Fifty mosses on five trees: comparing phylogenetic information in three types of non-coding mitochondrial DNA and two chloroplast loci

Given the frequent genomic recombinations in plant mitochondrial DNA, intergenic regions of this organelle genome had so far not been considered as loci of potential phylogenetic information. Based on the recent evidence that an evolutionary ancient mitochondrial nad5-nad4 gene continuum is conserved in bryophytes we have compiled a dataset for a phylogenetically wide sampling of 50 mosses covering this intergenic region. The length of the intergenic region was generally in the range of 585 (Diphyscium) to 646 bp (Tomentypnum) with rare exceptions, for example all Polytrichales taxa showing a 200 bp deletion as an apparent synapomorphy of this order. Phylogenetic information in the novel marker sequence was compared with that of a nad5 gene region containing a group I intron and a nad2 gene region containing a group II intron as well as with two widely sampled chloroplast data sets, rbcL and rps4. Indel evolution in the three types of non-coding mitochondrial sequences is obviously more taxon-dependent than locus-dependent, indicating lineage-specific insertion/deletion rates. For example, larger sequence deletions are a general feature in Schistostega and Tetraphis. Although confidence for particular nodes in the phylogeny was found to vary among data sets, gene trees were essentially without conflict with respect to well-supported ones and add up in information towards a reasonably well-resolved moss phylogeny. However, while a consensus on the latter is clearly emerging, sufficient confidence is still lacking for the first dichotomies among the arthrodontous mosses leading into subclasses Bryidae, Dicranidae and Funariidae and the relative placement of nematodontous mosses (Polytrichales and Tetraphidales) on the backbone of early moss phylogeny.     

PERISTOME DEVELOPMENT IN MOSSES IN RELATION TO SYSTEMATICS AND EVOLUTION. II. TETRAPHIS PELLUCIDA (TETRAPHIDACEAE)

The Tetraphidae is a small subclass of mosses with a nematodontous peristome that has frequently been interpreted as primitive among the true mosses. The developmental cell sequence leading to the formation of the four peristome teeth of Tetraphis pellucida is described for the first time. Comparisons are made with sequences known for other nematodontous and arthrodontous mosses. Peristome development in T. pellucida is more like that described previously for arthrodontous peristomes than to published developmental sequences for nematodontous peristomes of species in the Polytrichaceae. On the other hand, our observations confirm a basic uniformity of the earliest developmental stages in all mosses studied thus far, regardless of their systematic position.     

The phylogeny of mosses – Addressing open issues with a new mitochondrial locus: Group I intron cobi420

Mosses are an ancient clade of land plants, set apart from the two other monophyletic groups of bryophytes, the liverworts and the hornworts. Different molecular data sets seem to converge towards a consensus backbone phylogeny of mosses. Nevertheless, for some crucial nodes open questions remain, which obviously require additional phylogenetic information. We here report that a group I intron in the mitochondrial cob gene (cobi420) is universally conserved in the mosses, including basal genera such as Sphagnum and Takakia. Well resolved phylogenetic trees were obtained for 56 mosses of wide phylogenetic sampling, e.g. supporting a placement of Drummondia branching after the genera Timmiella and Catoscopium basal in the Dicranidae. Taxon gaps have been filled in the previously established data sets nad5i753, nad2i156, the nad5-nad4 intergenic region and chloroplast rbcL and rps4 genes. A concatenated 6-loci analysis suggests reconsideration of a Funariidae concept which includes Gigaspermaceae but leaves the isolated genus Timmia at the radiation of arthrodontous mosses unresolved.     

Organellar genomes of the four-toothed moss,Tetraphis pellucida

Background

Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systematics is the branching order of these peristomate clades. Organellar genome sequencing offers the potential to resolve this issue through the provision of both genomic structural characters and a greatly increased quantity of nucleotide substitution characters, as well as to elucidate organellar evolution in mosses. We publish and describe the chloroplast and mitochondrial genomes of Tetraphis pellucida, representative of the most phylogenetically intractable and morphologically isolated peristomate lineage.

Results

Assembly of reads from Illumina SBS and Pacific Biosciences RS sequencing reveals that the Tetraphis chloroplast genome comprises 127,489 bp and the mitochondrial genome 107,730 bp. Although genomic structures are similar to those of the small number of other known moss organellar genomes, the chloroplast lacks the petN gene (in common with Tortula ruralis) and the mitochondrion has only a non-functional pseudogenised remnant of nad7 (uniquely amongst known moss chondromes).

