Data from: Undescribed species diversity in Brewer’s Jewelflower illuminates potential mechanisms of diversification associated with serpentine endemism
Data files
May 15, 2025 version files 338.80 KB
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Appendix_S10_alignment_nexus.nexus
157.68 KB
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Figure1a_Sbreweri_collections_CCH2_November212023.csv
26.57 KB
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Figure1a_Sbreweri_collections.csv
2.35 KB
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Figure2_phenology_data.csv
15.51 KB
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Figure3_and_Figure4_crossing_data.csv
74.23 KB
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Figure5_leaf_morphometric_data.csv
29.10 KB
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FigureS2_selfing_data.csv
20.11 KB
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README.md
6.25 KB
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README.txt
7 KB
Abstract
Premise of study: Documenting species-level diversity is a fundamental goal of biology, yet undescribed species remain hidden even in well-studied groups. Inaccurate delimitation of species boundaries can limit our understanding of ecological and evolutionary processes and patterns of biodiversity, and may further impede conservation and management efforts.
Methods: We utilized an integrative approach, combining techniques from speciation biology, molecular phylogenetics, and geometric morphometrics to assess diversity in the Californian serpentine endemic Streptanthus breweri (Brewer’s Jewelflower). We assessed reproductive isolation resulting from flowering time differences, mating system differences, and interfertility among four distinct geographic clusters of S. breweri that span the geographic range of the species. We generated a gene tree based on the ribosomal DNA internal transcribed spacer region (ITS), a diagnostic species-level marker for this clade of jewelflowers, and additionally quantified leaf morphology in plants grown under common conditions.
Key Results: Four geographic clusters of S. breweri in northern California represent not a single species, but instead a species complex of at least three putative species. Independent data associated with Biological, Phylogenetic, and Morphological Species Concepts support these conclusions.
Conclusions: This work illustrates that latent biodiversity may be concealed even in well-studied groups and underscores the contribution of edaphic endemism generally, and serpentine endemism specifically, to California’s rich plant biodiversity. The existence of unrecognized species diversity within the S. breweri species complex highlights multiple factors, including 1) the spatial context of geologic discontinuities, 2) a selfing mating system, and 3) differential selection pressures across discontinuous specialized habitats as potential drivers of evolutionary divergence on serpentine.
American Journal of Botany
Kyle Christie, N. Ivalú Cacho, Jacob Macdonald, Deniss J. Martinez, and Sharon Y. Strauss
Corresponding author – Kyle Christie (kyle.christie@nau.edu; kylechristie1@gmail.com)
This dataset includes:
- six (6) .csv files,
- two (2) .Rdata input files,
- five (5) .R scripts used for data analysis and figure generation, and
- one (1) .nexus file
The .R files generate Figure 1, Figure 2, Figure S2 (Appendix S2), Figure 3 and Figure 4, and Figure 5, and rely on the associated input data (.csv and .Rdata files). All missing data represented as NA.
The .nexus file (Appendix_S10_alignment_nexus) was used to generate the phylogenetic tree shown in Figure 6.
