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.

The classification of the Bryopsida (mosses) has been based primarily on the variation of sporophytic characters i.e., architectural features of the peristome teeth that line the capsule mouth. Five arthrodontous peristome types have been recognized. Whether peristome types define natural groups and how they are evolutionary related has, however, remained unclear. Nucleotide sequence data from one nuclear and two chloroplast loci are generated and compiled to test two contrasting hypotheses regarding the ancestral peristome type in the Arthrodonteae. The genomic data partitions are incongruent with regard to the phylogenetic signal they carry. All phylogenetic analyses converge toward the polyphyly of the Funariineae and the Funariaceae. The Funariaceae are defined by the loss of a codon in therps4 gene. Goniomitrium acuminatum, the type of the genus, lacks this deletion, and is always resolved within the Haplolepideae. Consequently Goniomitrium is transferred to the Pottiaceae. The Ephemeraceae and Splachnobryaceae are tentatively retained as distinct, but with strong affinities to the Pottiineae. Neither the combined nor the independent data sets yield well supported topologies under the parsimony optimality criterion. Hence, the relationships among major lineages remain ambiguous. Inferences from chloroplast data alone yield a basal dichotomy between taxa with alternate peristomes (Orthotrichales and Bryales sensu lato) and those with opposite peristomes (Encalyptineae, Disceliaceae, Funariaceae, Timmiaceae, and the Haplolepideae). In contrast, analyses of the combined data resolve the Timmiaceae as sister to the split between the two peristomial lineages. It is hypothesized that the symmetric divisions of the IPL cells, is a synapomorphy for at least the Encalyptineae-Funariineae clade. The endostomial appendages of the timmiaceous peristome could, under either phylogenetic hypothesis, be regarded as homologous to the cilia in the bryoid peristome. Although the relationships among major lineages of arthrodontous mosses remain ambiguous, this study suggests that taxa with reduced or no peristomes, such as the Disceliaceae and the Gigaspermaceae, may be crucial in resolving the early evolutionary history of the Arthrodonteae when using DNA sequences.

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.

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.

Mosses with haplolepideous peristomes form a major lineage within the arthrodontous taxa, the Dicranidae. Relationships among lineages within the Dicranidae are explored using three cpDNA regions: rbcL, rps4, and the region spanning trnL(UAA)- trnF(GAA). Maximum parsimony analyses of combined data sets support robust clades that correspond to traditionally recognized families. Phylogenetic relationships of 71 exemplar taxa rooted with five outgroup taxa identify 13 major clades within the Dicranidae. Predominantly the monophyly of these groups is strongly supported, although relationships among the clades are ambiguous. The phylogenetic implications of the current taxon sampling include 1) the Dicranidae are monophyletic, 2) the Pottiales are polyphyletic with the Calymperaceae and Octoblepharaceae cladistically distant from the Pottiaceae, and these two former families should be transferred to the Dicranales, 3) the Dicranales are polyphyletic, with Ditrichaceae and Rhabdoweisiaceae more closely related to the Pottiaceae than other members of the Dicranales, 4) the Fissidentaceae are nested within the Dicranales, 5) the Rhachitheciaceae and Erpodiaceae are nested within the Dicranidae and sister to the Pottiaceae, 6) Amphidium is sister to the pottiaceous ^{clade, 7}) the Seligeriaceae form a well supported sister relationship to the Grimmiales, and 8) Scouleria aquatica, Bryoxiphium norvegicum, Ditrichum flexicaule, and Timmiella crassinervis appear to form basal lineages within the Dicranidae.

Most reconstructions of basal land plant relationships derived from morphological or molecular data suggest that the Sphagnopsida form a critical clade at or near the base of the mosses (Bryophyta s.s.). The Sphagnopsida include two orders: Sphagnales and Ambuchananiales, each with one family. The Ambuchananiaceae is monotypic, with A. leucobryoides of Tasmania. Nucleotide sequences from five genomic regions, two from the nuclear genome (ITS and 26S nuclear ribosomal DNA) and three from the chloroplast genome (psbT, rpl16, trnL) were subjected to cladistic analyses in order to assess 1) the relationship between Ambuchanania and Sphagnum, 2) the polarity of evolutionary change in Sphagnum (i.e., infer a root for the infrageneric phylogeny), 3) monophyly of the four large sections of Sphagnum (Acutifolia, Cuspidata, Sphagnum, and Subsecunda) and 4) phylogenetic relationships of the smaller or monotypic sections. Ambuchanania is resolved as the sister group to Sphagnum and is not nested within the latter as a highly derived species. Polarity of evolutionary change in Sphagnum is ambiguous; alternative hypotheses suggested by molecular data place either the sect. Subsecunda or the sect. Sphagnum as sister to all other species. The four large sections of Sphagnum are each monophyletic if circumscribed to include species traditionally placed in monotypic sections. Sphagnum macrophyllum ^{(sect. Isocladus),} is nested within the Subsecunda. Sphagnum pylaesii ^{(sect. Hemitheca),} is nested within the Cuspidata and is closely related to S. tenellum (sect. Mollusca). Sphagnum wulfianum ^{(sect. Polyclada),} is nested within the Acutifolia, closely related to S. fimbriatum and S. girgensohnii. Sphagnum aongstroemii ^{(sect. Insulosa)} is either nested within the Acutifolia, or is sister to other species of Acutifolia. Molecular evidence supports a sister group relationship between the sections Rigida and Sphagnum, and between the sections Squarrosa and Acutifolia. Molecular data suggest that phylogenetic structure in Sphagnum can be accommodated by four large sections without segregating morphologically distinctive taxa into smaller sections, as is traditionally done. A revised classification is proposed in which the genus is divided into four sections: Acutifolia, Cuspidata, Sphagnum, and Subsecunda.

