Out of Madagascar, repeatedly: The phylogenetics and biogeography of Dombeyoideae (Malvaceae s.l.).

Dispersals have been shown to be critical to the evolution of the long isolated but megadiverse flora of Madagascar and the surrounding islands of the western Indian Ocean, but we are just beginning to understand the directionality of these dispersals. With more than half of its species occurring in the western Indian Ocean region (WIOR), the paleotropical subfamily Dombeyoideae provides a particularly useful case study through which to better understand the biogeography of the WIOR, and yet its biogeography is poorly understood. Here we sampled six molecular markers from all 20 genera in the Dombeyoideae to reconstruct the most complete phylogeny to date for the subfamily. From this, divergence times, calibrated with three fossils (two dombeyoid, one malvoid), and ancestral range estimations were hypothesized. Biogeographic stochastic mapping (BSM) analyses on the maximum clade credibility tree were completed and compared to BSM analyses on 1,000 trees randomly sampled from the posterior distribution of trees resulting from the dating analysis. We found the Dombeyoideae crown node diverged ca. 53 million years ago out of a broad ancestral range involving all three major areas of its distribution: Madagascar, Africa, and Asia. The majority of diversification and dispersals in the subfamily occurred within the last ca. 10 million years, mostly from the Pliocene onwards. There were roughly five dispersals from Madagascar to Africa (and only one in reverse), at least six from Madagascar to surrounding islands of the WIOR (Mascarenes and Comoros), and one dispersal from Madagascar to Asia (and ca. 1 in reverse). Other long-distance dispersals included one from Africa to St. Helena and one from Africa to Australasia, both from within the most widespread clade, the Cheirolaena & allies clade, and one dispersal from Asia to Africa. Critically, the Dombeyoideae provide strong evidence for considering the island of Madagascar as a source for the colonization of continents, as well as the surrounding islands of the WIOR. Furthermore, narrow sympatry was a key process in the evolution of the subfamily, particularly in Madagascar and the Mascarenes.

Gains and losses of the epiphytic lifestyle in epidendroid orchids: review and new analyses of succulence traits.

BACKGROUND AND AIMS: Epiphytism has evolved repeatedly in plants and has resulted in a considerable number of species with original characteristics. Because water supply is generally erratic compared to that in soils, succulent forms in particular are widespread in epiphytic species. However, succulent organs also exist in terrestrial plants, and the question of the concomitant evolution of epiphytism and succulence has received little attention, not even in the epidendroid orchids, which account for 67.6 % of vascular epiphytes. METHODS: We built a new time-calibrated phylogenetic tree of Epidendroideae with 203 genera treated in genus Orchidacearum, from which we reconstructed the evolution of epiphytism as well as traits related to water scarcity (stem and leaf succulence and the number of velamen layers), while testing for the correlated evolution between the two. Furthermore, we estimated the ancestral geographical ranges to evaluate the palaeoclimatic context in which epiphytism evolved. KEY RESULTS: Epiphytism evolved at least three times: 39.0 million years ago (Mya) in the common ancestor of the Malaxideae and Cymbidieae that probably ranged from the Neotropics to Southeast Asia and Australia, 11.5 Mya in the Arethuseae in Southeast Asia and Australia, and 7.1 Mya in the neotropical Sobralieae, and it was notably lost in the Malaxidiinae, Collabieae, Calypsoeae, Bletiinae and Eulophiinae. Stem succulence is inferred to have evolved once, in a terrestrial ancestor at least 4.1 Mya before the emergence of epiphytic lineages. If lost, stem succulence was almost systematically replaced by leaf succulence in epiphytic lineages. CONCLUSIONS: Epiphytism may have evolved in seasonally dry forests during the Eocene climatic cooling, among stem-succulent terrestrial orchids. Our results suggest that the emergence of stem succulence in early epidendroids was a key innovation in the evolution of epiphytism, facilitating the colonization of epiphytic environments that later led to the greatest diversification of epiphytic orchids.

Quantification of complex modular architecture in plants.

