Biotic interactions promote local adaptation to soil in plants - Supplementary data
Data files
May 29, 2024 version files 699.50 KB
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README.md
8.52 KB
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Supplementary_Data_1.csv
183.56 KB
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Supplementary_Data_2.csv
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May 28, 2024 version files 699.49 KB
Abstract
Although different ecological factors shape adaptative evolution in natural habitats, we know little about how their interactions impact local adaptation. Here we used eight generations of experimental evolution with outcrossing Brassica rapa plants as a model system, in eight treatment groups that varied in soil type, herbivory (with/without aphids), and pollination mode (hand- or bumblebee-pollination), to study how biotic interactions affect local adaptation to soil. First, we show that several plant traits evolved in response to biotic interactions in a soil-specific way. Second, using a reciprocal transplant experiment, we demonstrate that significant local adaptation to soil-type evolved in the “number of open flowers”, a trait used as a fitness proxy, but only in plants that evolved with herbivory and bee pollination. Whole genome re-sequencing of experimental lines revealed that biotic interactions caused a 10-fold increase in the number of SNPs across the genome with significant allele frequency change, and that alleles with opposite allele frequency change in different soil types (antagonistic pleiotropy) were most common in plants with an evolutionary history of herbivory and bee pollination. Our results demonstrate that the interaction with mutualists and antagonists can facilitate local adaptation to soil type through antagonistic pleiotropy.
README: Supplementary Data
https://doi.org/10.5061/dryad.k98sf7mfm
Description of the data and file structure
File Name: Supplementary Data 1. Dataset.
Description: Traits values of plants growing in different soil (L = limestone, T= Tuff), and in different soil treatment (fertilizer: with use of fertilizer, nofertilizer: without use of fertilizer, standardized: grown in standardized soil, which provides optimal conditions for cultivation).
Plantlabel: Identity of plants during the experiment
PlantlabelDNA: Identity of plants for DNA collection (Labels used for DNA sequences, available on the platform NCBI).
Replicate: Replicate of the experiment
Generation: either plants from the initial population (generation one) or evolved plants (generation 10)
Soil: soil in which plants grew during the experiment
Soilline: Soil in which plants evolved during the experimental evolution
Herbivoryline: herbivory treatment in which plant evolved during the experiment evolution (NH: non herbivory; H: herbivory)
Pollinationline: pollination treatment in which plant evolved during the experiment evolution (B: bumblebee, H: hand pollination)
Treatment: overal treatment in which plant evolved during the experiment evolution
Native soil: Binary variable determining whether plants are growing in their native soil during the reciprical transplant experiment
Seedssownout: refers to the number of seeds used for germination
Germination: refers to the number of seeds that germinated
Germination rate (%)
Weightperseed: refers to the average weight per seed used for germination (mg)
NbFlowers: number of open flower during choice tests
Height: plant height during choice tests in cm
Leaf_size: product of leaf length and leaf width, divided by 2; expressed in cm2
Lengthperbranche: average length per branche (in cm)
Timetofirstflower: onset of flowering after germination (days)
Flowerproduction: total flower production between flowering onset and choice tests.
Flowerdiameter: average flower diameter of three flowers (in mm)
Petal_width: average petal width of three flowers (cm)
Style: average style length of three flowers (cm)
Stamen: average stamen length of three flowers (cm)
Herkogamy: average difference between style and stamen length (cm)
Visits: corresponds to how many bees visited the plants during the choice tests.
MatriceNb: corresponds to identity of the different matrices of choice tests
File name: Supplementary Data 2. Dataset.
Description: Phenotypic, attractiveness and reproductive traits among first and seven generation plants and those having evolved with or without aphid-herbivory, with or without bee-pollination and either in limestone or tuff soil. LHB: limestone line plants (L) growing with aphid-herbivory (H) and bee-pollination (B). LHH: limestone line plants (L) growing with aphid-herbivory (H) and hand-pollination (H). LNHB: limestone line plants (L) growing without herbivory (NH) and bee-pollination (B). LNHH: limestone line plants (L) growing without herbivory (NH) and hand-pollination (H). THB: tuff line plants (T) growing with aphid-herbivory (H) and bee-pollination (B). THH: tuff line plants (T) growing with aphid-herbivory (H) and hand-pollination (H). TNHB: tuff line plants (T) growing without herbivory (NH) and bee-pollination (B). TNHH: tuff line plants (T) growing without herbivory (NH) and hand-pollination (H).
