Ancient admixture is a powerful catalyst for evolutionary innovation, yet its long-term genomic consequences for newly formed lineages remain poorly understood. Here, using 53 whole genomes across 19 species of the Asian langur genus Trachypithecus, we explore ancient admixture's role in shaping a reticulated radiation. Anchoring our phylogenetic analysis on the X-linked recombination desert (XLRD), which shows an 84.5% reduction in introgression compared to autosomes, mitigates genome-wide historical noise to resolve the true ancestral species tree. 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, establishing reticulation as the dominant force shaping genomic diversity. Within this network, we identify Delacour's langur as a clear case of homoploid hybrid speciation, arising from ancient admixture with ~30:70 genomic contributions from northern and southern ancestral limestone langur lineages. This hybrid lineage appears to have fixed key loci related to reproductive isolation, including a chimeric RNF175 allele potentially determining its diagnostic pelage phenotype, illustrating how introgressed variation can underpin rapid phenotypic divergence. However, subsequent spatial isolation within fragmented karst landscapes forced a major conversion of genetic burden into realized load. Genus-wide, homozygous loss-of-function variants exceed 82%, consistent with the expression of lethal recessive mutations within long runs of homozygosity. Together, our findings demonstrate that ancient admixture can simultaneously trigger homoploid hybrid speciation and lock derived lineages into severe, long-term genomic erosion, revealing a fundamental trade-off at the heart of reticulate evolutionary radiations.
Qi, J., zhao, q., zhang, l., Rusitanmu, D., shen, y., liu, g., li, x., teng, y., Miguez, R. P., Truong, N. V., Le, M. D., Nadler, T., Schonfelder, R., Zhou, X., Liu, Z., Roos, C., Li, M.
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