<Emphasis Type="Italic">Cortinarius</Emphasis> sect. <Emphasis Type="Italic">Riederi</Emphasis>: taxonomy and phylogeny of the new section with European and North American distribution

Cortinarius is one of the most species-rich genera of mushroom-forming fungi. Based on phylogenetic and morphological evidence, Cortinarius, sect. Riederi, is introduced at sectional level (= subsect. Riederi sensu Brandrud & Melot). The taxonomy, phylogeny, ecology and distribution of not only mainly European but also including some North American taxa of this section are treated, which includes nine species and two varieties. Of these, three taxa are described as new (C. burlinghamiae, C. pallidoriederi and C. argenteolilacinus var. dovrensis). The sect. Riederi species possess morphological features similar to Phlegmacium group(s) and forms a phylogenetically isolated lineage, with no supported affinity to other phlegmacioid groups. Three taxa are known from both Europe and North America, two species are known only from North America and five only from Europe. Altogether, eight of the ten taxa are associated with conifers or northern (boreal-subalpine) deciduous trees (Betula spp.). Only two species occur in more temperate forests (Fagus forests), and no species have so far been found in thermophilous Quercus forests     

PHYLOGENY OF CARTERIA (CHLOROPHYCEAE) INFERRED FROM MOLECULAR AND ORGANISMAL DATA1

Comparative ultrastructural data have shown that at least two distinct groups exist within Carteria. Similarly, interpretations of variation in gross morphological features have led to the discovery of morphologically distinct groups within the genus. Partial sequences from the nuclear-encoded small- and large-subunit ribosomal RNA molecules of selected Carteria taxa were studied as a means of 1) testing hypotheses that distinct groups of species exist within the genus and 2) assessing monophyly of the genus. Parsimony analysis of the sequence data suggests that three Carteria species, C. lunzensis, C. crucifera, and C. olivieri, form a monophyletic group that is the basal sister group to all other ingroup flagellate taxa (including species of Chlamydomonas, Haematococcus, Stephanosphaera, Volvox, and Eudorina). Two other Carteria taxa, C. radiosa and Carteria sp. (UTEX isolate LB 762), form a clade that is the sister group to a clade that includes Haematococcus spp., Chlamydomonas spp., and Stephanosphaera. Thus, the sequence data support the interpretations of ultrastructural evidence that described two distinct Carteria lineages. Moreover, the sequence data suggest that these two Carteria groups do not form a monophyletic assemblage. Parsimony analysis of a suite of organismal (morphological, ultra-structural, life history, and biochemical) character data also suggest two distinct lineages among the five Carteria taxa; however, the organismal data are ambiguous regarding monophyly of these Carteria taxa. When the two independent data sets are pooled, monophyly of Carteria is not supported; therefore, the weight of available evidence, both molecular and organismal, fails to support the concept of Carteria as a natural genus.     

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia

Sponges are among the most species‐rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model‐based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single‐copy nuclear protein‐coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax, C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera, C. longissima, C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model‐based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.     

Chromosomal localization of 45S and 5S rDNA in 14 species and the implications for genome evolution of genus Epimedium

Studying the genome structure of Epimedium has been hindered by the large genomes and uniform karyotypes. Consequently our understanding of the genome organization and evolutionary changes of Epimedium is extremely limited. In the present study, the 45S and 5S rDNA loci of 14 Epimedium species were physically mapped by double-probe FISH for the first time. Results showed the following: (1) Chromosomes I and II of all 14 species examined, except for E. shuichengense, hosted one pair of 45S rDNA sites, respectively. Most of the 45S rDNA sites gave clear signals and were positioned in the distal regions of the short arms. (2) All species studied of section Diphyllon were found to have one pair of 5S rDNA sites localized in the interstitial regions of the long arm of chromosome IV, and the two species of section Epimedium, E. alpinum and E. pubigerum, had two pairs of 5S rDNA sites localized in the interstitial regions of the long arm of chromosomes IV and V, respectively. (3) In section Diphyllon, all species of small flower taxa, except E. shuichengense, had three pairs of 45S rDNA sites, clearly more than species of big flower taxa, except E. davidii, with two pairs of 45S rDNA sites. Based on the 45S and 5S rDNA distribution patterns and other chromosomal morphological characteristics, six pairs of chromosomes can be unambiguously identified in all 14 Epimedium species. The stable differentiation in 45S and 5S rDNA FISH patterns between the two sections suggests that chromosomal rearrangements and transpositional events played a role in the splitting of the two sections, and section Diphyllon may be more primitive than section Epimedium. In the same way, big flower taxa may be more primitive than small flower taxa in section Diphyllon.     

