Trait data of Primula elatior from common garden experiments and field campaigns
Data files
Nov 07, 2023 version files 1.19 MB
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Primula_elatior_common_garden_data.zip
1.17 MB
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README.md
15.03 KB
Abstract
- Climate change and the resulting increased drought frequencies pose considerable threats to forest herb populations, particularly where additional environmental challenges jeopardize responses to selection. Specifically, habitat fragmentation may impede climate adaptation through its impact on the distribution of adaptive genetic variation, and cause evolutionary shifts in mating systems.
- To assess how habitat fragmentation disrupts climate adaptation, we conducted a common garden experiment with Primula elatior offspring originating from 24 populations sampled along a latitudinal gradient with varying climate and landscape characteristics. We then quantified a range of vegetative, regulatory, and reproductive traits under distinct soil moisture regimes to evaluate imprints of local adaptation and phenotypic plasticity. Additionally, we conducted a more extensive field campaign in 60 populations along the same latitudinal gradient to evaluate the potential evolutionary breakdown of reciprocal herkogamy.
- For large, connected populations, our results demonstrated an evolutionary shift from a strategy in southern populations that seems aligned with drought avoidance — where plants minimize their exposure to dry conditions and optimize photosynthesis — to a drought tolerance strategy in northern populations, where plants adapted to function despite water scarcity. However, habitat fragmentation disrupted climate clines and the adaptive responses to drought stress in key traits related to growth, biomass allocation and water regulation. Additionally, our findings indicate the onset of evolutionary breakdown in reciprocal herkogamy and divergence in other key flower traits. The disruption of climate clines, drought responses, and adaptations in mating systems contributed to a substantially diminished flowering investment across the distribution range, with the most pronounced effects observed in southern fragmented populations.
- Synthesis: We present novel empirical evidence of how habitat fragmentation disrupts climate adaptation and drought tolerance in a wide range of traits along the range of the forest herb Primula elatior. These findings emphasize the need to account for habitat fragmentation while designing effective conservation strategies in order to preserve and restore resilient meta-populations of forest herbs amidst ongoing global changes.
README: Trait data for common garden Primula elatior
Dataset DOI: https://doi.org/10.5061/dryad.3j9kd51r8
Description of the data and file structure
The dataset provides comprehensive trait data for Primula elatior, focusing on the impacts of climate change and habitat fragmentation. It includes field-based herkogamy data from 60 populations as well as greenhouse-based common garden trait data originating from 24 populations. Data cover various aspects of the plant's life cycle, from germination to adult traits, including morphological characteristics and flowering metrics. Some of the data have been pre-processed by machine learning techniques for image segmentation and classification (e.g. stomate, trichomes, and bee view). For a full description see the methods and appendices of the original article.
The dataset is divided into multiple Excel files for related traits, each addressing different aspects of the lifecycle:
00_explanatory_data.xlsx
This file provides background and explanatory data for the populations of Primula elatior sampled in the study. It includes geographical coordinates, population size, and other environment-related metrics.
| Header | Description | Units |
|---|---|---|
| Pop_code | Identifier for the population, consistent across all files | N/A |
| X_LAEA | X coordinate in Lambert Azimuthal Equal-Area projection | Metres (m) |
| Y_LAEA | Y coordinate in Lambert Azimuthal Equal-Area projection | Metres (m) |
| N_I | Population size | N Individuals (count) |
| Climate_PC1 | Principal Component 1 derived from WorldClim climate data | Unitless |
| Frag_PC1_2000 | Principal Component 1 derived from landscape configuration metrics, calculated with a 2000m buffer | Unitless |
Note: This file contains no missing data.
A_germination.xlsx
This file contains data related to the germination traits of Primula elatior seeds, under different treatments in a common garden experiment. Metrics such as the number of days for germination and percentage of successful germination are included.
| Header | Description | Units |
|---|---|---|
| Pop_code | Identifier for the population, consistent across all files | N/A |
| ID | Unique identifier for the petri dish and the corresponding treatment | N/A |
| Parent_ID | Identifier linking the seed to the parent plant | N/A |
| CG_main | Type of common garden experiment: CGM for vernalisation, CGD for no vernalisation | N/A |
| Germination_days | Number of days taken for the seed to germinate | Days |
| Germination_perc | Percentage of successful germination | Percentage (%) |
| bin_weights | Count of seeds in the petri dish used for the experiment | Count (number of seeds) |
Note: The 'Germination_days' column exhibits 0.62% missing data, which is attributable to instances of germination failure caused by fungal contamination of seeds during the germination stage, as well as potential sampling errors.
