Sporogenesis in Eusporangiate Ferns: I. Monoplastidic Meiosis in Angiopteris (Marattiales)

Angiopteris (Marattiales) undergoes the more primitive form of monoplastidic meiosis, while other ferns have evolved the polyplastidic type typical of seed plants. In monoplastidic cell division, the single plastid divides and serves as site of the microtubule organizing center (MTOC) for spindle formation resulting in coordinated division of plastid, nucleus, and cytoplasm. In plants with polyplastidic cell division, the MTOC is diffuse and generally perinuclear. Monoplastidic cell division is seen as a plesiomorphic feature that was inherited from algal ancestors containing a single plastid and modified through evolution. Monoplastidic meiosis occurs in all groups of bryophytes (although in only a few hepatics), Isoetes, Selaginella, certain generic segregates of Lycopodium, and in members of the Marattiales. It is not known to occur in psilophytes, Equisetum, leptosporangiate ferns, or seed plants. Received 30 January 2001/ Accepted in revised form 24 April 2001     

Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences

The phylogenetic structure of ferns (= monilophytes) is explored here, with a special focus on the early divergences among leptosporangiate lineages. Despite considerable progress in our understanding of fern relationships, a rigorous and comprehensive analysis of the early leptosporangiate divergences was lacking. Therefore, a data set was designed here to include critical taxa that were not included in earlier studies. More than 5000 bp from the plastid (rbcL, atpB, rps4) and the nuclear (18S rDNA) genomes were sequenced for 62 taxa. Phylogenetic analyses of these data (1) confirm that Osmundaceae are sister to the rest of the leptosporangiates, (2) resolve a diverse set of ferns formerly thought to be a subsequent grade as possibly monophyletic (((Dipteridaceae, Matoniaceae), Gleicheniaceae), Hymenophyllaceae), and (3) place schizaeoid ferns as sister to a large clade of "core leptosporangiates" that includes heterosporous ferns, tree ferns, and polypods. Divergence time estimates for ferns are reported from penalized likelihood analyses of our molecular data, with constraints from a reassessment of the fossil record.     

STUDIES OF PALEOZOIC MARATTIALEANS: NEW SPECIES OF SCOLECOPTERIS (MARATTIALES) FROM THE PENNSYLVANIAN OF NORTH AMERICA

Two new species of the late Paleozoic fern Scolecopteris (Marattiales) are described and their relationships within the genus are discussed. Scolecopteris charma sp.n., from Steubenville, Ohio (Duquesne Coal, Upper Pennsylvanian), is similar to species in the Oliveri group, while S. gnoma sp.n. from Providence, Kentucky (Baker Coal, Middle Pennsylvanian), compares favorably with the Latifolia species group. Scolecopteris gnoma is most similar to S. fragilis but differs in its smaller synangia and spore type. S. charma appears generally similar to S. iowensis because of its large pedicel and histologically undifferentiated walls, but differs in a number of characters such as vasculature and spore type. Despite its occurrence late in the Pennsylvanian, S. charma is thought to possess a number of primitive character states (large trilete spores, vascularized pedicels, flat pinnules with downturned margins). Using the same criteria for the much older S. gnoma, we note a number of relatively apomorphic character states (small monolete spores, unvascularized pedicels, extended pinnule margins). An outgroup analysis of species-level characters of Scolecopteris gives a better concept of primitive versus derived traits in marattialean and other ferns. Genera in the Paleozoic fern orders Filicales (Ankyropteris) and Zygopteridales (Corynepteris, Musatea) were chosen as outgroups, and the comparisons support suggestions for the polarity of several important characters. Some of these agree with previously proposed evolutionary polarities based on the geological occurrence of marattialean ferns.     

THE CYTOHISTOLOGICAL AND CYTOHISTOCHEMICAL ZONATION OF THE SHOOT APEX OF BOTRYCHIUM MULTIFIDUM

Cytohistologically, the shoot apex of Botrychium multifidum is composed of three zones—a zone of surface initials in which there is usually a centrally located apical cell, a zone of subsurface initials, and a cup-shaped zone that is subdivided into a pheripheral zone and a rib meristem. The results of cytohistochemical tests for total protein, RNA, total carbohydrate, histones, and DNA localization support this concept. Thus, the cytohistological zonation of the apical meristem of the Ophioglossales is essentially identical to that of the Filicales, and furthermore, is comparable to that of the seed plants.     

Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes)

? Premise of the Study: The monilophytes (ferns and relatives)-the third largest group of land plants-exhibit a diverse array of vegetative and reproductive morphologies. Investigations into their early ecological and life-history diversification require accurate, well-corroborated phylogenetic estimates. We examined the utility of a large plastid-based data set in inferring backbone relationships for monilophytes. ? Methods: We recovered 17 plastid genes for exemplar taxa using published and new primers. We compared results from maximum-likelihood and parsimony analyses, assessed the effects of removing rapidly evolving characters, and examined the extent to which our data corroborate or contradict the results of other studies, or resolve current ambiguities. ? Key Results: Considering multifamily clades, we found bootstrap support comparable to or better than that in published studies that used fewer genes from fewer or more taxa. We firmly establish filmy ferns (Hymenophyllales) as the sister group of all leptosporangiates except Osmundaceae, resolving the second deepest split in leptosporangiate-fern phylogeny. A clade comprising Ophioglossaceae and Psilotaceae is currently accepted as the sister group of other monilophytes, but we recover Equisetum in this position. We also recover marattioid and leptosporangiate ferns as sister groups. Maximum-likelihood rate-class estimates are somewhat skewed when a long-branch lineage (Selaginella) is included, negatively affecting bootstrap support for early branches. ? Conclusions: Our findings support the utility of this gene set in corroborating relationships found in previous studies, improving support, and resolving uncertainties in monilophyte phylogeny. Despite these advances, our results also underline the need for continued work on resolving the very earliest splits in monilophyte phylogeny.     

Phylogenetic Information in the Mitochondrial nad5 Gene of Pteridophytes: RNA Editing and Intron Sequences

Abstract: A conserved coding region of the mitochondrial nad5 gene (1098–1107 bp of protein coding sequence) was amplified from 30 pteridophytes (26 ferns and 4 fern allies). A group II intron sequence conserved in all ferns except the eu-sporangiate genus Ophioglossum is also present in the whisk fern Psilotum nudum and the lycopod Huperzia selogo , but absent from the horsetails ( Equisetum ), the seed plants and the bryo-phytes. Phylogenetic trees constructed with different methods consistently suggest several monophyletic units. The conserved group II intron sequence provides valuable additional phylogenetic information. Leptosporangiate ferns are monophyletic with Osmunda as the basal-most branching genus followed by Trichomanes, Matonia and Lygodium . These genera are set distantly apart from other leptosporangiate ferns, including the tree and water ferns, which branch in close proximity. Species of Polypodiaceae, Dryopteridaceae, Thelypteridaceae, Aspleniaceae and Blechnaceae appear in a monophyletic crown group of derived leptosporangiate ferns with Dryopteridaceae as a paraphyletic taxon. Placement of Psilotum in a class of its own receives no support from the mitochondrial sequences, which rather suggest its inclusion among eusporangiate ferns (Ophioglossales). RNA editing is required to correct the genetic information of the nad5 gene in all species investigated and includes the removal of stop codons from the reading frames. The influence of RNA editing on phylogenetic tree construction is investigated and discussed.     

Chloroplast phylogenomics resolves key relationships in ferns

Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep nodes in ferns. We sequenced the chloroplast genomes from Cyrtomium devexiscapulae(Koidz.) Ching (eupolypod I) and Woodwardia unigemmata (Makino) Nakai (eupolypod II), and constructed the phylogeny of ferns based on both 48 genes and 64 genes. The trees based on 48 genes and 64 genes are identical in topology, differing only in support values for four nodes, three of which showed higher support values for the 48-gene dataset. Equisetum L. was resolved as the sister to the Psilotales–Ophioglossales clade, and Equisetales–Psilotales–Ophioglossales clade was sister to the clade of the leptosporangiate and marattioid ferns. The sister relationship between the tree fern clade and polypods was supported by 82% and 100% bootstrap values in the 64-gene and 48-gene trees, respectively. Within polypod ferns, Pteridaceae was sister to the clade of Dennstaedtiaceae and eupolypods with a high support value, and the relationship of Dennstaedtiaceae–eupolypods was strongly supported. With recent parallel advances in the phylogenetics of ferns using nuclear data, chloroplast phylogenomics shows great potential in providing a framework for testing the impact of reticulate evolution in the early evolution of ferns.     

