Jaakko Hyvönen

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.

Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects.

The nuclear ribosomal locus coding for the large subunit is represented in tandem arrays in the plant genome. These consecutive gene blocks, consisting of several regions, are widely applied in plant phylogenetics. The regions coding for the subunits of the rRNA have the lowest rate of evolution. Also the spacer regions like the internal transcribed spacers (ITS) and external transcribed spacers (ETS) are widely utilized in phylogenetics. The fact, that these regions are present in many copies in the plant genome is an advantage for laboratory practice but might be problem for phylogenetic analysis. Beside routine usage, the rDNA regions provide the great potential to study complex evolutionary mechanisms, such as reticulate events or array duplications. The understanding of these processes is based on the observation that the multiple copies of rDNA regions are homogenized through concerted evolution. This phenomenon results to paralogous copies, which can be misleading when incorporated in phylogenetic analyses. The fact that non-functional copies or pseudogenes can coexist with ortholougues in a single individual certainly makes also the analysis difficult. This article summarizes the information about the structure and utility of the phylogenetically informative spacer regions of the rDNA, namely internal- and external transcribed spacer regions as well as the intergenic spacer (IGS).

Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and beta-tubulin sequences, morphology, anatomy and secondary chemistry.

Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis on the heterogeneous group of cetrarioid lichens are reconstructed. The results are based on cladistic analyses of DNA-sequences, morphological and chemical data. Almost all currently recognized cetrarioid genera were included in the analyses together with parmelioid and alectorioid members of the presumably monophyletic family Parmeliaceae. We tried to sample taxonomic diversity of the family as widely as possible. The ITS1-5.8S-ITS2 region of the rDNA and a partial β-tubulin gene from 126 samples representing 82 species were analysed. Cetrarioid lichens were identified as a monophyletic group, supported by both ITS and β-tubulin characters. This group was reanalysed using 47 morphological, anatomical and secondary chemistry characters combined with the DNA data matrix. ITS and β-tubulin sequences provide congruent information, and a clear correlation between DNA-data and conidial shape is observed. The current taxonomy of the cetrarioid lichens is discussed and compared with the phylogenetic trees obtained here. A comprehensive study of the phylogeography of some bipolar or subcosmopolitic species with representatives from both hemispheres was performed. Cetraria aculeata is the only taxon where correlation between DNA-data and geographic origin is observed.

