Ancient admixture catalyzes homoploid hybrid speciation and intense genomic erosion in an Asian langur genus

Abstract

Ancient admixture catalyzes evolutionary innovation, yet its long-term genomic consequences for newly formed lineages remain poorly understood. Here, based on 53 genomes covering 19 species of the Asian langur genus Trachypithecus, we explore admixtures role in shaping a reticulated radiation. Genome-wide analyses of phylogenomic triplet topologies demonstrate that phylogenetic discordance across this radiation is primarily driven by widespread introgression rather than incomplete lineage sorting. To mitigate historical noise and resolve the ancestral species tree, we anchored our phylogenetic analysis on the X-linked recombination desert (XLRD), which exhibits an 84.5% introgression reduction compared to autosomes. We identify Delacours langur as a clear case of homoploid hybrid speciation, arising from ancient admixture with [~]70:30 genomic contributions from ancestral northern and southern limestone langur lineages. This hybrid species fixed key reproductive isolation loci; notably, alternate inheritance of pigmentation genes (SLC45A4, HPS5, ADCY10) systematically coupled with a fixed RNF175 chimeric allele to drive its diagnostic pelage phenotype. This illustrates how introgressed multi-gene networks rapidly establish prezygotic visual barriers and profound phenotypic divergence. However, subsequent spatial isolation within fragmented karst landscapes forced a major conversion of genetic burden into realized load. Genome-wide, over 82% of loss-of-function variants occur in a homozygous state, reflecting the expression of lethal recessive mutations within long runs of homozygosity. Together, our findings demonstrate that ancient admixture can trigger homoploid hybrid speciation, yet subsequent ecological restriction locks derived lineages into severe, long-term genomic erosion, revealing a fundamental trade-off in reticulate evolutionary radiations.