DOI: 10.5061/dryad.6t1g1jx79
title: Reproductive complexity, whole genome duplication, and genome size data across vascular plants

description: Whole genome duplication (WGD) may be an important factor in plant
 macroevolution, implicated in diversification rate shifts, structural
 innovations, and increased disparity. But general effects of WGD on plant
 evolution are challenging to evaluate, in part due to the difficulty of
 directly comparing morphological patterns across clades. We explored
 relationships between WGD and the evolution of complexity across vascular
 plants using a metric based on the number of reproductive part types. We
 used multiple regression models to evaluate the relative importance of
 inferred WGD events, genome size, and a suite of additional variables
 relating to growth habit and reproductive biology in explaining part type
 complexity. WGD was a consistent predictor of reproductive complexity only
 among angiosperms. Across vascular plants more generally, reproductive
 biology, clade identity, and the presence of bisexual strobili (those that
 produce microsporangiate and megasporangiate organs) were better
 predictors of complexity. Angiosperms are unique among vascular plants in
 combining frequent polyploidy with high reproductive complexity. Whether
 WGD is mechanistically linked to floral complexity is unclear, but we
 suggest widespread polyploidy and increased complexity were ultimately
 facilitated by the evolution of herbaceous growth habits in early
 angiosperms.
description: # Reproductive complexity, whole genome duplication, and genome size data
 across vascular plants GENERAL INFORMATION 1. Title of Dataset: Whole
 Genome Duplications and Reproductive Complexity 2. Author Information A.
 Principal Investigator Contact Information Name: Andrew Leslie
 Institution: Stanford University Address: 450 Jane Stanford Way, Building
 320, Room 118, Stanford, CA 94305, USA.\ Email:
 [aleslieb@stanford.edu](mailto:aleslieb@stanford.edu) B. Associate or
 Co-investigator Contact Information Name: Luke Mander Institution: The
 Open University Address: Walton Hall, Milton Keynes, MK7 6AA, UK. Email:
 [luke.mander@gmail.com](mailto:luke.mander@gmail.com) DATA & FILE
 OVERVIEW File List: 1. ComplexityWGD_data.csv 2. Analysis Scripts.R 3.
 Data_Citations.txt 4. Forest2018.tree 5. Janssens2020.tree 6.
 Nitta2022.tree 7. Testo2018.tree 8. Angio_reorder.tree
 "ComplexityWGD_data.csv"" contains the data and character
 scorings used in our analyses. The various .tree files include
 phylogenetic trees used to generate the phylogeny in this study or
 subtrees used in figures.\ The data and tree files can be imported into
 the provided R script ("Analysis Scripts.R") to reproduce the
 results, main figures, and supplemental figures reported in the
 manuscript. DATA-SPECIFIC INFORMATION FOR: ComplexityWGD_data.csv 1.
 Number of variables: 44 2. Number of cases/rows: 1291 3. Variable List: 1.
 Taxon: species to which each reproductive structure belongs. 2. in_tree:
 whether (1) or not (0) taxon is included in a phylogenetic tree used in
 this analysis. 3. phyloname: taxonomic name used to represent each taxon
 in the phylogenetic trees. In some cases, the species we scored was not
 the same as that included in the phylogeny. We substituted our species
 into the phylogeny in cases where this did not change the topology. 4.
 group1-5: nested taxonomic affiliations for each reproductive structure.
 5. group1-5: nested taxonomic affiliations for each reproductive
 structure. 6. group1-5: nested taxonomic affiliations for each
 reproductive structure. 7. group1-5: nested taxonomic affiliations for
 each reproductive structure. 8. group1-5: nested taxonomic affiliations
 for each reproductive structure. 9. group6: a binary character used in
 some analyses to identify all angiosperms that are not monocots. 10.
