DOI: 10.5061/dryad.pvmcvdnxr
title: Novel major loci shape habitat-associated flowering time variation in Yellowstone monkeyflowers

description: Plants harbor remarkable genetic diversity in flowering phenology,
 particularly in their responses to environmental cues such as photoperiod.
 Understanding the genetic basis of repeated evolution in flowering cues,
 which are key to reproduction, illuminates adaptation with gene flow and
 parallel evolution. We characterized variation in minimum critical
 daylength for flowering (MCD) in yellow monkeyflower (Mimulus guttatus)
 accessions from a geothermal soil mosaic in Yellowstone National Park,
 mapped loci underlying the most extreme MCD in focal thermal annuals, and
 investigated environmental variables shaping phenology in the field.
 Yellowstone monkeyflowers range in MCD from 12-15 hours, paralleling
 range-wide variation in M. guttatus; plants from thermal habitats flower
 under significantly shorter daylengths. Two QTLs govern the most extreme
 12-hour MCD. Both contain candidates from gene families previously
 implicated in phenological evolution in monkeyflowers and other
 angiosperms, but the major loci appear novel. The frequency of 12-hour
 flowering across a microgeographic gradient is predicted by variation in
 soil temperature and the timing of dry-down. Adaptation to Yellowstone’s
 geothermal soil mosaic has generated dramatic evolution of flowering cues
 over short spatial scales. The genetic basis of 12-hour flowering does not
 indicate re-use of known M. guttatus alleles, but strong candidate genes
 nonetheless suggest molecular parallelism.
description: # Novel major loci shape habitat-associated flowering time variation in
 Yellowstone monkeyflowers Dataset DOI:
 [10.5061/dryad.pvmcvdnxr](10.5061/dryad.pvmcvdnxr) ## Description of the
 data and file structure These files contain the data for experiments
 investigating the diversity, genomic basis, and environmental influences
 on minimum daylength for flowering in Yellowstone National Park (YNP)
 *Mimulus guttatus*. * inbredLine_Daylength_screen_forDryad.txt contains
 information about which YNP inbred lines flowered under 12, 13, 14, and
 15-hour days. - AHQsd_linkage_mapforDryad and AHQsd_QTL_map_forDryad.txt
 contain the data from QTL mapping of 12-hour flowering using an AHQT x
 AHQN (thermal x nonthermal) F2 mapping population. *
 sd6_inbredLines_genotypes_forDryad.txt contains genotypes from
 whole-genome sequenced inbred lines, within the strongest daylength QTL on
 Chr 6. - sd11_mafClust_WGS_med_stand_coverage_forDryad.txt contains
 median-standardized coverage values for each site within a cluster of MADs
 affecting flowering transcription factors, which are within the second
 12-hour flowering QTL on Chr 11. * AHQCanyon_12h_growout_forDryad.txt
 contains data from a growout of wild-collected seeds in a gradient from
 highly thermal habitat to highly nonthermal habitat, under 12-hour days. -
 AHQgradient_tempscleansynched_forDryad.txt contains soil and air
 temperature data in the field along quadrats in a thermal - nonthermal
 gradient. * AHQ_soilMoisture_forDryad.txt contains soil moisture
 measurements in the field in the same quadrats as the temperature data.
 ### Files and variables **File:
 sd11_mafClust_WGS_med_stand_coverage_forDryad.txt**
 **Description:** median-standardized coverage at each site in the cluster
 of MADs affecting flowering transcription factors on Chr 11. **Variables**
 * CHROM: chromosome. All genes are on Chromosome 11. * POS: bp position on
 chromosome 11 * gene_name: Gene name from the AHQTv1 reference genome *
 AHQN: inbred line whole genome sequence from nonthermal parent. The AHQN
 column shows median-standardized coverage for AHQN. at those sites. *
 AHQT: inbred line whole genome sequence from thermal parent. The AHQT
 column shows median-standardized coverage for AHQT. **File:
 sd6_inbredLines_genotypes_forDryad.txt** **Description:** contains
 genotypes from whole-genome sequenced inbred lines, within the 12-hour
 flowering QTL on Chr 6. **Variables** * bp: base pair position on
 Chromosome 6, AHQTv1 reference genome * individual: all other columns are
 individual inbred line. genotypes are coded as 0 for homozygous reference,
 1 for heterozygous, and 2 for homozygous alternate. **File:
 AHQsd_QTL_map_forDryad.txt** **Description:** QTLCartographer mapping
 results for 12-hour flowering in an AHQTxAHQN F2 mapping population
 **Variables** * Chromosome: M. guttatus IM62v2 Chromosome Number (1 - 14)
 * Marker: Marker number * Position (cM): position in centimorgans *
 columns D - U: QTLCartographer mapping results **File:
 inbredLine_Daylength_screen_forDryad.txt** **Description:** contains
 information about which YNP inbred lines flowered under 12, 13, 14, and
 15-hour days. **Variables** * Light: hours of daylength (12, 13, 14,
 15-hour days) * Site-habitat: Habitat call (thermal annual or nonthermal
 perennial\_ * Line: inbred line identity * N Rows: number of replicates *
 proportion_flowered: proportion of replicates that flowered * canFlower:
 whether a line can flower under the specified daylength **File:
 AHQsd_linkage_mapforDryad.txt** **Description:** Linkage map from AHQT x
 AHQN (thermal x nonthermal) F2 mapping population. F2 ddRAD sequence were
 aligned to the M. guttatus IM62v2 reference genome. **Variables** * pos:
 chromosome_bp position on the *M. gutattus* IM62v2 reference genome. * cm:
 centimorgan position of the marker * remaining columns: individual F2
 names. Flowered.yes.no indicates whether they flowered under 12-hour days.
