An open and continuously updated fern tree of life

Phylogenetic diversity sheds light on the evolution of the unique fern flora of Mount Kinabalu, Borneo

BACKGROUND AND AIMS

Mount Kinabalu is an isolated, geologically young mountain (Pliocene and early Pleistocene) in northern Borneo harbouring a highly diverse flora with a high level of endemism. It is one of the global centres of fern diversity, but how this diversity has evolved has not been studied to date. We assess patterns of evolutionary legacies in the fern flora of Mount Kinabalu, with an emphasis on testing the tropical niche conservatism hypothesis.

METHODS

We used several metrics of phylogenetic structure, including phylogenetic diversity (PD), mean nearest taxon distance (MNTD), mean pairwise distance (MPD), and their respective standardized effect sizes (PDses, MNTDses and MPDses), which represent different depths of evolutionary history, to investigate patterns of evolutionary legacies in the fern flora of Mount Kinabalu.

KEY RESULTS

We found that there was a decrease of PDses with elevation, reflecting a tropical origin of ferns and a gradual evolutionary adaptation to colder environments by fewer successive lineages. However, when separating the evolutionary old non-polypod lineages from the modern polypod radiation, we found a decrease of MNTD with elevation for the former, reflecting an ongoing upslope evolutionary trend, whereas for the modern polypod radiation, the inverse was true. Within the polypods, terrestrial and epiphytic species also showed different patterns, with the former showing a hump-shaped pattern for all phylogenetic diversity metrics, whereas the latter showed a more or less linear decline. Again, this suggests different evolutionary histories for ferns inhabiting the forest floor and canopy, due to the influence of the different habitat conditions. Finally, we found that mean annual temperature had a much stronger effect on phylogenetic diversity metrics than annual precipitation.

CONCLUSIONS

We found that the current fern assemblages on Mount Kinabalu show a strong evolutionary legacy that mirrors that of other mountains, suggesting a global consistency in phylogenetic diversity patterns of ferns along elevational transects, presumably due to a combination of dispersal between mountains and evolutionary convergence.

Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls

Ferns are essential for understanding plant evolution; however, their large and intricate genomes have kept their genetic landscape largely unexplored, with only a few genomes sequenced and limited transcriptomic data available. To bridge this gap, we generated extensive RNA-sequencing data across various organs from 22 representative fern species, resulting in high-quality transcriptome assemblies. These data enabled us to construct a time-calibrated phylogeny for ferns, encompassing all major clades, which revealed numerous instances of whole-genome duplication. We highlighted the distinctiveness of fern genetics, discovering that half of the identified gene families are unique to ferns. Our exploration of fern cell walls through biochemical and immunological analyses uncovered the presence of the lignin syringyl unit, along with evidence of its independent evolution in ferns. Additionally, the identification of an unusual sugar in fern cell walls suggests a divergent evolutionary trajectory in cell wall biochemistry, probably influenced by gene duplication and sub-functionalization. To facilitate further research, we have developed an online database that includes preloaded genomic and transcriptomic data for ferns and other land plants. We used this database to demonstrate the independent evolution of lignocellulosic gene modules in ferns. Our findings provide a comprehensive framework illustrating the unique evolutionary journey ferns have undertaken since diverging from the last common ancestor of euphyllophytes more than 360 million years ago.

Population genomics of the gametophyte-only fern Vittaria appalachiana provides insights into clonal plant evolution

How asexually reproducing organisms maintain genetic diversity and adaptive potential is a long-standing question in evolutionary biology. Asexual lineages have historically been thought of as evolutionary dead ends, yet some exhibit remarkable persistence through time. The gametophyte-only fern Vittaria appalachiana is a clonal eukaryote, the focus of extensive study due to its peculiar habit and life history, and is an excellent system to explore the consequences of asexuality. Using reduced representation sequencing and life cycle simulations, we assess theoretical expectations for genomic consequences of long-term asexual reproduction and test hypotheses about its origin and demographic history. We show that V. appalachiana colonies are not patches of single genotypes but are mosaics of genetic diversity, and the accumulation of mutations in the absence of recombination plays an important role in driving this diversity. We identify increased genomic variation, excess heterozygosity, decreased population differentiation, and increased effective population size, all of which are consistent with the expectations for prolonged clonality. Our analyses support the hypothesis that the loss of sexual reproduction in V. appalachiana occurred during the Last Glacial Maximum. Our results from empirical and simulation-based analyses illuminate how an asexual eukaryote generates, retains, and partitions genomic diversity.

