2026/05/20 by Jill S. Miller, Dan J. González‐Kosasky, Kathleen F. Harris +2
Biochemistry, Genetics and Molecular Biology · Agricultural and Biological Sciences · #Genomics and Phylogenetic Studies #Plant Diversity and Evolution #Chromosomal and Genetic Variations
paper · doi:10.1002/tax.70135
Abstract DNA sequence data derived from chloroplast gene regions (or intergenic spacers) has yielded important insights into the phylogeny of green plants, and technological and bioinformatic advancements have enhanced the efficiency of data recovery from the chloroplast genome, making whole chloroplast genomes readily obtainable and assembled. The success of chloroplast data to infer relationships at finer taxonomic scales, however, remains mixed. In some cases, well‐supported phylogenies are recovered, whereas a lack of resolution, heteroplasmy, or non‐monophyly of taxa remain a challenge in other groups. We use a genome skimming approach to recover whole chloroplast genomes from 113 individuals and 61 species in Lycium and 5 species in outgroups from Nolana , Sclerophylax , and Jaborosa . Our sampling included a diverse set of Lycium collected from across its cosmopolitan distribution. Importantly, we include multiple individuals from 20 species, which enables us to explore the extent of intraspecific variation and test the utility of whole chloroplast genomes to infer species‐level relationships. Complete chloroplast genomes were obtained, assembled, and annotated, and surveyed for the presence of short inversions described previously in Solanaceae. We used maximum likelihood to reconstruct phylogenomic relationships and constraint analyses to test the monophyly of individuals within species. Plastomes for Lycium , Nolana , Sclerophylax , and Jaborosa were similar in length and structure to those previously reported in Solanaceae. Six short (4–31 bp) inversions were identified and were homoplasious in Lycium . Phylogenetic resolution varied depending on geographical region. Evolutionary relationships among American Lycium were well resolved and strongly supported, whereas resolution was limited in the recently diverged Eastern Hemisphere clade, which had shorter branch lengths and lower nucleotide diversity. Species with multiple individuals were not often recovered as monophyletic, and we argue that sampling within species is critical. We discuss our results in comparison to previous studies using chloroplast and nuclear data, noting both synergies and inconsistencies, and suggest that incomplete lineage sorting and chloroplast capture likely explain the non‐monophyly and incongruence. Finally, we caution against including herbarium specimens in genomic studies without first ensuring taxonomic accuracy.