Fern Lineages Research Articles

An early cladoxylopsid with complex vascular architecture: Paracladoxylon kespekianum gen. et sp. nov. from the Lower Devonian (Emsian) of Quebec, Canada.

Cladoxylopsids, one of the first lineages with complex organization to rise from the plexus of structurally simple plants that comprised the earliest euphyllophyte floras, are moniliformopsid euphyllophytes. They formed Earth's earliest forests by the Middle Devonian and are thought to have given rise to the equisetopsids and probably some fern lineages. The Lower Devonian (Emsian) Battery Point Formation (Quebec, Canada) contains previously unrecognized cladoxylopsids preserved anatomically. One of these provides new data on structural evolution among euphyllophytes and is described here. The anatomy and morphology of permineralized axes of the new plant were studied with light and electron microscopy on sections produced using the cellulose acetate peel technique. Morphological comparisons and phylogenetic analysis were used for taxonomic placement of the plant. The plant represents a new species, Paracladoxylon kespekianum Chu et Tomescu, gen. et sp. nov., that has tracheids with modern-looking bordered pits and the complex cauline vascular architecture characteristic of the genus Cladoxylon. Its dissected ultimate appendages have complex regular taxis and a pattern of vascularization that suggests bilateral symmetry. Paracladoxylon kespekianum is one of the largest Early Devonian euphyllophytes, among the oldest representatives of the cladoxylopsid group, and older than any species of the closely related Cladoxylon by at least 35 million years. It is also one of the oldest anatomically preserved representatives of the cladoxylopsid group. Its anatomical organization pushes the rise of complex vascular architecture among moniliformopsid euphyllophytes deeper in time than previously recognized.

Genomic signatures of inbreeding and mutation load in tree ferns.

Ferns (Pteridophyta), as the second largest group of vascular plants, play important roles in ecosystem functioning. Homosporous ferns exhibit a remarkable range of mating systems, from extreme inbreeding to obligate outcrossing, which may have significant evolutionary and ecological implications. Despite their significance, the impact of genome-wide inbreeding on genetic diversity and mutation load within the fern lineage remain largely unexplored. In this study, we utilized whole-genome sequencing to investigate the genomic signatures of inbreeding and genetic load in three Alsophila tree fern species. Our analysis revealed extremely high inbreeding in A. spinulosa, in contrast to the predominantly outcrossing observed in A. costularis and A. latebrosa. This difference likely reflects divergent mating systems and demographic histories. Consistent with its extreme inbreeding propensity, A. spinulosa exhibits reduced genetic diversity and a pronounced decline in effective population size. Comparison of genetic load revealed an overall reduction in deleterious mutations in the highly inbred A. spinulosa, highlighting that long-term inbreeding may have contributed to the purging of strongly deleterious mutations, thereby prolonging the survival of A. spinulosa. Despite this, however, A. spinulosa carries a substantive realized genetic load that may potentially instigate future fitness decline. Our findings illuminate the complex evolutionary interplay between inbreeding and mutation load in homosporous ferns, yielding insights with important implications for the conservation and management of these species.

Biotic interactions, evolutionary forces and the pan-plant specialized metabolism.

Plant specialized metabolism has a complex evolutionary history. Some aspects are conserved across the green lineage, but many metabolites are unique to certain lineages. The network of specialized metabolism continuously diversified, simplified or reshaped during the evolution of streptophytes. Many routes of pan-plant specialized metabolism are involved in plant defence. Biotic interactions are recalled as major drivers of lineage-specific metabolomic diversification. However, the consequences of this diversity of specialized metabolism in the context of plant terrestrialization and land plant diversification into the major lineages of bryophytes, lycophytes, ferns, gymnosperms and angiosperms remain only little explored. Overall, this hampers conclusions on the evolutionary scenarios that shaped specialized metabolism. Recent efforts have brought forth new streptophyte model systems, an increase in genetically accessible species from distinct major plant lineages, and new functional data from a diversity of land plants on specialized metabolic pathways. In this review, we will integrate the recent data on the evolution of the plant immune system with the molecular data of specialized metabolism and its recognition. Based on this we will provide a contextual framework of the pan-plant specialized metabolism, the evolutionary aspects that shape it and the impact on adaptation to the terrestrial environment.This article is part of the theme issue 'The evolution of plant metabolism'.