Conclusions

Structural genomic features exist with the potential to be informative for phylogenetic relationships amongst the peristomate moss lineages, and thus organellar genome sequences are urgently required for exemplars from other clades. The unique genomic and morphological features of Tetraphis confirm its importance for resolving one of the major questions in land plant phylogeny and for understanding the evolution of the peristome, a likely key innovation underlying the diversity of mosses. The functional loss of nad7 from the chondrome is now shown to have occurred independently in all three bryophyte clades as well as in the early-diverging tracheophyte Huperzia squarrosa.     

Responses of bryophytes to wood-ash recycling are related to their phylogeny and pH ecology

Ash generated by the combustion of solid biofuels is increasingly being returned to the fuel's place of origin (mostly forests). In this way, nutrient depletion and acidification caused by biofuel harvest is counteracted and a waste problem is solved. Concerns about the potential negative effects of ash spreading on forest biodiversity (in particular mosses) have been raised, but little is known. I studied the effects of the application of two types of ash (the most used self-hardened crushed ash including fine particles and a less reactive type, pellets without fine particles) on 28 moss species and 17 liverwort species. In two field experiments, one on transplants of ground-living species and one on wood-inhabiting species in situ, I measured the response during the first two months after ash application. Visible damage (discoloration from green to brown) was assessed for all species and the growth response was measured for 24 ground-living species. The responses to crushed ash were clearly related to the species’ pH ecology and phylogenetic position. The growth of bryophytes associated with acidic conditions (pooled data from 10 species) or considered as being indifferent to pH (4 species) was negatively affected, whereas there was no effect on the growth of bryophytes of non-acidic habitats (10 species). The connection to phylogeny was even clearer. Most taxa responded negatively, but transplants from the moss order Bryales (4 species) and the family Brachytheciaceae (2 species; order Hypnales) grew better when treated with ash. The genera with the clearest negative responses were Sphagnum mosses (5 species), Tetraphis mosses (1 species), Dicranum mosses (6 species), and Barbilophozia liverworts (2 species). The four red-listed wood-inhabiting liverworts studied were not significantly damaged. Concerning ash type, pellets caused smaller effects than crushed ash, both on the positive and negative side. The results show that responses to ash recycling of the bryophyte species included in this study are predictable from their phylogenetic position and/or pH ecology. Further studies are needed to determine the generality of these results and to sort out if phylogeny or current relationship to pH is the primary determinant of the response.     

PRELIMINARY INFERENCES OF THE PHYLOGENY OF BRYOPHYTES FROM NUCLEAR-ENCODED RIBOSOMAL RNA SEQUENCES

Ribosomal RNA sequences and cladistic analysis were used to infer a phylogeny for eight bryophyte taxa. Portions of the cytoplasmic large (26S-like) and small (18S-like) subunit ribosomal RNA genes were sequenced for three marchantioid liverworts (Asterella, Conocephalum, and Riccia), three mosses (Atrichum, Fissidens, and Plagiomnium), and two hornworts (Phaeoceros and Notothylas). Cladistic analysis of these data suggests that the hornworts are the sister group to the mosses, the mosses and hornworts form a clade that is sister to the tracheophytes, and the liverworts form a clade sister to the other land plants. These results differ from previous cladistic analyses based on morphology, ultrastructure, and biochemistry, wherein the mosses alone are sister group to the tracheophytes. We conclude that cladistic analysis of molecular data can provide an independent data set for the study of bryophyte phylogeny, but the differences between the molecular and morphological results are a topic for further investigation.     

A light, scanning electron, and transmission electron microscopic study of pollen wall architecture in the subtribe Gnaphaliinae (Gnaphalieae, Asteraceae)

To better understand relationships within the Asteroideae, the pollen morphology and exine structure of 10 genera and 15 species of Gnaphaliinae were investigated using light, scanning electron, and transmission electron microscopy. All taxa have a Gnaphalioid pattern of exine with an evidently rough foot layer. The tectal complex consists of three main layers that differ in morphology and thickness: a tectum, a median columellar layer, and an internal interlaced sub-columellar layer. The apertural system consists of an ectoaperture, a mesoaperture, and an endoaperture, which intersect, respectively, the tectal complex, the foot layer and the upper part of the endexine, and the inner part of the endexine. On the basis of pollen characteristics, especially those of the spines, all the species examined may be gathered into two groups, one including Helichrysum foetidum, H. italicum, Plecostachys serpyllifolia, and Pseudognaphalium luteo-album and the other including the other 11 species of Gnaphaliinae now investigated. In addition, because Gnaphalieae has been proposed as sister group to several tribes and clades of Asteroideae, a comparison was made between exine pattern in the Gnaphalieae and that in its putatively related tribes. On the basis of previous phylogenetic studies and our present pollen data we suggest that either Astereae, Astereae-Anthemideae clade, or Heliantheae s.l.-Anthemideae clade are the best candidates for the sister taxon/sister group of Gnaphalieae.     

