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Background <p>The polymorphic swallowtail butterfly <i>Papilio bootes</i> displays pronounced subspecific differentiation and extensive wing-pattern variation, offering an exceptional system to investigate lineage diversification and phenotypic evolution. However, the genetic mechanisms underlying its intraspecific divergence and morphological polymorphism remain poorly understood.</p> Results <p>We assembled a chromosome-level reference genome for <i>P. bootes</i> and performed whole-genome resequencing of 66 individuals from six subspecies and 12 outgroup <i>P. janaka</i>. Population genomic analyses delineated three major genetic lineages (northern, central, southern), whose divergences aligned with Pleistocene glacial cycles. Historical hybridization was evident, with the <i>nigricauda</i> group originating from admixture between <i>dealbatus</i> and <i>rubicundus</i> (east) populations. The Z chromosome exhibited significantly elevated differentiation and selective sweep signatures, underscoring its role in early intraspecific divergence. Comparative analyses between black-winged and white-spotted morphs identified candidate genomic regions containing <i>spalt</i> and <i>fpps</i>, two genes with known links to wing pigmentation and melanin-associated processes, that may be associated with wing-pattern polymorphism in this species.</p> Conclusions <p>Our study demonstrates how climatic oscillations, hybridization, rapid evolution of sex chromosomes, and natural selection have jointly shaped lineage diversification and adaptive wing-pattern evolution in <i>P. bootes</i>, offering new insights into the genomic architecture of speciation and phenotypic diversification in <i>Papilio</i> butterflies.</p>

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Whole-genome analyses illuminate demographic history and lineage differentiation of polymorphic swallowtail butterfly Papilio bootes

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月20日

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  • Xiao Xu,
  • Jingyi Zeng,
  • Hao Li,
  • Adam Miles Cotton,
  • Dan Liang,
  • Shao-Ji Hu,
  • Peng Zhang

摘要

Background

The polymorphic swallowtail butterfly Papilio bootes displays pronounced subspecific differentiation and extensive wing-pattern variation, offering an exceptional system to investigate lineage diversification and phenotypic evolution. However, the genetic mechanisms underlying its intraspecific divergence and morphological polymorphism remain poorly understood.

Results

We assembled a chromosome-level reference genome for P. bootes and performed whole-genome resequencing of 66 individuals from six subspecies and 12 outgroup P. janaka. Population genomic analyses delineated three major genetic lineages (northern, central, southern), whose divergences aligned with Pleistocene glacial cycles. Historical hybridization was evident, with the nigricauda group originating from admixture between dealbatus and rubicundus (east) populations. The Z chromosome exhibited significantly elevated differentiation and selective sweep signatures, underscoring its role in early intraspecific divergence. Comparative analyses between black-winged and white-spotted morphs identified candidate genomic regions containing spalt and fpps, two genes with known links to wing pigmentation and melanin-associated processes, that may be associated with wing-pattern polymorphism in this species.

Conclusions

Our study demonstrates how climatic oscillations, hybridization, rapid evolution of sex chromosomes, and natural selection have jointly shaped lineage diversification and adaptive wing-pattern evolution in P. bootes, offering new insights into the genomic architecture of speciation and phenotypic diversification in Papilio butterflies.