On the uniqueness of fern-insect interactions

This article is a Commentary on Porto et al. (2025), 246: 747–757.

The chromosome-level genome assembly of Broad-Leaf Fern (Dipteris shenzhenensis)

Dipteris is a relic plant genus and an important indicator of global climate warming and plant geography during the Mesozoic era. However, the lack of genomic resources has hindered the study of paleoclimate, systematic evolution, and medicinal value of this genus. Here, we sequenced and assembled the first chromosome-level genome of Dipteris shenzhenensis. The assembled genome was 1.9 Gb with a contig N50 length of 4.75 Mb, GC content of 42.28% and BUSCO value of 98.3%, and 98.37% of the assembled sequences were anchored onto 33 pseudochromosomes. 71.97% of the genome were predicted to be repetitive sequences, and 45 telomeres were identified, including 15 paired telomeres. A total of 26,471 protein coding genes were predicted, of which 24,485 (92.5%) genes were functionally annotated. The first high-quality genome of Dipteris will provide important genome resources for understanding the systematic evolution, paleoclimate and medicinal value of ferns.

Spatial diversity and distribution of fern and lycophyte species in karst and non-karst landscapes towards conservation needs

Karst formations are distinguished by their high levels of species diversity and endemism, including ferns and lycophytes. However, the existing data on plant community composition in karst formations remains deficient. Addressing these knowledge gaps is imperative, given the current accelerated rates of species loss, to enhance efforts to conserve biodiversity in these habitats. This study documents and explains patterns of fern and lycophyte species diversity within karst landscapes (KL) and non-karst landscapes (NKL) in the Philippines. Our comprehensive analysis involved aggregating 19,529 occurrence points encompassing 1,024 fern and lycophyte species sourced from field expeditions, voucher records from local herbaria, and online databases. Indices for species richness, weighted endemism, and corrected weighted endemism were then computed across KL and NKL areas to describe spatial diversity and identify fern and lycophyte hotspot areas. Gap analyses were also performed to determine if established protected areas (PAs) were sufficient to cover the identified fern and lycophyte diversity hotspots. Principal Component Analysis (PCA) was conducted to determine potential ecological drivers of distribution between KL and NKL areas. The findings reveal that most fern and lycophyte species were recorded to occur in NKL areas, with 995 (97.16%) species identified, while 676 (66.02%) species were documented to occur in KLs, including 29 (2.83%) exclusive to karsts. Identified hotspots for NKL are within mountain ecosystems, which are already under existing legal protection. In contrast, KLs have five areas identified as congruent hotspots but considered gap areas due to their exclusion from current PA boundaries. Existing PAs thus provide less protection to karst habitats and their associated floras. PCA did not reveal any significant environmental predictors, suggesting separation of KL and NKL species distributions, possibly due to lack of high-resolution environment data available for karsts. To facilitate the conservation of fern and lycophyte species in karsts, we propose installing and expanding existing PA boundaries, along with conducting more focused surveys in karst regions to better understand their ecological dynamics.

Genomic correlates of vascular plant reproductive complexity and the uniqueness of angiosperms

Whole genome duplication (WGD) likely plays an important role in plant macroevolution, and has been implicated in diversification rate shifts, structural innovations, and increased disparity. But the general effects of WGD are challenging to evaluate, in part due to the difficulty of directly comparing morphological patterns across disparate clades. We explored relationships between WGD and the evolution of reproductive complexity across vascular plants using a metric based on the number of reproductive part types. We used multiple regression models to evaluate the relative importance of inferred WGD events, genome size, and a suite of additional variables relating to growth habit and reproductive biology in explaining part type complexity. WGD was a consistent predictor of reproductive complexity only among angiosperms. Across vascular plants generally, reproductive biology, clade identity, and the presence of bisexual strobili (those that produce microsporangiate and megasporangiate organs) were better predictors of complexity. Angiosperms are unique among vascular plants in combining frequent polyploidy with high-reproductive complexity. Whether WGD is mechanistically linked to floral complexity is unclear, but we suggest widespread polyploidy and increased complexity were ultimately facilitated by the evolution of herbaceous growth habits in early angiosperms.

