Evolutionary history of endangered and relict tree species <i>Dipteronia sinensis</i> in response to geological and climatic events in the Qinling Mountains and adjacent areas

Shahzad, Khurram; Liu, Mi‐Li; Zhao, Yuhe; Zhang, Tingting; Liu, Jian-Ni; Li, Zhong-Hu

doi:10.1002/ece3.6996

Cited by 9 publications

(10 citation statements)

References 85 publications

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“…S11). Phylogeographic studies have revealed that the uplift of the Qinling Mountains played an important role in the genetic differentiation of many plant species in China (Guo et al, 2014;Xia et al, 2018;Shahzad et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Linked selection, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence in Quercus dentata

Zhou

Shi

Chen

et al. 2022

J of Systematics Evolution

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Multiple evolutionary forces contribute to heterogeneous genomic landscapes; however, disentangling their relative contributions is challenging. We sampled nine populations across the distribution of Quercus dentata, a dominant forest tree in East Asia, and used whole-genome sequencing data to investigate mechanisms underlying divergence. We identified two genetic groups (north and south) that diverged ~1.84 million years ago, consistent with the uplift of the Qinling Mountains during the Pleistocene. The north group experienced a bottleneck during the middle-late Pleistocene and expanded from multiple refugia. The south group experienced a more severe bottleneck and showed high population differentiation, probably due to long-term isolation and habitat fragmentation. We detected genomic islands with elevated relative differentiation (F ST ) scattered across the genome. Among these, 65.9% showed reduced absolute divergence (d XY ) consistent with linked selection, while the remaining (34.1%) showed elevated d XY suggestive of divergent sorting of ancient polymorphisms. The recombination rate in genomic islands was lower than background, suggesting the importance of genome structure in shaping the genomic landscape. We detected 108 single nucleotide polymorphisms significantly associated with environmental factors, 12 of which clustered in a region of ~500 kb. This region showed multiple signals of positive selection in the north group, including the enrichment of XP-extended haplotype homozygosity scores, an elevated population branch statistic, and an excess of high-frequency derived alleles. In addition, we found that linkage disequilibrium was low and derived haplotypes declined rapidly in this region, indicating selection on standing variation. Our results clarify the evolutionary processes driving genomic divergence in Q. dentata.

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Section: Discussionmentioning

confidence: 99%

Linked selection, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence in Quercus dentata

Zhou

Shi

Chen

et al. 2022

J of Systematics Evolution

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“…The QM provides a natural boundary between northern and southern China, and served as a geographical and ecological barrier for species with low dispersal ability ( Yan et al, 2010 ; Hu et al, 2021 ). Its isolation also promoted the divergence of some relict species ( Shahzad et al, 2020 ). Mount Taibai, belonging to the QM, is the highest peak (3,500 m a.s.l.)…”

Section: Discussionmentioning

confidence: 99%

Population genomics reveal deep divergence and strong geographical structure in gentians in the Hengduan Mountains

Sun

Hollingsworth

et al. 2022

Front. Plant Sci.

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Understanding the evolutionary and ecological processes driving population differentiation and speciation can provide critical insights into the formation of biodiversity. Here, we examine the link between population genetic processes and biogeographic history underlying the generation of diversity in the Hengduan Mountains (HM), a region harboring a rich and dynamic flora. We used restriction site-associated DNA sequencing to generate 1,907 single-nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the Gentiana hexaphylla complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing diversification of G. hexaphylla in the HM. We find the G. hexaphylla complex is characterized by geographic genetic structure with clusters corresponding to the South, North and the central HM. Phylogenetic reconstruction and pairwise FST analyses showed deep differentiation between Southern and Northern populations in the HM. The population in Mount Taibai exhibited the highest genetic similarity to the North HM. Ancestral range estimation indicated that the G. hexaphylla complex originated in the central HM and then diverged in the Pliocene and the Early Pleistocene, before dispersing widely, resulting in the current distinct lineages. Overall, we found deep genomic differentiation in the G. hexaphylla complex corresponds to geographic barriers to dispersal in the HM and highlights a critical role of the uplift of the Daxue Mountains and subsequent climatic fluctuations underlying diversification. The colonization of G. hexaphylla in the Mount Taibai region suggests directional dispersal between the alpine flora of the Qinling Mountains and the HM.

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“…Due to the high geographic and environmental heterogeneity in central China, an IBD effect on genetic divergence has been found widely in some low to moderate altitude plant species, such as Dipteronia sinensis Oliv. (Shahzad et al, 2020), and Euptelea pleiosperma J. D. Hooker & Thomson (Meng et al, 2020). Our results indicate that the Qinling Mountains in East Asia comprised an important east–west isolation barrier that led to the intraspecific differentiation of the perennial alpine cold‐tolerant herb N .…”

Section: Discussionmentioning

confidence: 99%

Drivers of intraspecific differentiation of an alpine cold‐tolerant herb, Notopterygium oviforme: Roles of isolation by distance and ecological factors

Liu

Shang

Cheng

et al. 2022

J of Sytematics Evolution

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Determining the mechanisms that drive phenotypic and genetic divergence by species has been a central topic in evolutionary biology for many years. However, the relative contributions of isolation by distance (IBD) and environment factors to species divergence are largely unknown in perennial herbs in East Asia. In this study, we collected population genetic samples of the cold-tolerant perennial herb Notopterygium oviforme R. H. Shan in central China. We integrated the population transcriptomes, whole chloroplast genomes, genotyping-bysequencing, microsatellite markers, and ecological factors to determine the relative contributions of geography, climate, and soil factors to genetic, chemical, and phenotypic divergence. A clear genetic distinction was identified between the West Qinling and East Qinling Mountains geographical groups of N. oviforme based on various molecular datasets. Interestingly, obvious niche conservation might have been responsible for the similarity of most of the leaf functional traits in the two groups. Multiple matrix regression with randomization analysis showed that the spatial intraspecific divergence pattern was mainly due to IBD rather than isolation by environment. In addition, transcriptomic expression divergence and some ecological factors have played key roles in intraspecific lineage differentiation. Approximate Bayesian Computation showed that both lineages have experienced historical population expansion and recent range contraction. Molecular dating suggested that intraspecific divergence was closely associated with dramatic uplifts of the Qinling Mountains in East Asia. These results demonstrate that geographical, geological, and environmental factors together shaped cryptic intraspecific diversification and shifts in the population dynamics of the perennial cold-tolerant herb N. oviforme.

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Evolutionary history of endangered and relict tree species Dipteronia sinensis in response to geological and climatic events in the Qinling Mountains and adjacent areas

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 9 publications

References 85 publications

Linked selection, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence in Quercus dentata

Linked selection, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence in Quercus dentata

Population genomics reveal deep divergence and strong geographical structure in gentians in the Hengduan Mountains

Drivers of intraspecific differentiation of an alpine cold‐tolerant herb, Notopterygium oviforme: Roles of isolation by distance and ecological factors

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