DOI: 10.5061/dryad.xsj3tx9s2
title: Investigating putative hybrids of <em>Fremontodendron decumbens</em> and <em>F. californicum</em> in the Sierra foothills

description: 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. 
description: # Investigating putative hybrids of *Fremontodendron decumbens* and *F.
 californicum* in the Sierra foothills Dataset DOI:
 [10.5061/dryad.xsj3tx9s2](https://doi.org/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](https://github.com/reedjohnkenny/Fremontodendron)