Identification of a tetrahedral apical cell preserved within a fossilized fern fiddlehead

The gradual unfurling of fronds from tightly coiled tips, termed fiddleheads or croziers, is one of the most recognizable features of the fern lineage, but its evolutionary origin remains unclear. Here, we identify that fiddleheads and their development, termed circinate vernation,1,2 are not ubiquitous across ferns. Instead, they are a synapomorphy of a clade we term the circinatophytes that includes extant marattioid and leptosporangiate ferns. Circinatophytes encompass the vast majority of extant ferns,3 and fossil evidence demonstrates the antiquity of the group at over 315 million years. Despite their overall conservation, a comparative investigation of extant species suggests that during fiddlehead evolution, there was a transition from a tetrahedral to a wedge-shaped apical cell in the leaf meristem. We predict that a tetrahedral leaf apical cell was likely ancestral in circinatophytes, despite being present in less than 2% of modern species,3 and that this cell mirrored the tetrahedral cell found in the shoots of all major groups of ferns. This is supported by our description of a tetrahedral apical cell in, to our knowledge, the oldest preserved fossil fern leaf meristem of the ca. 315-million-year-old fern Ankyropteris corrugata. We conclude that fiddleheads have been highly conserved in the circinatophytes, and the similarities in leaf and shoot apical cells in early diverging groups of ferns add support to the hypothesis that fern leaves evolved through the modification of shoots, as proposed by the telome theory.4.

Untangling poikilohydry and desiccation tolerance: evolutionary and macroecological drivers in ferns

BACKGROUND AND AIMS

Poikilohydry describes the inability of plants to internally regulate their water content (hydroregulation), whereas desiccation tolerance (DT) refers to the ability to restore normal metabolic functions upon rehydration. The failure to clearly separate these two adaptations has impeded a comprehensive understanding of their unique evolutionary and ecological drivers. Unlike bryophytes and angiosperms, these adaptations in ferns are sometimes uncorrelated, offering a unique opportunity to navigate their intricate interplay.

METHODS

We classified ferns into two syndromes: the Hymenophyllum-type (H-type), encompassing species with filmy leaves lacking stomata that experience extreme poikilohydry and varying degrees of DT, and the Pleopeltis-type (P-type), consisting of resurrection plants with variable hydroregulation but high DT.

KEY RESULTS

The H-type evolved during globally cool Icehouse periods, as an adaptation to low light levels in damp, shady habitats, and currently prevails in wet environments. Conversely, the P-type evolved predominantly under Greenhouse periods as an adaptation to periodic water shortage, with most extant species thriving in warm, seasonally dry habitats.

CONCLUSIONS

Out study underscores the fundamental differences between poikilohydry and DT, emphasizing the imperative to meticulously differentiate and qualify the strength of each strategy as well as their interactions, as a basis for understanding the genetic and evolutionary background of these ecologically crucial adaptations.

A DNA barcode reference of Asian ferns with expert-identified voucher specimens and DNA samples

Ferns belong to species-rich group of land plants, encompassing more than 11,000 extant species, and are crucial for reflecting terrestrial ecosystem changes. However, our understanding of their biodiversity hotspots, particularly in Southeast Asia, remains limited due to scarce genetic data. Despite harboring around one-third of the world's fern species, less than 6% of Southeast Asian ferns have been DNA-sequenced. In this study, we addressed this gap by sequencing 1,496 voucher-referenced and expert-identified fern samples from (sub)tropical Asia, spanning Malaysia, the Philippines, Taiwan, and Vietnam, to retrieve their rbcL and trnL-F sequences. This DNA barcode collection of Asian ferns encompasses 956 species across 152 genera and 34 families, filling major gaps in fern biodiversity understanding and advancing research in systematics, phylogenetics, ecology and conservation. This dataset significantly expands the Fern Tree of Life to over 6,000 species, serving as a pivotal and global reference for worldwide barcoding identification of ferns.

