Jean-Yves Dubuisson

A TAXONOMIC REVISION OF HYMENOPHYLLACEAE

SUMMARY A new classification of Hymenophyllaceae, consisting of nine genera (Hymenophyllum, Didymoglossum, Crepidomanes, Polyphlebium, Vandenboschia, Abrodictyum, Trichomanes, Cephalomanes and Callistopteris) is proposed. Every genus, subgenus and section chiefly corresponds to the mono phyletic group elucidated in molecular phylogenetic analyses based on chloroplast sequences. Brief descriptions and keys to the higher taxa are given, and their representative members are enumerated, including some new combinations.

Molecular systematics of the fern genus Hymenophyllum s.l. (Hymenophyllaceae) based on chloroplastic coding and noncoding regions.

We investigated the phylogenetic relationships of the filmy fern genus Hymenophyllum s.l. using the rbcL and rps4 genes and the intergenic spacer rps4-trnS. Because of variation in length of the noncoding marker, we tested and compared three methods for integrating indels. They proved to be useful for estimating a phylogeny of the genus. The rps4-trnS marker, with coded indels integrated, produced better resolution than analysis of either rps4 or rbcL, and combining the three data sets allowed us to obtain a well resolved and strongly supported topology. We interpret our data as showing support for the classical bigeneric system for the family, and call into question several classifications proposed in the past century. The segregate genera Cardiomanes, Hymenoglossum, Serpyllopsis, and Rosenstockia are embedded within Hymenophyllum s.l. Although the deepest relationships within the genus remain uncertain, two subgenera described by Morton do have some support: (1) Sphaerocionium, in which the problematic section Microtrichomanes is embedded; and (2) a diverse Hymenophyllum, including species that were placed originally in Serpyllopsis, Rosenstockia, Hemicyatheon, and Craspedophyllum by Copeland. Subgenus Mecodium appears to be polyphyletic; nevertheless, a subgroup within Mecodium is strongly supported. Several unexpected associations gain support from cytological data and certain morphological characters not previously used to distinguish species groups within Hymenophyllum s.l.

rbcL Phylogeny of the Fern Genus Trichomanes (Hymenophyllaceae), with Special Reference to Neotropical Taxa

In order to estimate evolutionary relationships within the filmy fern genus Trichomanes (Hymenophyllaceae), we performed a phylogenetic analysis using rbcL nucleotide data from 46 species of Trichomanes belonging to all four of C. V. Morton’s subgenera: Achomanes, Didymoglossum, Pachychaetum, and Trichomanes. Outgroups included four species of Hymenophyllum in three different subgenera, plus the monotypic genus Cardiomanes, from New Zealand. We find high resolution and robust support at most nodes, regardless of the phylogenetic optimization criterion used (maximum parsimony or maximum likelihood). Two species belonging to Morton’s Asiatic sections Callistopteris and Cephalomanes are in unresolved basal positions within Trichomanes s.l., suggesting that rbcL data alone are inadequate for estimating the earliest cladogenetic events. Out of the four Morton trichomanoid subgenera, only subg. Didymoglossum appears monophyletic. Other noteworthy results include the following: (1) lianescent sect. Lacostea is more closely related to sect. Davalliopsis (traditionally placed in subg. Pachychaetum) than to other members of subg. Achomanes; (2) sections Davalliopsis and Lacostea, together with species of the morphologically different subg. Achomanes, make up a strongly supported Neotropical clade; (3) all hemiepiphytes (but not true lianas) and strictly epiphytic or epipetric species (Morton’s subgenera Trichomanes and Didymoglossum) group together in an ecologically definable clade that also includes the terrestrial sect. Nesopteris; and (4) sect. Lacosteopsis (sensu Morton) is polyphyletic and comprises two distantly related clades: large hemiepiphytic climbers and small strictly epiphytic/epipetric taxa. Each of these associations is somewhat unexpected but is supported by cytological, geographical, and/or ecological evidence. We conclude that many morphological characters traditionally used for delimiting groups within Trichomanes are, in part, plesiomorphic or homoplastic. Additionally, we discuss probable multiple origins of Neotropical Trichomanes.

