The molecular phylogenetics of Trachymyrmex Forel ants and their fungal cultivars provide insights into the origin and coevolutionary history of ‘higher‐attine’ ant agriculture

The fungus‐growing ants and their fungal cultivars constitute a classic example of a mutualism that has led to complex coevolutionary dynamics spanning c. 55–65 Ma. Of the five agricultural systems practised by fungus‐growing ants, higher‐attine agriculture, of which leaf‐cutter agriculture is a derived subset, remains poorly understood despite its relevance to ecosystem function and human agriculture across the Neotropics and parts of North America. Among the ants practising higher‐attine agriculture, the genus Trachymyrmex Forel, as currently defined, shares most‐recent common ancestors with both the leaf‐cutter ants and the higher‐attine genera Sericomyrmex Mayr and Xerolitor Sosa‐Calvo et al. Although previous molecular‐phylogenetic studies have suggested that Trachymyrmex is a paraphyletic grade, until now insufficient taxon sampling has prevented a full investigation of the evolutionary history of this group and limited the possibility of resolving its taxonomy. Here we describe the results of phylogenetic analyses of 38 Trachymyrmex species, including 27 of the 49 described species and at least 11 new species, using four nuclear markers, as well as phylogenetic analyses of the fungi cultivated by 23 species of Trachymyrmex using two markers. We generated new genetic data for 112 ants (402 new gene sequences) and 95 fungi (153 new gene sequences). Our results corroborate previous findings that Trachymyrmex, as currently defined, is paraphyletic. We propose recognizing two new genera, Mycetomoellerius gen.n. and Paratrachymyrmex gen.n. , and restricting the continued use of Trachymyrmex to the clade of nine largely North American species that contains the type species [Trachymyrmex septentrionalis (McCook)] and that is the sister group of the leaf‐cutting ants. Our fungal cultivar phylogeny generally corroborates previously observed broad patterns of ant–fungus association, but it also reveals further violations of those patterns. Higher‐attine fungi are divided into two groups: (i) the single species Leucoagaricus gongylophorus (Möller); and (ii) its sister clade, consisting of multiple species, recently referred to as Leucoagaricus Singer ‘clade B’. Our phylogeny indicates that, although most non‐leaf‐cutting higher‐attine ants typically cultivate species in clade B, some species cultivate L. gongylophorus, whereas still others cultivate fungi typically associated with lower‐attine agriculture. This indicates that the attine agricultural systems, which are currently defined by associations between ants and fungi, are not entirely congruent with ant and fungal phylogenies. They may, however, be correlated with as yet poorly understood biological traits of the ants and/or of their microbiomes.     

A molecular phylogeny of the <Emphasis Type="Italic">Lecanora varia</Emphasis> group,including a new species from western North America

The phylogeny of the Lecanora varia group is inferred from ITS sequences using Bayesian and ML phylogenetic analysis methods. According to our data, usnic acid-containing, corticolous Lecanora species do not form a monophyletic group but occur in three major clades together with other groups of Lecanora and Protoparmeliopsis. The new combination Lecanora filamentosa (Stirt.) Elix & Palice is proposed. The new species Lecanora schizochromatica is described from northwestern North America. It produces atranorin as a major substance and is closely related to the morphologically and chemically similar L. filamentosa. The American Biatora pullula Tuck. is synonymised with Lecanora anopta Nyl., which is hereby reported for continental North America for the first time. The phylogenetic relationships between the major clades of Lecanora are still largely unresolved and require more intensive taxon and character sampling.     

Taxonomic studies of nectrioid fungi in Japan. II: The genus <Emphasis Type="Italic">Bionectria</Emphasis>

Based on the result of morphological and the phylogenetic analyses, three Bionectria (Bionectriaceae: Hypocreales) species are added to the mycobiota of Japan. Among them, one found in Okinawa and Kagoshima Prefectures is described as a new species, Bionectria pseudostriatopsis (anamorph: Clonostachys pseudostriatopsis). The other two, B. grammicospora and B. sporodochialis, are new records from Japan. Additional distribution records are given for Bionectria species hitherto known in Japan.     

