Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera

Abstract

Background and Aims Understanding adaptive genetic variation and whether it can keep pace with predicted future climate change is critical in assessing the genetic vulnerability of species and developing conservation management strategies. The lack of information on adaptive genetic variation in relict species carrying abundant genetic resources hinders the assessment of genetic vulnerability. Using landscape genomics approach, this study aimed to determine how adaptive genetic variation shapes population divergence and predict the adaptive potential of Pterocarya macroptera (a vulnerable relict species in China) under future climate scenarios. Methods We applied restriction site-associated DNA sequencing (RAD-seq) to obtain 8,244 single nucleotide polymorphisms (SNPs) from 160 individuals across 28 populations. We examined the pattern of genetic diversity and divergence, and then identified outliers by genetic differentiation (FST) and genotype–environment association (GEA) methods. We further dissected the effect of geographic/environmental gradients on genetic variation. Finally, we predicted genetic vulnerability and adaptive risk under future climate scenarios. Key Results We identified three genetic lineages within P. macroptera: the Qinling-Daba-Tianmu Mountains (QDT), Western Sichuan (WS), and Northwest Yunnan (NWY) lineages, which showed significant signals of isolation by distance (IBD) and isolation by environment (IBE). IBD and IBE explained 3.7–5.7% and 8.6–12.8% of the genetic structure, respectively. The identified GEA SNP-related genes were involved in chemical defence and gene regulation and may exhibit higher genetic variations to adapt to the environment. Gradient forest analysis revealed that the genetic variation was mainly shaped by temperature-related variables, indicating its adaptation to local thermal environments. A limited adaptive potential was suggested by the high levels of genetic vulnerability in marginal populations. Conclusions Environmental gradient mainly shaped the population differentiation of P. macroptera. Marginal populations may be at high risk of extinction, and thus, proactive management measures, such as assisted gene flow, are required to ensure the survival of these populations.

Understanding Plant Diversity from Ecological and Evolutionary Perspectives

“…In such a context, the concept that habitat suitability has been altered by climate change at the regional scale or global scale, which is causing local extinctions of biodiversity, seems possible [1]. Thus, the notion of whether adaptive genetic variation can keep pace with future climate change is a very critical factor in developing conservation management strategies when the genetic vulnerability of species is assessed [16]. And now, climate change and human activity have been considered to be major drivers of biodiversity loss and species range shifts [17].…”