B_growth_rate.xlsx
This file contains data on the growth rates of Primula elatior from various life stages, ranging from seedling to adult. The data include metrics measured at different time points during the plant's growth.
| Header | Description | Units |
|---|---|---|
| Plant_ID | Unique identifier for the individual plant | N/A |
| Parent_ID | Identifier linking the plant to its parent | N/A |
| Pop_code | Identifier for the population, consistent across all files | N/A |
| CG_main | Type of common garden experiment: CGM for normal conditions, CGD for drought stress | N/A |
| GR_germ_to_adult | Growth rate from germination to adult stage | mm per day |
| GR_germ_to_seedling | Growth rate from germination to seedling stage | mm per day |
| GR_seedling_to_adult | Growth rate from seedling to adult stage | mm per day |
| GR_adult_to_final | Growth rate from adult stage to the end of the experiment | mm per day |
Note: In the 'B_growth_rate.xlsx' dataset, missing values within the 'GR_germ_to_adult' column (2.63%) and the 'GR_adult_to_final' column (15.76%) are attributable to instances of plant mortality, with the latter reflecting a loss of individuals at the final measurement interval.
C_allocation_all.xlsx
This file contains data on resource allocation in Primula elatior, focusing on metrics such as the root-shoot ratio. These metrics give insights into how the plant allocates its resources under different conditions.
| Header | Description | Units |
|---|---|---|
| Plant_ID | Unique identifier for the individual plant | N/A |
| Parent_ID | Identifier linking the plant to its parent | N/A |
| Pop_code | Identifier for the population, consistent across all files | N/A |
| CG_main | Type of common garden experiment: CGM for normal conditions, CGD for drought stress | N/A |
| BGM_AGM_ratio | Ratio of below-ground mass (root mass in grams) to above-ground mass (shoot mass in grams) | unitless |
| SLA_sqmm_mg | Specific leaf area, leaf area per unit leaf mass | mm²/mg |
Note: In the 'C_allocation_all.xlsx' dataset, the 'BGM_AGM_ratio' column, which denotes the root-to-shoot ratio, presents a missing data percentage of 1.78%. This absence is mainly attributed to fungal infections compromising root biomass and insect herbivory reducing leaf biomass, thereby impacting the measurement of biomass allocation between below-ground and above-ground plant parts.
D_stom_trich.xlsx
This file contains data on the leaf stomatal and trichome density of Primula elatior. These metrics are crucial for understanding the plant's response to environmental conditions like drought stress.
| Header | Description | Units |
|---|---|---|
| Plant_ID | Unique identifier for the individual plant | - |
| Parent_ID | Identifier linking the plant to its parent | - |
| Pop_code | Identifier for the population, consistent across all files | - |
| CG_main | Type of common garden experiment: CGM for normal conditions, CGD for drought stress | - |
| Sample_ID | Unique identifier for the leaf sample | - |
| stomata_abaxial | Density of stomata on the abaxial (lower) leaf surface | number/mm² |
| stomata_adaxial | Density of stomata on the adaxial (upper) leaf surface | number/mm² |
| trichome_abaxial | Density of trichomes on the abaxial (lower) leaf surface | number/mm² |
Note: In the 'D_stomatal_traits.xlsx' dataset, missing values for both 'stomata_abaxial' and 'trichome_abaxial' are reported at 14.20%, with 'stomata_adaxial' showing a lower missing data percentage at 3.11%. These gaps in data can be attributed to damage to the samples, which occurred during the process of creating imprints with nail varnish – a technique that did not uniformly succeed in producing clear, analyzable samples for microscopy.
E_flower_investment_phenology.xlsx
This file contains data on flowering investment and phenology of Primula elatior. It includes metrics related to the timing and investment in flowering.
| Header | Description | Units |
|---|---|---|
| Plant_ID | Unique identifier for the individual plant | N/A |
| Parent_ID | Identifier linking the plant to its parent | N/A |
| Pop_code | Identifier for the population, consistent across all files | N/A |
| CG_main | Type of common garden experiment: CGM for normal conditions, CGD for drought stress | N/A |
| mean_spring_days_4_degrees | Average number of spring days with temperatures above 4 degrees Celsius | days |
| flower_total | Total flower count | count |
| flower_means | Mean flower count | count |
| flowerMax | Maximum flower count | count |
| stalk_n | Number of stalks | count |
| stalk_height_mean | Mean height of flower stalks | cm |
| stalk_height_max | Maximum height of flower stalks | cm |
| FD_max | Maximum flower duration | days |
| FD_min | Minimum flower duration | days |
| FD_mean | Mean flower duration | days |
Note: In the 'F_floral_traits.xlsx' dataset, missing data for the columns 'flower_total', 'flower_means', 'flowerMax', 'stalk_n', 'stalk_height_mean', and 'stalk_height_max' is reported at approximately 14.61%. The 'mean_spring_days_4_degrees' column has a slightly lower missing percentage at 13.80%. The most substantial gaps in data are seen in 'FD_max', 'FD_min', and 'FD_mean', each with a missing percentage of 20.97%. These missing data occurrences are primarily due to the biological variability of the perennial species Primula elatior, which does not consistently produce flowers or stalks in its first or second year, leading to the absence of these measurements in a proportion of the samples.
