<Emphasis Type="Italic">Ceriporiopsis kunmingensis</Emphasis> sp. nov. (Polyporales,Basidiomycota) evidenced by morphological characters and phylogenetic analysis

A new poroid wood-inhabiting fungal species, Ceriporiopsis kunmingensis sp. nov., is proposed based on morphological and molecular characters. The species is characterized by resupinate basidiocarps with pale cinnamon-buff to ochreous color when dry; generative hyphae unbranched and subparallel along the tubes; presence of hyphal ends; allantoid basidiospores, 4.5–5 × 1.5–2 μm. The internal transcribed spacer (ITS) and large subunit (LSU) regions of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. The phylogenetic analysis based on molecular data of ITS?+?nLSU sequences showed that C. kunmingensis belonged to the phlebioid clade, formed a monophyletic lineage with a strong support (100% BS, 100% BP, 1.00 BPP), and was closely related to Phlebia aurea, and then grouped with P. livida and P. subserialis. Both morphological and molecular characters confirmed the placement of the new species in Ceriporiopsis.     

Phylogenetic diversity of Fusarium incarnatum-equiseti species complex isolated from Spanish wheat

Wheat is the most important cereal grown in the European Union and Spain is its fifth largest wheat producer. There is little information about Fusarium species associated with wheat in Spain. Phylogenetic diversity of 51 strains belonging to Fusarium incarnatum-equiseti species complex (FIESC) isolated from Spanish wheat was investigated using partial sequences of the translation elongation factor gene (EF-1α). Maximum-parsimony and Bayesian analysis of aligned DNA sequences resolved 18 haplotypes and 7 phylogenetic species. Strains morphologically identified as F. equiseti belonged to two different phylogenetic species, FIESC-5 and FIESC-14. Some correlation between phylogenetic species and geographical region was found. The present results highlight the potential contribution of FIESC to the mycotoxin contamination of Spanish wheat.     

<Emphasis Type="Italic">Leifiporia rhizomorpha</Emphasis> gen. et sp. nov. and <Emphasis Type="Italic">L. eucalypti</Emphasis> comb. nov. in Polyporaceae (Basidiomycota)

A new poroid wood-inhabiting fungal genus, Leifiporia, is proposed, based on morphological and molecular evidence, which is typified by L. rhizomorpha sp. nov. The genus is characterized by an annual growth habit, resupinate basidiocarps with white to cream pore surface, a dimitic hyphal system with generative hyphae bearing clamp connections and branching mostly at right angles, skeletal hyphae present in the subiculum only and distinctly thinner than generative hyphae, IKI–, CB–, and ellipsoid, hyaline, thin-walled, smooth, IKI–, CB– basidiospores. Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analysis based on molecular data of ITS + nLSU sequences showed that Leifiporia belonged to the core polyporoid clade and was closely related to Diplomitoporus overholtsii and Lopharia cinerascens, and then grouped with Pycnoporus and Trametes. Further investigation was obtained for more representative taxa in the Polyporaceae based on nLSU sequences, in which the results demonstrated that the genus Leifiporia formed a monophyletic lineage with a strong support (100 % BS, 100 % BP, 1.00 BPP). Both morphological and molecular evidence confirmed the placement of the new genus in the core polyporoid clade. In addition, a new combination, Leifiporia eucalypti, is proposed based on examination of its type material and phylogeny.     

Phylogenetic selection of target species in Amaryllidaceae tribe Haemantheae for acetylcholinesterase inhibition and affinity to the serotonin reuptake transport protein

