DOI: 10.5061/dryad.3bk3j9kwz
title: Data from: Undescribed species diversity in Brewer’s Jewelflower illuminates potential mechanisms of diversification associated with serpentine endemism

description: 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.
description: 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).
description: # Undescribed species diversity in Brewer’s Jewelflower illuminates
 potential mechanisms of diversification associated with serpentine
 endemism 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](mailto:kyle.christie@nau.edu);
 [kylechristie1@gmail.com](mailto: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]