Phylogenetic relationships among the ciliate arthrodontous mosses: Evidence from chloroplast and nuclear DNA sequences

Parsimony and maximum likelihood analyses of combinedtrnL (UAA) 5 exon —trnF (GAA) andrps4 exon cpDNA, and 18S nrDNA sequences of 60 arthrodontous moss taxa indicate strong support for the monophyly of a clade containing theSplachnineae, Orthotrichineae, and diplolepideous alternate sub-orders. A clade including theSplachnineae, Meesiaceae andLeptobryum (Bryaceae) is similarly well supported and forms the sister group to a clade comprising theOrthotrichineae and the other diplolepideous alternate mosses. Within this latter clade a number of well supported lineages are identified, but relationships among these remain poorly resolved. These analyses indicate that the Splachnaceous and Orthotrichaceous peristomes have been independently derived from an ancestral perfect bryoid peristome.     

Ultrastructure and development of the gametophyte vaginula-sporophyte foot complex in the liverwort Targionia hypophylla L.

The development of the placental complex including the gametophyte vaginula and the bulbous foot of the sporophyte in the liverwort Targionia hypophylla L. (Marchantiales) was studied by transmission electron microscopy. The vaginula and foot are separated by an intervening space and each consist of parenchymatous cells without intercellular spaces. Transfer cells begin to differentiate at the gametophyte-sporophyte interface just prior the onset of meiosis. While a single epidermal transfer-cell layer has developed in the foot by the end of meiosis, a multilayered pattern of transfer cells is formed in the vaginula. Gametophyte transfer cells have wall labyrinths which decrease in complexity with distance from the foot, lack plasmodesmata, and show signs of degeneration in the proximity of the foot. During meiosis, amyloplasts of both vaginula and foot lack starch and develop some thylakoid grana. In the subsequent stage of spore maturation, obliteration of the wall labyrinth occurs in both gametophyte and sporophyte transfer cells. The developmental pattern of the placental complex in Targionia is discussed in relation to that of mosses.     

Development of the enigmatic peristome of Timmia megapolitana (Timmiaceae; Bryophyta)

The Timmiaceae (Bryophyta) have been traditionally classified within the Bryales based on peristome architecture. Phylogenetic analyses of nucleotide sequences have revealed relationships that are incongruent with this hypothesis and have implicated an origin for this lineage early in the radiation of arthrodontous mosses (Bryopsida). This unexpected phylogenetic placement raises important questions about the evolutionary significance of the Timmia peristome, which differs from all other mosses by 64 isomorphic filaments topping the endostomial membrane. A developmental study of the peristome in Timmia megapolitana was undertaken to examine alignments of anticlinal cell walls in the inner peristomial layer (IPL) with those of the primary peristomial layer (PPL), a character that has been used to define major arthrodontous lineages. Criteria were established for assessing longitudinally homologous regions that contribute to the peristome-forming region. Young sporophytes were examined using histological techniques, and the alignment of the cell wall divisions was quantified. Critical divisions in the IPL of T. megapolitana were determined to be symmetrical, similar to patterns in the Funariales. This research provides novel developmental observations for a putative ancestral lineage of arthrodontous mosses, reevaluates criteria used to compare developmental studies of different lineages and discusses the phylogenetic implications of these observations.     

Evaluation of chromium phytoremediation potential of some plant species of Dir Lower,Khyber Pakhtunkhwa,Pakistan