The classification of the fern family Gleicheniaceae, with the description of a new genus, segregated from Sticherus

Abstract Gleicheniaceae is an early diverging lineage of leptosporangiate ferns. Although the family can be readily recognized by the pseudodichotomous branching pattern of its fronds, generic circumscription has long been debated. Phylogenetic analyses based on genomic data supported the monophyly of six genera (Dicranopteris, Diplopterygium, Gleichenella, Gleichenia, Rouxopteris, and Stromatopteris) but indicate the paraphyly of Sticherus. To accommodate this latter result, we describe a new genus, Sticheropsis, gen. nov., segregated from Sticherus. We provide a new taxonomic treatment of Gleicheniaceae, including an identification key to all eight genera, descriptions of the genera with comments and notes concerning geographic distributions and phylogenetic affinities, as well as an overview of the morphology of the family with a revised and unified terminology for the fronds. We recognize 149 species plus two hybrids for the family, distributed into eight genera, and propose six new combinations.

The third opinion on fern phylogenetics with novel insights into their mitogenome evolution

The current understanding of fern phylogeny is primarily based on plastid and nuclear sequences, but the third genome—the mitogenome—has remained practically unstudied. We inferred the first broad scale fern phylogeny based on mitogenomic data, obtained from the One Thousand Plant Transcriptomes Initiative project, and compared it with the plastid phylogeny. The trees were mostly congruent and corresponded to the current understanding of the fern phylogeny, but we observed different evolutionary patterns between the two genomes. Protein-coding markers located in the plastome had, on average, over two times higher substitution rate than the markers from the mitogenome. The similar rate variation pattern between the genomes in different fern lineages supports the idea that a common mechanism, like life history traits, drives the rates of molecular evolution. The few conflicting nodes we observed have also been difficult to resolve in other studies, suggesting that even genomic data may not suffice to resolve them.

Modified CTAB protocols for high-molecular-weight DNA extractions from ferns.

Efficient protocols for extracting high-molecular-weight (HMW) DNA from ferns facilitate the long-read sequencing of their large and complex genomes. Here, we perform two cetyltrimethylammonium bromide (CTAB)-based protocols to extract HMW DNA and evaluate their applicability in diverse fern taxa for the first time. We describe two modified CTAB protocols, with key adjustments to minimize mechanical disruption during lysis to prevent DNA shearing. One of these protocols uses a small amount of fresh tissue but yields a considerable quantity of HMW DNA with high efficiency. The other accommodates a large amount of input tissue, adopts an initial step of nuclei isolation, and thus ensures a high yield in a short period of time. Both methods were proven to be robust and effective in obtaining HMW DNA from diverse fern lineages, including 33species in 19 families. The DNA extractions mostly had high DNA integrity, with mean sizes larger than 50 kbp, as well as high purity (A260/A230 and A260/A280 > 1.8). This study provides HMW DNA extraction protocols for ferns in the hope of facilitating further attempts to sequence their genomes, which will bridge our genomic understanding of land plant diversity.

Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns

Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.

Target Capture Methods Offer Insight into the Evolution of Rapidly Diverged Taxa and Resolve Allopolyploid Homeologs in the Fern Genus Polypodium s.s.

