DOI: 10.5061/dryad.wh70rxww8
title: Data from: Predicting fitness in future climate: Insights from temporally replicated field experiments in Arabidopsis thaliana

description: Organisms are already facing climate change driven by recent anthropogenic
 activities. In an attempt to understand and mitigate the negative effects
 of climate change on wild and farmed species, recent research focused on
 predicting the fitness of organisms or populations in future climates. The
 accuracy of these predictions is, however, seldom tested. To test such
 predictions, we grew 800 genetic families of the annual selfing plant
 Arabidopsis thaliana in the same field site for two consecutive years with
 contrasted climates. Despite observing, in both years, a clear association
 between fitness and climatic distance between our field site and the
 climate of origin of the genetic families, the diverse set of methods we
 used failed to accurately predict fitness from a year to another. This
 impossibility resulted from different contributions of climatic factors in
 climate adaptation every year, which impeded the definition of a
 meaningful climatic descriptor across years. Our results also show that,
 for our study populations at least, vegetative growth is a more important
 trait for climate adaptation than phenology. We discuss the implications
 of our results for predicting the fitness of wild organisms in future
 climates and for breeding programs.
description: <strong>Plant material</strong>
 The plant material we used has already been described in a
 previous study (Brachi et al. 2013) but we provide a short description of
 this material hereafter. In 2009, we collected 800 individuals of the
 annual plant species <em>A. thaliana</em> from 49 natural
 populations in four regions of France with different climatic regimes
 (Brittany: oceanic climate - 11 populations; Burgundy: continental climate
 - 11 populations; Languedoc: Mediterranean climate - 16 populations; North
 of France: semi-continental climate, 11 populations; Table S1- Figure S1
 of the associated publication). We collected an average of 16 plants per
 population (mean=16.3 ±5.6). We collected these plants before they
 initiated flowering, and grew them in isolation with aratubes
 (https://www.arasystem.com/asn003-aratubes-360) in the greenhouse (16h
 photoperiod, 20°C) to prevent cross-pollination and harvest seeds. The
 seeds we obtained from each individual plant therefore constitute a
 genetic family. Because <em>A. thaliana </em>is a highly
 selfing species, each genetic family is quasi-homozygous (Platt et al.
 2010). To reduce the impact of maternal effects in our experiments
 (Rossiter 1996) and increase the proportion of variance due to genetic
 factors, we grew each genetic family in isolation with aratubes for an
 additional generation in a common environment (<em>i.e.</em>,
 greenhouse conditions, 16h photoperiod, 20°C) and harvested their seeds.
 These seeds are the starting material for the experiments described in
 this study. <strong>Field
 experiments</strong> We set the same experiment
 for two consecutive years in the same field site in the north of France
 (Villeneuve-d’ascq, France, GPS coordinates: 50°36'27.2"N,
 3°08'37.0"E). For convenience, we refer to the first experiment
 as the ‘2011 experiment’ and the second experiment as the ‘2012
 experiment’. For each experiment, we aimed at growing two individuals from
 each genetic family. We sowed seeds on a similar Julian day of the year
 for both experiments (the 27th of September 2010 for the 2011 experiment,
 and the 26th of September 2011 for the 2012 experiment). The following
 design and protocol were identical for both experiments.
 For each genetic family replicate, at least four seeds were
 placed within an individual well of a 66-well botanical tray (TEKU, JP
 3050/66) filled with damp standard soil culture (007B Florafleur, France),
 so that a given well contained only seeds from a given genetic family.
