Historical biogeography of the ancient lycophyte genusSelaginella: early adaptation to xeric habitats on Pangea

Phylogeny, character evolution, and classification of Selaginellaceae (lycophytes)

Selaginella is the largest and most taxonomically complex genus in lycophytes. The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes. Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions (74% increase of the earlier largest sampling) representing ca. 300 species to infer a new phylogeny. The evolution of 10 morphological characters is studied in the new phylogenetic context. Our major results include: (1) the nuclear and plastid phylogenies are congruent with each other and combined analysis well resolved and strongly supported the relationships of all but two major clades; (2) the Sinensis group is resolved as sister to S. subg. Pulviniella with strong support in two of the three analyses; (3) most morphological characters are highly homoplasious but some characters alone or combinations of characters well define the major clades in the family; and (4) an infrafamilial classification of Selaginellaceae is proposed and the currently defined Selaginella s.l. is split into seven subfamilies (corresponding to the current six subgenera + the Sinensis group) and 19 genera (the major diagnosable clades) with nine new species-poor genera. We support the conservation of Selaginella with a new type, S. flabellata, to minimize nomenclatural instability. We provide a key to subfamilies and genera, images illustrating their morphology, their morphological and geographical synopses, a list of constituent species, and necessary new combinations. This new classification will hopefully facilitate communication, promote further studies, and help conservation.

Five long-distance dispersals shaped the major intercontinental disjunctions in Tectariaceae s.l. (Polypodiales, Polypodiopsida)

Intercontinental disjunct distributions can arise either from vicariance, from long-distance dispersal, or through extinction of an ancestral population with a broader distribution. Tectariaceae s.l., a clade of ferns in Polypodiales with ca. 300 species mainly distributed in the tropics and subtropics, provide an excellent opportunity to investigate global distribution patterns. Here, we assembled a dataset of eight plastid markers and one nuclear marker of 636 (92% increase of the earlier largest sampling) accessions representing ca. 210 species of all eight genera in Tectariaceae s.l. (Arthropteridaceae, Pteridryaceae, and Tectariaceae s.s.) and 35 species of other families of eupolypods Ⅰ. A new phylogeny is reconstructed to study the biogeography and trait-associated diversification. Our major results include: (1) a distinct lineage of Tectaria sister to the rest of the American Tectaria is identified; (2) Tectariaceae s.l., and the three families: Arthropteridaceae (Arthropteris), Pteridryaceae (Draconopteris, Malaifilix, Polydictyum, Pteridrys), and Tectariaceae s.s. (Hypoderris, Tectaria, and Triplophyllum), might have all originated in late Cretaceous; (3) only five intercontinental dispersals occurred in Pteridryaceae and Tectariaceae s.s. giving rise to their current intercontinental disjunction; (4) we provide the second evidence in ferns that a long-distance dispersal between Malesia and Americas during the Paleocene to Eocene led to the establishment/origin of a new genus (Draconopteris); and (5) diversification rate of each state of leaf dissection is different, and the lowest is in the simple-leaved taxa.

Selaginelladensiciliata (subg. Heterostachys, Selaginellaceae), a new spikemoss species from China based on morphological and molecular data

A new species of spikemoss, Selaginelladensiciliata in S.subg.Heterostachyssect.Tetragonostachyae, China, is described from southeastern Xizang, based on morphological and molecular phylogenetic data. Morphologically, S.densiciliata is similar to S.repanda, S.subvaginata and S.vaginata, but the new species can be easily distinguished from them by having sterile leaves margins densely ciliate, symmetrical axillary leaves oblong ovate to ovate-triangular, and ovate dorsal leaves obviously carinate. Molecular phylogenetic analysis resolves S.densiciliata as sister to the clade comprised with S.vaginata and S.xipholepis, which confirms the recognition of the new species.

