DOI: 10.5061/dryad.547d7wmhm
title: Data and code for: Adaptive evolution of freezing tolerance in oaks is key to their dominance in North America

description: Freezing tolerance plays a pivotal role in shaping the distribution and
 diversification of organisms across diverse habitats and was likely
 crucial to the expansion and adaptive radiation of the American oaks. We
 investigated the dynamics of adaptation to climate and potential
 trade-offs between stem freezing tolerance and growth rate in 48 Quercus
 species from five genus sections grown under temperate and tropical
 conditions. Species from colder regions exhibit higher freezing tolerance,
 lower growth rates and higher acclimation potential compared to species
 from warmer climates, suggesting evolutionary adaptations to seasonal
 climate fluctuations. Deciduous species show marked variability in
 freezing tolerance across their broad climatic range while evergreen
 species, confined to warm climates, display low freezing tolerance. While
 annual growth rates are constrained in deciduous species, we found no
 direct trade-off between freezing tolerance and growth because deciduous
 species that evolved in warm latitudes lost freezing tolerance. Despite an
 evolutionary lag, freezing tolerance in Quercus species is closely aligned
 with its optimal state. The capacity to withstand cold and adapt to a wide
 range of thermal environments was likely critical to adaptive radiation
 and current dominance of the North American oaks. Data and code are
 provided here.
description: We examined 48 species of <em>Quercus</em> from 5
 different sections: Cerris (3 species), Lobatae (19), Protobalanus (1),
 Quercus (26), and Virentes (3 species; Table S1). The species are
 characterized by different growth forms, leaf phenology (34 deciduous and
 14 evergreen species), ecological niches, and distribution ranges. Acorns
 were collected from one to five populations within each of the 48 oak
 species in the fall of 2010 or 2011 to capture variation across the range
 of the species and to maximize the phylogenetic coverage of the oaks
 within North America. Acorns from the Cerris section were gathered from
 locations outside North America, as these species are not indigenous to
 the region. Seeds were collected from California, Florida, Illinois,
 Michigan, Minnesota, North Carolina, New York, Ohio, Utah, and Wyoming
 from trees occurring in natural areas within each population. The length
 and width of each acorn were measured, and the acorns were stored for
 several months at 4ºC at the University of Minnesota until synchronous
 planting (25 to 40 seedlings per species) in glasshouse facilities at the
 Franklinville Experimental Research Station in Franklinville, New York or
 at the University of Minnesota (UMN).                
 Seeds were germinated and grown in two replicated climate
 treatments in each of the two greenhouse locations for two years in (1) a
 tropical treatment, in which daytime temperature was maintained between 30
 and 35ºC, and night-time temperature between 22º and 26ºC; and (2) a
 temperate treatment, in which winter growth temperatures (mid-November to
 March) reached a minimum night-time temperature of 4ºC with a minimum
 daytime temperature of 15ºC, simulating species’ range limits.  Plants in
 the temperate treatment were acclimated to the winter temperature regime
 approximately 3 months prior to measurement. In New York, each climate
 regime was replicated in three independently controlled glasshouse rooms
 (for a total of six rooms) and in Minnesota, each climate regime was
 replicated in two independently controlled rooms (total of four). Summer
 photoperiods were left at ambient levels with a maximum of 15.4 hours in
 Minnesota and 15.16 in New York. The photoperiod was extended to 12 hours
 during the winter. These climate treatments were repeated every year for
 three subsequent years.<em>            </em>
 Three months after the start of the winter climate treatment, all
 individuals were monitored for maximum height (h; root collar to apex of
 tallest stem), the number of leaves (total leaves on all stems), and stem
 diameter (d; measured at the root collar). Allometric equations used to
 estimate the biomass for each species. Above-ground biomass was estimated
 using the maximum height, total number of leaves, and stem diameter. Acorn
 mass was estimated using the acorn volume.  Absolute growth rate (AGR; g
 yr<sup>-1</sup>) was calculated as AGR =
 (V<sub>final</sub> -V<sub>initial) </sub>⁄
 (T<sub>final </sub>- T<sub>initial</sub>), and
 Relative growth rate (RGR; mm<sup>3</sup>
 mm<sup>-3</sup> yr<sup>-1</sup>) was calculated as
 RGR= [log<sub>e</sub>(V<sub>final</sub>) -
 log<sub>e</sub>(V<sub>initial</sub>)] ⁄
 (T<sub>final </sub>- T<sub>initial</sub>). Where
 V<sub>final </sub>and V<sub>initial</sub> were
 calculated as the volume of a cylinder:  V<sub>final/initial
 ­</sub>=
 (d<sub>final/initial</sub>/2)­<sup>2</sup> x P x
 h<sub>final/initial</sub>.
