Showing papers in "Phytotaxa in 2014"

Moss diversity: A molecular phylogenetic analysis of genera

Abstract: In this study we present phylogenetic and molecular phylogenetic diversity analyses of moss taxa from a total of 655 genera of mosses. Three loci were sampled: chloroplast ribosomal small protein 4, the intronic region of the mitochondrial NADH dehydogenase subunit 5, and partial sequences of the nuclear 26S ribosomal RNA. Maximum likelihood and Bayesian phylogenetic analyses were performed on individual loci and on multilocus data sets. A measure of phylogenetic diversity was calculated and constrasted among major lineages of mosses. We reveal many instances of incongruence among genomic partitions, but, overall, our analyses describe relationships largely congruent with previous studies of the major groups of mosses. Moreover, our greater sampling highlights the possible non-monophyly of many taxonomic families, particularly in the haplolepideous and pleurocarpous mosses. Comparisons of taxic and phylogenetic diversity among genera indicate that the Dicranidae (haplolepideous taxa) include about 15% of moss genera, but nearly 30% of the phylogenetic diversity. By contrast, the Hypnanae (hypnalian pleurocarps) contain about 45% of moss genera, but a lower percentage of phylogenetic diversity. Agreement between numbers of genera and phylogenetic diversity within other moss clades are remarkably consistent.

An updated classification for Apocynaceae

Abstract: An updated suprageneric classification is provided for Apocynaceae to bring the family into better agreement with recent morphological and molecular, mainly phylogenetic-based, results. A total of 366 genera are recognized and placed within five subfamilies, 25 tribes and 49 subtribes. In Apocynaceae s. str., one new tribe (Amsonieae) and two new subtribes (Tonduziinae and Vincinae) are described in Rauvolfioideae, and one new tribe (Rhabdadenieae) and nine new subtribes (Amphineuriinae, Beaumontiinae, Chonemorphinae, Galactophorinae, Papuechitinae, Peltastinae, Pentalinoninae, Prestoniinae and Urceolinae) are described or validated in Apocynoideae. Within Asclepiadoideae, one new tribe (Eustegieae) and three subtribes (Diplolepinae, Pentacyphinae and Tassadiinae) are described or validated.

An inventory of vascular plants endemic to Italy

Abstract: For the purpose of the present study we considered as Italian endemics those specific and subspecific taxa occurring in Italy that are not found elsewhere with the exception of Corsica (France) and Malta. This study presents an updated list of the endemic taxa in the Italian flora, including their geographical distribution at regional level. Italy is characterized by 1371 endemic species and subspecies (18.9% of the total vascular flora): three taxa belong to Lycopodiidae, one to Polypodiidae, two to Pinidae and 1365 to Magnoliidae (three paleoherbs, 221 monocots and 1144 eudicots). The endemic flora belongs to 29 orders, 67 families and 304 genera. Sicily, Sardinia, Calabria and Abruzzo are the four regions richest in endemics. About 58% of endemics are confined to a single administrative region. The most represented orders, families and genera are: Asterales, Caryophyllales and Asparagales, Asteraceae, Plumbaginaceae and Caryophyllaceae, Limonium , Centaurea and Hieracium , respectively. The phytogeographic isolation of Sardinia and Sicily and the separation of peninsular Italy from Northern Italy is confirmed. The relative isolation of Puglia with respect the remaining southern Italian pensinsular regions is also confirmed. Alpine region endemics (from northern Italy) are underrepresented.

Fungal symbioses in bryophytes: New insights in the Twenty First Century

Abstract: Fungal symbioses are one of the key attributes of land plants. The twenty first century has witnessed the increasing use of molecular data complemented by cytological studies in understanding the nature of bryophyte-fungal associations and unravelling the early evolution of fungal symbioses at the foot of the land plant tree. Isolation and resynthesis experiments have shed considerable light on host ranges and very recently have produced an incisive insight into functional relationships. Fungi with distinctive cytology embracing short-lived intracellular fungal lumps, intercellular hyphae and thick-walled spores in Treubia and Haplomitrium are currently being identified as belonging to a more ancient group of fungi than the glomeromycetes, previously assumed to be the most primitive fungi forming symbioses with land plants. Glomeromycetes, like those in lower tracheophytes, are widespread in complex and simple thalloid liverworts. Limited molecular identification of these as belonging to the derived clade Glomus Group A has led to the suggestion of host swapping from tracheophytes. Ascomycetes, all identified to date as Rhizoscyphus ericae and having an extremely wide host range extending into the Ericales, occur in the rhizoids of a range of leafy liverwort families that are sister to the Schistochilaceae, where the fungus induces rhizoid branching and septation. Dating of the Schistochilaceae suggests that these liverwort rhizoid associations predated ericoid mycorrhizas. A more restricted distribution of basidiomycetes, all identified as members of the genus Sebacina, is interpreted as a secondary acquisition in leafy liverworts following the loss of ascomycetes. Unlike the latter and ectomycorrhizal basidiomycetes in tracheophytes, these are host specific. Whereas there is no evidence of host digestion for either the ascomycetes or basidiomycetes in leafy liverworts, basidiomycetes in the Aneuraceae display regular colonization and digestion cycles. Considerable molecular diversity in the aneuracean fungi, mainly in the genus Tulasnella with occasional sebacinoids, mirrors the same in the host liverworts. Nesting of the only mycoheterotrophic liverwort Cryptothallus within Aneura is congruent with the phylogeny of the endophytes. Glomeromycete fungi have been identified in Phaeoceros and Anthoceros whereas Dendroceros, Megaceros and Nothoceros lack endophytes but the distribution of fungi across hornworts has yet to be explored. In contrast to liverworts and hornworts, there is no evidence of mycorrhiza-like associations in mosses. Claims that the fossil Prototaxites was a fossil fungus-associated liverwort are discounted.

