A settled sub-family for the orphan tree: The phylogenetic position of the endemic Colombian genus <Emphasis Type="Italic">Orphanodendron</Emphasis> in the Leguminosae

Orphanodendron is a taxonomically and geographically isolated South American genus of two species. When first described by Barneby and Grimes in 1990, the genus was placed in Leguminosae subfamily Caesalpinioideae, but that placement was doubted and the name Orphanodendron (Gr. orphanos, orphan + dendron, tree) was chosen to reflect the uncertain subfamilial relationship of the genus. In this study, nucleotide sequence data from five Orphanodendron specimens were added to 662 other, previously sampled, Leguminosae taxa representing all three currently recognized subfamilies (Caesalpinioideae, Mimosoideae and Papilionoideae) in a matK maximum parsimony analysis that resolved Orphanodendron as a member of the genistoid s.l. clade of subfamily Papilionoideae. Two additional Bayesian phylogenetic analyses with reduced taxon sampling of plastid (matK combined with trnL-F) and nuclear (ITS) loci strongly support the monophyly of Orphanodendron and unambiguously establish Orphanodendron as a member of the genistoid sensu lato clade. Although our plastid phylogenetic analysis finds relatively low support for a sister-group relationship with the African genus Camoensia, the nuclear-encoded ITS resolves Orphanodendron as sister to the Bowdichia clade with strong support and Camoensia as sister to other core genistoids. The phylogenetic resolution of Orphanodendron as a member of the genistoid s.l. legumes based on nuclear and plastid sequences will undoubtedly advance future evolutionary investigations of this Colombian endemic tropical tree genus.     

Species tree phylogeny,character evolution,and biogeography of the Patagonian genus <Emphasis Type="Italic">Anarthrophyllum</Emphasis> Benth. (Fabaceae)

Geologic events promoting the aridization of southern South America contributed to lineage divergences and species differentiation through geographic (allopatric divergence) and biotic and abiotic factors (ecological divergence). For the genus Anarthrophyllum, which is distributed in arid and semi-arid regions of Patagonia, we assessed how these factors affected species diversification and reconstructed its possible biogeographic history in South American arid environments. Sequences were obtained from two molecular markers: the ITS nuclear region and the trnS-trnG plastid region. Using Parsimony, Maximum likelihood and Bayesian inference individual gene trees were reconstructed, and a species tree was obtained using multi-species coalescent analysis. Divergence times among species were estimated using secondary calibrations. Flexible Bayesian models and stochastic character mapping were used to elucidate ancestral geographic distributions and the evolution of the floral and vegetative phenotypes in the genus. Gene trees and species tree analyses strongly support Anarthrophyllum as monophyletic; all analyses consistently retrieved three well-supported main clades: High Andean Clade, Patagonian Clade 1, and Patagonian Clade 2. Main diversification events occurred concomitant with the Andean uplift and steppe aridization; the Andean mountain range possibly acted as a species barrier for the High Andean Clade. Vegetative traits showed adaptations to harsh climates in some clades, while pollinator-related floral features were associated with independent diversification in bee- and bird-pollinated clades within both Patagonian Clades. In conclusion, evolutionary and biogeographic history of Anarthrophyllum resulted from the action of ecological, historical, and geographic factors that acted either alternatively or simultaneously.     

Polyphyletic origin in <Emphasis Type="Italic">Pimpinella</Emphasis> (Apiaceae): evidence in Western Europe

The genus Pimpinella L. comprises about 150 species, being one of the largest genera within the family Apiaceae (subfamily Apioideae). Previous molecular phylogenetic studies have shown that Pimpinella is a taxonomically complex group. In this study, evolutionary relationships among representatives from Western Europe have been inferred from phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer (ITS 1 and ITS 2) and plastid sequences (trnL intron and the trnL-F spacer), with a representative sampling included (168 accessions in the ITS analysis, representing 158 species; and 42 accessions in the cpDNA analysis representing 35 taxa of Pimpinella and closely related species). All analyses resolved that Pimpinella is a non-monophyletic group, and Pimpinella’s taxa that grow in Western Europe are part of phylogenetically independent groups that correspond to three different tribes of the subfamily Apioideae: Pimpinelleae (core group), Pyramidoptereae and Smyrnieae.     