Diversity of the Pteridoflora of Montane Northwestern Mexico

This study compiles and updates the checklist of ferns and lycophytes from the Sierra Madre Occidental (SMOc). For this, we revised information on these taxa from regional floristic studies, databases, and herbaria. Our updated list includes 312 species, of which 276 are ferns and 36 are lycophytes integrated into 27 families and 75 genera. The richest families are Pteridaceae (118), Polypodiaceae (31), Selaginellaceae (30), Aspleniaceae (25), and Dryopteridaceae (25). The three most diverse genera were Selaginella (30), Asplenium (25), and Myriopteris (22). The species-rich Mexican states that include the SMOc are Durango (166 species), Chihuahua (149), and Jalisco (146). As in other tropical mountains, species richness in the SMOc is concentrated at the elevation interval of 1500 to 2000 m (236 species). The mid-mountain vegetation forests (Quercus and Pinus-Quercus forests) harbor the most pteridoflora richness (52% of the species). Four species of ferns are listed as threatened in the Mexican Official Norm NOM-059-SEMARNAT-2010, 17 species are listed in the IUCN, and only one tree ferns are in CITES. The SMOc has a Nearctic affinity, and its fern and lycophyte diversity are lower than in other Mexican Transition Zone mountain chains, such as the Sierra Madre del Sur, the Trans-Mexican Volcanic Belt, and the Sierra Madre Oriental. Notwithstanding, its biological composition is unique and distinctive. The species number reported in the SMOc represents 31% of the pteridoflora diversity recorded in Mexico.

Comparative transcriptome analysis suggests convergent evolution of desiccation tolerance in Selaginella species

BACKGROUND

Desiccation tolerant Selaginella species evolved to survive extreme environmental conditions. Studies to determine the mechanisms involved in the acquisition of desiccation tolerance (DT) have focused on only a few Selaginella species. Due to the large diversity in morphology and the wide range of responses to desiccation within the genus, the understanding of the molecular basis of DT in Selaginella species is still limited.

RESULTS

Here we present a reference transcriptome for the desiccation tolerant species S. sellowii and the desiccation sensitive species S. denticulata. The analysis also included transcriptome data for the well-studied S. lepidophylla (desiccation tolerant), in order to identify DT mechanisms that are independent of morphological adaptations. We used a comparative approach to discriminate between DT responses and the common water loss response in Selaginella species. Predicted proteomes show strong homology, but most of the desiccation responsive genes differ between species. Despite such differences, functional analysis revealed that tolerant species with different morphologies employ similar mechanisms to survive desiccation. Significant functions involved in DT and shared by both tolerant species included induction of antioxidant systems, amino acid and secondary metabolism, whereas species-specific responses included cell wall modification and carbohydrate metabolism.

CONCLUSIONS

Reference transcriptomes generated in this work represent a valuable resource to study Selaginella biology and plant evolution in relation to DT. Our results provide evidence of convergent evolution of S. sellowii and S. lepidophylla due to the different gene sets that underwent selection to acquire DT.

Drought-induced lacuna formation in the stem causes hydraulic conductance to decline before xylem embolism in Selaginella

Lycophytes are the earliest diverging extant lineage of vascular plants, sister to all other vascular plants. Given that most species are adapted to ever-wet environments, it has been hypothesized that lycophytes, and by extension the common ancestor of all vascular plants, have few adaptations to drought. We investigated the responses to drought of key fitness-related traits such as stomatal regulation, shoot hydraulic conductance (K_shoot ) and stem xylem embolism resistance in Selaginella haematodes and S. pulcherrima, both native to tropical understory. During drought stomata in both species were found to close before declines in K_shoot , with a 50% loss of K_shoot occurring at -1.7 and -2.5 MPa in S. haematodes and S. pulcherrima, respectively. Direct observational methods revealed that the xylem of both species was resistant to embolism formation, with 50% of embolized xylem area occurring at -3.0 and -4.6 MPa in S. haematodes and S. pulcherrima, respectively. X-ray microcomputed tomography images of stems revealed that the decline in K_shoot occurred with the formation of an air-filled lacuna, disconnecting the central vascular cylinder from the cortex. We propose that embolism-resistant xylem and large capacitance, provided by collapsing inner cortical cells, is essential for Selaginella survival during water deficit.

