Devonian origin and Cenozoic radiation in the clubmosses (Lycopodiaceae)

Together with the heterosporous lycophytes, the clubmoss family (Lycopodiaceae) is the sister lineage to all other vascular land plants. Given the family’s important position in the land-plant phylogeny, studying the evolutionary history of this group is an important step towards a better understanding of plant evolution. Despite this, little is known about the Lycopodiaceae, and a well-sampled, robust phylogeny of the group is lacking. The goal of this dissertation is to resolve the relationships among evolutionary lineages in the Lycopodiaceae and provide insight into the timing and drivers of diversification in the family. First, to place the evolution of the family within a global and historical context, I generated a densely sampled, time-calibrated phylogeny of the family. I sampled 50% of the estimated 400 extant species in the Lycopodiaceae and used eight fossils to calibrate the age of major divergence events in the family and across the land-plant phylogeny. Further, we used a probabilistic biogeographic model to infer the historical biogeography of the family. Together, these analyses indicate that the Lycopodiaceae originated in the late Devonian, began its early diversification in the Carboniferous, and accumulated much of its extant diversity during the Cenozoic. From a geographical perspective, major cladogenesis events in the family’s history appear to be linked to the breakup of the Pangaean and Gondwanan supercontinents, with long-distance dispersal playing a role in the establishment of younger evolutionary lineages. Second, I examined the drivers of diversification in the species-rich genus Phlegmariurus in the Neotropics. This clade includes an estimated 150 species and is most diverse in high-elevation habitats in the tropical Andes of South America. Using a time-calibrated phylogeny of the group and species distribution and niche data, I demonstrate a strong positive association between lineage diversification rates and the mean elevation of species’ distributions as well as a strong negative correlation between diversification rates and the size of species’ ranges. Further, we employ a paleoelevation-dependent diversification model to test for an association between the uplift of the Andes and diversification in the clade and demonstrate that speciation rates in Neotropical Phlegmariurus are positively associated with increasing elevations in the Andes. Third, I use a phylogenetic framework to test the monophyly of morphology-based species groups in Neotropical Phlegmariurus. I demonstrate that most groups are not monophyletic, and that convergent evolution is widespread in the genus. We use ancestral character-state reconstruction methods for six morphological traits to elucidate patterns of trait evolution and to circumscribe new species groups. A total of eleven new monophyletic species groups are proposed and defined

The relationship between chlorophyllous spores and mycorrhizal associations in ferns: evidence from an evolutionary approach

Premise: Approximately 14% of all fern species have physiologically active chlorophyllous spores that are much more short-lived than the more common and dormant achlorophyllous spores. Most chlorophyllous-spored species (70%) are epiphytes and account for almost 37% of all epiphytic ferns. Chlorophyllous-spored ferns are also overrepresented among fern species in habitats with waterlogged soils, of which nearly 60% have chlorophyllous spores. Ferns in these disparate habitat types also have a low incidence of mycorrhizal associations. We therefore hypothesized that autotrophic chlorophyllous spores represent an adaptation of ferns to habitats with scarce mycorrhizal associations. Methods: We evaluated the coevolution of chlorophyllous spores and mycorrhizal associations in ferns and their relation to habitat type using phylogenetic comparative methods. Results: Although we did not find support for the coevolution of spore type and mycorrhizal associations, we did find that chlorophyllous spores and the absence of mycorrhizal associations have coevolved with epiphytic and waterlogged habitats. Transition rates to epiphytic and waterlogged habitats were significantly higher in species with chlorophyllous spores compared to achlorophyllous lineages. Conclusions: Spore type and mycorrhizal associations appear to play important roles in the radiation of ferns into different habitat types. Future work should focus on clarifying the functional significance of these associations. Keywords: arbuscular mycorrhizae; chlorophyllous spores; correlated evolution; dark septate endophytes; epiphytes; grammitid; green spores; pteridophyte

Target Sequence Capture of Nuclear-Encoded Genes for Phylogenetic Analysis in Ferns

Premise of the Study Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one documented case. However, it not yet clear what effect such hybridization has on fern evolution, in part due to a paucity of available biparentally inherited (nuclear‐encoded) markers. Methods We designed oligonucleotide baits to capture 25 targeted, low‐copy nuclear markers from a sample of 24 species spanning extant fern diversity. Results Most loci were successfully sequenced from most accessions. Although the baits were designed from exon (transcript) data, we successfully captured intron sequences that should be useful for more focused phylogenetic studies. We present phylogenetic analyses of the new target sequence capture data and integrate these into a previous transcript‐based data set. Discussion We make our bait sequences available to the community as a resource for further studies of fern phylogeny

Madagascar’s extraordinary biodiversity: Threats and opportunities

Madagascar's unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar's terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as themost prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique living laboratory for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity

Goniopteris ×tico (Thelypteridaceae), a new hybrid fern from Costa Rica

<p><em>Goniopteris</em> ×<em>tico</em>, a new hybrid fern from La Selva Biological Station in Heredia Province, Costa Rica, is described based on morphology and analysis of target-capture DNA sequence data. The hybrid co-occurs with its two putative progenitors, <em>Goniopteris</em> <em>mollis</em> and <em>Goniopteris</em> <em>nicaraguensis</em>, and is readily recognizable by its intermediate leaf dissection and venation. It is also intermediate in pinnae size and shape and presents irregularly lobed pinnae. Despite the broad overlap in the geographic distribution of its parental taxa, <em>Goniopteris</em> ×<em>tico</em> is only known from two collections from a single area of the La Selva Biological Station, highlighting the importance of close observation of ferns from even well-collected areas.</p><p>Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/021nxhr62<br>Award Number: DEB-2045319</p&gt

Gametophyte Ecology of the American Hart’s-Tongue Fern: Effects of Temperature and Calcium Availability

This study investigated the gametophyte ecology and physiology of the American hart’s-tongue fern, Phyllitis scolopendrium var. americana. A federally-listed threatened species, the fern is native to eastern North America and found only in lime sinks and glacial plunge ravines with calcium-rich substrates. Greater than ninety percent of the approximately 4000 plants remaining in the United States are found in two counties in central New York, where populations have declined dramatically in recent years. The goal of this work was to generate an improved understanding of potential reasons for the species’ decline through study of its ecology. Gametophytes were grown at 20°C and 25°C and in low-(2.5g/L), medium-(5g/L), and high-(7.5g/L) calcium treatments. Spore germination was of the Vittaria-type, and prothallial plate formation was of the Aspidium-type. Germination rates were similar in all treatments, but growth was significantly slowed in the 25°C, with gametophytes remaining in the protonemal stage of development indefinitely. Calcium affected sexual development, with gametophytes grown in the high-calcium treatments developing gametangia earlier and having higher sporophyte recruitment rates (13.9%) than those grown in medium-(2.3%) or lowcalcium (0.3%) treatments. These findings suggest that P. scolopendrium is particularly susceptible to the effects of climate change and habitat disturbance, and may be outcompeted by other species on account of its slow growth, limited reproductive potential, and extreme habitat specificity

Overcoming among-lineage rate heterogeneity to infer the divergence times and biogeography of the clubmoss family Lycopodiaceae

Aim: To infer divergence times and historical biogeography of the cosmopolitan lycophyte family Lycopodiaceae. Location: Worldwide. Methods: We generated time‐calibrated phylogenies of the Lycopodiaceae based on six regions of chloroplast DNA using a node‐dating approach implemented in beast with eight fossil calibrations. To investigate effects of among‐lineage substitution rate heterogeneity on divergence time estimation, we compared the performance of two relaxed clock models: an uncorrelated lognormal clock model and a random local clock (RLC) model. The historical biogeography of the family was inferred using two Bayesian models implemented in BioGeoBEARS. Results: Divergence time estimates for major groups of the Lycopodiaceae obtained using the two substitution clock models differed substantially, and the RLC model was a better fit. The Lycopodiaceae crown group age is estimated to be late Devonian, and most deep divergence events date to the Carboniferous, with most extant species diversity accumulating during the Cenozoic. The timing of divergences of major clades in the Lycopodiaceae corresponds to the breakup of the Pangaean and Gondwanan supercontinents. Long‐distance dispersal events are relatively common, but generally do not appear to be followed by subsequent radiations. Main conclusions: Accounting for among‐lineage substitution rate heterogeneity improves divergence time estimates for the Lycopodiaceae. The family has a deep evolutionary history, and continent‐scale vicariance events in the Mesozoic appear to have been associated with major cladogenesis events, with long‐distance dispersal playing a relatively minor role

Data from: On the widespread capacity for and functional significance of extreme inbreeding in ferns

Homosporous vascular plants utilize three different mating systems, one of which, gametophytic selfing, is an extreme form of inbreeding only possible in homosporous groups. This mating system results in complete homozygosity in all progeny and has important evolutionary and ecological implications. Ferns are the largest group of homosporous land plants, and the significance of extreme inbreeding for fern evolution has been the subject of debate for decades. We cultured gametophytes in the laboratory and quantified the relative frequencies of sporophyte production from isolated and paired gametophytes, and examined associations between breeding systems and several ecological and evolutionary traits. The majority of fern species studied show a capacity for gametophytic selfing, producing sporophytes from both isolated and paired gametophytes. While we did not follow sporophytes to maturity to investigate potential detrimental effects of homozygosity at later developmental stages, our results suggest that gametophytic selfing may have greater significance for fern evolution and diversification than has previously been realized. We present evidence from the largest study of mating behavior in ferns to date that capacity for extreme inbreeding is prevalent in this lineage, and we discuss its implications and relevance and make recommendations for future studies of fern mating systems