Multilocus Sequence Typing of Listeria monocytogenes by Use of Hypervariable Genes Reveals Clonal and Recombination Histories of Three Lineages

In an attempt to develop a method to discriminate among isolates of Listeria monocytogenes, the sequences of all of the annotated genes from the fully sequenced strain L. monocytogenes EGD-e (serotype 1/2a) were compared by BLASTn to a file of the unfinished genomic sequence of L. monocytogenes ATCC 19115 (serotype 4b). Approximately 7% of the matching genes demonstrated 90% or lower identity between the two strains, and the lowest observed identity was 80%. Nine genes (hisJ, cbiE, truB, ribC, comEA, purM, aroE, hisC, and addB) in the 80 to 90% identity group and two genes (gyrB and rnhB) with approximately 97% identity were selected for multilocus sequence analysis in two sets of L. monocytogenes isolates (a 15-strain diversity set and a set of 19 isolates from a single food-processing plant). Based on concatenated sequences, a total of 33 allotypes were differentiated among the 34 isolates tested. Population genetics analyses revealed three lineages of L. monocytogenes that differed in their history of apparent recombination. Lineage I appeared to be completely clonal, whereas representatives of the other lineages demonstrated evidence of horizontal gene transfer and recombination. Although most of the gene sequences for lineage II strains were distinct from those of lineage I, a few strains with the majority of genes characteristic of lineage II had some that were characteristic of lineage I. Genes from lineage III organisms were mostly similar to lineage I genes, with instances of genes appearing to be mosaics with lineage II genes. Even though lineage I and lineage II generally demonstrated very distinct sequences, the sequences for the 11 selected genes demonstrated little discriminatory power within each lineage. In the L. monocytogenes isolate set obtained from one food-processing plant, lineage I and lineage II were found to be almost equally prevalent. While it appears that different lineages of L. monocytogenes can share habitats, they appear to differ in their histories of horizontal gene transfer.     

Salinomyces polonicus: A moderately halophilic kin of the most extremely halotolerant fungus Hortaea werneckii

A clade where the most halotolerant fungus in the world – Hortaea werneckii, belongs (hereafter referred to as Hortaea werneckii lineage) includes five species: Hortaea werneckii, H. thailandica, Stenella araguata, Eupenidiella venezuelensis, and Magnuscella marina, of which the first species attracts increasing attention of mycologists. The species diversity and phylogenetic relationships within this lineage are weakly known. In this study two moderately halophilic black yeast strains were isolated from brine of graduation tower in Poland. Molecular phylogenetic analyses based on the rDNA ITS1-5.8S-ITS2 (=ITS), rDNA 28S D1–D2 (=LSU), and RNA polymerase II (rpb2) sequences showed that the two strains belong to Hortaea werneckii lineage but cannot be assigned to any described taxa. Accordingly, a new genus and species, Salinomyces and Salinomyces polonicus, are described for this fungus. Furthermore, molecular phylogenetic analyses have revealed that Hortaea thailandica is more closely related to S. polonicus than to H. werneckii. A new combination Salinomyces thailandicus is proposed for this fungus.     

Checklist of fauna found in zooplankton samples from the Barents Sea

We present a list of zooplankton taxa occurring in the Barents Sea based on our analysis of 360 samples from the upper 100 m of the water column as well as on reports from published sources. Moreover, we provide information on adult size, ecological and geographical distribution, habitat preference and frequency of occurrence of each taxon. The list encompasses a total of 374 species and higher taxa. Most are mesozooplankton, with Copepoda prevailing (153 species), and belong to the holoplankton. However, pseudoplankton, organisms only circumstantially occurring in the water column, also comprise a significant part of the fauna (86 taxa). The coastal zooplankton (264 neritic species) was richer than the fauna of the open sea. In our samples, the majority of the zooplankton taxa were rarely found (94 of 157 taxa, equivalent of 60%), 46 taxa (29%) were moderate and only 17 taxa (11%) were common (found in >80% of the samples). Among these, the copepods Calanus finmarchicus, C. glacialis, Oithona similis and Pseudocalanus minutus were most frequent.     