The subfamilies and tribes of the family Bovidae

In this paper 112 skeletal characters in 27 living species of bovids are used in cladistic and phenetic analyses of the relationships among the tribes in the family. Consideration and modification of the cladistic analysis leads to the conclusion that bovids cluster around four foci in ascending evolutionary sequence: Boselaphini and allies; Antilopini and some Neotragini; the Caprinae; and a group of African antelopes containing Aepyceros , Alcelaphini, Reduncini and Hippotragini. This conclusion is quite closely compatible with the phenetic distance analysis of the same data, provided die latter is read as if primitive or early bovids share more similarities than divergently advanced ones and hence associate more closely. Given the primitiveness of Boselaphini and allies, the crucial finding is that Caprinae link with African antelopes and that Antilopini are more remote. Cladistic and phenetic analyses of 32 characters in 12 extinct bovid species produce similar groupings, but also throw doubt on the classification of Aepyceros , Reduncini and Hippotragini alongside Alcelaphini within a clade of African antelopes. As a result of these two sets of studies, of living and of extinct bovids, minimal alterations are proposed to the arrangement of bovid tribes. In addition, Saiga is placed in the Antilopini, and, with less assurance, Pelea in the Neotragini, Aepyceros in the Alcelaphinae, and Pantholops in the Caprinae. The contribution of the fossil record to understanding bovid evolution is considered.     

Phylogeny of the water strider genus Rheumatobates (Heteroptera: Gerridae)

The genus Rheumatobates comprises thirty‐seven species and subspecies of New World water striders belonging to subfamily Rhagadotarsinae. Among species, males vary dramatically in the degree and nature of modifications of the antennae, three pairs of legs and abdominal and genital segments. Characters describing this modification have traditionally been used to differentiate and group species. The general assumption has been that modified species belong to one group and unmodified species to another. These two ‘species groups’ are subdivided into ‘subgroups’, but little effort has been made to resolve relationships among them. We conduct the first numerical cladistic analysis of Rheumatobates using a data set comprised of 102 characters, primarily describing modification of male external morphology. To address concerns about the inclusion of characters to be optimized on the phylogeny, characters describing modification of antennae and hind legs were included and then excluded in separate analyses. A preferred phylogeny was chosen from the four equally parsimonious cladograms found after successive reweighting of characters. There was good resolution at all levels of the phylogeny. Most of the major clades and terminal relationships were moderately to strongly supported, whereas the basal relationships were less well supported. The general assumption that unmodified and modified species form two monophyletic groups was not supported. However, traditionally recognized ‘subgroups’ within the modified species group were largely upheld. The analysis also suggested several major clades and relationships among these clades that were not previously recognized. The exclusion of characters describing modification of antennae and hind legs did not change the resolved major clades of the reconstructed phylogeny.     

The systematics of right whales (Mysticeti: Balaenidae)

Balaenidae (right whales) are large, critically endangered baleen whales represented by four living species. The evolutionary relationships of balaenids are poorly known, with the number of genera, relationships to fossil taxa, and position within Mysticeti in contention. This study employs a comprehensive set of morphological characters to address aspects of balaenid phylogeny. A sister‐group relationship between neobalaenids and balaenids is strongly supported, although this conflicts with molecular evidence, which may be an artifact of long‐branch attraction (LBA). Monophyly of Balaenidae is supported, and three major clades are recognized: (1) extinct genus Balaenula, (2) extant and extinct species of the genus Eubalaena, and (3) extant and extinct species of the genus Balaena plus the extinct taxon, Balaenella. The relationships of these clades to one another, as well as to the early Miocene stem balaenid, Morenocetus parvus, remain unresolved. Pliocene taxa, Balaenula astensis and Balaenula balaenopsis, form a clade that is the sister group to the Japanese Pliocene Balaenula sp. Eubalaena glacialis and Pliocene Eubalaena belgica, are in an unresolved polytomy with a clade including E. japonica and E. australis. Extant and fossil species of Balaena form a monophyletic group that is sister group to the Dutch Pliocene Balaenella, although phylogenetic relationships within Balaena remain unresolved.     