Molecular phylogenies of the complex-thalloid liverworts (Marchantiales) were reconstructed using independent nuclear and plastid data sets to explore relative age, relationships, and character evolution in this ancient group. The sample includes 10 carpocephalate taxa and 24 acarpocephalate taxa (emphasizing Riccia) within Marchantiales sensu stricto. In addition, Monoclea, Sphaerocarpos, Riella, three Metzgeriales (Fossombronia, Pellia, and Blasia), the hornwort Anthoceros, four mosses, and outgroup Coleochaete are also sampled. Two nucleotide sequence alignments were used 1) partial nuclear-encoded Large Subunit rDNA (LSU rDNA) for all 48 taxa and 2) the plastid-encoded trnL-F region for the marchantioids and outgroup Blasia. Alignment-ambiguous regions of each alignment were culled. A combined matrix consisting of concatenated nuclear and plastid culled alignments was assembled for marchantioids and Blasia. The two alignments were utilized in four analyses: 1) nuclear LSU rDNA for all taxa, 2) nuclear LSU rDNA for marchantioids Blasia, 3) plastid trnL-F region for marchantioids plus Blasia, and 4) combined nuclear and plastid data for marchantioids plus Blasia. Selected pairwise comparisons reveal significant rate heterogeneity in the nuclear LSU rDNA data; metzgerioid liverworts, hornworts and primitive mosses evolve significantly slower than other taxa relative to the outgroup Coleochaete. The LSU rDNA genes of some marchantioid taxa and sampled bryalean mosses are apparently evolving relatively fast. Rate heterogeneity is also documented within Marchantiales. Lunularia positions as the most basal of sampled Marchantiopsida; Sphaerocarpales, Marchantia, and Corsinia represent early diverging lines. A monophyletic Aytoniaceae, Cleveaceae, and Riccia are indicated. Topologies imply that extant acarpocephalate taxa are derived from carpocephalate forms. Monoclea positions well within Marchantiales sensu stricto. A well-supported long branch (Decay Index = 19) unites all sampled Marchantiopsida and isolates this clade from other liverworts and bryophytes. This long branch may suggest extensive extinction of proto- and eomarchantioid forms that led to modern taxa. A recurring theme in the topologies presented here is the unresolved marchantioid polytomy that follows well-supported basal nodes. A similar polytomy results from either independent data set and may correspond to a rapid radiation of marchantioid forms (e.g., Aytoniaceae, Cleveaceae, Targionia, Monoclea, and riccioids) coincident with extreme conditions and ecological reorganizations of the Permo-Triassic. The origin of Marchantiopsida probably occurred long before; amidst, perhaps, a series of long-extinct Blasia-like ancestors that colonized and innovated on any of various xeric surfaces (either cool or warm) that were available throughout embryophyte history in the Paleozoic.

