Evolution of Land Plants

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

Title: Climatic Effects of Early Land Plant Evolution
Authors: Bo Chen1 & Thomas J. Algeo2,3
Affiliation: 1 Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China; 2 China University of Geosciences, Wuhan, China; 3 University of Cincinnati, Ohio, USA
Abstract: The expansion of early land plants is widely accepted to have played a key role in cooling the Earth and generating modern levels of atmospheric oxygen. However, there is considerable debate regarding the timing and rate of this process, e.g., whether it commenced in the Devonian or possibly as early as the Ordovician, and how it was related to coeval oceanic anoxic events and marine extinction crises. In this contribution, we undertake a high-resolution review of extant paleoclimatic (e.g., oxygen isotope, pCO2), weathering (e.g., strontium and lithium isotopes), and redox (e.g., uranium isotope) proxies as well as the timing and magnitude of marine biotic extinctions. We then compare these records with the history of terrestrial floral evolution, including paleobotanic innovations, biodiversity changes, and geographic distribution patterns in order to assess the role of land plant evolution as a driver of penecontemporaneous environmental and climatic changes.

Title: Chemical (Terpenoid) Evolution in Land Plants
Authors: Feng Chen
Affiliation: University of Tennessee, Knoxville, USA

Title: Molecular Phylogenomics Reveals the Deep Evolutionary History of Carnivory across Land Plants
Authors: Richard W. Jobson1 & Steven Fleck2
Affiliation: 1National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Locked Bag 6002, Mount Annan, New South Wales 2567, Australia 2Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260,
Abstract: Early Sanger sequenced molecular phylogenies that broadly sampled multiple angiosperm lineages found the carnivorous syndrome had evolved at least 10 times independently across four major lineages. Within and between these clades the different prey capture strategies involving flypaper and pitfall structures had arisen in parallel with subsequent evolution of other strategies such as snap traps and suction bladders. Attempts to discern deep ontological history of carnivorous structures using multigene phylogenies has so far mostly failed to determine 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) that was assembled by the Kew Plant Trees of Life initiative that is attempting to complete the tree of life for plants. The phylogeny includes all carnivorous and protocarnivorous families and provides for the first time an overview of generic relationships among and between carnivorous genera. We found that most carnivorous families are not affiliated with any one family but instead are sister to large clades consisting of multiple families. We also review recent genomic studies in several of the carnivorous clades that addressed questions of the evolution of the carnivorous syndrome.

Title: Phylogeny and Ages of Land Plants and Major Subclades
Authors: Yin-Long Qiu 1 & Brent D. Mishler 2
Affiliation: 1 University of Michigan, Ann Arbor, USA; 2 University of California, Berkeley, USA
Abstract: Land plants represent one of the major clades of eukaryotes and have played an instrumental role in building the terrestrial biosystem. Reconstructing phylogenetic relationships and estimating divergence times of the major clades of land plants are essential to understand their evolutionary history as well as their interaction with and impact on the environment. In this article, we review recent molecular phylogenetic and divergence time studies, especially those based on nuclear phylogenomic data, to examine various aspects of study design: selection of characters, homology assessment, relative balance of character vs. taxon sampling, quality and quantity of fossil calibration points, dealing with evolutionary rate variation, model and parameter choices, and search thoroughness. We aim to discover potential causes of the considerable disagreement that has been seen in different studies using various types of data and methods, and develop a set of suggested measures to move towards agreement on the actual historical patterns.

Title: Evolution of Fossil Soils and Plants
Authors: Gregory J. Retallack
Affiliation: University of Oregon, Eugene, USA,

Title: Evolution of Land Plants: A Cornucopia of Novel Reproductive Structures
Authors: Günter Theißen & Lydia Gramzow
Affiliation: Matthias Schleiden Institute / Genetics, Friedrich Schiller University, Jena, Germany
Abstract: Explaining the mechanisms by which fundamental novelties originated is a key goal of evolutionary developmental biology (evo-devo) since decades. Attractive systems for respective investigations are provided by embryophytes („land plants“). In this case a single monophyletic lineage (clade) generated numerous remarkable reproductive structures, such as archegonia, ovules, carpels, stamens, and the flower as a whole within 450 million years. Besides some vegetative traits, these organs and compound structures have largely contributed to the „success“ of embryophytes in terms of species number, biomass, and land coverage. Here we review what is known about the origin of these structures from both a paleobotanical and a neobotanical point of view, and how they provided land plants with adaptive advantages that were never achieved by other plant lineages. We discuss as to whether there are special genetic features in land plants that have fostered this evolutionary creativity.

