Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae)

Abstract

Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from nine to two. To verify this taxonomic proposal, we employed a genome skimming approach to recover the plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions of 51 individual plants across the nine described species of P. sect. Axiparis by sampling multiple accessions per species. The species boundaries within P. sect. Axiparis were explored using phylogenetic inference and three different sequence-based species delimitation methods (ABGD, mPTP, and SDP). The mutually reinforcing results indicate that there are two species-level taxonomic units in P. sect. Axiparis (Paris forrestii s.l. and P. vaniotii s.l.) that exhibit morphological uniqueness, non-overlapping distribution, genetic distinctiveness, and potential reproductive isolation, providing strong support to the proposed species delimitation scheme. This study confirms that previous morphology-based taxonomy overemphasized intraspecific and minor morphological differences to delineate species boundaries, therefore resulting in an overestimation of the true species diversity of P. sect. Axiparis. The findings clarify species limits and will facilitate robust taxonomic revision in P. sect. Axiparis.

Genome skimming as an efficient tool for authenticating commercial products of the pharmaceutically important Paris yunnanensis (Melanthiaceae)

“…2 ) resolved both species as fully supported monophyletic entities (BS = 100%), and the two species were phylogenetically distinct from each other in the tree topology. Similar to previous studies [ 49 , 55 ], ML analysis of the nrDNA arrays generated tree topologies that were completely different from the plastome phylogeny (Fig. 3 ).…”

Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes

“…This study describes a protocol for rapidly obtaining a primary species delimitation scheme. In some cases, plastome data contributes to discovering cryptic diversity or sorting out problematic taxonomic treatments [ 24 , 74 , 75 ], and have formed the primary basis of formal taxonomic revisions [ 25 , 76 ]. In other cases, an integrative strategy including plastome data has been applied for delimiting species.…”

Target capture and genome skimming for plant diversity studies

“…For example, a couple of dozen samples can be sequenced and combined with hundreds of previously available sequences to produce a densely sampled new phylogeny (Mo et al, 2022 ). Recent studies have shown that an increase in the number of plastid loci and nrDNA greatly improves the resolution of phylogenetic trees for taxonomically difficult groups, although unresolved relationships may remain (Loiseau et al, 2021 ; D'haijère et al, 2022 ; Fu et al, 2022 ; Ji et al, 2022 ). The lower resolution might result from missing data due to the varying sequencing coverage in genome skimming data, or actual low informativeness that might not be sufficient to resolve some evolutionary relationships, resulting in phylogenies that are less resolved toward the tips.…”