Chloroplast Genome Evolution in Early Diverged Leptosporangiate Ferns

In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnV-GCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of co-dons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.     

Spore morphology and wall ultrastructure of Trachypteris species (Pteridaceae)

Trachypteris is a small genus consisting of four species native to America and Madagascar: Trachypteris induta, T.?pinnata, T.?gilliana, and T.?drakeana. The spores of the genus were studied using light microscopy and scanning and transmission electron microscopy. They are trilete, triangular to globose, with equatorial diameter of 29?C58???m and polar diameter of 26?C53???m. The exospore is 0.5?C1.1???m thick, plane, and two-layered. The perispore is 0.3?C6.8???m thick and two-layered. Depending on the species, two different ornamentations were observed: cristated with partially fused cristae, and ridged with partially fused ridges, forming an incomplete reticulum. Globules immersed in the perispore were occasionally observed. The systematic value of the Trachypteris spores is discussed, and their morphology and ultrastructure are compared with those of other related cheilanthoid ferns. The palynological characteristics presented here may be useful for phylogenetic studies within the Pteridaceae, and particularly within the cheilanthoid ferns.     

Sur les fougères Anachoropteris et Tubicaulis du Stéphanienfrançais. Description de Tubicaulis grandeuryi nov. sp.

New information is presented on the morphology of leaves and stems of the ferns Anachoropteris and Tubicaulis preserved in silicified material from the Stephanian of Grand'Croix (France). A rachis of Anachoropteris involuta bears laterally, in association with a pinna, an epiphyllous stem, with a vitalized protostele. This stem bears nine petioles and is almost identical in anatomy to the american species, Tubicaulis stewartii. A hand-ground section from the Grand'Eury collection, Paris, is described as Tubicaulis sp. and identified as a more distal region of a similar stem. Tubicaulis grandeuryi nov. sp. is another type, with haplostelic stem and petioles bearing pinna traces near their base. Axillary branching is described in this genus for the first time. The problem of redefining the systematic position of Tubicaulis and its relationship to Anachoropteris is discussed.     

Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis

BackgroundSome ferns have medicinal properties and are used in therapeutic interventions. However, the classification and phylogenetic relationships of ferns remain incompletely reported. Considering that chloroplast genomes provide ideal information for species identification and evolution, in this study, three unpublished and one published ferns were sequenced and compared with other ferns to obtain comprehensive information on their classification and evolution.Materials and MethodsThe complete chloroplast genomes of Dryopteris goeringiana (Kunze) Koidz, D. crassirhizoma Nakai, Athyrium brevifrons Nakai ex Kitagawa, and Polystichum tripteron (Kunze) Presl were sequenced using the Illumina HiSeq 4,000 platform. Simple sequence repeats (SSRs), nucleotide diversity analysis, and RNA editing were investigated in all four species. Genome comparison and inverted repeats (IR) boundary expansion and contraction analyses were also performed. The relationships among the ferns were studied by phylogenetic analysis based on the whole chloroplast genomes.ResultsThe whole chloroplast genomes ranged from 148,539 to 151,341 bp in size and exhibited typical quadripartite structures. Ten highly variable loci with parsimony informative (Pi) values of > 0.02 were identified. A total of 75–108 SSRs were identified, and only six SSRs were present in all four ferns. The SSRs contained a higher number of A + T than G + C bases. C‐to‐U conversion was the most common type of RNA editing event. Genome comparison analysis revealed that single‐copy regions were more highly conserved than IR regions. IR boundary expansion and contraction varied among the four ferns. Phylogenetic analysis showed that species in the same genus tended to cluster together with and had relatively close relationships.ConclusionThe results provide valuable information on fern chloroplast genomes that will be useful to identify and classify ferns, and study their phylogenetic relationships and evolution.     

Yanliaoa, an extinct genus of Cupressaceae s. l. from the Middle Jurassic,northeastern China

Yanliaoa is a common fossil in the Middle Jurassic of western Liaoning, eastern Inner Mongolia and northern Hebei Province, China. It is an important element of the Yanliao biota. The genus was established by Pan in 1977 for fossil plants from the Middle Jurassic Haifanggou Formation in Xiasanjiaochengzi, western Liaoning Province, and in present paper, the genus Yanliaoa is studied based on new material. Pan never designated a type specimen and his fossil material cannot be located. We designate a type specimen here for Yanliaoa, so that the genus name Yanliaoa remains valid. Yanliaoa sinensis Pan emend. Tan et al., is found in the same locality and formation as the lost specimens, Y. sinensis of Pan, 1977. Yanliaoa daohugouensis n. sp., a new species with epidermal anatomy, is from the Middle Jurassic Daohugou, Inner Mongolia. A holotype is also selected from the new material for this new species. Characters of the leafy shoots and ovulate cones of Yanliaoa are emended. The epidermal anatomy of this genus is described for the first time. Compared with other extant and extinct species of Cupressaceae s. l., the current species can be distinguished from any known species both by the leafy shoot characters and its epidermal anatomy. It further indicates that Yanliaoa is an extinct and endemic conifer found in the Middle Jurassic of northeastern China.     

