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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Systematics, Taxonomy, Nomenclature and Classification".

Deadline for manuscript submissions: closed (30 June 2025) | Viewed by 6534

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Dr. Dengfeng Xie

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Guest Editor

Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
Interests: plant taxonomy; molecular phylogenetics; speciation; phylogeography; conservation biology; species diversification and distribution

Special Issue Information

Dear Colleagues,

This Special Issue compiles research on plant classification, phylogeny, and evolution, spanning the following areas:

(1) Taxonomic studies of plants: This encompasses determining the systematic position of species, conducting taxonomic revisions, or publishing new species through rigorous scientific investigations. It also involves comprehensive statistical comparisons of morphology and molecular phylogenetic analyses.

(2) Plant phylogenetic analysis: This involves gathering morphological data and conducting phylogenetic reconstructions at various taxonomic levels (e.g., family or genus) using diverse molecular data sources (e.g., the transcriptome or resequencing). The aim is to elucidate the phylogenetic relationships among species as well as analyze the origins and evolution of species within different clades.

(3) Evolutionary biology of plants: This field combines morphological data with a range of molecular tools to explore the mechanisms underlying species formation and evolution. It seeks to detect evolutionary events, such as hybridization and ancestral lineage divergence, and analyze potential factors influencing species evolution.

Dr. Dengfeng Xie
Guest Editor

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Keywords

morphological characteristics
phylogeny
speciation
hybridization
adaptation

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Published Papers (9 papers)

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Research

19 pages, 3730 KiB

Open AccessArticle

Phylogenomic Analyses Reveal Species Relationships and Phylogenetic Incongruence with New Member Detected in Allium Subgenus Cyathophora

by Kun Chen, Zi-Jun Tang, Yuan Wang, Jin-Bo Tan, Song-Dong Zhou, Xing-Jin He and Deng-Feng Xie

Plants 2025, 14(13), 2083; https://doi.org/10.3390/plants14132083 - 7 Jul 2025

Viewed by 134

Abstract

Species characterized by undetermined clade affiliations, limited research coverage, and deficient systematic investigation serve as enigmatic entities in plant and animal taxonomy, yet hold critical significance for exploring phylogenetic relationships and evolutionary trajectories. Subgenus Cyathophora (Allium, Amayllidaceae), a small taxon comprising approximately five species distributed in the Qinghai–Tibet Plateau (QTP) and adjacent regions might contain an enigmatic species that has long remained unexplored. In this study, we collected data on species from subgenus Cyathophora and its close relatives in subgenus Rhizirideum, as well as the enigmatic species Allium siphonanthum. Combining phylogenomic datasets and morphological evidence, we investigated species relationships and the underlying mechanism of phylogenetic discordance. A total of 1662 single-copy genes (SCGs) and 150 plastid loci were filtered and used for phylogenetic analyses based on concatenated and coalescent-based methods. Furthermore, to systematically evaluate phylogenetic discordance and decipher its underlying drivers, we implemented integrative analyses using multiple approaches, such as coalescent simulation, Quartet Sampling (QS), and MSCquartets. Our phylogenetic analyses robustly resolve A. siphonanthum as a member of subg. Cyathophora, forming a sister clade with A. spicatum. This relationship was further corroborated by their shared morphological characteristics. Despite the robust phylogenies inferred, extensive phylogenetic conflicts were detected not only among gene trees but also between SCGs and plastid-derived species trees. These significant phylogenetic incongruences in subg. Cyathophora predominantly stem from incomplete lineage sorting (ILS) and reticulate evolutionary processes, with historical hybridization events likely correlated with the past orogenic dynamics and paleoclimatic oscillations in the QTP and adjacent regions. Our findings not only provide new insights into the phylogeny of subg. Cyathophora but also significantly enhance our understanding of the evolution of species in this subgenus. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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21 pages, 7485 KiB