A catalogue of the vascular plants of the Caatinga Phytogeographical Domain: a synthesis of floristic and phytosociological surveys

Abstract: A catalogue is presented of plant names in use in the Caatinga Phytogeographical Domain (CPD), the largest semiarid ecoregion of South America. We compiled all pubished papers we could locate with floristic and/or phytosociological data relating to the CPD and created a database of all site-based surveys, all names reported in these surveys and the basic ecological data associated with each species. We then mapped the names used in survey reports to those currently accepted in Brazil, consulting specialists to resolve taxonomic and nomenclatural issues before synthesizing the data in order to present here a list of all names in use. Thus this compilation represents the taxonomic data in use by generalist botanists on a sub continental scale. Synthesizing the previously dispersed ecological data available for the species, we explored general ecological patterns in the CPD. We also classified each survey as documenting the flora of a specific type of environment within the CPD and compared the general floristic resemblance between different environments within CPD on a biogeographical scale. Rarefaction curves and species richness estimator indices were employed in order to address the question as to whether or not the Caatinga Phytogeographical Domain can be described as well-sampled. To date over 1700 species have been reported in site-based floristic and phytosociological studies in the CPD. Most surveys focused only on woody plants, ignoring the non woody component, but we show here that a large proportion of the plant biodiversity in the Caatinga is comprised of non woody plants. We estimate that 40% of the existing species were not sampled by site-based surveys. Moreover, most of the species in our database were recorded from a single site, while a few species were considered widespread. When comparing the number of widespread species in our dataset to results published for the cerrado savannas, we show that species in Caatinga seems to have a much more restricted distribution than plants in the Cerrado. We present here a catalogue of all plant names recorded and discuss sampling and geographical issues related to the floristic study of Caatinga.

Checklist of the hornworts and liverworts of Java

Abstract: In this checklist all hornworts and liverworts reports for Java are listed. The horn-and liverwort flora of the island consists of 568 known and accepted species (plus 39 invalid or illegitimate names). In addition 12 recorded species are considered dubious and another 111 species are excluded from the flora of Java. Most of the species are reported from West Java. The genus Stenolejeunea is synonymized with Lejeunea and we make the new combination Lejeunea thallophora (Eifrig) Gradst. and the new name Lejeunea propagulifera Gradst. (nom. nov. pro Trachylejeunea schiffneri Herzog; non Lejeunea schiffneri Steph. ex Schiffn.). A new synonym of Lejeunea papilionacea (Cardiolejeunea cardiantha R.M.Schust. et Kachroo syn. nov.) is proposed.

A synthesis of hornwort diversity: Patterns, causes and future work

Abstract: Hornworts are the least species-rich bryophyte group, with around 200-250 species worldwide. Despite their low species numbers, hornworts represent a key group for understanding the evolution of plant form because the best-sampled current phylogenies place them as sister to the tracheophytes. Despite their low taxonomic diversity, the group has not been monographed worldwide. There are few well-documented hornwort floras for temperate or tropical areas. Moreover, no species level phylogenies or population studies are available for hornworts. Here we aim at filling some important gaps in hornwort biology and biodiversity. We provide estimates of hornwort species richness worldwide, identifying centers of diversity. We also present two examples of the impact of recent work in elucidating the composition and circumscription of the genera Megaceros and Nothoceros. Important areas for further research are highlighted, particularly at taxonomic, ultrastructural, phylogenetic and genomic levels.

20,000 species and five key markers: The status of molecular bryophyte phylogenetics

Abstract: A number of reviews have accompanied and monitored the progress of molecular phylogenetic research on bryophytes, focusing on the publication record itself, bryophyte phylogeny and systematics in the molecular era, as well as the evolution and phylogenetic utility of markers from different genomes. However, none of the recent reviews include a detailed characterization of all molecular markers used in bryophyte phylogenetics. Here we provide an overview of the history and current state of marker utilization, including coding and non-coding sequence markers from all three genomes as well as fingerprinting approaches. The molecular architecture and evolutionary peculiarities, as well as practical aspects such as amplification and sequencing strategies, are outlined for the DNA sequence markers, with a focus on the most commonly employed regions. Their phylogenetic utility and potential for solving some of the remaining, pressing questions in bryophyte phylogeny, as well as their suitability for molecular species identification by DNA barcoding, are discussed.

One hundred and seventy-five new species of Graphidaceae: closing the gap or a drop in the bucket?