 WGDmincon: the "consensus" low number of possible WGD events in
 the history of a taxon. This number is based on WGD events that are either
 widely regarded as having occurred (such as at the base of the
 angiosperms), are recovered in many separate studies, or were recovered by
 multiple analytical methods (typically Ks plots plus MAPS analysis). This
 is the number of WGD events used throughout the manuscript as the low
 number. 11. WGDmin: the low number of possible WGD events in the history
 of a taxon after removing a debated WGD event at the base of angiosperms.
 12. WGDmax: the high number of possible WGD events in the history of a
 taxon. This number is based on WGD events recovered by any analysis method
 in any study. It is the number used as the high estimate of WGD events in
 the manuscript. 13. KPmin: the low number of possible WGD events recovered
 in the One Thousand Plant Transcriptomes Initiative and shown on the
 phylogeny in Supplemental Figure 8. This analysis is used as a consistent
 baseline for identifying WGD events across all vascular plants. The low
 number represents only WGD events found by two analytical methods (Ks
 plots, MAPS). 14. KPmax: the high number of possible WGD events recovered
 in the One Thousand Plant Transcriptomes Initiative and shown on the
 phylogeny in Supplemental Figure 8. This analysis is used as a consistent
 baseline for identifying WGD events across all vascular plants. The high
 number represents WGD events found by either or both of the analytical
 methods (Ks plots, MAPS). 15. Huang2020: WGD events among leptosporangiate
 ferns recovered by Huang et al. 2020 16. Huang2020+KP: WGD events among
 leptosporangiate ferns recovered by Huang et al. 2020 with added potential
 WGD events recovered in the 1KP analysis. These events correspond to two
 putative WGD events in the lineage leading to euphyllophytes but which was
 outside the coverage of the Huang et al. 2020 study. 17. Pelosi2020min:
 the low number of WGD events among leptosporangiate ferns recovered by
 Pelosi et al. 2020. The low number represents only WGD events found by two
 analytical methods (Ks plots, MAPS). 18. Pelosi2020max: the high number of
 WGD events among leptosporangiate ferns recovered by Pelosi et al. 2020.
 The high number represents WGD events found by Ks plots alone. 19.
 Pelosi2020min+KP: the low number of WGD events among leptosporangiate
 ferns recovered by Pelosi et al. 2020 with added WGD events recovered in
 the 1KP analysis. These events correspond to two putative WGD events in
 the lineage leading to euphyllophytes but which was outside the coverage
 of the Pelosi et al. 2020 study. 20. Pelosi2020max+KP: the high number of
 WGD events among leptosporangiate ferns recovered by Pelosi et al. 2020
 with added WGD events recovered in the 1KP analysis. These events
 correspond to two putative WGD events in the lineage leading to
 euphyllophytes but which was outside the coverage of the Pelosi et al.
 2020 study. 21. Stull2021: WGD events among acrogymnosperms recovered by
 Stull et al. 2021. 22. Stull2021+KP: WGD events among acrogymnosperms
 recovered by Stull et al. 2021 with added WGD events recovered in the 1KP
 analysis. These events correspond to two putative WGD events in the
 lineage leading to euphyllophytes but which was outside the coverage of
 the Stull et al. 2021 study. 23. Cvalue: DNA 1C-value (in pg) from the Kew
 C-Value Database 24. Cvalue_avg: whether (1) or not (0) and Cvalue is
 based on a genus average or was measured from the particular species in
 our data set. 25. fossil: whether reproductive structure was produced by
 an extinct (fossil) or extant taxon. 26. period: geologic age of
 reproductive structures; recorded to most finely resolved time interval.
