Phylogenetic Analysis of Salvia Species

The genus Salvia, comprising nearly 1 000 species, is one of the most diverse lineages within the mint family, with centres of diversity in the Mediterranean, East Asia and the Americas. Phylogenetic analysis of Salvia has advanced from single‐gene barcoding towards comprehensive phylogenomics, integrating complete chloroplast genomes, nuclear single‐copy genes and genome‐scale data sets. These approaches have refined our understanding of inter- and infrageneric relationships, resolved long-standing taxonomic ambiguities and revealed patterns of hybridisation, incomplete lineage sorting and biogeographical divergence. Chloroplast genome comparisons have delineated major clades corresponding to geographic regions, while nuclear-based analyses have illuminated reticulate evolution and gene-tree discordance. The integration of morphological, plastid and nuclear data has also enabled the identification of novel species, clarified sectional boundaries and provided molecular markers for species discrimination. Together, these developments underpin conservation strategies, guide the sustainable use of medicinal and ornamental Salvia species and inform the elucidation of adaptive radiation across heterogeneous habitats worldwide.

Research from Nature Portfolio

Recent studies employing complete chloroplast genomes from representative Salvia taxa across three principal distribution centres have demonstrated that plastome variation reflects geographic history. Species from the Central and Western Asia–Mediterranean region form an early‐diverging clade, exhibiting greater sequence variation and repeated elements, followed by distinct East Asian and Central/South American lineages. Comparative analyses revealed that chloroplast sequences cluster by origin, with variation hotspots correlating with biogeographical separation. These findings not only clarify the paraphyletic status of Salvia but also provide a robust framework for utilising global genetic resources in breeding, pharmacological exploration and conservation planning.

Phylogenetic Analysis of Salvia Species publication trend

The graph below shows the total number of articles in phylogenetic analysis of salvia species across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogenetic analysis: Reconstruction of evolutionary relationships among species based on genetic or morphological data.

Chloroplast genome (plastome): The circular DNA molecule found in chloroplasts, commonly used for resolving plant phylogeny.

Nuclear loci: Specific regions of the nuclear genome, including single-copy genes, used to infer species relationships.

Monophyletic: A group of organisms consisting of an ancestor and all its descendants.

Incomplete lineage sorting: The retention of ancestral genetic variation across speciation events, leading to gene‐tree discordance.

Horizontal gene flow: Transfer of genetic material between species through hybridisation or introgression.

References

1. Salvia guidongensis sp. nov.: unraveling a critical evolutionary link in East Asian Salvia from Central China integrating morphology, phylogeny, and plastid genomics. Frontiers in Plant Science (2024).
2. Comparative and phylogenetic analysis of complete chloroplast genome sequences of Salvia regarding its worldwide distribution. Scientific Reports (2023).
3. Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes. Frontiers in Plant Science (2021).
4. Comparative Genomics and Phylogenetic Analysis of the Chloroplast Genomes in Three Medicinal Salvia Species for Bioexploration. International Journal of Molecular Sciences (2022).