Sphagnum-dominated peatlands occupy extensive tracts of land throughout the Boreal and Subarctic regions of North America, extending north onto the Low Arctic of the Canadian Shield and south along the west coast of Oregon, Rocky Mountains of Wyoming, and Appalachians of West Virginia. In addition, short pocosins found along the southeastern coast also can be considered as Sphagnum-dominated peatlands, even though they differ significantly from traditional concepts of boreal peatlands. Along the southern limit of Sphagnum-dominated peatlands, where climate is limiting, edaphic factors allow for the development of outliers. As the current distribution of Sphagnum-dominated peatlands is related to Sphagnum spore rain, past distributions of Sphagnum-dominated peatlands can be constructed from spore records preserved in lakes and peatlands. Here we present six time slices extending back to the Last Glacial Maximum to determine how Sphagnum-dominated peatlands have varied in both time and space. The spore record indicates that Sphagnum-dominated peatlands were present in North America during the Last Glacial Maximum although they were spatially limited to central Alaska, the Olympic Peninsula and Puget Trough of Washington, and to a narrow band in the eastern states of Kentucky, North Carolina, Tennessee, and Maryland. During the Late Wisconsinan Sphagnum-dominated peatlands shifted northwards in eastern North America and expanded farther into Alaska and the Midwest. The Late Wisconsinan/Holocene transition marks a time of overall increase in the area supporting Sphagnum-dominated peatlands, while extending farther in eastern Canada and western continental and coastal regions, they almost completely disappear in the Midwest where they were extensive earlier. Sphagnum-dominated peatlands generally reach their current extent about 2,000–3,000 years ago. Sphagnum-dominated peatlands have dramatically changed their distribution and abundance since the Last Glacial Maximum, and hence the carbon that is stored in these present-day important sinks has also changed dramatically. When compared to the estimated 220 Pg of carbon stored in North American peatlands today, less than 10% of this carbon was present in these peatland during the LGM.

Phylogenetic analyses of nuclear and chloroplast DNA sequences resolve four major clades within the peatmosses, and these lineages correspond to sections that have traditionally been recognized based on morphology. The sectional placement of most species is unambiguous, but four taxa combine the nuclear sequences of one section with the chloroplast sequences of another. A hypothesis of past reticulate evolution is favored over lineage sorting to account for this incongruence, because single genome analyses (nuclear vs. chloroplast) indicate that the species are derived within their respective sections. Sphagnum mendocinum, from the Pacific coast of North America, has the nuclear DNA of section Subsecunda, but the chloroplast DNA of section Cuspidata. Sphagnum cuculliforme, from Ecuador, has the nuclear sequences of section Subsecunda, but the chloroplast sequences of section Sphagnum. Sphagnum falcatulum and S. ehyalinum, both from temperate Southern Hemisphere, have the nuclear sequences of section Cuspidata, but the chloroplast sequences of section Subsecunda. While morphological evidence alone would not be sufficient to hypothesize past reticulations, at least three of the four species are atypical and ambiguous with regard to sectional placement. Sphagnum mendocinum is morphologically intermediate between the Subsecunda and Cuspidata, S. cuculliforme has previously been classified in its own monotypic section because of a unique combination of morphological characters, and S. ehyalinum is highly unusual because of a near absence of differentiated chlorophyllose and hyaline cells in the branch leaves. S. ehyalinum is described as new in this paper. Sphagnum falcatulum is morphologically typical of the section Cuspidata, to which it appears to belong based on nuclear DNA sequences. These inferences of reticulation between widely divergent taxa add to growing evidence of hybridization in the peatmosses.

Syntrichia minor (Bizot) stat. et comb. nov. (basionym: Tortula papillosissima var. minor Bizot) is proposed at the rank of species and its geographical range is extended to Europe (Iberian Peninsula). The species is described, lectotypified, illustrated, and compared with Syntrichia virescens (De Not.) Ochyra, from which it can be distinguished by the type of papillosity.

One hundred eighty-two taxa of lichens including two lichen parasites are reported from Izembek National Wildlife Refuge on the tip of the Alaska Peninsula. Metasphaeria tartarina is new to North America; Scoliciosporum umbrinum is new to Alaska. Wide-ranging, arctic-alpine, and boreal species dominate the lichen flora; a coastal element is moderately represented, while amphi-Beringian species form a minor element. Epigeic lichen abundance is described along a lowland to alpine mesotopographic gradient selected to represent major landscape variation in the refuge. Of six major community types identified, three had significant lichen components.

The blepharoplast of Riccia gougetiana displays typical features of the subclass Marchantiidae. The spline reaches a maximum of 24 microtubules and has a closed aperture the equivalent of two microtubule diameters in width. The lamellar strip is longitudinally elongated and asymmetrically spatulate in shape, 1.96 μm long and 0.74 μm wide, the same as the overlying spline. The basal bodies are staggered in insertion, overlapping, and parallel with the spline over most of their lengths. The ABB, situated over the right side of the spline and 0.22 μm from the anterior spline margin, measures 0.71 μm in length including triplet extensions. The PBB is longer, at 1.16 μm, and is situated over the left side of the spline, 0.59 μm from the leading edge of the spline. The uniformity of blepharoplast features in the subclass Marchantiidae, and particularly within the Marchantiales, supports the concept of a monophyletic grouping. The overall similarity of the blepharoplast among those marchantialian genera studied in detail is striking and further supports the use of these features in studying the relationships among bryophytes.