Input data include:
Figure1a_Sbreweri_collections_CCH2_November212023.csv
Figure1a_Sbreweri_collections.csv
Figure2_phenology_data.csv
Figure3_and_Figure4_crossing_data.csv
Figure5_leaf_morphometric_data.csv
FigureS3_selfing_data.csv
CA.Rdata
serp.patches.Rdata
Analysis scripts include:
01_Figure1a_collection_map.R
02_Figure2_phenology.R
03_FigureS2_selfing.R
04_Figure3_and_Figure4_interfertility.R
05_Figure5_leaf_PCA.R
Description of METADATA (columns in input .csv files)
- Figure1a_Sbreweri_collections.csv
[S. breweri accessions used in the study]
species [species name]
site [site name]
lat [latitude (decimal degrees)]
lon [longitude (decimal degrees)]
elev [elevation (in feet)]
geography [category for geographic cluster (North, North Central, South Central, South)]
plot_color [hex code for plotting color]
- Figure1a_Sbreweri_collections_CCH2_November212023.csv
[S. breweri georeferenced herbarium specimens]
[online search conducted 11/21/2023, "PreservedSpecimens"]
[California Consortium of Herbaria]
id [California Consortium of Herbaria unique id field]
institutionCode [herbarium acronym]
catalogNumber [catalog number]
otherCatalogNumbers [alternate catalog numbers]
scientificName [scientific name]
eventDate [date of herbarium collection]
decimalLatitude [latitude (decimal degrees)]
decimalLongitude [longitude (decimal degrees)]
- Figure2_phenology_data.csv
[date of first flower of S. breweri individuals grown in a greenhouse common garden]
site [site name/sampling location]
greenhouse_code [greenhouse cell code; unique ID]
greenhouse_tray [greenhouse tray ID]
species [species]
maternal family [maternal family ID]
Julian_date_first_flower [Julian date of first flower]
lat [latitude (decimal degrees)]
lon [longitude (decimal degrees)]
geography [geographic cluster; North, North Central, South Central, South]
- FigureS2_selfing_data.csv
[data on autonomous selfing in a greenhouse common garden]
population [site name/sampling location]
cone_code [greenhouse cone code; unique ID]
prop_fruit_class [categorical estimate of proportion of flowers that autonomously produced fruits]
# 0 = 0
# 1 = 1-5% of flowers on a plant produced fruits
# 2 = 6-25%
# 3 = 26-50%
# 4 = 51-75%
# 5 = 76-100%
perc_self [continuous estimate of percentage of flowers that autonomously produced fruits, based on categorical mid-point]
species [species]
lat [latitude (decimal degrees)]
lon [longitude (decimal degrees)]
geography [geographic cluster; North, North Central, South Central, South]
- Figure3_and_Figure4_crossing_data.csv
[data from experimental crosses among individuals from S. breweri species complex]
maternal_site [site name/sampling location of maternal parent]
paternal_site [site name/sampling location of paternal parent]
mom [unique ID/greenhouse cell of maternal parent]
dad [unique ID/greenhouse cell of paternal parent]
fruit [fruit set success; 1 = fruit produced, 0 = no fruit produced]
seeds [seed set success; 1 = seeds produced, 0 = no seeds produced]
viable_seeds [viable seed set success; 1 = viable seeds produced, 0 = no viable seeds produced]
n_seeds [number of seeds produced in cross]
seed_mass [total mass of seeds produced in miligrams]
dehisced [fruit dehisced prior to collection; 1 = dehisced; 0 = not dehisced]
maternal_species [maternal species]
mat_fam [maternal family ID]
paternal_species [paternal species]
pat_fam [paternal family ID]
maternal_lat [latitude (decimal degrees) of maternal sampling location]
maternal_lon [longitude (decimal degrees) of maternal sampling location]
maternal_elev [elevation in feet of maternal sampling location]
maternal_geography [geographic cluster of maternal parent]
paternal_lat [latitude (decimal degrees) of paternal sampling location]
paternal_lon [longitude (decimal degrees) of paternal sampling location]
paternal_elev [elevation in feet of paternal sampling location]
paternal_geography [geographic cluster of paternal parent]
- Figure5_leaf_morphometric_data.csv
[morphometric data based on landmarks calculated in MorphoLeaf]
[leaves of plants grown in a greenhouse common garden]
Leaf_ID [collection site _ unique plant ID]
Geography [geographic cluster; North, North Central, South Central, South]
Blade_Length [length of leaf blade as calculated in MorphoLeaf]
Blade_Width_BB [widest width of leaf blade as calculated in MorphoLeaf]
Blade_Area [area of leaf blade as calculated in MorphoLeaf]
Blade_Perimeter [leaf blade perimeter length as calculated in MorphoLeaf]
Petiole_Width [petiole width as calculated in MorphoLeaf]
Upper_Teeth_Number [number of upper teeth]
Lower_Teeth_Number [number of lower teeth]
Total_Teeth_Number [total number of leaf teeth]
Tooth_Width [tooth width, length between sinuses]
Tooth_Height_altitude [tooth height, perpendicular to tooth width line]
Tooth_Height_median [tooth height, oblique to tooth width line]
Tooth_Height_to_Tooth_Width [tooth height to tooth width ratio]
Tooth_Area [tooth area as calculated in MorphoLeaf]
Tooth_Perimeter [tooth perimeter length as calculated in Morpholeaf]
Datasets were 1) generated in greenhouse common gardens at the University of California, Davis (Davis, California, USA); and 2) using Sanger sequencing of the ribosomal DNA internal transcribed spacer region (ITS).
