DOI: 10.5061/dryad.gqnk98sx2
title: Local adaptation and phenotypic plasticity drive leaf trait variation in the California endemic toyon dataset

description: Premise of the study: To survive climate change and habitat loss plants
 must rely on phenotypic changes to the environment, local adaptation, or
 migration. Understanding the drivers of intraspecific variation is
 critical to anticipate how plant species will respond to climate change
 and inform conservation decisions. Here we explore the extent of local
 adaptation and phenotypic plasticity in Heteromeles arbutifolia, toyon, a
 species endemic to the California Floristic Province. Methods: We
 collected leaves from 286 individuals across toyon’s range and used seeds
 from 37 individuals to establish experimental gardens in the northern and
 southern parts of toyon’s range. We measured leaf functional traits of the
 wild collected leaves, and functional and fitness traits of the offspring
 grown in the experimental gardens. We then investigated the relationships
 between traits and source environment. Key results: Most traits we
 investigated responded plastically to the environment, and some traits
 measured in young seedlings were influenced by maternal effects. We found
 strong evidence that variation in leaf margins is a result of local
 adaptation to variation in temperature and temperature range. However, the
 source environment was not related to fitness traits or survival in the
 experimental gardens. Conclusions: Our findings reiterate the adaptive
 role of toothed leaf margins in colder and more seasonally variable
 environments. Additionally, we provide evidence that fitness of toyon is
 not dependent on where they are sourced, and thus toyon can be sourced
 across its range for restoration purposes.
description: # Local adaptation and phenotypic plasticity drive leaf trait variation in
 the California endemic toyon dataset
 [https://doi.org/10.5061/dryad.gqnk98sx2](https://doi.org/10.5061/dryad.gqnk98sx2) This dataset contains the data used to answer the research questions 1. How do toyon traits vary along environmental gradients? 2. How do genetic differences and environmental maternal effects contribute to trait variation between individuals grown in a common environment and how does this trait variation relate to the source environment? 3. Are toyon individuals adapted to their local environment? 4. Are some traits more plastic than others and do maternal lines vary in plasticity? It contains the herbarium, seed, greenhouse, and two common garden data sets with climatic variables sourced from the Bioclim dataset.  ## Description of the data and file structure All files are in csv format. EnvironmentQ and GeneticQ are only used for creating figures. All other data frames are subsets of the whole body of data or are specifically manipulated for different questions. Details for all clean data.csv :  * Description: A csv input for the majority of data analyses including herbarium and common garden collected data.  * Variables:  * whole_name : The maternal line and the planted individual in one name. * Mom : The maternal line the individual was sourced from in California.  * Individual: Which individual planted in the greenhouse from the maternal line, from A through J and extras from X1 to X4.  * lat : The latitude of where the maternal line was sourced.  * long : The longitude of where the maternal line was sourced.  * coordinate : The coordinates of the lat and long of where the maternal line was sourced.  * bio_9 : Bioclim variable Mean temperature driest quarter.  * bio_8 : Bioclim variable Mean temperature of the wettest quarter.  * bio_7 : Bioclim variable temperature annual range. * bio_6 : Bioclim variable Minimum temperature of the coldest month.  * bio_5 : Bioclim variable maximum temperature of the warmest month.  * bio_4 : Bioclim variable temperature seasonality.  * bio_3 : Bioclim variable isothermality.  * bio_2 : Bioclim variable mean diurnal range.  * bio_19 : Bioclim variable precipitation of coldest quarter.  * bio_18 : Bioclim variable precipitation of warmest quarter.  * bio_17 : Bioclim variable precipitation of the driest quarter.  * bio_16 : Bioclim variable precipitation of the wettest quarter.  * bio_15 : Bioclim variable precipitation seasonality.  * bio_14 : Bioclim variable precipitation of the driest month.  * bio_13 : Bioclim variable precipitation of the wettest month.  * bio_12 : Bioclim variable of annual precipitation.  * bio_11 : Bioclim variable mean temperature of coldest quarter.  * bio_10 : Bioclim variable mean temperature of warmest quarter.  * bio_1 : Bioclim variable annual mean temperature. * elevation : elevation of maternal line in meters.  * lwr_mom : Length width ratio of the maternal line herbarium sample.  * sla_mom : Specific leaf area of the leaf area divided by the leaf mass of the maternal line herbarium sample. * density_mom: Stomatal density of the maternal line herbarium sample. Blank cells is for individual 277 that we were not able to collect a stomatal peel.  * mom_leaf_mass : Leaf mass of the  maternal line herbarium sample.  * new_mom_leaf_area : Leaf area of the maternal line herbarium sample calculated in imageJ. * mom_leaf_length : Length of maternal line herbarium sample calculated in imageJ. * mom_leaf_width: Width of maternal line herbarium sample calculated in imageJ. * tooth_ct_mom teeth_per_cm_mom : Number of teeth per 1 cm of  maternal line herbarium sample.  * avg_mj_tooth_mom : The average length of 3 major teeth of  maternal line herbarium sample. NAs were for a sample that did not have defined teeth.  * avg_mn_tooth_mom : The average length of 3 minor teeth of  maternal line herbarium sample. NAs were for a sample that did not have defined teeth.  * inside_area_mom : The inside area of the  maternal line herbarium sample not including the area of the teeth.  * total_tooth_area_mom :  The total area of the maternal line herbarium sample minus the inside leaf area * relative_tooth_area_mom : The tooth area divided by the total leaf area of the maternal line herbarium sample.  * block : The block from A to J in the greenhouse that the germinated seed was planted in. NAs for two individuals that were in a block on the side.  * rack_position : Where in the block the seed was planted in. NAs for two individuals that were in a block on the side.  * starting.day : What day the seed was placed in a moist petri dish for germination. * germination.day.extra_planting.day : The date the seed germinated or the date an extra seed was planted later in the germination cycle. Blank cells are for extra seeds when we did not record the germination data. * planting.day.transplanting.day : The date the germinated seed was planted or the date the extra seeds were moved into a larger pot in the main blocks. NAs for only two individuals that were mistakenly not tracked.  * planting_day: How many days since the seed germinated and they were outplanted into the common gardens. NAs for only two individuals that were mistakenly not tracked.  * rgrtime_gh : How many days since planting in the greenhouse before the heights were measured on June 7th, 2022. NAs for only two individuals that were mistakenly not tracked.  * height_6_7 : The height of the seedlings on June 7th, 2022.  * branches_6_7 : The number of branches on the seedlings on June 7th, 2022.  * leaf_num_6_7 : The number of leaves on the seedlings on June 7th, 2022.  All n/as for GH recorded measurements where for plants that were too small to measure.   * leaf_area_GH : Leaf area of the leaf measured in the greenhouse.  * leaf_length_GH : Leaf length of the leaf measured in the greenhouse.  * leaf_width_GH : Leaf width of the leaf measured in the greenhouse.  * tooth_ct_GH : The number of teeth of the leaf measured in the greenhouse.  * teeth_per_cm_GH : The number of teeth per cm of the leaf measured in the greenhouse.  * avg_mj_toothgh : The average length of 3 major teeth of the leaf measured in the greenhouse.  * minor_tooth_GH : The average length of 3 minor teeth of the leaf measured in the greenhouse.  * inside_area_GH : The inside area not including teeth of the leaf measured in the greenhouse.  * tooth_area_GH : The total area of the leaf minus the inside area of the leaf measured in the greenhouse. * relative_tooth_area_GH :  The tooth area divided by the total lead area of the leaf measured in the greenhouse. * lwr_gh : The length divided by the width of the leaf measured in the greenhouse.  * rgr_gh : The natural log of the height of the individual divided by the number of days growing since germination.  * garden.location : Which common garden the individual was out planted into. All n/as for the garden are for individuals that died in the field before measuring. * lwr_gar : The length width ratio of the collected leaves from the gardens in August, 2022.  * sla_garden :  The specific leaf area of the collected leaves from the gardens in August, 2022.  * rgr_gar9_14 : The relative growth rate of the individuals from outplanting to September 14th, 2022.  * total_leaf_9_14 : The number of leaves produced on an individual in the common garden until September 14th, 2022.  * total_branch_9_14 : The number of branches produced by September 14th, 2022.  * rgr_gar_nov : The relative growth rate from out planting to November.  total_leaf : The total number of new leaves in November.  * total_branch : The total number of new branches in November.  * density_garden : The stomatal density of leaves collected in the gardens.  * leaf_area_G : The leaf area of the collected leaf in the common gardens.  * leaf_length_G : The leaf length of the collected leaf in the common gardens.  * leaf_w_G : The leaf width of the collected leaf in the common gardens.  * tooth_ct_G : The number of teeth of the collected leaf in the common gardens.  * teeth_per_cm_G : The teeth per cm of the collected leaf in the common gardens.  * avg_mj_toothg : The average length of 3 major teeth of the collected leaf in the common gardens.  * minor_tooth_G :The average length of 3 minor teeth of the collected leaf in the common gardens.  * inside_area_G : The inside area not including teeth of the collected leaf in the common gardens.  * tooth_area_G : The total area minus the inside area of the collected leaf in the common gardens.  * relative_tooth_area_G : The tooth area divided by the total area of the collected leaf in the common gardens.  * leaf_weight_g : The mass in grams of the collected leaf in the common gardens.  * water_PC1 : The first principal component of the water related bioclim variables.   * water_PC2 : The second principal component of the water related bioclim variables.  * temp_PC1 : The first principal component of the temperature related bioclim variables.  * temp_PC2 :  The second principal component of the temperature related bioclim variables.  * average.seed.weight : The average weight of the seeds collected for the maternal line.  * height_9_14 : The height of the plants on September 14th, 2022.  Details for env mom leaf.csv :  * Description: A csv with all of the maternal lines examined from herbarium samples. The plants with seeds and individuals in the common garden are a subset of this dataset. All variables remain consistent with the all clean data.csv * Only NAs are for individual Harb-SMA-2 because it did not have defined teeth.  Details for env mom stomata.csv * Description: A csv with the stomatal density values for the maternal herbarium specimens for all of the individuals found in the common gardens. All variables are consistent with the prior data frames with the addition of these variables.  * Variables:  * average_num : The average number of stomata counted in 3 different images of the stomata peel.  * density : The average number of stomata divided by the area of the photo.  * Only NAs are for individual 277 that we were not able to collect a stomatal peel from.  Details for germination.csv :  * Description: A csv input for the majority of data analyses including herbarium and common garden collected data.  * The NAs are for germination.day and planting.day for seeds that weren't tracked.  * Variables:  * county: The county in California the seeds were collected.  * herbarium : Whether or not the seeds were collected from an herbarium specimen.  * number.of.seeds : The number of seeds being counted and weighed. * total.weight..g. : The mass of the seeds being weighed.  * average.seed.weight : The total weight divided by the number of seeds.  * germyn : Whether or not the seed germinated.  * germ_days : How many days it took for the seed to germinate.  * died : Whether or not the seed died after germinating.  * germ_dayslog : The number of days it took for the seed to germinate log transformed.  Details for seed_weight.csv :  * Description: A csv of a subset of data with all of the maternal lines that had seeds collected from them and were weighed. All variables are consistent with prior data frames.  Details for surv_data.csv :  * Description : A csv with all individuals in the common gardens with data on how long they survived and variables to run a survival analysis. It also has difference in the climate PC's from the common garden climates to analyze difference in climate in respect to survival.  * Variables:  * Date.of.Death : the date the plant individual died in the common garden. Blanks are for plants that did not die. * days_survived : The number of days the plant was alive in the common garden. NAs are for plants that did not die.  * status : A 0 if the plant did not die and a 1 if the plant did die.  * time : The number of days the plant was alive in the common garden.  * Individuals 97_*X1 and 97*\_ X2  was mistakenly not tracked and does not have block locations or germination information.  * Blanks in germination_day are for extra individuals who were planted after the initial germination tracking.  * All n/as for the garden measured variables* *are for individuals that died in the field before measuring. Details for big*model plotting2.csv and loo output.csv*:  * Description : 2 csvs with the outputs from plasticity anaylses for creating figures.  ## Sharing/Access information The data is only available here on Dryad. For additional resources and support analyzing the data, please reach out to the authors of the paper. Data was derived from the following sources: * WorldClim for the Bioclim variables: [https://www.worldclim.org/data/bioclim.html](https://www.worldclim.org/data/bioclim.html) ## Code/Software All code was conducted in R Studio. The final code for data analysis separated into general and plasticity analysis as well as the code used to create the figures are provided. The data analysis and plasticity analysis codes should be run before the figures code to have the correct outputs.