Phylogeography of &lt;I&gt;Davidia involucrata&lt;/I&gt; (Davidiaceae) Inferred from cpDNA Haplotypes and nSSR Data

Ma, Qing; Du, Yu-juan; Chen, Nan; Zhang, Luyi; Li, Jianhua; Fu, Chengxin

doi:10.1600/036364415x689267

Cited by 27 publications

(33 citation statements)

References 91 publications

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“…Despite its restricted and highly disjunct distribution range, P. subaequalis exhibits similar or even higher levels of cpDNA haplotype diversity ( H cp = 0.862) as compared to other Chinese endemic flowering plant taxa presented in previous studies by using similar markers (e.g., 0.893 for Davidia involucrata , Ma et al, 2015 ; 0.627 for Dipteronia dyeriana , Chen et al, 2017 ). The species-wide levels of haplotype diversity in P. subaequalis were also higher than the mean value of 170 seed plants estimated by maternally inherited markers (mean: h T = 0.67; Petit et al, 2005 ).…”

Section: Discussionmentioning

confidence: 51%

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

et al. 2018

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Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units.

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Section: Discussionmentioning

confidence: 51%

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

et al. 2018

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“…biloba , Davidia involucrata , Emmenopterys henryi , Euptelea pleiosperma , Liriodendron chinense , Tetracentron sinense ) are confined to relatively narrow, discontinuous ranges in subtropical China, where they often occur in small, isolated mountain populations on unstable sites, such as scree slopes and eroded rocky stream banks (reviewed in Shang et al ., 2016). Earlier phylogeographic studies, primarily based on organellar markers, indicated that these Tertiary relict trees, indeed, experienced repeated range contractions and expansions associated with Quaternary glacial–interglacial cycles (Qiu et al ., 2011; Sun et al ., 2014; Ma et al ., 2015; Cao et al ., 2016; Zhang et al ., 2016; Shen et al ., 2019). However, with the exception of a couple of studies (Tsumura et al ., 2012; Zhang et al ., 2016; Zhao et al ., 2019), there have so far been limited attempts to link those demographic changes with adaptive responses, even though one could expect that both are associated (Shaw & Etterson, 2012).…”

Section: Introductionmentioning

confidence: 99%

Genomic insights on the contribution of balancing selection and local adaptation to the long‐term survival of a widespread living fossil tree, Cercidiphyllum japonicum

et al. 2020

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Summary ‘Living fossils’ are testimonies of long‐term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations remains unclear. To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum, a widespread East Asian Tertiary relict tree, and resequenced 99 individuals of C. japonicum and its sister species, Cercidiphyllum magnificum (Central Japan). We dated this speciation event to the mid‐Miocene, and the intraspecific lineage divergence of C. japonicum (China vs Japan) to the Early Pliocene. Throughout climatic upheavals of the late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C. japonicum. However, this polymorphism loss was likely counteracted by, first, long‐term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance, and, second, selective sweeps at stress response and growth‐related genes likely involved in local adaptation. Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range; that is, both types of selection could be major factors contributing to the species' survival, resilience, and persistence.

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“…sinensis into eastern China. Postglacial dispersal and range expansion also occurred in other relict plants in China, such as Cercidiphyllum [ 64 ], Davidia [ 65 , 66 ], Euptelea [ 67 ] and Tetracentron [ 68 ].…”

Section: Discussionmentioning

confidence: 99%

Phylogeography and conservation genetics of the rare and relict Bretschneidera sinensis (Akaniaceae)

et al. 2018

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Bretschneidera sinensis, a class-I protected wild plant in China, is a relic of the ancient Tertiary tropical flora endemic to Asia. However, little is known about its genetics and phylogeography. To elucidate the current phylogeographic patterns and infer the historical population dynamics of B. sinensis, and to make recommendations for its conservation, three non-coding regions of chloroplast DNA (trnQ-rps16, rps8-rps11, and trnT-trnL) were amplified and sequenced across 256 individuals from 23 populations of B. sinensis, spanning 10 provinces of China. We recognized 13 haplotypes, demonstrating relatively high total haplotype diversity (hT = 0.739). Almost all of the variation existed among populations (98.09%, P < 0.001), but that within populations was low (1.91%, P < 0.001). Strong genetic differentiation was detected among populations (GST = 0.855, P < 0.001) with limited estimations of seed flow (Nm = 0.09), indicating that populations were strongly isolated from one another. According to SAMOVA analysis, populations of B. sinensis in China could be divided into five geographic groups: (1) eastern Yunnan to western Guangxi; (2) Guizhou-Hunan-Hubei; (3) central Guangdong; (4) northwestern Guangdong; and (5) the Luoxiao-Nanling-Wuyi -Yangming Mountain. Network analysis showed that the most ancestral haplotypes were located in the first group, i.e., the eastern Yungui Plateau and in eastern Yunnan, which is regarded as a putative glacial refugia for B. sinensis in China. B. sinensis may have expanded its range eastward from these refugia and experienced bottleneck or founder effects in southeastern China. Populations in Liping (Guizhou Province), Longsheng (Guangxi Province), Huizhou (Guangdong Province), Chongyi (Jiangxi Province), Dong-an (Hunan Province), Pingbian (Yunnan Province) and Xinning (Hunan Province) are proposed as the priority protection units.

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Phylogeography of <I>Davidia involucrata</I> (Davidiaceae) Inferred from cpDNA Haplotypes and nSSR Data

Cited by 27 publications

References 91 publications

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

Genomic insights on the contribution of balancing selection and local adaptation to the long‐term survival of a widespread living fossil tree, Cercidiphyllum japonicum

Phylogeography and conservation genetics of the rare and relict Bretschneidera sinensis (Akaniaceae)

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