Synopsis of <Emphasis Type="Italic">Mickelia</Emphasis>, a newly recognized genus of bolbitidoid ferns (Dryopteridaceae)

Our recent molecular phylogenetic study revealed a previously unrecognized clade of six species that is sister to Elaphoglossum. Within this clade, four species are currently classified in Bolbitis, one in Lomagramma, and one in Acrostichum. For this clade, we propose the name Mickelia, with M. nicotianifolia as the type species. We also make new combinations for the species in our phylogenetic study shown to belong to Mickelia (M. bernoullii, M. guianensis, M. hemiotis, M. nicotianifolia, M. oligarchica, and M. scandens) and two other species believed to belong to the clade based on morphology (M. lindigii, M. pergamentacea). A new hybrid and two new species are also described (M. ×atrans, M. furcata, and M. pradoi). In total, Mickelia consists of ten species and one hybrid. It is entirely neotropical. We provide a key to the genera of bolbitidoid ferns and a synopsis of Mickelia that gives for each species a complete synonymy, geographical distribution, comparative discussion, and illustration.     

New species and record of <Emphasis Type="Italic">Zygophiala</Emphasis> on apple fruit from China

Up to now, four species of Zygophiala have been recorded, most of them as agents of flyspeck disease on apples. Two species of Zygophiala associated with flyspeck on apple in China are described in this paper. Zygophiala cylindrica is described as a new fungal species based on morphological characteristics and analysis of DNA sequences, and a phylogenetic analysis of the DNA sequences data is presented. Zygophiala cryptogama is recorded for the first time in China.     

Phylogeny and biogeography of the lamioid genus <Emphasis Type="Italic">Phlomis</Emphasis> (Lamiaceae)

The genus Phlomis is one of the largest genera of subfamily Lamioideae (Lamiaceae) with more than 100 recognised species distributed in Asia, southern Europe and northern Africa. Morphological studies have suggested that the species can be split into two morphologically distinct groups that have previously been recognised as either sections or separate genera. The current study represents the first molecular phylogenetic study of the genus in which taxa representative of the entire genus are included. In contrast to considerable morphological and ecological variation among taxa, sequence variation in the trnL intron, the trnL – F intergenic spacer, and the rps16 intron was low, resulting in sparse phylogenetic resolution, particularly among the South West Asian and Mediterranean taxa. However, the results support a split of the genus into two separate groups that are recognised here as the genera Phlomoides and Phlomis in order to decrease taxonomic complexity. The close relationship between Phlomis s.l. and Eremostachys, pointed out by several authors, is confirmed, and in a noteworthy new finding, the small Asian genus Notochaete, is more closely related to the Phlomis s.l. lineage than previously assumed. The two monotypic genera Pseuderemostachys and Lamiophlomis as well as Notochaete hamosa are transferred to Phlomoides and three new combinations are made. Character optimisation analyses based on geographic distributions of all taxa show that the groups obtained by molecular phylogenetic analysis correlate well with biogeography. The results suggest that the Phlomis s.l. lineage has a Central Asian origin in an area around Western China.     

A novel clade of sporocarp-forming species of glomeromycotan fungi in the <Emphasis Type="Italic">Diversisporales</Emphasis> lineage