Three molecular markers suggest different relationships among three <Emphasis Type="Italic">Drepanocladus</Emphasis> species (Bryophyta: Amblystegiaceae)

Relationships among numerous specimens of Drepanocladus angustifolius (35 specimens), Drepanocladus lycopodioides (71 specimens), and Drepanocladus turgescens (102 specimens) are analysed based on the nuclear internal transcribed spacers 1 and 2 (ITS) and a portion of glyceraldehyde 3-phosphate dehydrogenase (gpd), and the plastid rpl16 G2 intron. Molecular data suggest that neither species is monophyletic as well as significant incongruence among molecular markers. No statistical support for recombination (ITS, gpd) was found. For some D. lycopodioides and D. turgescens specimens, the molecular information even suggests that they belong to the wrong one of these two species. All such specimens were collected in south Swedish areas where the two species are frequently found growing together and where sporophytes are often common. The occurrence of all such specimens only in these geographical areas is statistically unlikely and suggests that hybridisation occasionally occurs here. While molecular information suggests that the species are not monophyletic, geographical signals could be found for both D. angustifolius and D. turgescens.     

Phylogeny of anaerobic fungi (phylum <Emphasis Type="Italic">Neocallimastigomycota</Emphasis>), with contributions from yak in China

The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.     

Assessing <Emphasis Type="Italic">Azorella</Emphasis> (Apiaceae) and its allies: Phylogenetics and a new classification

Phylogenetic analyses of nuclear rDNA spacers (ITS and ETS) from Azorella and five closely related genera confirm earlier plastid results indicating that Azorella, Huanaca, Mulinum, and Schizeilema are all polyphyletic, and that the monotypic genus Laretia is nested within one of the six subclades of Azorella. Only Stilbocarpa is monophyletic, but that genus is embedded within a larger clade that includes representatives of three other genera (Azorella, Huanaca, and Schizeilema). Both nuclear and plastid datasets identify the same 10 clades, but the placement of these clades remains unstable. A new classification is presented in which these six genera are reduced to a single genus (Azorella) comprising 58 species arranged in 10 sections, one of which is newly described here (Azorella sect. Ranunculus), and one lectotypified (Azorella sect. Glabratae). A total of 13 new combinations are made (A. albovaginata, A. allanii, A. boelckei, A. burkartii, A. colensoi, A. echegarayi, A. echinus, A. hallei, A. lyallii, A. polaris, A. prolifera, A. robusta, A. ulicina), along with three replacement names (A. atacamensis, A. ruizii, A. schizeilema). For each of the 58 accepted species, a full synonymy is provided along with geographic ranges (and nomenclatural notes, where useful).     

Disentangling <Emphasis Type="Italic">Phialophora</Emphasis> section <Emphasis Type="Italic">Catenulatae</Emphasis>: disposition of taxa with pigmented conidiophores and recognition of a new subclass,Sclerococcomycetidae (Eurotiomycetes)

A new genus Rhopalophora is described for Phialophora clavispora, a lignicolous species formerly placed in Phialophora section Catenulatae that possesses pigmented conidiophores, phialides with a single conidiogenous locus that occasionally appear as schizophialides, and clavate, aseptate conidia arranged in chains or sometimes in heads. Sexual morphs are not known for this taxon. Phylogenetic analysis of DNA sequences from five loci (nucSSU, ITS, nucLSU, mitSSU, rpb1 and rpb2) of this and related fungi supports the introduction of a new family, Sclerococcaceae, for which we establish the order Sclerococcales. This order belongs to the new subclass Sclerococcomycetidae, a strongly supported clade within the Eurotiomycetes that is basal to a lineage containing the Chaetothyriomycetidae, Coryneliomycetidae and Eurotiomycetidae. Rhopalophora clavispora fits in this new family and is closely related to an isolate of Fusichalara minuta. The Sclerococcales also encompass marine, lignicolous species of Dactylospora, two species of the lichenicolous genus Sclerococcum, and a lineage comprised of strains from the digestive tracts of Neotropical wood-inhabiting beetles. We confirm that Dactylospora is polyphyletic; the phylogenetic placement of D. parasitica, the generic type, remains unknown.     

