Evolution of Land Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 23 December 2025 | Viewed by 11437

Special Issue Editors


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Guest Editor
Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI 48109, USA
Interests: land plant phylogeny and evolution; mitochondrial genome evolution
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Plant Sciences, The University of Tennessee, Knoxville, TN 37996, USA
Interests: biosynthesis; function and evolution of plant secondary metabolites

Special Issue Information

Dear Colleagues,

Land plants are the primary producers of the modern terrestrial biosystem and play a critical role in shaping the Earth’s environment and climate regime. Recent active research on phylogeny, genomes and phenomes of land plants, and their numerous model representatives has brought a new level of understanding of their evolution, function, and interaction with the environment. This Special Issue will publish a collection of review and primary research papers that report on the latest status of this important field. Submissions in phylogenetics, phylogenomics, evolutionary genomics, molecular evolution, evolutionary developmental biology, chemical evolution, evolutionary ecology, biogeography, and paleobotany are welcome.

Prof. Dr. Yinlong Qiu
Prof. Dr. Feng Chen
Guest Editors

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Keywords

  • land plants
  • evolution
  • phylogenetics
  • evolutionary genomics
  • biogeography
  • paleobotany
  • specialized metabolites
  • chemical evolution

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Published Papers (6 papers)

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Research

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20 pages, 5079 KiB  
Article
Paleovegetation Community and Paleoclimate Succession in Middle Jurassic Coal Seams in Eastern Coalfields in Dzungaria Basin, China
by Xingli Wang, Shuo Feng, Wenfeng Wang, Qin Zhang, Jijun Tian, Changcheng Han and Meng Wang
Plants 2025, 14(5), 695; https://doi.org/10.3390/plants14050695 - 24 Feb 2025
Viewed by 312
Abstract
The Dzungaria Basin is located north of Xinjiang and is one of the largest inland basins in China. The eastern coalfields in the Dzungaria Basin contain a large amount of coal resources, and the thickness of the coal seams is significant. Therefore, the [...] Read more.
The Dzungaria Basin is located north of Xinjiang and is one of the largest inland basins in China. The eastern coalfields in the Dzungaria Basin contain a large amount of coal resources, and the thickness of the coal seams is significant. Therefore, the aim of this study was to classify the paleovegetation types and develop paleoclimate succession models of the extra-thick coal seams. We conducted the sampling, separation, and extraction of spores and pollen and carried out microscopic observations in the Wucaiwan mining area of the eastern coalfields in the Dzungaria Basin. The vertical vegetation succession in the thick seam (Aalenian Stage) in the study area was divided into three zones using the CONISS clustering method. The results show that the types of spore and pollen fossils belong to twenty families and forty-five genera, including twenty-three fern, twenty gymnosperm, and two bryophyte genera. The types of paleovegetation in the study area were mainly Lycopodiaceae and Selaginellaceae herb plants, Cyatheaceae, Osmundaceae, and Polypodiaceae shrub plants, and Cycadaceae and Pinaceae coniferous broad-leaved trees. The paleoclimate changed from warm–humid to humid–semi-humid and, finally, to the semi-humid–semi-dry type, all within a tropical–subtropical climate zone. The study area was divided into four paleovegetation communities: the nearshore wetland paleovegetation community, lowland cycad and Filicinae plant community, slope broad-leaved and coniferous plant mixed community, and highland coniferous tree community. This indicates that there was a climate warming event during the Middle Jurassic, which led to a large-scale lake transgression and regression in the basin. This resulted in the transfer of the coal-accumulating center from the west and southwest to the central part of the eastern coalfields in the Dzungaria Basin. Full article
(This article belongs to the Special Issue Evolution of Land Plants)
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29 pages, 2280 KiB  
Article
Geometric Models of Speciation in Minimally Monophyletic Genera Using High-Resolution Phylogenetics
by Richard H. Zander
Plants 2025, 14(4), 530; https://doi.org/10.3390/plants14040530 - 9 Feb 2025
Viewed by 550
Abstract
High-resolution phylogenetics using both morphology and molecular data reveal surfactant-like trait buffering of peripatric descendant species that facilitate resilience for supra-specific entities across geologic time. Regular polygons inscribed in circles model balanced areas of survival of various numbers of new species in one [...] Read more.