Morphometrics, the assignment of quantities to biological shapes, is a powerful tool to address taxonomic, evolutionary, functional and developmental questions. We propose a novel method for shape quantification of complex modular architecture in thalloid plants, whose extremely reduced morphologies, combined with the lack of a formal framework for thallus description, have long rendered taxonomic and evolutionary studies extremely challenging. Using graph theory, thalli are described as hierarchical series of nodes and edges, allowing for accurate, homologous and repeatable measurements of widths, lengths and angles. The computer program MorphoSnake was developed to extract the skeleton and contours of a thallus and automatically acquire, at each level of organization, width, length, angle and sinuosity measurements. Through the quantification of leaf architecture in Hymenophyllum ferns (Polypodiopsida) and a fully worked example of integrative taxonomy in the taxonomically challenging thalloid liverwort genus Riccardia, we show that MorphoSnake is applicable to all ramified plants. This new possibility of acquiring large numbers of quantitative traits in plants with complex modular architectures opens new perspectives of applications, from the development of rapid species identification tools to evolutionary analyses of adaptive plasticity.

Chromosome number evolution in Hymenophyllum (Hymenophyllaceae), with special reference to the subgenus Hymenophyllum.

With about 100 species distributed worldwide, Hymenophyllum subg. Hymenophyllum is the largest subgenus of filmy ferns. It also displays morphological disparity and extreme chromosome numbers variation, with n=11, 12, 13, 14, 18, 21, 22, 26, 28, and 34. We use DNA sequences from the genes rbcL, part of accD, rps4, and the intergenic spacers rbcL-accD, rps4-trnS, and trnG-trnR to infer relationships within Hymenophyllum, with a focus on this subgenus. In the subgenus Hymenophyllum, two main clades are retrieved together with several minor clades whose placement within the subgenus remains ambiguous. We then investigate the evolution of chromosome numbers in the genus and the subgenus, using a maximum likelihood approach taking into account phylogenetic uncertainty. We provide evidence that Hymenophyllum experienced descending aneuploidy during its evolutionary history, especially within the subgenus Hymenophyllum. Reduction in chromosome numbers is particularly extreme in one clade of the subgenus, with the lowest number reported for homosporous ferns. In addition, this group of species displays a high instability in its chromosome number. Both the reduction and the instability in chromosome number may coincide with the distribution of these species in either temperate areas or at high elevations.

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.

A first checklist of the Pteridophytes of Togo (West Africa).

BACKGROUND: The present work proposes, for the first time, a study exclusively focused on the diversity of Pteridophytes in Togo.The study was based on fieldwork that resulted in 869 new collections gathered between 2013 and 2017 in the country and on yet existing herbarium specimens kept at the Herbaria of Lomé and Paris. Thus, a total number of 1092 specimens collected throughout the country served as a basis for this work, to which were added the known, published occurrences of Pteridophytes for the country. NEW INFORMATION: At the end of this study, a total diversity of 134 species belonging to 53 genera and 25 families and 12 orders were recorded and documented for the country. It results in 73 newly cited species for Togolese flora, including 61 spontaneous species. Lycopodiopsida (18 species) and Polypodiopsida (116 species) classes are both represented. The Polypodiales order is the most represented with 97 species. The Pteridaceae and Aspleniaceae families are the most diverse with 24 and 22 species respectively. Finally, notes were provided on species distribution at national level.

Adetogramma (Polypodiaceae), a new monotypic fern genus segregated from Polypodium.

Polypodiaceae is one of the most diverse and abundant families of ferns in tropical and subtropical forests. Despite multiple studies investigating its phylogeny and taxonomy, several generic boundaries within the family still need clarification. One of the most problematic circumscriptions is that of Polypodium L., and one species that still contributes to this uncertainty is Polypodium chrysolepis Hook. The main goal of this study was to use molecular and morphological data to clarify the relationships of P. chrysolepis inside the polygrammoid clade. Sequences from three plastid regions (cpDNA - rbcL, rps4 and rps4-trnS IGS) from fifty species belonging to thirty-two genera of Polypodiaceae were analyzed using maximum likelihood and Bayesian inference. Polypodium chrysolepis constitutes an isolated lineage among the neotropical polygrammoid ferns, close to Serpocaulon and the grammitids, and is recognized here in a new genus. It can be distinguished by its entire leaves with free veins and peltate, pedicellate, lanceolate paraphyses. A new combination, Adetogramma chrysolepis, is proposed and a new taxonomic treatment is presented; its conservation status was assessed using IUCN Red List Categories and Criteria.

