Data from: The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers
Data files
Nov 01, 2023 version files 6.22 MB
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F2-Greenhouse-2014.txt
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key.txt
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markerbp.map
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README.md
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Rqtl-pheno.csv
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tassel.ped
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Toll-v2-tassel_imputed_parents_FSFHap_DontUseHeterozygousCalls_kosambi_all2022.map
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Toll-v2-tassel_imputed_parents_FSFHap_DontUseHeterozygousCalls.csv
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Toll-v2-tassel_imputed_parents_FSFHap_DontUseHeterozygousCalls.raw
Abstract
The floras on chemically and physically challenging soils, such as gypsum, shale, and serpentine, are characterized by narrowly endemic species. The evolution of edaphic endemics may be facilitated or constrained by genetic correlations among traits contributing to adaptation and reproductive isolation across soil boundaries. The yellow monkeyflowers in the Mimulus guttatus species complex are an ideal system in which to examine these evolutionary patterns. To determine the genetic basis of adaptive and prezygotic isolating traits, we performed genetic mapping experiments with F2 hybrids derived from a cross between a serpentine endemic, M. nudatus, and its close relative M. guttatus. Few large effect and many small effect QTL contribute to interspecific divergence in life history, floral and leaf traits, and a history of directional selection contributed to trait divergence. Loci contributing to adaptive traits and prezygotic reproductive isolation overlap, and their allelic effects are largely in the direction of species divergence. These loci contain promising candidate genes regulating flowering time and plant organ size. Together our results suggest that genetic correlations among traits can facilitate the evolution of adaptation and speciation and may be a common feature of the genetic architecture of divergence between edaphic endemics and their widespread relatives.
README: The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers
Katherine Toll and John Willis:
Phenotype and genotype files used for QTL analysis
Description of the Data
F2-Greenhouse-2014.txt: Phenotype file of parental lines, F1 hybrids and F2 hybrids. Column headers:
- Plant individual plant ID
- Type Parental line, F1 or F2
- DTG days to germination from planting of seed
- DTF days to flowering (calculated by subtracting the flowering date by the germination date)
- Fl_Node the node of first flower
- First_Internode_cm the length of the first internode in centimeters, indicating whether plants bolted (transitioned to flowering) between the cotyledons and first leaf pair
- Height_cm plant height at flowering in centimeters
- Corolla_Width_cm the width of the corolla in centimeters
- Corolla_Length_cm the length of the corolla in centimeters
- bladeArea the area of the leaf in cm^2 (determined from leaf scans in ImageJ)
- WL leaf width to length ratio (leaf shape)
Individuals with missing data (indicated by NA) are plants that did not flower in the greenhouse or whose first leaf was damaged and could not be scanned, or have traits that were not measured on the date of first flower.
Rqtl-pheno.csv: Phenotype file of just F2s for QTL mapping. Column headers:
- DaysToFlowering - days to flowering (calculated by subtracting the flowering date by the germination date)
- FlowerNode the node of first flower
- FirstInternodeLength the length of the first internode in centimeters, indicating whether plants bolted (transitioned to flowering) between the cotyledons and first leaf pair
- Height plant height at flowering in centimeters
- CorollaWidth the width of the corolla in centimeters
- CorollaLength the length of the corolla in centimeters
- LeafArea the area of the leaf in cm^2 (determined from leaf scans in ImageJ)
- LeafWidthLengthRatio leaf width to length ratio (leaf shape)
Individuals with missing data (indicated by NA) are plants whose first leaf was damaged and could not be scanned or have traits that were not measured on the date of first flower.
key.txt - text file needed to parse F2s and parental sequences by barcode in TASSEL
tassel.ped - text file containing pedigree needed to run FSFHap
Toll-v2-tassel_imputed_parents_FSFHap_DontUseHeterozygousCalls.csv: F2 genotypes imputed using FSFHap in TASSEL. Column headers:
- id individual F2 ID
- remaining headers indicate the chromosome and base pair positions for corresponding genotypes (e.g., S1_138791 is chromosome 1 base pair position 138791)
Toll-v2-tassel_imputed_parents_FSFHap_DontUseHeterozygousCalls.raw the mapmaker file created in R/qtl by merging the phenotype and genotype files (Toll-v2-tassel_imputed_parents_FSFHap_DontUseHeterozygousCalls.csv)
Toll-v2-tassel_imputed_parents_FSFHap_DontUseHeterozygousCalls_kosambi_all2022.map: the linkage map generated with onemap (using onemap.R)
Description of R code on Zenodo
tassel.sh - commands for running the TASSEL5 GBS v2 pipeline on the cluster
phenotype_analysis.R - code to analyze parental, F1, and F2 data
onemap.R - code to generate linkage map
Rqtl_2022.R - code to perform QTL mapping
Methods
Phenotypic data was collected in a greenhouse, genotype data was generated using multiplexed shotgun genotyping.
Usage notes
All phenotypic and genetic data uploaded was analyzed in R. Additional files are included for analyzing raw sequence reads in TASSEL.