New Observations on the Branching of Carboniferous Ferns and Pteridosperms

Additional information is presented on the oldest known exampleof axillary branching seen in some Calamopitys from the lowermostCarboniferous of France; these putative pteridosperms are amongstthe earliest plants to be attributed to the spermatophytes.Comparative anatomical studies of coenopterid ferns from theLower and Upper Carboniferous show four categories of caulinebranching morphology: unbranched, dichotomous, lateral-monopodialand branches borne on leaves. It is suggested that leaf evolutionand thus, the axillary type of branching, was achieved earlierin the pteridosperms than in the ferns. Calamopitys, pteridosperms, coenopterid ferns, axillary branching, stem dichotomy, evolution, Carboniferous, fossil anatomy     

Krogia coralloides,a new lichen genus and species from Mauritius

Abstract:The new corticolous lichen genus Krogia and species K. coralloides are described from humid forest in Mauritius. The genus shows affinities with Phyllopsora, but differs in characters of the ascus, ascospores, and thallus anatomy. The ascal characters make its inclusion in the Bacidiaceae orPhyllopsoraceae problematic. The lichen contains boninic acid and an apparently related compound.     

Molecular phylogeny of the endemic fern genera Cyrtomidictyum and Cyrtogonellum (Dryopteridaceae) from East Asia

Cyrtomidictyum Ching and Cyrtogonellum Ching are two eastern Asian endemic genera whose taxonomic affinities and phylogenetic relationships have long been controversial. The main uncertainty surrounds the separation of the two genera from the species-rich genus Polystichum. Here we present a phylogenetic study focusing on the phylogenetic relationships of these polystichoid ferns. We reconstructed the relationships based on DNA sequence variation in four chloroplast genome regions, rbcL, atpB, and the intergenic spacers (IGS) rps4-trnS and trnL-trnF. Maximum likelihood and Bayesian inference analyses confirm earlier results that were based on less comprehensive taxon sampling and either only a single gene (rbcL) or two IGS (rps4-trnS and trnL-trnF). Cyrtomidictyum is the sister of the clade of polystichoid ferns that includes Cyrtogonellum, Cyrtomium subser. Balansana and three sections of Polystichum. Cyrtogonellum groups with several species of Polystichum, and constitutes the sister taxon to Polystichum sect. Sphaenopolystichum. We support the recognition of Cyrtomidictyum as circumscribed initially, rather than expansion of the genus to include either several Polystichum species or Cyrtogonellum, some Polystichum and Cyrtomium species. The monophyly of Cyrtomidictyum is supported by morphological characters such as once-pinnate leaves, free venation, prolongated leaf apices, and exindusiate sori. Two synapomorphic indels in the chloroplast genome, one 15-bp deletion in rps4-trnS, and one 3-bp insertion in trnL-trnF further differentiate Cyrtomidictyum from other polystichoid ferns. The close affinity of Cyrtogonellum to section Sphaenopolystichum of Polystichum s.s. is highly supported by molecular data. However, no shared morphological characters or molecular indels have been detected, although the distinctness of Cyrtogonellum is shown by a 13-bp insertion in the rps4-trnS alignment.     

An upright psaroniaceous stump and two surrounding pecopteroids from the early Permian Wuda Tuff Flora

An upright Psaronius stump was discovered in the upper part of Taiyuan Formation (Asselian) of Wuda Coalfield, Inner Mongolia, China. The stump is 47 cm high and truncated at the upper part of the ash layer in which it is preserved. At the height of 38 cm, the stem possesses a stelar configuration comprised of 3~4 cycles in 5 orthostichies. The Wuda Psaronius stump rapidly widens at the base until it attains a stable axial diameter; a root mantle is present in the proximal zone of primary body expansion, but not distal to that zone. This architecture is further demonstrated by a prostrate Psaronius trunk almost 7 m long with a stable stem diameter and two rows of frond scars visible over most of its length. This developmental mode is seen among extant leptosporangiate tree ferns but differs from that previously documented among North American Pennsylvanian marattialean tree ferns whereby the primary body of Psaronius stems increases continually in width towards the apex and is buttressed by a thick root mantle that compensates for the obconical nature of the stem. Two types of pecopteroid fronds associated with the Psaronius stump are identified as Pecopteris cf. polymorpha and Pecopteris orientalis based on their pinnule morphology. The Pecopteris orientalis frond possesses a penultimate rachis with stewartiopteroid anatomy and is more likely to be the leaf of the Psaronius stump based on a recently reported Psaronius specimen with stem and frond in connection from the same locality.     