Epiphytism in ferns: diversity and history.

As for other vascular plants, numerous adaptive strategies have been selected in epiphytic ferns in order to survive in a constraining and desiccating environment and thus to prevent dehydration and/or to access to water and nutrients. Here we present some of the specializations that allow ferns to survive in this particular habitat. Some of the most spectacular epiphytic specializations are observed in the Polypodiaceae family, involving humus-collectors which entrap humus in specialized organs, and ant-plant mutualism strategies. We then address the question of epiphytism in an evolutionary context. There is little fossil evidence of vascular epiphytes. Inferring the evolution of epiphytism in extant ferns shows that diversification of major living epiphytic groups mostly occurred in the Tertiary. Finally, we focus on the Hymenophyllaceae family which provides an original example of hygrophilous epiphytic strategy that is unique in vascular plants.

Multiple colonizations from Madagascar and converged acquisition of dioecy in the Mascarene Dombeyoideae (Malvaceae) as inferred from chloroplast and nuclear DNA sequence analyses

BACKGROUND AND AIMS In the Mascarenes, a young oceanic archipelago composed of three main islands, the Dombeyoideae (Malvaceae) have diversified extensively with a high endemism rate. With the exception of the genus Trochetia, Mascarene Dombeyoideae are described as dioecious whereas Malagasy and African species are considered to be monocline, species with individuals bearing hermaphrodite/perfect flowers. In this study, the phylogenetic relationships were reconstructed to clarify the taxonomy, understand the phylogeographic pattern of relationships and infer the evolution of the breeding systems for the Mascarenes Dombeyoideae. METHODS Parsimony and Bayesian analysis of four DNA markers (ITS, rpl16 intron and two intergenic spacers trnQ-rsp16 and psbM-trnD) was used. The molecular matrix comprised 2985 characters and 48 taxa. The Bayesian phylogeny was used to infer phylogeographical hypotheses and the evolution of breeding systems. KEY RESULTS Parsimony and Bayesian trees produced similar results. The Dombeyoideae from the Mascarenes are polyphyletic and distributed among four clades. Species of Dombeya, Trochetia and Ruizia are nested in the same clade, which implies the paraphyly of Dombeya. Additionally, it is shown that each of the four clades has an independent Malagasy origin. Two adaptive radiation events have occurred within two endemic lineages of the Mascarenes. The polyphyly of the Mascarene Dombeyoideae suggests at least three independent acquisitions of dioecy. CONCLUSIONS This molecular phylogeny highlights the taxonomic issues within the Dombeyoideae. Indeed, the limits and distinctions of the genera Dombeya, Trochetia and Ruizia should be reconsidered. The close phylogeographic relationships between the flora of the Mascarenes and Madagascar are confirmed. Despite their independent origins and a distinct evolutionary history, each endemic clade has developed a different breeding systems (dioecy) compared with the Malagasy Dombeyoideae. Sex separation appears as an evolutionary convergence and may be the consequence of selective pressures particular to insular environments.

DIVERGENCE TIMES AND THE EVOLUTION OF EPIPHYTISM IN FILMY FERNS (HYMENOPHYLLACEAE) REVISITED

Although the phylogeny of the filmy fern family (Hymenophyllaceae) is rapidly coming into focus, much remains to be uncovered concerning the evolutionary history of this clade. In this study, we use two data sets (108‐taxon rbcL + rps4, 204‐taxon rbcL) and fossil constraints to examine the diversification of filmy ferns and the evolution of their ecology within a temporal context. Our penalized likelihood analyses (with both data sets) indicate that the initial divergences within the Hymenophyllaceae (resulting in extant lineages) and those within one of the two major clades (trichomanoids) occurred in the early to middle Mesozoic. There was a considerable delay in the crown group diversification of the other major clade (hymenophylloids), which began to diversify only in the Cretaceous. Maximum likelihood and Bayesian character state reconstructions across the broadly sampled single‐gene (rbcL) phylogeny do not allow us to unequivocally infer the ancestral habit for the family or for its two major clades. However, adding a second gene (rps4) with a more restricted taxon sampling results in a hypothesis in which filmy ferns were ancestrally terrestrial, with epiphytism having evolved several times independently during the Cretaceous.

