Phylogeographic Analyses of the East Asian Endemic Genus Prinsepia and the Role of the East Asian Monsoon System in Shaping a North-South Divergence Pattern in China

Ma, Xiang-Guang; Wang, Zhiwei; Tian, Bin; Sun, Hang

doi:10.3389/fgene.2019.00128

Cited by 12 publications

(19 citation statements)

References 39 publications

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“…Three chloroplast fragments, psbJ-petA , psbB-psbF , and trnL-trnF , and two species-specific low-copy nuclear genes ( 6146 and 38274 ) developed using transcriptome data ( Fu et al, 2016 ) following the procedure described by Ye et al (2017c) were used to detect potential genetic variation in S. tuberculata ( Supplementary Table 1 ). The PCRs were performed following the protocol of Ma et al (2019) , except for different annealing temperatures ( Supplementary Table 1 ), and the products were sequenced by Sangon Biotech (Shanghai, China).…”

Section: Methodsmentioning

confidence: 99%

Insights Into the Significance of the Chinense Loess Plateau for Preserving Biodiversity From the Phylogeography of Speranskia tuberculata (Euphorbiaceae)

et al. 2021

Front. Plant Sci.

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The significance of the Chinese Loess Plateau (CLP) in maintaining biodiversity for northern China has rarely been shown, as previous phylogeographic studies are mostly woody species and they have revealed that Quaternary refugia are mainly located in mountain regions. We selected a drought-enduring endemic herb, Speranskia tuberculata (Euphorbiaceae), to determine its glacial refugia and postglacial demographic history. To this end, we sampled 423 individuals from 38 populations covering its entire geographic distribution. Three chloroplast DNA (cpDNA) fragments, two low-copy nuclear genes, and six nuclear microsatellites (nSSRs) were used and supplemented with ecological niche modeling (ENM) to infer the phylogeographic history of this species. Populations with private haplotypes and high haplotype diversity of cpDNA are mainly located in the CLP or scattered around northeastern China and the coastal region. Spatial expansion, detected using a neutrality test and mismatch distribution, may have resulted in a widely distributed ancestral cpDNA haplotype, especially outside of the CLP. For nuclear DNA, private haplotypes are also distributed mainly in the CLP. In nSSRs, STRUCTURE clustering identified two genetic clusters, which are distributed in the west (western cluster) and east (eastern cluster), respectively. Many populations belonged, with little to no admixture, to the western cluster while (hardly) pure populations of the eastern cluster were barely found. Genetic differentiation is significantly correlated with geographic distance, although genetic diversity is uniformly distributed. ENM suggests that the distribution of S. tuberculata has recently expanded northwards from the southern CLP, whereas it has experienced habitat loss in the south. Thus, S. tuberculata populations probably survived the last glacial maximum (LGM) in the southern CLP and experienced post-glacial expansion. Wind-dispersed pollen could bring the majority of genotypes to the front during spatial expansion, resulting in uniformly distributed genetic diversity. Based on evidence from molecular data and vegetation and climate changes since the LGM, we conclude that drought-enduring species, especially herbaceous species, are likely to have persisted in the CLP during the LGM and to have experienced expansion to other regions in northern China.

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Section: Methodsmentioning

confidence: 99%

Insights Into the Significance of the Chinense Loess Plateau for Preserving Biodiversity From the Phylogeography of Speranskia tuberculata (Euphorbiaceae)

et al. 2021

Front. Plant Sci.

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“…(Guo et al, 2014), Kalopanax septemlobus Koidz. (Sakaguchi et al, 2012), and Prinsepia Royle (Ma, Wang, Tian, & Sun, 2019). We suspect that this abrupt genetic break between L. obtusiloba populations could be attributed to the drought sensitivity of the species and that the arid belt located between NEA and SEA regions may represent a strong climatic barrier to the spread of L. obtusiloba .…”

Section: Introductionmentioning

confidence: 99%

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

Tian

Wang

et al. 2020

Ecology and Evolution

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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

