Special Issue "Phylogeny, Ages, Molecules and Fossils of Land Plants"

Dear Colleagues,

Land plants represent one of the most important groups of eukaryotes in the terrestrial biota. Recent active research on their phylogeny and evolution using gene and genomic sequences, as well as morphological characters of extant and extinct taxa, have greatly improved our understanding of relationships among many important clades. Furthermore, the availability of big data and advances in computational methods and software of molecular clock studies have made divergence time studies an active area of research. Tremendous progress has been made in improving our understanding of the evolutionary history of this large group. At the same time, some long-established hypotheses have been challenged and controversies have also been generated.

This Special Issue offers a collection of review and primary research papers that report on the latest status of this important field. Submissions on phylogenetics, phylogenomics, divergence time studies, and paleobotany of all groups of land plants are all welcome.

Prof. Dr. Yin-Long Qiu
Dr. Yang Liu
Guest Editors

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• land plants
• phylogeny
• divergence time
• molecular clock
• fossil
• evolution

A fossil record of spores before sporophytes

Paul K Strother (strother@bc.edu)

Department of Earth & Environmental Sciences, Boston College Weston Observatory, Weston, Massachusetts, USA

Because their resistant, sporopolleninous walls preserve a record of morphogenic change during spore formation. Fossil cryptospores provide a direct physical record of the evolution of sporogenesis during the algal-plant transition. That transition itself is a story of the evolution of development – it is not about phylogeny. Here I review the fossil record of terrestrially-derived spore/cryptospore assemblages, and attempt to place these microfossils into their evolutionary context with respect to the origin of complex multicellularity in plants. Cambrian cryptospores show features related to karyokinesis seen in extant charophytes, but they also possess ultrastructure similar to that seen in liverworts today. Dyadospora, a cryptospore dyad recovered from sporangia of Devonian embryophytes, first occurs in the earliest Ordovician. Tetrahedraletes, a likely precursor to the trilete spore, first occurs in the Middle Ordovician. These fossils correspond to evolutionary novelties that were acquired during a period of genome assembly prior to the existence of upright, axial sporophytes. The cryptospore/spore fossil record provides a temporal scaffold for the acquisition of novel characters relating to the evolution of plant sporogenesis during the Cambrian-Silurian interval.

Phylogenety and divergence in the complex thalloid liverworts 

David Bell¹ (DBell@rbge.org.uk), David Long¹ (DLong@rbge.org.uk), Juan Carlos Villarreal Aguilar² (juan-carlos.villarreal-aguilar@bio.ulaval.ca) & Laura Forrest¹ (LForrest@rbge.org.uk)

¹ Royal Botanic Garden Edinburgh, U.K.; ² Laval University, Québec, Canada 

Liverworts and mosses form a clade, the setaphytes. Within the liverworts three distinct classes are recovered: Haplomitriopsida, Marchantiopsida (complex thalloids) and Jungermanniopsida (simple thalloid and leafy liverworts). Complex thalloids include a morphologically heterogeneous assemblage, with the earliest split in the Marchantiopsida; this segregates the Marchantiidae (complex thalloids) from the Blasiidae, a lineage of two simple thalloid species with endophytic cyanobacteria. The Marchantiidae typically develop a complex thallus with air chambers. The ordinal relationships within the Marchantiidae vary in support, with conflicting results from recent multi-locus organellar phylogenies. The Marchantiales contain the majority of the species of the class (ca. 497 spp.), including the model species Marchantia polymorpha.  

We present a complete generic-level phylogeny of the complex thalloid liverworts using 228 genes from 120 species (ca. 25% of complex thalloid species-level diversity) using the goflag 408 probes. Maximum likelihood and coalescence-based approaches (ASTRAL) are used to estimate gene and species trees. Using a Bayesian framework, we estimate divergence times for the complex thalloids and compare with recent studies based on organellar loci to compare rates of evolution. Our phylogeny cements the branching order of complex thalloids, providing the foundations for further studies at infrageneric and population level. 

A phylogenomic approach to study rate and character evolution in hornworts.

Gabriel Peñaloza-Bojacá & Juan Carlos Villarreal Aguilar (juan-carlos.villarreal-aguilar@bio.ulaval.ca), Laval University, Québec, Canada

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.

 angiosperm nuclear phylogenomics (title tentative)

Hong Ma (hxm16@psu.edu)

Pennsylvania State University, State College, USA

land plant phylogeny inferred from chloroplast and mitochondrial genome structural characters

Yin-Long Qiu¹ (ylqiu@umich.edu), Yang Liu² (liuyang@szbg.ac.cn), Jeffrey P. Mower³ (jpmower@unl.edu) & Brent D. Mishler⁴ （bmishler@berkeley.edu)

 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

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.

How to recognize extant moss taxa among extinct moss taxa?

Michael S. Ignatov (misha_ignatov@list.ru)^1,2 & Tatyana V. Voronkova¹

¹ Tsitsin Main Botanical Garden, Russian Academy of Sciences, Moscow, Russia

² Lomonosov Moscow State University, Moscow, Russia

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.

A new genus of marattialean ferns from the Middle Permian of Angaraland

Serge V. Naugolnykh (naugolnykh@rambler.ru)

Geological Institute, Russian Academy of Sciences, Russia

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.

New data on Permian ginkgophytes of Angaraland, and morphological archetype of this group

Serge V. Naugolnykh (naugolnykh@rambler.ru)

Geological Institute, Russian Academy of Sciences, Russia

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.