DOI: 10.5061/dryad.0rxwdbs42
title: Data from: How important are functional and developmental constraints on phenotypic evolution? An empirical test with the stomatal anatomy of flowering plants

description: Quantifying the relative contribution of functional and developmental
 constraints on phenotypic variation is a longstanding goal of
 macroevolution, but it is often difficult to distinguish different types
 of constraints. Alternatively, selection can limit phenotypic
 (co)variation if some trait combinations are generally maladaptive. The
 anatomy of leaves with stomata on both surfaces (amphistomatous) presents
 a unique opportunity to test the importance of functional and
 developmental constraints on phenotypyic evolution. The key insight is
 that stomata on each leaf surface encounter the same functional and
 developmental constraints, but potentially different selective pressures
 because of leaf asymmetry in light capture, gas exchange, and other
 features. Independent evolution of stomatal traits on each surface implies
 that functional and developmental constraints alone likely do not explain
 trait covariance. Packing limits on how many stomata can fit into a finite
 epidermis and cell-size-mediated developmental integration are
 hypothesized to constrain variation in stomatal anatomy. The simple
 geometry of the planar leaf surface and knowledge of stomatal development
 makes it possible to derive equations for phenotypic (co)variance caused
 by these constraints and compare them with data. We analyzed evolutionary
 covariance between stomatal density and length in amphistomatous leaves
 from 236 phylogenetically independent contrasts using a robust Bayesian
 model. Stomatal anatomy on each surface diverges partially independently,
 meaning that packing limits and developmental integration are not
 sufficient to explain phenotypic (co)variation. Hence, (co)variation in
 ecologically important traits like stomata arises in part because there is
 a limited range of evolutionary optima. We show how it is possible to
 evaluate the contribution of different constraints by deriving expected
 patterns of (co)variance and testing them using similar but separate
 tissues, organs, or sexes.
description: This readme file was generated on 2022-09-10 by Chris Muir GENERAL
 INFORMATION Title of Dataset: How important are functional and
 developmental constraints on phenotypic evolution? An empirical test with
 the stomatal anatomy of flowering plants Author/Principal Investigator
 Information Name: Christopher D. Muir ORCID: 0000-0003-2555-3878
 Institution: University of Hawaiʻi at Mānoa Address: 2538 McCarthy Mall
 EDM 216 Honolulu, HI 96822 Email: cdmuir@hawaii.edu SHARING/ACCESS
 INFORMATION Licenses/restrictions placed on the data: No
 licenses/restrictions on processed data The ropenstomata R package
 contains raw data distributed under an MIT license Links to other publicly
 accessible locations of the data: Raw stomatal anatomical data:
 https://github.com/cdmuir/ropenstomata Processed data:
 https://github.com/cdmuir/stomata-independence Links/relationships to
 ancillary data sets: References to original stomatal anatomical data sets
 are provided in Table A5 of the Muir et al. (2022) and in the ropenstomata
 R package. The GBOTB.extended mega-tree came from V.phylomaker
 (https://onlinelibrary.wiley.com/doi/10.1111/ecog.04434) Sequence data
 came from GenBank Plant and Fungal sequences database division
 (https://www.ncbi.nlm.nih.gov/genbank/htgs/divisions/) Genome size data
 came from the Angiosperm DNA C-values database
 (https://cvalues.science.kew.org/) Recommended citation for this dataset:
 To cite ropenstomata in publications use: ``` Muir CD. 2022. ropenstomata:
 An Open Stomatal Database. https://github.com/cdmuir/ropenstomata. ```
 DATA & FILE OVERVIEW File List: \ stomatal-anatomy.csv - raw
 stomatal anatomical data from ropenstomata stomatal-anatomy-metadata.csv -
 metadata on raw stomatal anatomical data from ropenstomata
 plant-c-value.csv - raw data on plant C-value downloaded from the
 Angiosperm DNA C-values database trimmed-data.csv - trimmed data set of