Invasion facilitates hybridization with introgression in the Rattus rattus species complex

Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two nuclear gene sequences (Atp5a1 and DHFR) and nine microsatellite loci to examine the distribution of three invasive black rat lineages (Rattus tanezumi, Rattus rattus I and R. rattus IV) in the United States and Asia and to determine the extent of hybridization among these taxa. Our analyses revealed two mitochondrial lineages that have spread to multiple continents, including a previously undiscovered population of R. tanezumi in the south‐eastern United States, whereas the third lineage (R. rattus IV) appears to be confined to Southeast Asia. Analyses of nuclear DNA (both sequences and microsatellites) suggested significant hybridization is occurring among R. tanezumi and R. rattus I in the United States and also suggest hybridization between R. tanezumi and R. rattus IV in Asia, although further sampling of the latter species pair in Asia is required. Furthermore, microsatellite analyses suggest unidirectional introgression from both R. rattus I and R. rattus IV into R. tanezumi. Within the United States, introgression appears to be occurring to such a pronounced extent that we were unable to detect any nuclear genetic signal for R. tanezumi, and a similar pattern was detected in Asia.     

Italian neo-endemism in a widespread group of leafhoppers insects: A revision of the Eupteryx aurata group (Auchenorrhyncha: Cicadellidae: Typhlocybinae) using morphology,ecology and genetics

The Eupteryx aurata group is characterised by several features, primarily by colouration and aedeagus morphology. It is distributed mainly in Europe, with some species also in Asia and one species perhaps in North Africa. At least one species is introduced in North America. Until now 12 taxa were known. Two new species, Eupteryx divulsa from central Italy and Eupteryx oscorum from central and southern Italy, are described in this paper. Eupteryx petasitidis Ferrari, 1882, described as Eupteryx carpini petasitidis and later synonymised with Eupteryx atropunctata (Goeze, 1778), is reestablished on species level and redescribed including genital morphology. Ten taxa of the species group are studied in relation to their morphological and molecular characters. The colouration, aedeagus, and pygofer appendage are figured for all of these taxa. Molecular study showed that the E. aurata group is monophyletic. The little or moderate distances in sequences (below 6.0% for mtDNA and up to 2.5% for nuclear ITS2) between the different taxa of the E. aurata group and incongruence of genetic signals from mtDNA and nuclear DNA could be the result of incomplete lineage sorting in young species and/or hybridisation and introgression of DNA among taxa. Of particular importance in this study is material from Italy, a peripheral region in relation to the distribution of the species group and due to its geomorphological features favouring isolation and speciation. A distribution map for the E. aurata species group in Italy and an identification key for all 15 taxa of the aurata group are given. Phylogenetic relationships within the aurata group are discussed in relation to morphological, molecular, ecological, and zoogeographic aspects.     

Phylogenetic characterisation of Taenia tapeworms in spotted hyenas and reconsideration of the “Out of Africa” hypothesis of Taenia in humans

The African origin of hominins suggests that Taenia spp. in African carnivores are evolutionarily related to the human-infecting tapeworms Taenia solium, Taenia saginata and Taenia asiatica. Nevertheless, the hypothesis has not been verified through molecular phylogenetics of Taenia. This study aimed to perform phylogenetic comparisons between Taenia spp. from African hyenas and the congeneric human parasites. During 2010–2013, 233 adult specimens of Taenia spp. were collected from 11 spotted hyenas in Ethiopia. A screening based on short DNA sequences of the cytochrome c oxidase subunit 1 gene classified the samples into four mitochondrial lineages designated as I–IV. DNA profiles of nuclear genes for DNA polymerase delta (pold) and phosphoenolpyruvate carboxykinase (pepck) showed that lineages II and III can be assigned as two independent species. Common haplotypes of pold and pepck were frequently found in lineages I and IV, suggesting that they constitute a single species. Morphological observations suggested that lineage II is Taenia crocutae, but the other lineages were morphologically inconsistent with known species, suggesting the involvement of two new species. A phylogenetic tree of Taenia spp. was reconstructed by the maximum likelihood method using all protein-coding genes of their mitochondrial genomes. The tree clearly demonstrated that T. crocutae is sister to T. saginata and T. asiatica, whereas T. solium was confirmed to be sister to the brown bear tapeworm, Taenia arctos. The tree also suggested that T. solium and T. arctos are related to two species of Taenia in hyenas, corresponding to lineages I + IV and III. These results may partially support the African origin of human-infecting Taenia spp., but there remains a possibility that host switching of Taenia to hominins was not confined to Africa. Additional taxa from African carnivores are needed for further testing of the “Out of Africa” hypothesis of Taenia in humans.     