New Insights into the Phylogeny of the Genus Hymenophyllum s.l. (Hymenophyllaceae): Revealing the Polyphyly of Mecodium

Abstract With more than 100 species, Mecodium is the largest infrageneric taxon of Hymenophyllum s.l. It was long considered a natural and homogeneous group, but recent phylogenetic studies have questioned this assertion. Using rbcL, rbcL-accD, and rps4-trnS sequences, we demonstrate that Mecodium is highly polyphyletic. Several species of Mecodium form the derived clade “H. polyanthos”; one species is nested within a second derived clade; and the remaining species are assigned to five basal clades including taxa regarded as distantly related. These clades are strongly supported both by parsimony and Bayesian analyses, but the relative placement of the basalmost clades lacks support. We show that the members of “basal Mecodium” are characterized by features that are plesiomorphic for Hymenophyllum s.l.—a reduced or dorsi-ventral stele, a lamina generally at least partially thickened, and a chromosome number based on x = 36, whereas taxa in the “H. polyanthos” clade have a subcollateral stele, the one-cell thick lamina typical of the family, and x = 28. There is a high level of variation among the basal species, and, notably, the rhizome indumentum is shown to be an interesting character for distinguishing among the basal clades. These new findings stress the need for further studies on Hymenophyllum s.l., and reassessment of its classification.

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 insights into the systematics and evolution of the filmy fern genus Crepidomanes (Hymenophyllaceae) in the Mascarene Archipelago with a focus on dwarf species

Abstract The diversity of species belonging to the filmy fern genus Crepidomanes (Hymenophyllaceae) in the Mascarene archipelago was studied, based on morphological investigations and focusing especially on the most dwarf species that are easily confused in the field and in herbarium collections. Morphological potential clusters and discriminations were then compared with an rbcL phylogeny. As a result, we recognized at least eight morpho-species for the archipelago and defined characters for distinguishing the three smallest ones, Crepidomanes bonapartei, Crepidomanes minutum and Crepidomanes (Trichomanes) trinerve. Morphological evidence and molecules confirm the specific status for T. trinerve (newly combined in Crepidomanes), the inclusion of Crepidomanes mannii into a C. minutum complex, and new records of C. bonapartei for Mauritius. The neotropical Polyphlebium pyxidiferum is found to be closely related to Afro-Madagascan Crepidomanes inopinatum and Crepidomanes melanotrichum species and so is newly combined in Crepidomanes. A key for the eight species of the genus in the archipelago, description of a new section clustering Crepidomanes frappieri and Crepidomanes longilabiatum, and new enhanced descriptions for two dwarf taxa (C. bonapartei and C. trinerve) are provided, and biogeographical origins of the genus in the Western Indian Ocean area are discussed.

Anatomical diversity and regressive evolution in trichomanoid filmy ferns (Hymenophyllaceae): A phylogenetic approach

To infer the anatomical evolution of the Hymenophyllaceae (filmy ferns) and to test previously suggested scenarios of regressive evolution, we performed an exhaustive investigation of stem anatomy in the most variable lineage of the family, the trichomanoids, using a representative sampling of 50 species. The evolution of qualitative and quantitative anatomical characters and possibly related growth-forms was analyzed using a maximum likelihood approach. Potential correlations between selected characters were then statistically tested using a phylogenetic comparative method. Our investigations support the anatomical homogeneity of this family at the generic and sub-generic levels. Reduced and sub-collateral/collateral steles likely derived from an ancestral massive protostele, and sub-collateral/collateral types appear to be related to stem thickness reduction and root apparatus regression. These results corroborate the hypothesis of regressive evolution in the lineage, in terms of morphology as well as anatomy. In addition, a heterogeneous cortex, which is derived in the lineage, appears to be related to a colonial strategy and likely to a climbing phenotype. The evolutionary hypotheses proposed in this study lay the ground for further evolutionary analyses that take into account trichomanoid habitats and accurate ecological preferences.