Open AccessArticle

Endocarp Morphology of Premna (Lamiaceae) in Thailand and Its Taxonomic Significance

by Jiratthi Satthaphorn, Alan J. Paton, Pornsawan Sutthinon and Charan Leeratiwong

Plants 2025, 14(11), 1706; https://doi.org/10.3390/plants14111706 - 3 Jun 2025

Viewed by 1079

Abstract

Fruits and endocarps of 21 species within the genus Premna (Lamiaceae) in Thailand were examined using light (LM) and scanning electron microscopy (SEM) to evaluate taxonomic relevance. Overall, mature fruits were classified into two types: fully developed mericarp (fruit type I) and partly developed mericarp (fruit type II), with three shape patterns: broadly obovoid, narrowly obovoid, and clavoid. Fruit size ranged from 1.52 to 7.48 mm in length and 0.98 to 7.71 mm in width. In LM investigations, the endocarps were classified into three types based on the presence and shape of the protruding structure: saccate-like (protrusion type I), thorn-like (protrusion type II), and no protrusion (protrusion type III). The examination of endocarps under SEM showed that they consist of multilayers of sclerenchyma cells. The shape of the sculpturing cells on the endocarp surface can be divided into two patterns: irregular tetragonal and polygonal, with distinct or obscure straight cell faces. The morphological comparison and phenetic analyses using factor analysis of mixed data (FAMD) show that fruit and endocarp characteristics of Premna hold significant taxonomic value for distinguishing certain related species and classifying within the genus in Thailand. From the first two FAMD dimensions, fruit shape, shape of sculptured cells on the endocarp, and protrusion type of the endocarp are considered as the most significant contributing variables. The findings also support the reinstatement of species previously synonymized with P. serratifolia, namely P. cordifolia, P. paniculata, and P. punctulata. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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16 pages, 2138 KiB

Open AccessArticle

The Divergence History of Two Japanese Torreya Taxa (Taxaceae): Implications for Species Diversification in the Japanese Archipelago

by Qian Ou, Xin Huang, Dingguo Pan, Shulan Wang, Yuting Huang, Sisi Lu, Yujin Wang and Yixuan Kou

Plants 2025, 14(10), 1537; https://doi.org/10.3390/plants14101537 - 20 May 2025

Viewed by 424

Abstract

The Japanese archipelago as a continental island of the Eurasia continent and harboring high levels of plant species diversity provides an ideal geographical setting for investigating vicariant allopatric speciation due to the sea-level fluctuations associated with climatic oscillations during the Quaternary. In this study, three chloroplast DNA regions and 14 nuclear loci were sequenced for 31 individuals from three populations of Torreya nucifera var. nucifera and 52 individuals from three populations of T. nucifera var. radicans. Population genetic analyses (Network, STRUCTURE and phylogeny) revealed that the genetic boundaries of the two varieties are distinct, with high genetic differentiation (F_ST) of 0.9619 in chloroplast DNA and 0.6543 in nuclear loci. The relatively ancient divergence times between the two varieties were estimated to 3.03 Ma by DIYABC and 1.77 Ma by IMa2 when dated back to the late Pliocene and the early Pleistocene, respectively. The extremely weak gene flow (2Nm = 0.1) between the two varieties was detected by IMa2, which might be caused by their population expansion since the early Pleistocene (~2.0 Ma) inferred in the Bayesian skyline plots and DIYABC. Niche modeling showed that the two varieties had significant ecological differentiation (p < 0.001) since the Last Interglacial even earlier. These results demonstrate that vicariant allopatric speciation due to sea-level fluctuations may be a common mode of speciation in the Japanese archipelago. This finding provides insights into the understanding of species diversification in the Japanese Archipelago and even East Asian flora under climatic oscillations during the Quaternary. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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21 pages, 4530 KiB