 species found on phylogeny trimmed-phylogeny.new - trimmed phylogeny of
 species with stomatal anatomical data in newick format
 phylogenetic-contrasts.csv - phylogenetically independent contrasts used
 in final analyses Relationship between files: The column
 "resolved\_name" in trimmed-data.csv matches the tip names in
 trimmed-phylogeny.new. The column "tree\_node" in
 phylogenetic-contrasts.csv refers to the node in trimmed-phylogeny.new The
 columns "sp1" and "sp2" match
 "resolved\_name" in trimmed-data.csv matches the tip names in
 trimmed-phylogeny.new DATA-SPECIFIC INFORMATION FOR: stomatal-anatomy.csv
 Number of variables: 7 Number of rows: 5842 Variable List: source\_id,
 taxonomic ID in original source, Genus species trait, trait ID,
 {"abaxial\_stomatal\_density\_mm2" ,
 "abaxial\_stomatal\_length\_um",
 "abaxial\_stomatal\_width\_um",
 "adaxial\_stomatal\_density\_mm2",
 "adaxial\_stomatal\_length\_um",
 "adaxial\_stomatal\_width\_um",
 "abaxial\_pore\_length\_um"
 "adaxial\_pore\_length\_um"} mu, mean trait value, um or mm^2 n,
 sample size, 1 sd, trait standard deviation, um or mm^2 source, original
 source, first-author\_first-word\_year se, trait standard error of the
 mean, um or mm^2 Missing data codes: NA DATA-SPECIFIC INFORMATION FOR:
 stomatal-anatomy-metadata.csv Number of variables: 7 Number of rows: 38
 Variable List: source, original source, first-author\_first-word\_year
 taxa, taxomic group studies, open-ended location, location of data in
 source, tableX or figureX density\_unit, unit of stomatal density in
 source, open-ended length\_unit, unit of stomatal length in source,
 open-ended sample\_size, sample size, 1 notes, usage notes, open-ended
 Missing data codes: NA DATA-SPECIFIC INFORMATION FOR: plant-c-value.csv
 Number of variables: 9 Number of rows: 1033 Variable List: family, plant
 family genus, plant genus species, plant species subspecies, plant
 subspecies chromostome\_number\_2n, 2N chromosome number, 1
 ploidy\_level\_x, Ploidy level, 1 dna\_amount\_1c\_pg, 1C DNA amount, pg
 c\_value\_reference, reference c\_value\_note, note Missing data codes: NA
 DATA-SPECIFIC INFORMATION FOR: trimmed-data.csv Number of variables: 27
 Number of rows: 638 Variable List: resolved\_name, resolved taxonomic name
 family, plant family source, original source,
 first-author\_first-word\_year source\_id, taxonomic ID in original
 source, Genus species abaxial\_stomatal\_density\_mm2, abaxial stomatal
 density, mm^2 adaxial\_stomatal\_density\_mm2, adaxial stomatal density,
 mm^2 abaxial\_stomatal\_length\_um, abaxial stomatal length, um
 adaxial\_stomatal\_length\_um, adaxial stomatal length, um phy\_name, tip
 label in original phylogeny grass, is species a grass, boolean c,
 morphological constant used to calculate m for gmax, unitless h,
 morphological constant used to calculate m for gmax, unitless j,
 morphological constant used to calculate m for gmax, unitless m,
 morphological constant used to calculate gmax, unitless b, biophysical
 constant used to calculate gmax, mol / m / s abaxial\_stomatal\_area\_um2,
 abaxial stomatal area, um^2 adaxial\_stomatal\_area\_um2, adaxial stomatal
 area, um^2 abaxial\_gmax, abaxial maximum stomatal conductance, mol / m^2
 / s adaxial\_gmax, abaxial maximum stomatal conductance, mol / m^2 / s
 abaxial\_fs, abaxial fraction of epidermal area allocated to stomata,
 unitless adaxial\_fs, adaxial fraction of epidermal area allocated to
 stomata, unitless genus, plant genus subspecies, plant subspecies
 chromostome\_number\_2n, 2N chromosome number, 1 ploidy\_level\_x, Ploidy
 level, 1 c\_value\_reference, reference c\_value\_note, note
 dna\_amount\_2c\_pg, 2C DNA amount, pg Missing data codes: NA
 DATA-SPECIFIC INFORMATION FOR: phylogenetic-contrasts.csv Number of
 variables: 18 Number of rows: 236 Variable List: tree\_node, node in
 trimmed phylogeny, 1 pair\_age, divergence time between sp1 and sp2,
 millions of year sp1, resolved name species 1, Genus\_species sp2,
 resolved name species 2, Genus\_species All other columns are the
 log10-difference between sp1 and sp2 for the trait given by the column
 name Missing data codes: NA