Plastome phylogenomics and new fossil evidence from Dominican amber shed light on the evolutionary history of the Neotropical fern genus Pecluma

PREMISE

Molecular studies based on chloroplast markers have questioned the monophyly of the fern genus Pecluma (Polypodioideae, Polypodiaceae), which has several species of Polypodium nested within it. We explored the delimitation of Pecluma and its biogeographic pattern by evaluating the phylogenetic position of four Polypodium species not sequenced thus far and integrating the first fossil evidence of Pecluma.

METHODS

Using herbarium material, we applied a genome-skimming approach to obtain a phylogenetic hypothesis of Polypodioideae; assessed the combination of character states observed in the fossil from Miocene Dominican amber using a previously published phylogeny of Polypodioideae based on four plastid markers as framework; calculated divergence times; and conducted an ancestral area estimation.

RESULTS

Within Polypodioideae, Pecluma was recovered as sister to Phlebodium. Three of the newly sequenced species-Polypodium otites, P. pinnatissimum, and P. ursipes-were recovered with maximum support within the Pecluma clade, whereas P. christensenii remained within Polypodium. The closest combination of character states of the fossil was found within Pecluma. Our biogeographic analyses suggest an Eocene origin of the genus in South America, with several subsequent Oligocene and Miocene colonization events to Mexico-Central America and to the West Indies.

CONCLUSIONS

Although the circumscription of Pecluma is still challenging, our results elucidate the origin and age of the genus. The newly described fossil, Pecluma hispaniolae sp. nov., supports the hypothesis that the epiphytic communities of the Greater Antilles exhibit a constant generic composition since the Miocene. We propose new combinations (Pecluma otites, Pecluma pinnatissima, and Pecluma ursipes) to accommodate three species previously classified in Polypodium.

The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae

PREMISE

Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape.

METHODS

By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework.

RESULTS

We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other.

CONCLUSIONS

The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.

Stomatal behaviour and water relations in ferns and lycophytes across habits and habitats

Stomatal anatomy and behaviour are key to managing gas exchange fluxes, which require coordination with the plant vascular system to adequately supply leaves with water. Stomatal response times and regulation of water loss are generally understudied in ferns, especially across habits (i.e. epiphytic and terrestrial) and habitats (i.e. wet mesic and dry xeric environments). Our objectives were to (i) determine if hydraulic and anatomical traits that control water use are correlated with their habitats (i.e. xeric, mesic) and habits (i.e. epiphytic, terrestrial) for ferns and lycophytes across taxa, and (ii) explore how those traits and others like average leaf water residence time correlate with stomatal function using a subset of closely related species. Epiphytic species had lower vein densities than terrestrial species, while xeric species had higher vein densities than mesic species. Xeric ferns also had smaller stomata than mesic ferns but had similar stomatal densities. Further, in a subset of mesic and xeric ferns, the xeric ferns had higher maximum stomatal conductance and water content, as well as shorter average stomatal opening responses to light intensity, but stomatal closing times did not differ. Finally, shorter stomatal opening and closing responses were correlated with shorter water residence time. Our study highlights anatomical and physiological differences between ferns and lycophytes, which may partially explain habitat preference based on their optimization of light and water.

Convergent evolution of fern nectaries facilitated independent recruitment of ant-bodyguards from flowering plants

Plant-herbivore interactions reciprocally influence species' evolutionary trajectories. These interactions have led to many physical and chemical defenses across the plant kingdom. Some plants have even evolved indirect defense strategies to outsource their protection to ant bodyguards by bribing them with a sugary reward (nectar). Identifying the evolutionary processes underpinning these indirect defenses provide insight into the evolution of plant-animal interactions. Using a cross-kingdom, phylogenetic approach, we examined the convergent evolution of ant-guarding nectaries across ferns and flowering plants. Here, we discover that nectaries originated in ferns and flowering plants concurrently during the Cretaceous, coinciding with the rise of plant associations in ants. While nectaries in flowering plants evolved steadily through time, ferns showed a pronounced lag of nearly 100 My between their origin and subsequent diversification in the Cenozoic. Importantly, we find that as ferns transitioned from the forest floor into the canopy, they secondarily recruited ant bodyguards from existing ant-angiosperm relationships.