 27. epoch: geologic age of reproductive structures; recorded to most
 finely resolved time interval. 28. stage: geologic age of reproductive
 structures; recorded to most finely resolved time interval. 29. maximum
 absolute age: age (millions of years ago) of reproductive structures based
 on the age range of its most finely resolved geologic time interval or
 radiometric dating of its locality. 30. minimum absolute age: age
 (millions of years ago) of reproductive structures based on the age range
 of its most finely resolved geologic time interval or radiometric dating
 of its locality. 31. midpoint absolute age: age (millions of years ago) of
 reproductive structures based on the age range of its most finely resolved
 geologic time interval or radiometric dating of its locality. 32.
 reference: citation(s) used to score each reproductive structure; numbers
 correspond to those in "Data_Citations.txt". 33. habit: whether
 a given reproductive structure was produced by a free-sporing vascular
 plant ('freesporing') or a seed plant ('seed'). 34.
 heterospory: whether (1) or not (0) that taxon that produced the
 reproductive structure was heterosporous. 35. combined: a multistate
 character identifying how fertile organs are arranged in the reproductive
 structure. (0) unisexual: only microsporangiate or megasporangiate organs
 present, (1) bisexual: both microsporangiate and megasporangiate organs
 present, (2) artificially combined: separate unisexual reproductive
 structures produced by a single taxon were amalgamated into a single
 hypothetical structure, (3) artificially combined, interpreted: separate
 unisexual reproductive structures possibly produced by a single taxon were
 amalgamated into a single hypothetical structure, (4) bisexual structure,
 interpreted: both microsporangiate and megasporangiate organs are thought
 to be produced in a single structure but are not definitively known. 36.
 analysis_group: basic groups used in analyses presented in the main text.
 Where possible, these groups are based on resolved clades; for groups with
 unknown affinities, they may also represent heterogenous groupings used
 for convenience. 37. mega: whether (1) or not (0) a given reproductive
 structure has female functionality; that is, whether it produces either
 megaspores or seeds. Bisexual reproductive structures that produce seeds
 are scored as “1” because they have female functionality. 38.
 biotic.pollination: whether (1) or not (0) a reproductive structure is
 pollinated by animals. NA for free-sporing plants and fossil taxa where
 pollination is not known definitively. 39. seed.plant: whether (1) or not
 (0) a reproductive structure is produced by a seed plant. 40. angiosperm:
 whether (1) or not (0) a reproductive structure is produced by an
 angiosperm. 41. total.parts: the total number of part types in a
 reproductive structure. This number includes all part types expressed over
 ontogeny. 42. bisex.parts: part types directly associated with an
 additional reproductive organ; in structures that function as
 microsporangiate this would include sterile ovule parts, while in those
 that function to produce megaspores or seeds it would include
 microsporangiate parts. Scored as "NA" for artificially combined
 reproductive structures and for fossil taxa, which were not used in
 analyses with bisexuality as a predictor variable. 43. symmetry: floral
 symmetry scores for angiosperm taxa; 1=helical, 2=radial,
 3=zygomorphic/disymmetric, 4=asymmetric, 5=reduced flower lacking
 symmetry, NA=not applicable. 44. merism: floral organ arrangements;
 1=tri/hexamerous, 2=di/tetramerous, 3=pentamerous, NA=not applicable 4.
 Missing data codes: missing or inapplicable data given as "NA".
 SPECIFIC INFORMATION FOR: Analysis Scripts.R This annotated R script
 contains all commands necessary to reproduce the analyses and plots from
 Figures 1-4 and Table 1 in the main text, and Figure S1 and Tables S1-S2
 in the Supplement. It uses "ComplexityWGD_data.csv",
 "Angio_reorder.tree","Forest2018.tree","Janssens2020.tree","Nitta2020.tree", and "Testo2018.tree" as inputs. DATA-SPECIFIC INFORMATION FOR: Data_Citations.txt This text file contains a numbered list of all sources for morphological scorings. The numbers correspond to those associated with each reproductive structure in the "Reference" column of the "ComplexityWGD_data.csv" file. DATA-SPECIFIC INFORMATION FOR: Angio_reorder.tree, Forest2018.tree, Janssens2020.tree, Nitta2022.tree, Testo2018.tree These .tree files are used to build the vascular plant phylogeny for phylogenetic regression analyses in this study. Full citations for these studies are given in the main text.