DOI: 10.5061/dryad.9zw3r22f0
title: Data from: Phylogenetic history of vascular plant metabolism revealed using a macroevolutionary common garden

description: While the fundamental biophysics of C3 photosynthesis is highly conserved
 across plants, substantial variation in leaf structure and enzymatic
 activity translates into variability in rates of photosynthesis.
 Although this variation is well-documented, it remains poorly understood
 how photosynthetic rates evolve over short and long time scales, and
 whether these macroevolutionary changes are related to the evolution of
 key morphological and biochemical leaf traits. Large-scale comparative
 studies have been hampered by the substantial logistical and statistical
 challenges in disentangling evolutionary adaptation from environmental
 acclimation. Here we get around this limitation with a ‘macroevolutionary
 common garden’ approach in which we measured the metabolic traits Jmax and
 Vcmax from 111 phylogenetically diverse species in a shared environment.
 Using several phylogenetic comparative methods, we find substantial
 phylogenetic signal in these traits at shallow phylogenetic scales,
 but  this signal dissipates quickly at deeper time scales. Leaf
 morphological traits exhibit phylogenetic signal over much deeper time
 scales, suggesting that these traits are less evolutionarily constrained
 than metabolic traits. Furthermore, we find that while morphological and
 biochemical traits (LMA, Narea and Carea) are weakly predictive of Jmax
 and Vcmax, evolutionary changes in these traits are mostly decoupled from
 changes in metabolic traits. This lack of tight evolutionary coupling
 implies that it may not be possible to use changes in these functional
 traits in response to global change to infer that photosynthetic strategy
 is also evolving.
description: There are 3 sets of data files, corresponding to measurements
 taken for 138 individuals growing at the UBC and Van Dusen Botanical
 Gardens in Vancouver, BC, Canada. All of these data have been measured on
 the same set of leaves, between May and September of 2019. <br> n.b.
 Following data processing and quality checks, only data for 111 species
 were used in the final analysis.  
 <strong>1. Rapid A/Ci Response (RACiR)
 data</strong> Find these data in neto-bradley_et_al_2021_physiological_data.zip <br> Files are named in the following format yyyy-mm-dd-hhmm_genus_species<br> Provided in .txt format, as output by the LiCor6800 machine.   Blurb: RACiR curves (as described in Stinziano et al. 2017) characterize the change in Net photosynthesis A relative to changes in CO2. Functionally this describes the physiological constraints of how quickly and efficiently a plant can take up CO2. During our RACiR curve measurements, CO2 is ramped from 10 ppm to 1010 ppm at a rate of + 100 ppm per minute. While this is ongoing, CO2 accumulates in the chamber such that the true CO2 contents of the chamber are slightly out of sync with the concentration of CO2 measured by the machine. In order to correct for this lag, two curves are measured - a data curve and an empty curve for callibrating the data curve.   Data Specifics: The RACiR data is comprised of 2 data files: an "empty curve" and a "data curve" (see above.) The empty curve characterizes how CO2 accumulates in an empty chamber throughout the course of the A/Ci measurement, and the data curve characterizes a leaf's photosynthetic rates change in response to increasing CO2. Empty curves were collected every hour to two hours - for every empty curve multiple that were collected in close temporal proximity can be corrected (for the lag in CO2 measured - as described above.) Every measurement has its own txt file that was generated by the LiCor6800 machine when the measurement was finalized.   Time & Place: RACiR curves were measured on the youngest fully expanded leaves of each of the 138 species studied here. These measurements were taken between May 5th and July 18th 2019 at the UBC and VanDusen Botanical Garden.   <strong>2. Morphological data</strong> Find these data in neto-bradley_et_al_2021_morphological_data.csv    Blurb: After each RACiR curve was measured, the leaf (or several leaves in the case of small leaves/needles) on which this was taken were harvested and put in a sealed bag, which was stored in a cooler overnight. The next morning, the leaves were measured for fresh mass and leaf area. The leaves were then dried for 48 hours in an oven at 60 degrees Celsius. After this the leaves were weighed for dry mass.   Time & Place: These measurements were taken the day of, or the following day at the Beaty Biodiversity Research Centre at the UBC Vancouver Campus.   <strong>3. Biochemical data</strong> Find these data in neto-bradley_et_al_2021_biochemical_data.csv   Blurb: Once the leaf tissues were dried, these were sent off for chemical analysis for the Nitrogen and Carbon contents by combustion.   Time & Place: These measurements were done at the Analytical Chemical Services Laboratory (at the BC Ministry of Environment and Climate Change Strategy), during September 2019.