Strong population bottleneck and repeated demographic expansions of Populus adenopoda (Salicaceae) in subtropical China

Fan, Liqiang; Zheng, Honglei; Milne, Richard I.; Zhang, Lei; Mao, Kangshan

doi:10.1093/aob/mcx198

Cited by 28 publications

(21 citation statements)

References 82 publications

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“…Fragment sizes were read with the GeneMapper version 4.0. CERVUS [32] was used in eliminating four loci as existing null alleles (F (Null) > 0.4) [33]. PCR products by three cpDNA intergenic spacers were sequenced in both directions by Sangon Biotech Services Company Ltd. (Shanghai, China).…”

Section: Dna Extraction Pcr Amplification and Sequencingmentioning

confidence: 99%

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Zhang

Liu

Wang

et al. 2020

Plants

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Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (H E = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: F ST = 0.165***; cpDNA: F ST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000-100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex. Plants 2020, 9, 338 2 of 16 potential genetic resources for the development of new cultivars that can adapt to diverse environmental conditions [4]. In addition, plants in the genus Rhododendron L. produce numerous chemical constituents and are recognized as an important source of bioactive phytochemicals [5]. Some Rhododendron species are used as traditional medicine in China, India, Europe, and North America against various diseases, such as inflammation, pain, skin ailments, common cold, and gastrointestinal disorders [5]. However, as an important natural resource for human daily life and ecosystem composition, most Rhododendron species are facing risk of extinction due to the high frequency of anthropogenic disturbance [6]. Thus, research on the population genetic information of Rhododendron species is undoubtedly beneficial for germplasm protection and sustainable utilization [6][7][8][9].Inferring genetic information is recognized as the undisputed basis for the sustainable exploitation and conservation of plant diversity [10,11]. Different molecular markers are used in assessing genetic information and identifying distinct plant populations for management and conservation [12][13][14]. Microsatellite markers (SSRs) are used in revealing the genetic characteristics and related influence factors of plant species at individual and population levels due to their desirable advantages [13,15]. Chloroplast DNA (cpDNA), whic...

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Section: Dna Extraction Pcr Amplification and Sequencingmentioning

confidence: 99%

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Zhang

Liu

Wang

et al. 2020

Plants

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“…A substantially different modeled LIG distribution compared with those during the present interglacial period is not unique to the Emei mustache toad. Around the Sichuan Basin, such results have been commonly obtained for various animal [49,50,[68][69][70][71] and plant groups [45,55,72,73]. Because the LIG period at1 40-120 ka is relatively recent on an evolutionary scale, it is unlikely that the corresponding effects have been erased.…”

Section: Climatic Suitabilitymentioning

confidence: 86%

Dynamics behind disjunct distribution, hotspot-edge refugia, and discordant RADseq/mtDNA variability: insights from the Emei mustache toad

Dai

Guo

et al. 2020

BMC Evol Biol

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Background: The distribution of genetic diversity and the underlying processes are important for conservation planning but are unknown for most species and have not been well studied in many regions. In East Asia, the Sichuan Basin and surrounding mountains constitute an understudied region that exhibits a "ring" of high species richness overlapping the eastern edge of the global biodiversity hotspot Mountains of Southwest China. We examine the distributional history and genetic diversification of the Emei mustache toad Leptobrachium boringii, a typical "ring" element characterized by disjunct ranges in the mountains, by integrating time-calibrated gene tree, genetic variability, individual-level clustering, inference of population splitting and mixing from allele frequencies, and paleoclimatic suitability modeling. Results: The results reveal extensive range dynamics, including secondary contact after long-term isolation via westward dispersal accompanied by variability loss. They allow the proposal of a model that combines recurrent contractions caused by Quaternary climatic changes and some failed expansions under suitable conditions for explaining the shared disjunct distribution pattern. Providing exceptional low-elevation habitats in the hotspot area, the eastern edge harbors both long-term refugial and young immigrant populations. This finding and a synthesis of evidence from other taxa demonstrate that a certain contributor to biodiversity, one that preserves and receives low-elevation elements of the east in this case, can be significant for only a particular part of a hotspot. By clarifying the low variability of these refugial populations, we show that discordant mitochondrial estimates of diversity can be obtained for populations that experienced admixture, which would have unlikely left proportional immigrant alleles for each locus.

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“…Different studies showed that spatial separation of Populus spp. populations is governed by historical processes, mainly by events in the Pleistocene and Holocene (Keller et al, 2010;Macaya-Sanz et al, 2012;Dewoody et al, 2015;Meirmans et al, 2017;Fan et al, 2018). Therefore, the variability of P. laurifolia population structure in the Tom River basin is the subject for a further extended research.…”

Section: Discussionmentioning

confidence: 99%

Phenetic Analysis of Populus Nigra, P. Laurifolia and P. × Jrtyschensis in Natural Hybridization Zone

Klimov¹

2018

Vestn. VOGiS

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The wide spread of hybridization in the genus Populus, including spontaneous hybridization, caused by cultivars, requires studying the variability and inheritance of morphological traits by hybrids for initial tracking of these processes. The analysis of endogenous, intra- and inter-population variability was performed on 533 individual poplar trees in seven populations of P. nigra, seven populations of P. laurifolia and four populations of P. × jrtyschensis in the Tom river basin. On each specimen, 15 leaves from short mid-crown branches were collected to determine the shape of the leaf blade, the shape of its tip and base, as well as the branch morphotype. Some biometric indicators were proposed for geometric assessment of the leaf blade shapes of poplar species. The analysis showed that of all the traits examined only the leaf blade shape did not meet the criterion for “phene”, since it is usually represented by several forms in the crown of one and the same tree. In all the species studied, the level of their intra-population diversity was found to be much higher than the inter-population one. According to the increase of intra-population variability of qualitative traits, the taxa could be ranked as P. nigra < P. laurifolia < P. × jrtyschensis. The share of inter-population diversity differed among the species studied, accounting for 21.5% in P. laurifolia, 13.8% in P. nigra and 8.0% in P. × jrtyschensis. The P. laurifolia populations showed the greatest inter-population differentiation, most likely because of a disjunct distribution due to narrow specialization to the montane river environment. The lower differentiation in P. nigra is probably due to the facts that this species dominates the poplar stands of the Tom River basin; its populations are not fragmented and are linked by vast gene flow. In P. nigra, an increase in the diversity of qualitative characteristics and phenotypes was observed in populations confined to hybridization centers. Natural selection is most likely the factor governing the inter-population differentiation in P. × jrtyschensis, leading to the predominance of F1 hybrids in populations and hence to a sharp decrease in inter-population variability.

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Strong population bottleneck and repeated demographic expansions of Populus adenopoda (Salicaceae) in subtropical China

Cited by 28 publications

References 82 publications

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Dynamics behind disjunct distribution, hotspot-edge refugia, and discordant RADseq/mtDNA variability: insights from the Emei mustache toad

Phenetic Analysis of Populus Nigra, P. Laurifolia and P. × Jrtyschensis in Natural Hybridization Zone

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