F_bee_view.xlsx
This file contains data on flower colour metrics as they would be perceived by pollinators in Primula elatior. These metrics are crucial for studies related to pollinator attraction and plant reproduction.
| Header | Description | Units |
|---|---|---|
| flower_ID | Unique identifier for the individual flower | N/A |
| Plant_ID | Unique identifier for the individual plant | N/A |
| Parent_ID | Identifier linking the flower to its parent plant | N/A |
| Pop_code | Identifier for the population, consistent across all files | N/A |
| CG_main | Type of common garden experiment: CGM for normal conditions, CGD for drought stress | N/A |
| Q_25_UV_R | 0.25 quantile for UV Red | Reflectance (%) |
| Q_25_colour_B | 0.25 quantile for blue spectrum | Reflectance (%) |
| Q_25_colour_G | 0.25 quantile for green spectrum | Reflectance (%) |
| Q_50_UV_R | 0.5 quantile (median) for UV Red | Reflectance (%) |
| Q_50_colour_B | 0.5 quantile (median) for blue spectrum | Reflectance (%) |
| Q_50_colour_G | 0.5 quantile (median) for green spectrum | Reflectance (%) |
| Q_75_UV_R | 0.75 quantile for UV Red | Reflectance (%) |
| Q_75_colour_B | 0.75 quantile for blue spectrum | Reflectance (%) |
| Q_75_colour_G | 0.75 quantile for green spectrum | Reflectance (%) |
Note: In this table, the term "0.X quantile" is used to indicate the value below which a given percentage (X * 100%) of the data points fall. For example, the 0.5 quantile is the median value of the dataset. This file contains no missing data.
G_Herkogamy_plant.xlsx
This file contains data on herkogamy in Primula elatior, essential for assessing potential shifts in mating systems. It includes metrics such as stigma and anther heights, which were measured with a caliper, from two morph types: 'S' (short-styled) and 'L' (long-styled).
| Header | Description | Units |
|---|---|---|
| Pop_code | Identifier for the population, consistent across all files | N/A |
| P_ID | Unique identifier for the individual plant | N/A |
| Well_ID | Radseq genome sample ID | N/A |
| FL_MT | Morph type of a corresponding plant (ID) | S or L morph |
| MT_N | Flower count within that population | Count |
| MT_S | Count of evaluated S morphs within that population | Count |
| MT_L | Count of evaluated L morphs within that population | Count |
| SH | Stigma height, measured with a caliper | Millimetres (mm) |
| AH | Anther height, measured with a caliper | Millimetres (mm) |
| HE | Absolute difference between stigma and anther heights | Millimetres (mm) |
Note: This dataset comprises field-collected data spanning 60 populations across the species' range. In the "G_Herkogamy_plant.xlsx" dataset, the column 'Well_ID' has 78.33% missing data, which signifies that genomic analysis was not conducted for these samples. The remaining 21.67% of the samples that do possess 'Well_ID' information were subject to genomic analysis in conjunction with herkogamy trait assessment.
H_selfing.xlsx
This file contains data on self-compatibility in Primula elatior through manual self-pollination. It includes metrics such as the percentage of seeds pollinated and the count of evaluated flowers.
| Header | Description | Units |
|---|---|---|
| Plant_ID | Unique identifier for the individual plant | N/A |
| Parent_ID | Identifier linking the plant to its parent | N/A |
| Pop_code | Identifier for the population, consistent across all files | N/A |
| Seeds_poll_perc | Percentage of seeds that were successfully self-pollinated | Percentage (%) |
| bin_weights | Count of evaluated flowers | Count |
| MT | Morph type of the plant | S or L morph |
Note: In the 'H_selfing.xlsx' dataset, a small proportion of the morph type ('MT') data, representing either 'S' (short-styled) or 'L' (long-styled) morphs, is missing, which amounts to roughly 1.08%. This could potentially be attributed to occasional mislabelling or omissions during data collection.
