Angela E. Newton

The evolution of asexual reproduction in plants

Prologue. Patterns of reproduction in bryophytes and tracheophytes. The costs, benefits and constraints of asexual reproduction in plants. Cosexuality, asexuality and the male function. The genetic control of apomixis. At the court of the red queen. Reflections. References. Index.

Mid-Miocene cooling and the extinction of tundra in continental Antarctica

A major obstacle in understanding the evolution of Cenozoic climate has been the lack of well dated terrestrial evidence from high-latitude, glaciated regions. Here, we report the discovery of exceptionally well preserved fossils of lacustrine and terrestrial organisms from the McMurdo Dry Valleys sector of the Transantarctic Mountains for which we have established a precise radiometric chronology. The fossils, which include diatoms, palynomorphs, mosses, ostracodes, and insects, represent the last vestige of a tundra community that inhabited the mountains before stepped cooling that first brought a full polar climate to Antarctica. Paleoecological analyses, 40Ar/39Ar analyses of associated ash fall, and climate inferences from glaciological modeling together suggest that mean summer temperatures in the region cooled by at least 8°C between 14.07 ± 0.05 Ma and 13.85 ± 0.03 Ma. These results provide novel constraints for the timing and amplitude of middle-Miocene cooling in Antarctica and reveal the ecological legacy of this global climate transition.

Evolution of the major moss lineages: phylogenetic analyses based on multiple gene sequences and morphology

Abstract Evolutionary relationships of mosses are still poorly understood, with family, order, and subclass circumscription and relationships remaining especially obscure. Over the past decade, a considerable body of data has accumulated, including information on morphological, developmental, anatomical, and ultrastructural characteristics, as well as nucleotide sequences for a number of nuclear and plastid genes. We have combined data from these different sources to provide an overview of the relationships of the major lineages of mosses. We analyzed a data set that includes 33 moss species and ten outgroup taxa drawn from the liverworts, hornworts, and vascular plants. Molecular data consisted of nucleotide sequences from four DNA regions, (rbcL, trnL-trnF, rps4 and 18S). Morphological data included 41 characters of which many were derived from published anatomical and ultra-structural studies. Combining morphological and molecular data in the analyses showed that mosses, including Sphagnum, Takakia, Andreaea and Andreaeobryum, form a monophyletic group, provided improved resolution of higher level relationships, and further insight into evolutionary patterns in morphology.

Phylogenetic Relationships Among the Diplolepideous-alternate Mosses (Bryidae) Inferred from Nuclear and Chloroplast DNA Sequences

Abstract The diplolepideous-alternate peristome, when most highly developed, has endostome segments attached to a basal membrane and positioned alternate to the outer exostome teeth, with cilia often present between the segments. This peristome type defines the Bryidae ( sensu Vitt et al. 1998), which includes four orders: the Bryales, Leucodontales, Hypnales, and Hookeriales, of which the latter three are mainly pleurocarpous in their growth form. Chloroplast (rbcL, rps4, and trnL-trnF) and nuclear (18S rRNA) gene sequences have been analyzed using the parsimony optimality criterion to elucidate relationships among the Bryidae. The analyses strongly support the paraphyly of the Bryidae, with the Splachnidae, and possibly the Orthotrichidae, having arisen from ancestors within the Bryidae. The Leucodontales, Hypnales, and Hookeriales form a monophyletic group, as do the pleurocarpous members of the Bryidae. However, the two pleurocarpous clades are not resolved as sister groups, although their non-monophyly is not supported by the bootstrap. The phylogenetic hypothesis provides a context in which to infer evolutionary transitions in some key morphological characters relating to the peristome and the transition from the acrocarpous to pleurocarpous growth forms.

Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms.

Background High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms. Methodology/Principal Findings This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples. Conclusions/Significance These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography.

