Neil Bell

An annotated checklist of the mosses of Europe and Macaronesia

Abstract The moss flora of Europe and Macaronesia comprises 278 genera, 1292 species, 46 subspecies and 118 varieties. Of the total 1292 species, 53 are confined to Macaronesia and 21 are thought to be non-native. The checklist was derived from those for the various component countries and regions. It is based on results published up to the end of 2005. Subspecies and varieties are included; hybrids are omitted. The taxonomic hierarchy is based on one published by Goffinet & Buck in 2004. While it has been strongly influenced by results of modern molecular methods, there are still many remaining uncertainties, even at family level. Because of these uncertainties, taxonomic innovation has generally been avoided. There are four new combinations and one change of status.

Advances in plant gene-targeted and functional markers: a review

Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.

Phylogeny of the moss class Polytrichopsida (BRYOPHYTA): Generic-level structure and incongruent gene trees

Analysis of an extensive new molecular dataset for the moss class Polytrichopsida provides convincing support for many traditionally recognised genera and identifies higher level phylogenetic structure with a strong geographic component. A large apical clade that is most diverse in the northern hemisphere is subtended by a grade of southern temperate and tropical genera, while the earliest diverging lineages have widely separated relictual distributions. However, there is strongly supported topological incongruence between the nuclear 18S rRNA gene tree and the chloroplast and mitochondrial data for the positions of some taxa and notably for the status of Pogonatum. While Pogonatum is unambiguously paraphyletic in the 18S tree, it is well supported as monophyletic by the combined chloroplast and mitochondrial data, this being corroborated by several distinctive morphological synapomorphies and a 51-53 bp deletion in the rps4-trnS spacer. We explore various reticulate historical processes and methodological issues as possible explanations for incongruence, and suggest that either (1) the 18S topology is an artefact created by convergence of substitutions at specific sites due to functional and/or molecular-structural constraints not accounted for by the model, or (2) the incongruence is a product of ancient hybridization events. Under the latter scenario, incongruent topologies for Pogonatum are parsimoniously explained if Polytrichum (including Polytrichastrum sect. Aporotheca) is ultimately descended from a hybridization event involving an extinct maternal taxon derived from the branch ancestral to the combined Pogonatum/Polytrichum s.l. clade, and a paternal taxon belonging to (or ancestral to) the apical Pogonatum group to which the majority of extant species belong. Numerous novel relationships of taxonomic and evolutionary significance are supported. Notably, both Polytrichastrum and Oligotrichum are polyphyletic. While Polytrichastrum sect. Aporotheca is closely related to Polytrichum, other species, including the type, are not. The large majority of Oligotrichum species sampled occur in one of two distantly related clades with predominantly northern and southern hemisphere distributions, respectively, implying convergent evolution of this morphology in each of the two temperate zones.

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.

The Paraphyly of Hypnodendron and the Phylogeny of Related Non-Hypnanaean Pleurocarpous Mosses Inferred from Chloroplast and Mitochondrial Sequence Data

Abstract The phylogenetic integrity and relationships of the pleurocarpous moss Hypnodendron and several potentially related taxa are investigated using chloroplast rbcL, trnL-F, and rps4 sequence data, the mitochondrial nad5 region, and a set of 29 morphological characters. Strong support is obtained for the recognition of a monophyletic group, the “hypnodendroid pleurocarps,” that includes Hypnodendron, Braithwaitea, Pterobryella praenitens, the Cyrtopodaceae, Spiridentaceae, and Racopilaceae. This clade is resolved as sister to the Hypnanae with moderately strong support. Hypnodendron is paraphyletic, with H. section Sciadocladus resolved as sister to Pterobryella praenitens and outside of a very well supported clade that includes the other taxa of Hypnodendron in addition to the Spiridentaceae and Cyrtopodaceae. Chloroplast and mitochondrial sequence data show a high degree of congruence, and confidence in critical nodes is increased by long branches, high support values, and indels corresponding to radical modification of sequence and secondary structure within the nad5 group I intron. Based on morphological character state optimisation the hypnodendroid pleurocarps comprise a clade that includes plesiomorphically dendroid, palmate/umbellate terrestrial plants in addition to a number of derived lineages representing adaptive shifts towards epiphytism. These include the prostrate/creeping Racopilaceae, the dendroid-pinnate species in Hypnodendron section Phoenicobryum, and the simple, large-leaved Spiridentaceae and Cyrtopodaceae. Our data also support recognition of the hypnodendroid pleurocarps at the ordinal or superordinal level.

A phylogenetic circumscription of Polytrichastrum (Polytrichaceae): Reassessment of sporophyte morphology supports molecular phylogeny.

