Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae)

We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades – inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (..., We used custom-designed baits for anchored hybrid enrichment, preparing Illumina sequence libraries for 158 samples (156 Calochortus and 2 outgroups). Our final dataset consisted of 294 low-copy nuclear loci (provided here as alignments). Specific methods for generating these data are also follows:

Sampling. We included 1 to 2 samples per species and subspecies; herbarium vouchers for new samples were deposited in the herbaria noted in SI Appendix, Table S9. Total genomic DNAs were extracted from silica-dried leaf or floral tis- sue using DNeasy plant kits (Qiagen, Valencia CA) following the manufacturer’s instructions. We included all extant Calochortus species except extremely rare C. rustvoldii [known from only two sites/pixels in the western Transverse Ranges (76))]; including it would little affect our analyses.
Library Preparation. We prepared Illumina sequence libraries for 158 samples (156 Calochortus and 2 outgroups) following Lemmon et al. (77–79). We used a Covaris ultras..., , # Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae)

[https://doi.org/10.5061/dryad.kwh70rzbw](https://doi.org/10.5061/dryad.kwh70rzbw)

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This repository contains the molecular data used for the phylogenetic analyses conducted in Karimi et al. 2022 (https://doi.org/10.1073/pnas.2305) for Calochortus (Liliaceae). The nuclear data was derived from a custom-bait anchored hybrid enrichment set which resulted in 295 low-copy nuclear loci. Alignments for all Calochortus samples and outgroup species are provided here as standard fasta file alignments. In addition, for the BEAST dated phylogeny, we extracted five plastid genes from our Calochortus reads and aligned them to plastid data originally extracted from https://doi.org/10.1002/ajb2.1178. These new alignments are provided as standard fasta file alignments. The maximum clade credibility (MCC) tree derived from BEAST analyses that was used in all downs...