Evolution of Malacothrix and relatives (Cichorieae; Compositae), with special reference to taxa of California's Channel Islands
Data files
Jun 18, 2026 version files 13.93 MB
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Fig_S1_revised.pdf
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Fig_S12_revised.pdf
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Fig_S2_revised.pdf
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Fig_S3_revised.pdf
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Fig_S4_revised.pdf
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Fig_S5_revised.pdf
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Fig_S6_revised.pdf
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Fig_S7_revised.pdf
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Fig_S8_revised.pdf
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Fig_S9_revised.pdf
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Figs_S10_S11_revised.pdf
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Malacothrix_nrDNA_matrix.nex
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Malacothrix_nrDNA_ML_results.txt
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README.md
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Abstract
Biosystematic, cytogenetic, and morphological data and observations bring additional evolutionary context to an expanded molecular phylogenetic study of the primarily western North American Malacothrix and relatives (Cichoreae; Compositae) based on nuclear ribosomal (nr)DNA sequences. One of the two major clades resolved (Malacothrix 1) includes a subclade corresponding to the M. foliosa complex (M. incana, M. indecora, and all subspecies of M. foliosa), with all recognized taxa native to the California Channel Islands and all but one (M. incana) endemic there or to the California Islands more generally. The insular diploids of the M. foliosa complex mostly retain high interfertility and appear to be isolated geographically or ecologically, although recent introduction of M. incana to San Nicolas Island has resulted in extensive hybridization with the single-island endemic M. foliosa subsp. polycephala. Based on experimental cytogenetic, morphological, and molecular phylogenetic results, the recently described tetraploid M. junakii, endemic to Middle Anacapa Island, is evidently an allopolyploid from hybridization between diploid ancestors in the M. foliosa and M. clevelandii complexes, which are resolved as sister groups in the nrDNA tree. The tetraploid M. squalida, endemic to Anacapa and Santa Cruz islands, and the putative polyploid M. insularis, endemic to Las Islas Coronado, Mexico, belong to another subclade (Malacolepis) of the Malacothrix 1 clade that also includes the widespread diploid M. coulteri, which represents one of two subgenomes in M. squalida based on experimental cytogenetics and morphological considerations. The other major clade in Malacothrix (Malacothrix 2) includes the perennial M. saxatilis complex of highly interfertile, allopatric or putatively ecologically divergent diploids, wherein the endemic Channel Islands taxon M. saxatilis var. implicata is evidently sister to the other varieties, including the mainland and Santa Catalina Island native var. tenuifolia. Insular endemics across subclades of Malacothrix and their close mainland relatives are self-compatible, at least in part, in keeping with Baker’s Rule. These island endemics also generally have cypselae with characteristics associated with the insular syndrome of reduced dispersability, either lacking outer pappus (M. foliosa complex), unlike all mainland taxa except M. floccifera, or having outer pappus with no persistent bristles (M. saxatilis complex), unlike most mainland taxa of Malacothrix, including those inferred to have been bird-dispersed from North America to South America (M. clevelandii and M. coulteri). An expanded circumscription of Malacothrix to result in generic monophyly requires reinstating M. platyphylla and the new combinations Malacothrix acaulis (Torr. & A. Gray) B. G. Baldwin & Joongku Lee, Malacothrix parryi (A. Gray) B. G. Baldwin & Joongku Lee, and Malacothrix wrightii (A. Gray) B. G. Baldwin & Joongku Lee for all taxa previously treated in Atrichoseris, Anisocoma, and Calycoseris.
Dataset DOI: 10.5061/dryad.mkkwh71dj
Description of the data and file structure
The nuclear ribosomal DNA (nrDNA) matrix represents the aligned external transcribed spacer (ETS) and internal transcribed spacer (ITS) regions of Malacothrix and relatives, including the outgroup, with sample name abbreviations including: first three letters of genus name_first three or four letters of species name (or, if infraspecific taxon sample, the first letter of species name_first three or four letters of subspecies or varietal name)_a number that corresponds to the numbering of samples in this study or by Lee et al. (2003, Systematic Botany 28:616-626), if more than one sample of minimum-rank taxon was generated for this study or if more than one sample of a minimum-rank taxon was generated by Lee et al. (2003). If one sample of a minimum-rank taxon was generated by Lee et al. (2003) and another sample of the same taxon was generated in this study, then the sample from this study is indicated by an abbreviation of the collector name and number (first letter of collector name followed by their collection number).
The maximum-likelihood tree based on the nrDNA sequence matrix and all associated statistics are provided in a separate file. The sample names do not precisely correspond to those in the matrix, as the sample names were changed later in the matrix to be unambiguous.
