Integrative population genomics and ecological niche modelling analyses illuminates the demographic history and inform conservation strategies of Calycanthus chinensis, a critically endangered shrub in subtropical China

Abstract

Climate changes have profoundly influenced the evolutionary history of plants, particularly for endangered species with narrow habitat ranges, which renders them disproportionately vulnerable to the impacts of climate change. Elucidating the spatial distribution of genetic variation and demographic patterns within threatened species populations provides essential empirical evidence for designing biologically meaningful conservation interventions. Here, we integrated population genomics with species distribution modeling analyses to investigate the genetic diversity and changes in the suitability distribution of Calycanthus chinensis, an endangered shrub in subtropical China, ultimately informing evidence-based conservation strategies for this threatened species. We assembled 75 plastomes and obtained nuclear genome-wide SNP data to address evolutionary processes of C. chinensis. The plastome-based phylogeny revealed that C. chinensis lineage diversification started in the later Pliocene (2.75 Ma) and was concentrated in the Pleistocene. Analysis of genome-wide SNPs revealed that seven populations clustered into two lineages corresponding to the two main geographic distributions. The AMOVA analyses revealed that genetic variation occurred mainly within populations. Nucleotide diversity analyses suggested that low genetic diversity may be one of a threat to C. chinensis. Demographic analyses revealed a bottleneck event from 0.4–0.7 Ma, which was associated with the Wangkun glaciation. Ecological niche modelling analyses revealed that these two genetic groups are likely to face the loss of highly suitable habits in response to future climate change. Our findings provide novel insights into the evolutionary history of C. chinensis and inform evidence-based conservation strategies.