Different processes shape the patterns of divergence in the nuclear and chloroplast genomes of a relict tree species in East Asia

Abstract

Isolation by spatial distance (IBD), environment (IBE), and historical climatic instability (IBI) are three common processes assessed in phylogeographic and/or landscape genetic studies. However, the relative contributions of these three processes with respect to spatial genetic patterns have seldom been compared. Moreover, whether the relative contribution differs in different regions or when assessed using different genetic markers has rarely been reported. Lindera obtusiloba has been found to have two sister genetic clades of chloroplast (cpDNA) and nuclear microsatellite (nSSR), both of which show discontinuous distribution in northern and southern East Asia. In this study, we used the Mantel test and multiple matrix regression with randomization (MMRR) to determine the relative contributions of IBD, IBE, and IBI with respect to L. obtusiloba populations. Independent Mantel tests and MMRR calculations were conducted for two genetic data sets (cpDNA and nSSR) and for different regions (the overall species range, and northern and southern subregions of the range). We found a significant IBI pattern in nSSR divergence for all assessed regions, whereas no clear IBI pattern was detected with respect to cpDNA. In contrast, significant (or marginal) divergent IBD patterns were detected for cpDNA in all regions, whereas although a significant IBE was apparent with respect to the overall range, the effect was not detected in the two subregions. The differences identified in nSSR and cpDNA population divergence may be related to differences in the heredity and ploidy of the markers. Compared with the southern region, the northern region showed less significant correlation patterns, which may be related to the shorter population history and restricted population range. The findings of this study serve to illustrate that comparing between markers or regions can contribute to gaining a better understanding the population histories of different genomes or within different regions of a species' range. K E Y W O R D SEast Asia, genetic marker, isolation by distance, isolation by environment, isolation by instability, regional history

Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

“…Among these, two highly variable regions were found in the Northern population, but no high variable regions were detected in individuals from the Southern populations (Figure 3). It is speculated that the difference in cpDNA divergence patterns between the Northern and the Southern populations might be shaped by their specific evolutionary history (Tian et al, 2020). et al, 2017).…”

“…The demographic history of some species proves that subspecies living in separated subregions have experienced different selection pressures and have accumulated various mutations in their genomes (Tian et al, 2020). Intraspecific variation was recognized as a prerequisite for speciation (Bürger et al, 2006).…”

Genetic structure and trait variation within a maple hybrid zone underscore North China as an overlooked diversity hotspot

“…However, no morphological divergence, or reproductive barriers have been identified in this secondary contact zone 32,42,43 . Furthermore, Juglans mandshurica species complex 7 and Lindera obtusiloba 44 , have revealed signals of local adaptation by analysis based on isolation by environment. Hybridization of these pre-adapted lineages in North China can generate high levels of genetic and phenotypic diversity, which is important in the face of climate change and urbanization [45][46][47][48] .…”

Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China

“…Multiple glacial refugia correlated with centers of genetic diversity have been identified in subtropical China, out of which subsequent localized or rapid range expansions have been inferred (Chen et al, 2012 ; Gong et al, 2008 ; Li et al, 2012 ; Qiu et al, 2011 ; Tian et al, 2015 ). Previous research has elucidated the scenarios involved with the evolutionary history of plant species thought to be affected by glacial and postglacial cycles in subtropical China (Gong et al, 2016 ; Liu et al, 2012 ; Tian et al, 2020 ). This research suggests that climate change is considered the main driver in triggering genetic differentiation and population divergence in subtropical China (Chen et al, 2020 ; Qiu et al, 2011 ; Wang et al, 2015 , 2017 ).…”