The traditional utilization, biological activity and chemical composition of edible fern species

ETHNOPHARMACOLOGICAL RELEVANCE

Ferns form an important part of the human diet. Young fern fiddleheads are mostly consumed as vegetables, while the rhizomes are often extracted for starch. These edible ferns are also often employed in traditional medicine, where all parts of the plant are used, mostly to prepare extracts. These extracts are applied either externally as lotions and baths or internally as potions, decoctions and teas. Ailments traditionally treated with ferns include coughs, colds, fevers, pain, burns and wounds, asthma, rheumatism, diarrhoea, or skin diseases (eczema, rashes, itching, leprosy).

AIM OF THE REVIEW

This review aims to compile the worldwide knowledge on the traditional medicinal uses of edible fern species correlating to reported biological activities and isolated bioactive compounds.

MATERIALS AND METHODS

The articles and books published on edible fern species were searched through the online databases Web of Science, Pubmed and Google Scholar, with critical evaluation of the hits. The time period up to the end of 2022 was included.

RESULTS

First, the edible fern species were identified based on the literature data. A total of 90 fern species were identified that are eaten around the world and are also used in traditional medicine. Ailments treated are often associated with inflammation or bacterial infection. However, only the most common and well-known fern species, were investigated for their biological activity. The most studied species are Blechnum orientale L., Cibotium barometz (L.) J. Sm., Diplazium esculentum (Retz.) Sw., Marsilea minuta L., Osmunda japonica Thunb., Polypodium vulgare L., and Stenochlaena palustris (Burm.) Bedd. Most of the fern extracts have been studied for their antioxidant, anti-inflammatory and antimicrobial activities. Not surprisingly, antioxidant capacity has been the most studied, with results reported for 28 edible fern species. Ferns have been found to be very rich sources of flavonoids, polyphenols, polyunsaturated fatty acids, carotenoids, terpenoids and steroids and most of these compounds are remarkable free radical scavengers responsible for the outstanding antioxidant capacity of fern extracts. As far as clinical trials are concerned, extracts from only three edible fern species have been evaluated.

CONCLUSIONS

The extracts of edible fern species exert antioxidant anti-inflammatory and related biological activities, which is consistent with their traditional medicinal use in the treatment of wounds, burns, colds, coughs, skin diseases and intestinal diseases. However, studies to prove pharmacological activities are scarce, and require chemical-biological standardization. Furthermore, correct botanical classification needs to be included in publications to simplify data acquisition. Finally, more in-depth phytochemical studies, allowing the linking of traditional use to pharmacological relevance are needed to be done in a standardized way.

Polyploid goldback and silverback ferns (Pentagramma) occupy a wider, colder, and wetter bioclimatic niche than diploid counterparts

PREMISE

The western North American fern genus Pentagramma (Pteridaceae) is characterized by complex patterns of ploidy variation, an understanding of which is critical to comprehending both the evolutionary processes within the genus and its current diversity.

METHODS

We undertook a cytogeographic study across the range of the genus, using a combination of chromosome counts and flow cytometry to infer ploidy level. Bioclimatic variables and elevation were used to compare niches.

RESULTS

We found that diploids and tetraploids are common and widespread, and triploids are rare and sporadic; in contrast with genome size inferences in earlier studies, no hexaploids were found. Diploids and tetraploids show different geographic ranges: only tetraploids were found in the northernmost portion of the range (Washington, Oregon, and British Columbia) and only diploids were found in the Sierra Nevada of California. Diploid, triploid, and tetraploid cytotypes were found to co-occur in relatively few localities: in the southern (San Diego County, California) and desert Southwest (Arizona) parts of the range, and along the Pacific Coast of California.

CONCLUSIONS

Tetraploids occupy a wider bioclimatic niche than diploids both within P. triangularis and at the genus-wide scale. It is unknown whether the wider niche of tetraploids is due to their expansion upon the diploid niche, if diploids have contracted their niche due to competition or changing abiotic conditions, or if this wider niche occupancy is due to multiple origins of tetraploids.

Organellar phylogenomics of Ophioglossaceae fern genera

Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.