 T<sub>initial</sub><sub> </sub>is the approximate
 date plants were measured in March 2012 and T<sub>final</sub>
 is the date plants. We used the most comprehensive
 phylogenetic tree for the genus <em>Quercus</em> and performed
 a comparative analysis using the ‘SLOUCH’ package in R. SLOUCH models
 traits as evolving under an Ornstein-Uhlenbeck (OU) model of evolution in
 a maximum likelihood framework. Traits are modeled as evolving toward a
 primary optimum, which is influenced by a continuous, randomly changing
 predictor variable, in our case, minimum temperature. Estimates of the
 phylogenetic signal or phylogenetic inertia are given by the phylogenetic
 half-life
 (<em>t</em><em><sub>1/2</sub></em>)
 and are interpreted relative to the absolute time associated with the
 phylogeny. When
 <em>t</em><em><sub>1/2</sub></em> is
 close to 0, the trait is evolving under strong selection by the predictors
 included in the model, without any influence from the ancestral trait
 value, whereas increasing values of
 <em>t</em><em><sub>1/2
 </sub></em>reflect an increasing effect of the ancestral trait
 value on present-day trait values. We used index of
 injury measured at -15<sup>o</sup>C as the response variable
 of the model, while minimum temperature of the coldest month in the native
 climate was treated as a predictor variable modeled as evolving according
 to a Wiener (Brownian motion) process. We compared models with and without
 the predictor variable to test the role of climatic niche in freezing
 tolerance evolution. For all statistical analyses, we used R v.3.4.2 with
 base packages R core Team (2018).
description: # Data and code for: Adaptive evolution of freezing tolerance in oaks is
 key to their dominance in North America
 [https://doi.org/10.5061/dryad.547d7wmhm](https://doi.org/10.5061/dryad.547d7wmhm) ## Description of the data and file structure ### Files and variables #### File: Critical\_temperature\_for\_MN-NY\_dataset.csv **Description:** Mean and SD for critical freezing temperatures and climate variables for each species     ##### Variables * species: Latin binomial * Dataset: plants grown in NY or MN greenhouses * critical_temp_25: critical freezing temperature at which 25% of cells have lysed * critical_temp_50: critical freezing temperature at which 50% of cells have lysed * Section: Section or major lineage within the genus -&gt; Cerris, Lobatae, Quercus, Virentes * LP: Leaf phenology -&gt; Evergreen or Deciduous * min_min_temp: mean minimum temperature, averaged across the distribution for each species * sd_min_temp: SD of the minimum temperature, across the distribution for each species * se_min_temp: SE of the minimum temperature, across the distribution for each species * mean_bio6c: bioclim variable 6, which is the mean minimum temperature of the coldest month, averaged across the distribution for each species * sd_bio6c: SD of bioclim variable 6 across the distribution for each species * se_bio6c: SE of bioclim variable 6 across the distribution for each species #### File: Species\_section\_phenology.csv **Description:** Phylogenetic section each species belongs to ##### Variables * species: Latin binomial * Section: Section or major lineage within the genus -&gt; Cerris, Lobatae, Quercus, Virentes * LP: Leaf phenology -&gt; Evergreen or Deciduous #### File: MN\_NY\_Index\_of\_injury\_mean\_se\_climatic\_variables.csv **Description:** Mean, SD, and SE for the Index of injury after freezing for each species and the greenhouse location ##### Variables * species: Latin binomial * Location: plants grown in NY or MN greenhouses -&gt; NY or MN * IJ_mean: mean index of injury after freezing at -15 degrees C for each species * log_IJ_mean: log (base 10) of the index of injury after freezing at -15 degrees C, calculated from the mean of each species * IJ_sd: SD of the index of injury after freezing at -15 degrees C for each species * IJ_se: SE of the index of injury after freezing at -15 degrees C for each species * mean_min_temp: mean minimum temperature of the coldest month, averaged across the distribution for each species * min_min_temp: minimum temperature, averaged across the distribution for each species * log_min_min_temp: log (base 10) of the minimum temperature for each species * sd_min_temp: SD of the minimum temperature, across the distribution for each species * se_min_temp: SE of the minimum temperature, across the distribution for each species    * mean_bio6c: bioclim variable 6, which is the mean minimum temperature of the coldest month, averaged across the distribution for each species * sd_bio6c: SD of bioclim variable 6 across the distribution for each species * se_bio6c: SE of bioclim variable 6 across the distribution for each species #### File: RGR\_cylinder\_cold\_all\_data.csv **Description:** relative growth rate and other growth related variables for all species in tropical and temperate treatments ##### Variables * species: specific epithet * ID: Individual plant identification number or code * zone: greenhouse room in which plants were grown – climatic regimes in zones were set to simulate tropical (zones 3,4,5) or temperate (zones 1,2,6) growth environments * d0: stem basal diameter at time zero (start of growth; first measurement) in mm * d1: stem basal diameter at time one (end of growing season; second measurement) in mm * h0: stem height at time zero (start of growth; first measurement) in cm * h1: stem height at time one (end of growing season; second measurement) in cm * t0: time 0 (in units of days) * t1: time 1 (in units of days) * v0: calculated cylindrical plant volume at time 0 in units of cm^3    * v1: calculated cylindrical plant volume at time 1 in units of cm^3 * biom0: estimated dry plant biomass at time 0 in units of g * biom1: estimated dry plant biomass at time 1 in units of g * rgr_cyl: relative growth rate calculated based on the cylindrical volume of the plant in units of cm^3 per cm^3 per day * rgr_biom: relative growth rate calculated based on the estimated biomass in units of g per g per day * rgr_h: relative growth rate calculated based on height in units of cm per cm per day * rgr_d: relative growth rate calculated based on stem basal diameter in units of mm per mm per day * rgr_av: average of all of the relative growth rate calculations #### File: tree\_MN\_NY\_spp **Description:** Phylogeny of the 48 oak species in the dataset #### File: Trait\_data\_RGR\_bio6.csv **Description:** mean trait values, growth related traits, acclimation potential and climate variables Missing data codes: NA ##### Variables * Species: Latin binomial * Section: Section or major lineage within the genus Cerris, Lobatae, Quercus, Virentes * Leaf_P: leaf phenology * Vess_Diam: average vessel diameter * Wood_Density: stem specific density (g per cm^3) * Habit: tree or shrub * Region: Tropical, Temperate or Mediterranean * critical_temp_25: critical freezing temperature at which 25% of cells have lysed * critical_temp_50: critical freezing temperature at which 50% of cells have lysed * IJ: index of injury when stems were frozen at -15 degrees C * cold: index of injury when stems were frozen at -15 degrees C for plants grown in temperate conditionsindex of injury when stems were frozen at -15 degrees C for plants grown in temperate conditions * warm: index of injury when stems were frozen at -15 degrees C for plants grown in tropical conditions * mean_rgr_cold: relative growth rate for plants grown in temperate conditions * sd_rgr_cold: SD of relative growth rate for plants grown in temperate conditions * mean_rgr_warm: relative growth rate for plants grown in tropical conditions * sd_rgr_warm: SD of relative growth rate for plants grown in tropical conditions * bio6c: bioclim variable 6, which is the mean minimum temperature of the coldest month, averaged across the distribution for each species * diff_RGR: difference between rgr in temperate and tropical conditions    * min_min_temp: minimum temperature averaged across the distribution for each species * acclimation: cold acclimation capacity based on the difference in index of injury in temperate and tropical growth conditions #### File: sp\_means\_bio6\_min\_temp\_se.csv **Description:** freezing vulnerability and mean minimum temperatures in source locations for each species ##### Variables * species: Latin binomial * cold: mean index of injury at -15 degrees C after growth in temperate treatment * warm: mean index of injury at -15 degrees C after growth in tropical treatment * cold_se: standard error of index of injury at -15 degrees C after growth in temperate treatment * warm_sd: standard deviation of index of injury at -15 degrees C after growth in tropical treatment * warm_se: standard error of index of injury at -15 degrees C after growth in tropical treatment * mean_min_temp: mean minimum temperature in source location * min_min_temp: minimum temperature in source location * sd_min_temp: standard deviation of minimum temperature in source location * se_min_temp: standard error of minimum temperature in source location * mean_bio6c: mean minimum temperature of coldest month * sd_bio6c: standard deviation of minimum temperature of coldest month * se_bio6c: standard error of minimum temperature of coldest month * diff_mean: difference in index of injury between seedlings of the same mother grown in temperate and tropical environments * diff_sd: standard deviation of difference in index of injury between seedlings of the same mother grown in temperate and tropical environments * diff_se: standard error of difference in index of injury between seedlings of the same mother grown in temperate and tropical environments * Section: Section or major lineage within the genus Cerris, Lobatae, Quercus, Virentes * LP: Leaf phenology, Evergreen or Deciduous * diff: difference in mean index of injury in temperate and tropical treatment for each species ## Code/software R (R Core Team 2018) Acclimation potential.R  Critical temperature MN and NY data.R Extracting climatic variables.R Index of injury - MN_NY - Phylo regression.R  RGR-Mixed Models.R Slouch-evolutionary model.R ## Access information Other publicly accessible locations of the data: * WorldClim database ([http://www.worldclim.org/](http://www.worldclim.org/)) for climatic variables