 Following sowing, we placed the trays in a cold chamber (4°C) for four
 days, to stratify the seeds and promote germination. We then placed the
 trays in a frost-free greenhouse, without additional light or heating. We
 treated the trays with Vectobac (8mL per liter) on the day of their
 placement in the frost-free greenhouse, to protect them against a possible
 episodic outbreak of the pest dark-winged fungus gnats. We monitored the
 trays daily for 17 days after their placement in the frost-free greenhouse
 to score germination date. Germination rates (measured as the percentage
 of sown wells for which at least one germination was observed) were very
 high with 96.4% and 96.3% of the wells containing germination for the 2011
 experiment and the 2012 experiment, respectively. On day 18, when
 possible, we transplanted two seedlings of a specific genetic family
 replicate that germinated into a replicate of the same genetic family that
 did not germinate. On that same day, we thinned all individual wells to
 keep two seedlings per well and moved the trays onto the experimental
 field, located outside the greenhouse at the University of Lille 1 France
 (GPS coordinates: 50°36'27.2"N, 3°08'37.0"E). To
 facilitate root development (the wells have a hole allowing root
 development into the soil), we tilled the soil below the trays to be able
 to bury them slightly into the ground. The field was far enough from any
 surrounding buildings to have direct sunlight all day. We did not place
 any object or plastic covering on top of the plants, as we aimed to let
 the plants experience the climatic conditions at the field site (sunlight,
 temperature, and precipitation). A week after placement in the field, we
 thinned all wells to only retain a single seedling per well.
 We organized each experiment into two experimental blocks, with
 one replicate of each genetic family within each block. Each block
 comprised 19 trays, with genetic families organized randomly within the 19
 trays. We placed trays belonging to the same block near each other in four
 rows and five columns. We placed blocks approximately five meters apart.
 To reduce the impact of micro-environmental variations, we rotated trays
 daily in the cold chamber and the frost-free greenhouse. To control for
 possible micro-environmental variations within blocks in the field, we
 placed two individuals from the same genetic line (Bg-2 line, referred to
 as control hereafter) at the same two positions within each tray. Another
 set of 398 worldwide or French genetic families was also included in these
 two field experiments for another study that investigated the genetics
 underlying natural variation in glucosinolate profiles (Brachi et al.
 2015). In total, the 2011 experiment and the 2012
 experiment involved the monitoring of 3,352 individual plants (1,676
 plants per experiment). To score phenological and vegetative traits as
 accurately as possible, we monitored individual plants on the field site
 every two or three days during the entirety of the experiments, from the
 placement of trays on the field site to the production of the last mature
 fruit. <strong>Estimating phenology, vegetative
 growth, and seed production</strong> We measured
 four phenological traits (germination time, bolting time, the interval
 from bolting to flowering, and the length of the reproductive period), one
 vegetative trait (diameter at bolting), and an estimator of fitness (seed
 production) on all plants. We measured germination time
 (GERM hereafter) as the number of days elapsed from the end of the
 stratification treatment to germination. We measured bolting time (BT
 hereafter) as the number of days elapsed between germination and the onset
 of bolting. We measured the flowering interval (INT hereafter) as the
 number of days elapsed between bolting and the opening of the first
 flower. We measured the length of the reproductive period as the number of
 days elapsed between the opening of the first flower and the maturation of
 the last fruit. To facilitate trait value comparison across years, we
 rescaled these four phenological traits in photothermal units (PTU) using
 a phenological model integrating both daily photoperiod length and daily
 temperatures measured in the greenhouse and at the field site (Brachi et
 al. 2010). As an estimator of vegetative growth, we
 measured the maximum diameter of the rosette at bolting (DIAM hereafter)
 using a plastic ruler (~0.5mm accuracy), as this trait is a good
 descriptor of plant size in <em>A. thaliana </em>(Weinig et
 al. 2006). The lifetime fitness of each plant (seed
 production hereafter) was estimated by the total length of fruits
 produced, which strongly correlates with seed count (Roux et al. 2004;
 Roux et al. 2005). Plants that germinated but did not survive to produce
 any mature fruit were given a total fruit length value of zero.
 <strong>Climatic data</strong> We
 obtained past climatic data for our 49 populations for the worldclim 2.1
 database (Fick and Hijmans 2017). Specifically, we downloaded the 19
 bioclimatic variables for these populations using the finest resolution
 data (30 seconds = ~1km resolution). These estimates are the average for
 the years 1970-2000. To characterize the climate
 experienced by plants in our experiments, we used the meteorological
 reports (temperature and precipitation) from the nearest meteorological
 station (Lille-Lesquin, 59, France) for the years 2011 and 2012. We
 transformed these raw records into 19 bioclimatic variables, similar to
 the one mentioned above, but for our field site for the years 2011 and
 2012. We performed this transformation using the function calc_biovars
 from the package QBMS (v 0.9.1) (Al-Shamaa 2023).