I_Corolla Tube Width.xlsx
This file encompasses measurements pertaining to the corolla tube width of Primula elatior individuals. The data facilitate the examination of floral morphological variations within and across populations.
| Header | Description | Units |
|---|---|---|
| F_ID | Unique identifier for the flower | N/A |
| Plant_ID | Unique identifier for the individual plant | N/A |
| Parent_ID | Identifier linking the plant to its parent | N/A |
| Pop_code | Identifier for the population, consistent across all files | N/A |
| CG_main | Code for common garden experiment: CGM or CGD | N/A |
| CTW | Corolla tube width, measured with a caliper | Millimetres (mm) |
| MT | Morph type of the flower | S or L morph |
Note: This file contains no missing data and provides a comprehensive overview of the corolla tube widths across different morphs and populations.
Relationships Between Data Files, Missing Data Codes, and Abbreviations
- Pop_code: This is the identifier for the population and is consistent across all files. It allows for cross-referencing and merging data from different files.
- Parent_ID: This links the offspring plant to its parent.
- CG_main: Indicates the type of common garden experiment—either main treatment (CGM) or drought treatment (CGD). This is crucial for interpreting plant responses under different environmental conditions.
Additional Context
- Germination Experiment: The data related to germination was collected in a separate initial experiment. Seeds were monitored for germination success and lag time under controlled conditions.
- Common Garden: All other data (everything except germination and herkogamy) was collected in a common garden experiment but specimens originated from a subset of populations (24) that was analysed for herkogamy (60) and originated from a subset from the germination experiment.
- Herkogamy Field Data: The herkogamy metrics were collected in the field and include measurements such as stigma and anther heights, using a caliper. These are crucial for studies on potential shifts in mating systems.
Methods
The trait dataset was generated through a comprehensive research design aimed at investigating the impacts of climate change and habitat fragmentation on Primula elatior, a European forest herb. Data collection was structured into two main components: field-based seed and flower collection, and greenhouse-based common garden experiments.
Field-Based Seed and Flower Collection
Seeds were collected from 24 distinct populations of P. elatior, spanning a latitudinal gradient from southern France to northern Denmark. Each pair among the 24 populations was designed to include one population from a highly fragmented forest patch and another from a well-connected forest area, resulting in 12 unique pairs. These pairs were selected based on specific criteria that included measures of habitat fragmentation and connectivity, such as the Mean Patch Proximity Index and Mean Nearest Neighbour distance, population size, and a maximum elevation of 200m. In addition to seed collection, herkogamy was assessed in 60 populations (comprising 30 pairs) with a total of 2116 evaluated individuals, to examine the potential evolutionary breakdown in mating systems.
Greenhouse-Based Common Garden Experiment
The collected seeds underwent an initial germination experiment in petri dishes with perlite and water, under two treatments: one with vernalisation and one without. These seeds were monitored for germination success and lag time under controlled climate conditions. Seedlings were then transitioned into a controlled common garden greenhouse experiment, where they were cultivated under two distinct soil moisture regimes to assess their drought stress responses.
Additional Data Collection for Response Variables
A comprehensive array of response variables was meticulously recorded to cover the plant's lifecycle, from seed to adult.
- Germination Traits: Seeds in petri dishes were monitored for germination success and lag time under controlled conditions.
- Juvenile Growth Rate: Measured at specific time points from seedling to juvenile stage, capturing metrics such as growth rate in mm/day.
- Adult Plant Traits: Includes adult growth rate, root-shoot ratio, and specific leaf area, measured at designated time points.
- Leaf Morphology: Both abaxial and adaxial stomatal density, as well as abaxial glandular trichome density, were evaluated using microscopic imaging and a custom convolutional neural network model.
- Flower Phenology: Captured metrics related to the timing of flowering events, such as the lag time before flowering.
- Flowering Investment Metrics: A composite metric of flower traits was derived using PCA, including the total count of produced flowers, stalk height, and flower opening duration.
- Flower Colour Metrics: Evaluated using macro-photography and image segmentation algorithms to assess visual pollinator signalling.
- Self-Compatibility: Assessed through manual self-pollination techniques in a controlled environment.
- Herkogamy: Stigma and anther heights were measured in the field using a digital caliper for 60 populations to assess potential evolutionary breakdown in mating systems.
The dataset has been subjected to rigorous quality assurance, including validation steps for the neural network models used for image classification. For detailed methodologies, including the procedures and tools used for each trait, please see the main manuscript and appendices.