The role of Hydropteris pinnata gen. et sp. nov. in reconstructing the cladistics of heterosporous ferns

Large segments of intact plants that represent a heterosporous fern have been discovered within an aquatic plant community from the Late Cretaceous St. Mary River Formation near Cardston in southern Alberta, Canada. Branching rhizomes of Hydropteris pinnata gen. et sp. nov. are 1–2 mm wide. They produce fronds at intervals of 2–12 mm and bear numerous elongated roots. Fronds, up to approximately 6 cm long, are pinnate with subopposite to alternate pinnae that exhibit anastomosing venation. Large, multisoral sporocarps occur at the junctures of the rhizome and frond rachides. Both microsporangiate massulae and megaspore complexes occur within each sporocarp. Megaspore complexes are assignable to the sporae dispersae genus Parazolla Hall. Microspores are trilete, smooth-walled, and are embedded in episporal material of the massulae. A numerical cladistic analysis indicates that the heterosporous aquatic ferns are monophyletic, and not as closely related to either schizaeaceous or hymenophyllaceous ferns as they are to some other filicaleans. Systematic revisions are proposed to reflect newly recognized cladistic relationships within the heterosporous clade, and character originations in the evolution of heterosporous aquatic ferns are evaluated. Hydropteridaceae fam. nov. is proposed, and included with Salviniaceae and Azollaceae in the Hydropteridineae subord. nov., and the Hydropteridales Willdenow.     

Conantiopteris schuchmanii, gen. et sp. nov., and the Role of Fossils in Resolving the Phylogeny of Cyatheaceae s.l.

Conantiopteris schuchmanii gen. et sp. nov. The specimen, 23.2 cm long and 11.7 cm wide, shows helically arranged persistent frond bases embedded in adventitious roots, and is clothed by multicellular trichomes. A parenchymatous pith with mucilaginous cells and sclerotic nests is surrounded by an amphiphloic distyostele, parenchymatous inner cortex, and outer sclerenchymatous cortex. Sclerenchyma also surrounds the cauline vasculature and leaf traces. Medullary and cortical bundles are absent. Phloem contains both axially elongated and tangential sieve elements. Frond bases are oval in outline with three vascular bundles, including an undulating abaxial arc and an adaxial pair. Protoxylem of the stipe is endarch and is associated with cavity parenchyma. These characters are indicative of tree fern affinities. A cladistic analysis using trunk characters of both living and fossil tree ferns was conducted to help establish relationships of the new species and other fossil ferns, and to test hypotheses of general tree fern relationships. Additional analyses of living taxa only were also performed. Results from the analysis using both living and fossil taxa compare favorably with those that included only living species when either morphological characters or molecular sequences of the chloroplast gene rbcL are utilized. Although there are variations in the topologies of the various trees, results indicate that the new genus is nested among a paraphyletic assemblage of dicksoniaceous, lophosoriaceous, and metaxyaceous species that subtend a monophyletic Cyatheaceae s.s. Received 26 April 1999/ Accepted in revised form 15 July 1999     

A phylogenetic supertree of the bats (Mammalia: Chiroptera)