In the early times of taxonomy of arbuscular mycorrhizal fungi (Glomeromycota), exclusively sporocarpic species were described. Since then the focus has mainly shifted to species forming spores singly. For many of the sporocarpic species, no molecular data have been made available, and their phylogenetic position has remained unclear. We obtained small subunit ribosomal rDNA and internal transcribed spacer data from specimens of glomeromycotan sporocarps from tropical areas that were assigned to three morphospecies. The complete sequence of the 18S small rDNA subunit sequence, internal transcribed spacers (ITS) 1 and 2 and 5.8S rDNA subunit, was determined from a sporocarp of Glomus fulvum. Partial sequences of the small subunit and the other regions were obtained from Glomus pulvinatum and the newly described species Glomus megalocarpum. Molecular phylogenetic analyses placed all species analyzed as a monophyletic sister group to the Diversispora spurca/Glomus versiforme clade group (“Glomus group C”) within the Diversisporales. The phylogenetic divergence from other known species suggests that this clade may constitute a new genus. These findings will have important consequences for taxon definition in the Diversisporales. They will facilitate identification of these fungi using rDNA sequences within colonized roots or the environment. Taxonomic novelties: Glomus megalocarpum D. Redecker     

<Emphasis Type="Italic">Micronematobotrys</Emphasis>, a new genus and its phylogenetic placement based on rDNA sequence analyses

A new hyphomycetous fungus, Micronematobotrys verrucosus, isolated as an endophyte from Quercus liaotungensis and Ulmus macrocarpa in the Dongling Mountain of Beijing is described as a new monotypic genus represented by M. verrucosus. This new species differs morphologically from Botrytis-like fungi and other similar genera in possessing micronematous conidiophores and colored verrucose conidia. The phylogenetic relationships of Micronematobotrys among sexual ascomycetes are examined based on 18S and 28S rDNA sequence data using maximum parsimony and Bayesian methods. The phylogenetic analyses suggest that M. verrucosus is a member of Pyronemataceae in Pezizales.     

<Emphasis Type="Italic">Prorocentrum rivalis</Emphasis> sp. nov. (Dinophyceae) and its phylogenetic affinities inferred from analysis of a mixed morphological and LSU rRNA data set

A new freshwater epiphytic Prorocentrum species, Prorocentrum rivalis, from the temperate region of the Haute-Vienne, France, is described. This species is the third freshwater species identified among approximately 60 marine Prorocentrum species. This new species is described using scanning electron microscope and phylogenetic analyses by a polyphasic approach (LSU rRNA sequences combined with 9 morphological characters). The phylogenetic analysis attests that P. rivalis is close to other planktonic freshwater species and the freshwater Prorocentrum clade is evolutionarily derived from an epiphytic freshwater prorocentroid ancestor. The unique marine species in the freshwater clade results from an ecophysiological reversion. P. rivalis differs from other epiphytic taxa by its rarity, its temperate distribution and its ecophysiological needs. The phylogeny confirms also that all planktonic Prorocentrum species are evolutionarily derived from epiphytic/benthic ancestors.     

Unmasking cryptic species: morphometric and phylogenetic analyses of the Ibero‐North African Linaria incarnata complex

Linaria incarnata has been treated as a widely distributed Ibero‐North African species in the latest taxonomic reviews. Morphological and phylogenetic disparity between populations of this species has been previously reported. Here we present new morphological and phylogenetic evidence for the disintegration of L. incarnata into three distinct species: L. incarnata from the western Iberian Peninsula; L . mamorensis sp. nov. from north‐western Morocco; and L. onubensis from south‐western Spain. The relatively poor morphological differentiation between these taxa (which can be regarded as cryptic species) and their distinct phylogenetic positions indicate that characters of the L. incarnata morphotype have been acquired multiple times in the evolution of Linaria section Versicolores. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00, 000–000.     

More than meets the eye: a morphological and phylogenetic comparison of long‐spurred,white‐flowered Satyrium species (Orchidaceae) in South Africa

Superficial similarities among unrelated species are often a result of convergent evolution and can cause considerable taxonomic confusion. A case in point is Satyrium eurycalcaratum , described here as a new species, which has been confused with several other Satyrium spp. with similar long‐spurred, white flowers. A phylogenetic analysis, based on molecular data, indicated that S. eurycalcaratum is not closely related to any of the species with which it has been previously confused. A comparative analysis of morphological characters in the seven South African Satyrium spp. with long‐spurred, white flowers showed that each of these, including S. eurycalcaratum , is characterized by a unique combination of traits. Despite the similarity in pollination syndrome characters, such as spur length and flower colour, variation in rostellum structure was particularly pronounced and four distinctive forms were present. There was no phylogenetic signal in patterns of interspecific rostellum variation, as some closely related species had different rostella, whereas some distantly related species shared similar rostellum structures. We therefore conclude that the use of rostellum traits in conjunction with phylogenetic evidence can resolve species delimitations among orchid species that share the same pollination syndrome. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 166 , 417–430.     