Open AccessArticle

Leaf Morpho-Anatomy of Twelve Cymbidium (Orchidaceae) Species from China and Their Taxonomic Significance

by Xiangke Hu, Lei Tao, Jialin Huang, Kaifeng Tao, Dong Ma and Lu Li

Plants 2025, 14(9), 1396; https://doi.org/10.3390/plants14091396 - 6 May 2025

Viewed by 444

Abstract

Cymbidium are endangered and ornamental orchids, and the taxonomy and species identification of this genus have been debated due to some overlapping morphological features between taxa and limited data being available. The leaf morpho-anatomy of 12 Cymbidium species from China was investigated using light microscopy and paraffin sectioning. Based on a comparative analysis, some leaf morphological features that varied between species were selected and used for taxonomic differentiation as follows: (1) The shape and structure of leaves were varied and could be used for species delimitation. (2) Microscopic characteristics show that the leaves lacked trichomes and displayed polygonal to rectangular epidermal cells on both surfaces, with larger adaxial cells and more abaxial stigmata. Stomata were mostly distributed only on the abaxial side, but on both sides in Cymbidium mastersii, which exhibited a rare amphistomatic type. The stomatal complex was uniformly tetracytic in 11 species, while it was observed to be anomocytic in C. floribundum. (3) Anatomically, two distinct midrib configurations were identified, a shallow V-shape and V-shape. The mesophyll cells were homogeneous in 10 species, with the exception of a layer of parenchyma cells resembling palisade cells occurring in C. lancifolium and C. qiubeiense. The thickness of the cuticle varied between species, with the adaxial surface covered by a thicker cuticle than the abaxial surface and displaying either a smooth or corrugated surface. A fiber bundle was observed in six species, but absent in the other six. In the former group, the fiber bundle occurred adjacent to both epidermal cells in C. mastersii and C. hookerianum, while it was adjacent to the abaxial epidermis in four other species. The stegmata, with conical, spherical silica bodies, were associated with fiber bundles and mesophyll in seven species, but absent in the other five (C. kanran, C. defoliatum, C. floribundum, C. lancifolium, and C. serratum). Three kinds of crystals were identified, namely the terete bundle, the long tube bundle, and the raphide. (4) It was suggested that some of these variable features could be selected and used for the delimitation of the species and taxonomy of Cymbidium. In addition, a key to the 12 Cymbidium species based on their leaf morpho-anatomic features was proposed, which could lead to a better understanding of the taxonomy and conservation of Orchidaceae. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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25 pages, 6250 KiB

Open AccessArticle

Morphology and Phylogenetic Positions of Two Novel Gogorevia Species (Bacillariophyta) from the Han River, South Korea

by Weihan Wang, Yuyao Li, Byeong-Hun Han, Su-Ok Hwang and Baik-Ho Kim

Plants 2025, 14(9), 1272; https://doi.org/10.3390/plants14091272 - 22 Apr 2025

Viewed by 490

Abstract

This study reports two novel species, Gogorevia contracta sp. nov. and G. recticentralis sp. nov., which were isolated from freshwater environments in South Korea. Using an integrative taxonomic approach, we conducted morphological analyses using light microscopy and scanning electron microscopy, along with molecular phylogenetic investigations using SSU rRNA and rbcL gene sequences. Phylogenetic reconstructions highlighted the distinct characteristics of both species, confirming their classification within the genus Gogorevia and elucidating their evolutionary relationships. Morphologically, G. contracta was characterized by a bow-tie-shaped central area and circular depressions in the rapheless valve, whereas G. recticentralis exhibited a rectangular-to-wedge-shaped central area with parallel striae near the center of the raphe valve. Our findings highlighted the ecological significance of Gogorevia species and suggested their potential role as bioindicators of water quality in relatively unpolluted freshwater systems. Over the past decade, our research has focused on the taxonomic and ecological study of diatoms in the Han River system and identified 136 species, including nine newly described taxa. The findings of the present study contribute to a growing understanding of Gogorevia diversity, underscore the importance of region-specific diatom indices, and support the integration of morphological and molecular methods into diatom systematics. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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19 pages, 11784 KiB

