AI Article Synopsis
- Ghost introgression involves the transfer of genetic material from extinct lineages into currently existing species, with limited evidence found in plants, particularly for Carya sinensis and Carya cathayensis.
- Researchers assembled chromosome-level genomes for these species and re-sequenced 43 C. sinensis individuals and 11 diploid hickory species to explore genetic patterns and confirm ghost introgression.
- Their analysis, employing methods like D-statistic and BPP alongside phylogenetic network analysis, provided strong evidence of ghost introgression in C. sinensis from an extinct lineage, enhancing the understanding of Carya's evolutionary history and biogeography.
Article Abstract
Ghost introgression, or the transfer of genetic material from extinct or unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost introgression, especially in plant species, remains scarce. Here, we newly assembled chromosome-level genomes for both Carya sinensis and Carya cathayensis, and additionally re-sequenced the whole genomes of 43 C. sinensis individuals as well as 11 individuals representing 11 diploid hickory species. These genomic datasets were used to investigate the reticulation and bifurcation patterns within the genus Carya (Juglandaceae), with a particular focus on the beaked hickory C. sinensis. By combining the D-statistic and BPP methods, we obtained compelling evidence that supports the occurrence of ghost introgression in C. sinensis from an extinct ancestral hickory lineage. This conclusion was reinforced through the phylogenetic network analysis and a genome scan method VolcanoFinder, the latter of which can detect signatures of adaptive introgression from unknown donors. Our results not only dispel certain misconceptions about the phylogenetic history of C. sinensis but also further refine our understanding of Carya's biogeography via divergence estimates. Moreover, the successful integration of the D-statistic and BPP methods demonstrates their efficacy in facilitating a more precise identification of introgression types.
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