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Massive Inter-species Introgression Overwhelms Phylogenomic Relationships Among Jaguar, Lion, and Leopard.

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Phylogenomic analysis reveals that the dominant genome tree in big cats is not the species tree. Instead, rampant hybridization between lions and leopards, not speciation, shaped their evolutionary history.

Keywords:
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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Phylogenetics

Background:

  • Phylogenetic reconstruction is challenged by interspecies hybridization, where hybridization can obscure the true speciation tree.
  • The evolutionary relationships among Panthera species (jaguar, lion, leopard) are complex and difficult to resolve.
  • Previous studies suggest hybridization may have played a role in Panthera evolution.

Purpose of the Study:

  • To investigate the phylogenetic relationships among jaguar, lion, and leopard using whole-genome data.
  • To determine if hybridization has influenced the predominant phylogenetic signal in these species.
  • To assess the impact of hybridization on inferring species trees from genomic data.

Main Methods:

  • Whole-genome sequencing of jaguar, lion, and leopard individuals.
  • Phylogenomic analyses using maximum-likelihood trees from genomic fragments of varying sizes.
  • Divergence time estimation corrected for recombination rates.
  • Introgression analyses and multi-species-coalescence-with-introgression (MSci) modeling.

Main Results:

  • Maximum-likelihood trees consistently supported species monophyly but showed a dominant topology uniting lion and leopard.
  • This dominant topology was prevalent in high-recombination regions, while alternative topologies were enriched in low-recombination segments.
  • Divergence time analyses indicated a younger lion-leopard split, suggesting post-speciation admixture.
  • Introgression analyses and MSci models confirmed pervasive hybridization between lions and leopards, rejecting models without introgression.

Conclusions:

  • The predominant genome-wide tree topology in Panthera does not reflect the speciation tree but is a result of extensive post-speciation admixture.
  • Hybridization between lions and leopards significantly impacts phylogenetic inference, complicating the resolution of their evolutionary history.
  • Understanding introgression is crucial for accurate phylogenomic reconstruction in species with complex evolutionary dynamics.