Open AccessArticle

Comprehensive Chloroplast Genomic Insights into Amaranthus: Resolving the Phylogenetic and Taxonomic Status of A. powellii and A. bouchonii

by Jizhe Han, Chuhang Lin, Tingting Zhu, Yonghui Liu, Jing Yan, Zhechen Qi and Xiaoling Yan

Plants 2025, 14(5), 649; https://doi.org/10.3390/plants14050649 - 20 Feb 2025

Cited by 1 | Viewed by 741

Abstract

Amaranthus, a genus in Amaranthaceae, is divided into three subgenera—Amaranthus, Acnida, and Albersia—and contains approximately 70 to 80 species. Understanding its phylogenetic relationships is essential for species classification, genetic diversity assessment, and evolutionary studies. This knowledge is vital for improving Amaranthus utilization in crop improvement and managing the ecological impacts of invasive weeds. In this study, we analyzed the chloroplast genomes of 27 Amaranthus species across all three subgenera to characterize their genomic features and construct a comprehensive phylogenetic tree. Our aim was to elucidate the phylogenetic relationships within the genus and evaluate interspecific affinities among the subgenera. We also addressed the taxonomic ambiguity surrounding A. bouchonii and A. powellii to determine their distinct species within the genus. Chloroplast genome sizes ranged from 149,949 to 150,818 bp, with GC content varying between 36.52% and 36.63%. Comparative structural analyses confirmed highly conserved quadripartite structures, gene content, and organization, comprising 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat and codon usage analyses revealed conserved repeat patterns and a preference for codons ending in A or U. Selection pressure analysis indicated a predominantly purifying selection, with matK showing signs of positive selection, particularly in A. spinosus. Phylogenetic analysis of 80 protein-coding genes confirmed the monophyly of subgenus Amaranthus but found Alberisa and Acnida to be paraphyletic. Despite their morphological similarity, A. bouchonii and A. powellii were placed in separate clades within subgenus Amaranthus, with A. bouchonii clustering with A. retroflexus, and A. powellii aligning with the A. hybridus complex. Additionally, we identified 16 variable regions as potential molecular markers for species identification. Our study provides the most comprehensive Amaranthus chloroplast genome dataset to date, offering new insights into its evolutionary relationships and valuable genomic resources for taxonomy, germplasm management, and invasive risk assessment. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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21 pages, 9949 KiB

Open AccessArticle

Investigating the Variation in Leaf Traits Within the Allium prattii C.H. Wright Population and Its Environmental Adaptations

by Shuai-Shuai Zhang, Zi-Jun Tang, Kun Chen, Xiao-Jing Ma, Song-Dong Zhou, Xing-Jin He and Deng-Feng Xie

