Nathalie Nagalingum

California Academy of Sciences

Premise: New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, f...

Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or “tip-dating”) approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data, and 2) the fossilized birth-death (FBD) c...

Full genome sequencing of organisms with large and complex genomes is intractable and cost ineffective under most research budgets. Cycads (Cycadales) represent one of the oldest lineages of the extant seed plants and, partly due to their age, have incredibly large genomes up to ~60Gbp. Restriction site associated DNA sequencing (RADseq) offers an...

The gymnosperm genus Cycas is the sole member of Cycadaceae, and is the largest genus of extant cycads. There are about 115 accepted Cycas species mainly distributed in the paleotropics. Based on morphology, the genus has been divided into six sections and eight subsections, but this taxonomy has not yet been tested in a molecular phylogenetic fram...

The lastreopsid ferns are a group of mostly terrestrial ferns within the Dryopteridaceae, found in parts of Africa, Madagascar, the Neotropics, southern Asia, Australasia, and some Pacific Islands. Within this group is the paraphyletic genus Lastreopsis s. l., which has been segregated into Lastreopsis s. s. and Parapolystichum. However, there rema...

Taxonomic descriptions contain valuable phenotypic data that is often not directly accessible for modern evolutionary, ecological, or biodiversity analyses. We describe a process for building a consensus-based controlled vocabulary from taxonomic descriptions for plants, which also can be applied for building controlled vocabularies for other taxon...

Xylem vulnerability to embolism is emerging as a major factor in drought-induced tree mortality events across the globe. However, we lack understanding of how and to what extent climate has shaped vascular properties or functions. We investigated the evolution of xylem hydraulic function and diversification patterns in Australia's most successful g...

Ferns, lycophytes, mosses, liverworts, and hornworts (the latter three are collectively termed bryophytes) reproduce via spores. The fossil record of spore-bearing plants is extensive, beginning with the cryptophytes that were the first plants to invade the land. Today, there are about 25 000 spore-bearing plant species that have a complex, dynamic...

Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community-based a...

The Albian Alexander Island macrofossil flora from the Antarctic Peninsula preserves a diverse community of liverworts (Marchantiophyta), ferns (Polypodiopsida), Lycopodiales, Equisetales, Cycadales, Ginkgoales, seed-ferns (Bennettitales and Pentoxylales), Coniferales, and the first representatives of angiospermous leaves in Antarctica. Despite the...

Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of plant evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic est...

Because ferns have a wide range of habitat preferences and are widely distributed, they are an ideal group for understanding how diversity is distributed. Here we examine fern diversity on a broad-scale using standard and corrected richness measures as well as phylogenetic indices; in addition we determine the environmental predictors of each diver...

Bryophytes are significant contributors to floristic diversity, but they are often neglected in field surveys and collections. Thus, in order to obtain more accurate estimates of plant richness, there must be reliable estimates of bryophyte diversity. To address this, we examined whether another plant group, namely the ferns, could be used as a sur...

The largest digitized dataset of land plant distributions in Australia assembled to date (750,741 georeferenced herbarium records; 6,043 species) was used to partition the Australian continent into phytogeographical regions. We used a set of six widely distributed vascular plant groups and three non-vascular plant groups which together occur in a v...

Ferns of the genus Marsilea (water clover) are potentially invasive aquatic and wetland plants. They are difficult to identify to species because of subtle diagnostic characters, the sterile condition of many specimens, and unresolved taxonomic problems. We sequenced four plastid regions (rbcL, rps4, rps4-trnS spacer, and trnL-F spacer) from 223 ac...

Modern survivors of previously more diverse lineages are regarded as living fossils, particularly when characterized by morphological stasis. Cycads are often cited as a classic example, reaching their greatest diversity during the Jurassic-Cretaceous (199.6 to 65.5 million years ago) then dwindling to their present diversity of ~300 species as flo...

Dated molecular phylogenies are the basis for understanding species diversity and for linking changes in rates of diversification with historical events such as restructuring in developmental pathways, genome doubling, or dispersal onto a new continent. Valid fossil calibration points are essential to the accurate estimation of divergence dates, bu...

Heterosporous ferns (Salviniales) are a group of approximately 70 species that produce two types of spores (megaspores and microspores). Earlier broad-scale phylogenetic studies on the order typically focused on one or, at most, two species per genus. In contrast, our study samples numerous species for each genus, wherever possible, accounting for...

Three new taxa from Albian, Early Cretaceous assemblages in Gondwana (Australia and Antarctica) and two previously described fossils from the Late Cretaceous and Eocene of North America are attributable to the heterosporous semi-aquatic fern family Marsileaceae. They are assigned to Marsileaceaephyllum, a morphotaxon erected here for sterile remain...

Using six plastid regions, we present a phylogeny for 26 species of the heterosporous fern genus Marsilea. Two well-supported groups within Marsilea are identified. Group I includes two subgroups, and is relatively species-poor. Species assignable to this group have glabrous leaves (although land leaves may have a few hairs), sporocarps lacking bot...

and yAlbrecht-von-Haller Institut fü r Pflanzenwissenschaften, Abteilung Systematische Botanik, Georg-August-Universität, Untere Karspü le 2, 37073 Gö ttingen, Germany Heterosporous water ferns (Marsileaceae and Salviniaceae) are the only extant group of plants to have evolved heterospory since the Paleozoic. These ferns possess unusual reproductiv...

The first Cretaceous representatives of Matoniaceae and Gleicheniaceae in the Antarctic are described from the Albian flora of Alexander Island. Two new species are recognized, one is assigned to Matonia, and another to the emended gleicheniaceous form-genus Gleicheniaceaephyllum. The taxonomy of fossil genera assigned to Gleicheniaceae is problema...

Six new records of ferns from the late Albian flora of Alexander Island, Antarctic Peninsula, provide further evidence for a widespread Cretaceous Austral flora. Phyllopteroides antarctica sp. nov. is the first record of this genus from Antarctica, extending its range from Australia, New Zealand, and India. It appears that Phyllopteroides forms an...

A new species of fossil conifer foliage, Bellarinea richardsii, is described and illustrated from Neocomian (Early Cretaceous) sediments of the Tyers River Subgroup in south-eastern Victoria. The specimens consist of intact seasonal shoots and isolated leaves, and their depositional setting in prominent leaf mats suggests a seasonal, deciduous habi...

Fossil assemblages are described from the Tyers River Subgroup (late Berriasian to Hauterivian), Gippsland Basin, Victoria. The assemblages include plant macrofossils referable to 33 form-species including five new species (Isoetites abundans Tosolini & McLoughlin, Coniopteris victoriensis Nagalingum & McLoughlin, Otozamites douglasii Drinnan, Brac...

Changes in the Cretaceous fern flora of Australia were analysed by compiling data from the palynological literature. A decline in the relative diversity and abundance of free-sporing plants during the Late Cretaceous was concurrent with a rise in angiosperms, while the relative contribution of gymnosperms was unchanged. Ferns and lycophytes were th...