We present the first estimate of the phylogenetic relationships among all 916 extant and nine recently extinct species of bats Mammalia: Chiroptera), a group that accounts for almost one-quarter of extant mammalian diversity. This phylogeny was derived by combining 105 estimates of bat phylogenetic relationships published since 1970 using the supertree construction technique of Matrix Representation with Parsimony (MRP). Despite the explosive growth in the number of phylogenetic studies of bats since 1990, phylogenetic relationships in the order have been studied non-randomly. For example, over one-third of all bat systematic studies to date have locused on relationships within Phyllostomidae, whereas relationships within clades such as Kerivoulinae and Murinae have never been studied using cladistic methods. Resolution in the supertree similarly differs among clades: overall resolution is poor (46.4%, of a fully bifurcating solution) but reaches 100% in some groups (e.g. relationships within Mormoopidae). The supertree analysis does not support a recent proposal that Microchiroptera is paraphyletic with respect to Megachiroptera, as the majority of source topologies support microbat monophyly. Although it is not a substitute for comprehensive phylogenetic analyses of primary molecular and morphological data, the bat supertree provides a useful tool for future phylogenetic comparative and macroevolutionary studies. Additionally, it identifies clades that have been little studied, highlights groups within which relationships are controversial, and like all phylogenetic studies, provides preliminary hypotheses that can form starting points for future phylogenetic studies of bats.     

Is the anthophyte hypothesis alive and well? New evidence from the reproductive structures of Bennettitales

Bennettitales is an extinct group of seed plants with reproductive structures that are similar in some respects to both Gnetales and angiosperms, but systematic relationships among the three clades remain controversial. This study summarizes characters of bennettitalean plants and presents new evidence for the structure of cones and seeds that help clarify relationships of Bennettitales to flowering plants, Gnetales, and other potential angiosperm sister groups. Bennettitales have simple mono- or bisporangiate cones. Seeds are borne terminally on sporophylls. They have a unique structure that includes a nucellus with a solid apex, no pollen chamber, and a single integument, and they are clearly not enclosed by a cupule or other specialized structures. Such features differ substantially from Gnetales, flowering plants, and the seed fern Caytonia, providing no compelling evidence for the origin of the angiospermous carpel. Cladistic tests were performed to assess the strength of the "anthophyte hypothesis" and possible relationships of Bennettitales, Gnetales, and Caytonia to flowering plants. Our results do not support the anthophyte hypothesis for the origin of angiosperms by a transformation of fertile organs that were already aggregated into a cone or flower-like structure. However, the anthophyte topology of the seed plant tree continues to be supported by morphological analyses of living and extinct taxa.     

SUMMARY OF GREEN PLANT PHYLOGENY AND CLASSIFICATION

Abstract— A cladogram of green plants involving all major extant groups of green algae, bryophytes, pteridophytes, and seed plants is presented. It is partly based on contributions by B. Mishler and S. Churchill, H. Wagner, and P. Crane. The relationships of green plants to other green organisms ( Prochloron , euglenophytes) are discussed. The characters and subclades of the cladogram are briefly discussed, with an attempt to indicate weak points. The possibility of including some major extinct groups is considered. A cladistic classification consistent with the cladogram is presented. Grades are abandoned as taxa and major clades like the division Chlorophyta (green algae excluding micro-monadophytes and charophytes sensu Mattox and Stewart), the division Streptophyta (charophytes + embryophytes), the subdivision Embryophytina (land plants or embryophytes), the superclass Tracheidatae (tracheophytes), and the class Spermatopsida (seed plants) are recognized.     

First combined cladistic analysis of marsupial mammal interrelationships

We combine osteological, dental, and soft tissue data with sequences from three nuclear and five mitochondrial genes, sampling all major living clades of marsupials plus several extinct taxa, to perform a simultaneous analysis of marsupial interrelationships. These data were analyzed using direct optimization and sensitivity analysis on a parallel supercomputing cluster, and compared with trees produced with conventional parsimony and likelihood algorithms using a static alignment. A major issue in marsupial phylogeny is the relationships among australidelphians. Optimal analyses using direct optimization and those based on the static alignment support the basal positions of peramelians (bandicoots) and Dromiciops ('monito del monte') within Australidelphia, and in all but one case these analyses support a monophyletic Eometatheria, a group consisting of all australidelphians excluding peramelians. Dromiciops is basal within Eometatheria in analyses that maximize congruence across partitions, including the equally weighted parameter set. The topologies resulting from direct optimization under all parameter sets show some differences, but all show a high degree of resolution. Direct optimization supports high-level clades supported by analyses of partitioned molecular (e.g., Notoryctes as sister group of Dasyuromorphia) and morphological (e.g., Diprotodontia) data.     