Abstract: Recent studies of the global diversity of the lichenized fungal family Graphidaceae suggest that there are a large number of species remaining to be discovered. No less than 640 species have been described since 2002, including 175 new species introduced in a collaborative global effort in a single issue in this journal. These findings suggest that the largest family of tropical crustose lichens may have an even higher number of species than Parmeliaceae. To estimate whether the discovery of 175 new species is a significant step forward in cataloguing extant diversity in this family, we employed a parametric method to predict global species richness of Graphidaceae using a GIS-based grid map approach. The model employs linear regression between observed species richness and sample score and vegetation composition per grid to predict individual grid species richness, and interpolation of species grid distributions to predict global species richness. We also applied a non-parametric species-area curve approach and non-parametric species richness estimators (Chao, Jackknife, Bootstrap) to compare the results from the different methods. Our approach resulted in a prediction of 4,330 species of Graphidaceae, including approximately 3,500 (sub-)tropical species in the core subfamilies Fissurinoideae, Graphidoideae, Redonographoideae, plus 125 species restricted to extratropical regions (outside the zone between 30° northern and 30° southern latitude) and 700 species in subfamily Gomphilloideae. Currently, nearly 2,500 species are known in the family, including species not yet formally described. Thus, our model suggests that even after describing 175 species in this issue and with another approximately 140 awaiting publication, the number of species still to be discovered and described is more than 1,800, and much work remains to be done to close this substantial gap. Based on our approach, we predict that most of this undiscovered diversity is to be found in Mexico, the northern Andean region, the eastern Amazon and central and southern Brazil, tropical West Africa, continental Southeast Asia, Indonesia, and Papua New Guinea.

Roussoellaceae , a new pleosporalean family to accommodate the genera Neoroussoella gen. nov., Roussoella and Roussoellopsis

Abstract: Roussoella and Roussoellopsis species are mostly known from monocotyledons (large grasses, bamboo and palms). Detailed phylogenies for this group are lacking and thus their family placement and relationships with other genera are unclear. Fresh collections of several Roussoella -like species, including the type species Roussoella nitidula were made from bamboo and palms in Thailand. In order to obtain a phylogenetic understanding of Roussoella -like species within the order Pleosporales , we carried out the phylogenetic analyses of ITS, LSU, TEF1α and RPB2 loci. The 15 target strains formed a well-supported clade (100% BS/1.00 PP) in phylogenetic reconstructions of individual and combined datasets, supporting the introduction of a new family Roussoellaceae . The Roussoellaceae clade can be distinguished into three well-supported sections, namely Roussoella / Roussoellopsis (93% BS/1.00 PP), Roussoella (88% BS/1.00 PP) and Neoroussoella . Based on both morphology and phylogenetic analyses, we introduce Neoroussoella gen. nov., epitypify Roussoella nitidula which is the type species of the genus, and introduce the new species Neoroussoella bambusae , Roussoella chiangraina , R. japanensis , R. neopustulans , R. siamensis , R. thailandica and R. verrucispora .

Mesophyllum erubescens (Corallinales, Rhodophyta)—so many species in one epithet

Abstract: The name Mesophyllum erubescens has been applied to protuberant rhodolith specimens which sometimes occur abundantly, as well as to encrusting specimens in tropical and temperate waters in the Western Pacific, Indian and Western Atlantic Oceans. A DNA sequence, representing about 20% of the rbc L gene, was obtained from the 140 year old holotype specimen collected in the Fernando de Noronha Archipelago by the Challenger Expedition. This sequence was identical to field-collected topotype specimens as well as to specimens ranging south along the coast of Brazil. Sequences for psb A from these same Brazilian specimens and specimens from the east coast of Mexico were identical or differed by 1 base pair. In contrast, specimens called M. erubescens based on morpho-anatomical characters in the Pacific Ocean differed from Western Atlantic Ocean specimens by 2.5–13.1%, indicating that these represent numerous distinct species. All reports of non-geniculate coralline species said to be widely distributed across different oceans or in different biogeographic provinces based on morpho-anatomical characters need to be verified by DNA sequences.

The application of molecular data to the phylogenetic delimitation of species in bryophytes: A note of caution

Abstract: Molecular phylogenetics has been of prime importance in revisiting traditional taxonomic hypotheses, and this is especially true in taxa with reduced morphologies like bryophytes. Sequence identity at one or a few loci, as well as evidence for species para-or polyphyly, have been increasingly used to lump species. While sequence identity at loci that are usually variable within the group of interest can provide some incentive for additional study of such species, it does by no means alone provide sufficient evidence for synonymization. Similarly, the strict requirement that all species must be demonstrably monophyletic is equivalent to adopting an uncompromsing view that reproductive isolation (i.e., the biological species concept) is the only valid evidence for species status, and that all species have to be 100% isolated. Some modes of speciation lead to paraphyletic species or even phylogenetic networks. We therefore encourage case by case evaluation of all available data rather than applying a single criterion such as monophyly. We make some suggestions about how to use molecular data in the circumscription of bryophyte species.

Polyphasic characterization of Trichocoleus desertorum sp. nov. (Pseudanabaenales, Cyanobacteria) from desert soils and phylogenetic placement of the genus Trichocoleus

Abstract: Little is known about the taxonomic diversity of cyanobacteria in deserts, despite their important ecological roles in these ecosystems. In this study, cyanobacterial strains from the Atacama, Colorado, and Mojave Deserts were isolated and characterized using molecular, morphological, and ecological information. Phylogenetic placement of these strains was revealed through Bayesian and parsimony-based phylogenetic analyses utilizing sequences of the 16S rRNA gene and the associated 16S–23S ITS region. Based on the combined evidence of this polyphasic approach, a new species from desert soils morphologically corresponding to the genus Trichocoleus was described. Trichocoleus desertorum sp. nov. Muhlsteinova, Johansen et Pietrasiak was used to obtain a phylogenetic reference point for Trichocoleus, a genus so far characterized by morphological description only. Through characterization of this new taxon in desert soils we hope to contribute to the general understanding of cyanobacterial diversity in extreme arid habitats.