ON PHYLOGENY OF THE POLYTRICHALES

Phylogenetic analyses on Polytrichales were conducted using morphological characters as well as sequence data from the chloroplast genes rbcL and rps4 and the nuclear-encoded 18S rRNA gene. Our analyses included 22 species representing all genera of Polytrichales, plus eight outgroup species. Sequence data were obtained from 25, 22, and 19 taxa for 18S, rbcL and rps4 genes, respectively. Phylogenetic trees were constructed with parsimony analyses. Results lend support for recognition of Polytrichales as a distinct, monophyletic entity. After successively approximated weighting, Oedipodium griffithianum appears as the sister-group to Polytrichales. Within Polytrichales, Alophosia, Bartramiopsis, and Lyellia have the most basal placement outside a clade including all other genera. Atrichopsis, Dendroligotrichum, Itatiella, Meiotrichum, and Notoligotrichum are distinguished as a resolved monophyletic group while other genera are left as an unresolved entity. Resolution between these genera is achieved by successive weighting of data. After this, Dawsonia is resolved in the basal position within the clade and Polytrichastrum appears as a sister-taxon to Eopolytrichum and Polytrichum. Polytrichales are typically pioneer plants of open, sometimes even dry, habitats. Despite comprising only a small number of species, the order exhibits great diversity of shapes and sizes, from miniature plants such as Pogonatum piliferum (Dozy & Molk.) Touw of SE Asia and P. pensilvanicum (Hedw.) P. Beauv. of E North America to giants of Papua New Guinea like Dawsonia gigantea Geh. with stems reaching up to 80 cm. The most typical features of Polytrichales are the adaxial leaf lamellae and differentiation of leaves into a distinct blade and sheathing base. The hairy calyptra has given the group its name, although most genera have practically naked calyptrae. Sporophytes of Polytrichales normally have a well-developed peristome with at least 16 teeth that consist of whole cells. The epiphragm that covers the mouth of the capsule is a unique character that distinguishes most of the genera from all other groups of mosses. Size and shape of the urn vary greatly among genera (Schofield 1985; Smith 1971). The number of currently accepted genera in the Polytrichales is 19, and the approximate number of species in each genus is given in Table 1. One genus, along with its sole species Eopolytrichum antiquum Konopka, Herendeen, Merrill & Crane, is known only from beautifully preserved late Cretaceous fossils that reveal its structures in fine detail (Konopka et al. 1997). Many of the remaining genera are monotypic and all the others, with the exception of Pogonatum and Polytrichum, are fairly small. Schofield (1985) gives a conservative estimate of about 370 for the number of species in Polytrichales, but on the basis of recent critical revisions (e.g., Hyvinen 1989) it is realistic to assume that the number is actually closer to, or even less than, 200. Some species, like Polytrichum juniperinum Hedw., are almost cosmopolitan, while others, like the Macaronesian Alophosia azorica (Ren. & Card.) Card., are narrow endemics and possibly 1 This paper was presented at the 1997 Montr6al ABLS symposium sponsored by the Green Plant Phylogeny Research Coordination Group (with funding provided by DOE/NSF/USDA Panel on Collaborative Research in Plant Biology, USDA grant 94-7105-0713, Co-Pls Mark A. Buchheim, Brent D. Mishler, Russell L. Chapman). 0007-2745/98/489-504

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

1.75/0 This content downloaded from 207.46.13.162 on Fri, 01 Jul 2016 05:45:45 UTC All use subject to http://about.jstor.org/terms 490 THE BRYOLOGIST [VOL. 101 TABLE 1. The approximate number of species in the genera of Polytrichales. t-fossil. Alophosia 1 Meiotrichum 1 Atrichopsis 1 Notoligotrichum 10 Atrichum 15 Oligotrichum 10 Bartramiopsis 1 Pogonatum 50 Dawsonia 10 Polytrichadelphus 10 Dendroligotrichum 2 Polytrichastrum 10 t Eopolytrichum 1 Polytrichum 30 Hebantia 1 Psilopilum 2 Itatiella 1 Steereobryon 1 Lyellia 4 even threatened by extinction. Ecologically, the Polytrichales range from xerophytes like Polytrichum piliferum Hedw. to species of peaty, wet habitats like P. commune Hedw. Although their structure appears so obviously adapted to dry environments, the Polytrichales are largely absent from extremely arid regions, and the group exhibits greatest diversity in areas with humid or moist climates like SE Asia and Central America-northern South America. Phylogenetic relationships of the Polytrichales are particularly relevant to considerations of moss evolutionary history since the group is probably among the first of the lineages that diverged from the common ancestor of all mosses (Mishler & Churchill 1984). Smith (1971) presented a dendrogram with assumed phylogenetic trends for Polytrichales, and these ideas were further developed in his study of epiphragm structure and spore ornamentation (Smith 1974). Hyv6nen (1989), in a revision of Pogonatum that included cladistic analysis based on manual Hennigian argumentation, tentatively distinguished three entities in the Polytrichales as an unresolved basal trichotomy. These, and many other authors, viewed Polytrichastrum G. L. Sm. as the closest extant approximation to the common ancestor of Polytrichales. Forrest (1995) presented the first computer-aided analyses of Polytrichalean phylogeny based on a matrix of 50 characters compiled from the literature. The cladogram from her successively weighted analysis of these data is presented in Figure 1 (fig. 3b in Forrest 1995). In contrast to the views noted above, the position of Atrichum as sister to the remaining Polytrichales suggests that relatively simple members of the group more closely approximate the ancestral condition. This is congruent with ideas presented previously by Fleischer (1923). Forrests (1995) analyses resolved both strongly and weakly supported groups as implied by the number of characters supporting each clade. To test the strength of the phylogenetic hypotheses based on morphology and to determine whether they are congruent with other sources of data we explored Tetraphis

Multiple origins of symbioses between ascomycetes and bryophytes suggested by a five-gene phylogeny

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.

