Samuli Lehtonen

A community-derived classification for extant lycophytes and ferns

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 approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.

Towards resolving the complete fern tree of life.

In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a ‘supermatrix’ approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.

Cladistic analysis of Echinodorus (Alismataceae): simultaneous analysis of molecular and morphological data

Echinodorus is the second largest genus in the aquatic plant family Alismataceae. The genus is naturally distributed in the New World, but many species are known world‐wide as popular aquarium plants. The views upon species delimitation and infrageneric classification of the genus have been controversial. Phenotypic plasticity of aquatic plants combined with reduced and presumably convergent morphological structures pose serious problems to classification, emphasizing the need for molecular‐level data. A simultaneous cladistic analysis of molecular and morphological data was conducted to resolve the phylogeny of the genus. The results showed Echinodorus (as it is currently circumscribed) to be polyphyletic. None of the currently proposed infrageneric classifications of the genus were supported in the light of phylogenetic evidence. Also, many species and subspecies level rankings were found to be unnatural. Monophyly of Echinodorus is ascertained by separating Helanthium and the monotypic genus Albidella from Echinodorus. As a result, two new combinations (Helanthium bolivianum and H. zombiense) are made, and a detailed description of the genus Helanthium is provided.

Global patterns and drivers of phylogenetic structure in island floras

Islands are ideal for investigating processes that shape species assemblages because they are isolated and have discrete boundaries. Quantifying phylogenetic assemblage structure allows inferences about these processes, in particular dispersal, environmental filtering and in-situ speciation. Here, we link phylogenetic assemblage structure to island characteristics across 393 islands worldwide and 37,041 vascular plant species (representing angiosperms overall, palms and ferns). Physical and bioclimatic factors, especially those impeding colonization and promoting speciation, explained more variation in phylogenetic structure of angiosperms overall (49%) and palms (52%) than of ferns (18%). The relationships showed different or contrasting trends among these major plant groups, consistent with their dispersal- and speciation-related traits and climatic adaptations. Phylogenetic diversity was negatively related to isolation for palms, but unexpectedly it was positively related to isolation for angiosperms overall. This indicates strong dispersal filtering for the predominantly large-seeded, animal-dispersed palm family whereas colonization from biogeographically distinct source pools on remote islands likely drives the phylogenetic structure of angiosperm floras. We show that signatures of dispersal limitation, environmental filtering and in-situ speciation differ markedly among taxonomic groups on islands, which sheds light on the origin of insular plant diversity.

An integrative approach to species delimitation in Echinodorus (Alismataceae) and the description of two new species

SummaryTaxonomy of the genus Echinodorus is partially revisited in the light of current understanding of the phylogenetic relationships of the genus. As a result of new taxonomy, the species status of some previously synonymised taxa are restored, other names are synonymised, and some nomenclatural problems unnoticed by previous authors are resolved. Two new species, Echinodorus reptilis and E. emersus are described. The subgeneric divisions of the genus are not accepted, and all subspecific taxa are either rejected or established as species. As a result, 28 species based on a phylogenetic species concept are now recognised in Echinodorus and an identification key to these species is provided.

Historical herbarium specimens in plant molecular systematics — an example from the fern genus Lindsaea (Lindsaeaceae)

We extracted, amplified and sequenced DNA from historical herbarium specimens and silica-dried samples of the fern genus Lindsaea in order to study the sequencing success between the two kinds of samples. High quality sequences were obtained from 57% of the herbarium samples. The specimens age was found to be of little importance for sequencing success when less than 75 years, but the colour of a specimen was found more indicative of sequencing success. Shorter DNA fragments were sequenced successfully twice as often as longer fragments from the herbarium material; in relatively recently collected silica-dried material longer sequences were obtained almost as frequently as short ones. No obvious differences in sequencing success between material originating from different herbaria was observed. We conclude that by using specifically designed DNA extraction protocols and by sequencing short DNA fragments from carefully selected specimens, herbarium material and type specimens can be successfully used in molecular systematics. Typical material or specimens from the type locality (topotypes) should be preferred, when placing a species in a phylogeny.

Phylogenetic Placement of the Enigmatic Fern Genus Dracoglossum

Abstract The phylogenetic position of Dracoglossum Christenh. is studied here for the first time using DNA sequence data. Based on a broad sampling of eupolypod ferns and four plastid genes (atpA, atpB, rbcL, rps4), we show that Dracoglossum does not belong to the genus Tectaria Cav., in which it was previously placed, nor is it closely related to that genus or any other member of Tectariaceae. Our results provide strong support to suggest that Dracoglossum forms a rather isolated lineage, which is sister to Lomariopsis Fée, and that the genus should therefore be placed in Lomariopsidaceae.

Environmentally driven extinction and opportunistic origination explain fern diversification patterns.

Combining palaeontological and neontological data offers a unique opportunity to investigate the relative roles of biotic and abiotic controls of species diversification, and the importance of origination versus extinction in driving evolutionary dynamics. Ferns comprise a major terrestrial plant radiation with an extensive evolutionary history providing a wealth of modern and fossil data for modelling environmental drivers of diversification. Here we develop a novel Bayesian model to simultaneously estimate correlations between diversification dynamics and multiple environmental trajectories. We estimate the impact of different factors on fern diversification over the past 400 million years by analysing a comprehensive dataset of fossil occurrences and complement these findings by analysing a large molecular phylogeny. We show that origination and extinction rates are governed by fundamentally different processes: originations depend on within-group diversity but are largely unaffected by environmental changes, whereas extinctions are strongly affected by external factors such as climate and geology. Our results indicate that the prime driver of fern diversity dynamics is environmentally driven extinction, with origination being an opportunistic response to diminishing ecospace occupancy.

Newly discovered diversity in the tropical fern genus Metaxya based on morphology and molecular phylogenetic analyses

SummaryFor a long time, the genus Metaxya was treated as monotypic with a single species, M. rostrata. A second species, M. lanosa, was described in 2001 on the basis of morphological features and rbcL gene sequences with a suggestion that the genus may contain even more species. We have now systematically compared morphological traits in a large number of Metaxya specimens collected in tropical America. We have also carried out phylogenetic analyses of 32 Metaxya and 5 outgroup specimens based on four markers of the plastid genome (rbcL, matK, and rps4 genes, and trnG-trnR intergenic spacer). Based on the morphological variation among the Metaxya specimens, we accept six distinct species, three of which we describe as new in this paper. Molecular phylogenetic analyses resolved five distinct clades. Four of these corresponded with the morphologically delineated species (M. contamanensis sp. nov., M. elongata sp. nov., M. lanosa, and M. parkeri). The fifth clade contained all the individuals of the remaining two species, of which M. rostrata was rendered paraphyletic by M. scalaris sp. nov. being nested within it. Since M. scalaris was resolved as monophyletic, and the two are clearly distinguishable morphologically, we consider them true species despite the incomplete genetic differentiation.

Can sensitivity analysis help to detect long-branch attraction?

The behavior of nodal support and stability in the presence of long branches were examined under simulations and an analysis of real data. Relatively short branches were typically correctly resolved, received high bootstrap support, and were stable in sensitivity analyses. Longer branches received lower support and stability measures, and were often incorrectly resolved due to the long-branch attraction. Support and stability does not always correlate, and in the case of mammalian mitochondrial tree, well supported but unstable nodes were typically associated with long-branch attraction. Very long branches, on the other hand, may be incorrectly resolved with high support and stability indices. These patterns were observed both in simulations, and in the real data. The results indicate that sensitivity analysis may help to reveal phylogenetic uncertainty hidden behind artificially high support.