Diversification of <Emphasis Type="Italic">Caiophora</Emphasis> (Loasaceae subfam. Loasoideae) during the uplift of the Central Andes

Andean orogeny and the ecological changes that followed promoted diversification in plant and animal lineages since the Early Miocene. The angiosperm genus Caiophora (Loasaceae, subfam. Loasoideae) comprises around 50 species that are endemic to South America. These are distributed from southern Ecuador to Central Chile and Argentina. Bee pollination and distribution at low-intermediate elevations probably represent the ancestral condition in the lineage that includes Caiophora and its allied genera. The majority of Caiophora species grow at high elevations in the Andes, where some depend on vertebrate pollination. Previous studies did not resolve phylogenetic relationships within Caiophora, which precluded the dating of the origin and divergence of this group. We used markers of one nuclear (ITS) and one plastid region (trnS ^GCU -trnG ^UUC ) to solve phylogenetic relationships among 19 Caiophora species (including different accessions). We also included 10 species of the allied genera Blumenbachia and Loasa. Aosa rostrata and Xylopodia klaprothioides were used as outgroups. Phylogenetic reconstruction strongly supports the monophyly of Caiophora, and although several clades within this genus are poorly supported, our study yielded a better infra-generic resolution than previous studies. The origin of Caiophora is dated to the Early-Middle Miocene and can be related to the uplift of the Cordilleras Frontal and Principal and to Pacific marine transgressions. According to our estimations, Caiophora began to diversify during the Middle-Late Miocene and this unfolding proceeded eastwards during the Pliocene and the Pleistocene, in parallel to the uplift of different Andean mountain ranges.     

<Emphasis Type="Italic">Calcarisporium xylariicola</Emphasis> sp. nov. and introduction of <Emphasis Type="Italic">Calcarisporiaceae</Emphasis> fam. nov. in Hypocreales

During a survey of fungicolous fungi, a novel taxon from the surface of stroma of an unidentified Xylaria species was collected. Phylogenetic analyses showed that this taxon clustered with Calcarisporium sp. and C. arbuscula isolates, but was resolved as a distinct species. A detailed morphological examination coupled with phylogenetic analysis indicated that the taxon represented a new species. Calcarisporium xylariicola sp. nov. is thus introduced. The new taxon is characterized by short conidiophores with swollen bases and less length/width ratio of conidia that distinguish it from other Calcarisporium species. Calcarisporium is presently placed in Hypocreales genera, incertae sedis genus. Species in the genus are largely fungicolous, or occasionally caulicolous or foliicolous, and have hyaline, erect, verticillate conidiophores and sympodial, polyblastic conidiation. A phylogenetic analysis of combined SSU, ITS, LSU, TEF and RPB2 sequence data from Calcarisporium species and other taxa in Hypocreales indicate that Calcarisporium is a distinct lineage from other families. Therefore, a new family, Calcarisporiaceae, in Hypocreales is introduced.     

<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.     

Heteroplasmy due to chloroplast paternal leakage: another insight into <Emphasis Type="Italic">Phragmites</Emphasis> haplotypic diversity in North America

Chloroplasts contain several copies of their DNA, and intra-individual haplotypic variation (heteroplasmy) is common in plants, but unexplored in the cosmopolitan genus Phragmites. The aims of this study were to assess if heteroplasmy due to paternal leakage of the chloroplast occurs in Phragmites and which new insights into the evolutionary history of Phragmites australis in North America can be identified from the heteroplasmic variation. Eight non-native P. australis haplotypes occur in North America and can interbreed with P. australis ssp. americanus and P. australis var. berlandieri, creating opportunities for biparental inheritance of distinctive haplotypes. The polymorphism in the trnT-trnL sequence length revealed seventeen cases of heteroplasmy worldwide, in contact zones of distantly related haplotypes and in known hybrid populations, nine of which occurred in North America. In America, the cloned sequences, combined with nuclear markers, identified recombined haplotypes between native P. australis ssp. americanus and invasive P. australis haplotype M, and between the species P. mauritianus and P. australis, due to chloroplast paternal leakage. The occurrence of heteroplasmy and recombined haplotypes suggest a local origin for some of the rare non-native haplotypes occurring in North America, and plastid leakage events in the evolutionary histories of P. australis ssp. americanus and P. australis var. berlandieri.     