Abstract— Like many fern lineages comprising reticulate species complexes, Polypodium s.s. (Polypodiacaeae) has a history shaped by rapid diversification, hybridization, and polyploidy that poses substantial challenges for phylogenetic inference with plastid and single-locus nuclear markers. Using target capture probes for 408 nuclear loci developed by the GoFlag project and a custom bioinformatic pipeline, SORTER, we constructed multi-locus nuclear datasets for diploid temperate and Mesoamerican species of Polypodium and five allotetraploid species belonging to the well-studied Polypodium vulgare complex. SORTER employs a clustering approach to separate putatively paralogous copies of targeted loci into orthologous matrices and haplotype phasing to infer allopolyploid haplotypes across loci, resulting in datasets amenable to both concatenated maximum likelihood and multi-species coalescent phylogenetic analyses. By comparing phylogenies derived from maximum likelihood and multi-species coalescent analyses of unphased and phased datasets, as well as evaluating discordance among gene trees and species trees, we recover support for incomplete lineage sorting within Polypodium s.s., novel relationships among diploid taxa of the Polypodium vulgare complex and its Mesoamerican sister clade, and the placement of several Polypodium species within other genera. Additionally, we were able to infer well-supported phylogenies that identified the hypothesized progenitors of the allotetraploid species, indicating that SORTER is an effective and accurate tool for reconstructing homeolog haplotypes of allopolyploids in fern taxa and other non-model organisms from target capture data.

Organ Patterning at the Shoot Apical Meristem (SAM): The Potential Role of the Vascular System

Auxin, which is transported in the outermost cell layer, is one of the major players involved in plant organ initiation and positioning at the shoot apical meristem (SAM). However, recent studies have recognized the role of putative internal signals as an important factor collaborating with the well-described superficial pathway of organogenesis regulation. Different internal signals have been proposed; however, their nature and transport route have not been precisely determined. Therefore, in this mini-review, we aimed to summarize the current knowledge regarding the auxin-dependent regulation of organ positioning at the SAM and to discuss the vascular system as a potential route for internal signals. In addition, as regular organ patterning is a universal phenomenon, we focus on the role of the vasculature in this process in the major lineages of land plants, i.e., bryophytes, lycophytes, ferns, gymnosperms, and angiosperms.

Flora de samambaias de Viçosa, Estado de Minas Gerais, Brasil: Dennstaedtiaceae, Lindsaeaceae e Saccolomataceae

ABSTRACT As part of an ongoing project treating the ferns and lycophytes from the region of Viçosa, Minas Gerais State, Brazil, we here present the taxonomic treatment of the early divergent lineages of the leptosporangiate ferns: the families Dennstaedtiaceae, Lindsaeaceae and Saccolomataceae. We have been sampling the remnant forest patches since 2012; we also fully reviewed the collection of herbarium VIC and other online collections: F, IAN, NY, PH, RB, U, UC, UPCB, US, and WTU. In the region of Viçosa, six taxa belonging to those families occur: Dennstaedtia cicutaria and Pteridium esculentum subsp. arachnoideum (Dennstaedtiaceae); Lindsaea lancea var. lancea, L. quadrangularis subsp. quadrangularis, and L. stricta var. stricta (Lindsaeaceae); and Saccoloma elegans (Saccolomataceae). Among these taxa, only L. quadrangularis subsp. quadrangularis and S. elegans are endemic to the Brazilian Atlantic Rainforest; the remaining are widespread in the Neotropics. We present keys, descriptions, illustrations, examined specimens, and comments.

Revisiting ancient polyploidy in leptosporangiate ferns.

Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building KS -age distributions and applying substitution rate corrections and by conducting statistical gene tree-species tree reconciliation analyses. Our integrative analyses not only identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree-species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues.

