Alan R. Smith

A classification for extant ferns

We present a revised classification for extant ferns, with emphasis on ordinal and familial ranks, and a synopsis of included genera. Our classification reflects recently published phylogenetic hypotheses based on both morphological and molecular data. Within our new classification, we recognize four monophyletic classes, 11 monophyletic orders, and 37 families, 32 of which are strongly supported as monophyletic. One new family, Cibotiaceae Korall, is described. The phylogenetic affinities of a few genera in the order Polypodiales are unclear and their familial placements are therefore tentative. Alphabetical lists of accepted genera (including common synonyms), families, orders, and taxa of higher rank are provided.

Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants

Most of the 470-million-year history of plants on land belongs to bryophytes, pteridophytes and gymnosperms, which eventually yielded to the ecological dominance by angiosperms 90 Myr ago. Our knowledge of angiosperm phylogeny, particularly the branching order of the earliest lineages, has recently been increased by the concurrence of multigene sequence analyses. However, reconstructing relationships for all the main lineages of vascular plants that diverged since the Devonian period has remained a challenge. Here we report phylogenetic analyses of combined data—from morphology and from four genes—for 35 representatives from all the main lineages of land plants. We show that there are three monophyletic groups of extant vascular plants: (1) lycophytes, (2) seed plants and (3) a clade including equisetophytes (horsetails), psilotophytes (whisk ferns) and all eusporangiate and leptosporangiate ferns. Our maximum-likelihood analysis shows unambiguously that horsetails and ferns together are the closest relatives to seed plants. This refutes the prevailing view that horsetails and ferns are transitional evolutionary grades between bryophytes and seed plants, and has important implications for our understanding of the development and evolution of plants.

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.

Cytotaxonomical Atlas of the Pteridophyta.

Cytotaxonomical atlas of the pteridophyta , Cytotaxonomical atlas of the pteridophyta , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی

Phylogenetic Relationships and Evolution of Extant Horsetails, Equisetum, Based on Chloroplast DNA Sequence Data (rbcL and trnL‐F)

Equisetum is a small and morphologically distinct genus with a rich fossil record. Two subgenera have been recognized based principally on stomatal position and stem branching: subg. Equisetum (eight species; superficial stomates; stems branched) and subg. Hippochaete (seven species; sunken stomates; stems generally unbranched). Prior attempts at understanding Equisetum systematics, phylogeny, and character evolution have been hampered by the high degree of morphological plasticity in the genus as well as by frequent hybridization among members within each subgenus. We present the first explicit phylogenetic study of Equisetum, including all 15 species and two samples of one widespread hybrid, Equisetum ×ferrissii, based on a combined analysis of two chloroplast markers, rbcL and trnL‐F. Our robustly supported phylogeny identifies two monophyletic clades corresponding to the two subgenera recognized by earlier workers. The phylogenetic placement of Equisetum bogotense, however, is ambiguous. In maximum likelihood analyses, it allies with subg. Hippochaete as the most basal member, while maximum parsimony places it as sister to the rest of the genus. A consensus phylogeny from the two analyses is presented as a basal trichotomy (E. bogotense, subg. Hippochaete, subg. Equisetum), and morphological character evolution is discussed. We detected rate heterogeneity in the rbcL locus between the two subgenera that can be attributed to an increased rate of nucleotide substitution (transversions) in subg. Hippochaete. We calculated molecular‐based age estimates using the penalized likelihood approach, which accounts for rate heterogeneity and does not assume a molecular clock. The Equisetum crown group appears to have diversified in the early Cenozoic, whereas the Equisetaceae total group is estimated to have a Paleozoic origin. These molecular‐based age estimates are in remarkable agreement with current interpretations of the fossil record.

Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy

We conducted phylogenetic analyses of the fern family Grammitidaceae using sequences from two cpDNA genes and from morphological characters. Data were obtained for 73 species from most recognized genera in the family. Thegenera Adenophorus, Ceradenia, Calymmodon, Cochlidium, Enterosora, and Melpomene were each strongly supported as being monophyletic. Other recognized genera that were not supported as monophyletic included Ctenopteris, Grammitis, Lellingeria, Micropolypodium, Prosaptia, and Terpsichore. Several previously unrecognized clades were identified, some of which are characterized by distinctive morphological features. Analyses of the distribution of morphological character states on our inferred phylogeny showed extremely high levels of homoplastic evolution for many different characters. Homoplasy for morphological characters was considerably greater than for molecular characters. Many of the characters that exhibited high levels of convergent or parallel evolution across the phylogeny are features that have been commonly used to circumscribe genera in this group (e.g., leaf blade dissection, various rhizome scale characters, and glandular paraphyses). Conversely, some of the characters that exhibited relatively low levels of homoplasy have either not been regarded as having taxonomic value or have been ignored (e.g., root insertion, rhizome scale sheen). Our data support a New World origin of Grammitidaceae, with Old World taxa generally being more evolutionarily derived. Several clades are either primarily Neotropical or primarily Paleotropical but also have a few members distributed in the opposite hemisphere. Thus, we postulate multiple, independent dispersal and colonization events in several lineages.

Phytogeographic relationships between neotropical and African-Madagascan pteridophytes

The purpose of this study is to determine the floristic affinities of pteridophytes between the neotropics and Africa-Madagascar and examine how these affinities might have arisen. We present an annotated list that contains two kinds of affinities: 1) species in common between both regions (excluding pantropical species) and 2) species pairs (or clusters of species paris) where one of the species (or infrageneric group) occurs in the Neotropics and the other in Africa and/or Madagascar. There are 114 examples on the list, of which 27 are same-species and 87 are species pairs or closely related taxa at some infrageneric level. About 13% of the African pteridoflora and 14% of the Madagascan pteridoflora show affinities with the Neotropics. To determine how these similarities might have originated, we assess three hypotheses: 1) the boreotropics hypothesis, 2) continental drift, and 3) long-distance dispersal. The boreotropics hypothesis is difficult to assess without further phylogenetic information on the groups to which the species belong. Continental drift seems to best explain one example in the geologically old family Schizaeaceae (species inAnemia subgen.Coptophyllum sect.Tomentosae). Nearly all the other examples seem best explained by long-distance dispersal because they belong to families that first appeared during the Paleocene, more than 30 million yearsafter drift had effectively separated South America and Africa. Most of the dispersal events appear to have taken place from the neotropics to Africa-Madagascar, but recent African extinctions may have obscured directionality. Species with green spores or gemmiferous gametophytes were slightly overrepresented on the list compared to pteridophytes as a whole.ResumenLos propósitos de este estudio son determinar las afinidades florísticas de pteridofitas entre el neotrópico y la región de África-Madagascar y examinar como estas han ocurrido. Se presenta una lista con anotaciones que contiene dos tipos de afinidades: 1) especies en común entre las dos regiones (omitiendo las especies pantropicales) y 2) parejas de especies (grupos de especies) donde una de las especies (o grupo infragenérico) existe en el neotrópico y la otra en África y/o Madagascar. Hay 114 ejemplos en la lista, de los cuales 27 son la misma especie y 87 son parejas o taxa cercanamente relacionadas en algun nivel infragenérico. Casi el 13% de la pteridoflora de África y 14% de la pteridoflora de Madagascar presentan afinidades al neotrópico. Para determinar como se originaron estas similaridades, se examinaron tres hipóteses: 1) la hipótesis boreotrópica, 2) deriva continental, y 3) dispersión a larga distancia. La hipótesis boreotrópica es difícil de evaluar sin suficiente información filogenética sobre los grupos a los que las especies pertenecen. La deriva continental parece explicar mejor un ejemplo en la familia geológicamente antigua Schizaeaceae (especies enAnemia subgen.Coptophyllum sect.Tomentosae). Casi todos los otros ejemplos parecen explicarse mejor por dispersión a larga distancia ya que pretenecen a familias que aparecieron por primera vez durante el Paleoceno, más de 30 millones de años antes de que deriva continental separara América del Sur y África. La mayoría de los casos de dispersión aparecen haber tomado lugar desde el neotrópico hasta África-Madagascar, pero extinciones recientes quizás han obscurecido la direcionalidad. Las especies con esporas verdes o gametofitos gemíferos están representadas con más frecuencia en nuestra lista en contraste con las pteridofitas en general.

