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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 ., Competing Interests: G-JW and MR were employed by Taiwan Semiconductor Manufacturing Company and Wildland Consultants. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ke, Wang, Labiak, Rouhan, Chen, Shepherd, Ohlsen, Renner, Karol, Li and Kuo.)

Background: The Atlantic Forest is one of the most threatened biomes in the world. Despite that, this biome still includes many areas that are poorly known floristically, including several protected areas, such as the "Floresta Nacional do Rio Preto" ("Flona do Rio Preto"), located in the Brazilian State of Espírito Santo. This study used a published vascular plant species list for this protected area from the "Catálogo de Plantas das Unidades de Conservação do Brasil" as the basis to synthesise the species richness, endemism, conservation and new species occurrences found in the "Flona do Rio Preto"., New Information: The published list of vascular plants was based on field expeditions conducted between 2018 and 2020 and data obtained from herbarium collections available in online databases. Overall, 722 species were documented for the "Flona do Rio Preto", 711 of which are native to Brazil and 349 are endemic to the Atlantic Forest. In addition, 60 species are geographically disjunct between the Atlantic and the Amazon Forests. Most of the documented species are woody and more than 50% of these are trees. Twenty-three species are threatened (CR, EN and VU), while five are Data Deficient (DD). Thirty-two species are new records for the State of Espírito Santo. Our results expand the knowledge of the flora of the Atlantic Forest and provide support for the development of new conservation policies for this protected area., (Anderson Alves-Araújo, Marina M Moreira, Tatiana T Carrijo, Lúcia G Lohmann, Adriana Q Lobão, Alana F Scheidegger, Aline D Firmino, Aline Vieira de Melo Silva, Álvaro Nepomuceno, Amélia C Tuler, André MA Amorim, André LC Moreira, Braz AP Cosenza, Brenno G Sossai, Christian Silva, Claudia R Lopes, Daniele Monteiro, Dayvid R Couto, Duane F Lima, Eduardo C Dalcin, Eliana Ramos, Elton J Lírio, Fatima Salimena, Felipe Alves de Oliveira, Fernanda RM Fraga, Filipe Torres-Leite, Guilherme M Antar, Gustavo H Shimizu, Haroldo C Lima, Herison Medeiros, Jaquelini Luber, Jheniffer A Christ, João Lanna, João Paulo F Zorzanelli, Joelcio Freitas, José FB Pastore, José IM Melo, Juliana Paula-Souza, Juliana RPM Oliveira, Leandro C Pederneiras, Leandro Freitas, Leandro L Giacomin, Leonardo D Meireles, Luis AE Silva, Luiz JS Pinto, Luiz Menini Neto, Marcelo Trovó, Mário L Garbin, Marli P Morim, Michel Ribeiro, Nelson TL Pena, Paulo H Labiak, Pedro H Cardoso, Pedro L Viana, Pedro LR Moraes, Quélita S Moraes, Raquel F Zorzanelli, Renara N Amaral, Renata C Asprino, Renato Goldenberg, Ricardo Magnago, Ricardo S Couto, Sandrine C Dutra, Saúl E Hoyos-Gómez, Tamara AF Vieira, Thiago B Flores, Valquíria F Dutra, Víctor S Miranda, Vitor C Manhães, Rafaela C Forzza.)

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., (© 2021 Breinholt et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.)

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., (Luiza F. A. de Paula, Luísa O. Azevedo, Luana Paula Mauad, Leandro Jorge Telles Cardoso, João Marcelo Alvarenga Braga, Ludovic J.C. Kollmann, Claudio N. Fraga, Luiz Menini Neto, Paulo H. Labiak, Renato Mello-Silva, Stefan Porembski, Rafaela Campostrini Forzza.)

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., (Marina M Moreira, Tatiana T Carrijo, Anderson Alves-Araújo, André M A Amorim, Alessandro Rapini, Andrews V S da Silva, Braz A P Cosenza, Claudia R Lopes, Camila N Delgado, Cíntia Kameyama, Dayvid R Couto, Daniel E F Barbosa, Daniele Monteiro, Diego R Gonzaga, Eduardo C Dalcin, Elsie F Guimarães, Elton John de Lírio, Fernando B Matos, Fátima R G Salimena, Felipe A Oliveira, Gustavo Heiden, João M Lanna, José Fernando Baumgratz, José F B Pastore, Juliana R P M Oliveira, Laísa B Barcelos, Lana S Sylvestre, Leandro Freitas, Leandro L Giacomin, Leandro Pederneiras, Leonardo D Meireles, Lúcia G Lohmann, Luciana C Pereira, Luis Alexandre E Silva, Luiz M Neto, Marcelo C Souza, Marcelo Trovó, Marcos E G Sobral, Mário Luís Garbin, Mario Gomes, Marli P Morim, Michelle Christine A Mota, Paulo H Labiak, Pedro L Viana, Pedro Luís R de Moraes, Renato Goldenberg, Rubens Luiz G Coelho, Samyra G Furtado, Sebastião José da Silva-Neto, Thiago B Flores, Valquíria F Dutra, Vinícius R Bueno, Rafaela C Forzza.)

Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events., (© 2019 The Authors. Ecology © 2019 The Ecological Society of America.)

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., (© 2017 Botanical Society of America.)

• 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., (© 2014 Botanical Society of America, Inc.)

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.