Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments.

Abstract

Understanding how organisms adapt to their environments is a central question in evolutionary biology. Limestone langurs are unique among primates, as they are exclusively found in karst limestone habitats and have evolved mechanisms to tolerate high levels of mineral ions, which are typically associated with metal toxicity affecting organs, cells, and genetic material. We generated a high-quality reference genome (Tfra_5.0) for the limestone langur (Trachypithecus francoisi), along with genome re-sequencing data for 48 langurs representing 15 Trachypithecus species. Genes coding for ion channels (e.g., Na+, K+, and Ca2+) exhibited significantly accelerated evolution in limestone langurs. Limestone langur-specific mutations in Na+ and Ca2+ channels were experimentally confirmed to modify inward ion currents in vitro. Unexpectedly, scans for positive selection also identified genes involved in DNA damage response/repair pathways, a previously unknown adaption. This finding highlights an evolutionary adaptation in limestone langurs that mitigate the increased risk of DNA damage posed by elevated metal ion concentrations. Notably, a limestone langur-specific mutation (E94D) of the melanocortin 1 receptor was associated with increased basal cyclic adenosine monophosphate (cAMP) production, contributing to the species' darker coat color, which likely serves as camouflage on limestone rocks. Our findings reveal novel adaptive evolutionary mechanisms of limestone langurs and offer broader insights into organismal adaptation to extreme environments, with potential implications for understanding human health, biological evolution, and biodiversity conservation.