DOI: 10.5061/dryad.t1g1jwt64
title: Data from: The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers

description: 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.
description: Phenotypic data was collected in a greenhouse, genotype data was
 generated using multiplexed shotgun genotyping.
description: All phenotypic and genetic data uploaded was analyzed in R.
 Additional files are included for analyzing raw sequence reads in
 TASSEL.
description: # 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