High selectivity in symbiotic associations of lichenized ascomycetes and cyanobacteria

Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked and their identity and nutritional strategies are mostly unknown. Most of these bryosymbiotic fungi belong to the Ascomycota. Their fruit‐bodies are extremely small, often reduced and simply structured, which is why they cannot be reliably identified and classified by their morphological and anatomical characters. A phylogenetic hypothesis of bryosymbiotic ascomycetes is presented. New sequences of 78 samples, including 61 bryosymbionts, were produced, the total amount of terminals being 206. Of these, 202 are Ascomycetes. Sequences from the following five gene loci were used: rDNA SSU, rDNA LSU, RPB2, mitochondrial rDNA SSU, and rDNA 5.8S. The program TNT was used for tree search and support value estimation. We show that bryosymbiotic fungi occur in numerous lineages, one of which represents a newly discovered lineage among the Ascomycota and exhibits a tripartite association with cyanobacteria and sphagna. A new genus Trizodia is proposed for this basal clade. Our results demonstrate that even highly specialized life strategies can be adopted multiple times during evolution, and that in many cases bryosymbionts appear to have evolved from saprobic ancestors.

Phylogenetic hypotheses: Cladoniaceae, Stereocaulaceae, Baeomycetaceae, and Icmadophilaceae revisited

The selectivity of mycobionts and cyanobionts in lichen symbioses were examined. We analyzed symbiotic cyanobionts, collected from different sample sites, and compared them to free‐living cyanobacteria Nostoc. Cyanobionts were obtained from lichens assigned to the genera Pseudocyphellaria and Sticta, in particular. Multiple gene loci were screened and direct optimization was used in the phylogenetic analyses. We show that many lichen fungi are strongly selective towards their cyanobionts. Lichenized ascomycetes seem to be able to identify and choose a specific strain, species or a species group of Nostoc with which to associate. The present analyses also suggest that some of the Nostoc taxa may be specialized in symbiotic life with only lichenized ascomycetes. Despite the selectivity observed in fungi, there appears to be no coevolution between the partners. We have also discussed the problems of using the tRNALeu intron as a marker in phylogenetic analyses.

On the origin of Solanum nigrum: can networks help?

Parsimony analyses of SSU rDNA sequences were conducted to examine phylogenetic relationships of selected genera within the families Cladoniaceae, Stereocaulaceae, Icmadophilaceae and Baeomycetaceae (lichen-forming ascomycetes). The analyses included 93 taxa (84 species) representing various groups of ascomycetous fungi. Analyses of the matrix with pre-aligned sequences were performed using heuristic and parsimony ratchet searches, and support values for the same matrix were calculated using parsimony jackknifing. The results support the recognition of the four families. Cladoniaceae are recircumscribed to accommodate Cladia, Cladonia, Heterodea, Metus, Pilophorus, Pycnothelia, Ramalea, Thysanothecium and the newly erected genus Carassea. Myelorrhiza is excluded from the family, while the status of other potential members, Calathaspis, Gymnoderma s.str. and Squamella, remains unresolved. Baeomycetaceae include Baeomyces and Phyllobaeis. Stereocaulaceae include Stereocaulon only, although the status of Muhria is still unclear. Finally, Icmadophilaceae include Dibaeis, Endocena, Knightiella, Icmadophila, Siphula and Thamnolia, while the status of Pseudobaeomyces and Siphulella requires further elucidation. The genus Cladonia appeared to be a polyphyletic assemblage, and accordingly, a new genus Carassea S. Stenroos, gen. nov., represented by C. connexa (Vain.) S. Stenroos, comb. nov., is described. Carassea is most closely related to Pycnothelia and Metus in the Cladoniaceae. Siphula, represented in the present analysis by six species, is not monophyletic, and is in need of reclassification.