DOI: 10.5061/dryad.931zcrjvm
title: Phylogenomic insights into species relationships, reticulate evolution, and biogeographic diversification of the ginseng genus Panax (Araliaceae), with an emphasis on the diversification in the Himalayan – Hengduan Mountains

description: Panax (Araliaceae) is a small genus with several well-known medicinally
 important species. It has a disjunct distribution between eastern Asia and
 eastern North America, with most species from eastern Asia,
 especially the Himalayan – Hengduan Mountains (HHM). This study
 used the genomic target enrichment method to obtain
 358 nuclear ortholog loci and complete plastome
 sequences from 59 accessions representing all 18 species of the
 genus. Divergence time estimation and biogeographic analyses
 suggest that Panax was likely widely distributed from North
 America to Asia during the middle Eocene. During the late Eocene
 to Oligocene Panax may have experienced extensive
 extinctions during global climate cooling. It survived
 and diverged early in the mountains of southwest China
 and tropical Indochina, where some taxa migrated northwestward to
 the Himalayan-Hengduan Mountains, eastward to central and eastern China,
 and then onward towards Japan and North America. Gene flow is identified
 as the main contributor to phylogenetic discordance (33.46%) within Panax.
 We hypothesize that the common ancestors of the medicinally
 important P. ginseng+P. japonicus+P. quinquefolius clade had experienced
 allopolyploidization, which increased adaptability to cooler and
 drier environments. During the middle to late Miocene, several
 dispersals occurred from the region of the HHM to contiguous areas,
 suggesting that HHM acted as a refugium and also served as a secondary
 diversification center for Panax. Our findings highlight that the
 interplay of orographic uplift and climatic changes in the HHM greatly
 contributed to the species diversity of Panax.
description: Raw sequencing reads were quality filtered using Trimmomatic
 v.0.39 (Bolger et al., 2014) to remove bases at read ends and low-quality
 bases with a minimum quality score of 20. Subsequently, the HybPiper
 pipeline v.1.3.1 (Johnson et al., 2016) was used to assemble nuclear loci.
 The process includes three major steps: using the nuclear sequences of
 936 genes for bait design as the references to capture all the reads from
 sequenced accessions via the BWA 0.7.17 (Li & Durbin 2009) option
 with default settings, applying the SPAdes 3.12.0 (Bankevich et al. 2012)
 to assemble reads into contigs, and implementing the Python and R scripts
 from HybPiper to obtain the recovered sequences. Potential paralogs were
 detected and removed from the sequence dataset for subsequent phylogenetic
 analyses using the "paralog investigator" tool included in
 HybPiper. This resulted in 578 loci being removed from the final dataset
 and subsequent analyses. Therefore, the final dataset
 included 358 orthologues. To obtain bycatch plastid
 sequences from the clean reads, a reference assembly strategy was used. We
 employed BWA for reference-guided (<em>Panax notoginseng</em>,
 Genbank KP036468) assembly based on clean reads. 
description: # Phylogenomic insights into species relationships, reticulate evolution,
 and biogeographic diversification of the ginseng genus Panax (Araliaceae),
 with an emphasis on the diversification in the Himalayan – Hengduan
 Mountains
 [https://doi.org/10.5061/dryad.931zcrjvm](https://doi.org/10.5061/dryad.931zcrjvm) ## Description of the data and file structure The nuclear gene data matrix consisted of 358 ortholog genes with a total length of 303,894 bp. The plastome data matrix had a length of 156,100 bp. The nuclear datasets assembled by HybPiper.  We employed BWA for reference-guided (*Panax notoginseng*, Genbank KP036468) assembly based on clean reads to obtained the plastome sequences.