Systematics and Plastome Evolution in Schizaeaceae

While the family Schizaeaceae (Schizaeales) represents only about 0.4% of the extant fern species diversity, it differs from other ferns greatly in gross morphologies, niche preferences, and life histories. One of the most notable features in this family is its mycoheterotrophic life style in the gametophytic stage, which appears to be associated with extensive losses of plastid genes. However, the limited number of sequenced plastomes, and the lack of a well-resolved phylogenetic framework of Schizaeaceae, makes it difficult to gain any further insight. Here, with a comprehensive sampling of ~77% of the species diversity of this family, we first inferred a plastid phylogeny of Schizaeaceae using three DNA regions. To resolve the deep relationships within this family, we then reconstructed a plastome-based phylogeny focusing on a selection of representatives that covered all the major clades. From this phylogenomic backbone, we traced the evolutionary histories of plastid genes and examined whether gene losses were associated with the evolution of gametophytic mycoheterotrophy. Our results reveal that extant Schizaeaceae is comprised of four major clades-Microschizaea, Actinostachys, Schizaea, and Schizaea pusilla. The loss of all plastid NADH-like dehydrogenase (ndh) genes was confirmed to have occurred in the ancestor of extant Schizaeaceae, which coincides with the evolution of mycoheterotrophy in this family. For chlorophyll biosynthesis genes (chl), the losses were interpreted as convergent in Schizaeaceae, and found not only in Actinostachys, a clade producing achlorophyllous gametophytes, but also in S. pusilla with chlorophyllous gametophytes. In addition, we discovered a previously undescribed but phylogenetically distinct species hidden in the Schizaea dichotoma complex and provided a taxonomic treatment and morphological diagnostics for this new species-Schizaea medusa. Finally, our phylogenetic results suggest that the current PPG I circumscription of Schizaea is non-monophyletic, and we therefore proposed a three-genus classification moving a subset of Schizaea species sensu PPG I to a third genus-Microschizaea.

The southernmost distribution range of Isoetes panamensis Maxon & C.V. Morton (Lycopodiopsida, Isoetaceae) in the relicts of the Cerrado in southern Brazil

Establishing the geographical distribution limits of species may provide not only data to understand their range of adaptation to conservation proposals but also records of the dynamics in the vegetation across the time. Here we report the southernmost limit of the occurrence of Isoetes panamensis Maxon & C.V. Morton within a relict of the Cerrado in Paraná, Brazil. This find highlights the importance of fieldwork in relicts of the Cerrado to enhance the knowledge about the flora of Paraná and the vegetational dynamic of the Cerrado in the past.

A target enrichment probe set for resolving the flagellate land plant tree of life

PREMISE

New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms.

METHODS

We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages.

RESULTS

Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics.

CONCLUSIONS

A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

A target enrichment probe set for resolving the flagellate land plant tree of life

PREMISE

New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms.

METHODS

We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages.

RESULTS

Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics.

CONCLUSIONS

A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

Sugarloaf Land in south-eastern Brazil: a tropical hotspot of lowland inselberg plant diversity

Background

Isolated monoliths of granitic and/or gneissic rock rising abruptly from the surrounding landscape are known as inselbergs. Dome-shaped inselbergs are common throughout the Atlantic Forest in south-eastern Brazil, a region known as Sugarloaf Land (SLL). This study aimed to create the first checklist of vascular plant species occurring on lowland inselbergs in SLL, with a focus on vegetation islands. We used information from online databases, our own field sampling and data from previously-published studies. We found 548 vascular plant species (505 angiosperms; 43 ferns and lycophytes) belonging to 69 families and 212 genera. Of all identified species, 536 are native and 12 are naturalised.

New information

We updated the information currently available in Flora do Brasil 2020, as 59% of the angiosperms and 63% of the ferns and lycophytes on our checklist were not previously characterised as occurring on rock outcrops. As a first step towards generating a Virtual Herbarium of lowland inselberg vascular plants, we added barcode vouchers with images available online for 75% of the total number of vascular species. In the official lists of endangered species, 115 angiosperms and five ferns and lycophytes are mentioned. However, the conservation status of many species have not yet been evaluated (77% angiosperms; 88% ferns and lycophytes), thus this list is an important step towards their conservation. The information provided herein is essential for management programmes related to rock outcrops in Brazil as they are facing serious threats to conservation.

Using online databases to produce comprehensive accounts of the vascular plants from the Brazilian protected areas: The Parque Nacional do Itatiaia as a case study

Background

Brazil is one of the most biodiverse countries in the world, with about 37,000 species of land plants. Part of this biodiversity is within protected areas. The development of online databases in the last years greatly improved the available biodiversity data. However, the existing databases do not provide information about the protected areas in which individual plant species occur. The lack of such information is a crucial gap for conservation actions. This study aimed to show how the information captured from online databases, cleaned by a protocol and verified by taxonomists allowed us to obtain a comprehensive list of the vascular plant species from the "Parque Nacional do Itatiaia", the first national park founded in Brazil. All existing records in the online database JABOT (15,100 vouchers) were downloaded, resulting in 11,783 vouchers identified at the species level. Overall, we documented 2,316 species belonging to 176 families and 837 genera of vascular plants in the "Parque Nacional do Itatiaia". Considering the whole vascular flora, 2,238 species are native and 78 are non-native.