We present phylogenetic analyses of 37 taxa of Amaryllidaceae, tribe Haemantheae and Amaryllis belladonna L. as an outgroup, in order to provide a phylogenetic framework for the selection of candidate plants for lead discoveries in relation to Alzheimer's disease and depression. DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and the plastid trnL-F regions were used. Maximum parsimony analyses provide increased support for the sister relationship of Haemanthus and Scadoxus. Within Haemanthus, a well supported clade (89% BS) corresponds to a summer rainfall group (mainly Eastern Cape) with white-pale pink flowers. A second strongly supported clade (100% BS) corresponds to a winter rainfall group (mainly Western Cape) with red-pale pink flowers. Haemanthus montanus, which is from the summer rainfall region, is sister to the winter rainfall group. Alkaloid profiles and bioactivity profiles were investigated for 16 taxa using gas chromatography-mass spectrometry (GC-MS) and assays measuring acetylcholinesterase (AChE) inhibition and affinity to the serotonin reuptake transport protein (SERT). No alkaloids were detected by GC-MS in extracts of the two species of Gethyllis included in the present study suggesting that Gethyllis (and possibly Apodolirion) species may not produce the alkaloids characteristic for the family. AChE inhibitory activity was found in all investigated clades except the Apodolirion-Gethyllis clade, which can be explained by the apparent lack of alkaloids in this clade. In spite of infra-specific variability of alkaloid profiles observed, dose-dependent SERT activity appears to be pronounced and restricted to the genus Haemanthus within tribe Haemantheae. Three of eight Haemanthus species tested had IC₅₀ < 10 μg/ml. Two of the most active extracts in the present study contained primarily montanine type alkaloids which have not been tested for SERT affinity previously. Simultaneous evaluation of bioactivity and alkaloid profiles in a phylogenetic framework can potentially be used to select candidate species for phytotherapy and drug discovery.     

Phylogenetics of the Antopocerus-Modified Tarsus Clade of Hawaiian Drosophila: Diversification across the Hawaiian Islands

The Hawaiian Drosophilidae radiation is an ecologically and morphologically diverse clade of almost 700 described species. A phylogenetic approach is key to understanding the evolutionary forces that have given rise to this diverse lineage. Here we infer the phylogeny for the antopocerus, modified tarsus and ciliated tarsus (AMC) clade, a lineage comprising 16% (91 of 687 species) of the described Hawaiian Drosophilidae. To improve on previous analyses we constructed the largest dataset to date for the AMC, including a matrix of 15 genes for 68 species. Results strongly support most of the morphologically defined species groups as monophyletic. We explore the correlation of increased diversity in biogeography, sexual selection and ecology on the present day diversity seen in this lineage using a combination of dating methods, rearing records, and distributional data. Molecular dating analyses indicate that AMC lineage started diversifying about 4.4 million years ago, culminating in the present day AMC diversity. We do not find evidence that ecological speciation or sexual selection played a part in generating this diversity, but given the limited number of described larval substrates and secondary sexual characters analyzed we can not rule these factors out entirely. An increased rate of diversification in the AMC is found to overlap with the emergence of multiple islands in the current chain of high islands, specifically Oahu and Kauai.     

Genetic diversity among different species of the genus Leiurus (Scorpiones: Buthidae) in Saudi Arabia and the Middle East

The molecular phylogenetic relationship among two species of genus Leiurus, from Saudi Arabia with additional comparative sequence data available from Egypt, Oman and Turkey is presented. The molecular phylogeny was performed using maximum parsimony, neighbor joining and bayesian inference. Our results indicate a clear deep splitting between the Western clade, which represented by L. quinuestriatus sequences from Egypt and those from the Eastern clade which encompassing different Leiurus species from Saudi Arabia, Oman and Turkey was shown. Also, the phylogenetic relationship represents additional support for the taxonomic status of Arabian Leiurus species.     

Xylodon kunmingensis sp. nov. (Hymenochaetales,Basidiomycota) from southern China

A new wood-inhabiting fungal species, Xylodon kunmingensis, is proposed based on morphological and molecular evidences. The species is characterized by an annual growth habit, resupinate basidiocarps with cream to buff hymenial, odontioid surface, a monomitic hyphal system with generative hyphae bearing clamp connections and oblong-ellipsoid, hyaline, thin-walled, smooth, inamyloid and indextrinoid, acyanophilous basidiospores, 5–5.8 × 2.8–3.5 μm. The phylogenetic analyses based on molecular data of ITS sequences showed that X. kunmingensis belongs to the genus Xylodon and formed a single group with a high support (100% BS, 100% BP, 1.00 BPP) and grouped with the related species X. astrocystidiatus, X. crystalliger and X. paradoxus. Both morphological and molecular evidences confirmed the placement of the new species in Xylodon.     