Transatlantic disjunction in fleshy fungi. I. The Sparassis crispa complex

Phylogenies based on ITS and LSU sequences show that the Sparassis crispa complex comprises several monophyletic clades, in some cases co\rresponding to named taxa (i.e. S. crispa, S. radicata), but others lacking names (i.e. eastern and southwestern North American S. “crispa”). In our study, morphological examination of numerous collections also distinguished subtle differences correlated with geographic distribution. Underlying these problems, several taxa lacked type specimens for taxonomic analysis. In this paper, appropriate epitypes are designated and names assigned. Extensive sexual compatibility experiments, described within, indicate that monokaryon, haploid isolates of collections from North America and Europe are consistently sexually compatible to some degree. Inherent in the study, different “species concepts” were tested, with the “biological species concept,” based on sexual compatibility, being the least restrictive. We propose two new taxa, S. americana and S. americana f. arizonica.     

Cortinarius sect. Brunnei (Basidiomycota, Agaricales) in North Europe

The section Brunnei was extensively studied based on material from North Europe. To stabilise the nomenclature we studied the relevant types of taxa included in this section. Phylogenetic relationships and species limits were investigated using rDNA ITS sequences and the results were compared with the morphological data. We recognised 11 species: Cortinarius brunneus, C. clarobrunneus comb. nov., C. coleoptera, C. ectypus, C. gentilis, C. glandicolor (neotypified), C. pseudorubricosus, and four species described as new C. caesiobrunneus, C. albogaudis, C. carabus, and C. cicindela. They are described here and their taxonomy, ecology, distribution, and relationships are discussed. In addition, a key to species of the section Brunnei is provided. A total of 77 new sequences of 11 species are published including nine type sequences. Also the taxonomic assignments of sequences in the public databases belonging to the section Brunnei are revised.     

Hybridization and introgression in Carex aquatilis and C. paleacea

The diversification and distribution of Abies species throughout the Mediterranean region has led to a complex of species which are difficult to classify. An open question is whether these mainly allopatric taxa have exchanged genetic information via secondary contact. We studied the variation and geographic distribution of paternally inherited chloroplast DNA markers in nine Mediterranean Abies taxa. Markers with high and low mutation rates were applied in order to differentiate among a scenario of secondary genetic contact and a scenario of complete isolation after speciation. The observed molecular variation was analysed using statistical parsimony, geostatistics, and measures of population genetic differentiation. Ancient paternal lineages, represented by markers with low mutation rates, were shared among species. The central and widespread A. alba retained all ancient lineages whereas other species exhibited fewer, down to a single lineage. In contrast, modern lineages, depicted by markers with high mutation rates, were largely separated among species. The western Mediterranean A. pinsapo and A. numidica were clearly separated from each other and from the remaining Abies species. This indicates the absence of secondary contact. The same scenario applies to the eastern Mediterranean Abies species. An exception is the parapatric complex of A. alba, A. cephalonica, and their supposed hybrid A. borisii regis, which exhibited evidence of secondary contact.     

Morphological and phylogenetic studies of Cytospora (Valsaceae,Diaporthales) isolates from Chinese scholar tree,with description of a new species

Cytospora species are the most serious and widespread pathogens associated with canker disease on multiple plants. In this study, three species, i.e., Cytospora sophoricola, C. chrysosperma, and C. sophorae, which were isolated from Sophora in China, are described and illustrated based on their morphological characteristics and phylogenetic analyses. Cytospora sophoricola was distinguished clearly by its larger disc, multiple ostioles, cystic and multiple locules, and specific cultural characteristics, i.e., protruding fruiting bodies. Maximum parsimony and maximum likelihood analysis showed that it did not cluster with any known species of Cytospora, so it is described as a new species. Cytospora sophorae is a previously reported species from Sophora, which is redescribed based on new isolates and additional observations. Another species was identified as C. chrysosperma, which is reported for the first time on Sophora, so Papilionaceae is shown to be a new host family for C. chrysosperma. The morphological affinities of these species with related taxa are discussed, while the phylogenetic relationships of these species with other fungus in the genus Cytospora were elucidated based on their internal transcribed spacer (ITS) rRNA region sequences.     