Aetokthonos hydrillicola gen. et sp. nov. : Epiphytic cyanobacteria on invasive aquatic plants implicated in Avian Vacuolar Myelinopathy

Abstract: Research into the taxonomy of a novel cyanobacterial epiphyte in locations where birds, most notably Bald eagle and American coots, are dying from a neurologic disease (Avian Vacuolar Myelinopathy—AVM) has been ongoing since 2001. Field investigations revealed that all sites where birds were dying had extensive invasive aquatic vegetation with dense colonies of an unknown cyanobacterial species growing on the underside of leaves. Morphological evaluation indicated that this was a true-branching, heterocystous taxon falling within the former order Stigonematales. However, 16S rRNA gene sequence demonstrated that it did not match closely with any described genus or species. More recent sequence analysis of the 16S rRNA gene and associated ITS region from additional true branching species resulted in a unique phylogenetic placement distant from the other clades of true-branching cyanobacteria. Light, epifluorescent, and transmission and scanning electron micrographs confirm the novel characteristics of this species, which is true-branching form with uniseriate basal filaments. It is encased within a firm sheath and has heterocytes both within the filaments and at the tips of the branches. The species is in a new genus of uncertain family assignment, and is herein named Aetokthonos hydrillicola gen. et sp. nov.

Remarkable diversity of the lichen family Graphidaceae in the Amazon rain forest of Rondônia, Brazil

Abstract: In a continuation of our investigation of lichenized fungi in Rondonia and adjacent areas, we present a preliminary treatment of the graphidoid and thelotremoid core Graphidaceae (subfamilies Fissurinoideae and Graphidoideae). A total of 122 identified species are reported here, almost all of which are new reports to Rondonia, and 37 of which are new to science. This includes three new, monospecific genera, viz. Aggregatorygma triseptatum M. Caceres, Aptroot & Lucking, a new, phylogenetically distinct genus and species similar to Diorygma but with corticate thallus, aggregated and branched lirellae, very small, 3-septate ascospores and unknown secondary substances; Byssotrema mirabile M. Caceres, Aptroot & Lucking, a new genus and species similar to Glaucotrema but with partially carbonized excipulum with pilose inner margin and cinchonarum unknown chemistry; and Corticorygma stellatum M. Caceres, Feuerstein, Aptroot & Lucking, a new, phylogenetically distinct genus and species similar to Diorygma but with non-amyloid ascospores and corticate thallus. The following further species are described as new to science: Cruentotrema amazonum M. Caceres, Aptroot & Lucking, differing from Cruentotrema kurandense in the 3-septate ascospores; Fissurina amazonica M. Caceres, Aptroot & Lucking, differing from F. dumastii in the small, closed, much branched and dense lirellae and the apically smooth paraphyses; F. amyloidea M. Caceres, Aptroot & Lucking, differing from F. subnitidula in the weakly carbonized lirellae and thick-walled, strongly amyloid ascospores; F. chrysocarpa M. Caceres, Aptroot & Lucking, differing from F. chrysocarpoides in the short lirellae with distinct labia; F. duplicans M. Caceres, Aptroot & Lucking, differing from F. pseudostromatica in the endoperidermal thallus and double margin of the lirellae; F. macrospora M. Caceres, Aptroot & Lucking, differing from F. undulata in the much larger ascospores; F. subfurfuracea M. Caceres, Aptroot & Lucking, differing from F. furfuracea in the thin margin of the lirellae (distinctly fissurinoid rather than hemithecioid); Glaucotrema stegoboloides M. Caceres, Aptroot & Lucking, differing from G. glaucophaenum in the papillose thallus and complex columella; Graphis amazonica M. Caceres, Aptroot & Lucking, differing from G. pitmanii in the inspersed hymenium and larger ascospores; G. pustulosa M. Caceres, Aptroot & Lucking, differing from G. hyphosa in the pustulate thallus and larger ascospores; G. rondoniana M. Caceres, Aptroot & Lucking, differing from G. pinicola in the pruinose labia and smaller ascospores; Gyrotrema flavum M. Caceres, Aptroot & Lucking, differing from G. sinuosum in the yellow apothecial disc; Myriotrema foliaceum M. Caceres, Aptroot & Lucking, differing from M. rugiferum in the gall-forming thallus; M. inspersum M. Caceres, Aptroot & Lucking, differing from M. foliicola in the hyaline, smaller ascospores; M. subclandestinum M. Caceres, Aptroot & Lucking, differing from Myriotrema clandestinum in the larger ascospores with more numerous septa; Ocellularia brasiliensis M. Caceres, Aptroot & Lucking, differing from O. africana in the carbonized excipulum and columella and cinchonarum unknown chemistry; O. diminuta M. Caceres, Aptroot & Lucking, differing from O. papillata in the smaller ascomata lacking a columella; O. flavostroma M. Caceres, Aptroot & Lucking, differing from O. fecunda in the ecolumellate ascomata; O. halei M. Caceres, Aptroot & Lucking, differing from O. protoinspersa in the grey thallus, narrow columella, and shorter ascospores; O. immersocarpa M. Caceres, Aptroot & Lucking, differing from O. terebrata in the immersed ascomata lacking carbonization; O. lacerata M. Caceres, Aptroot & Lucking, differing from O. margaritacea in the irregularly chroodiscoid, weakly carbonized ascomata and the white medulla; O. myriotrema M. Caceres, Aptroot & Lucking, differing from M. inspersum in the papillose thallus and erumpent, grouped ascomata; O. ornata M. Caceres, Aptroot & Lucking, differing from O. perforata in the ridged thallus and the gall-forming ascomata with carbonized excipulum and columella; O. pseudochapsa M. Caceres, Aptroot & Lucking, differing from O. referta in the larger ascospores and cinchonarum unknown as accessory substance; O. pseudostromatica M. Caceres, Aptroot & Lucking, differing from Ocellularia barroensis in the grouped, pseudostromatic ascomata and unknown secondary compound; O. rondoniana M. Caceres, Aptroot & Lucking, differing from O. terebrata in the ridged thallus and non-carbonized excipulum; O. rubropolydiscus M. Caceres, Aptroot & Lucking, differing from O. polydiscus in the red pigment covering the ascoma disc; Platygramme unirana M. Caceres, Aptroot & Lucking, differing from P. caesiopruinosa in the erumpent lirellae with thinly white-pruinose disc and the 1-spored asci; Platythecium biseptatum M. Caceres, Aptroot & Lucking, differing from other Platythecium species in the consistently 2-septate ascospores; Pseudochapsa amylospora M. Caceres, Aptroot & Lucking, differing from other species of Pseudochapsa in the apically spinulose paraphyses and periphysoids; Rhabdodiscus crassoides M. Caceres, Aptroot & Lucking, differing from R. crassus in the transversely septate, hyaline ascospores; R. inspersus M. Caceres, Aptroot & Lucking, differing from R. subemersus in the inspersed hymenium and irregularly verrucose thallus and ascomata; R. planus M. Caceres, Aptroot & Lucking, differing from R. crassoides in the immersed ascomata and smaller ascospores; and Stegobolus amazonus M. Caceres, Aptroot & Lucking, differing from S. berkeleyanus in the smaller, submuriform ascospores. In addition, the new combinations Fissurina chrysocarpoides (Vain.) Lucking, Ocellularia margaritacea (Redinger) Lucking, and Pseudochapsa subdactylifera (Sipman) Lucking [syn.: Chapsa isidiifera Frisch & Kalb] are proposed. Rondonia is one of the areas in the world with the highest diversity in Graphidaceae. The Graphidaceae flora differs markedly between the collecting areas, although they are in similar forest types and less than 50 km apart, with the Parque Municipal yielding the greatest diversity over the full breath of the family, featuring e.g. several Gyrotrema species, a pustulose Graphis and the first Graphidaceae with consistently 2-septate ascospores, while the Cunia forest showing the highest diversity in Rhabdodiscus and Stegobolus species. New species are even described from a university campus and from the historic town center of the large city of Porto Velho.

