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

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 m..., 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...., , # 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.

人参属（Panax，五加科Araliaceae）是一个小型类群，包含多个广为人知的药用重要物种。该属呈现东亚与北美东部的间断分布格局，绝大多数物种分布于东亚，尤以喜马拉雅-横断山区（HHM）为核心分布区。本研究采用基因组靶向富集技术，从覆盖该属全部18个物种的59份样品中，成功获取了358个核直系同源基因座与完整的质体基因组序列。分化时间估算与生物地理分析结果表明，人参属在始新世中期可能曾广泛分布于北美至亚洲区域。在始新世晚期至渐新世全球气候变冷事件期间，人参属大概率经历了大规模物种灭绝。该属最终在中国大陆西南部山地与热带印度支那地区存活下来并发生早期分化，其中部分类群向西北迁移至喜马拉雅-横断山区，向东扩散至中国中东部区域，随后进一步向日本及北美迁徙。研究已鉴定出基因流为[原文未完成内容]。原始测序读段使用Trimmomatic v.0.39（Bolger等，2014）进行质量过滤，去除读段末端碱基及最低质量分值低于20的低质量碱基。随后，采用HybPiper流程v.1.3.1（Johnson等，2016）组装核基因座，该流程包含三大核心步骤：以936个基因的核序列作为诱饵设计参考，通过默认参数的BWA 0.7.17（Li & Durbin 2009）工具捕获所有测序材料的读段；使用SPAdes 3.12.0（Bankevich等，2012）将读段组装为重叠群；并运行HybPiper自带的Python与R脚本以获取回收的序列。利用HybPiper内置的旁系同源基因检测工具（paralog investigator）对序列数据集进行潜在旁系同源基因的检测与移除，以用于后续系统发育分析。最终从数据集中移除了578个基因座，因此最终数据集包含358个直系同源基因座。

# 系统发育组学解析人参属（Panax，五加科Araliaceae）的物种关系、网状进化与生物地理分化——以喜马拉雅-横断山区的物种分化为重点
https://doi.org/10.5061/dryad.931zcrjvm

## 数据与文件结构说明
核基因数据矩阵包含358个直系同源基因，总长度为303894 bp。质体基因组数据矩阵长度为156100 bp。
核数据集由HybPiper组装得到。我们以清洁读段为基础，采用BWA进行参考引导组装（参考序列为三七*Panax notoginseng*，GenBank登录号KP036468），以获取质体基因组序列。