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.

Fern cell walls and the evolution of arabinogalactan proteins in streptophytes

Significant changes have occurred in plant cell wall composition during evolution and diversification of tracheophytes. As the sister lineage to seed plants, knowledge on the cell wall of ferns is key to track evolutionary changes across tracheophytes and to understand seed plant-specific evolutionary innovations. Fern cell wall composition is not fully understood, including limited knowledge of glycoproteins such as the fern arabinogalactan proteins (AGPs). Here, we characterize the AGPs from the leptosporangiate fern genera Azolla, Salvinia, and Ceratopteris. The carbohydrate moiety of seed plant AGPs consists of a galactan backbone including mainly 1,3- and 1,3,6-linked pyranosidic galactose, which is conserved across the investigated fern AGPs. Yet, unlike AGPs of angiosperms, those of ferns contained the unusual sugar 3-O-methylrhamnose. Besides terminal furanosidic arabinose, Ara (Araf), the main linkage type of Araf in the ferns was 1,2-linked Araf, whereas in seed plants 1,5-linked Araf is often dominating. Antibodies directed against carbohydrate epitopes of AGPs supported the structural differences between AGPs of ferns and seed plants. Comparison of AGP linkage types across the streptophyte lineage showed that angiosperms have rather conserved monosaccharide linkage types; by contrast bryophytes, ferns, and gymnosperms showed more variability. Phylogenetic analyses of glycosyltransferases involved in AGP biosynthesis and bioinformatic search for AGP protein backbones revealed a versatile genetic toolkit for AGP complexity in ferns. Our data reveal important differences across AGP diversity of which the functional significance is unknown. This diversity sheds light on the evolution of the hallmark feature of tracheophytes: their elaborate cell walls.

U.PhyloMaker: An R package that can generate large phylogenetic trees for plants and animals

The previously released packages of the PhyloMaker series (i.e. S.PhyloMaker, V.PhyloMaker, and V.PhyloMaker2) have been broadly used to generate phylogenetic trees for ecological and biogeographical studies. Although these packages can be used to generate phylogenetic trees for any groups of plants and animals for which megatrees are available, they focus on generating phylogenetic trees for plants based on the megatrees provided by the packages. How to use these packages to generate phylogenetic trees based on other megatrees is not straightforward. Here, we present a new tool, which is called 'U.PhyloMaker', and a simple R script that can be used to easily generate large phylogenetic trees for both plants and animals at a relatively fast speed.

Simplified Genomic Data Revealing the Decline of Aleuritopteris grevilleoides Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China

Understanding the evolutionary history of endangered species is crucial for identifying the main reasons for species endangerment in the past and predicting the changing trends and evolutionary directions of their future distribution. In order to study the impact of environmental changes caused by deep valley incision after the uplift of the Qinghai-Tibet Plateau on endangered species, we collected 23 samples belonging to four populations of Aleuritopteris grevilleoides, an endangered fern endemic to the dry-hot valleys (DHV) of Yunnan. Single-nucleotide variation sites (SNPs) were obtained by the genotyping-by-sequencing (GBS) method, and approximately 8085 SNP loci were identified. Through the reconstruction and analysis of genetic diversity, population structure, population dynamics, evolution time, and ancestral geographical distribution, combined with geological historical events such as the formation of dry-hot valleys, this study explores the formation history, current situation, reasons for endangerment and scientifically sound measures for the protection of A. grevilleoides. In our study, A. grevilleoides had low genetic diversity (Obs_Het = 0.16, Exp_Het = 0.32, Pi = 0.33) and a high inbreeding coefficient (Fis = 0.45). The differentiation events were 0.18 Mya, 0.16 Mya, and 0.11 Mya in the A. grevilleoides and may have been related to the formation of terraces within the dry-hot valleys. The history of population dynamics results shows that the diversion of the river resulted in a small amount of gene flow between the two clades, accompanied by a rapid increase in the population at 0.8 Mya. After that, the effective population sizes of A. grevilleoides began to contract continuously due to topographic changes resulting from the continuous expansion of dry-hot valleys. In conclusion, we found that the environmental changes caused by geological events might be the main reason for the changing population size of A. grevilleoides.