Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic

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.

Genome-wide data reveal bi-direction and asymmetrical hybridization origin of a fern species Microlepia matthewii

Introduction

Natural hybridization is common and plays a crucial role in driving biodiversity in nature. Despite its significance, the understanding of hybridization in ferns remains inadequate. Therefore, it is imperative to study fern hybridization to gain a more comprehensive understanding of fern biodiversity. Our study delves into the role of hybridization in shaping fern species, employing Microlepia matthewii as a case study to investigate its origins of hybridization.

Methods

We performed double digest Genotyping-by-sequencing (dd-GBS) on M. matthewii and its potential parent species, identifying nuclear and chloroplast SNPs. Initially, nuclear SNPs were employed to construct the three cluster analysis: phylogenetic tree, principal component analysis, and population structure analysis. Subsequently, to confirm whether the observed genetic mixture pattern resulted from hybridization, we utilized two methods: ABBA-BABA statistical values in the D-suite program and gene frequency covariance in the Treemix software to detect gene flow. Finally, we employed chloroplast SNPs to construct a phylogenetic tree, tracing the maternal origin.

Results and discussion

The analysis of the nuclear SNP cluster revealed that M. matthewii possesses a genetic composition that is a combination of M. hancei and M. calvescens. Furthermore, the analysis provided strong evidence of significant gene flow signatures from the parental species to the hybrid, as indicated by the two gene flow analyses. The samples of M. matthewii cluster separately with M. hancei or M. calvescens on the chloroplast systematic tree. However, the parentage ratio significantly differs from 1:1, suggesting that M. matthewii is a bidirectional and asymmetrical hybrid offspring of M. hancei and M. calvescens.

'Out of Africa' origin of the pantropical staghorn fern genus Platycerium (Polypodiaceae) supported by plastid phylogenomics and biogeographical analysis

BACKGROUND AND AIMS

The staghorn fern genus Platycerium is one of the most commonly grown ornamental ferns, and it evolved to occupy a typical pantropical intercontinental disjunction. However, species-level relationships in the genus have not been well resolved, and the spatiotemporal evolutionary history of the genus also needs to be explored.

METHODS

Plastomes of all the 18 Platycerium species were newly sequenced. Using plastome data, we reconstructed the phylogenetic relationships among Polypodiaceae members with a focus on Platycerium species, and further conducted molecular dating and biogeographical analyses of the genus.

KEY RESULTS

The present analyses yielded a robustly supported phylogenetic hypothesis of Platycerium. Molecular dating results showed that Platycerium split from its sister genus Hovenkampia ~35.2 million years ago (Ma) near the Eocene-Oligocene boundary and began to diverge ~26.3 Ma during the late Oligocene, while multiple speciation events within Platycerium occurred during the middle to late Miocene. Biogeographical analysis suggested that Platycerium originated in tropical Africa and then dispersed eastward to southeast Asia-Australasia and westward to neotropical areas.

CONCLUSIONS

Our analyses using a plastid phylogenomic approach improved our understanding of the species-level relationships within Platycerium. The global climate changes of both the Late Oligocene Warming and the cooling following the mid-Miocene Climate Optimum may have promoted the speciation of Platycerium, and transoceanic long-distance dispersal is the most plausible explanation for the pantropical distribution of the genus today. Our study investigating the biogeographical history of Platycerium provides a case study not only for the formation of the pantropical intercontinental disjunction of this fern genus but also the 'out of Africa' origin of plant lineages.

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.