Ordinal Phylogeny within the Hypnobryalean Pleurocarpous Mosses Inferred from Cladistic Analyses of Three Chloroplast DNA Sequence Data Sets: trnL-F, rps4, and rbcL

Abstract Classification of families of hypnobryalean mosses into the Hypnales, Leucodontales, and Hookeriales has been taxonomically difficult. Several researchers have sequenced different genes for independent phylogenetic studies of these three pleurocarp groups. Our goal is to summarize available molecular data and compile the largest data set to infer phylogenetic relationships among families as basis for classification at ordinal level. Sequences of rbcL, trnL-F, and rps4 loci for 38 exemplars of most families of Hypnales, Leucodontales, and Hookeriales were analyzed to evaluate whether or not each of the three orders is monophyletic. Cladistic analyses of combined sequences, using five taxa in the Bryales as outgroups, reveal a robust clade (decay > 5) including all hypnobryalean pleurocarps. Within this group, one clade (decay = 2) includes only taxa of the Hookeriales, and is sister to a large monophyletic group (Hypnales sensu lato) containing all other taxa (decay = 2) previously in the Leucodontales and Hypnales. These relationships suggest that the ordinal level taxonomy needs to be reconsidered since major lineages detected do not correspond to the traditional Leucodontales or Hypnales. These two orders are not supported by any molecular evidence from rbcL, trnL-F, or rps4, either analyzed singly or in different combinations. Additionally, present results indicate the need for changes to the current system of three suborders of Hypnales and four of the Leucodontales. Phylogenetic reconstructions based on molecular data emphasize the need for a re-examination of the taxonomic relevance of morphological characters and corroborate previous interpretations of sporophytic morphological similarities as multiple transitions to similar solutions to epiphytism among the pleurocarps.

Taxonomy and phylogeny in the earliest diverging pleurocarps: square holes and bifurcating pegs

Abstract The extant members of the earliest diverging pleurocarpous moss lineages comprise few species but span a wide range of structural and molecular diversity, most of it restricted to temperate and high-altitude tropical forests in the Southern Hemisphere. We present the most comprehensive molecular phylogenetic study of these lineages to date, based on parsimony and Bayesian analyses of four regions from the chloroplast and mitochondrial genomes. In addition to corroborating the findings of parsimony methods in this and previous studies, the results of heterogeneous Bayesian analyses provide strong support for sub-topologies that are also consistently found under parsimony, but are rarely well supported. Careful model specification and investigation of potential sources of error increase confidence in the Bayesian results, which provide the basis for a substantially revised classification reflecting the best currently available hypothesis of evolutionary history. The genera previously classified in the Rhizogoniaceae, together with Orthodontium, Orthodontopsis, Aulacomnium and Calomnion, are recognized in three families, the Orthodontiaceae, Rhizogoniaceae and Aulacomniaceae, and three monofamilial orders, the Orthodontiales ord. nov., Rhizogoniales and Aulacomniales ord. nov. Many of the species previously recognized in Hypnodendron are placed in Sciadocladus, Touwiodendron gen. nov., Dendro-hypnum or Mniodendron. These genera, with the exception of Sciadocladus, are placed in the Hypnodendraceae together with Spiridens, Franciella, Cyrtopus and Bescherellia. Braithwaitea is excluded from the Hypnodendraceae and recognized in the monogeneric Braithwaiteaceae fam. nov., while Sciadocladus is placed with Pterobryella and Cyrtopodendron in the Pterobryellaceae. The Hypnodendraceae, Pterobryellaceae, Braithwaiteaceae and Racopilaceae are recognized in the order Hypnodendrales comb. et stat. nov. We discuss the advantages and limitations of ranked classification systems and propose the abandonment of intercalated Linnaean ranks between order and class levels in Bryopsida. Three node-based informal names, the Pleurocarpids, the Core Pleurocarps and the Homocostate pleurocarps, are defined to represent evolutionarily significant clades within the pleurocarpous group.

