Investigating putative hybrids of Fremontodendron decumbens and F. californicum in the Sierra foothills
Data files
Oct 20, 2025 version files 21.12 GB
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blm_frem_raw.vcf.gz
21.12 GB
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FREM_samples_master_clean.csv
39.22 KB
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Fremontodendron_Morph_Study_8-28-23.csv
19.22 KB
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README.md
4.84 KB
Abstract
Fremontodendron (Flannelbush, Fremontia, Malvaceae) is a genus of shrubs native to California, Arizona, and Baja California Norte. There are three species in the genus: Fremontodendron californicum is widespread throughout the range and is highly variable in its appearance, F. mexicanum is endemic to Otay mountain in Southern California, and F. decumbens is endemic to gabbro soils in the Sierra Nevada foothills. Fremontodendron decumbens is currently only known from the Pine Hill Preserve and adjacent areas in El Dorado County and was listed as endangered in 1996. Fremontodendron decumbens is mainly distinguished from F. californicum by its orange or reddish flowers and decumbent habit. Many plants with a decumbent habit but lacking the floral characters to be placed in F. decumbens have been collected over the years, primarily in the Northern Sierra Nevada/Cascade foothills and there has long been speculation as to whether these could be hybrids between F. californicum and F. decumbens. Here we investigated the potential hybrid origin of morphologically intermediate individuals using full genome resequencing data from 99 individuals of F. californicum, F. decumbens and potential hybrids, mapped to a F. californicum reference genome. We investigated population structure and potential admixture using principal components analysis, model-based evolutionary clustering, and D-statistics, as well as additional analyses. We also systematically investigated the morphology of F. californicum, F. decumbens, and potentially intermediate individuals, by measuring a suite of 10 characters in the field on 68 individuals. We found no evidence that the morphologically intermediate forms are of hybrid origin; rather, they generally group genetically with F. californicum. We also found that specimens from populations noted to be morphologically intermediate showed considerable overlap with F. californicum, but not F. decumbens, based on a morphological principal components analysis. The results lead us to conclude that F. decumbens is indeed a genetically distinct taxon, and that individuals of F. californicum with a decumbent habit, but lacking the distinct floral characters of F. decumbens, are not the results of hybridization. This dataset archives the VCF used for performing all analyses as well as the morphological data.
Dataset DOI: 10.5061/dryad.xsj3tx9s2
Description of the data and file structure
These data were collected in part to be used to determine whether some individuals of identified as Fremontodendron californicum might be hybrids between F. californicum and the federally endangered F. decumbens.
Files and variables
File: blm_frem_raw.vcf.gz
Description: Raw vcf file containing SNP data for all individuals in the study.
File: Fremontodendron_Morph_Study_8-28-23.csv
Description: Morphological data collected from F. decumbens, F. californicum and putative hybrid individuals. Missing values are indicated by NA and represent measurements that could not be collected. Color values are with reference to a color chart.
Variables
- Plant ID: Unique ID
- vcf_name: VCF identifier to link results to genetic data
- County: County where plant occurred.
- population: Population name
- sp_hyp: Hypothesized species identity based off of morphology
- Width: Plant width at widest point
- Height: Plant height at highest point
- Ratio_W/H: Ratio of width to height
- sepal_color_1: sepal color
- sepal_color_2: sepal color
- sepal_color_3: sepal color
- sepal_color_4: sepal color
- sepal_color_5: sepal color
- sepal_color_Mean: mean of the 5 observations of sepal color
- base_color_1: sepal base color
- base_color_2: sepal base color
- base_color_3: sepal base color
- base_color_4: sepal base color
- base_color_5: sepal base color
- base_color_Mean: mean of the five observations of sepal base color
- Ped_length_1: Pedicel length mm
- Ped_length_2: Pedicel length mm
- Ped_length_3: Pedicel length mm
- Ped_length_4: Pedicel length mm
- Ped_length_5: Pedicel length mm
- Ped_length_Mean: mean of the five observations of pedicel length mm
- lf_length_mm_1: leaf length at longest point mm
- lf_length_mm_2: leaf length at longest point mm
- lf_length_mm_3: leaf length at longest point mm
- lf_length_mm_4: leaf length at longest point mm
- lf_length_mm_5: leaf length at longest point mm
- lf_length_mm_Mean: mean of five observations of leaf length at longest point mm
- pet_length_1: petiole length mm
- pet_length_2: petiole length mm
- pet_length_3: petiole length mm
- pet_length_4: petiole length mm
- pet_length_5: petiole length mm
- pet_length_Mean: mean of five observations of petiole length mm
- lf_width_1: leaf width at widest point mm
- lf_width_2: leaf width at widest point mm
- lf_width_3: leaf width at widest point mm
- lf_width_4: leaf width at widest point mm
- lf_width_5: leaf width at widest point mm
- lf_width_Mean: mean of five observations of leaf width at widest point mm
- lf_lobes_1: number of leaf lobes
- lf_lobes_2: number of leaf lobes
- lf_lobes_3: number of leaf lobes
- lf_lobes_4: number of leaf lobes
- lf_lobes_5: number of leaf lobes
- lf_lobes_Mean: mean number of leaf lobes across five leaves
- ray_length_1: length of the ray of a stellate hair mm
- ray_length_2: length of the ray of a stellate hair mm
- ray_length_3: length of the ray of a stellate hair mm
- ray_length_4: length of the ray of a stellate hair mm
- ray_length_5: length of the ray of a stellate hair mm
- ray_length_Mean: mean of five observations of length of the ray of a stellate hair mm
- ray_length_Range: range of five observations length of the ray of a stellate hair mm
File: FREM_samples_master_clean.csv
Description: Sample ID's and meta data about each sample. Missing data stored as NA, and indicating either that a value was not applicable for a sample or not assigned.
Variables
- Population: Geographic population
- geo_pop: Variant of geographic population
- geo_pop2: Variant of geographic population
- Individual: Individual number in population, not used in analysis
- Original.ID: Original identifier used by collecter
- sample_name: Unique ID for the sample
- vcf_name: Unique sample ID used in vcf
- phylo: Used for phylogenetic analyses? (1 or NA)
- popgen: Used for popgen analyses? (2 or NA)
- CCGP: Data generated by the CCGP
- BLM/CNPS: Data generated as part of BLM/CNPS funded project
- organism: Species
- organism.pop: Slight alteration of organism to remove F. aff. califoricum
- geo_loc_name: location recorded by collecters
- county: County collected in
- collection_date: date collected
- passed_QC1: did sample pass initial QC check?
- longitude: longitude collected
- latitude: latitude collected.
Code/software
Scripts used to perform the analyses can be found at https://github.com/reedjohnkenny/Fremontodendron