Diffusional limitations explain the lower photosynthetic capacity of ferns as compared with angiosperms in a common garden study

Ferns are thought to have lower photosynthetic rates than angiosperms and they lack fine stomatal regulation. However, no study has directly compared photosynthesis in plants of both groups grown under optimal conditions in a common environment. We present a common garden comparison of seven angiosperms and seven ferns paired by habitat preference, with the aims of (1) confirming that ferns do have lower photosynthesis capacity than angiosperms and quantifying these differences; (2) determining the importance of diffusional versus biochemical limitations; and (3) analysing the potential implication of leaf anatomical traits in setting the photosynthesis capacity in both groups. On average, the photosynthetic rate of ferns was about half that of angiosperms, and they exhibited lower stomatal and mesophyll conductance to CO₂ (g_m), maximum velocity of carboxylation and electron transport rate. A quantitative limitation analysis revealed that stomatal and mesophyll conductances were co‐responsible for the lower photosynthesis of ferns as compared with angiosperms. However, g_m alone was the most constraining factor for photosynthesis in ferns. Consistently, leaf anatomy showed important differences between angiosperms and ferns, especially in cell wall thickness and the surface of chloroplasts exposed to intercellular air spaces.     

Early Cretaceous Gleicheniaceae and Matoniaceae (Gleicheniales) from Alexander Island,Antarctica

The first Cretaceous representatives of Matoniaceae and Gleicheniaceae in the Antarctic are described from the Albian flora of Alexander Island. Two new species are recognized, one is assigned to Matonia, and another to the emended gleicheniaceous form-genus Gleicheniaceaephyllum. The taxonomy of fossil genera assigned to Gleicheniaceae is problematic, and as an alternative to the invalid genus Gleichenites, we propose that Microphyllopteris be utilised as a form-genus for species that have either an unknown branching pattern or pseudo-dichotomous branching without resting buds; Microphyllopteris is reserved for ferns that cannot be ascribed conclusively to Gleicheniaceae. Alternatively, Gleicheniaceaephyllum should be used for gleicheniaceous material that has a resting bud amongst two to four primary branches. Gleicheniaceaephyllum acutum sp. nov. is preserved as sterile and fertile fronds, pinnae and pinnules. The other new species, Matonia jeffersonii sp. nov., occurs as sterile and fertile pinnae and pinnules, and is aligned to Matoniaceae based on the presence of circular-oval sori with peltate indusia. The two taxa are inferred to have either a pedate or scrambling habit. These morphologies are relatively common at Alexander Island, compared to other high latitude fossil floras, and are interpreted as an adaptation to the high disturbance, polar conditions and unusual photoperiod experienced at Alexander Island during the Early Cretaceous. The theory that angiosperms caused the demise of ferns is discussed in relation to the Matoniaceae and Gleicheniaceae, and there does not appear to be association between angiosperm expansion and the decline of these two fern families.     

Sinephropteris,a new genus of scolopendrioid ferns

A new genus of ferns,Sinephropteris, is described from southeast Asia. Its one species,S. delavayi (Franch.) Mickel, has most recently been placed inSchaffneria, an otherwise monotypic Mexican genus, but there is evidence that they are not closely related.     

Spore morphology of the genus Dryopteris Adans. (Dryopteridaceae) in Korea

Spore morphology of the Korean members of the genus Dryopteris was examined by scanning electron microscopy. In particular, spores of D. hangchowensis, D. woodsiisora, D. saxifragivaria, and D. subexaltata were examined here for the first time. Three perispore types were recognized on the basis of the shape of macro-ornamentations on perispore: these include rugate, echinate, and spinose. The rugate perispore type appeared to be the most common in the genus, and probably represents plesiomorphic condition in the genus Dryopteris. The echinate perispore type is found in D. expansa, and spinose perispore type in D. formosana. The results of this study demonstrate that the perispore characteristics, particularly the shape of macro-ornamentation and surface texture, have diagnostic value at the species level. Indeed, most of the Dryopteris taxa in Korea could be distinguished by their perispore characters. In addition, spores of sexual diploid individuals of D. saxifraga were much smaller than those of agamosporous triploid individuals, supporting the contention that the size of spores in ferns is generally related to ploidy levels.     