Phylogenomics indicates the "living fossil" Isoetes diversified in the Cenozoic

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

An Ancient Peptide Family Buried within Vicilin Precursors

New proteins can evolve by duplication and divergence or de novo, from previously noncoding DNA. A recently observed mechanism is for peptides to evolve within a "host" protein and emerge by proteolytic processing. The first examples of such interstitial peptides were ones hosted by precursors for seed storage albumin. Interstitial peptides have also been observed in precursors for seed vicilins, but current evidence for vicilin-buried peptides (VBPs) is limited to seeds of the broadleaf plants pumpkin and macadamia. Here, an extensive sequence analysis of vicilin precursors suggested that peptides buried within the N-terminal region of preprovicilins are widespread and truly ancient. Gene sequences indicative of interstitial peptides were found in species from Amborellales to eudicots and include important grass and legume crop species. We show the first protein evidence for a monocot VBP in date palm seeds as well as protein evidence from other crops including the common tomato, sesame and pumpkin relatives, cucumber, and the sponge loofah ( Luffa aegyptiaca). Their excision was consistent with asparaginyl endopeptidase-mediated maturation, and sequences were confirmed by tandem mass spectrometry. Our findings suggest that the family is large and ancient and that based on the NMR solution structures for loofah Luffin P1 and tomato VBP-8, VBPs adopt a helical hairpin fold stapled by two internal disulfide bonds. The first VBPs characterized were a protease inhibitor, antimicrobials, and a ribosome inactivator. The age and evolutionary retention of this peptide family suggest its members play important roles in plant biology.

From the Guiana Highlands to the Brazilian Atlantic Rain Forest: four new species of Selaginella (Selaginellaceae - Lycopodiophyta: S. agioneuma, S. magnafornensis, S. ventricosa, and S. zartmanii)

We describe four new species in the genus Selaginella (i.e., S. agioneuma, S. magnafornensis, S. ventricosa, and S. zartmanii) from Brazil, all presently classified in subg. Stachygynandrum. For each of the new taxa we discuss taxonomic affinities and provide information on habitat, distribution, and conservation status. In addition, line drawings and scanning electron microscope (SEM) images of stems sections, leaves, and spores (when present) are included. Selaginella agioneuma and S. magnafornensis are from the State of Espíritu Santo where they inhabit premontane to montane Atlantic rain forests in the Reserva Biológica Augusto Ruschi and Parque Estadual Forno Grande, respectively. Selaginella ventricosa was collected in upper montane forests at Parque Nacional Serra da Mocidade, State of Roraima and S. zartmanii in premontane Amazon rain forests on upper Rio Negro at Mpio. São Gabriel da Cachoeira, Amazonas State in both Serra Curicuriari and the Morro dos Seis Lagos Biological Reserve.

The adaptive value of heterospory: Evidence from Selaginella

Heterospory was a pivotal evolutionary innovation for land plants, but it has never been clear why it evolved. We used the geographic distributions of 114 species of the heterosporous lycophyte Selaginella to explore the functional ecology of microspore and megaspore size, traits that would be correlated with many aspects of a species' regeneration niche. We characterized habitats at a global scale using leaf area index (LAI), a measure of foliage density and thus shading, and net primary productivity (NPP), a measure of growth potential. Microspore size tends to decrease as habitat LAI and NPP increase, a trend that could be related to desiccation resistance or to filtration of wind-borne particles by leaf surfaces. Megaspore size tends to increase among species that inhabit regions of high LAI, but there is an important interaction with NPP. This geographical pattern suggests that larger megaspores provide an establishment advantage in shaded habitats, although in open habitats, where light is less limiting, higher productivity of the environment seems to give an advantage to species with smaller megaspores. These results support previous theoretical arguments that heterospory was originally an adaptation to the increasing height and density of Devonian vegetative canopies that accompanied the diversification of vascular plants with leaves.