The Pteridaceae family diversity in Togo.

BACKGROUND: The Pteridaceae family is the largest fern family in Togo by its specific and generic diversity. Like all other families of ferns in the country, Pteridaceae are poorly studied and has no identification key. The objective of this study is to perform a taxonomic revision and list establishment of this family of leptosporangiate ferns in the light of current available knowledge about the family. Pteridaceae was also assessed in terms of its diversity and conservation status, this was conducted through the recent field data and the existing herbaria specimens. The current study permits to confirm the presence of Pteris similis Kuhn. which brought the number of Pteridaceae to 17 in Togo. NEW INFORMATION: This study provides first local scientific information about the fern flora of Togo. It confirmed the presence of Pterissimilis Kuhn. in Togo and brought the Pteridaceae family diversity to 17 species. A species identification key is provided for the easy identification of the Pteridaceae of Togo.

Coding of insertion-deletion events of the chloroplastic intergene atp beta-rbcL for the phylogeny of the Valerianeae tribe (Valerianaceae).

A preliminary analysis of the sequence alignment of the chloroplast intergene atp beta-rbcL in tribe Valerianeae reveals that insertion-deletion evolutionary events ('indels'), combined with nucleotide substitutions, have occurred in large zones in some of the studied taxa. Due to the frequent occurrence and large size of indels within this tribe, intergene length varies from 531 to 788 base pairs within the studied species. This situation poses gap coding problems that we had to tackle before phylogenetic analysis. Four methods of gap coding were used: elimination of gapped sites ('complete omission'), 'missing data', 'fifth base' and Barriel's coding method, which translates indels into new multistate characters in the data matrix. After application of these four methods of data treatment, phylogenetic analyses (maximum parsimony) did not lead to very different results. Three robust clades emerged in each case, corresponding to the Centranthinae subtribe (genus Centranthus), the Fediinae subtribe (genera Fedia and Valerianella), and the American species of Valeriana. The theoretical basis and biological significance of these four methods are discussed in order to apply the best ones in future studies.

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.

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.

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.

Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: contributions of species from the Indian Ocean area.

We performed a phylogenetic analysis of the fern genus Elaphoglossum using two non-coding chloroplast spacers: trnL-trnF and rps4-trnS. The sampling includes 123 species, of which 80 have not been previously sequenced, and for the first time includes species from Africa and the Indian Ocean area. The results of this expanded study largely agree with an earlier molecular study based on a smaller group of neotropical species and with the morphology-based classification of Mickel and Atehortua. We found, however, that some infrageneric groups such as section Elaphoglossum are not monophyletic. Besides section Elaphoglossum pro parte, we recognize six sections: two new monospecific, unnamed sections, and the previously established sections Lepidoglossa, Squamipedia, Amygdalifolia, and "Subulate-scaled clade." We divide the subulate-scaled clade into subsection Setosa (hydathodes present) and Polytrichia (hydathodes absent), and section Elaphoglossum is divided into subsections Platyglossa and Pachyglossa, two groups that do not appear to be supported by any single morphological character. In general, however, the main clades are supported by morphology. Finally, we discuss the species of the Indian Ocean region and their affinities with the neotropical ones. Out of the 11 species pairs postulated by Moran and Smith on the basis of morphology, two are well supported (E. eximium-E. aubertii; E. piloselloides-E. spatulatum) and three are not supported (E. ciliatum-E. humbertii; E. muscosum-E. poolii; E. paleaceum-E. deckenii), and two remain unresolved (E. erinaceum-E. hybridum; E. glabellum-E. acrostichoides) because our molecular markers were not variable enough. Four species pairs could not be tested because specimens were lacking. Unsupported species pairs are best interpreted as morphological convergences. Two additional species pairs are proposed: E. cuspidatum-E. succisaefolium; E. doanense-E. hornei. Placement of the species from the Indian Ocean suggests that at least 13 long-distance dispersal events occurred between the Neotropics and the Indian Ocean-Africa.