Molecular systematics of small-eared shrews (Soricomorpha,Mammalia) within Cryptotis mexicanus species group from Mesoamérica

Cryptotis mexicanus species group is the most diverse group of Cryptotis shrews in the Mesoamerican highlands (ca.13 species). In México, eight endemic species occurs and several taxa are endangered. The species’ limits and phylogenetic relationships of these taxa have been recently examined using morphology; nevertheless, little is known about phylogenetic relationships among Cryptotis species at the molecular level. Therefore, our research included a mitochondrial DNA marker as a source of additional information to corroborate taxonomic identification and produce a phylogenetic hypothesis of the C. mexicanus species group. We were particularly interested in the status of Cryptotis magnus, a species considered as relict on the basis of primitive characters. Based on the analyses of genetic sequences of a high number of Cryptotis species, outgroups, and phylogenetic analyses of parsimony and Bayesian inference, we confirmed that Cryptotis genus consists of different lineages that represent species groups. A detailed analysis suggests that C. magnus is a species that shares an evolutionary history with the C. mexicanus species group because it is imbedded within this group. In particular, our data strongly support that C. magnus and Cryptotis phillipsii are sister groups, a pair of species that inhabit allopatrically Southern México.     

New species and distinctive geographical divergences of the genus Sparassis (Basidiomycota): evidence from morphological and molecular data

Species of the genus Sparassis in East Asia were investigated using morphology and DNA sequences data. Phylogenetic analyses inferred from sequences of the internal transcribed spacer (ITS), the nuclear gene coding for the ribosomal large subunit (nLSU) and partial gene coding RNA polymerase subunit II (rpb2) strongly supported lineages corresponding to morphological features. Three taxa, S. subalpina, S. cystidiosa f. flabelliformis and S. latifolia were recognized from East Asia, and the former two taxa are new to science. The occurrence of S. latifolia in Japan and in the Russian Far East was confirmed. Geographical divergences of Sparassis in the Holarctic were observed. Most species have relatively narrow distribution ranges, and taxa with intercontinental distributions were not detected. Divergence of species in the Northern Hemisphere in different clades appears to have taken place at different times: the S. latifolia-crispa-radicata species complex appears to have undergone a recent radiation, while the S. subalpina-brevipes-spathularia species complex represents a relatively ancient speciation.     

Characterization of a Plasmopara species on Ambrosia artemisiifolia, and notes on P. halstedii, based on morphology and multiple gene phylogenies

Common ragweed (Ambrosia artemisiifolia) is an invasive and highly allergenic plant species, on which two species, Plasmopara halstedii and Plasmopara angustiterminalis, have been recognized to cause downy mildew disease. In this study, morphological and molecular patterns of seven Plasmopara specimens collected from A. artemisiifolia in Canada, Hungary, and USA were compared with those of P. halstedii and P. angustiterminalis from Helianthus and Xanthium, respectively. Analyses of partial sequences of three genes, namely those for the large subunit (28S) of rDNA, cytochrome c oxidase subunit II (COX2), and NADH dehydrogenase subunit I (ND1) of mtDNA, were carried out to examine the phylogenetic relationships among these specimens using both Bayesian and maximum parsimony methods. All the phylogenetic analyses revealed that the downy mildew pathogens infecting A. artemisiifolia in Hungary and North America clearly represent a lineage distinct from other Plasmopara taxa investigated. The shape of sporangia and the width of trunks and branches also allowed the separation of the specimens parasitic to A. artemisiifolia from P. halstedii on Helianthus annuus and P. angustiterminalis on Xanthium strumarium. Surprisingly, the Hungarian and the Canadian specimens were more closely related to each other than to those from the USA based on COX2 and ND1 mtDNA data, although the D1/D2/D3 sequences of 28S rDNA were identical in all these Plasmopara specimens. The regional distribution of the mtDNA haplotypes seen in this study suggests a transatlantic migration has occurred and would be interesting to follow up with a more detailed sampling. To investigate the diversity within P. halstedii sensu lato, infecting different host plant species, specimens from six asteraceous genera, Ambrosia, Flaveria, Helianthus, Siegesbeckia, Solidago, and Xanthium, were also included in molecular analyses. These represented six distinct lineages according to the host plant genera. These findings might serve as a basis for a taxonomical reassessment of the P. halstedii complex and also for the delimitation of several well-defined species within this complex.     

Specialization and iterative evolution of some Western Tethyan Bathonian ammonites [Benatinites (B.) nov., B. (Lugariceras) nov. and Hemigarantia]

Late Bajocian to Early Bathonian ammonites, now attributed to Benatinites and Lugariceras, and Late Bathonian Hemigarantia, previously considered as cryptogenic taxa, share very similar sutural and ornamentation characters, suggesting their derivation from the stephanoceratid stock, most probably from the Cadomites-Polyplectites line. The palaeogeographical distribution of these taxa is limited to the North-Western African and European margins of Western Tethys. Palaeontologically, they represent the result of the iterative evolution rather than a poorly known lineage.