Ancient polyploidization events influence the evolution of the ginseng family (Araliaceae)

The raw reads (FASTQ files) used in this study are available in the NCBI Sequence Read Archive (SRA) database (Bioproject ID: PRJNA841627).

[Introduction]: Whole genome duplication events (WGDs) have been recognized as major drivers of evolution in plants, especially when they involve hybridization (allopolyploidization). In this study we evaluated if WGDs acted as evolutionary forces at the origin and early divergence of the Asian Palmate group (AsPG) of the plant family Araliaceae. This clade encompasses most of the generic and species diversity as well as most of the polyploids of the family, and a role of hybridization in its origin has been suggested.

[Methods]: In order to test this hypothesis, we obtained nuclear and plastid time-calibrated phylogenomic trees including 80% of Araliaceae genera (37 genera, 237 species) using the Hyb-Seq approach. The role of WGDs in the early evolution of the AsPG was tested using ancestral chromosome number reconstructions based on chromosome counts for 62% of the sampled genera, while recent polyploidization events were explored by inferring ploidy of the sequenced species from allelic frequencies.

[Results]: Phylogenetic analyses of nuclear and plastid sequences provided highly resolved but incongruent topologies consistent with ancient hybridization not only for the origin of the AsPG, but also in the second most highly diverse clade of the family. Our ancestral chromosome number reconstructions supported that one or two WGDs preceded the origin of two of the three main clades of Araliaceae (AsPG and Polyscias-Pseudopanax), which could have acted as background variables necessary for the posterior diversification of these lineages. Ploidy inference based on allelic frequencies provided signal of recent polyploidization in the AsPG and the third main clade of Araliaceae (Aralia-Panax).

[Conclusions]: In summary, WGDs are linked to the origin of the main clades of the Araliaceae family, but the drivers of the strong diversification of the AsPG remain an open question.

This study was supported by the Spanish Ministry of Economy, Industry, and Competitiveness (CGL2017-87198-P), the Spanish Ministry of Science and Innovation (PID2019-106840GA-C22 and PID2022-140985NB-C22), the Laboratories of Analytical Biology of the Smithsonian National Museum of Natural History (https://ror.org/05b8c0r92), and the Smithsonian Institution DNA Barcode Network (SIBN). A. Gallego-Narbón was supported by the program “Contratos predoctorales para Formación de Personal Investigador FPIUAM” of Universidad Autónoma de Madrid (FPI-UAM 2018) and the Smithsonian Institution Fellowship program (Graduate Student Fellowship 2022, Peter Buck Postdoctoral Fellowship 2024). M. Fernández-Mazuecos was supported by a Ramón y Cajal Fellowship (RYC2022-036418-I), funded by the Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033) and the European Social Fund Plus (FSE+).

Peer reviewed