Title: Fossil History of Land Plants
Authors: Alexandru M. F. Tomescu
Affiliation: California Polytechnic State University Humboldt, Arcata, USA

Title: Phylogenetic and Divergence Time Analyses of Liverworts
Authors: Laura Forrest1 , David Bell1 , David Long1 & Juan Carlos Villarreal Aguilar2
Affiliation: 1 Royal Botanic Garden Edinburgh, U.K.; 2 Laval University, Québec, Canada

Title: A Phylogenomic Approach to Study Rate and Character Evolution in Hornworts
Authors: Gabriel Peñaloza-Bojacá, J.C. Villarreal et al.
Affiliation: Laval University, Québec, Canada
Abstract: Recent plant phylogenomic studies strongly support bryophytes (hornworts, mosses and liverworts) as a clade. Hornworts are the least species-rich bryophyte group (~220 spp.) and they are sister to setaphytes (liverworts plus hornworts). A renewed interest in hornworts has been fueled by nuclear genomic analyses of their unique traits such as endophytic cyanobacterial symbiosis and the atavistic presence of pyrenoids, a physical carbon concentrating site found otherwise in algae. In previous analyses based on five organellar loci, hornwort relationships seemed to be stable with Leiosporoceros (Leiosporocerotales) reconstructed as sister to all other species. This solid topology has been the base of multiple ancestral character reconstruction, divergence times and diversification studies. For example, pyrenoids were reconstructed as a derived condition in hornworts simply because Leiosporoceros lacks this trait. We present ongoing phylogenomic analyses of 421 genes from 79 species (ca. 35% of hornwort diversity) encompassing all five orders and eleven hornwort genera, using the goflag 408 probes. Maximum likelihood and ASTRAL will be used to estimate gene and species trees. Using a topological approach, rate evolution will be assessed across the hornwort phylogeny. The reconstructed topology will be used as template to reconstruct character evolution. We will present divergence times and ancestral character reconstructions and propose new scenarios of character evolution, including the pyrenoid.

Title: Angiosperm Nuclear Phylogenomics
Authors: Hong Ma
Affiliation: Pennsylvania State University, State College, USA

Title: Land Plant Phylogeny Inferred from Chloroplast and Mitochondrial Genome Structural Characters
Authors: Yin-Long Qiu1, Yang Liu2, Jeffrey P. Mower3 & Brent D. Mishler4
Affiliation: 1 University of Michigan, Ann Arbor, USA; 2 Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China; 3 University of Nebraska, Lincoln, USA; 4 University of California, Berkeley, USA
Abstract: Land plants have evolved over a period of around 500 million years, yet the diversification of the major extant subclades appears to have happened relatively rapidly, early in their history. The antiquity of their origin and the rapidity of the major early divergences makes inference of their phylogeny quite challenging. Phylogenetic signal decays over time in faster-evolving genes, and the more clocklike nucleotide evolution is in a gene, the less likely it can reliably detect such deep, rapid divergences. In such cases we need a different type of marker, one that evolves relatively slowly and episodically. Genome structural characters are promising in that regard. In this study, we conducted a parsimony analysis of a matrix of chloroplast and mitochondrial genome structural characters, including gene synteny blocks, intron positions, and intron splicing patterns, from over 150 species of green algae and land plants. These characters appear to have evolved slowly and have low levels of homoplasy in comparison to most gene sequences. The extensive taxon sampling adopted here also allows detection of hidden homoplasy that might have been missed in previous such analyses with low taxon coverage. This study thus provides a well-supported, independent assessment of land plant phylogeny, which has been controversial from analyses of nucleotide sequence data.

Title: How to Recognize Extant Moss Taxa among Extinct Moss Taxa?
Authors: Michael S. Ignatov1,2 & Tatyana V. Voronkova1
Affiliation: 1 Tsitsin Main Botanical Garden, Russian Academy of Sciences, Moscow, Russia 2 Lomonosov Moscow State University, Moscow, Russia
Abstract: The paper discusses the Upper Paleozoic mosses from one collection especially rich in fossil mosses in Aristovo, Subangaraland in Permian, currently NE Europe. These fossils have numerous features in common with the main lineages of extant mosses. However, some structural distinctions hamper their placements in any of the survived moss lineages. Possible pitfalls of misinterpretation the fossil moss identity is discussed based on examples of the newly described mosses from this locality. The importance on the expanded circumscription of totally extinct lineages is highlighted.

Title: A New Genus of Marattialean Ferns from the Middle Permian of Angaraland
Authors: Serge V. Naugolnykh
Affiliation: Geological Institute, Russian Academy of Sciences, Russia
Abstract: This paper will be focused on a new representative of Marattiales, including data both on macromorphology, structure of synangia, and the spores preserved in situ.

Title: New Data on Permian Ginkgophytes of Angaraland, and Morphological Archetype of This Group
Authors: Serge V. Naugolnykh
Affiliation: Geological Institute, Russian Academy of Sciences, Russia
Abstract: The paper will deal with the general overview of Paleozoic representatives of Ginkgoales (mostly Permian), in general context of morphogenetic trends, which took place in this plant group evolution.