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.

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#### **Step 1: Reference Assembly and SNP Calling**

**Script:** `Step1.Reference_assembly_and_SNPs_calling.sh`
**Description:** Performs genome alignment, variant calling, and SNP extraction.

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#### **Step 2: Population Structure and Admixture Analysis**

**Script:** `Step2.Population_struc...,