Chromium is the second most common metal pollutant in the soil, sediments and groundwater, due to its extensive industrial application, hence posing a serious environmental concern. Various remediation approaches including phytoremediation have been proposed to remediate chromium polluted waters and soils. In the present research, a total of sixty-one plant species belongs to thirty families were analyzed for the concentration of Chromium. Chromium was analyzed in the soil of the root zone, root and shoot of each plant. The concentration of chromium in the soil of different sites and plant parts (roots and shoots) was found in mg/kg in the range of 0.33–48.73, 8–1233.3 and 10.23–568.33 respectively. The highest concentration of chromium was found in the soil of site Site 41 (48.73 mg/kg) followed by Site 18 (47.83 mg/kg) and Site 6 (45.33 mg/kg). Among the analyzed plants, the highest concentration of chromium in mg/kg was found in the root of Cannabis sativa (1233.3) while its highest concentration was found in the shoot of Allium griffithianum (568.33). Phytoremediation potential of the analyzed plants was evaluated by the calculation of Bioconcentration Factor (BCF), Translocation Factor (TF) and Biological Accumulation Coefficient (BAC). Thirty-eight plant species showed feasibility for the phytostabilization of chromium (Cr_Excluders) based on BCF value and the concentration of chromium in the root. Plants i.e. Argyrolobium stenophyllum, Silybum marianum, Bryophyllum daigremontianum, Limonium macrorhabdon, Calendula arvensis and Delphinium suave were found the most efficient plant for the phytostabilization of chromium. Fifteen plant species showed feasibility for the phytoextraction of chromium (Cr_Indicators) based on TF value. The most efficient plant's species among them for the phytoextraction of chromium are Rosularia adenotricha, Catharanthus roseus, Allium griffithianum, Himalaiella heteromalla, Stellaria media, Salvia moorcroftiana and Marrubium vulgare. Based on BCFs, TFs and BACs value and the concentration of chromium in plant shoot six plant species Allium griffithianum, Catharanthus roseus, Himalaiella heteromalla, Geranium rotundifolium, Marrubium vulgare and Solanum nigrum were found chromium hyperaccumulators.     

Introducing Intron Locus cox1i624 for Phylogenetic Analyses in Bryophytes: On the Issue of Takakia as Sister Genus to All Other Extant Mosses

Liverworts are well supported as the sister group to all other land plants (embryophytes) by molecular data. Observations strongly supporting this earliest dichotomy in embryophyte evolution are the strikingly different introns occurring in the mitochondrial DNAs of liverworts versus non-liverwort embryophytes (NLE), including the mosses. A final conclusion on the most basal lineages of mosses, for which genera such as Sphagnum and Takakia are the most likely candidates, is lacking. We have now investigated cox1i624, a mitochondrial group I intron conserved between the moss Physcomitrella patens and the liverwort Marchantia polymorpha. Focusing on a sampling of liverwort and moss genera, which had previously been identified as early branching taxa in their respective clades, we find that group I intron cox1i624 is universally conserved in all 33 mosses and 11 liverworts investigated. The group I intron core secondary structure is well conserved between the two ancient land plant clades. However, whereas dramatic size reductions are seen in the moss phylogeny, exactly the opposite is observed for liverworts. The cox1i624g1 locus was used for phylogenetic tree reconstruction also in combination with data sets of nad5i753g1 as well as chloroplast loci rbcL and rps4. The phylogenetic analyses revealed (i) very good support for the Treubiopsida as sister clade to all other liverworts, (ii) a sister group relationship of the nematodontous Tetraphidopsida and Polytrichopsida and (iii) two rivalling hypotheses about the basal-most moss genus with mitochondrial loci suggesting an isolated Takakia as sister to all other mosses and chloroplast loci indicating a Takakia–Sphagnum clade.     

Patterns of clade support across the major lineages of moss phylogeny

Relationships among the major branches of moss phylogeny are understudied compared with other major land‐plant groups. We addressed this by surveying 14–17 plastid genes from taxa representing the major lineages, using different phylogenetic methods (parsimony, likelihood) and codon‐ and gene‐based data partitioning schemes (likelihood). Our phylogenetic inferences generally corroborated the best supported clades across multiple recent studies, with comparable or higher levels of clade support here. We resolved persistent ambiguities with strong to moderate support across analyses, including several early nodes in subclass Dicranidae, and relationships among other subclasses of peristomate mosses. In particular, we resolved a sister‐group relationship between Bryidae and Dicranidae, between these subclasses and Timiidae, and between this entire clade and Funariidae. We consistently recovered Tetraphidopsida (a nematodontous class) as the sister group of arthrodontous mosses (Bryopsida), although with only weak support. Strongly conflicting arrangements at the base of moss phylogeny concerning Takakiopsida and Sphagnopsida, two non‐peristomate moss lineages, were inferred in parsimony and likelihood analysis, but this depended on how base‐frequency parameters were estimated and how data were partitioned in likelihood analysis. Relationships inferred for the remaining peristomate and non‐peristomate moss clades, and their associated support values, were otherwise broadly congruent across analyses.     