Six new species of Pythiogeton in Taiwan,with an account of the molecular phylogeny of this genus

Pythiogeton is a little-studied genus of pythialean Oomycete. The genus is characterized by producing its zoospores outside of the sporangium within an apparently naked protoplasmic mass, which formed from a discharge tube-vesicle complex. A total of nine morphologically distinct Pythiogeton species were identified, of which six were new species (Pythiogeton abundans, Pythiogeton microzoosporum, Pythiogeton oblongilobum, Pythiogeton paucisporum, Pythiogeton proliferatum, and Pythiogeton puliensis). A phylogenetic analysis based on internal transcribed spacer sequences revealed that all isolates of Pythiogeton formed a highly supported clade, nested within the wider clade of Pythium species. Each newly recognized Pythiogeton species that was established on the basis of morphological characters was found to occur in a well-supported subgroup within the Pythiogeton clade, confirming their assignment to new species. Pythiogeton shares a common ancestor with the monophyletic group of Pythium species that have predominantly filamentous sporangia rather than with the separate clade of Pythium species that have predominantly globose or ovoid sporangia. This study confirms that Pythium is an extremely heterogenous and polyphyletic genus containing a number of distinct clades of species, including Pythiogeton, which possess morphologically distinguishable characters. A synoptic key to all the described Pythiogeton species is provided.     

An ITS-based phylogenetic framework for the genus Vorticella: finding the molecular and morphological gaps in a taxonomically difficult group

Vorticella includes more than 100 currently recognized species and represents one of the most taxonomically challenging genera of ciliates. Molecular phylogenetic analysis of Vorticella has been performed so far with only sequences coding for small subunit ribosomal RNA (SSU rRNA); only a few of its species have been investigated using other genetic markers owing to a lack of similar sequences for comparison. Consequently, phylogenetic relationships within the genus remain unclear, and molecular discrimination between morphospecies is often difficult because most regions of the SSU rRNA gene are too highly conserved to be helpful. In this paper, we move molecular systematics for this group of ciliates to the infrageneric level by sequencing additional molecular markers—fast-evolving internal transcribed spacer (ITS) regions—in a broad sample of 66 individual samples of 28 morphospecies of Vorticella collected from Asia, North America and Europe. Our phylogenies all featured two strongly supported, highly divergent, paraphyletic clades (I, II) comprising the morphologically defined genus Vorticella. Three major lineages made up clade I, with a relatively well-resolved branching order in each one. The marked divergence of clade II from clade I confirms that the former should be recognized as a separate taxonomic unit as indicated by SSU rRNA phylogenies. We made the first attempt to elucidate relationships between species in clade II using both morphological and multi-gene approaches, and our data supported a close relationship between some morphospecies of Vorticella and Opisthonecta, indicating that relationships between species in the clade are far more complex than would be expected from their morphology. Different patterns of helix III of ITS2 secondary structure were clearly specific to clades and subclades of Vorticella and, therefore, may prove useful for resolving phylogenetic relationships in other groups of ciliates.     

A Remarkable New Species of Liparis (Orchidaceae) from China and Its Phylogenetic Implications

In the present study, we formally describe Liparis pingxiangensis as a new species from Guangxi, China on the basis of morphological and molecular phylogenetic analyses. It is easily distinguished from closely related species by strongly curved column without column wings, and broadly rhombic-elliptic lip with 2 uncinate calli at the base. In particular, it differs most markedly from its congeners in possessing two pollinia attached by long and prominent caudicles (not stipes), to a distinct sticky disc. This type of pollinarium, as far as we know, is not found in any other species of Liparis, and is also unique among the orchids with waxy pollinia. We then proceeded to a phylogenetic analysis to ascertain the systematic position of this enigmatic species. Molecular study based on nuclear ribosomal ITS and plastid matK DNA sequence data supports L. pingxiangensis as a distinct species, which forms an independent lineage sister to L. nervosa and its allies (93% BS, 1.00 BPP). In the light of previous work, the findings have important implications for a better understanding of the well-supported pattern mainly based on vegetative features in Malaxideae.     

Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.     

Phylogenetic analysis of the Plagiotheciaceae (Musci) and its relatives based on rbcL gene sequences

Phylogenetic relationships are investigated using nucleotide sequences of the chloroplast gene, rbcL, for members of the family Plagiotheciaceae and its relatives. Nucleotide sequences of the rbcL were determined in 32 species (38 samples). In some species small differences in the nucleotide sequences of rbcL were recognized between the materials from different localities. The phylogenetic tree deduced from the sequences of the rbcL loci indicates the following: (1) pleurocarpous mosses form a monophyletic clade; (2) Plagiothecium is monophyletic; (3) Taxiphyllum is not closely related to Plagiothecium; (4) the family Hypnaceae is paraphyletic; (5) Pylaisiella is heterogeneous.     

