Genomic insights into historical population dynamics, local adaptation, and climate change vulnerability of the East Asian Tertiary relict Euptelea (Eupteleaceae)

Abstract

The warm‐temperate and subtropical climate zones of East Asia are a hotspot of plant species richness and endemism, including a noticeable number of species‐poor Tertiary relict tree genera. However, little is understood about when East Asian Tertiary relict plants diversified, how they responded demographically to past environmental change, and to what extent their current genomic composition (and adaptive capacity) might mitigate the effects of global warming. Here, we obtained genomic (RAD‐SNP) data for 171 samples from two extant species of Euptelea in China (24 E. pleiosperma populations) and Japan (11 E. polyandra populations) to elucidate their divergence and demographic histories, genome‐wide associations with current environmental variables, and genomic vulnerability to future climate change. Our results indicate that Late Miocene changes in climate and/or sea level promoted species divergence, whereas Late Pliocene uplifting in southwest China likely fostered lineage divergence within E. pleiosperma. Its subsequent range expansion into central/east (CE) China bears genomic signatures of climate‐driven selection, yet extant CE populations are predicted to be most vulnerable to future climate change. For E. polyandra, geography was the only significant predictor of genomic variation. Our findings indicate a profound impact of Late Neogene geological and climate change on the evolutionary history of Euptelea, with much stronger signals of local adaptation left in China than in Japan. This study deepens our understanding of the complex evolutionary forces that influence the distribution of genetic variation of Tertiary relict trees, and provides insights into their susceptibility to global change and potential for adaptive responses. Our results lay the groundwork for future conservation and restoration programs for Euptelea.

Population Genetic Structure and Biodiversity Conservation of a Relict and Medicinal Subshrub Capparis spinosa in Arid Central Asia

“…The genetic diversity of C. spinosa (Pi = 0.2644) (Table 1) through RAD-seq is higher than that of other relic species (such as Euptelea pleiosperma and Gymnocarpos przewalskii) [11,48] because widespread species have a higher genetic diversity than species with endemic distribution. The total diversity index in arid central Asia is also different from that obtained by previous research using AFLP, RAPD and EST-SSR for C. spinosa in the Mediterranean coast (southern Europe, north Africa and west Asia) [18,20,21].…”

“…In recent years, they have been increasingly widely applied in research fields of phylogenetics, molecular ecology, conservation genetics and biogeography [41][42][43]. As a high-efficiency next-generation highthroughput sequencing technology (NGS) that has been developed and commonly used, restriction-site-associated DNA sequencing (RAD-Seq) can rapidly identify and score highresolution SNP data from thousands of orthologous sites, while reducing the complexity of genomic sequences, even in the absence of reference genomes [44,45], becoming one of the main effective methods to address critical issues in the fields of evolution and genetics at the genomic level [46], especially for studies of species groups with ancient origins and complex evolutionary and genetic structures [47,48].…”

Inferring historical survivals of climate relicts: the effects of climate changes, geography, and population-specific factors on herbaceous hydrangeas

“…To investigate the species and population responses to historical climate changes, phylogeographic studies have been performed mainly for widespread woody taxa in East Asia. These studies have contributed to our understanding by reconstructing demographic histories in relation to environmental changes (Cao et al 2020;Chou et al 2011;Lu et al 2020;Qi et al 2012;Sakaguchi et al 2012) and by detecting climate refugia that contributed to long-term persistence (Qi et al 2014;Worth et al 2013). However, our knowledge is still inadequate regarding whether the species' life history could predict how climate relicts survived in East Asia through the climate deterioration in the Tertiary and glacial-interglacial cycles in the Quaternary (Harrison and Noss 2017), because most genetic studies in this region focused on widespread trees with high fecundity and dispersal abilities.…”

Closely Related Tree Species with Overlapping Ranges Exhibit Divergent Adaptation to Climate

“…Therefore, the characterisation of these suite of SNPs and their associated genes allows for further analysis and investigation of the influence they may have upon climate adaptation. Previous studies have performed GDM analyses on SNP datasets to categorise the allele frequency shift (or allelic turnover), and genomic vulnerability across the landscape (Ahrens et al, 2019;Cao et al, 2020;Fitzpatrick & Keller, 2015;Supple et al, 2018). Our data did not highlight one or few SNPs of large allelic turnover across the landscape, therefore we subsequently performed this analysis on a collection of SNPs associated with the common enriched GO term found among both eucalypts.…”