How diverse were ferns in the Baltic amber forest?

Diverse temperate forest types and a high atmospheric humidity have recently been suggested for the Eocene source area of Baltic amber. However, ferns are astonishingly rare as inclusions in this amber, which is in contrast to other seed‐free land plants, fungi, and lichens. Moreover, the identities of some of the few described putative fern taxa are dubious, and some fossils were even assigned to the Paleozoic seed fern genera Alethopteris, Pecopteris and to the form genus Sphenopteris containing Paleozoic and Mesozoic fern‐like leaf fossils. Here, we review previously described fern inclusions from Baltic amber and identify further fern‐like leaf inclusions as belonging to the extant angiosperm genus Comptonia (sweet ferns, Myricaceae). We conclude that only one taxon, Matonia striata (Matoniaceae), can with confidence be identified as a Polypodiopsida representative. Although “Pecopteris” humboldtiana is so far only known as sterile foliage, its leaf morphology strongly suggests that also this taxon belongs to the Polypodiopsida rather than to any other tracheophyte lineage. We propose accommodating “Pecopteris” humboldtiana in the new genus Berendtiopteris. “Alethopteris” serrata and “Sphenopteris” phyllocladoides are not to be regarded as evidence of ferns from Baltic amber. Reinvestigation of the holotypes of these two taxa did not reveal to which tracheophyte lineages these fossils belong. We suggest that the scarcity of fern remains from Baltic amber may reflect both a relatively low fern diversity in the source area of the fossil resin, and an absence or rarity of epiphytic and climbing ferns as observed in modern temperate forest ecosystems.     

Leonophyllum tenellum nov. gen., nov. sp., an enigmatic plant from the Early Jurassic of the Mecsek Mts (Hungary)

The Early Jurassic flora of the Mecsek Mountains is diverse, with numerous representatives of ferns, seed ferns, cycadophytes, ginkgophytes, and conifers. Its (para-)autochthonous deposition, good preservation and low collection bias has permitted researchers to save delicate, small plant remains that would generally be missing from the fossil record. These plant fossils are characterized by having a “filmy” (probably unilayered) structure, thin stalks with flat leaf-like branches and ultimate irregular segments with streamlined epidermal cells having thick cell walls. Due to the absence of sporangia, the plant remains cannot be confidently assigned to any higher plant group, although they show some similarities to thalloid liverworts with raised vegetative bodies and also have some resemblance to the fern family Hymenophyllaceae. The new genus and species Leonophyllum tenellum Barbacka et Kustatscher is erected.     

Invasive feral pigs impact native tree ferns and woody seedlings in Hawaiian forest

Invasive mammals can fundamentally alter native plant communities, especially on isolated islands where plants evolved without them. The globally invasive feral pig (Sus scrofa) can be particularly destructive to native plant communities. Tree ferns are an important understory component in many forests facilitating the establishment of a variety of species. However, the extent and effects of feral pig damage to tree ferns, and associated impacts on plant community regeneration, are largely unknown. We quantified the effect that feral pig damage has on tree fern growth, survival, and epiphytic woody seedling abundance over 1 year on 438 randomly selected tree ferns of three endemic species (Cibotium chamissoi, Cibotium glaucum, and Cibotium menziesii) in a Hawaiian montane wet forest with high tree fern and feral pig densities. Across all tree fern species, feral pigs damaged 13 % of individuals over 1 year. Compared with undamaged tree ferns, moderately- to heavily-damaged individuals had decreases of 4 to 27 % in trunk length increment and lost tenfold more fronds. Tree fern angle (standing, leaning, prone, or semi-prone) and woody seedling abundance co-varied with feral pig damage. Specifically, damaged tree ferns were more often prone or semi-prone and supported more seedlings, but also had annual mortality up to 34 % higher than undamaged tree ferns. Overall, feral pig damage had substantial negative effects on tree ferns by reducing growth and survival. Given the importance of tree ferns as regeneration sites for a variety of native plants, feral pig damage to tree ferns will likely alter future forest composition and structure. Specifically, feral pig damage to tree ferns reduces potential establishment sites for species that either regenerate preferentially as epiphytes or are currently restricted to epiphytic establishment due to ground rooting by feral pigs.     

Xenostegia,a new genus of Convolvulaceae

Stigma anatomy, pollen morphology, cotyledon structure and other traits suggest that two species formerly considered members ofMerremia fall outside an acceptable range of variation for that genus. A new genus,Xenostegia, is proposed for these two species.