The Use of DNA Barcoding on Recently Diverged Species in the Genus Gentiana (Gentianaceae) in China

Liu, Juan; Yan, Hai‐Fei; Ge, Xue‐Jun

doi:10.1371/journal.pone.0153008

Cited by 35 publications

(30 citation statements)

References 59 publications

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“…This high resolution was also found in previous research (e.g., Li et al, 2011; Liu et al, 2016; Wirta et al, 2016), for example, in Rhododendron (Yan et al, 2015), Venus Slipper (Guo et al, 2016) and in Rosewood (Hartvig et al, 2015). These previous results showed that the ITS marker performed well as a single barcode for species identification, although the ITS marker was considered to have drawbacks, including incomplete lineage sorting and homogeneous concerted evolution (Liu et al, 2011, 2016; Wang et al, 2011; Wirta et al, 2016). However, in a recent study, Li et al (2011) found that the nuclear ITS barcode had high species discrimination power, and they proposed that it should be incorporated into the core barcode marker for land plants.…”

Section: Discussionsupporting

confidence: 86%

“…Thus, the ITS fragment has a larger effective population size than the chloroplast DNA regions, which makes the ITS marker is not easily quicker to complete lineage sorting than the cpDNA markers (Wachowiak et al, 2011). However, the nuclear ITS marker showed a higher evolutionary rate and higher inter-species differentiation than the chloroplast regions, and the nuclear ITS region in plants comprises multiple (reiterated) copies and usually undergoes concerted evolution (Alvarez and Wendel, 2003; Liu et al, 2016). During this process, different copies become homogenized to the same sequence type (becoming almost identical types) as a result of mechanisms such as high-frequency unequal crossing over or gene conversion (Alvarez and Wendel, 2003; Hartvig et al, 2015; Wirta et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

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Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

Han

Duan

et al. 2016

Front. Plant Sci.

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Aceraceae is a large forest tree family that comprises many economically and ecologically important species. However, because interspecific and/or intraspecific morphological variations result from frequent interspecific hybridization and introgression, it is challenging for non-taxonomists to accurately recognize and identify the tree species in Aceraceae based on a traditional approach. DNA barcoding is a powerful tool that has been proposed to accurately distinguish between species. In this study, we assessed the effectiveness of three core standard markers (matK, rbcL and ITS) plus the chloroplast locus trnS-trnG as Aceraceae barcodes. A total of 231 sequences representing 85 species in this forest family were collected. Of these four barcode markers, the discrimination power was highest for the ITS (I) region (50%) and was progressively reduced in the other three chloroplast barcodes matK (M), trnS-trnG (T) and rbcL (R); the discrimination efficiency of the ITS marker was also greater than any two-locus combination of chloroplast barcodes. However, the combinations of ITS plus single or combined chloroplast barcodes could improve species resolution significantly; T+I (90.5% resolution) and R+M+T+I (90.5% resolution) differentiated the highest portion of species in Aceraceae. Our current results show that the nuclear ITS fragment represents a more promising DNA barcode marker than the maternally inherited chloroplast barcodes. The most efficient and economical method to identify tree species in Aceraceae among single or combined DNA barcodes is the combination of T+I (90.5% resolution).

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Section: Discussionsupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

Han

Duan

et al. 2016

Front. Plant Sci.

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“…In contrast, many studies have considered only M. azedarach as an accepted species (Dassanayake 1995;Ahmed et al 2012;Dharmalingam et al 2014;Lake 2015). The existing complexity of whether M. azedarach and M. dubia are the same or different species can be D r a f t resolved using DNA barcoding, which was reported to be efficient in species differentiation and identification of cryptic species (Ragupathy et al 2009;Liu et al 2016).…”

Section: Despite Its Multipurpose Values and Importance Species Levementioning

confidence: 99%

Species delimitation of Melia dubia Cav. from Melia azedarach L. complex based on DNA barcoding

