Uncovering Ghost Introgression Through Genomic Analysis of a Distinct East Asian Hickory Species

Abstract

ABSTRACTAlthough the possibility of introgression from ghost lineages (all unsampled extant and extinct taxa) is now widely recognized, detecting and characterizing ghost introgression remains a challenge. Here, we propose a combined use of the popularD-statistic method, which tests for the presence of introgression, and the full-likelihood method BPP, which determines which of the possible gene-flow scenarios, including ghost introgression, is truly responsible. We illustrate the utility of this approach by investigating the reticulation and bifurcation history of the genusCarya(Juglandaceae), including the beaked hickoryCarya sinensis. To achieve this goal, we generated two chromosome-level reference genomes respectively forC. sinensisandC. cathayensis. Furthermore, we re-sequenced the whole genomes of 43 individuals fromC. sinensisand one individual from each of the 11 diploid species ofCarya. The latter dataset with one individual per species is used to reconstruct the phylogenetic networks and estimate the divergence time ofCarya. Our results unambiguously demonstrate the presence of ghost introgression from an extinct lineage into the beaked hickory, dispelling certain misconceptions about the phylogenetic history ofC. sinensis. We also discuss the profound implications of ghost introgression intoC. sinensisfor the historical biogeography of hickory species. [BPP;Carya;D-statistic; gene flow; ghost introgression]