Dietmar Quandt

The deepest divergences in land plants inferred from phylogenomic evidence.

Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.

Noncoding plastid trnT‐trnF sequences reveal a well resolved phylogeny of basal angiosperms

Recent contributions from DNA sequences have revolutionized our concept of systematic relationships in angiosperms. However, parts of the angiosperm tree remain unclear. Previous studies have been based on coding or rDNA regions of relatively conserved genes. A phylogeny for basal angiosperms based on noncoding, fast‐evolving sequences of the chloroplast genome region trnT‐trnF is presented. The recognition of simple direct repeats allowed a robust alignment. Mutational hot spots appear to be confined to certain sectors, as in two stem‐loop regions of the trnL intron secondary structure. Our highly resolved and well‐supported phylogeny depicts the New Caledonian Amborella as the sister to all other angiosperms, followed by Nymphaeaceae and an Austrobaileya–Illicium–Schisandra clade. Ceratophyllum is substantiated as a close relative of monocots, as is a monophyletic eumagnoliid clade consisting of Piperales plus Winterales sister to Laurales plus Magnoliales. Possible reasons for the striking congruence between the trnT‐trnF based phylogeny and phylogenies generated from combined multi‐gene, multi‐genome data are discussed.

Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

UNLABELLED PREMISE OF THE STUDY Land plants play an essential role in the evolution of terrestrial life. Their time of origin and diversification is fundamental to understanding the evolution of life on land. We investigated the timing and the rate of molecular evolution of land plants, evaluating the effects of different types of molecular data, including temporal information from fossils, and using different molecular clock methods. • METHODS Ages and absolute rates were estimated independently with two substitutionally different data sets: a highly conserved 4-gene data set and matK, a fast-evolving gene. The vascular plant backbone and the crown nodes of all major lineages were calibrated with fossil-derived ages. Dates and absolute rates were estimated while including or excluding the calibrations and using two relaxed clocks that differ in their implementation of temporal autocorrelation. • KEY RESULTS Land plants diverged from streptophyte alga 912 (870-962) million years ago (Mya) but diversified into living lineages 475 (471-480) Mya. Ages estimated for all major land-plant lineages agree with their fossil record, except for angiosperms. Different genes estimated very similar ages and correlated absolute rates across the tree. Excluding calibrations resulted in the greatest age differences. Different relaxed clocks provided similar ages, but different and uncorrelated absolute rates. • CONCLUSIONS Whole-genome rate accelerations or decelerations may underlie the similar ages and correlated absolute rates estimated with different genes. We suggest that pronounced substitution rate changes around the angiosperm crown node may represent a challenge for relaxed clocks to model adequately.

Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA

Introns and spacers are a rich and well-appreciated information source for evolutionary studies in plants. Compared to coding sequences, the mutational dynamics of introns and spacers is very different, involving frequent microstructural changes in addition to substitutions of individual nucleotides. An understanding of the biology of sequence change is required for correct application of molecular characters in phylogenetic analyses, including homology assessment, alignment coding, and tree inference. The widely used term “indel” is very general, and different kinds of microstructural mutations, such as simple sequence repeats, short tandem repeats, homonucleotide repeats, inversions, inverted repeats, and deletions, need to be distinguished. Noncoding DNA has been indispensable for analyses at the species level because coding sequences usually do not offer sufficient variability. A variety of introns and spacers has been successfully applied for phylogeny inference at deeper levels (major lineages of angiosperms and land plants) in past years, and phylogenetic structure R in intron and spacer data sets usually outperforms that of coding-sequence data sets. In order to fully utilize their potential, the molecular evolution and applicability of the most important noncoding markers (the trnT–trnF region comprising two spacers and a group I intron; the trnS–G region comprising one spacer and a group II intron in trnG; the group II introns in petD, rpl16, rps16, and trnK; and the atpB–rbcL and psbA–trnG spacers) are reviewed. The study argues for the use of noncoding DNA in a spectrum of applications from deep-level phylogenetics to speciation studies and barcoding, and aims at outlining molecular evolutionary principles needed for effective analysis.

Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family

The authors report the structure of ten plastid genomes from hemi- and holoparasitic plants and their closest nonparasitic relative. Structural plastome reconfiguration is associated with obligate parasitism. The extent of genome reduction after the loss of photosynthesis is governed by dispensable genes’ proximity to essential genes and the position in operons or by alternative gene function. Nonphotosynthetic plants possess strongly reconfigured plastomes attributable to convergent losses of photosynthesis and housekeeping genes, making them excellent systems for studying genome evolution under relaxed selective pressures. We report the complete plastomes of 10 photosynthetic and nonphotosynthetic parasites plus their nonparasitic sister from the broomrape family (Orobanchaceae). By reconstructing the history of gene losses and genome reconfigurations, we find that the establishment of obligate parasitism triggers the relaxation of selective constraints. Partly because of independent losses of one inverted repeat region, Orobanchaceae plastomes vary 3.5-fold in size, with 45 kb in American squawroot (Conopholis americana) representing the smallest plastome reported from land plants. Of the 42 to 74 retained unique genes, only 16 protein genes, 15 tRNAs, and four rRNAs are commonly found. Several holoparasites retain ATP synthase genes with intact open reading frames, suggesting a prolonged function in these plants. The loss of photosynthesis alters the chromosomal architecture in that recombinogenic factors accumulate, fostering large-scale chromosomal rearrangements as functional reduction proceeds. The retention of DNA fragments is strongly influenced by both their proximity to genes under selection and the co-occurrence with those in operons, indicating complex constraints beyond gene function that determine the evolutionary survival time of plastid regions in nonphotosynthetic plants.

Restless 5S: the re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants.

Among eukaryotes two types of nuclear ribosomal DNA (nrDNA) organization have been observed. Either all components, i.e. the small ribosomal subunit, 5.8S, large ribosomal subunit, and 5S occur tandemly arranged or the 5S rDNA forms a separate cluster of its own. Generalizations based on data derived from just a few model organisms have led to a superimposition of structural and evolutionary traits to the entire plant kingdom asserting that plants generally possess separate arrays. This study reveals that plant nrDNA organization into separate arrays is not a distinctive feature, but rather assignable almost solely to seed plants. We show that early diverging land plants and presumably streptophyte algae share a co-localization of all rRNA genes within one repeat unit. This raises the possibility that the state of rDNA gene co-localization had occurred in their common ancestor. Separate rDNA arrays were identified for all basal seed plants and water ferns, implying at least two independent 5S rDNA transposition events during land plant evolution. Screening for 5S derived Cassandra transposable elements which might have played a role during the transposition events, indicated that this retrotransposon is absent in early diverging vascular plants including early fern lineages. Thus, Cassandra can be rejected as a primary mechanism for 5S rDNA transposition in water ferns. However, the evolution of Cassandra and other eukaryotic 5S derived elements might have been a side effect of the 5S rDNA cluster formation. Structural analysis of the intergenic spacers of the ribosomal clusters revealed that transposition events partially affect spacer regions and suggests a slightly different transcription regulation of 5S rDNA in early land plants. 5S rDNA upstream regulatory elements are highly divergent or absent from the LSU-5S spacers of most early divergent land plant lineages. Several putative scenarios and mechanisms involved in the concerted relocation of hundreds of 5S rRNA gene copies are discussed.

When morphology and molecules tell us different stories: a case-in- point with Leptodon corsicus, a new and unique endemic moss species from Corsica

Abstract Leptodon corsicus (Neckeraceae) is described as the first endemic moss species from Corsica. It strikingly differs from the other species of the genus by the lack of a dense and pinnate to bipinnate mode of branching; about 10 times smaller shoots that do not inroll upon drying; the lack of paraphyllia; and few, occasional small pseudoparaphyllia. Due to its small size and several leaf characters, L. corsicus shares at first glance more similarities with Homalia webbiana and Neckera besseri than with Leptodon. Yet, phylogenetic analysis of chloroplast and nuclear DNA sequences unambiguously shows that L. corsicus is deeply nested within L. smithii. The numerous morphological characters that distinguish L. corsicus from L. smithii cannot be attributed to plasticity. Consequently, we interpret the phylogenetic position of L. corsicus as the result of a recent speciation process, involving mutations at one or a few coding loci or differences in gene expression, which have tremendous consequences for phenotypic appearance, and retention of ancestral polymorphism in the non-coding sequences used for phylogenetic reconstruction. Such an explanation might also apply to other species of mosses, which exhibit a striking morphology, and yet share identical non-coding sequences with the common species they derive from. The notion of species in mosses is discussed in this context.

