Phylogenomic evolutionary insights in the fern family Gleicheniaceae.

The pantropical fern family Gleicheniaceae comprises approximately 157 species. Seven genera are currently recognized in the family, although their monophyly is still uncertain due to low sampling in phylogenetic studies. We examined the monophyly of the genera through extended sampling, using the first phylogenomic inference of the family including data from both nuclear and plastid genomes. Seventy-six samples were sequenced (70 Gleicheniaceae species and six outgroups) using high throughput sequencing, including all seven currently recognized genera. Plastid and nuclear data were recovered and assembled; the nuclear data was phased to reduce paralogy as well as hybrid noise in the final recovered topology. Maximum likelihood trees were built for each locus, and a concatenated dataset was built for both datasets. A species tree based on a multispecies coalescent model was generated, and divergence time analyses performed. We here present the first genomic phylogenetic inferences concerning Gleicheniaceae, confirming the monophyly of most genera except Sticherus, which we recovered as paraphyletic. Although most of the extant genera of Gleicheniaceae originated during the Mesozoic, several genera show Neogene and even Quaternary diversifications, and our results suggest that reticulation and polyploidy may have played significant roles during this diversification. However, some genera, such as Rouxopteris and Stromatopteris, appear to represent evolutionary relicts.

HybPhaser identifies hybrid evolution in Australian Thelypteridaceae.

Hybridisation has been proposed to play an important role in fern evolution, but has been difficult to investigate. This study explores the utility of target sequence capture and read-to-reference phasing of putative hybrids to investigate the role of evolutionary reticulation in ferns using Australian Thelypteridaceae as a model. The bioinformatics workflow HybPhaser was used to assess divergence between alleles, phase sequence reads to references and construct accessions resembling parental haplotypes. These accessions were included in phylogenetic and network analyses to detect hybrids and infer their parentage. This approach identified two novel hybrid lineages in Thelypteridaceae, one occurring between two different genera (Abacopteris and Christella), and another as part of a complex of Christella. In addition, hybrid phasing successfully reduced conflicting data and improved overall resolution in the Thelypteridaceae phylogeny, highlighting the power of this approach for reconstructing evolutionary history in reticulated lineages.

A comprehensive checklist of vascular epiphytes of the Atlantic Forest reveals outstanding endemic rates.

Knowledge of the geographic distribution of plants is essential to underpin the understanding of global biodiversity patterns. Vascular epiphytes are important components of diversity and functionality of Neotropical forests but, unlike their terrestrial counterparts, they are under-represented in large-scale diversity and biogeographic analyses. This is the case for the Atlantic Forest - one of the most diverse and threatened biomes worldwide. We provide the first comprehensive species list of Atlantic Forest vascular epiphytes; their endemism patterns and threatened species occurrence have also been analyzed. A list with 2,256 species of (hemi-)epiphytes - distributed in 240 genera and 33 families - is presented based on the updated Brazilian Flora Checklist. This represents more than 15% of the total vascular plant richness in the Atlantic Forest. Moreover, 256 species are included on the Brazilian Red List. More than 93% of the overall richness is concentrated in ten families, with 73% represented by Orchidaceae and Bromeliaceae species alone. A total of 78% of epiphytic species are endemic to the Atlantic Forest, in contrast to overall vascular plant endemism in this biome estimated at 57%. Among the non-endemics, 13% of epiphytic species also occur either in the Amazon or in the Cerrado - the other two largest biomes of Brazil - and only 8% are found in two or more Brazilian biomes. This pattern of endemism, in addition to available dated phylogenies of some genera, indicate the dominance of recent radiations of epiphytic groups in the Atlantic Forest, showing that the majority of divergences dating from the Pliocene onwards are similar to those that were recently reported for other Neotropical plants.

Isolated in biogeographic islands: discovery of a disjunct population of a fern in Northeastern Atlantic Forest / Aislados en islas biogeográficas: descubrimiento de una población disyunta de un helecho en el Bosque Atlántico Septentrional

Brejos Nordestinos (northeastern highland wet forests) is a unique ecosystem within the Northeastern Atlantic Forest. This area encompasses a mosaic of humid forests above 600 meters in the semi-arid region, forming an ecotone area. These environmental conditions create an optimal ecosystem for the diversification of plants, including ferns. Pico do Jabre in Paraíba state, with an elevation of 1,208 meters above sea level, is an example of Brejo Nordestino. This study reports the occurrence of Pleopeltis pleopeltidis in the Northeastern Atlantic Forest, particularly at Pico do Jabre, a new record of P. pleopeltifolia for Paraíba state, and the local fern flora. Additional records of P. pleopeltidis were found in the municipalities of Triunfo, and Floresta, in Pernambuco state, which are also classified as Brejos Nordestinos with elevations exceeding 1,000 meters above sea level. These findings extend the species' known extent of occurrence by approximately 40%. The conservation status of P. pleopeltidis is suggested as Vulnerable (VU) across its entire range and Endangered (EN) in Northeast Brazil. The distance between populations in the Northeastern Atlantic Forest and the nearest populations in Bahia state ranges from 763-931 km, indicating a potential disjunction. Although the species occurs in three relatively close Brejos Nordestinos, the fragmented nature of the Northeastern Atlantic Forest results in isolated populations on these biogeographical islands, surrounded by a Caatinga (seasonally dry tropical forest) matrix.

Los Brejos Nordestinos (bosques húmedos de tierras altas del noreste) son un ecosistema único dentro del Bosque Atlántico del Nordeste. Esta área abarca un mosaico de bosques húmedos por encima de los 600 metros en la región semiárida, formando una zona de ecotono. Estas condiciones ambientales crean un ecosistema óptimo para la diversificación de plantas, incluidos los helechos. El Pico do Jabre, en el estado de Paraíba, con una altitud de 1208 metros sobre el nivel del mar, es un ejemplo de Brejo Nordestino. Este estudio reporta la ocurrencia de Pleopeltis pleopeltidis en el Bosque Atlántico del Nordeste, particularmente en el Pico do Jabre, un nuevo registro de P. pleopeltifolia para el estado de Paraíba, y en la flora local de helechos. Se encontraron registros adicionales de P. pleopeltidis en los municipios de Triunfo y Floresta, en el estado de Pernambuco, que también están clasificados como Brejos Nordestinos con elevaciones superiores a los 1000 metros sobre el nivel del mar. Estos hallazgos amplían la extensión conocida de ocurrencia de la especie en aproximadamente un 40%. Se sugiere que el estado de conservación de P. pleopeltidis sea vulnerable (VU) en toda su área de distribución y en peligro (EN) en el noreste de Brasil. La distancia entre las poblaciones del Bosque Atlántico del Nordeste y las poblaciones más cercanas en el estado de Bahía varía entre 763 y 931 km, lo que indica una posible disyunción. Aunque la especie ocurre en tres Brejos Nordestinos relativamente cercanos, la naturaleza fragmentada del Bosque Atlántico del Nordeste da como resultado poblaciones aisladas en estas islas biogeográficas, rodeadas por una matriz de Caatinga (bosque tropical seco estacionalmente).