A revised subfamilial classification of Polypodiaceae based on plastome, nuclear ribosomal, and morphological evidence

Abstract

The polygrammoid fern family Polypodiaceae represents one of the most diversified epiphytic fern groups, with more than 1600 species distributed on all continents except Antarctica, with the highest species diversity in tropical and subtropical regions. Despite progress in recent phylogenetic studies of Polypodiaceae, the infrafamilial classification of this group of ferns is still problematic. Here, we explore the phylogenetic relationship within Polypodiaceae using plastid genome (plastome) and nuclear ribosomal cistron genome data obtained from high-throughput sequencing. Although genome skimming data strongly support the monophyly of many genera and clades of Polypodiaceae, relationships within some clades and along the backbone of the phylogeny remain incongruent between plastome and nuclear data. The explanation is possibly a factor of complex evolutionary history found in these clades, such as rapid radiation, incomplete lineage sorting, ancient hybridization, and recent introgression. Based on the concatenated dataset, our phylogenetic analyses support nine major clades in Polypodiaceae, which merit the recognition as subfamilies, Crypsinoideae, Grammitidoideae, Loxogrammoideae, Microsoroideae, Platycerioideae, Polypodioideae, Adetogrammoideae, Campyloneuroideae, and Serpocauloideae, while the latter three are separated from Polypodioideae as new subfamilies. All of these infrafamilial divisions, identified with molecular data, are further supported by non-molecular features including leaf dissection, venation, scales and paraphyses, soral features, and geographical distributions. Systematic and taxonomic discussions on the subfamilial treatment are also provided.

An open and continuously updated fern tree of life

“…However, a tree derived from plastid data may not necessarily mirror those inferred from other data sources. Conflict between plastid and nuclear phylogenies has been frequently observed in narrowly focused (e.g., genus level) studies using traditional Sanger sequencing (e.g., Sessa et al, 2012;Zhou and Zhang, 2017;Wei et al, 2021) and has recently been demonstrated at deeper levels within Polypodiaceae using phylogenomic approaches (Wei and Zhang, 2022). Such conflict does not necessarily reflect insufficient methodology or sampling, but rather may be due to processes including (but not limited to) introgression, lineage sorting, and hybridization at deep phylogenetic levels.…”

Plastome phylogenomic analysis reveals evolutionary divergences of Polypodiales suborder Dennstaedtiineae

“…4 Museum of New Zealand Te Papa Tongarewa, Cable Street, Wellington 6011, New Zealand. 5 Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China. 6 Taiwan Forestry Research Institute, Taipei 10066, Taiwan.…”

“…Numerous phylogenetic studies have been conducted since the publication of the PPG classification [ 3 ], especially on those globally distributed families, e.g., Lycopodiaceae [ 4 ], Polypodiaceae [ 5 , 6 ], Pteridaceae [ 7 ], and Thelypteridaceae [ 8 , 9 ]. The increase in the number of samples, especially in regions and groups with low sampling density, and the accumulation of molecular data, have improved the ability of taxon delimitation and identification and prompted the publication of some new taxa.…”

“…One new family was published by Zhou et al [ 10 ], and some new genera have continued to be recognized (e.g., [ 11 , 12 , 13 , 14 , 15 , 16 ]). The systematic positions of several remaining enigmatic groups in the PPG classification [ 3 ] were resolved [ 5 , 6 , 17 , 18 , 19 , 20 ]. In addition, some hybrid genera have been found (e.g., × Cyclobotrya , [ 21 ]; × Woodsimatium Li Bing Zhang, N.T.…”

Integrative species delimitation of Selaginella labordei and closely related species: Uncovering the mysterious identity of S. jugorum and S. tibetica, and description of a new species

“…Although nuclear genes have been considered informative for species delimitation in lycophytes (Zhang & al., 2021), ferns (Liang & al., 2019, 2021), and seed plants (Bratzel & al., 2020), low‐copy nuclear gene sequences have always remained difficult to obtain, especially from historical specimens (Staats & al., 2013). With the rapid development of high‐throughput sequencing technology, plastid genomes can be effectively obtained by genome skimming sequencing, and can greatly increase resolution in plant phylogenetics at familial, generic, or species level (Li & al., 2015; Ye & al., 2020; Zhang & al., 2020; Qin & al., 2022; Wei & Zhang, 2022). Due to the typical mode of uniparental inheritance and high content of informative loci, an increasing number of studies pointed out that plastid genomes may provide more variation to discriminate closely related species, among which hybridization and polyploidization is less frequently reported (Parks & al., 2009; Li & al., 2015; Magwé‐Tindo & al., 2018).…”