Microlepia burmasia sp. nov., a new fern species from mid-Cretaceous Kachin amber of norther Myanmar (Dennstaedtiaceae, Polypodiales)

The rise of angiosperms during the Cretaceous was thought to be related to the radiation of polypod ferns, a fern lineage that represent 80% of the modern fern diversity. However, although the proposed palo-diversity from DNA based studies, Mesozoic polypod fern fossils with preserved fertile pinnae are scarcely. Here, we investigated the fragment of polypod fern preserved in mid-Cretaceous Kachin amber from northern Myanmar and assigned a new fossilized fertile pinnule into the genus Microlepia (Dennstaedtiaceae), described as Microlepia burmasia Long, Wang and Shi, sp. nov. The new species is mainly characterized by the 2-pinnate-pinnatifid pinnule with surface and margin covering short tomentum and articulate hairs. Vein free, pouch-shaped indusia, submarginal and terminal on one vein of sori, sporangium with interrupted, vertical annulus and spores trilete. This discovery adds to polypod fern diversity in the Cretaceous and dates the origin of Microlepia to at least 60 million years earlier, which is evidence for an early origin of polypod ferns and coincides with the rise of angiosperms.

Filmy Ferns (Hymenophyllaceae) and Associated Spike-Mosses (Selaginellaceae) from the Mid-Cretaceous Kachin Amber, Myanmar.

Filmy ferns (Hymenophyllaceae) are the most diverse lineage of the early-diverging leptosporangiate ferns with ca. 430 species widely distributed around the world but with the highest diversity in the humid tropics. However, their fossil record is scarce because of the low preservation potential of the delicate, membranous laminae. So far, no Hymenophyllaceae fossils have been reported from tropical Asia. Here, we describe some fern remains and their syninclusions (spike-mosses) in four pieces of Kachin amber from the mid-Cretaceous of Hukawng Valley, Northern Myanmar, as Hymenophyllites angustus sp. nov., H. kachinensis sp. nov., H. setosus sp. nov. (Hymenophyllaceae) and Selaginella alata sp. nov. (Selaginellaceae), respectively. These fern remains are assigned to Hymenophyllaceae based on the filmy, one-cell thick, decompound pinnatifid laminae and dichotomous venation. They represent the first fossil record of Hymenophyllaceae in tropical Asia. The growth habits of these ferns and associated spike-mosses and their implication for paleoenvironment are discussed. Our study expands the diversity of the cryptogams in mid-Cretaceous Kachin amber. Together with other contemporaneous findings, the present fossils indicate that Hymenophyllaceae have already accumulated some notable diversity in the Cretaceous.

Revisiting R.H. Tschudy’s fern-spore spike concept 40 years later: connecting Tschudy’s ‘disaster taxon’ concept with paleopolyploidization in Stenochlaena J. Sm

The Cretaceous/Paleogene (K/Pg) boundary fern-spore spike concept was first introduced by R.H. Tschudy 40 years ago and established the precept that ferns are so-called ‘disaster taxa’ that flourish after natural disasters because of the high colonization potential of their wind-blown spores. Among the least understood topics at the crux of contemporary K/Pg boundary fern-spike studies is whether Stenochlaena-like or other stem blechnaceous ferns were among those that flourished after the K/Pg event, contributing to the Laevigatosporites-dominated phase of the fern-spore spike. For instance, dispersed Stenochlaena-like spores – e.g. Polypodiisporites usmensis (van der Hammen) Khan & Martin – first appear in the upper Eocene stratigraphic record of South America, whereas megafossils of Stenochlaena-like ferns are first known from the upper Paleocene strata of this same region. Beyond this traditional focus on taphonomic and taxonomic uncertainty regarding the identity of dispersed spore producers, however, there is further discordance between contemporary paleobotanical and molecular phylogenetic perspectives on the timing of diversification of stem lineages of blechnaceous ferns in relation to the K/Pg boundary. This investigation reconciles these two perspectives by constraining molecular clock divergence time estimates using contemporary fossil data. If this reconciliation is correct, then paleopolyploidization (whole genome duplication or WGD) associated with the origin of the genus Stenochlaena J. Sm. predated evolution of polocytic stomata, a heavily ornamented exospore, and a hemi-epiphytic to epiphytic habit observed in the crown lineage. Critically, this novel perspective elicits a merger of the K/Pg boundary fern spike and K/Pg boundary-WGD concepts, suggesting a link between polyploidy and the ‘disaster taxon’ concept.