Morphological and molecular studies of Neosynechococcus sphagnicola, gen. et sp. nov. (Cyanobacteria, Synechococcales)

Abstract: The genus Synechococcus represents an enigmatic group of cyanobacteria with very simple unicellular morphology and polyphyletic evolutionary origin. Here, we describe a new genus based on strain of Synechococcus -like cyanobacterium. The strain was isolated from the peat bog Klin (Slovakia), where it occupies different niches such as hyaline cells of Sphagnum , sheaths of cyanobacteria, dead cells of desmids, carapaces of dead crustaceans, and solitary in detritus. We describe this new genus using a combination of molecular, morphological and ecological features. A phylogeny of the 16S rRNA gene, 16S-23S ITS and rbc L loci showed a separate position of the investigated strain and its close proximity to filamentous cyanobacteria. Therefore, it is a novel lineage of Synechococcus -like cyanobacteria illustrating the polyphyletic nature of the genus Synechococcus . Moreover, the strain exhibits unique morphological and ecological features, which allow us to erect the new monospecific genus Neosynechococcus .

Cyanocohniella calida gen. et sp. nov. (Cyanobacteria: Aphanizomenonaceae) a new cyanobacterium from the thermal springs from Karlovy Vary, Czech Republic

Abstract: The thermal springs of Karlovy Vary (Carlsbad) is the locus classicus of the well-known thermal cyanobacterium Mastigocladus laminosus . In addition to the nominate variety, several other varieties and forms were described based on differences in morphology (true-branching versus non-branching) or ecology (thermal versus non-thermal). The cyanobacterial strain Kastovský 1996/2, which was provisionally identified as M. laminosus f. nostocoides , was also isolated from this locality and discussed in previous work. Based on both morphological and molecular (SSU) analyses, this strain was found to not belong to Mastigocladus , but rather to an undescribed genus, presumably within the Nostocaceae. This strain was subsequently lost, and absence of type materials prevented the description of the genus. The species was successfully re-isolated in 2012. The new strain is identical in morphology, life cycle, and 16S rRNA sequence to the lost strain 1996/2. It is herein described as Cyanocohniella calida gen. et sp. nov. The genus differs from all other Nostocaceae and Aphanizomenonaceae by the unique combination of these characteristics: 1) thermal-tolerant ecology, 2) life cycle that includes Pseudanabaenaceae-like, Nostoc -like and Chlorogloeopsis -like stages, 3) absence of aerotopes, and 4) phylogenetic placement in the Aphanizomenonaceae. The sister taxa, based on 16S rRNA gene sequence phylogenetic analysis, are Cyanospira and Anabaenopsis , both spiral, planktonic, aerotope-bearing, tropical genera and species clearly distinct from C. calida.

Early Land Plants Today (ELPT): How many liverwort species are there?