New information

The "Parque Nacional do Itatiaia" houses 13% of the angiosperm and 37% of the fern species known from the Brazilian Atlantic Forest. Amongst these species, 82 have been cited as threatened, following IUCN categories (CR, EN or VU), seven are data deficient (DD) and 15 have been classified as a conservation priority, because they are only known from a single specimen collected before 1969.

The ferns and lycophytes of Reserva Natural Guaricica, Antonina, Paraná, Brazil

We found 204 species of pteridophytes in Reserva Natural Guaricica, a private natural heritage reserve (RPPN) in Antonina, Paraná, Brazil. With approximately 8,600 ha and elevations ranging from sea level to 600 m, RPPN Guaricica has more species of pteridophytes than any other area in Paraná. Ferns are represented by 194 species in 82 genera and 26 families, whereas lycophytes comprise 10 species in four genera and two families. The RPPN is the type locality of two recently described species: Hypolepis acantha Schwartsb. and Oleandra australis Schwartsb. & J.Prado. It is also the only place of occurrence of Didymoglossum angustifrons Fée, Diplazium riedelianum (Bong. ex Kuhn) C.Chr., Pteris ensiformis Burm.f., P. tripartita Sw., Saccoloma elegans Kaulf., and Steiropteris polypodioides (Raddi) Salino & T.E.Almeida in Paraná. Pteris ensiformis and Saccoloma brasiliense (C.Presl) Mett. are new state records. Additional species are expected to occur in the area, in view of their known geographical ranges.

Samambaias e Licófitas da Pedra do Elefante, Espírito Santo, Brasil

Resumo Os resultados aqui apresentados fazem parte de um trabalho maior que consiste na Flora Vascular da Pedra do Elefante, Nova Venécia, Espírito Santo. As expedições a campo foram realizadas de março de 2010 a julho de 2016, em um total de 23 visitas ao local. As amostras foram incorporadas principalmente nos herbários CEPEC, MBML, RB, UPCB, VIC e VIES. Sessenta e três espécies, uma subespécie, três variedades e dois híbridos de samambaias e licófitas foram registradas, distribuídas em 32 gêneros e 15 famílias. As famílias mais representativas foram Pteridaceae (14 spp.), Polypodiaceae (11 spp.), Anemiaceae (9 spp.) e Selaginellaceae (5 spp.). Os gêneros mais representativos foram Anemia (9 spp), Selaginella (5 spp.), Adiantum e Pteris (4 spp. cada). Dentre estas, três espécies são novas ocorrências para o Espírito Santo e oito táxons apresentam estado de conservação. Chaves de identificações em nível genérico e específico, comentários, e distribuição geográfica para todos os táxons são apresentados. Inventários florísticos no Espírito Santo são importantes, principalmente em áreas que possuem afloramentos rochosos, pois o baixo esforço de amostragem e a alta pressão antrópica, causam impactos negativos na preservação da vegetação nativa.

Checklist of ferns and lycophytes from the highlands of Pico Paraná State Park, Paraná, Brazil

Abstract We present a checklist for the ferns and lycophytes from Pico Paraná State Park, in Southern Brazil. The Park is entirely located at the Serra do Mar mountains, and represents an important remnant of the Atlantic Rain Forest with altitude achieving 1,887 m. In this locality is the Pico Paraná, the highest mountain in Southern Brazil. This study was focused on the altitudes above 1,000 m, which are mainly represented by dwarf forests and altitudinal fields. A total of 142 species were recorded, three of them (Ceradenia maackii, Diplazium tamandarei, and Stenogrammitis wittigiana) are only found in the park in Southern Brazil. Besides of the checklist of the species, we highlight some important aspects related to endangered species, geographic distribution, and life forms. The high level of endemism, the presence of endangered species, and the phylogenetic diversity as represented by distinct families of ferns and lycophytes show the biogeographic importance of this area for the conservation of these groups of plants.

Plastome sequences of an ancient fern lineage reveal remarkable changes in gene content and architecture

PREMISE OF THE STUDY

Comparative analyses of plastid genomes have suggested that gene order and content are relatively stable across the main groups of land plants, with significant changes rarely reported. We examine plastome organization and RNA editing in ferns and report changes that add valuable information on plastome evolution in land plants.

METHODS

Using next-generation sequencing methods, we fully sequenced plastomes from three species of Schizaeaceae, and compared their plastomes with other groups of land plants to study changes in gene composition, plastome architecture, and putative RNA editing sites. We also performed maximum likelihood and Bayesian inference phylogenetic analyses using 46 plastid-encoded genes, including 26 ferns, two gymnosperms, and five angiosperms.

KEY RESULTS

Within Schizaeaceae, plastomes were similar to each other in gene content and architecture. Striking changes compared with other ferns include the complete loss of ndh genes and reduction of the small single copy. Putative RNA editing was identified in all three plastomes, a characteristic that is shared with other fern groups. The monophyly of Schizaeales and Schizaeaceae was confirmed.

