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Plant Taxonomy, Phylogeny, and Evolution
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Plant Taxonomy, Phylogeny, and Evolution

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: 30 June 2025 | Viewed by 3616

Special Issue Editor

Dr. Dengfeng Xie

E-Mail Website
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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • morphological characteristics
  • phylogeny
  • speciation
  • hybridization
  • adaptation

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Published Papers (6 papers)

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Research

21 pages, 4530 KiB  
Article
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
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 [...] Read more.
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  
Article
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 304
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 [...] Read more.
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  
Article
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
Viewed by 567
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 [...] Read more.
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  
Article
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 462
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 [...] Read more.
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  
Article
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 598
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 [...] Read more.
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  
Article
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 1040
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 [...] Read more.
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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