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 after
the initiation of Quaternary climate oscillations. Ecological niche
modeling showed low niche overlap, reflecting adaptations to different
climatic conditions—C. cashmeriana to warmer, wetter habitats and C.
torulosa to colder, drier habitats. We identified positively selected
genes related to environmental stress responses, highlighting the crucial
role of ecological selection. Genotype–environment association and partial
redundancy analysis emphasized that ecological factors significantly drive
genetic variation. Under future climate scenarios, both species show
increased genomic vulnerability, particularly C. torulosa. Our findings
underscore the importance of ecological selection in initiating speciation
despite strong gene flow and have significant implications for managing
mountain biodiversity in the face of climate change.