Phylogenetic relationships,molecular taxonomy,biogeography of <Emphasis Type="Italic">Betula</Emphasis>, with emphasis on phylogenetic position of Iranian populations

Birch trees inhabiting the high-altitude Hyrcanian forest (the southern shores of the Caspian Sea of Iran and Azerbaijan) are classified in the EN (endangered) category of the International Union for Conservation of Nature (IUCN). Taxonomic status and phylogenetic relationship of Iranian populations, molecular taxonomy, and biogeography of the genus Betula in the world have been considered. Four remnant populations of Betula were selected from north and northwestern parts of Iran. The internal ITS and trnH-psbA intergenic spacer regions were sequenced. Based on the trnH-psbA and ITS, Iranian birch and white birch were placed in a clade, but based on trnH-psbA divided into two subclades. Phylogenetic trees based on ITS and trnH-psbA data did not completely support the morphological classification. Network analysis confirms a close relationship of B. pendula with B. platyphylla and B. papyrifera with B. humilis, and B. ermanii were in a group with the other tetraploid species of the subgenus Neurobetula. Divergence time analysis showed that about 75 Ma ago the Betula genus separated from the other genus of Betulaceae and then divided into two main clades in Oligocene. Our divergence analysis supports that two subgenera of Betulenta and Betulaster are the oldest subgenera in the genus Betula and they date back to Eocene. The ancestral reconstruction suggests that ancestors of the genus Betula originated from Southeast Asia.     

<Emphasis Type="Italic">Luteoamylascus aculeatus</Emphasis> (Pezizomycetes,Pezizaceae): a new genus and species near the <Emphasis Type="Italic">Pachyphlodes</Emphasis>–<Emphasis Type="Italic">Amylascus</Emphasis> lineage

The new taxon Luteoamylascus aculeatus described in this article is proposed to accommodate two collections of a hypogeous ascomycete from central Spain, characterized by a tomentose yellowish peridium, labyrinth-like gleba filled with whitish hyphae, and intensely reacting amyloid asci. ITS, 28S, and RPB2 data suggest that this new taxon is an independent lineage proposed here as the new genus Luteoamylascus. Until now, this lineage was only known from ectomycorrhizal root tips and mitotic spore mats. In phylogenetic analyses, the Luteoamylascus lineage is placed close to the genera Amylascus, Pachyphlodes, and Scabropezia. Morphological data suggest an affinity with Amylascus.     

Molecular phylogeny of the genus <Emphasis Type="Italic">Bolusiella</Emphasis> (Orchidaceae,Angraecinae)

Recent molecular studies have suggested the monophyly of Bolusiella, a small orchid genus comprising five species and one subspecies from Continental Africa, but sampling has been limited. Using the species delimitation presented in the recent taxonomic revision of the genus, this study aimed to confirm the monophyly of Bolusiella and assess the interspecific relationships using a comprehensive sampling and various analytical methods. DNA sequences of one nuclear spacer region (ITS-1) and five plastid regions (matK, rps16, trnL–trnF, trnC–petN, and ycf1) from 20 specimens representing all five species of the genus were analyzed using static homology, dynamic homology, and Bayesian methods. The monophyly of both the genus Bolusiella and each of its five species was confirmed, corroborating the previously published taxonomic revision. The use of dynamic homology methods was not conclusive for this particular group. The results of the total evidence analysis (combining all six sequence regions) using the dynamic homology approach yielded a slightly different hypothesis regarding interspecific relationships (namely the exchange of B. talbotii and Bolusiella iridifolia as the earliest diverging lineage), probably because the nodes in question are supported by a small subset of conflicting characters, compared to the hypotheses resulting from the static homology and Bayesian methods, which are congruent with the results of previous studies.     