Abstract: Estimates of extant liverwort species range from 4,500 to 9,000, with estimates in the past decade converging on 5,000 to 6,000 Potential problems and pitfalls of deriving species estimates are addressed, including binomial accumulation, the impact of synonymy, taxonomic inflation, the impact of unrevised species-rich genera, species concepts and cryptic species We present a revised mean estimate of 7,500 for the number of liverwort species based on estimating rates of synonymy in a sample of recently monographed and revised taxa This estimate does not include infraspecific names and may underestimate global diversity as a result We also present a databased estimate of about 8,500 species derived from the Early Land Plants Today data set We argue higher estimates are supported by: 1) the number of published species has not reached a plateau and new species continue to be discovered; 2) not all regions have been thoroughly explored and with equal intensity, with survey effort being historically biased toward northern temperate regions; 3) synonymy rates are not uniform across taxonomic groups; 4) novel discovery of species outpaces new species derived from elevation in rank (taxonomic inflation); and 5) species numbers are not necessarily distorted by large unrevised genera A standardized global worldwide liverwort checklist with strong community participation coupled with the critical need for ongoing monographs and revisions, will aid in arriving at a clearer estimates of liverwort diversity We promote and encourage interest in the topic using an evidence-based approach and quantitative data

A new genus, Rubroboletus, to accommodate Boletus sinicus and its allies

Abstract: Rubroboletus is erected as a new genus to accommodate Boletus sinicus and its allies based on morphological and molecular evidence. Morphologically, Rubroboletus differs from the remaining genera in Boletaceae by the combination of a reddish pileal surface, an orange-red to blood red surface of the hymenophore, yellow tubes, pink to red reticula or spots on the yellow background of the stipe, a bluish color-change when injured, a non-amyloid context, smooth spores which are olive-brown in deposit, and an interwoven trichodermal pileipellis. Our phylogenetic analyses based on five gene markers (ITS, nrLSU, tef1-alpha, rpb1 and rpb2) recognized eight species in the genus, including one new species and seven new combinations. A key to the eight species is provided.

New higher taxa in the lichen family Graphidaceae (lichenized Ascomycota: Ostropales) based on a three-gene skeleton phylogeny

Abstract: We provide an updated skeleton phylogeny of the lichenized family Graphidaceae (excluding subfamily Gomphilloideae), based on three loci (mtSSU, nuLSU, RPB2 ), to elucidate the position of four new genera, Aggregatorygma , Borinquenotrema , Corticorygma , and Paratopeliopsis , as well as the placement of the enigmatic species Diorygma erythrellum , Fissurina monilifera , and Redingeria desseiniana . Based on the resulting topology, in addition to three tribes described previously, we recognize four further tribes in the subfamily Graphidoideae: Acanthothecieae Lumbsch, Kraichak & Lucking, Diploschisteae (Zahlbr.) Lumbsch, Kraichak & Lucking, Leptotremateae Lumbsch, Kraichak & Lucking, and Wirthiotremateae Lumbsch, Kraichak & Lucking. The phylogenetic position of Aggregatorygma and Borinquenotrema was not resolved with support, whereas Corticorygma forms part of Acanthothecieae, supported sister to Acanthothecis , and Paratopeliopsis belongs in Thelotremateae, unsupported sister to Leucodecton . Diorygma erythrellum is confirmed as a member of the Diorygma - Thalloloma clade, while Fissurina monilifera , inspite of its myriotremoid ascomata, belongs in Fissurina s.str. Redingeria dessiniana , although resembling the genus Phaeographopsis , is supported sister to R. glaucoglyphica . Topeliopsis darlingtonii forms the sister group to Gintarasia megalophthalma . Consequently, T. darlingtonii and the closely related T. elixii are recombined in Gintarasia as Gintarasia darlingtonii (Frisch & Kalb) Lumbsch, Kraichak & Lucking, and G. elixii (Frisch & Kalb) Lumbsch, Kraichak & Lucking.

Pyropia orbicularis sp. nov. (Rhodophyta, Bangiaceae) based on a population previously known as Porphyra columbina from the central coast of Chile

Abstract: A new species of bladed Bangiales, Pyropia orbicularis sp. nov., has been described for the first time from the central coast of Chile based on morphology and molecular analyses. The new species was incorrectly known previously as Porphyra columbina (now Pyropia columbina), and it can be distinguished from other species of Pyropia through a range of morphological characteristics, including the shape, texture and colour of the thallus, and the arrangement of the reproductive structures on the foliose thalli. Molecular phylogenies based on both the mitochondrial COI and plastid rbcL gene regions enable this species to be distinguished from other species within Pyropia. P. orbicularis sp. nov. belongs to a well-supported clade of Pyropia from the southern oceans that include specimens from the South Pacific (North, South, Chatham, Stewart, Auckland, and Campbell Island, New Zealand, New South Wales, and Macquarie Island, Australia) including P. columbina and P. plicata. Within this clade, the highest sequence identity was observed between Pyropia orbicularis sp. nov. and Pyropia sp. FIC from the Falkland Islands.

Multi-gene analysis of Pseudocercospora spp. from Iran

Abstract: Species of Pseudocercospora have gained much attention in recent years owing to their phytopathogenic relevance, and worldwide occurrence on a wide range of economically important hosts. Although these fungi are common in Iran, they have generally been poorly studied and no cultures have been preserved for molecular analyses. The present paper represents the first study of Pseudocercospora species from Iran evaluated by employing the Consolidated Species Concept. Nineteen isolates were obtained from seven host plant families in the northern zone of Iran. A phylogenetic analysis based on a combination of LSU, ITS, TEF1-α and ACT loci clustered these isolates into eight clades, of which five are phylogenetically new, delineating two novel species, viz. P. mazandaranensis on Nerium oleander and P. sophoricola on Sophora alopecuroides. Furthermore, P. punicae is recorded on a wild - grown cultivar of Punica granatum , and two additional species reported, namely Pseudocercospora sp. A on Phaseolus vulgaris and Pseudocercospora sp. B on Diospyros lotus . Pseudocercospora norchiensis is recorded for the first time in Asia, where it occurs on a wide host range, contrary to most other species of Pseudocercospora , which appear to be highly host specific.