Phylogenetic relationships of Puccinia horiana and other rust pathogens of Chrysanthemum × morifolium based on rDNA ITS sequence analysis

Isolates of the most important Puccinia species that have been reported on Chrysanthemum × morifolium were collected and the sequences of their ribosomal DNA internal transcribed spacers ITS1 and ITS2 were determined and used as phylogenetic markers. The focus of this study was on Puccinia horiana, due to its quarantine status and its impact in commercial chrysanthemum production. Three technical adjustments were needed to reliably obtain the nucleotide sequences starting from fresh or dried samples. The complete rDNA ITS nucleotide sequences of P. horiana, Puccinia chrysanthemi, and Puccinia tanaceti isolates of varying age and geographic origin were determined. We also identified an as yet undescribed Puccinia species on six old herbarium samples from chrysanthemum. This new species is morphologically similar to P. chrysanthemi and near identical to recent rust samples from Artemisia tridentata. P. tanaceti could not be confirmed as a pathogen of chrysanthemum. Different rDNA ITS sequences were present in P. horiana, with intra-isolate and inter-isolate variability in the length of three nucleotide repeat regions in the different rDNA tandem copies. We also identified three ITS types within P. horiana, with the rarer types displaying up to 67 bp nucleotide sequence differences. These rarer ITS types were detected at low copy number in all isolates. In general, very little rDNA ITS sequence variation was observed between P. horiana isolates from 1903 and 2003, and among isolates from different continents. Phylogenetic analyses using distance, Maximum Likelihood and Bayesian methods confirmed P. horiana, P. chrysanthemi, and the new Puccinia sp. as well-resolved groups, with P. horiana clustering in the clade where the economically important rust species of the Poaceae are located, and P. chrysanthemi and the new Puccinia sp. clustering in the clade where the majority of the rust fungi with hosts in the Asteraceae is located.     

Chloroplast phylogenomic analyses maternal relationships among sections in the genus Populus

The genus Populus L. has been divided into five sections based on morphological characters, but the phylogenetic relationships among sections remain uncertain. Topological discrepancies have been reported between trees obtained using nuclear and plastid sequences. We selected nine chloroplast genomes from all five sections, including two new sequenced species in this study for analyses of maternal phylogenetic relationships in the genus Populus at the sectional level. Phylogenetic analyses were performed using various subsets of data, coding sequences, noncoding sequences, and different districts of the genome, yielding contradictory outcomes for various subsets. According to our phylogenetic analyses, (1) a robust maternal phylogenetic relationship among sections based on complete chloroplast genomes was obtained; (2) Sect. Tacamahaca can be divided into two clades based on maternally inherited loci, i.e. cladeⅠ, distributed in North America and northeast China, and cladeⅡ, distributed in southwest China; (3) SSC-noncoding regions revealed an inconsistent topology compared with all other subsets; (4) this discrepancy may be resulted from incomplete lineage sorting between species of Populus. We tested multiple partitioning schemes to resolve deep-level phylogenetic relationships in Populus, and complete noncoding subset is most recommended.     

A new species of Lenzitopsis (Thelephorales,Basidiomycota) and its phylogenetic placement

Lenzitopsis (Thelephorales, Basidiomycota), typified by Lenzitopsis oxycedri, was monotypic before we described the second species of this genus, Lenzitopsis daii in this study. L. daii resembles L. oxycedri in producing lenzitoid hymenophore as well as brown hyphae and echinulate spores, but it differs from the type species by its annual basidiocarps, amyloid spores and growth exclusively on Juniperus chinensis (Cupressaceae). In the phylogenetic perspective inferred with nuclear large subunit ribosomal DNA sequences, the two species were separated from each other and formed a strongly supported clade in the Thelephorales. The two Lenzitopsis species showed a more than 5% difference in internal transcribed spacer sequences. Lenzitopsis species are wood-decaying fungi, and this is the second genus of the order where mycorrhizal life style is unknown, besides of Amaurodon.     