A New Contribution to the Moss Flora of Dominican Amber

Abstract The largest collection studied so far of mosses in Dominican amber is reported here. The collection, in the Smithsonian Institution, consists of 76 pieces of amber containing bryophyte material, with a range of one to seven species of mosses and liverworts per piece. Nearly all specimens could be attributed to extant taxa and a total of 18 distinct moss species were identified in this collection, which raises the total number of mosses known from Dominican amber to 28. Six taxa assignable with some confidence to extant species are reported for the first time from Dominican amber: Calymperes levyanum, Calymperes smithii, Mniomalia viridis, Octoblepharum cylindricum, Orthostichopsis praetermissa, Plagiomnium rhynchophorum. A list of all species of mosses so far known from Dominican amber is given with an indication of their frequency in amber, and present distribution and altitudinal range. Some species are very rare at present and may be approaching extinction today. The main component of mosses so far found from the amber forest consists of species of Leucobryaceae, Calymperaceae, and Neckeraceae. Most species are widespread and found today in the West Indies as well as in Central and South America, thus representing an old stock of neotropical species. The present altitudinal distribution of the species ranges from lowland-submontane to montane, indicating climate changes within the period of amber production. In contrast to the liverworts reported from Dominican amber, the mosses can mostly be attributed to extant species, indicating perhaps a slower rate of evolution than in liverworts. Assemblages of several bryophyte species in amber show the presence of extinct liverworts together with extant mosses, the latter in combinations which are still found today.

The Transition to Pleurocarpy: A Phylogenetic Analysis of the Main Diplolepidous Lineages Based on rbcL Sequences and Morphology

Hypotheses of character evolution require a phylogeny for polarization of transformations and optimization of state changes. Our goal is to provide a phylogenetic hypothesis for diplolepidous mosses to investigate the evolution of morphological features associated with the transition to pleurocarpy. We performed cladistic analyses of morphological and molecular data sets for exemplars of the main diplolepidous lineages. These analyses were designed to sample families commonly included in the Leucodontales, Hookeriales, and Hypnales with some exemplars also from the Bryales. Diplolepidous taxa (Bryaceae, Splachnaceae, Orthotrichaceae, Macromitriaceae, and Hedwigiaceae) were included as close outgroups, and Dicranum scoparium, Grimmia apocarpa, and Funaria hygrometrica were included as distant outgroups. We constructed a molecular data set derived from sequences of the chloroplast rbcL gene for 36 species, 22 of which were pleurocarp exemplars. In the molecular analysis, the bryalean pleurocarps were the sister group of acrocarp exemplars from the Bryales. However, in the analyses of combined morphological and rbcL data, the bryalean pleurocarps were the sister group of a clade that includes the 11 exemplars from the Leucodontales, Hypnales, and Hookeriales, thus pleurocarpy appeared monophyletic. Decay analyses suggested that the grouping of bryalean and hypnobryalean pleurocarps together was weak, whereas both the hypnobryalean and bryalean pleurocarp clades were individually robust. Present cladistic analyses provide an inferential basis for structural investigations of branching systems and the evolution of pleurocarpy in a phylogenetic

Disentangling knots of rapid evolution: origin and diversification of the moss order Hypnales

Abstract The Hypnales are the largest order of mosses comprising approximately 4200 species. Phylogenetic reconstruction within the group has proven to be difficult due to rapid radiation at an early stage of evolution and, consequently, relationships among clades have remained poorly resolved. We compiled data from four sequence regions, namely, nuclear ITS1–5·8S–ITS2, plastid trnL–F and rps4, and mitochondrial nad5, for 122 hypnalean species and 34 species from closely related groups. Tree topologies from both Bayesian and parsimony analyses resolve the order as monophyletic. Although inferences were made from fast-evolving genes, and despite strong phylogenetic signal in the nuclear ITS1–5·8S–ITS2 data, monophyly, as well as backbone nodes within the Hypnales, remains rather poorly supported except under Bayesian inferences. Ancestral distribution based on Bayesian dispersal-vicariance analysis supports a Gondwanan origin of the Hypnales and subsequent geographical radiation in the area of the former Laurasian supercontinent. Reconstruction of historical biogeography is congruent with mainly tropical and Gondwanan distributions in the sister groups Hypnodendrales, Ptychomniales, and Hookeriales, and with the dating for the oldest pleurocarp and hypnalean fossils. We contrast groupings in the phylogenetic tree with recent classifications and other phylogenetic inferences based on molecular data, and summarise current knowledge on the evolutionary history of, and relationships among, the Hypnales.