A new species of Paris sect. Axiparis (Melanthiaceae) from Yunnan, China

Ji, Yunheng; Yang, Chengjin; Huang, Yu‐Ling

doi:10.11646/phytotaxa.306.3.6

Cited by 14 publications

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“…We sampled 33 accessions to represent all 29 species and five varieties recognized by Li [7] and those described since then [9, 84, 117–119]. The original sources of the plant materials used in this study and voucher information are presented in Additional file 4: Table S3.…”

Section: Methodsmentioning

confidence: 99%

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Yang

Chase

et al. 2019

BMC Plant Biol

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BackgroundParis (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus.ResultsAll 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary.ConclusionsOur results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

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Section: Methodsmentioning

confidence: 99%

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Yang

Chase

et al. 2019

BMC Plant Biol

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“…Therefore, it is reasonable to recognized them as distinct species under the unified species concept (de Queiroz, 2007), given that the species boundary proposed by our data reflects the unity of morphological uniqueness, genetic distinctiveness, and evolutionary independence. The findings suggest that previous morphology-based taxonomic studies (Li, 1984;He, 1990;Li, 1992;Ji et al, 2017;Xu et al, 2019;Yang et al, 2019) overemphasize intraspecific and minor morphological differences to establish species, therefore leading to the proliferation of synonyms. As a result, it is necessary to reduce P. axialis , P. guizhouensis , P. lihengiana , and P. variabilis as the synonyms of P. vaniotii , and to merge P. dulongensis ,P. rugosa and P. tengchongensis into P. forrestii .…”

Section: Species Delimitation Scenariomentioning

confidence: 79%

“…For instance, among the nine nominal species of P.sect. Axiparis , P. dulongensis and P. lihengianaare categorized as critically endangered (Qin et al, 2017;Xu et al, 2019); P. forrestii , P. guizhouensis , P. rugosa ,P. tengchongensis and P. vaniotii are classified as endangered (Ji et al, 2017;Qin et al, 2017); P. axialis andP. variabilis are identified as Vulnerable (Qin et al, 2017;Yang et al, 2019).…”

Section: Conservation Implicationsmentioning

confidence: 99%

“…section Axiparis H. Li (Melanthiaceae), a well-supported monophyletic clade including nine described species restricted to southwest China and the Himalayas (Li, 1998;Ji et al, 2006Ji et al, , 2019bHuang et al, 2016). Discovery of the first species (Paris vaniotii ) of this group, dating back to 1906, was based on collections from Guizhou, southwestern China (Léveillé, 1906), with the remaining species have been described since the 1980s (Takhtajan, 1983;Li, 1984Li, , 1992He, 1990;Ji et al, 2017;Xu et al, 2019;Yang et al, 2019). The rapidly increasing species count in the last 40 years led to considerable taxonomic confusion inP.…”

Section: Introductionmentioning

confidence: 99%

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From nine to two: Ultra-barcoding develops a rigorous species delimitation framework in Paris section Axiparis (Melanthiaceae)

Yang

Landis

et al. 2021

Preprint

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Species delimitation is a difficult task in traditional morphology-based taxonomy. The ultra-barcoding approach, which uses whole plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions as extended DNA barcodes for species identification and delimitation, has been recommended as one of the candidate techniques for plant barcoding 2.0. Yet, the efficacy of this approach in delineating species boundaries remains poorly understood. Here, we attempt to decipher species delimitation in the taxonomically challenging clade, Paris L. section Axiparis H. Li, using phylogenetic inference and multiple sequence-based species delimitation methods (ABGD, SDP, and mPTP) utilizing complete plastomes and nrDNA clusters from multiple accessions per described species. The results suggest that only two species-level taxonomic units that possess not only morphological uniqueness but also genetic distinctiveness and evolutionary independence can be recognized in P. sect. Axiparis. Therefore, previous taxonomic work overemphasized minor intraspecific morphological differences to establish species, and thus resulted in proliferation of as many as seven synonyms in this clade. Inferred from ultra-barcoding analyses, we propose a taxonomic revision of P. sect. Axiparis which will help inform future decisions regarding species conservation in the commercially valuable and severely threatened genus Paris. This case study indicates that the ultra-barcoding approach has great promise for developing a rigorous species delimitation framework that will facilitate credible taxonomic revision especially in taxonomically difficult plant taxa.

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“…The genus Paris comprises about 27 species accepted in The Plant List (http://www.theplantlist.org/) and divides into two subgenera, Paris and Daiswa (Huang et al 2016). In recent years, several new Paris species, such as P. lihengiana (Xu et al 2019), P. tengchongensis (Ji et al 2017) and P. nitida (Wang et al 2017) were reported. In this study, we constructed the phylogenetic tree and analyzed the phylogenetic position of P. delavayi based on the maximum likelihood (ML) and Bayesian inference (BI) methods (Ronquist et al 2012;Stamatakis 2014).…”

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confidence: 99%

The complete chloroplast genome and phylogenetic analysis of Paris delavayi (Melanthiaceae)

Ling

Zhang

2020

Mitochondrial DNA Part B

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Paris delavayi Franchet is a perennial herb of the family Melanthiaceae. In this study, the complete chloroplast (cp) genome sequence of P. delavayi was characterized. The cp genome is 164,195 bp in length and contains a pair of inverted repeats (33,415 bp) separated by a large (84,400 bp) and small (12,965 bp) single-copy regions. A total of 112 unique genes were predicted, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis suggested that P. delavayi is sister to P. mairei but with low support.

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A new species of Paris sect. Axiparis (Melanthiaceae) from Yunnan, China

Cited by 14 publications

References 0 publications

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

From nine to two: Ultra-barcoding develops a rigorous species delimitation framework in Paris section Axiparis (Melanthiaceae)

The complete chloroplast genome and phylogenetic analysis of Paris delavayi (Melanthiaceae)

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