Laurencia majuscula var. elegans (Rhodophyta,Rhodomelaceae) is reinstated to specific rank as L. elegans

Laurencia majuscula has recently been determined to be conspecific with Laurencia dendroidea. To determine the correct taxonomic placement of its only non‐typical variety, L. majuscula var. elegans, mitochondrial COI‐5P and chloroplast rbcL gene sequences were analyzed and its phylogenetic position was inferred. Laurencia majuscula var. elegans consistently formed a well‐supported clade distinctly separate from the L. dendroidea clade. Molecular analyses revealed that L. majuscula var. elegans generally shows two distinct forms; a long‐branched form, and a compact form. Often the compact form has been identified as a different species based on morphology alone. Included in these analyses were topotype sequences of two species with which L. majuscula var. elegans is most often misidentified; Laurencia nidifica and Laurencia mcdermidiae. Laurencia nidifica formed a well‐supported clade separate from L. majuscula var. elegans. Laurencia mcdermidiae, however, formed a well‐defined clade sister to the L. majuscula var. elegans clade. Morphological comparisons were also made. It is concluded that L. majuscula var. elegans is morphologically distinct from L. dendroidea, L. nidifica, and L. mcdermidiae. It is proposed that L. majuscula var. elegans be reinstated to species level as L. elegans.     

Systematics of the subgenus of mouse opossums Marmosa (Micoureus) (Didelphimorphia,Didelphidae) with noteworthy records from Paraguay

The subgenus Marmosa (Micoureus) Lesson, 1842 includes six species of long-tailed, black masked mouse-opossums widely distributed in forested areas of the Neotropics from northern Argentina to Belize. Most of the nominal forms of Marmosa (Micoureus) have not been revised since 1933 and some currently accepted synonymies are in need of revision; similarly distributions of these forms remain for the most part unclear. Herein, we report Paraguayan new and noteworthy locality records for Marmosa (Micoureus), including the first records for the western Dry Chaco region. Specimens were identified to the species level on the basis of morphological and molecular data. In addition, we conducted a phylogenetic analysis that includes sequences of five of the six species currently recognized of Micoureus incorporating a total of 70 sequences of the subgenus. This constitute the most taxonomically and geographically dense phylogenetic analysis of Micoureus. Results show that the most basal dichotomy of the Micoureus clade does not delimit cis- and trans-Andean reciprocally monophyletic groups, rending the cis group paraphyletic to the single trans-species included, suggesting that the colonization of the western (trans) side of the Andes was a relatively late event in the biogeographic history of Micoureus. In addition, the phylogenetic analysis shows that additional taxonomic work is much needed to clarify the number of distinct biological units, either species or subspecies, within Micoureus.     

Trichoderma eijii and T. pseudolacteum, two new species from Japan

Trichoderma eijii and T. pseudolacteum, are described here as new species from Japan. These species were isolated from decaying wood in the Tomakomai Experimental Forest in Hokkaido Prefecture and from bedlogs on shiitake mushroom (Lentinula edodes) farms, respectively. The species were characterized using a combined approach that included cultural studies, holomorph morphology, and phylogenetic analyses of internal transcribed spacer and protein coding gene sequences (RNA polymerase subunit II, translation elongation factor 1-α, endochitinase, and actin). The results of phylogenetic analyses of these gene sequences indicate that T. eijii belongs to the Hamatum clade and is closely related to Hypocrea pezizoides, H. flaviconidia, and H. atroviridis/T. atroviride, from which it differs mainly in part-ascospore size and anamorphic characteristics. Trichoderma pseudolacteum, which was previously recognized as H. lactea sensu Doi, is morphologically distinct from H. lactea (= Hypocrea citrina) and is strongly supported as a separate lineage based on our phylogenetic analyses.     

Molecular phylogenetics and population structure of Sousa chinensis in Chinese waters inferred from mitochondrial control region sequences

Phylogenetic analyses of the genus Sousa were carried out across their geographic range and focused especially on the genetic variation patterns and population structure of Sousa chinensis in Chinese waters. The analyses were based on 287-bp of the mitochondrial control region from 122 Indo-Pacific humpback dolphins (Sousa chinensis) and two Atlantic humpback dolphins (Sousa teuszii). All specimens from China grouped together in a well-supported clade with high bootstrap (BS) and Bayesian posterior probability values (BPP), strongly suggesting that only one species of Sousa exists in China. Six haplotypes were identified in 65 individuals from Xiamen and Pearl River Estuary in China. The extremely low level of detected mtDNA genetic diversity strongly suggests a high priority in conservation of Sousa. The highly significant genetic differentiation between the two populations in Xiamen and Pearl River Estuary supports the designation of these two populations as separate management units (MUs) when designing management programs for this species.