Origin of Hawaiian ferns of the genus Ctenitis (Dryopteridaceae)

ABSTRACT The Hawaiian Islands are an emblematic field to study evolution, with their very high rates of endemism and spectacular cases of insular speciation. Nevertheless, many Hawaiian lineages still deserve investigation, such as in the fern lineage. In this study, we address the question of the origin of the fern genus Ctenitis, which is present in the archipelago with two endemic species, Ctenitis squamigera and C. latifrons. Using a taxonomic sampling covering the pantropical distribution of the genus and three chloroplast DNA regions, we provide evidence that the genus in the Hawaiian Islands originated from a single long-distance dispersal from the Neotropics. This area is less represented than Asia and the South Pacific in the origin of Hawaiian ferns, but a Neotropical origin may be explained by the transportation of spores by tropical storms originating near Central America. Furthermore, the colonization of the Hawaiian Islands is estimated to have occurred between 4 [9–2] and 3 [7–1] mya. This timing is consistent with the ages of all main and extant islands of the archipelago, which already provided habitats for the establishment of the initial Ctenitis colonizer. In turn, this relatively late arrival to the islands and the related potentially low availability of ecological niches may have hampered diversification of the genus beyond the two extant species.

Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns.

Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns were sampled, making it the most comprehensive plastomic analysis of fern lineages to date. The samples included 42 novel plastomes of 15 families with a focus on Hymenophyllales and Gleicheniales. We reconstructed a well-supported phylogeny of all extant fern families, detected significant structural synapomorphies, including 9 large inversions, 7 invert repeat region (IR) boundary shifts, 10 protein-coding gene losses, 7 tRNA gene losses or anticodon changes, and 19 codon indels (insertions or deletions) across the deep phylogeny of ferns, particularly on the backbone nodes. The newly identified inversion V5, together with the newly inferred expansion of the IR boundary R5, can be identified as a synapomorphy of a clade composed of Dipteridaceae, Matoniaceae, Schizaeales, and the core leptosporangiates, while a unique inversion V4, together with an expansion of the IR boundary R4, was verified as a synapomorphy of Gleicheniaceae. This structural evidence is in support of our phylogenetic inference, thus providing key insight into the paraphyly of Gleicheniales. The inversions of V5 and V7 together filled the crucial gap regarding how the “reversed” gene orientation in the IR region characterized by most extant ferns (Schizaeales and the core leptosporangiates) evolved from the inferred ancestral type as retained in Equisetales and Osmundales. The tRNA genes trnR-ACG and trnM-CAU were assumed to be relicts of the early-divergent fern lineages but intact in most Polypodiales, particularly in eupolypods; and the loss of the tRNA genes trnR-CCG, trnV-UAC, and trnR-UCU in fern plastomes was much more prevalent than previously thought. We also identified several codon indels in protein-coding genes within the core leptosporangiates, which may be identified as synapomorphies of specific families or higher ranks. This study provides an empirical case of integrating structural and sequence information of plastomes to resolve deep phylogeny of plants.

Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity.

The formation of spatial genetic structure with the presence of extensive gene flow, an evolutionary force which is generally expected to eliminate population-specific variation and maintain genetic homogeneity, remains poorly understood. Homosporous ferns, which spread by spores through wind and possess long distance dispersal capacity, provide an ideal system to investigate such a process. Here, using a homoploid fern lineage, the Athyrium sinense complex, we used reduced-representation genomic data to examine spatial genetic structure and explored potential driving forces including geographical distance, environment, climatic history and external dispersal constraints. Our findings showed a clear north-south divergence at the genetic, morphological and ecological levels between both sides of 35°N in East Asia. Fluctuant and heterogeneous climatic condition was demonstrated to play a crucial role during the formation of the divergence. Our results suggested that this lineage was able to migrate southward and colonize new habitat as a result of the Quaternary climatic fluctuation. Furthermore, the present genetic structure is attributed to adaptation to heterogeneous environments, especially temperature difference. In addition to ecological adaptation, we found clues showing that canopy density, wind direction as well as habitat continuity were all likely to constrain the effect of gene flow. These results demonstrated a diversification process without ploidy changes in ferns providing new insights for our present knowledge on ferns' spatio-temporal evolutionary pattern. In particular, our study highlights the influence of environmental heterogeneity in driving genetic divergence against strong dispersal capacity.