Taxonomy and phylogeny in the earliest diverging pleurocarps: square holes and bifurcating pegs

Abstract The extant members of the earliest diverging pleurocarpous moss lineages comprise few species but span a wide range of structural and molecular diversity, most of it restricted to temperate and high-altitude tropical forests in the Southern Hemisphere. We present the most comprehensive molecular phylogenetic study of these lineages to date, based on parsimony and Bayesian analyses of four regions from the chloroplast and mitochondrial genomes. In addition to corroborating the findings of parsimony methods in this and previous studies, the results of heterogeneous Bayesian analyses provide strong support for sub-topologies that are also consistently found under parsimony, but are rarely well supported. Careful model specification and investigation of potential sources of error increase confidence in the Bayesian results, which provide the basis for a substantially revised classification reflecting the best currently available hypothesis of evolutionary history. The genera previously classified in the Rhizogoniaceae, together with Orthodontium, Orthodontopsis, Aulacomnium and Calomnion, are recognized in three families, the Orthodontiaceae, Rhizogoniaceae and Aulacomniaceae, and three monofamilial orders, the Orthodontiales ord. nov., Rhizogoniales and Aulacomniales ord. nov. Many of the species previously recognized in Hypnodendron are placed in Sciadocladus, Touwiodendron gen. nov., Dendro-hypnum or Mniodendron. These genera, with the exception of Sciadocladus, are placed in the Hypnodendraceae together with Spiridens, Franciella, Cyrtopus and Bescherellia. Braithwaitea is excluded from the Hypnodendraceae and recognized in the monogeneric Braithwaiteaceae fam. nov., while Sciadocladus is placed with Pterobryella and Cyrtopodendron in the Pterobryellaceae. The Hypnodendraceae, Pterobryellaceae, Braithwaiteaceae and Racopilaceae are recognized in the order Hypnodendrales comb. et stat. nov. We discuss the advantages and limitations of ranked classification systems and propose the abandonment of intercalated Linnaean ranks between order and class levels in Bryopsida. Three node-based informal names, the Pleurocarpids, the Core Pleurocarps and the Homocostate pleurocarps, are defined to represent evolutionarily significant clades within the pleurocarpous group.

Phylogenetic analyses reveal high levels of polyphyly among pleurocarpous lineages as well as novel clades

Abstract Phylogenetic analyses of the Hypnales usually show the same picture of poorly resolved trees with a large number of polyphyletic taxa and low support for the few reconstructed clades. One odd clade, however, consisting of three genera that are currently treated either within the Leskeaceae (Miyabea) or Neckeraceae (Homaliadelphus and Bissetia), was retrieved in a previously published phylogeny based on chloroplast rbcL. In order to elucidate the reliability of the observed Homaliadelphus - Miyabea - Bissetia -clade (HMB-clade) and to reveal its phylogenetic relationships a molecular study based on a representative set of hypnalean taxa was performed. Sequence data from all three genomes, namely the ITS1 and 2 (nuclear), the trnS-rps4-trnT-trnL-trnF cluster (plastid), the nad5 intron (mitochondrial), were analyzed. Although the phylogenetic reconstruction of the combined data set was not fully resolved regarding the backbone it clearly indicated the polyphyletic nature of various hypnalean families, such as the Leskeaceae, Hypnaceae, Hylocomiaceae, Neckeraceae, Leptodontaceae and Anomodontaceae with respect to the included taxa. In addition the results favor the inclusion of the Leptodontaceae and Thamnobryaceae in the Neckeraceae. The maximally supported HMB-clade consisting of the three genera Homaliadelphus (2–3 species), Miyabea (3 species) and Bissetia (1 species) is resolved sister to a so far unnamed clade comprising Taxiphyllum aomoriense, Glossadelphus ogatae and Leptopterigynandrum. The well-resolved and supported HMB-clade, here formally described as the Miyabeaceae, fam. nov. is additionally supported by morphological characters such as strongly incrassate, porose leaf cells, a relatively weak and diffuse costa and the presence of dwarf males. The latter are absent in the Neckeraceae and the Leskeaceae. It is essentially an East Asian family, with one species occurring in North America.