High-resolution phylogenetics using both morphology and molecular data reveal surfactant-like trait buffering of peripatric descendant species that facilitate resilience for supra-specific entities across geologic time. Regular polygons inscribed in circles model balanced areas of survival of various numbers of new species in one genus. This model maximizes the peripatric survival of descendant species, with populations partly in allopatric habitats and in sympatric areas. It extends the theory advanced with Willis’s Age and Area hypothesis. Hollow curves of the areas bounded between a series of inscribed regular polygons and their containing circles show a ranked progression governed by similar power laws of other phenomena, including Zipf’s law and a universal meta-law in physics. This model matches best the physics meta-law (law of laws) but is only one of several somewhat different curves generated by somewhat different processes. A rule of four can explain why most genera in vascular plants exhibit a hollow curve of optimally one to five species per genus. It implies a constraint on variation that enhances survival and provides a physics explanation for the monophyletic skeleton of macrogenera. A high-resolution form of ancestor–descendant analysis is compared to traditional phylogenetic analysis to best modeling of the demonstrable results of evolutionary processes. Arguments are advanced for the preservation of scientific concepts of taxa over cladistic clades. Full article
(This article belongs to the Special Issue Evolution of Land Plants)
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29 pages, 7901 KiB  
Article
Origin and Early Evolution of Hydrocharitaceae and the Ancestral Role of Stratiotes
by Silvia Ulrich, Manuel Vieira, Mario Coiro, Johannes M. Bouchal, Christian Geier, Bonnie F. Jacobs, Ellen D. Currano, Olaf K. Lenz, Volker Wilde, Reinhard Zetter and Friðgeir Grímsson
Plants 2024, 13(7), 1008; https://doi.org/10.3390/plants13071008 - 31 Mar 2024
Cited by 4 | Viewed by 2423
Abstract
The combined morphological features of Stratiotes (Hydrocharitaceae) pollen, observed with light and electron microscopy, make it unique among all angiosperm pollen types and easy to identify. Unfortunately, the plant is (and most likely was) insect-pollinated and produces relatively few pollen grains per flower, [...] Read more.
The combined morphological features of Stratiotes (Hydrocharitaceae) pollen, observed with light and electron microscopy, make it unique among all angiosperm pollen types and easy to identify. Unfortunately, the plant is (and most likely was) insect-pollinated and produces relatively few pollen grains per flower, contributing to its apparent absence in the paleopalynological record. Here, we present fossil Stratiotes pollen from the Eocene of Germany (Europe) and Kenya (Africa), representing the first reliable pre-Pleistocene pollen records of this genus worldwide and the only fossils of this family discovered so far in Africa. The fossil Stratiotes pollen grains are described and compared to pollen from a single modern species, Stratiotes aloides L. The paleophytogeographic significance and paleoecological aspects of these findings are discussed in relation to the Hydrocharitaceae fossil records and molecular phylogeny, as well as the present-day distribution patterns of its modern genera. Full article
(This article belongs to the Special Issue Evolution of Land Plants)
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20 pages, 3898 KiB  
Article
Phylotranscriptomics Shed Light on Intrageneric Relationships and Historical Biogeography of Ceratozamia (Cycadales)
by Sadaf Habib, Yiqing Gong, Shanshan Dong, Anders Lindstrom, Dennis William Stevenson, Hong Wu and Shouzhou Zhang
Plants 2023, 12(3), 478; https://doi.org/10.3390/plants12030478 - 19 Jan 2023
Cited by 8 | Viewed by 2458
Abstract
Ceratozamia Brongn. is one of the species-rich genera of Cycadales comprising 38 species that are mainly distributed in Mexico, with a few species reported from neighboring regions. Phylogenetic relationships within the genus need detailed investigation based on extensive datasets and reliable systematic approaches. [...] Read more.
Ceratozamia Brongn. is one of the species-rich genera of Cycadales comprising 38 species that are mainly distributed in Mexico, with a few species reported from neighboring regions. Phylogenetic relationships within the genus need detailed investigation based on extensive datasets and reliable systematic approaches. Therefore, we used 30 of the known 38 species to reconstruct the phylogeny based on transcriptome data of 3954 single-copy nuclear genes (SCGs) via coalescent and concatenated approaches and three comparative datasets (nt/nt12/aa). Based on all these methods, Ceratozamia is divided into six phylogenetic subclades within three major clades. There were a few discrepancies regarding phylogenetic position of some species within these subclades. Using these phylogenetic trees, biogeographic history and morphological diversity of the genus are explored. Ceratozamia originated from ancestors in southern Mexico since the mid-Miocene. There is a distinct distribution pattern of species through the Trans-Mexican Volcanic Belt (TMVB), that act as a barrier for the species dispersal at TMVB and its southern and northern part. Limited dispersal events occurred during the late Miocene, and maximum diversification happened during the Pliocene epoch. Our study provides a new insight into phylogenetic relationships, the origin and dispersal routes, and morphological diversity of the genus Ceratozamia. We also explain how past climatic changes affected the diversification of this Mesoamerica-native genus. Full article
(This article belongs to the Special Issue Evolution of Land Plants)
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Review

