Calvo-Yuste&_2026_Mol.Phyl.Evol

This repository contains 1) raw 150 bp paired-end Illumina reads generated for Petrocoptis using the Angiosperms353 target enrichment kit and 2) the datasets and R scripts used to perform phylogenetic comparative analyses in Petrocoptis. The materials provided here allow full reproducibility of all analyses presented in the associated manuscript. Raw sequence reads Total genomic DNA was extracted from silica-dried leaf tissue using a CTAB protocol. Indexed libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit, size-selected to ~150 bp, and amplified by PCR. Target enrichment was performed with the myBaits Angiosperms353 probe set following the manufacturer’s protocol. Enriched libraries were sequenced on an Illumina HiSeq platform. The dataset includes raw FASTQ files and associated sample metadata to enable independent sequence assembly, locus recovery, and phylogenomic analyses. Datasets and R scripts The repository also includes: Phylogenetic tree (dated species-level tree in Newick/Nexus format). Continuous trait datasets: Seed area (searea). Strophiole area (strarea). Strophiole/seed area ratio. Calyx length. Discrete trait datasets: Strophiolar hair type. Petal colour. Environmental variables: Annual precipitation. Annual maximum temperature. Genetic data summaries: Highly Heterozygous SNP counts (HH-SNP) SNP frequency thresholds SNP-derived predictors used in phylogenetic mixed models Analyses implemented The R scripts reproduce the following analyses: Phylogenetic signal estimation Pagel’s λ Blomberg’s K Ancestral state reconstruction Continuous traits using simulation-based fastAnc Discrete traits using stochastic character mapping Discrete trait evolution model comparison ER, SYM, ARD models Custom ordered and directional models AIC-based model selection Trait–environment relationships Linear models (non-phylogenetic) Phylogenetic independent contrasts (PICs) Adaptive regime analyses (OU models) Reversible-jump MCMC (bayou) Multi-regime OU and BM models (mvMORPH) Phylogenetic mixed models (MCMCglmm) Continuous and categorical response variables SNP-derived predictors Multiple chains and convergence diagnostics Highly heterozygous SNP exploration Interactive heatmaps Group-specific SNP threshold summaries All analyses were performed in R. The repository is structured to allow direct execution of scripts provided that file paths are preserved. Random seeds are set where appropriate to ensure reproducibility of stochastic analyses.