Intrafamilial Relationships of the Thelypteroid Ferns (Thelypteridaceae)

Abstract Data from three chloroplast genes (rps4 + trnS spacer, + trnL spacer; 1350 base pairs) for 27 of the recognized segregates show the Thelypteridaceae to be monophyletic and sister to an unresolved alliance of blechnoid, athyrioid, onocleoid, and woodsioid ferns. The family comprises two primary lineages, one phegopteroid, the other thelypteroid (including cyclosoroid). The phegopteroid lineage (Macrothelypteris, Pseudophegopteris, and Phegopteris) includes those elements that are the most dissected, lack adaxial grooves on the frond axes, and are generally morphologically the most distinct elements within the family. Within the thelypteroid-cyclosoroid lineage, three predominantly north-temperate subgroups, including Thelypteris s.s., form a free-veined clade that is in turn sister to the rest of the family. All segregates possessing x=36 (Cyclosorus sensu Smith, with predominantly anastomosing veins) form a strongly supported clade. Those groups with dysploid base chromosome numbers (x=27, 29, 30, 31, 32, 33, 34, 35) form a series of smaller clades basal to Cyclosorus s.l. Although our sampling is not yet sufficient to favor one classification over another, recognition of an intermediate number of genera may be the most reasonable taxonomic course.

Is Morphology Really at Odds with Molecules in Estimating Fern Phylogeny

Abstract Using a morphological dataset of 136 vegetative and reproductive characters, we infer the tracheophyte phylogeny with an emphasis on early divergences of ferns (monilophytes). The dataset comprises morphological, anatomical, biochemical, and some DNA structural characters for a taxon sample of 35 species, including representatives of all major lineages of vascular plants, especially ferns. Phylogenetic relationships among vascular plants are reconstructed using maximum parsimony and Bayesian inference. Both approaches yield similar relationships and provide evidence for three major lineages of extant vascular plants: lycophytes, ferns, and seed plants. Lycophytes are sister to the euphyllophyte clade, which comprises the fern and seed plant lineages. The fern lineage consists of five clades: horsetails, whisk ferns, ophioglossoids, marattioids, and leptosporangiate ferns. This lineage is supported by characters of the spore wall and has a parsimony bootstrap value of 76%, although the Bayesian posterior probability is only 0.53. Each of the five fern clades is well supported, but the relationships among them lack statistical support. Our independent phylogenetic analyses of morphological evidence recover the same deep phylogenetic relationships among tracheophytes as found in previous studies utilizing DNA sequence data, but differ in some ways within seed plants and within ferns. We discuss the extensive independent evolution of the five extant fern clades and the evidence for the placement of whisk ferns and horsetails in our morphological analyses.

Phylogenetic Relaitionships of the Enigmatic Fern Families Hymenophyllopsidaceae and Lophosocoriaceae: Evidence From rbcL Nucleotide Sequences

Nucleotide sequences fromrbcL were used to infer relationships of Lophosoriaceae and Hymenophyllopsidaceae. The phylogenetic positions of these two monotypic fern families have been debated, and neither group had been included in recent molecular systematic studies of ferns. Maximum parsimony analysis of our data supported a sister relationship betweenLophosoria andDicksonia, and also betweenHymenophyllopsis andCyathea. Thus, both newly-examined families appear to be part of a previously characterized and well-supported clade of tree ferns. The inferred relationships ofLophosoria are consistent with most (but not all) recent treatments. However,Hymenophyllopsis includes only small delicate plants superficially similar to filmy ferns (Hymenophyllaceae), very different from the large arborescent taxa. Nevertheless, some synapomorphic characteristics are shared with the tree fern clade. Further studies on gametophytes ofHymenophyllopsis are needed to test these hypotheses of relationship.