DOI: 10.5061/dryad.bcc2fqznn
title: Data from: Inversions contribute disproportionately to parallel genomic divergence in dune sunflowers

description: The probability of parallel genetic evolution is a function of the
 strength of selection and constraints imposed by genetic architecture.
 Inversions capture locally adapted alleles and suppress recombination
 between them, which limits the range of adaptive responses. Also, the
 combined phenotypic effect of alleles within inversions is likely to be
 greater than that of individual alleles, which should further increase the
 contributions of inversions to parallel evolution. We tested the
 hypothesis that inversions contribute disproportionately to parallel
 genetic evolution in independent dune ecotypes of Helianthus petiolaris.
 We analyzed habitat data and identified variables underlying parallel
 habitat shifts. Genotype-environment association analyses of these
 variables indicated parallel responses of inversions to shared selective
 pressures. We also confirmed larger seed size across the dunes and
 performed quantitative trait locus (QTL) mapping with multiple crosses.
 QTL shared between locations fell into inversions more than expected by
 chance. We used whole-genome sequencing data to identify selective sweeps
 in the dune ecotypes and found that the majority of shared swept regions
 were found within inversions. Phylogenetic analyses of shared regions
 indicate that within inversions the same allele typically was found in the
 dune habitat at both sites. These results confirm predictions that
 inversions drive parallel divergence in the dune ecotypes. 
description: This dataset includes:  Habitat
 data collected from areas where wild <em>H. petiolaris
 </em>sunflowers grow Seed size data collected
 from <em>H. petiolaris</em> growing in the wild and under
 common garden conditions Unfiltered vcfs used for QTL
 mapping seed size and looking for genotype environement
 associations Genomic locations of previously
 identified haploblocks (inversions) within <em>H.
 petiolaris</em>  Inversion genotypes for the
 QTL mapping populations  Please see the
 README file and associated publication for more complete descriptions of
 each dataset.
description: # Data from: Inversions contribute disproportionately to parallel genomic
 divergence in dune sunflowers
 [https://doi.org/10.5061/dryad.bcc2fqznn](https://doi.org/10.5061/dryad.bcc2fqznn) ## Description of the data and file structure ### Files and variables #### File: Habitat\_data\_clean.csv **Description:** Habitat data collected from multiple locations where dune and non-dune populations of sunflowers grow. New data was collected for the populations near Monahans Sandhills State Park in Texas. We established a transect through each population and picked 5 sites for habitat analysis at even intervals along those transects. At each site, we took a photo of a 0.65 m2 quadrat and used ImageJ to determine the proportion of vegetative cover and grass cover. Soil samples were taken from 25 cm deep, dried at 60 °C for 24 h, and pooled from the 5 sites at each population. Available phosphorus, and exchangeable potassium, magnesium, and calcium were measured at A&L Eastern Laboratories (Richmond, VA) and total nitrogen content was determined by Micro-Dumas Combustion (NA1500, Carlo Erba Strumentazione, Milan, Italy) at the University of Georgia Analytical Chemistry Laboratory. The data for populations near Great Sand Dunes National Park and Preserve is from Andrew, R.L., Ostevik, K.L., Ebert, D.P. and Rieseberg, L.H., 2012. Adaptation with gene flow across the landscape in a dune sunflower. *Molecular Ecology* 21: 2078-2091. ##### Variables * location: whether a population was near Monahans Sandhills State Park (MON) or Great Sand Dunes National Park and Preserve (GSD) * pop: population name * type: whether a population is dune (D) or non-dune (N)  * mean.percent.cover: proportion of quadrats covered by vegetation (average of 5 sites)  * percent.grass: proportion of quadrats covered by grass (average of 5 sites)  * total.N: total nitrogen (%*1000) in soil * P: phosphorus (ppm) in soil * K: potassium (ppm) in soil * Mg: magnesium (ppm) in soil * Ca: calcium (ppm) in soil #### File: haploblocks.petfal.txt **Description:** The locations of haploblocks (inversions) in *Helianthus petiolaris* based on Todesco, M., Owens, G.L., Bercovich, N., Légaré, J.S., Soudi, S., Burge, D.O., Huang, K., Ostevik, K.L., Drummond, E.B., Imerovski, I. and Lande, K., 2020. Massive haplotypes underlie ecotypic differentiation in sunflowers. *Nature* 584: 602-607. ##### Variables * name: haploblock name * chr: chromosome location of haploblock * start: base pair position of the start of the haploblock * end: base pair position of the end of the haploblock #### File: inv\_gt.WGS\_RF.NEG1.txt **Description:** Inversion genotypes for mapping population MON1. For genotyping scripts, see [https://github.com/hkchi/Dune_parallelism](https://github.com/hkchi/Dune_parallelism) ##### Variables * haploblock: name of the haploblock (inversion) * name: mapping population individual ID * WGS-FR-genotype: genotype of the inversion (0=homozygous for wildtype, 1=heterozygous, 2=homozygous for inversion) #### File: inv\_gt.WGS\_RF.NEG2.txt **Description:** Inversion genotypes for mapping population MON2. For genotyping scripts, see [https://github.com/hkchi/Dune_parallelism](https://github.com/hkchi/Dune_parallelism) ##### Variables * haploblock: name of the haploblock (inversion) * name: mapping population individual ID * WGS-FR-genotype: genotype of the inversion (0=homozygous for wildtype, 1=heterozygous, 2=homozygous for inversion) #### File: inv\_gt.WGS\_RF.PET1.txt **Description:** Inversion genotypes for mapping population GSD2. For genotyping scripts, see [https://github.com/hkchi/Dune_parallelism](https://github.com/hkchi/Dune_parallelism) ##### Variables * haploblock: name of the haploblock (inversion) * name: mapping population individual ID * WGS-FR-genotype: genotype of the inversion (0=homozygous for wildtype, 1=heterozygous, 2=homozygous for inversion) #### File: inv\_gt.WGS\_RF.PET2.txt **Description:** Inversion genotypes for mapping population GSD1. For genotyping scripts, see [https://github.com/hkchi/Dune_parallelism](https://github.com/hkchi/Dune_parallelism) ##### Variables * haploblock: name of the haploblock (inversion) * name: mapping population individual ID * WGS-FR-genotype: genotype of the inversion (0=homozygous for wildtype, 1=heterozygous, 2=homozygous for inversion) #### File: MON\_seed\_size\_data.csv **Description:** Seed size data collected from plants grown in the wild and in a common garden ##### Variables * experiment: whether seeds were collected from plants grown in the wild or in a common garden * ecotype: the ecotypes (dune or non-dune) of the plant phenotyped * pop: the population that the plant phenotyped was collected * mom: the individual ID of the plant phneotyped * weight: the average weight of a seed (mg) produced by the plant #### File: GSD\_SS\_GBS\_NGM\_GATK\_total.vcf.gz **Description:** An unfiltered vcf that includes genotype calls for all the individuals sequenced as part of the GSD seed size QTL mapping. For the genotyping scripts, see [https://github.com/hkchi/Dune_parallelism](https://github.com/hkchi/Dune_parallelism) #### File: QTL\_SS\_data.csv **Description:** Seed size data collected from all the individuals from MON and GSD mapping populations grown in a common garden ##### Variables * type: variable based on map_pop, generation, and cytoplasm (see below) * map_pop: which of the four mapping populations (MON1, MON2, GSD1, GSD2) the individual belongs to * generation: the generation (parent, F1, F2) that the individual belongs to * cytoplasm: whether the individual has a dune or non-dune cytoplasm (this depends on the direction of cross made) * weight: the weight of an average seed (mg) produced by this individual #### File: MON\_SS\_GBS\_NGM\_GATK\_total.vcf.gz **Description:** An unfiltered vcf that includes genotype calls for all the individuals sequenced as part of the MON seed size QTL mapping. For the genotyping scripts, see [https://github.com/hkchi/Dune_parallelism](https://github.com/hkchi/Dune_parallelism) #### File: NegPG\_GBS\_NGM\_GATK\_total.vcf.gz **Description:** An unfiltered vcf that includes genotype calls for all the individuals sequenced for the GEA analyses at MON. For the genotyping scripts, see [https://github.com/hkchi/Dune_parallelism](https://github.com/hkchi/Dune_parallelism) ## Access information Other publicly accessible locations of the data: * Andrew, R.L., Ostevik, K.L., Ebert, D.P. and Rieseberg, L.H., 2012. Adaptation with gene flow across the landscape in a dune sunflower. Molecular Ecology 21: 2078-2091. * Todesco, M., Owens, G.L., Bercovich, N., Légaré, J.S., Soudi, S., Burge, D.O., Huang, K., Ostevik, K.L., Drummond, E.B., Imerovski, I. and Lande, K., 2020. Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584: 602-607. Data was derived from the following sources: * vcfs were derived from sequences uploaded to the SRA ([PRJNA1145483](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1145483) and [PRJNA1145296](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1145296)) and scripts found at [https://github.com/hkchi/Dune_parallelism](https://github.com/hkchi/Dune_parallelism)