ID: Identity of plants during the experiment
Generation: Corresponds the generation to which plants belong (1:10)
Replicate: Replicate of the experiment
Soilline: Soil in which plants evolved during the experimental evolution
Pollinationline: pollination treatment in which plant evolved during the experiment evolution (B: bumblebee, H: hand pollination)
Herbivoryline: herbivory treatment in which plant evolved during the experiment evolution (NH: non herbivory; H: herbivory)
Treatment: overal treatment in which plant evolved during the experiment evolution
Nb_silliques: number of silliques produced by plants
Nb_seeds: number of seeds produced by plants during the experimental evolution
Nb_seeds_per_sillique: average number of seeds contained in each sillique
Relativeseedset: relative seed set of the plant within the population. This value is proportionnal to the number of seeds produced by other plants of the same population (see paper for more details on formula).
Visits: corresponds to how many bees visited the plants during pollination
Timetofirstflower: onset of flowering after germination (days)
Height: plant height during pollination in cm
NbFlowers: number of open flower during pollination
logNectar: corresponds to nectar production of plants per flower (expressed in uL and then log(x+1) transformed)
Flowerdiameter: average flower diameter of three flowers (in mm)
Petal_area: average petal area of three flowers (cm2)
Petal_length: average petal length of three flowers (cm)
Petal_width: average petal width of three flowers (cm)
Style: average style length of three flowers (cm)
Stamen: average stamen length of three flowers (cm)
Herkogamy: average difference between style and stamen length (cm)
LNBenzaldehyde: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1) transformed)
LN_1_Butene_4_isothiocyanate: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1) transformed)
LN_Methyl_benzoate: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1) transformed)
LN_Phenylethyl_Alcohol: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1) transformed)
LN_2_Amino_benzaldehyde: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1) transformed)
LN_p_Anisaldehyde: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1) transformed)
LN_Methyl_anthranilate: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1)transformed)
LN_Z_3_Hexen_1_ol_acetate: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1)transformed)
LN_Phenylacetaldehyde: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1)transformed)
LN_Benzyl_nitrile: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1)transformed)
LN_Methyl_salicylate: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1)transformed)
LN_Indole: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1) transformed)
LN_E.E_a_Farnesene: floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1) transformed)
LN_Totalvolatiles: total floral volatile emission expressed in pg.l-1
.h-1
.flower-1
(LN(x+1) transformed)
Software uploaded to Zenodo
File name: Supplementary Data 3. R Script.
Description: Script to produce the allele frequency change matrix. Fq.gz files are available on NCBI under the project PRJNA1105729. Both generation 1 and generation 10 of our experimental evolution were sequenced when growing in either local or foreign soil. This script requires the loading of the following packages: library('learnPopGen'), library ('tidyverse'), library ('vroom'), library(data.table), library (poolSeq), library (harmonicmeanp), library (remotes), library(ACER), library(plyr)
File name: Supplementary Data 4. R Script.
Description: Script for calculating the breeding values for markers, and merge them with the AF change matrix; check for conditional neutrality and antagonistic pleiotropy pattern in AF change. Fq.gz files are available on NCBI under the project PRJNA1105729. Both generation 1 and generation 10 of our experimental evolution were sequenced when growing in either local or foreign soil. This script requires the loading of the following packages: library(data.table), library(R.utils), library(rrBLUP), library(tidyverse), library (ggplot2), library(wesanderson),l ibrary("RColorBrewer"), library(plyr)
File name: Supplementary Data 5. R Script.
Description: Script to produce the list of annotate genes from the marker matrix. Fq.gz files are available on NCBI under the project PRJNA1105729. Both generation 1 and generation 10 of our experimental evolution were sequenced when growing in either local or foreign soil. This script requires the loading of the following packages: library(dplyr), library(GenomicRanges), library(data.table), library(tidyverse)
Methods
Plant, Brassica rapa, phenotype and genotype were measured. Samples result from a 8 generations experimental evolution where selective agents were different soils, herbivory and pollinators (Dorey and Schiestl 2024). Sample size for trait measurements was 36 per replicate, this was chosen according to previous studies, and values published in the literature (Gervasi and Schiestl 2017, Ramos and Schiestl 2020, Dorey and Schiestl 2024). For trait measurements and DNA extraction, we used all individuals if available (some plants lacked sufficient leaf tissue for DNA extraction).