Phylogeny, character evolution, and classification of Selaginellaceae (lycophytes)

Selaginella is the largest and most taxonomically complex genus in lycophytes. The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes. Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions (74% increase of the earlier largest sampling) representing ca. 300 species to infer a new phylogeny. The evolution of 10 morphological characters is studied in the new phylogenetic context. Our major results include: (1) the nuclear and plastid phylogenies are congruent with each other and combined analysis well resolved and strongly supported the relationships of all but two major clades; (2) the Sinensis group is resolved as sister to S. subg. Pulviniella with strong support in two of the three analyses; (3) most morphological characters are highly homoplasious but some characters alone or combinations of characters well define the major clades in the family; and (4) an infrafamilial classification of Selaginellaceae is proposed and the currently defined Selaginella s.l. is split into seven subfamilies (corresponding to the current six subgenera + the Sinensis group) and 19 genera (the major diagnosable clades) with nine new species-poor genera. We support the conservation of Selaginella with a new type, S. flabellata, to minimize nomenclatural instability. We provide a key to subfamilies and genera, images illustrating their morphology, their morphological and geographical synopses, a list of constituent species, and necessary new combinations. This new classification will hopefully facilitate communication, promote further studies, and help conservation.

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.

Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism

Orchidaceae (with >28,000 orchid species) are one of the two largest plant families, with economically and ecologically important species, and occupy global and diverse niches with primary distribution in rainforests. Among orchids, 70% grow on other plants as epiphytes; epiphytes contribute up to ~50% of the plant diversity in rainforests and provide food and shelter for diverse animals and microbes, thereby contributing to the health of these ecosystems. Orchids account for over two-thirds of vascular epiphytes and provide an excellent model for studying evolution of epiphytism. Extensive phylogenetic studies of Orchidaceae and subgroups have ;been crucial for understanding relationships among many orchid lineages, although some uncertainties remain. For example, in the largest subfamily Epidendroideae with nearly all epiphytic orchids, relationships among some tribes and many subtribes are still controversial, hampering evolutionary analyses of epiphytism. Here we obtained 1,450 low-copy nuclear genes from 610 orchid species, including 431 with newly generated transcriptomes, and used them for the reconstruction of robust Orchidaceae phylogenetic trees with highly supported placements of tribes and subtribes. We also provide generally well-supported phylogenetic placements of 131 genera and 437 species that were not sampled by previous plastid and nuclear phylogenomic studies. Molecular clock analyses estimated the Orchidaceae origin at ~132 million years ago (Ma) and divergences of most subtribes from 52 to 29 Ma. Character reconstruction supports at least 14 parallel origins of epiphytism; one such origin was placed at the most recent common ancestor of ~95% of epiphytic orchids and linked to modern rainforests. Ten occurrences of rapid increase in the diversification rate were detected within Epidendroideae near and after the K-Pg boundary, contributing to ~80% of the Orchidaceae diversity. This study provides a robust and the largest family-wide Orchidaceae nuclear phylogenetic tree thus far and new insights into the evolution of epiphytism in vascular plants.

Splitting one species into 22: an unusual tripling of molecular, morphological, and geographical differentiation in the fern family Didymochlaenaceae (Polypodiales)

The pantropical fern genus Didymochlaena (Didymochlaenaceae) has long been considered to contain one species only. Recent studies have resolved this genus/family as either sister to the rest of eupolypods I or as the second branching lineage of eupolypods I, and have shown that this genus is not monospecific, but the exact species diversity is unknown. In this study, a new phylogeny is reconstructed based on an expanded taxon sampling and six molecular markers. Our major results include: (i) Didymochlaena is moderately or weakly supported as sister to the rest of eupolypods I, highlighting the difficulty in resolving the relationships of this important fern lineage in the polypods; (ii) species in Didymochlaena are resolved into a New World clade and an Old World clade, and the latter further into an African clade and an Asian-Pacific clade; (iii) an unusual tripling of molecular, morphological and geographical differentiation in Didymochlaena is detected, suggesting single vicariance or dispersal events in individual regions and no evidence for reversals at all, followed by allopatric speciation at more or less homogeneous rates; (iv) evolution of 18 morphological characters is inferred and two morphological synapomorphies defining the family are recognized-the elliptical sori and fewer than 10 sori per pinnule, the latter never having been suggested before; (v) based on morphological and molecular variation, 22 species in the genus are recognized contrasting with earlier estimates of between one and a few; and (vi) our biogeographical analysis suggests an origin for Didymochlaena in the latest Jurassic-earliest Cretaceous and the initial diversification of the extant lineages in the Miocene-all but one species diverged from their sisters within the last 27 Myr, in most cases associated with allopatric speciation owing to geologic and climatic events, or dispersal.

