DOI: 10.5061/dryad.9zw3r22nb
title: Data and scripts from: Analyzing ontogenetic changes in Cupressaceae seed cone size

description: Ontogenetic shape change has long been recognized to be important in
 generating patterns of morphological diversity and may be especially
 important in plant reproductive structures. We explore how seed cone
 disparity in Cupressaceae changes over ontogeny by comparing
 pollination-stage and mature cones.   We sampled cones at pollen
 release and seed release and measured cone scales using basic morphometric
 shape variables. We used multivariate statistical methods, particularly
 hypervolume overlap calculations, to measure morphospace occupation and
 disparity.   Cone scales at both pollination and maturity exhibit
 substantial variability, although disparity is greater at maturity. Mature
 cone scales are also more clustered in trait space, showing less overlap
 with other taxa than at pollination. These patterns reflect two growth
 strategies that generate closed cones over maturation, either through thin
 laminar scales or relatively thick, peltate scales, resulting in two
 distinct regions of morphospace occupation.   
   Disparity patterns in Cupressaceae seed cones change over
 development as cone scales grow to meet shifting functional demands. For
 seed plants generally, the evolution of reproductive disparity represents
 the evolution of entire trajectories of ontogenetic shape
 change.   
description: # Data and scripts from: Analyzing ontogenetic changes in Cupressaceae
 seed cone size \[Access this dataset on Dryad] (10.5061/dryad.9zw3r22nb)
 ``` An analysis of how inter-taxon morphological disparity changes across
 ontogeny in Cupressaceae seed cone scales. The dataset consists of
 measurements of the cone scales of 10 species of conifers with multiple
 cones per species. Analysis is primarily done through the creation of
 hypervolumes from the 3-dimensional measurements of cone scales then
 comparing the resulting hypervolumes to contextualize both total
 morphospace occupance, via overlaps with the aggregate of each
 developmental stage, as well as morphospace position, via taxon-to-taxon
 overlap scores. Scores are measured via a calculated Jaccard Index Score.
 Code within the dataset is provided for the generation of these
 hypervolumes and overlap scores, for the creation of three sampling curves
 gauging how additional cones contribute to overall morphological disparity
 within a specific species at a developmental stage (these being
 Platycladus orientalis at pollination and Metasequoia glyptostroboides at
 pollination and maturity), and for the creation of the various plots and
 figures presented in NPH19482. Also provided are processed datasets of
 overlap scores for ease of figure construction, without needing to rerun
 the full overlap code. ``` ## Description of the data and file structure
 Data consists of 3 R documents of code and four csv files for data.
 FileList- Cupressaceae_Disparity_Analyses.R
 Hypvervolume_and_Overlap_Construction.R Ontogeny_data.csv
 Overlaps_pooled.csv Overlaps_randomized.csv Overlaps_taxa.csv
 Sampling_Curve_Construction.R Raw data from the measurements is provided
 in Ontogeny_data.csv, a csv spreadsheet consisting of four thousand eight
 hundred and ninety-six rows organized into thirteen columns. Each row
 represents a single cone scale. Columns and what each means are as
 follows: Taxon: Species as identified either by the botanical gardens or
 the authors. Phylogenetic order: Order of appearance within the
 phylogenetic structure of each taxon, used for creating some figures.
 Individual: Individual specimen cones were collected from, with numbers
 assigned to specific trees at time of collection. Cone: Identification of
 which cone each cone scale belongs to with all scales from a given
 individual and cone number combination belonging to the same cone.
 Cone_ID: A unique marker given to each cone scale in the form X_y where X
 represents the cone number and y the scale number from that cone. Stage:
 Ontogenetic stage of cone scale at time of collection and measurement,
 with pollination being the point where ovules were exposed to windborne
 pollens and maturity being the point of seed dispersal. Length: Length of
 the cone scale as measured in millimetres from the connection of a cone
 scale to the central axis outwards to the furthest point. Width: Width of
 the cone scale as measured in millimetres from the longest distance within
 an adaxial/abaxial plane. Thickness: Thickness of the cone scale as
 measured in millimetres from the largest line between the adaxial and
 abaxial surfaces. Thickness_Bract.only: Thickness of the cone scale bract
 as measured in millimetres from the largest line between the adaxial and
 abaxial surfaces excluding structures defined as belonging to a
 ovuliferous scale of a bract-scale complex. This is identical in most
 respects to Thickness except for Cryptomeria japonica specimens. lLength:
 The base 10 log of cone scale length. lWidth: The base 10 log of cone
 scale width. lThickness: The base 10 log of cone scale thickness. Other
 datasheets represent analysed and pooled data on hypervolume overlaps
 (recorded as Jaccard scores) which are presented as csv files. All scores
 are generated by the code contained within the file
 Hypervolume_and_Overlap_Construction.R These datasheets include:
 Overlaps_taxa.csv: Taxon to taxon overlaps at both stages. Each column
 represents a different taxon and developmental stage with Taxon names
 given in a shortened form with the addition of a single letter for stage
 .p for pollination or .m for mature. For example column Cun.p would be the
 overlaps between Cunninghamia lanceolata at pollination and all other
 taxon at pollination, with each row representing the Jaccard score of a
 different taxon at pollination overlapping with Cunninghamia lanceolata.
 Overlaps_pooled.csv: Overlap scores between taxa and the aggregate at each
 stage. Columns are the Taxon name, Jaccard score at Pollination, and
 Jaccard score at Maturity. Overlaps_randomized.csv: The overlap scores
 generated by the bootstrapping process, presented as two columns one for
 each stage. The three coding documents include:
 Hypervolume_and_Overlap_Construction.R: The main data processing code
 which constructs hypervolumes and compares overlaps as annotated within.
 Cupressaceae_Disparity_Analyses: Additional data processing and figure
 construction for figures contained within NPH19482.
 Sampling_Curve_Construction: Construction of the sampling curves shown in
 the Supplementary Information for NPH19482, specifically SF1. All coding
 documents are annotated for ease of repeat use. ## Sharing/Access
 information This is currently the most accessible form of this data. ##
 Code/Software ``` Code is provided as R files (R Studio version
 information provided below). Various packages have been loaded as well,
 each is specified within the code documents, but they include shape,
 dendextend, dplyr, hypervolume, ggplot2, and readxl. Data for figure
 construction outlined in Cupressaceae_Disparity_Analyses.R was generated
 using code found in Hypervolume_and_Overlap_Construction.R. The data was
 then extracted to an xl/csv file and reformatted to the version found
 within slightly rearranging the position of the various scores for ease in
 graphing. Other file transformations should take place within the code
 documents themselves. ``` RStudio 2023.06.0+421 "Mountain
 Hydrangea" Release (583b465ecc45e60ee9de085148cd2f9741cc5214,
 2023-06-05) for windows Mozilla/5.0 (Windows NT 10.0; Win64; x64)
 AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.06.0+421
 Chrome/110.0.5481.208 Electron/23.3.0 Safari/537.36