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

Climate change and human activities present substantial threats to the biodiversity of the Qinghai-Tibet Plateau (QTP), a region renowned for its rich endemic species. We aimed to examine genomic diversity and evolutionary trajectory of Achnatherum breviaristatum, a critically endangered monotypic grass genus endemic to the QTP. Diverging from its sister clade approximately 15 million years ago, A. breviaristatum stands in contrast to two widespread, ecologically dominant monotypic genera within the same clade—Neotrinia splendens and Psammochloa villosa—which thrive in arid northwestern China and neighboring regions. By analyzing high-quality chromosome-level genome assemblies and population resequencing data from all three species, we reveal that A. breviaristatum exhibits markedly low genetic diversity and heterozygosity. All species underwent parallel demographic declines since the Quaternary glaciation. During the Holocene, population sizes of all three species continued to diminish further, with A. breviaristatum ultimately becoming the smallest. The species’ current critically endangered status likely stems from its inability to reproduce clonally compared with two widespread relatives, coupled with Holocene vegetation shift and anthropogenic activities. Intriguingly, a significantly reduced genetic load in A. breviaristatum may have counteracted its low diversity, enabling provisional persistence on the QTP. This study highlights the interplay of historical climatic shifts, genetic constraints, and anthropogenic impacts in shaping the fate of endemic species, offering insights for conservation strategies in vulnerable ecosystems.