Germinal Rouhan

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.

Spore Morphology in Relation to Phylogeny in the Fern Genus Elaphoglossum (Dryopteridaceae)

The perispore structure of Elaphoglossum was studied using a scanning electron microscope. Of the species examined, 119 corresponded to those used in a previously published phylogenetic analysis of the genus based on two chloroplast noncoding DNA regions, trnL‐trnF and rps4‐trnS. The spores of 102 additional species were examined for comparative purposes. Five perispore characters were scored for each species and optimized onto the previously published molecular tree. The morphology of the perispore and its character state changes are described and discussed in a phylogenetic context. Synapomorphies for major clades within the genus were identified, such as spines for the Neotropical species of sect. Squamipedia and perforations, spines, and cristae for subsect. Pachyglossa and a large subclade within sect. Setosa. This study is the largest done on perispore morphology in relation to phylogeny in a genus of ferns. Spore images of all species studied are available at http://www.plantsystematics.org.

AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae)

PREMISE OF THE STUDY Despite its small size, New Caledonia is characterized by a very diverse flora and striking environmental gradients, which make it an ideal setting to study species diversification. Thirteen of the 19 Araucaria species are endemic to the territory and form a monophyletic group, but patterns and processes that lead to such a high species richness are largely unexplored. METHODS We used 142 polymorphic AFLP markers and performed analyses based on Bayesian clustering algorithms, genetic distances, and cladistics on 71 samples representing all New Caledonian Araucaria species. We examined correlations between the inferred evolutionary relationships and shared morphological, ecological, or geographic parameters among species, to investigate evolutionary processes that may have driven speciation. KEY RESULTS We showed that genetic divergence among the present New Caledonian Araucaria species is low, suggesting recent diversification rather than pre-existence on Gondwana. We identified three genetic groups that included small-leaved, large-leaved, and coastal species, but detected no association with soil preference, ecological habitat, or rainfall. The observed patterns suggested that speciation events resulted from both differential adaptation and vicariance. Last, we hypothesize that speciation is ongoing and/or there are cryptic species in some genetically (sometimes also morphologically) divergent populations. CONCLUSIONS Further data are required to provide better resolution and understanding of the diversification of New Caledonian Araucaria species. Nevertheless, our study allowed insights into their evolutionary relationships and provides a framework for future investigations on the evolution of this emblematic group of plants in one of the worlds biodiversity hotspots.

Global phylogeny and biogeography of grammitid ferns (Polypodiaceae).

We examined the global historical biogeography of grammitid ferns (Polypodiaceae) within a phylogenetic context. We inferred phylogenetic relationships of 190 species representing 31 of the 33 currently recognized genera of grammitid ferns by analyzing DNA sequence variation of five plastid DNA regions. We estimated the ages of cladogenetic events on an inferred phylogeny using secondary fossil calibration points. Historical biogeographical patterns were inferred via ancestral area reconstruction. Our results supported four large-scale phylogenetic and biogeographic patterns: (1) a monophyletic grammitid clade that arose among Neotropical polypod ancestors about 31.4 Ma; (2) a paraphyletic assemblage of clades distributed in the Neotropics and the Afro-Malagasy region; (3) a large clade distributed throughout the Asia-Malesia-Pacific region that originated about 23.4 Ma; and, (4) an Australian or New Zealand origin of the circumaustral genus Notogrammitis. Most genera were supported as monophyletic except for Grammitis, Oreogrammitis, Radiogrammitis, and Zygophlebia. Grammitid ferns are a well-supported monophyletic group with two biogeographically distinct lineages: a primarily Neotropical grade exhibiting several independent successful colonizations to the Afro-Malagasy region and a primarily Paleotropical clade exhibiting multiple independent dispersals to remote Pacific islands and temperate, austral regions.

Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae)

UNLABELLED PREMISE OF THE STUDY The recognition of monophyletic genera for groups that have high levels of homoplastic morphological characters and/or conflicting results obtained by different studies can be difficult. Such is the case in the grammitid ferns, a clade within the Polypodiaceae. In this study, we aim to resolve relationships among four clades of grammitid ferns, which have been previously recovered either as a polytomy or with conflicting topologies, with the goal of circumscribing monophyletic genera. • METHODS The sampling included 89 specimens representing 61 species, and sequences were obtained for two genes (atpB and rbcL) and four intergenic spacers (atpB-rbcL, rps4-trnS, trnG-trnR, and trnL-trnF), resulting in a matrix of 5091 characters. The combined data set was analyzed using parsimony, likelihood, and Bayesian methods. Ninety-six morphological characters were optimized onto the generated trees, using the parsimony method. • KEY RESULTS Lellingeria is composed of two main clades, the L. myosuroides and the Lellingeria s.s. clades, which together are sister to Melpomene. Sister to all three of these is a clade with two species of the polyphyletic genus Terpsichore. In the L. myosuroides clade, several dispersal events occurred between the neotropics, Africa, and the Pacific Islands, whereas Lellingeria s.s. is restricted to the neotropics, with about 60% of its diversity in the Andes. • CONCLUSIONS Overall, our results suggest that Lellingeria is monophyletic, with two clades that are easily characterized morphologically and biogeographically. Morphological characters describing the indument are the most important to define the clades within the ingroup. A small clade, previously considered in Terpsichore, should be recognized as a new genus.

Identifying a mysterious aquatic fern gametophyte

Süßwassertang, a popular aquatic plant that is sold worldwide in aquarium markets, has been long considered a liverwort because of its ribbon-like thallus. However, its antheridia are remarkably fern-like in morphology. To corroborate the hypothesis that Süßwassertang is a fern gametophyte and to determine its closest relative, we have sequenced five chloroplast regions (rbcL, accD, rps4–trnS, trnL intron, and trnL-F intergenic spacer), applying a DNA-based identification approach. The BLAST results on all regions revealed that Süßwassertang is a polypod fern (order: Polypodiales) with strong affinities to the Lomariopsidaceae. Our phylogenetic analyses further showed that Süßwassertang is nested within the hemi-epiphytic fern genus Lomariopsis (Lomariopsidaceae) and aligned very close to L. lineata. Our study brings new insights on the unexpected biology of Lomariopsis gametophytes—the capacity of retaining a prolonged gametophytic stage under water. It is of great interest to discover that a fern usually known to grow on trees also has gametophytes that thrive in water.

Preliminary phylogenetic analysis of the fern genus Lomariopsis (Lomariopsidaceae)

A preliminary phylogenetic analysis is presented forLomariopsis based on sequence data from the chloroplast intergenic spacertrnL-trnF. The analysis includes 27 (60%) of the approximately 45 species in the genus. A strict consensus of six most parsimonious trees supports two main clades—theSorbifolia-group and theJapurensis-group—previously proposed based on heteroblastic leaf development. TheSorbifolia-group is entirely neotropical and includes all the Antillean species. The species in this clade had either smooth or crested spores, but the tree was ambiguous whether these spore types define two separate clades. TheJapurensis-group consists of two clades, one primarily neotropical and the other entirely paleotropical. Within the neotropical clade nests a clade of two African species, which have long-spiny spores typical of the neotropical clade and unlike those found in the African-Madagascan clade. The occurrence of these two species in Africa is best explained by longdistance spore dispersal of their ancestral species from the neotropics to Africa. Within the paleotropical clade of theJapurensis-group, a clade of three African species is nested among seven species from Madagascar (all the species from that island). Within the genus as a whole, a derived character—the abortion of the rachis apex and its replacement by the distal lateral pinna assuming a terminal position—was found to have evolved separately in each of the four species with this kind of leaf apex. A scanning electron microcope study of the spores revealed five types, and a transformation series for these different types is proposed. Characters of spore morphology and heteroblastic leaf development agreed with many of the clades in the phylogenetic tree. This study represents the first phylogeny for the genus.ResumenSe presenta un análisis filogenético preliminar paraLomariopsis basado en datos de secuencias del espaciador intergenético del cloroplastotrnL-trnF. El análisis incluye 27 (60%) de las aproximadamente 45 especies del género. Un consenso estricto de seis árboles más parsimoniosos soporta dos clados principales—el grupoSorbifolia y el grupoJapurensis—previamente propuestos en análisis basados en el desarrollo heteroblástico de las hojas. El grupoSorbifolia es completamente neotropical e incluye todas las especies de las Antillas. Las especies de este clado presentan esporas lisas o crestadas, sin embargo el árbol fue ambiguo con respecto a si este tipo de esporas define dos clados separados. El grupoJapurensis está compuesto por dos clados, uno principalmente neotropical y otro completamente paleotropical. Dentro del clado neotropical se encuentra anidado un clado de dos especies Africanas, que poseen un tipo de esporas con espinas largas que es típico del clado neotropical y diferente al encontrado en el clado compuesto por especies Africanas y de Madagascar. La mejor explicación para la presencia de estas dos especies en Africa es dispersión a largas distancias de esporas de sus especies ancestrales desde el neotrópico hacia África. Dentro del clado paleotropical del grupoJapurensis, un clado de tres especies africanas se encuentra anidado entre siete especies de Madagascar (la totalidad de las especies de esta isla). Para el género completo un carácter derivado, el aborto del ápice del raquis y su reemplazo por la pinna lateral distal asumiendo una posición terminal, se encontró que ha evolucionado por separado en cada una de las cuatro especies con esta clase de ápice de la hoja. Un estudio de microscopio electrónico de barrido de las esporas reveló cinco tipos, se propone una serie de transición para estos diferentes tipos. Los caracteres de la morfología de la espora y del desarrollo heteroblástico de la hoja proporcionaron soporte adicional para muchos de los clados en el árbol filogenético. Este estudio representa la primera filogenia del género.

Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)

BACKGROUND AND AIMS Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented. METHODS A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications. KEY RESULTS The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions. CONCLUSIONS This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris.

The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept

Adaptive radiation is one of the most emblematic concepts in evolutionary biology. However, the current lack of a consensual definition and the diversity of methods used to assess the extent and speed of adaptive radiation indicate the need for a reappraisal of this research field. In order to depict how adaptive radiations have been studied in recent years, we performed a scientometric assessment of 765 articles published between 2003 and 2012 in five journals known to serve a broad audience. From each study, we extracted and analyzed data relative to the taxon and geographical area investigated and to the methodological setup, and we categorized its outcomes and conclusions. This scientometry-oriented work allowed us to identify and discuss trends relative to the way research about adaptive radiations was carried out during the 10-year period starting in 2003. We then provided some recommendations for how to conduct a reliable study of a suspected adaptive radiation. The associated database resulting from our study will be a valuable source of information for biologists as they design a study or put their results in perspective. Our work may also inspire a critical assessment of the relevance of this pivotal concept in evolutionary biology.

New combinations in Lastreopsis and Parapolystichum (Dryopteridaceae)

Recent molecular phylogenetic studies have shown that Lastreopsis is paraphyletic. Twenty-seven of its species belong to a separate clade for which the previously published generic name Parapolystichum is available. Parapolystichum is widely distributed, with four species in the Neotropics, six in Africa, nine in Madagascar, and eight in Australia and New Zealand. We make the following 25 new combinations in Parapolystichum:P. acuminatum, P. acutum, P. barterianum, P. boivinii, P. confine, P. coriaceosquamatum, P. currorii subsp. currorii, P. currorii subsp. eglandulosum, P. excultum, P. fideleae, P. glabellum, P. hornei, P. manongarivense, P. microsorum ssp. microsorum, P. microsorum ssp. pentangulare, P. munitum, P. nigritianum, P. perrierianum, P. pseudoperrierianum, P. rufescens, P. smithianum, P. subsimile, P. tinarooense, P. vogelii, and P. windsorense. Also, we designate a lectotype for Dryopteris exculta var. squamifera (=Parapolystichum excultum). No known morphological characters distinguish Parapolystichum from Lastreopsis s.s. Certain species of Parapolystichum, however, bear buds distally along the rachis, whereas Lastreopsis lacks such buds. Because no morphological character, or suite of characters, consistently separates the two genera, nine species of Lastreopsis s.l., which were not included in the previous phylogenetic analyses, could not be classified in either Lastreopsis or Parapolystichum. New combinations are also made for L. dissecta, L. tripinnata and L. poecilophlebia, species previously classified in Oenotrichia and Coveniella. Because Coveniella was considered monotypic, it is here reduced to a synonym of Lastreopsis. As re-circumscribed here, Lastreopsis now consists of about 16 species, all restricted to southeastern Asia and Oceania.