Mosses arguably possess the most structurally complex sporangia of any extant land plants, a consequence of being the monosporangiophyte lineage most strongly adapted to terrestrial environments. Morphological and functional variation in the mechanisms that regulate spore release in one of the major classes of mosses, the Polytrichopsida, is largely unexplored, while recent research indicates that the most distinctive structure, the peristome, has evolved independently in the Polytrichopsida and in other mosses. The genus Polytrichastrum was separated from Polytrichum on the basis of such sporangial characters, although the critical features had until recently only been examined using light microscopy, and strong evidence from molecular data indicated that Polytrichastrum as currently circumscribed is polyphyletic. Here we use Bayesian ancestral character state reconstruction in conjunction with extensive scanning electron micrographic studies to elucidate probable morphology at ancestral nodes and define natural taxa. As well as clarifying the structure, evolution, and aspects of development of the peristome-epiphragm complex in this highly prominent group of mosses, the results provide a basis for a revised phylogenetic taxonomy in which the species of Polytrichastrum sect. Aporotheca are recognized once more within Polytrichum.

Gametophytic simplicity in Laurasian and Gondwanan Polytrichopsida — the phylogeny and taxonomy of the Oligotrichum morphology

Abstract Phylogenetic analyses have largely resolved generic and higher level relationships within the Polytrichopsida, enabling polarisation of characters and the identification of macro-evolutionary trends. Topologies show strong geographic patterning, with major groups having predominantly Northern or Southern Hemisphere distributions and some general morphologies having arisen independently on either side of the equator. While most cases of apparent convergence have been taxonomically visible due to sufficient higher-level characters being present to distinguish unrelated genera, convergent reduction may have resulted in conflation of similar gametophytic morphologies in classification. We present further evidence for the polyphyly of Oligotrichum DC. as currently circumscribed, showing how this morphology has probably arisen through reduction on multiple occasions to produce distinct lineages that have lacked taxonomic identity. We present a preliminary arrangement of the species currently recognised in Oligotrichum, accommodating selected Southern Hemisphere taxa in Itatiella G.L.Sm., and combining Atrichopsis compressa (Hook.f. & Wilson) G.L.Sm. and Oligotrichum tenuirostre (Hook.) A.Jaeger under Notoligotrichum G.L.Sm. For several species that clearly do not belong in Oligotrichum but remain of ambiguous affinity to other genera we avoid making new combinations, as ongoing combined molecular and morphological studies have considerable potential to elucidate their relationships in the near future.

Ombronesus stuvensis, a new genus and species of the Ptychomniaceae (Bryophyta) from south west Chile

A new genus of the Ptychomniaceae (Ptychomniales) is described from Juan Stuven Island, south west Chile. Molecular phylogenetic analyses and morphology independently confirm the position of the taxon in the family, but features of the sporophyte (in particular a highly reduced endostome), a unique combination of gametophytic characters and a significant number of molecular autapomorphies indicate that the plant is clearly distinct from previously described genera. Molecular data demonstrate that the new genus is one of the earlier diverging lineages within the order, part of a basal grade that includes Hampeella, Ptychomniella, Tetraphidopsis, and Cladomniopsis, although its precise position remains ambiguous. The Ptychomniales occupy a key phylogenetic position as one of the earliest diverging pleurocarpous lineages with features that are intermediate between the most basal, predominantly orthotropic pleurocarps and the more derived plagiotropic taxa. The new taxon is thus of considerable phylogenetic significance and contributes to the nature conservation value of the locality.

Imre Festetics and the Sheep Breeders’ Society of Moravia: Mendel’s Forgotten “Research Network”

Poczai and coauthors introduce us to a Moravian Count, Imre Festetics, who formulated many principles of genetics before Mendel was born and helped establish the “research network” within which Mendel later developed his own ideas.

Genomics Meets Biodiversity: Advances in Molecular Marker Development and Their Applications in Plant Genetic Diversity Assessment

Genetic diversity is the fundamental source of biodiversity – the total number of genetic characters contributing to variation within species. In other words it is the measure that quantifies the variation found within a population of a given species. Genetic diversity among individuals reflects the presence of different alleles in the gene pool, and hence different genotypes within populations. Genetic diversity should be distinguished from genetic variability, which describes the tendency of genetic traits found within populations to vary (Laikre et al., 2009). Since the beginning of the 20th century, the study of genetic diversity has been the major focus of core evolutionary biology. The theoretical metrics developed, such as genetic variance and heritability (Fisher, 1930; Wright, 1931), provided the quantitative standards necessary for the evolutionary synthesis. Further research has focused on the origin of genetic diversity, its maintenance and its role in evolution. Simple questions such as “who breeds with whom” initiated studies on the relatedness of populations. These investigations led to the formation of metapopulation theory, where a group of spatially separated populations of the same species interact at some level and form a coherent larger group (Hanski, 1998). The discovery of spatial structure in populations was a key element in the early concepts and models of population ecology, genetics and adaptive evolution (Wright, 1931; Andrewartha & Birch, 1954). How different levels of genetic variance affect the rate of evolutionary change within populations has also been intensively studied. Such changes were originally studied using phenotypic markers: variation among individual plants in traits, such as leaf shape or flower color (Ward et al., 2008). Subsequently the detection of genetic variation has become more sensitive, firstly through the utilization of variation in enzymes (allozymes) and then through PCR-based marker systems allowing direct examination of DNA sequence variation. The precise detection of genetic variation/diversity has greatly enhanced studies of evolution. There is