Data from: How important are functional and developmental constraints on phenotypic evolution? An empirical test with the stomatal anatomy of flowering plants
Data files
Apr 26, 2023 version files 883.38 KB
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phylogenetic-contrasts.csv
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plant-c-value.csv
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README
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stomatal-anatomy-metadata.csv
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stomatal-anatomy.csv
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trimmed-data.csv
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trimmed-phylogeny.new
Oct 26, 2023 version files 889.43 KB
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phylogenetic-contrasts.csv
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plant-c-value.csv
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README
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README.md
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stomatal-anatomy-metadata.csv
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stomatal-anatomy.csv
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trimmed-data.csv
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trimmed-phylogeny.new
Abstract
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.
README
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