Genome size evolution of the extant lycophytes and ferns

Ferns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.

Plant abundance, but not plant evolutionary history, shapes patterns of host specificity in foliar fungal endophytes

AbstractUnderstanding the origins and maintenance of host specificity, or why horizontally‐acquired symbionts associate with some hosts but not others, remains elusive. In this study, we explored whether patterns of host specificity in foliar fungal endophytes, a guild of highly diverse fungi that occur within the photosynthetic tissues of all major plant lineages, were related to characteristics of the plant community. We comprehensively sampled all plant host species within a single community and tested the relationship between plant abundance or plant evolutionary relatedness and metrics of endophyte host specificity. We quantified host specificity with methods that considered the total endophyte community per plant host (i.e., multivariate methods) along with species‐based methods (i.e., univariate metrics) that considered host specificity from the perspective of each endophyte. Univariate host specificity metrics quantified plant alpha‐diversity (structural specificity), plant beta‐diversity (beta‐specificity), and plant phylogenetic diversity (phylogenetic specificity) per endophyte. We standardized the effect sizes of univariate host specificity metrics to randomized distributions to avoid spurious correlations between host specificity metrics and endophyte abundance. We found that more abundant plant species harbored endophytes that occupied fewer plant species (higher structural specificity) and were consistently found in the same plant species across the landscape (higher beta‐specificity). There was no relationship between plant phylogenetic distance and endophyte community dissimilarity. We still found that endophyte community composition significantly varied among plant species, families, and major groups, supporting a plant identity effect. In particular, endophytes in angiosperm lineages associated with narrower phylogenetic breadths of plants (higher phylogenetic specificity) compared to endophytes within conifer and fern lineages. Overall, an effect of plant species abundance may help explain why horizontally‐transmitted endophytes vary geographically within host species ranges.

Phylogenetic diversity of ferns reveals different patterns of niche conservatism and habitat filtering between epiphytic and terrestrial assemblages

Much attention has been directed to understanding species richness patterns, but adding an evolutionary perspective allows us to also consider the historical processes determining current diversity patterns. We analyzed phylogenetic patterns of fern species assemblages in 868 plots along a wide range of elevational (0-4000 m) and latitudinal (0°-23°N) gradients in the Neotropics to allow a deeper understanding of evolutionary processes underlying current patterns of diversity and community assembly. Overall, we found that phylogenetic mean pairwise distance (sMPD) and mean nearest taxon distance (sMNTD) decreased with increasing latitude and elevation, but that these geographical factors per se were weak explanatory variables. Incorporating environmental variables strongly enhanced the power of the predictive model, indicating that fern assemblages are phylogenetically more diverse under wet and warm to cool conditions at low latitudes and elevations. Further, whereas epiphytic fern assemblages were strongly influenced by climatic factors, this was not the case for terrestrial ones, suggesting that edaphic conditions and vegetation structure may have a stronger influence on the evolution and diversification of terrestrial ferns. We conclude that fern assemblages are strongly influenced by phylogenetic niche conservatism and environmental filtering. This has also been found for angiosperms, but the direction of the environment-phylogenetic relationship is often opposed in the two groups, suggesting that the older age of many fern lineages includes historical signals that are not evident in the more recent angiosperm radiation.