidates co-occurrence
of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae
(Asparagaceae). Am. J. Bot. 99, 397–406 (2012).
67. Vanneste, K., Sterck, L., Myburg, A. A., Van de Peer, Y. & Mizrachi, E. Horsetails Are
Ancient Polyploids: Evidence from Equisetum giganteum. Plant Cell 27, 1567–1578 (2015).
68. Iorizzo, M. et al. A high-quality carrot genome assembly provides new insights into
carotenoid accumulation and asterid genome evolution. Nat. Genet. 48, 657–666 (2016).
69. Lee, H. et al. The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri).
Plant Physiol. 172, 272–283 (2016). 70. Ming, R. et al. The pineapple genome and the evolution of CAM photosynthesis. Nat.
Genet. 47, 1435–1442 (2015).
71. Tang, H., Bowers, J. E., Wang, X. & Paterson, A. H. Angiosperm genome comparisons
reveal early polyploidy in the monocot lineage. Proc. Natl. Acad. Sci. U. S. A. 107, 472–477
(2010).
72. Wang, X. et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet.
43, 1035–1039 (2011).
73. Kim, Y.-M. et al. Genome analysis of Hibiscus syriacus provides insights of polyploidization
and indeterminate flowering in woody plants. DNA Res. 24, 71–80 (2017).
74. Hoshino, A. et al. Genome sequence and analysis of the Japanese morning glory Ipomoea
nil. Nat. Commun. 7, 13295 (2016).
75. Luo, Y.-J. et al. The Lingula genome provides insights into brachiopod evolution and the
origin of phosphate biomineralization. Nat. Commun. 6, 8301 (2015).
76. Qin, G. et al. The pomegranate (Punica granatum L.) genome and the genomics of
punicalagin biosynthesis. Plant J. 91, 1108–1128 (2017).
77. Sveinsson, S. et al. Phylogenetic pinpointing of a paleopolyploidy event within the flax
genus (Linum) using transcriptomics. Ann. Bot. 113, 753–761 (2014).
78. Bombarely, A. et al. Insight into the evolution of the Solanaceae from the parental genomes
of Petunia hybrida. Nat Plants 2, 16074 (2016).
79. Unver, T. et al. Genome of wild olive and the evolution of oil biosynthesis. Proc. Natl. Acad.
Sci. U. S. A. 114, E9413–E9422 (2017).
80. Devos, N. et al. Analyses of transcriptome sequences reveal multiple ancient large-scale
duplication events in the ancestor of Sphagnopsida (Bryophyta). New Phytol. 211, 300–318
(2016).
81. Blanc, G. & Wolfe, K. H. Widespread paleopolyploidy in model plant species inferred from
age distributions of duplicate genes. Plant Cell 16, 1667–1678 (2004). 82. Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy
fruit evolution. Nature 485, 635–641 (2012).
83. Garsmeur, O. et al. Two evolutionarily distinct classes of paleopolyploidy. Mol. Biol. Evol.
31, 448–454 (2014).
84. Freeling, M. The distribution of ancient polyploidies in the plant phylogenetic tree is a
spandrel of occasional sex. Plant Cell (2017). doi:10.1105/tpc.16.00836
85. Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in
major angiosperm phyla. Nature 449, 463–467 (2007).
86. Tang, H. et al. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene
maps. Genome Res. 18, 1944–1954 (2008).
87. Clark, J. W. & Donoghue, P. C. J. Constraining the timing of whole genome duplication in
plant evolutionary history. Proc. Biol. Sci. 284, (2017).
88. Sayyari, E., Whitfield, J. B. & Mirarab, S. DiscoVista: Interpretable visualizations of gene
tree discordance. Mol. Phylogenet. Evol. 122, 110–115 (2018).