Phylogenetic Studies of Piperaceae Species
Summary
Phylogenetic investigations of the pepper family (Piperaceae) have progressed from early morphology-based classifications towards genome-scale reconstructions that resolve deep and shallow divergences alike. The family comprises two large lineages, Piper and Peperomia, each displaying remarkable species richness and ecological breadth. Comparative analyses of chloroplast and nuclear markers have elucidated monophyletic clades, revealed instances of rapid radiation and reticulation, and clarified relationships among epiphytic, terrestrial and climber growth forms. Plastid genomes (plastomes) exhibit conserved gene content but variable structural features—such as inverted repeat boundaries and single-copy region lengths—that provide phylogenetic signal at multiple taxonomic levels. Nuclear single-copy genes have emerged as powerful complements to chloroplast loci, enhancing resolution in species-rich groups where traditional markers show limited polymorphism. Integrative approaches combining herbarium sampling, field collections and high-throughput sequencing have mapped biogeographical patterns across tropical regions, uncovering centres of endemism and elucidating evolutionary drivers of fruit morphology and dispersal strategies. These phylogenetic frameworks underpin conservation efforts for rare and endemic taxa, inform sustainable utilisation of spice and medicinal species, and offer a foundation for future comparative genomics within Piperales and adjacent angiosperm clades.
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Phylogenetic Studies of Piperaceae Species publication trend
The graph below shows the total number of articles in phylogenetic studies of piperaceae species across all publications each year (not limited to Nature Index journals).
Technical terms
Phylogeny: The evolutionary history and branching relationships among species or higher taxa.
Phylogenomics: Reconstruction of evolutionary relationships using genome-scale data.
Plastome: The complete DNA sequence of a chloroplast genome.
Inverted repeat (IR): A duplicated sequence region in plastomes that flanks single-copy regions and influences genome structure.
Large single-copy region (LSC): The major unique segment of a plastome outside the inverted repeats, often used for phylogenetic markers.
Small single-copy region (SSC): The minor unique segment of a plastome, frequently exhibiting higher rates of sequence variation.
Nuclear single-copy gene: A gene present as one copy in the nuclear genome, valuable for resolving relationships at and below species level.
References
- Discordant Phylogenomic Placement of Hydnoraceae and Lactoridaceae Within Piperales Using Data From All Three Genomes. Frontiers in Plant Science (2021).
- Comparative analysis of the chloroplast genomes of eight Piper species and insights into the utilization of structural variation in phylogenetic analysis. Frontiers in Genetics (2022).
- A comparative analysis of plastome evolution in autotrophic Piperales. American Journal of Botany (2024).
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