Scripts and detailed command lines supporting: Ecological selection as drivers during early speciation: Insights from two allopatric cypress species in the Himalaya

Understanding the factors driving speciation is fundamental to evolutionary biology. While geographic isolation has long been considered a primary factor, the role of ecological selection during early speciation stages is poorly understood. The Himalaya, a biodiversity hotspot, offers a unique opportunity to study these processes. We investigated two closely related conifer species, Cupressus torulosa and C. cashmeriana, which are geographically separated yet exhibit distinct ecological adaptations. Using target-capture sequencing of 52 C. cashmeriana samples from Bhutan and 46 C. torulosa samples from Nepal, we surveyed their genetic diversity, demographic history, and adaptive evolution. Genomic analyses revealed moderate genetic differentiation between them, yet confirmed they are genetically distinct sister species. Demographic modeling indicated their divergence began around 6.57 million years ago, with strong gene flow persisting until approximately 2.08 million years ago, shortly..., , # Scripts and detailed command lines supporting: Ecological selection as drivers during early speciation: Insights from two allopatric cypress species in the Himalaya Dataset DOI: [10.5061/dryad.6t1g1jxbg](10.5061/dryad.6t1g1jxbg) ## Description of the data and file structure ### Files and variables #### File: Ecological-selection-of-two-cypress-species.zip **Description:** This archive contains all necessary scripts and auxiliary files used in the analysis pipeline for this study. This workflow provides a comprehensive pipeline for analyzing genomic data, including reference alignment, SNP calling, population structure inference, demographic modeling, and gene functional annotation. --- #### **Step 1: Reference Assembly and SNP Calling** **Script:** `Step1.Reference_assembly_and_SNPs_calling.sh` **Description:** Performs genome alignment, variant calling, and SNP extraction. --- #### **Step 2: Population Structure and Admixture Analysis** **Script:** `Step2.Population_struc...,阐明驱动物种形成的因素是进化生物学的核心议题。长期以来，地理隔离被视为物种形成的首要驱动因素，但物种形成早期阶段生态选择所扮演的角色仍有待深入解析。作为全球生物多样性热点地区之一，喜马拉雅山脉为研究此类过程提供了独特契机。本研究聚焦两个近缘针叶树物种：喜马拉雅柏木（Cupressus torulosa）与喀什米尔柏木（C. cashmeriana），二者地理分布相互隔离，但表现出显著的生态适应性分化。我们针对不丹的52份喀什米尔柏木样本与尼泊尔的46份喜马拉雅柏木样本开展目标捕获测序（target-capture sequencing），以此分析二者的遗传多样性、种群历史与适应性进化过程。基因组分析结果显示二者存在中等程度的遗传分化，同时证实它们为遗传上独立的姊妹物种。种群历史建模结果表明，二者的分化始于约657万年前，持续的强基因流直至约208万年前方才减弱，…… 支持性脚本与详细命令行：生态选择驱动早期物种形成：来自喜马拉雅地区两个异域柏木物种的研究启示 数据集DOI：10.5061/dryad.6t1g1jxbg 数据与文件结构说明 ### 文件与变量 #### 文件：Ecological-selection-of-two-cypress-species.zip **描述：** 此归档文件包含本研究分析流程所需的全部脚本与辅助文件。 本工作流提供一套完整的基因组数据分析流程，涵盖参考基因组比对、单核苷酸多态性（Single Nucleotide Polymorphism，SNP）检测、种群结构推断、种群历史建模以及基因功能注释。 --- #### **步骤1：参考基因组组装与SNP检测** **脚本：** `Step1.Reference_assembly_and_SNPs_calling.sh` **描述：** 执行基因组比对、变异检测与SNP提取。 --- #### **步骤2：种群结构与混合分析** **脚本：** `Step2.Population_struc...,`