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18 pages, 2721 KiB  
Review
Function and Evolution of the Plant MES Family of Methylesterases
by Timothy A. Chaffin, Weijiao Wang, Jin-Gui Chen and Feng Chen
Plants 2024, 13(23), 3364; https://doi.org/10.3390/plants13233364 - 29 Nov 2024
Viewed by 832
Abstract
Land plant evolution has been marked by numerous genetic innovations, including novel catalytic reactions. Plants produce various carboxyl methyl esters using carboxylic acids as substrates, both of which are involved in diverse biological processes. The biosynthesis of methyl esters is catalyzed by SABATH [...] Read more.
Land plant evolution has been marked by numerous genetic innovations, including novel catalytic reactions. Plants produce various carboxyl methyl esters using carboxylic acids as substrates, both of which are involved in diverse biological processes. The biosynthesis of methyl esters is catalyzed by SABATH methyltransferases, and understanding of this family has broadened in recent years. Meanwhile, the enzymes catalyzing demethylation—known as methylesterases (MESs)—have received less attention. Here, we present a comprehensive review of the plant MES family, focusing on known biochemical and biological functions, and evolution in the plant kingdom. Thirty-two MES genes have been biochemically characterized, with substrates including methyl esters of plant hormones and several other specialized metabolites. One characterized member demonstrates non-esterase activity, indicating functional diversity in this family. MES genes regulate biological processes, including biotic and abiotic defense, as well as germination and root development. While MES genes are absent in green algae, they are ubiquitous among the land plants analyzed. Extant MES genes belong to three groups of deep origin, implying ancient gene duplication and functional divergence. Two of these groups have yet to have any characterized members. Much remains to be uncovered about the enzymatic functions, biological roles, and evolution of the MES family. Full article
(This article belongs to the Special Issue Evolution of Land Plants)
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15 pages, 1782 KiB  
Review
Molecular Phylogenomics Reveals the Deep Evolutionary History of Carnivory across Land Plants
by Steven J. Fleck and Richard W. Jobson
Plants 2023, 12(19), 3356; https://doi.org/10.3390/plants12193356 - 22 Sep 2023
Cited by 3 | Viewed by 3764
Abstract
Plastid molecular phylogenies that broadly sampled angiosperm lineages imply that carnivorous plants evolved at least 11 times independently in 13 families and 6 orders. Within and between these clades, the different prey capture strategies involving flypaper and pitfall structures arose in parallel with [...] Read more.
Plastid molecular phylogenies that broadly sampled angiosperm lineages imply that carnivorous plants evolved at least 11 times independently in 13 families and 6 orders. Within and between these clades, the different prey capture strategies involving flypaper and pitfall structures arose in parallel with the subsequent evolution of snap traps and suction bladders. Attempts to discern the deep ontological history of carnivorous structures using multigene phylogenies have provided a plastid-level picture of sister relationships at the family level. Here, we present a molecular phylogeny of the angiosperms based on nuclear target sequence capture data (Angiosperms-353 probe set), assembled by the Kew Plant Trees of Life initiative, which aims to complete the tree of life for plants. This phylogeny encompasses all carnivorous and protocarnivorous families, although certain genera such as Philcoxia (Plantaginaceae) are excluded. This study offers a novel nuclear gene-based overview of relationships within and between carnivorous families and genera. Consistent with previous broadly sampled studies, we found that most carnivorous families are not affiliated with any single family. Instead, they emerge as sister groups to large clades comprising multiple non-carnivorous families. Additionally, we explore recent genomic studies across various carnivorous clades that examine the evolution of the carnivorous syndrome in relation to whole-genome duplication, subgenome dominance, small-scale gene duplication, and convergent evolution. Furthermore, we discuss insights into genome size evolution through the lens of carnivorous plant genomes. Full article
(This article belongs to the Special Issue Evolution of Land Plants)
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