The Bryophyta (Mosses): Systematic and Evolutionary Inferences from an rps4 Gene (cpDNA) Phylogeny

Phylogenetic analyses of nucleotide and amino acid sequencesof the chloroplast protein coding generps4 were performed for225 species of mosses, representing 84% of families recognizedby Vitt (1984. In: Schuster RM, ed. New manual of bryology,vol 2. Nichinan: Hattori Botanical Laboratory), under the criterionof maximum parsimony with Takakia and Sphagnum as outgroups.Most parsimonious topologies converge to a scenario whereinthe Andreaeidae are monophyletic and sister to the Bryidae (peristomatemosses), the Nematodonteae and the Buxbaumiaceae form a monophyleticlineage, the Diphysciaceae are sister to the Arthrodonteae and,within the latter, the Funarineae-Encalyptineae-Timmiaceae-Haplolepideaecompose a monophyletic clade sister to remaining diplolepideousmosses. This hypothesis suggests that early in the evolutionof the Arthrodonteae, two major lineages diverged, with oppositeand alternate peristomes, respectively. Bootstrap support forthe deep dichotomies is poor or lacking but increases when proteintranslations ofrps 4 sequences are included in the analysis.Several novel systematic hypotheses are raised, including (a)a diplolepideous rather than haplolepideous origin of the Pleurophascaceae;(b) an affinity of the Catascopiaceae with the Funariineae ratherthan the Bryineae; and (c) a close relationship of the Calomniaceaeand Mitteniaceae to the Rhizgoniaceae. The advantages and disadvantagesof a single gene phylogeny are discussed with respect to theidentification of polyphyletic familial or suprafamilial taxa.Copyright 2001 Annals of Botany Company Bryophyta, mosses, phylogeny, rps4, evolution, peristome, parsimony, sequences     

Mesodermal Gene Expression in the Acoel Isodiametra pulchra Indicates a Low Number of Mesodermal Cell Types and the Endomesodermal Origin of the Gonads

Acoelomorphs are bilaterally symmetric small marine worms that lack a coelom and possess a digestive system with a single opening. Two alternative phylogenetic positions of this group within the animal tree are currently debated. In one view, Acoelomorpha is the sister group to all remaining Bilateria and as such, is a morphologically simple stepping stone in bilaterian evolution. In the other, the group is a lineage within the Deuterostomia, and therefore, has derived a simple morphology from a more complex ancestor. Acoels and the closely related Nemertodermatida and Xenoturbellida, which together form the Acoelomorpha, possess a very limited number of cell types. To further investigate the diversity and origin of mesodermal cell types we describe the expression pattern of 12 orthologs of bilaterian mesodermal markers including Six1/2, Twist, FoxC, GATA4/5/6, in the acoel Isodiametra pulchra. All the genes are expressed in stem cells (neoblasts), gonads, and at least subsets of the acoel musculature. Most are expressed in endomesodermal compartments of I. pulchra developing embryos similar to what has been described in cnidarians. Our molecular evidence indicates a very limited number of mesodermal cell types and suggests an endomesodermal origin of the gonads and the stem cell system. We discuss our results in light of the two prevailing phylogenetic positions of Acoelomorpha.     

Molecular Systematics and Evolution of the Growth Hormone Introns in the Salmoninae

DNA sequence data was collected for the C and D introns in the duplicate growth hormone loci (GH1 and GH2) from Brachmystax lenok, two subspecies of Hucho hucho, Hucho (Parahucho) perryi, Salmo salar, Salmo trutta, Acantholingua ohridana (Salmothymus), six species of Salvelinus, eight species of Oncorhynchus including O. masou, and three outgroups including Thymallus thymallus, Coregonus artedi, and Coregonus clupeaformis. Phylogenetic analyses were performed using maximum parsimony and maximum likelihood (PAUP, version 4.08beta) with gaps as missing data and as a fifth base. B. lenok was basal in all of the trees and all of the other genera were monophyletic with the exception that A. ohridana always placed within Salmo, and H. hucho sp. often placed with B. lenok. The GH1 introns supported a sister relationship between Oncorhynchus and Salvelinus, while the combined GH2 introns were ambiguous at this node. This result contrasts with trees based on morphology and the ribosomal ITS1 sequences that support a sister relationship between Salmo and Oncorhynchus. The only estrogen response element (ERE) in the gene is found in the C intron and has mutated in GH2 in all of the species except B. lenok. The ERE element in GH1 has undergone another mutation in all of the species except for B. lenok, and members of the two genera Salvelinus and Oncorhynchus. Thus these latter two genera are the only ones with a difference in expression of GH1 and GH2 in the presence of estrogen. Differences in selective pressure on the introns in the duplicate genes in different taxa could account for the conflicting results obtained in the phylogenetic analysis.