 Genotypes are coded as A, H, B. Genotypes are coded as A, H, B. A =
 homozygous nonthermal genotype, H = heterozygote, B = homozygous thermal
 genotype. **File: AHQCanyon_12h_growout_forDryad.txt** **Description:**
 data from a growout of wild-collected seeds in a gradient from highly
 thermal habitat to highly nonthermal habitat, under 12-hour days.
 **Variables** * Plate: Number of 96-well flat the individual was planted
 in during the experiment. * ID: identity of the maternal individual from
 which the seeds were collected in the greenhouse * Flower_binary: whether
 the individual flowered under 12-hour days. A blank line means the
 individual died before flowering was recorded. * Flowered yes/no: verbal
 description of whether individual flowered. “dead” means the individual
 died before flowering was recorded. * Habitat: area in which the maternal
 individual was collected (Canyon, AHQT, or AHQN). **File:
 AHQgradient_tempscleansynched_forDryad.txt** **Description:** soil and air
 temperature data in the field along quadrats in a thermal - nonthermal
 gradient. Blank cells indicate that no temperature was recorded.
 **Variables** * Quad#: Number of the quadrat at which temperature data was
 collected * Quadname: name of the quadrat at which temperature data was
 collected * AHQlocation: area of the gradient at which temperature was
 collected (T_upper for AHQT, T_canyon for AHQ Canyon, or N_bog for AHQN *
 Type: indicates wither plant temperature (at plant height) or soil
 temperature (beneath the soil) * Date/Time: Time stamp from data logger in
 the format m/dd/yyyy  h:mm:ss AM/PM * Date: Date in format m/dd/yy * Year:
 Year temperature was recorded * Month: month temperature was recorded (1 –
 12) * Day: day of month temperature was recorded * Time: time temperature
 was recorded (0 – 24) * tempC: temperature in degrees Celsius * am/pm:
 whether time recorded was AM or PM **File: AHQ_soilMoisture_forDryad.txt**
 **Description:** soil moisture measurements in the field in the same
 quadrats as the temperature data. **Variables** * year: year moisture data
 was collected * month: month moisture data was collected (1 – 12) * day:
 day of month moisture data was collected * Sample Date: date sample was
 collected (mm/dd/yy) * Quad#: number of the quadrat at which data was
 collected * Quadname: name of quadrat at which data was collected * T0:
 Mass of soaked toothpick (mg) * T2: Mass of dried toothpick (Mg) * Water:
 difference in mass between wet and dry toothpick * Habitat: area of
 quadrat (N_bog = AHQN, Canyon = AHQCanyon, AHQT = AHQT) * Max: proportion
 water saturation of toothpick (0 – 1), calibrated to maximum saturation.
 If T2 &gt; T0, saturation was considered to be 1 (fully saturated) ##
 Code/software ddRAD sequence of AHQT x AHQN F2's were processed using
 the Fishman Lab genotype processing pipeline, described in detail here:
 [https://www.protocols.io/view/processing-ddrad-data-from-raw-fastqs-to-vcf-q26g7bor3lwz/v1](https://www.protocols.io/view/processing-ddrad-data-from-raw-fastqs-to-vcf-q26g7bor3lwz/v1) Whole genome sequences were aligned with the package bwa mem with default parameters and genotypes with the package GATK-4.0. ## Access information Other publicly accessible locations of the data: * All ddRAD sequence are available on the sequence read archive, [PRJNA1051082](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1051082) * All whole genome sequence data are available on the sequence read archive, [PRJNA1050826](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1050826)