Plants 2025, 14(4), 541; https://doi.org/10.3390/plants14040541 - 10 Feb 2025

Viewed by 572

Abstract

Morphological and micro-morphological traits of characteristics serve as the cornerstone for species identification and taxonomy, and they also ensure the adaptive responses of species to specific environmental conditions. Allium prattii C.H. Wright is mainly distributed in the mountains of southwestern China (MSC) and adjacent regions, and exhibits pronounced variations in leaf morphology and micro-morphology across different growth environments, making it an ideal taxa to study species adaptation to diverse conditions. In this study, we conducted extensive field surveys, sample collections, and morphological experiments, amassing data on leaf morphological and micro-morphological traits from 45 populations of A. prattii. Specifically, we explored the differences in leaf morphology among populations and the patterns of geographical distribution. Consequently, we examined the correlation between seven climatic factors, longitude, latitude, and leaf morphological traits, and simulated the changes in the A. prattii distribution area during different historical periods. Our results indicate that all populations of A. prattii can be categorized into four distinct lineages, characterized by significant leaf morphological divergence and distinct geographical distribution patterns. Populations located in the Hengduan Mountains and neighboring regions demonstrated elevated coefficients of variation (CV) in leaf morphology. The correlation analysis between morphological traits and climatic factors highlighted substantial links between the density of stomata on the upper epidermis and environmental variables, as well as significant correlations between leaf length/width and geographical distribution (latitude and longitude). Simulations of the distribution area revealed that the distribution ranges of A. prattii underwent a significant fluctuation from the Last Interglacial Period (LIG) to the Last Glacial Maximum (LGM), the Mid-Holocene (MH), and the current period, accompanied by expansion of its potential distribution area in the future. These results underscore that the leaf morphology of A. prattii has significantly varied in response to climatic environmental factors across different regions, with a decrease in leaf width and an increase in stomatal density on the upper epidermis. The heterogeneous environment of the southwestern mountain region, characterized by variations in altitude, temperature, and precipitation, is the primary driver of morphological variation and geographical distribution patterns in A. prattii leaves. Our findings hold substantial scientific significance, shedding light on the evolutionary adaptation of species in the MSC and adjacent areas. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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12 pages, 1492 KiB

Open AccessArticle

Phylogenetic Relationships in the Miracle Berry Genus, Synsepalum, Sensu Lato, and Relatives (Sapotaceae)

by Daniel Potter and Mark Uleh

Plants 2025, 14(1), 41; https://doi.org/10.3390/plants14010041 - 26 Dec 2024

Viewed by 675

Abstract

Synsepalum and Englerophytum are two closely related genera of the sub-family Chrysophylloideae in the family Sapotaceae. It has been reported that the two genera are a monophyletic group, and their generic limitations are uncertain. Synsepalum is an economically important genus that includes the medicinally and culinarily important plant, -miracle berry, S. dulcificum. The phylogenetic relationships among the species are poorly understood. This study has been conducted to refine the phylogenetic relationships between and within the two genera utilizing nuclear and chloroplast DNA data. Bayesian analyses and Maximum likelihood of nuclear internal transcribed spacer (ITS) and plastid (trnH-psbA) sequences were used to reconstruct the phylogeny of the two genera. Phylogenetic trees generated for both regions (nuclear and plastid) resulted in the resolution of six clades. Four of the clades correspond to species in the genus Synsepalum and two clades include species of Englerophytum. The two clades of Englerophytum are nested within Synsepalum suggesting that the two genera are closely related and may not merit their current circumscription as distinct genera. Also, Synsepalum is confirmed to constitute more than one lineage suggesting it is not monophyletic in its current definition. Overall, the study suggests the need for a comprehensive evaluation of all species currently recognized in the two genera. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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14 pages, 2769 KiB

Open AccessArticle

Study on the Genus Drymaria (Caryophyllaceae)—A New Species from North-East India

by Sindhu Arya, Harsh Singh, Kalarikkal Walsan Vishnu and Duilio Iamonico

Plants 2024, 13(23), 3378; https://doi.org/10.3390/plants13233378 - 30 Nov 2024

Cited by 2 | Viewed by 1152

Abstract

A new species of Drymaria from the Kohima District (Nagaland of North-East India) is described and illustrated based on both molecular data (the ITS region of nuclear DNA) and morphometric analyses (clustering, PCA, DA, and MANOVA). The new species resembles D. cordata but differs with respect to the shape of the sepal (oblong, incurved at the margin vs. lanceolate, not incurved at the margin), petals (oblong or linear vs. ovate–lanceolate), and bract (foliaceous, glabrous, non-prominent vs. non-foliaceous, pubescent, and prominent). For nomenclatural purposes, the typification of Drymaria villosa by Duke (in 1961) was corrected according to Art. 9.10 of the Shenzhen Code. Full article

(This article belongs to the Special Issue Plant Taxonomy, Phylogeny, and Evolution)

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