Irusappan

Nithaniyal²,

Bhooma

et al. 2018

Botany

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The genus Melia L., which belongs to the 'Mahogany' family Meliaceae, is a source of important phytochemicals with marked medicinal properties. Species identification in Melia is complex due to the existence of overlapping morphological features. Though Melia dubia Cav. is listed as a synonym of Melia azedarach L., it is not clear from the available literature whether they are the same species or different, and the species complexity still remains unresolved. In the present study, ten accessions of M. dubia and M. azedarach were analysed by DNA barcoding using three chloroplast DNA markers (rbcL, matK, and trnH-psbA), and one nuclear marker (ITS2). Intra-specific divergence was not found in any of the four markers. However, the inter-specific divergence between M. azedarach and M. dubia ranged between 0.3% (rbcL) and 4.7% (ITS2) for individual markers, and for the combined dataset, it was 8.5%. Among the four markers, ITS2 was found to be the most suitable marker for

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“…To understand the mechanisms that facilitate these processes, we however need to resolve the phylogenetic relationships between closely related species. This task is usually difficult to achieve with traditional genetic markers (e.g., rbcL, matK, ITS), especially for genera that harbor high species richness and experience hybridization during their evolution, such as Primula L. (Guggisberg, Mansion, & Conti, 2009;Schmidt-Lebuhn, de Vos, Keller, & Conti, 2012) and Gentiana L. (Liu, Yan, & Ge, 2016). This problem may be overcome by using many thousands of DNA markers (e.g., Pante et al, 2015;Wagner et al, 2013), for example, using recently developed next-generation sequencing methods such as restriction site associated DNA (RAD) sequencing (Baird et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Species divergence and maintenance of species cohesion of three closely related Primula species in the Qinghai–Tibet Plateau

Ren

Mateo

Guisan

et al. 2018

Journal of Biogeography

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Aim Understanding the relative roles of geography and ecology in driving speciation, population divergence and maintenance of species cohesion is of great interest to molecular ecology. Closely related species that are parapatrically distributed in mountainous areas provide an ideal model to evaluate these key issues, especially when genomic data are analyzed within a spatially and ecologically explicit context. Here, we used three closely related species of Primula that occur in the Himalayas, the Hengduan Mountains and north‐east Qinghai–Tibet Plateau (QTP) to examine spatial and ecological effects on interspecific divergence and maintenance of species cohesion. Location Himalayas, the Hengduan Mountains and north‐east QTP. Methods We used genomic data for 770 samples of the three species using double‐digest restriction site‐associated DNA (ddRAD) sequencing and combined approximate Bayesian computation (ABC) modeling, generalized linear mixed modeling (GLMM) and niche‐based species distribution modeling (SDM). Results The three species are clearly delimited by the RADseq data. Further ABC modeling indicates that Primula tibetica diverged first followed by a later divergence between Primula nutans and Primula fasciculata. The time frames of the divergences among the three species coincide with the uplifts of the Hengduan Mountains and the northern QTP during the late Miocene and Pliocene followed by a long period of founder events. SDMs indicate that the three species might have survived in different refugia during glaciations and came into secondary contact during the postglacial expansions but with no significant introgression. Finally, GLMM suggests that both the geographical and ecological factors play roles in population differentiation in P. fasciculata and P. tibetica, while for P. nutans, geography is the major driver of genomic variation. The different roles played by geographical and ecological factors in the three species may have affected the maintenance of species cohesion. Main conclusion Our results provide insights of unprecedented details into the start and maintenance of interspecific divergence in the context of changing environments in mountains. Our findings highlight the significance of combining population genomics with environmental data when evaluating the effects of geography and ecology on interspecific divergence and maintenance of closely related species.

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The Use of DNA Barcoding on Recently Diverged Species in the Genus Gentiana (Gentianaceae) in China

Cited by 35 publications

References 59 publications

Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

Species delimitation of Melia dubia Cav. from Melia azedarach L. complex based on DNA barcoding

Species divergence and maintenance of species cohesion of three closely related Primula species in the Qinghai–Tibet Plateau

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