 <strong>BLUEs estimation</strong>
 We used raw data for most analyses unless specified otherwise.
 For some analyses we used BLUEs values. We calculated them as
 follow.  For each experiment, we estimated the
 genotypic value for each trait of each genetic family within each
 experiment by running the following mixed model for each trait:
 Trait<sub><em>ij</em></sub> =
 <em>b</em><sub>1</sub><sub>
 </sub>block<sub><em>i</em></sub> +
 <em>b</em><sub>2</sub><sub>
 </sub>family<sub><em>j </em></sub>+
 <em>b</em><sub>2</sub>
 control<sub><em>ij </em></sub>+ intercept
 (equation 3) Where ‘trait’ corresponds to the trait
 value for a given plant, ‘block<em>’</em> corresponds to
 differences between the two blocks, ‘family’ corresponds to variation
 among the 800 genetic families, and ‘control’ corresponds to the mean
 trait value for the two control plants located on the same tray than this
 plant. In this model, the family effect was considered as random, and all
 other effects as fixed. We extracted BLUPs (Best Linear Unbiased
 Predictions) for each family from this model, and obtained genotypic
 values (BLUEs - Best Linear Unbiased Estimates) by adding the trait mean
 computed from raw trait values to these BLUPs. We then perform the same
 analyses as described in the previous paragraph to obtain genotypic
 gradients of selection both at the population and genetic family levels.
 We fitted our mixed models using the lmer function from the lme4 package
 in R (v4.3.2) (Bates et al. 2015; R-Core-Team 2020) and extracted BLUPs
 with the ranef function from the same package.
 <strong>References</strong>
 Al-Shamaa, K. 2023. QBMS: Query the Breeding Management
 System(s). Bates, D., M. Mächler, B. Bolker, and S.
 Walker. 2015. Fitting Linear Mixed-Effects Models Using lme4. Journal of
 Statistical Software 67:1 - 48. Brachi, B., N. Faure,
 M. Horton, E. Flahauw, A. Vazquez, M. Nordborg, J. Bergelson, J. Cuguen,
 and F. Roux. 2010. Linkage and association mapping of Arabidopsis thaliana
 flowering time in nature. PLoS genetics 6:e1000940.
 Brachi, B., R. Villoutreix, N. Faure, N. Hautekeete, Y. Piquot,
 M. Pauwels, D. Roby, J. Cuguen, J. Bergelson, and F. Roux. 2013.
 Investigation of the geographical scale of adaptive phenological variation
 and its underlying genetics in Arabidopsis thaliana. Molecular ecology
 22:4222-4240. Platt, A., M. Horton, Y. S. Huang, Y. Li,
 A. E. Anastasio, N. W. Mulyati, J. Agren, O. Bossdorf, D. Byers, K.
 Donohue, M. Dunning, E. B. Holub, A. Hudson, V. Le Corre, O. Loudet, F.
 Roux, N. Warthmann, D. Weigel, L. Rivero, R. Scholl, M. Nordborg, J.
 Bergelson, and J. O. Borevitz. 2010. The scale of population structure in
 Arabidopsis thaliana. PLoS genetics 6:e1000843.
 R-Core-Team. 2020. R: A language and environment for statistical
 computing. R Foundation for Statistical Computing, Vienna,
 Austria. Rossiter, M. 1996. INCIDENCE AND CONSEQUENCES
 OF INHERITED ENVIRONMENTAL EFFECTS. Annual Review of Ecology, Evolution
 and Systematics 27:451-476. Roux, F., C. Camilleri, A.
 Bérard, and X. Reboud. 2005. MULTIGENERATIONAL VERSUS SINGLE GENERATION
 STUDIES TO ESTIMATE HERBICIDE RESISTANCE FITNESS COST IN ARABIDOPSIS
 THALIANA. Evolution 59:2264-2269. Roux, F., J. Gasquez,
 and X. Reboud. 2004. The Dominance of the Herbicide Resistance Cost in
 Several Arabidopsis thaliana Mutant Lines. Genetics 166:449-460.
 Weinig, C., J. Johnston, Z. M. German, and L. M. Demink. 2006.