Ple_sp1 = Ple_spi1 (Lee et al.);
Pre_ex = Pre_exi (Lee et al.);
Ste_ci_1 = Ste_cic_1 (Lee et al.);
Raf_ca_2 = Raf_cal_2 (Lee et al.);
Mun_br = Mun_bla (Lee et al.);
Ani_ac = Ani_aca (Lee et al.);
Mal_so = Mal_sonc (Lee et al.);
Cal_pa = Cal_par (Lee et al.);
Cal_wr = Cal_wri (Lee et al.);
Mal_gl_1 = Mal_gla_1 (Lee et al.);
Mal_gl2 = Mal_gla_2 (Lee et al.);
Mal_to = Mal_tor (Lee et al.);
Mal_tor180 = Mal_torT6796 (this study);
Mal_ca = Mal_cal (Lee et al.);
Mal_s_te = Mal_s_ten (Lee et al.);
Mal_s_al179 = Mal_s_ten_S12266 (this study);
Mal_s_sa = Mal_s_sax (Lee et al.);
Mal_s_co = Mal_s_com (Lee et al.);
Mal_s_ar = Mal_s_ara (Lee et al.);
Mal_s_im = Mal_s_imp (Lee et al.);
Mal_xa = Mal_xan (Lee et al.);
Atr_pl = Atr_pla_1 (Lee et al.);
Atr_pl_92 = Atr_pla_2 (Lee et al.);
Mal_in = Mal_inc (Lee et al.);
Mal_i_su176 = Mal_inc_D875992;
H125_newal = Mal_jun_3 (this study);
Mal_in_124 = Mal_ind_2 (this study);
Mal_f_cr116 = Mal_f_cri_2 (this study);
Mal_f_cr175 = Mal_f_cri_1 (this study);
Mal_f_ph161 = Mal_f_phi_2 (this study);
Mal_f_ph174 = Mal_f_phi_1 (this study);
Mal_f_phi121 = Mal_f_phi_3 (this study);
Mal_in_173 = Mal_ind_1 (this study);
Mal_PO = Malf_pol (Lee et al.);
Mal_f_fo115 = Mal_f_fol_1 (this study);
Mal_f_fol167 = Mal_f_fol_2 (this study);
Mal_cl = Mal_cle (Lee et al.);
Mal_si_163 = Mal_sim (this study);
Mal_st_169 = Mal_ste (this study);
Mal_ju_172 = Mal_jun_1 (this study);
H126_newal = Mal_jun_2 (this study);
Mal_sr_170 = Mal_sono (this study);
Mal_ph = Mal_pha (Lee et al.);
Mal_fe = Mal_fen (Lee et al.);
Mal_fl = Mal_flo (Lee et al.);
Mal_sq_118 = Mal_squ_2 (this study);
Mal_sq_168 = Mal_squ_1 (this study);
Mal_sq_117 = Mal_squ_3 (this study);
Mal_co = Mal_cou (Lee et al.);
Mal_insul = Mal_ins (this study).
The supplementary figures were produced by the late W. S. Davis and provide important context for this study, especially as regards chromosomal and micro-morphological (SEM) data. Prof. Davis was incapacitated prior to finalization of these figures, and the original images could not be obtained by his co-authors, who provide them here so that this invaluable information is available to all and not lost, with the understanding that Prof. Davis would have greatly preferred to have provided cleaner versions of these images and data.
Files and variables
File: Fig_S1_revised.pdf
Description: Habitats of Malacothrix foliosa subsp. foliosa, M. incana, M. indecora, and M. squalida in California’s Channel Islands. Photos by W. S. Davis.
File: Fig_S2_revised.pdf
Description: Morphological variation in the Malacothrix foliosa complex of subclade Malacomeris.
File: Fig_S3_revised.pdf
Description: Scanning Electron Microscopy (SEM) images of receptacular, cypselae, and other micromorphological details of taxa of Malacothrix and relatives.
File: Fig_S4_revised.pdf
Description: Morphological variation in the Malacolepis clade of Malacothrix, in comparison with M. foliosa subsp. philbrickii.
File: Fig_S5_revised.pdf
Description: Malacothrix foliosa subsp. polycephala, M. incana, and hybrids between them on San Nicolas Island. Photos by W. S. Davis.
File: Fig_S6_revised.pdf
Description: Growth-chamber grown plants from wild-collected cypselae of putative hybrids between Malacothrix foliosa subsp. polycephala and M. incana at Corral Harbor, San Nicolas Island. Photos by W. S. Davis.
File: Fig_S7_revised.pdf
Description: Flower heads (in profile) of different wild plants judged to be hybrids between Malacothrix foliosa subsp. polycephala and M. incana at Corral Harbor, San Nicolas Island. Photos by W. S. Davis.
File: Fig_S8_revised.pdf
Description: Phase microscopy image of five bivalents and ring of four chromosomes from meiosis in Malacothrix clevelandii × M. foliosa subsp. foliosa. Photo by W. S. Davis.
File: Fig_S9_revised.pdf
Description: Phase microscopy images of seven bivalents and seven univalents from meiosis in (a) Malacothrix coulteri (diploid) × M. squalida (tetraploid) and (b) Malacothrix foliosa subsp. foliosa (diploid) × M. squalida (tetraploid). Photos by W. S. Davis.
File: Figs_S10_S11_revised.pdf
Description: Fig. S10 -- Phase microscopy images of meiotic chromosomes of Malacothrix saxatilis var. saxatilis (left) and M. xanti (right). Photos by W. S. Davis. Fig. S11 -- Comparison of median total chromosome lengths of Malacothrix clevelandii, M. phaeocarpa, M. sonorae, and M. torreyi.
File: Fig_S12_revised.pdf
Description: Phase microscopy images of mitotic chromosomes of Malacothrix clevelandii, M. coulteri, M. fendleri, and M. glabrata. Photos by W. S. Davis.
File: Malacothrix_nrDNA_matrix.nex
Description: Aligned nuclear ribosomal (nr)DNA sequences of the external and internal transcribed spacer (ETS/ITS) regions of Malacothrix and relatives (and outgroup).
File: Malacothrix_nrDNA_ML_results.txt
Description: Results of maximum-likelihood (ML) phylogenetic analysis of the Malacothrix nrDNA matrix.
Code/software
The nrDNA matrix and maximum-likelihood results can be opened with any text browser. The supplementary figures are all pdfs and can be opened with Adobe Acrobat Reader or other pdf-viewing software.