Confusion surrounding Didymosphaeria-phylogenetic and morphological evidence suggest Didymosphaeriaceae is not a distinct family

Abstract: Didymosphaeriaceae is a ubiquitous fungal family that is reported to include saprobic, endophytic and pathogenic species associated with a wide variety of substrates. The family is characterized by 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci. In recent treatments Appendispora, Didymosphaeria, Roussoella, Phaeodothis and Verruculina were placed in the family. The aim of the present study is to delineate phylogenetic lineages within Didymosphaeriaceae and allied genera. A new species, Didymosphaeria rubi-ulmifolii, was isolated and identified based on morphological characters and phylogenetic analyses of partial 18S nrDNA and 28S nrDNA nucleotide sequence data. Didymosphaeria rubi-ulmifolii clustered with Montagnulaceae as a separate genus, while two putative strains (HKUCC 5834 and CMW 22186) of D. futilis from GenBank clustered with Cucurbitariaceae and Didymellaceae, respectively. The new species is characterized by immersed to slightly erumpent ascomata immersed under a clypeus, a peridium with compressed cells of textura intricata, long trabeculate pseudoparaphyses, anastomosing mostly above the asci and brown, 1-septate ascospores with granulate ornamentation. Phylogenetic analysis in combination with morphology and a review of literature show that Appendispora, Phaeodothis, Roussoella and Verruculina should be excluded from the family. Phaeodothis belongs in Montagnulaceae, Verruculina in Testudinaceae, while Appendispora and Roussoella belong in Roussoellaceae. The position of Didymosphaeriaceae as a distinct family, based on 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci is doubtful. Fresh collections of more Didymosphaeria strains are needed for epitypification and to obtain sequence data to establish if this family can be maintained.

Phylogenetic position of the diatom genus Geissleria Lange-Bertalot & Metzeltin and description of two new species from Siberian mountain lakes

Abstract: Two new Geissleria species from Siberian mountain lakes Baikal and Frolikha are described based on molecular and morphological data. The two new species are Geissleria baicalosimilis Kulikovskiy, Gusev, Andreeva & Annenkova sp. nov. and G. frolikhiensis Kulikovskiy, Gusev, Andreeva & Annenkova sp. nov. According to partial 18S rDNA and rbcL gene fragment analyses, Geissleria does not belong to the large catch-all genus Navicula as it was previously thought. Morphological features such as slit like areolae without hymenes, presence of one isolated pore near the central nodule and presence of props in areolae and an annulus structure support this conclusion. Plastid morphology of Geissleria species is typical for the Cymbellales, with one large chloroplast divided into two plates lying one against each valve, connected by a broad column. All of our data show that Geissleria is most closely to the genus Placoneis, with which they share naviculoid symmetry. Given these results, Geissleria should be included in the order Cymbellales. (Less)

A phylogenetic analysis of the Cryptocarya group (Lauraceae), and relationships of Dahlgrenodendron , Sinopora , Triadodaphne , and Yasunia

Abstract: A phylogenetic analysis based on nuclear ITS and plastid trnK intron sequences confirms that Dahlgrenodendron , Sinopora , Triadodaphne , and Yasunia are members of the Cryptocarya group, as expected from morphology. Dahlgrenodendron from South Africa is sister to Aspidostemon from Madagascar. Triadodaphne inaequitepala is nested within Endiandra (both from Australasia), and Yasunia from South America is nested among South American Beilschmiedia species. Sinopora is a member of the Beilschmiedia clade, but its precise position is still uncertain. Among large genera of the group, Cryptocarya is clearly monophyletic, and Endiandra appears to be as well, if T. inaequitepala is included. Beilschmiedia is paraphyletic with respect to (at least) Potameia and Yasunia . Most well-supported clades within genera are geographically homogeneous, except a clade including the Chilean Cryptocarya alba and two New Caledonian species. Both Beilschmiedia and Cryptocarya have reached the Americas more than once. Four-locular anthers are plesiomorphic in the Cryptocarya group; two-locular anthers have arisen by fusion of the two pollen sacs of a theca. In the plesiomorphic fruit type, the ovary is completely enclosed in receptacular tissue; a superior fruit, seated free on its pedicel, is a synapomorphy of the Beilschmiedia clade.

Early Land Plants Today: Taxonomy, systematics and nomenclature of Gymnomitriaceae

Abstract: There remains a critical need to synthesize the vast amount of nomenclatural, taxonomical and global distributional data for liverworts. This is fundamental in taxonomists' efforts towards developing a working list of all known plant species under the auspices of the Convention on Biological Diversity (CBD) as well as having far reaching implications and applications, including providing a valuable tool for taxonomists and systematists. We here provide the first synthesis of the taxonomy, systematics, and nomenclature of the family Gymnomitriaceae. The family is here conservatively treated to include ten genera representing 73 accepted species. We propose 149 new synonyms, 102 of them for validly published names. Significantly, we briefly discuss recent developments based on molecular studies and we predict future investigations will dramatically redefine the family. Detailed taxonomy and nomenclature is treated for almost 800 names associated with the family. Noteworthy remarks on various aspects of the distribution, ecology, conservation, and biology of members of the family are also included.