 Local and global costs of adaptive plasticity to density in Arabidopsis
 thaliana. Am Nat 167:826-836.
description: # Data from: Predicting fitness in future climate: Insights from
 temporally replicated field experiments in Arabidopsis thaliana
 [https://doi.org/10.5061/dryad.wh70rxww8](https://doi.org/10.5061/dryad.wh70rxww8) ## Description of the data and file structure ### Files and variables #### File: Ecological\_variables\_CG\_Popfr\_2025-03-25.txt **Description:** Climate data for the study populations. The climate data extracted from worldclim2.1 have been blanked in the file for license reasons but can be downloaded with the archived script 'get-popfr-bioWC2-compute-CG-bioclim.R'. Data for the common garden (years 2011 and 2012) are not blanked as they were not extracted from worldclim 2.1. The units of variables are similar to one used by the worldclim project: [https://www.worldclim.org/data/bioclim.html](https://www.worldclim.org/data/bioclim.html) ##### Variables Pop: Population name. These correspond to abbreviations of the closest locality's name. See the following table. | Pop | Locality | | :------- | :------------------------ | | ABA | Abaty | | ARR-1 | Arrigas | | ARR-2 | Arrigas | | ARR-3 | Arrigas | | BAU | Bauvin | | BEZ | Bez et Esparon | | BRE | Brendaouez | | BRI | Brillon | | CAT-S | Mont des Cats | | CAT-T | Mont des Cats | | CIRY | Ciry-le-Noble | | CON | Conforgien | | DIR-2.80 | Dirinon | | DIR-8.50 | Dirinon | | ENC-1 | Mont de l'Enclus | | ENC-2 | Mont de l'Enclus | | ESP1 | Esplechin | | ESP2 | Esplechin | | ETA-1 | Etang sur Arroux | | ETA-2 | Etang sur Arroux | | FOR | La Forest Landerneau | | GEN | Genech | | ISS | Issensac | | LCL | Lecelles | | LEC | Lecques | | LIE | Liernais | | MAR-3 | Marigny l'Eglise | | MAR-4 | Marigny l'Eglise | | MIL | Milizac | | MOL | Saint- Léger sous Beuvray | | MOU1-1 | Moussac | | MOU1-2 | Moussac | | MOU1-3 | Moussac | | MOU2 | Moussac | | NOZ | Nozières-Brignon | | PCH | Puechredon | | PLO | Plougastel-Daoulas | | PLY | Ploudiry | | QUI | Quissac | | RAD | Sainte-Radegonde | | ROC | La Roche Maurice | | RUM | Rumiqueal | | SAL | Salinelles | | TOU-J2 | Toulon sur Arroux | | TOU-M1 | Toulon sur Arroux | | TRE | Treflaouenan | | VED | St Jean de Vedas | | VEN | Vendargue | | WAV | Wavrin | * Region: Region of origin * Long: longitude, in decimal degree * Lat: Latitude, in decimal degree * Bio_1 = Annual Mean Temperature * Bio_2 = Mean Diurnal Range (Mean of monthly (max temp - min temp)) * Bio_3 = Isothermality (BIO2/BIO7) (×100) * Bio_4 = Temperature Seasonality (standard deviation ×100) * Bio_5 = Max Temperature of Warmest Month * Bio_6 = Min Temperature of Coldest Month * Bio_7 = Temperature Annual Range (BIO5-BIO6) * Bio_8 = Mean Temperature of Wettest Quarter * Bio_9 = Mean Temperature of Driest Quarter * Bio_10 = Mean Temperature of Warmest Quarter * Bio_11 = Mean Temperature of Coldest Quarter * Bio_12 = Annual Precipitation * Bio_13 = Precipitation of Wettest Month * Bio_14 = Precipitation of Driest Month * Bio_15 = Precipitation Seasonality (Coefficient of Variation) * Bio_16 = Precipitation of Wettest Quarter * Bio_17 = Precipitation of Driest Quarter * Bio_18 = Precipitation of Warmest Quarter * Bio_19 = Precipitation of Coldest Quarter Missing values: NA #### File: TE-clim-reformated-2023-09-13.csv **Description:** Climatic measurements for our common garden (years 2011 and 2012). One line for each month of the year (in month order: the first line corresponds to January, the second to February etc.). ##### Variables * year: Year of measurement * ppt: precipication in mm * tmin: minimum temperature in °C * tmax: maximum temperature in °C Missing values: NA #### File: Genotypic-values\_BLUPs\_Sep\_2010-2011\_2014-04-18.txt **Description:** BLUEs values for the 2011 experiment (one measure per genetic family) ##### Variables * Nom: Genetic family name * Region: Region of origin * Stands: Population of origin. These correspond to abbreviations of the closest locality's name * GERM_PTT: Time to germination in photothermal unit * BT_PTT: Time to bolting in photothermal unit * INT_PTT: Interval between bolting and flowering in photothermal unit * RP_PTT: reproductive period in in photothermal unit * DIAM_M: Diameter at bolting in mm * FITTOT2: total fruit length (set at 0 for plants that did not survive) in mm Missing values: NA #### File: Genotypic-values\_BLUPs\_Sep\_2011-2012\_2014-04-18.txt **Description:** BLUEs values for the 2012 experiment (one measure per genetic family) ##### Variables * Nom: Genetic family name * Region: Region of origin * Stands: Population of origin. These correspond to abbreviations of the closest locality's name. See the following table. | Pop | Locality | | :------- | :------------------------ | | ABA | Abaty | | ARR-1 | Arrigas | | ARR-2 | Arrigas | | ARR-3 | Arrigas | | BAU | Bauvin | | BEZ | Bez et Esparon | | BRE | Brendaouez | | BRI | Brillon | | CAT-S | Mont des Cats | | CAT-T | Mont des Cats | | CIRY | Ciry-le-Noble | | CON | Conforgien | | DIR-2.80 | Dirinon | | DIR-8.50 | Dirinon | | ENC-1 | Mont de l'Enclus | | ENC-2 | Mont de l'Enclus | | ESP1 | Esplechin | | ESP2 | Esplechin | | ETA-1 | Etang sur Arroux | | ETA-2 | Etang sur Arroux | | FOR | La Forest Landerneau | | GEN | Genech | | ISS | Issensac | | LCL | Lecelles | | LEC | Lecques | | LIE | Liernais | | MAR-3 | Marigny l'Eglise | | MAR-4 | Marigny l'Eglise | | MIL | Milizac | | MOL | Saint- Léger sous Beuvray | | MOU1-1 | Moussac | | MOU1-2 | Moussac | | MOU1-3 | Moussac | | MOU2 | Moussac | | NOZ | Nozières-Brignon | | PCH | Puechredon | | PLO | Plougastel-Daoulas | | PLY | Ploudiry | | QUI | Quissac | | RAD | Sainte-Radegonde | | ROC | La Roche Maurice | | RUM | Rumiqueal | | SAL | Salinelles | | TOU-J2 | Toulon sur Arroux | | TOU-M1 | Toulon sur Arroux | | TRE | Treflaouenan | | VED | St Jean de Vedas | | VEN | Vendargue | | WAV | Wavrin | * GERM_PTT: Time to germination in photothermal unit * BT_PTT: Time to bolting in photothermal unit * INT_PTT: Interval between bolting and flowering in photothermal unit * RP_PTT: reproductive period in in photothermal unit * DIAM_M: Diameter at bolting in mm * FITTOT2: total fruit length (set at 0 for plants that did not survive) in mm Missing values: NA #### File: september.2011.data.light.txt **Description:** Raw data for the 2011 experiment (one measure per replicate) ##### Variables * Code: Positional code * Bloc: Bloc number * Traitement: Experimental year (2011 here) * Plateau: Tray number * Ligne: Line number on the tray * Colonne: Column number on the tray * Nom: Genetic family name * Region: Region of origin * Stands: Population of origin. These correspond to abbreviations of the closest locality's name * Type: Experiment name (Popfr here) * GERM_PTT: Time to germination in photothermal unit * BT_PTT: Time to bolting in photothermal unit * INT_PTT: Interval between bolting and flowering in photothermal unit * RP_PTT: reproductive period in in photothermal unit * DIAM_M: Diameter at bolting in mm * FITTOT2: total fruit length (set at 0 for plants that did not survive) in mm * TGERM_PTT: Time to germination in photothermal unit of the