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Abstract Winter annuals comprise a large fraction of warm-desert plant species, but the drivers of their diversity are little understood. One factor that has generally been overlooked is the lack of obvious means of long-distance seed dispersal in many desert-annual lineages, which could lead to genetic differentiation at small spatial scales and, ultimately, to speciation and narrow endemism. If our gene-flow hypothesis is correct, individual winter-annual species should have populations with genetic spatial structures implying short distances of gene flow. To test this idea, we sampled six populations of Eschscholzia parishii (Papaveraceae) in three pairs of watersheds within a 28-km radius in southern California. We quantified genetic diversity and structure and inferred the distance of gene flow in these populations using single nucleotide polymorphisms derived from genotyping-by-sequencing. Estimated distances of gene flow were quite small (σ = 10.4–14.9 m), with strong genetic structure observed within and between populations. Kinship declined steeply with ln distance (r2 = 0.85). Petal size and shape differed significantly between the northernmost and southernmost populations. These findings support the hypothesis that the high diversity of warm-desert winter annuals might result, in part, from genetic differentiation within species at small spatial scales driven by poor seed dispersal. 

Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia . We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia , are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia . Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.