ITS rDNA sequence comparisons resolve phylogenetic relationships in <Emphasis Type="Italic">Orostachys</Emphasis> subsection <Emphasis Type="Italic">Appendiculatae</Emphasis> (Crassulaceae)

Orostachys (Crassulaceae) is a small genus of succulent plants having a predominantly East Asian distribution. Recent DNA sequence comparisons revealed polyphyletic nature of the genus and found distant relationship between its infrageneric taxa. Here we present the first molecular phylogeny of Orostachys subsection Appendiculatae based on a large number of ITS rDNA sequences representing most currently recognized members of the subsection and utilizing secondary structure information. Ribosomal spacer was a highly informative marker and provided a phylogenetic signal sufficient to resolve relationships at different scales, from affinities between species to a fine geographic structure in broadly sampled species. It was also conservative enough to allow unambiguous alignment and construction of consensus secondary structure models for ITS1 and ITS2. These models displayed a number of molecular synapomorphies defining most lineages established in our analyses. We revealed a major split in the subsection placing three species, O. spinosa, O. japonica and O. chanetii, into a strongly supported clade to the exclusion of O. thyrsiflora. Phenotypically distinct monotypic genus Meterostachys was also resolved as a part of the subsection’s clade and showed affinity to O. thyrsiflora. Our data suggested that morphology-based species concept for O. thyrsiflora requires reassessment.     

Phylogenetic relationships in Iranian <Emphasis Type="Italic">Scutellaria</Emphasis> (Lamiaceae) based on nuclear ribosomal ITS and chloroplast <Emphasis Type="Italic">trn</Emphasis>L-F DNA data

The genus Scutellaria (Lamiaceae, Scutellarioidae) includes taxa with a wide range of pharmacological traits, which make this genus economically important. Previous taxonomical studies on Scutellaria were mainly based on morphological and chromosomal characters. The infrageneric classification of the genus has been the subject of a long controversy among authors, and delimitation of taxa remains problematic. In this study, the phylogeny of the genus was evaluated using nrDNA ITS and trnL-F sequences, with a focus on the 42 Iranian taxa belonging to subgenera Apeltanthus and Scutellaria. In both ITS and trnL-F trees, there were two main clades within the genus corresponding to the two subgenera Scutellaria and Apeltanthus. In the subg. Scutellaria, the sect. Anaspis was monophyletic, but the monophyly of sect. Scutellaria was not supported. In this subgenus, S. galericulata was located away from other species in both trees, supported the isolation of this species from the sect. Scutellaria and inclusion in the sect. Galericularia as was previously considered by some authors. In subg. Apeltanthus, sect. Apeltanthus and sect. Lupulinaria were not monophyletic; furthermore, the monophyly of subsect. Lupulinaria was not supported. Based on the results of this study, it can be suggested that the sectional classification of both subgenera Apeltanthus and Scutellaria should be revised.     

Molecular phylogenetic and biogeographical analysis of <Emphasis Type="Italic">Nitraria</Emphasis> based on nuclear and chloroplast DNA sequences

Based upon DNA sequences from six plastid regions (rbcL, psbB-psbH, trnL-trnF, rpS16, psbA-trnH, rpS16-trnK) and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, the phylogenetic relationships in the genus Nitraria and family Nitrariaceae are investigated by using methods of maximum parsimony, maximum likelihood, and Bayesian inference. Our study strongly supports the monophyly of Nitraria. Nitraria can be divided into four parts, namely, the N. sphaerocarpa group, N. retusa group, the N. roborowskii and N. tangutorum group, and a group consisting of N. schoberi, N. komarovii, N. sibirica, and N. billardieri. Ancestral area reconstruction using S-Diva shows that eastern Central Asia is most likely the place of origin, and then dispersals occurred to western Central Asia, Africa, and Australia.