control genotype (Bg-2) * TBT_PTT: Time to bolting in photothermal unit of the control genotype (Bg-2) * TINT_PTT: Interval between bolting and flowering in photothermal unit of the control genotype (Bg-2) * TRP_PTT: reproductive period in in photothermal unit of the control genotype (Bg-2) * TDIAM_M: Diameter at bolting of the control genotype (Bg-2) of the control genotype (Bg-2) in mm * TFITTOT2: total fruit length (set at 0 for plants that did not survive) of the control genotype (Bg-2) in mm Missing values: NA #### File: september.2012.data.light.txt **Description:** Raw data for the 2012 experiment (one measure per replicate) ##### Variables * Code: Positional code * Bloc: Bloc number * Traitement: Experimental year (2012 here) * Plateau: Tray number * Ligne: Line number on the tray * Colonne: Column number on the tray * Nom: Genetic family name * Region: Region of origin - Stands: Population of origin. These correspond to abbreviations of the closest locality's name. See the following table. | Pop | Locality | | :------- | :------------------------ | | ABA | Abaty | | ARR-1 | Arrigas | | ARR-2 | Arrigas | | ARR-3 | Arrigas | | BAU | Bauvin | | BEZ | Bez et Esparon | | BRE | Brendaouez | | BRI | Brillon | | CAT-S | Mont des Cats | | CAT-T | Mont des Cats | | CIRY | Ciry-le-Noble | | CON | Conforgien | | DIR-2.80 | Dirinon | | DIR-8.50 | Dirinon | | ENC-1 | Mont de l'Enclus | | ENC-2 | Mont de l'Enclus | | ESP1 | Esplechin | | ESP2 | Esplechin | | ETA-1 | Etang sur Arroux | | ETA-2 | Etang sur Arroux | | FOR | La Forest Landerneau | | GEN | Genech | | ISS | Issensac | | LCL | Lecelles | | LEC | Lecques | | LIE | Liernais | | MAR-3 | Marigny l'Eglise | | MAR-4 | Marigny l'Eglise | | MIL | Milizac | | MOL | Saint- Léger sous Beuvray | | MOU1-1 | Moussac | | MOU1-2 | Moussac | | MOU1-3 | Moussac | | MOU2 | Moussac | | NOZ | Nozières-Brignon | | PCH | Puechredon | | PLO | Plougastel-Daoulas | | PLY | Ploudiry | | QUI | Quissac | | RAD | Sainte-Radegonde | | ROC | La Roche Maurice | | RUM | Rumiqueal | | SAL | Salinelles | | TOU-J2 | Toulon sur Arroux | | TOU-M1 | Toulon sur Arroux | | TRE | Treflaouenan | | VED | St Jean de Vedas | | VEN | Vendargue | | WAV | Wavrin | * Type: Experiment name (Popfr here) * GERM_PTT: Time to germination in photothermal unit * BT_PTT: Time to bolting in photothermal unit * INT_PTT: Interval between bolting and flowering in photothermal unit * RP_PTT: reproductive period in in photothermal unit * DIAM_M: Diameter at bolting in mm * FITTOT2: total fruit length (set at 0 for plants that did not survive) in mm * TGERM_PTT: Time to germination in photothermal unit of the control genotype (Bg-2) * TBT_PTT: Time to bolting in photothermal unit of the control genotype (Bg-2) * TINT_PTT: Interval between bolting and flowering in photothermal unit of the control genotype (Bg-2) * TRP_PTT: reproductive period in in photothermal unit of the control genotype (Bg-2) * TDIAM_M: Diameter at bolting of the control genotype (Bg-2) of the control genotype (Bg-2) in mm * TFITTOT2: total fruit length (set at 0 for plants that did not survive) of the control genotype (Bg-2) in mm Missing values: NA ## Code/software Analyses.R: R code with all the analyses and graphics presented in the manuscript. get-popfr-bioWC2-compute-CG-bioclim.R: R code to download and compute worldclim 2.1 bioclimatic variables with the populations gps coordinates and climatic variables from our fieldsite in 2011 and 2012. ## Access information Other publicly accessible locations of the data: * na Data was derived from the following sources: * na