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“…More specifically, the drier and colder EAWM may more dominantly function than EASM in the responsive process due to obstructed EASM by complex topography in the regions of the QTP, such as the uplift of the QTP and many mountains. The EAMS is believed to have had a tremendous influence during the Pleistocene on the genetic diversification and speciation of plants in the regions of the QTP [ 23 , 24 , 25 , 26 , 27 ]. For example, intraspecific divergence, population growth, and gene flow in two species of desert plants, Reaumuria soongarica and Agriophyllum squarrosum , appear to have been driven by the onset and stabilization of the EAMS [ 23 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

“…For example, intraspecific divergence, population growth, and gene flow in two species of desert plants, Reaumuria soongarica and Agriophyllum squarrosum , appear to have been driven by the onset and stabilization of the EAMS [ 23 , 28 ]. Notably, the origin of Prinsepia species was suggested to have occurred prior to the establishment of EAMS based on a phylogenetic analysis of the Rosaceae [ 26 ]. Ma et al reported that the divergence of Prinsepia species was potentially induced by the EASM, which produced a zone of humid forest vegetation during the late Oligocene [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

“…Notably, the origin of Prinsepia species was suggested to have occurred prior to the establishment of EAMS based on a phylogenetic analysis of the Rosaceae [ 26 ]. Ma et al reported that the divergence of Prinsepia species was potentially induced by the EASM, which produced a zone of humid forest vegetation during the late Oligocene [ 26 ]. This result provided an indirect evidence for the onset of a paleoclimatic event.…”

Section: Introductionmentioning

confidence: 99%

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The East Asian Winter Monsoon Acts as a Major Selective Factor in the Intraspecific Differentiation of Drought-Tolerant Nitraria tangutorum in Northwest China

Yin

Wang

Shi

et al. 2020

Plants

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The influence of Quaternary climate fluctuation on the geographical structure and genetic diversity of species distributed in the regions of the Qinghai–Tibet Plateau (QTP) has been well established. However, the underlying role of the East Asian monsoon system (EAMS) in shaping the genetic structure of the population and the demography of plants located in the arid northwest of China has not been explored. In the present study, Nitraria tangutorum, a drought-tolerant desert shrub that is distributed in the EAMS zone and has substantial ecological and economic value, was profiled to better understand the influence of EAMS evolution on its biogeographical patterns and demographic history. Thus, the phylogeographical structure and historical dynamics of this plant species were elucidated using its five chloroplast DNA (cpDNA) fragments. Hierarchical structure analysis revealed three distinct, divergent lineages: West, East-A, and East-B. The molecular dating was carried out using a Bayesian approach to estimate the time of intraspecies divergence. Notably, the eastern region, which included East-A and East-B lineages, was revealed to be the original center of distribution and was characterized by a high level of genetic diversity, with the intraspecific divergence time dated to be around 2.53 million years ago (Ma). These findings, combined with the data obtained by ecological niche modeling analysis, indicated that the East lineages have undergone population expansion and differentiation, which were closely correlated with the development of the EAMS, especially the East Asian winter monsoon (EAWM). The West lineage appears to have originated from the migration of N. tangutorum across the Hexi corridor at around 1.85 Ma, and subsequent colonization of the western region. These results suggest that the EAWM accelerated the population expansion of N. tangutorum and subsequent intraspecific differentiation. These findings collectively provide new information on the impact of the evolution of the EAMS on intraspecific diversification and population demography of drought-tolerant plant species in northwest China.

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Phylogeographic Analyses of the East Asian Endemic Genus Prinsepia and the Role of the East Asian Monsoon System in Shaping a North-South Divergence Pattern in China

Cited by 12 publications

References 39 publications

Insights Into the Significance of the Chinense Loess Plateau for Preserving Biodiversity From the Phylogeography of Speranskia tuberculata (Euphorbiaceae)

Insights Into the Significance of the Chinense Loess Plateau for Preserving Biodiversity From the Phylogeography of Speranskia tuberculata (Euphorbiaceae)

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

The East Asian Winter Monsoon Acts as a Major Selective Factor in the Intraspecific Differentiation of Drought-Tolerant Nitraria tangutorum in Northwest China

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