Plastid genome sequencing,comparative genomics,and phylogenomics: Current status and prospects

Abstract More than 190 plastid genomes have been completely sequenced during the past two decades due to advances in DNA sequencing technologies. Based on this unprecedented abundance of data, extensive genomic changes have been revealed in the plastid genomes. Inversion is the most common mechanism that leads to gene order changes. Several inversion events have been recognized as informative phylogenetic markers, such as a 30‐kb inversion found in all living vascular plants minus lycopsids and two short inversions putatively shared by all ferns. Gene loss is a common event throughout plastid genome evolution. Many genes were independently lost or transferred to the nuclear genome in multiple plant lineages. The trnR‐CCG gene was lost in some clades of lycophytes, ferns, and seed plants, and all the ndh genes were absent in parasitic plants, gnetophytes, Pinaceae, and the Taiwan moth orchid. Certain parasitic plants have, in particular, lost plastid genes related to photosynthesis because of the relaxation of functional constraint. The dramatic growth of plastid genome sequences has also promoted the use of whole plastid sequences and genomic features to solve phylogenetic problems. Chloroplast phylogenomics has provided additional evidence for deep‐level phylogenetic relationships as well as increased phylogenetic resolutions at low taxonomic levels. However, chloroplast phylogenomics is still in its infant stage and rigorous analysis methodology has yet to be developed.     

Morphological Evidence for the Phylogeny of Cetacea

A cladistic analysis of 54 extant and extinct cetacean taxa scored for 304 morphological characters supports a monophyletic Odontoceti, Mysticeti, Autoceta, and Cetacea. Forcing a sister-group relationship between Mysticeti and Physeteridae, as suggested by some, but not all, molecular studies, requires an additional 72 steps. In agreement with recent molecular studies, morphological data divide extant mysticetes into two clades: Balaenopteroidea (Eschrichtiidae + Balaenopteridae) and Balaenoidea (Balaenidae + Neobalaenidae). Cetotheriopsinae is removed from Cetotheriidae, elevated to Family Cetotheriopsidae, and placed within the Superfamily Eomysticetoidea. All extant mysticetes and all cetotheriids are placed in a new Parvorder Balaenomorpha, which is diagnosed by many morphological characters, including fusion of the anterior and posterior processes of petrosal to ectotympanic bulla, pronounced median keel on palate, and absence of ventral margin of sigmoid process of bulla. Many of the clades within Odontoceti in the most parsimonious trees of this study are at odds with recent phylogenetic analyses. For example, Platanistidae is not closely related to the extinct odontocete families Squalodontidae and Squalodelphinidae. Instead, it is more closely related to extant river-dwelling odontocetes (i.e., Lipotes, Inia), suggesting a single dispersal of odontocetes into freshwater habitats. We found several characters to support Physeteroidea (Physeteridae + Ziphiidae), a taxon considered paraphyletic by several molecular and some morphological analyses. Lack of agreement on the phylogeny within Odontoceti indicates that additional analyses, which include molecular and anatomical data as well as extant and extinct taxa, are needed.     

Spatial genetic analyses reveal strong genetic structure in two populations of the outcrossing tree fern Alsophila firma (Cyatheaceae)

The development of spatial genetic structure (SGS) in seed plants has been linked to several biological attributes of species, such as breeding system and life form. However, little is known about SGS in ferns, which together with lycopods are unique among land plants in having two free‐living life stages. We combined spatial aggregation statistics and spatial genetic autocorrelation analyses using five plastid microsatellites and one nuclear gene to investigate SGS in two populations of the outcrossing tree fern Alsophila firma (Cyatheaceae). We assessed how the observed patterns compare with those estimated for other ferns and seed plants. Populations of A. firma exhibited strong SGS, spatial clustering of individuals, substantial clonal diversity and no inbreeding. SGS in ferns appears to be higher than in most seed plants analysed to date. Contrary to our expectations, an outcrossing breeding system, wind dispersal and an arborescent life form did not translate into weak or no SGS. In ferns, SGS is probably being affected by the life cycle with two free‐living life stages. The reproductive biology of ferns appears to be more complex than previously thought. This implies that SGS in ferns is affected by some factors that cannot be inferred from the study of flowering plants. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 439–449.