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.

A plastid phylogenomic framework for the palm family (Arecaceae)

BACKGROUND

Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical rainforests bearing great cultural and economic significance. Taxonomy and phylogeny of the family have been extensively investigated by a series of molecular phylogenetic studies in the last two decades. Nevertheless, some phylogenetic relationships within the family are not yet well-resolved, especially at the tribal and generic levels, with consequent impacts for downstream research.

RESULTS

Plastomes of 182 palm species representing 111 genera were newly sequenced. Combining these with previously published plastid DNA data, we were able to sample 98% of palm genera and conduct a plastid phylogenomic investigation of the family. Maximum likelihood analyses yielded a robustly supported phylogenetic hypothesis. Phylogenetic relationships among all five palm subfamilies and 28 tribes were well-resolved, and most inter-generic phylogenetic relationships were also resolved with strong support.

CONCLUSIONS

The inclusion of nearly complete generic-level sampling coupled with nearly complete plastid genomes strengthened our understanding of plastid-based relationships of the palms. This comprehensive plastid genome dataset complements a growing body of nuclear genomic data. Together, these datasets form a novel phylogenomic baseline for the palms and an increasingly robust framework for future comparative biological studies of this exceptionally important plant family.

Insights into the evolutionary history and taxonomic status of Sinopteris (Pteridaceae)

As an endemic Chinese genus, Sinopteris C. Chr. & Ching was once considered an early diverged taxon of cheilanthoid ferns, and its taxonomic status has long been controversial. In this study, eight datasets spanning the complete chloroplast genomes and three nuclear genes were used to reconstruct the phylogeny of Sinopteris and its relatives. In addition, combining morphological analyses, divergence time estimation, and ancestral trait reconstruction, the origin and evolutionary history of Sinopteris were comprehensively discussed. Based on the complete chloroplast genome dataset, our analyses yielded a phylogram with all clades strongly supported (ML-BS = 100, BI-PP = 1.0), and the topology was almost identical to that based on the concatenated sequences of nrDNA, CRY2, and IBR3. Two species of Sinopteris were united and sister to Aleuritopteris niphobola (C. Chr.) Ching. They constituted a stable monophyletic group embedded in Aleuritopteris Fée. This was also consistent with the results of morphological analyses. Divergence time estimation indicated that the clade of Aleuritopteris and Sinopteris originated in the early Miocene (ca. 16.80 Ma) and experienced two rapid diversifications, which could coincide with environmental heterogeneity caused by the progressive uplift of the Himalayas and the intense uplift of the Hengduan Mountains. Sinopteris originated in the late Miocene (ca. 6.96 Ma), accompanied by the sharp intensifications of Asian Monsoon, and began to diversify at 2.34 Ma, following the intense uplift of the Hengduan Mountains. Ancestral character reconstruction showed that monangial sori and subsessile sporangia were clearly late derived states rather than early diverged states. Both the molecular phylogenetic and morphological analyses support the inclusion of Sinopteris in Aleuritopteris.

Phylogeny, character evolution, and biogeography of the fern genus Bolbitis (Dryopteridaceae)

Bolbitis is a pantropical fern genus of Dryopteridaceae with ca. 80 species mainly in tropical Asia. Earlier studies confirmed the monophyly of Bolbitis when Mickelia is excluded and identified three major clades in Bolbitis. However, earlier studies are based on relatively small sampling and the majority of Asian species are not sampled. In this study, DNA sequences of three plastid markers of 169 accessions representing ca. 68 (85 % of total) species of Bolbitis in nine out of the 10 series recognized by Hennipman (1977), and 54 accessions representing the five remaining bolbitidoid genera are used to infer a global phylogeny with a focus on Asian species. The major results include: (1) Bolbitis is strongly supported as monophyletic; (2) species of Bolbitis are resolved into four major clades and their relationships are: the Malagasy/Mascarene clade is sister to the rest, followed by the African clade which is sister to the American clade + the Asian clade; (3) six well-supported subclades are identified in the most speciose Asian clade; (4) the free-veined Egenolfia is embedded in Bolbitis and is paraphyletic in relation to species with anastomosing venation; (5) three series sensu Hennipman (1977), B. ser. Alienae, B. ser. Egenolfianae, and B. ser. Heteroclitae, are paraphyletic or polyphyletic; (6) evolution of six morphological characters is analyzed and free venation is found to have evolved from anastomosing venation and reversed to free venation in Bolbitis; and (7) biogeographical implications are drawn and it is shown that a single recent dispersal from Asia resulted in continental disjunction of closely related ferns of Bolbitis between Africa and America.

Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns

Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.

Plastome phylogenomic analysis reveals evolutionary divergences of Polypodiales suborder Dennstaedtiineae

BACKGROUND

Polypodiales suborder Dennstaedtiineae contain a single family Dennstaedtiaceae, eleven genera, and about 270 species, and include some groups that were previously placed in Dennstaedtiaceae, Hypolepidaceae, Monachosoraceae, and Pteridaceae. The classification and phylogenetic relationships among these eleven genera have been poorly understood. To explore the deep relationships within suborder Dennstaedtiineae and estimate the early diversification of this morphologically heterogeneous group, we analyzed complete plastomes of 57 samples representing all eleven genera of suborder Dennstaedtiineae using maximum likelihood and Bayesian inference.

RESULTS

The phylogenetic relationships of all the lineages in the bracken fern family Dennstaedtiaceae were well resolved with strong support values. All six genera of Hypolepidoideae were recovered as forming a monophyletic group with full support, and Pteridium was fully supported as sister to all the other genera in Hypolepidoideae. Dennstaedtioideae (Dennstaedtia s.l.) fell into four clades with full support: the Microlepia clade, the northern Dennstaedtia clade, the Dennstaedtia globulifera clade, and the Dennstaedtia s.s. clade. Monachosorum was strongly resolved as sister to all the remaining genera of suborder Dennstaedtiineae. Based on the well resolved relationships among genera, the divergence between Monachosorum and other groups of suborder Dennstaedtiineae was estimated to have occurred in the Early Cretaceous, and all extant genera (and clades) in Dennstaedtiineae, were inferred to have diversified since the Late Oligocene.

CONCLUSION

This study supports reinstating a previously published family Monachosoraceae as a segregate from Dennstaedtiaceae, based on unique morphological evidence, the shady habitat, and the deep evolutionary divergence from its closest relatives.

Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.

An open and continuously updated fern tree of life

Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree-species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.

Phylogenomic Analysis Reconstructed the Order Matoniales from Paleopolyploidy Veil

Phylogenetic conflicts limit our understanding of the evolution of terrestrial life under multiple whole genome duplication events, and the phylogeny of early terrestrial plants remains full of controversy. Although much incongruence has been solved with so-called robust topology based on single or lower copy genes, the evolutionary mechanisms behind phylogenetic conflicts such as polyploidization remain poorly understood. Here, through decreasing the effects of polyploidization and increasing the samples of species, which represent all four orders and eight families that comprise early leptosporangiate ferns, we have reconstructed a robust phylogenetic tree and network with 1125 1-to-1 orthologs based on both coalescent and concatenation methods. Our data consistently suggest that Matoniales, as a monophyletic lineage including Matoniaceae and Dipteridaceae, should be redefined as an ordinal rank. Furthermore, we have identified and located at least 11 whole-genome duplication events within the evolutionary history of four leptosporangiates lineages, and associated polyploidization with higher speciation rates and mass extinction events. We hypothesize that paleopolyploidization may have enabled leptosporangiate ferns to survive during mass extinction events at the end Permian period and then flourish throughout the Mesozoic era, which is supported by extensive fossil records. Our results highlight how ancient polyploidy can result in rapid species radiation, thus causing phylogenetic conflicts yet allowing plants to survive and thrive during mass extinction events.