CONCLUSIONS

The plastomes of Schizaea are the smallest reported for a fern so far. The loss of the ndh gene suite is associated with the reduction of the small single copy, instead of the inverted repeat as noted for other groups of plants. Putative C-to-U and U-to-C transitions were observed in several instances in the three plastomes, suggesting that posttranscriptional modification of RNA is likely a common phenomenon in this clade as well.

Diversity of ferns and lycophytes in Brazil

Abstract This compilation of ferns and lycophytes in Brazil is an update of the one published in 2010 in Catálogo de Plantas e Fungos do Brasil. The methodology consisted in collecting data from regional checklists, taxonomic revisions, and selected databases. Invited specialists improved the list accessing a website housed at the Jardim Botânico do Rio de Janeiro. The results show 1,253 species: 1,111 of ferns and 142 of lycophytes. This number is 6.5% higher than the previous one (1,176 spp.). The percentage of endemic species decreased from 38.2% to 36.7%. We recognized 36 families and 133 genera (vs. 33 families, 121 genera in 2010). The 10 most diverse families are Pteridaceae (196 spp.), Dryopteridaceae (179), Polypodiaceae (164), Hymenophyllaceae (90), Thelypteridaceae (86), Aspleniaceae (78), Lycopodiaceae (64), Selaginellaceae (55), Anemiaceae (51), and Cyatheaceae (45). The three most diverse genera are still Elaphoglossum (87 spp.), Thelypteris (85), and Asplenium (74). The richest phytogeographic domain continues to be in the Atlantic Rainforest with 883 species which also has the largest number of endemic and threatened species, followed by the Amazon Rainforest (503), Cerrado (269), Pantanal (30), Caatinga (26), and Pampa (eight). Minas Gerais remains as the richest state (657 spp. vs. 580 in 2010).

Phylogeny and historical biogeography of the lastreopsid ferns (Dryopteridaceae)

• Premise of the study: As currently circumscribed, Lastreopsis has about 45 species and occurs in Australia, southern Asia, Africa, Madagascar, and the neotropics. Previous molecular phylogenetic studies suggested that Lastreopsis is paraphyletic. Our study focuses on resolving relationships among the lastreopsid ferns (Lastreopsis, Megalastrum, and Rumohra), the evolution of morphological characters, and an understanding of the temporal and spatial patterns that have led to the current diversity and geographical distribution of its extant species.• Methods: Phylogenetic relationships were recovered under Bayesian, maximum likelihood, and maximum parsimony methods, using a data set of four plastid markers. Divergence time estimates were made using BEAST, and the biogeographic hypotheses were tested under the DEC model and the RASP/S-DIVA methods.• Key results: Lastreopsis was recovered as paraphyletic, and at least one of its clades should be recognized as a distinct genus, Parapolystichum. Coveniella poecilophlebia and Oenotrichia tripinnata were nested within Lastreopsis s.s., Megalastrum and Rumohra as sister to the Lastreopsis s.s., and the Lastreopsis amplissima clades. The initial diversification of the lastreopsids took place at about 56.55 Ma, from a neotropical ancestor.• Conclusions: Taxonomic recognition of Parapolystichum is warranted to preserve the monophyly of Lastreopsis. Diversification among the main clades of the lastreopsid ferns was influenced by climatic and geological changes in the southern hemisphere. The biogeographic history of the group is intimately related to the trans-Antarctic corridor between Australia and South America, with evidence for multiple lineage interchanges between Australia and South America during the Oligocene and the Eocene epochs.

Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae)

PREMISE OF THE STUDY

The recognition of monophyletic genera for groups that have high levels of homoplastic morphological characters and/or conflicting results obtained by different studies can be difficult. Such is the case in the grammitid ferns, a clade within the Polypodiaceae. In this study, we aim to resolve relationships among four clades of grammitid ferns, which have been previously recovered either as a polytomy or with conflicting topologies, with the goal of circumscribing monophyletic genera. •

METHODS

The sampling included 89 specimens representing 61 species, and sequences were obtained for two genes (atpB and rbcL) and four intergenic spacers (atpB-rbcL, rps4-trnS, trnG-trnR, and trnL-trnF), resulting in a matrix of 5091 characters. The combined data set was analyzed using parsimony, likelihood, and Bayesian methods. Ninety-six morphological characters were optimized onto the generated trees, using the parsimony method. •

KEY RESULTS

Lellingeria is composed of two main clades, the L. myosuroides and the Lellingeria s.s. clades, which together are sister to Melpomene. Sister to all three of these is a clade with two species of the polyphyletic genus Terpsichore. In the L. myosuroides clade, several dispersal events occurred between the neotropics, Africa, and the Pacific Islands, whereas Lellingeria s.s. is restricted to the neotropics, with about 60% of its diversity in the Andes. •

CONCLUSIONS

Overall, our results suggest that Lellingeria is monophyletic, with two clades that are easily characterized morphologically and biogeographically. Morphological characters describing the indument are the most important to define the clades within the ingroup. A small clade, previously considered in Terpsichore, should be recognized as a new genus.