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From nine to two: Ultra-barcoding develops a rigorous species delimitation framework in Paris section Axiparis (Melanthiaceae)
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  • Yunheng Ji,
  • Jin Yang,
  • Jacob Landis,
  • Shuying Wang,
  • Zhenyan Yang,
  • Lei Jin,
  • Li Li,
  • Jun-Bo Yang,
  • Ting Shuang Yi
Yunheng Ji
Kunming Institute of Botany Chinese Academy of Sciences
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Jin Yang
Kunming Institute of Botany Chinese Academy of Sciences
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Jacob Landis
Cornell University
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Shuying Wang
Kunming Institute of Botany Key Laboratory of Plant Diversity and Biogeography of East Asia
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Zhenyan Yang
Kunming Institute of Botany Chinese Academy of Sciences
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Lei Jin
Kunming Institute of Botany Chinese Academy of Sciences
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Li Li
Kunming Institute of Botany Key Laboratory of Plant Diversity and Biogeography of East Asia
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Jun-Bo Yang
Kunming Institute of Botany Chinese Academy of Sciences
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Ting Shuang Yi
Kunming Institute of Botany,Chinese Academy of Sciences
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Abstract

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.