Species clarification of the most important and cultivated Auricularia mushroom “Heimuer”: evidence from morphological and molecular data

Abstract: Phylogenetic analysis of the Auricularia auricula-judae complex was carried out using ITS and nLSU ribosomal RNA gene regions, and morphology of the A. auricula-judae complex and related species is examined based on 33 wild collections and 10 cultivated samples worldwide. The phylogenetic analysis presented here showed that the wild and cultivated samples previously identified as A. auricula-judae in China are different from those from Europe (the type locality). So far no exist name for the most important Chinese Auricularia species is available, and thus a new specie s , Auricularia heimuer , is described and illustrated. The new species is characterized by effused-reflexed or substipitate basidiomata with fawn to reddish brown color when fresh and vinaceous gray to dark gray when dry, pilose upper surface usually with a few folds when dry, short abhymenial hairs without branching and measured as 50–150 × 4–6.5 µm, usually presence of medulla, long clavate basidia with oil guttules and measured as 40–67 × 3.0–6.5 µm, and allantoid spores measured as 11–13 × 4–5 µm. A. auricula-judae is not found in China, and most probably has a distribution in Europe only. In addition, A. americana and A. villosula are the first time reported in China. Both A. heimuer and A. villosula grow on angiosperm wood, while A. americana is found on gymnosperm wood exclusively.

Molecular phylogeny and phylogeography of Holarctic species of Pluteus section Pluteus (Agaricales: Pluteaceae), with description of twelve new species

Abstract: The taxonomy and phylogeography of Pluteus section Pluteus in the Holarctic region was investigated using morphological and molecular data. Over 300 specimens spanning the major areas of boreal and temperate forests of the Northern Hemisphere were studied and nrITS and tef1 were obtained for phylogenetic analyses. In order to stabilize the taxonomy of the group all available type collections were studied and, if possible, sequenced. A total of 26 species occurring in Eurasia and North America were recovered in the phylogenetic analyses. Twelve species are described as new ( Pluteus rangifer , P. elaphinus, P. hibbettii, P. eos, P. orestes, P. methvenii, P. shikae, P. kovalenkoi, P. leucoborealis, P. sepiicolor, P. oreibatus, P. atrofibrillosus ), one is provisionally named ( P. parilis ) and one variety is raised to species rank ( P. americanus ). In many cases separation of the species based on morphology alone is challenging. In general, tef1 distinguishes the species better than nrITS. Structured infraspecific genetic variation was detected in the nrITS phylogenies for five species ( P. atromarginatus, P. hibbettii, P. orestes, P. primus and P. shikae ) and in the tef1 phylogenies for P. cervinus . Phylogeographic patterns are strikingly different among the species in this group and include widespread Holarctic species, exclusively Palearctic, putative disjuncts and endemics in each Holarctic subregion (Eastern/Western Palearctic and Nearctic). Identification keys are provided for each subregion.

DNA barcoding allows the accurate assessment of European maerl diversity: a Proof-of-Concept study

Abstract: Two non-geniculate coralline red algae (Lithothamnion corallioides and Phymatolithon calcareum) are partially protected under the assumption that they are the main components of maerl beds in Atlantic Europe. However, what we know about the composition of maerl relies mainly on morphology-based identifications that are notoriously difficult due to a lack of diagnostic features, convergence, and widespread phenotypic plasticity. Now, this state of affairs can be improved with new alternatives that, unlike morphology, allow the unambiguous partition of a large number of rhodoliths into species regardless of their size, shape, and condition (fertile or sterile). Here, we report the first DNA barcoding assessment of the relative abundance of maerl-forming algae. The plastidial gene psbA was sequenced for 1140 rhodoliths from 15 maerl beds scattered along 2000 km from the British Isles to South Portugal; rhodoliths were randomly collected along linear transects to obtain quantitative estimates of species composition. Most (97%) of our collections belonged to three, rather than two, species that often appeared intermixed along a single transect. Lithothamnion corallioides and P. calcareum dominated in the British Isles and Brittany (NW France), but they were gradually replaced by Phymatolithon sp3 in Galicia (NW Spain) and became extremely rare in Algarve (S Portugal). Morphology (rhodolith size and shape, branch diameter, habit) varied considerably between and within beds but the three species converged to a remarkably similar habit when living in sympatry. Still, P. calcareum and L. corallioides seemed to perform best in Brittany while Phymatolithon sp3 produced the largest rhodoliths with thickest branches in Algarve. Altogether, our study shows that the replacement of species of maerl seen in northern latitudes continues to the south along the coasts of Iberia. It also serves as a proof-of-concept of the benefits of DNA barcoding for ecological and biogeographic research of these taxonomically challenging taxa.

Polyphasic characterization of Kastovskya adunca gen. nov. et comb. nov. (Cyanobacteria: Oscillatoriales), from desert soils of the Atacama Desert, Chile

Abstract: Recent taxonomic revisions within the cyanobacteria have shown that the traditional simple filamentous genera often represent large polyphyletic clusters of not-so-closely-related taxa. In this study, the new cyanobacterial genus Kastovskya is described based on a combination of morphological, molecular, and ecological evidence. Kastovskya was first described as Schizothrix adunca , a morphospecies discovered in the Atacama Desert, Chile more than 50 years ago. This species has been transferred to Kastovskya and serves as the generitype. Kastovskya adunca currently represents a unique and probably endemic taxon for the soils of the Atacama Desert region. Description of this new genus contributes to the revision of the Phormidiaceae by providing a clear taxonomic definition to one of the clades within the Schizothrix/Microcoleus/Phormidium cluster.