Phylogeny, character evolution, and systematics of the fern family Ophioglossaceae based on Sanger sequence data, plastomes, and morphology

Adder's tongue ferns or Ophioglossaceae are best known among evolutionary biologists and botanists for their highest chromosome count of any known organisms, the presence of sporophores, and simple morphology. Previous studies recovered and strongly supported the monophyly of the family and the two multi-generic subfamilies, Botrychioideae and Ophioglossoideae, but the relationships among these and two other subfamilies (Helminthostachyoideae and Mankyuoideae) are not well resolved preventing us from understanding the character evolution. The monophyly of and the relationships in the species-rich genus, Ophioglossum, have not well been understood. In this study, new phylogenetic trees are reconstructed based on four datasets: Sanger sequences of eight plastid markers of 184 accessions, 22 plastomes (12 are new), 29 morphological characters, and combined Sanger and morphological data. Our major results include: (1) the relationships among the four subfamilies are well resolved and strongly supported in Bayesian and parsimony analyses based on plastomes: Mankyua is sister to the rest, followed by Ophioglossoideae which are sister to Helminthostachys + Botrychioideae; (2) Sanger data, plastomes, and combined Sanger and morphological data recovered and strongly supported the monophyly of Ophioglossum in its current circumscription (sensu lato; s.l.) in Bayesian and/or parsimony analyses; (3) within Ophioglossum s.l., four deeply diverged clades are identified and the relationships among the four clades are well resolved; (4) evolution of 34 morphological characters is analyzed in the context of the new phylogeny, among which shape of rhizomes, germination time of spores, shape of early gametophytes, and a number of other characters are found to contain interesting phylogenetic signal; and (5) based on the new phylogeny and character evolution, we propose a new classification of Ophioglossaceae in which the currently circumscribed Ophioglossum is divided into four genera including three new ones: Goswamia, Haukia, and Whittieria considering their molecular, morphological, ecological, and biogeographical distinctiveness.

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.

The Angiosperm Terrestrial Revolution and the origins of modern biodiversity

Biodiversity today has the unusual property that 85% of plant and animal species live on land rather than in the sea, and half of these live in tropical rainforests. An explosive boost to terrestrial diversity occurred from c. 100-50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth-life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species diversity of terrestrial environments. This boost in terrestrial biodiversity coincided with innovations in flowering plant biology and evolutionary ecology, including their flowers and efficiencies in reproduction; coevolution with animals, especially pollinators and herbivores; photosynthetic capacities; adaptability; and ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern biodiversity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.

Phylogeny, biogeography, and character evolution in the fern family Hypodematiaceae

The Old World fern genera Hypodematium and Leucostegia had long been placed in the families Dryopteridaceae and Davalliaceae, respectively, before the advent of molecular phylogenetics. Recent molecular studies confirmed the recognition of the family Hypodematiaceae composed of these two genera, but the relationships within each of these two genera have been unclear. In the present study we performed phylogenetic analyses (MP, ML, BI) based on DNA data from six plastid markers (atpB, atpB-rbcL, matK, rbcL, rps4 & rps4-trnS, and trnL & trnL-F) of 165 accessions representing 31 species in two genera of Hypodematiaceae as the ingroup and 26 accessions representing Cystopteridaceae, Didymochlaenaceae, Dryopteridaceae, Davalliaceae, Oleandraceae, and Woodsiaceae as the outgroups. Our analyses supported the monophyly of the currently defined Hypodematiaceae only including Hypodematium and Leucostegia and found that the family to be sister to the remaining eupolypods I. Our data resolved three taxa of Leucostegia into two clades. In Hypodematium, 28 taxa are resolved into seven strongly supported clades or single-accession clades. The evolution of important morphological characters are inferred in the phylogenetic context. Our dated phylogeny suggested a latest Jurassic-earliest Cretaceous origin of the family and Upper Cretaceous origin of two genera, with Hypodematiaceae originated from East Asia; extant lineages of Hypodematium originated from East Asia and subsequently into Africa, the Indian region, the Madagascar region, and Southeast Asia; and Leucostegia originated from East Asia and/or Southeast Asia.