Evolutionary genomics of ancient and endangered Achnatherum breviaristatum on the Qinghai-Tibet Plateau

Climate change and human activities threaten biodiversity on the Qinghai-Tibet Plateau (QTP), renowned for its endemic species. We examined genomic diversity and evolution of Achnatherum breviaristatum, an endangered grass species endemic to the QTP. A. breviaristatum diverged from its sister lineage ~15 million years ago, and contrasts with two widespread and ecologically dominant monotypic genera within the same lineage—Neotrinia splendens and Psammochloa villosa—which thrive in arid northwestern China. Using newly generated chromosome-level genome assemblies and population resequencing data for A. breviaristatum and N. splendens, together with publicly available genomic data for P. villosa, we reveal that A. breviaristatum exhibits lower genetic diversity and heterozygosity based on resequencing reads mapped to the respective reference genomes. All species experienced parallel demographic declines since the Quaternary glaciation, with reductions during the Pleistocene. The endangered status of A. breviaristatum likely results from weaker clonal reproduction relative to its relatives, combined with Pleistocene vegetation shifts and anthropogenic activities. A reduced genetic load in A. breviaristatum may mitigate the effects of its low genetic diversity and contribute to its persistence. This study highlights interactions among climatic shifts, reproductive strategy, and human impact in shaping endemic species’ fates, providing genetic insights for conservation in vulnerable ecosystems. A comparative genomics study on grasses from the Qinghai–Tibet Plateau reveals how demographic decline, reduced clonal reproduction, and Pleistocene climate shifts have driven low diversity in an endangered endemic species, while reduced genetic load may have enabled its persistence.