<Emphasis Type="Italic">Erysiphe monascogera</Emphasis> sp. nov., an unusual powdery mildew fungus found on fruits of <Emphasis Type="Italic">Styrax japonica</Emphasis>

Morphological observations using light and scanning electron microscopes and molecular phylogenetic analysis revealed that the fungus growing on the surface of fruits or sepals of Styrax japonica collected at Nagano, Japan, is a new powdery mildew with an unusual morphology, described here as Erysiphe monascogera. This fungus has mainly a single ascus in a chasmothecium, but molecular phylogenetic analysis and the shape of the hyphal appressoria suggest that it is an Erysiphe species. Erysiphe monascogera is a sister-species to E. nomurae on Symplocos chinensis var. leucocarpa f. pilosa, although there are obvious morphological differences between the two species. This inconsistency between molecular phylogeny and morphology may be explained by the unique habitat of E. monascogera. Erysiphe monascogera and E. nomurae are included in a clade composed of the E. alphitoides complex, which suggests that these two species diverged by host jumping of the E. alphitoides complex, having oaks as major host plants.     

A comparative morphological study of the kinorhynch genera <Emphasis Type="Italic">Antygomonas</Emphasis> and <Emphasis Type="Italic">Semnoderes</Emphasis> (Kinorhyncha: Cyclorhagida)

Detailed information revealed through combined use of light- and scanning electron microscopy, is given for two species of kinorhynchs, representing the cyclorhagid genera Semnoderes and Antygomonas. The two species have not previously been examined using SEM, and the new observations point out several similarities between species of the two genera, which could indicate a potential close relationship. The generated data is meant to be incorporated in a future phylogenetic analysis in order to clarify the phylogenetic relationships among kinorhynchs.     

A new species of <Emphasis Type="Italic">Pustula</Emphasis> (Oomycetes,Albuginales) is the causal agent of sunflower white rust

White blister rust of sunflower is an emerging disease that is among the most important diseases in this crop in South Africa and has recently spread to Europe. For the genus Albugo, it has been demonstrated that species are mostly at least host genus specific and that several previously overlooked species are present on Brassicaceae. It thus seems likely that previously unrecognised species are also present in the genus Pustula. Based on previous phylogenetic reconstruction in combination with differences in oospore ornamentation, it is revealed that Pustula on sunflower, previously attributed to Pustula tragopogonis (syn. Albugo tragopogonis), is distinct from Pustula on Tragopogon. Therefore, this pathogen is described as a new species, Pustula helianthicola. In addition, taxonomic observations revealed that Pustula tragopogonis is an incorrect name and is replaced by the new combination, Pustula obtusata.     

Molecular phylogeny of South‐East Asian arboreal murine rodents

Recent phylogenetic studies and taxonomic reviews have led to nearly complete resolution of the phylogenetic divisions within the old world rats and mice (Muridae, Murinae). The Micromys division and Pithecheir division are two notable exceptions where groupings of species into these divisions based on morphology and arboreal lifestyle have not been supported by phylogenetic evidence. Several enigmatic species from these divisions have been missing from molecular studies, preventing a rigorous revision of phylogenetic relationships. In this study, we sequenced for the first time one mitochondrial and three nuclear genes from South‐East Asian keystone species of these two arboreal divisions: Hapalomys delacouri (Micromys division), Lenothrix canus and Pithecheir parvus (Pithecheir division). We also complemented the molecular data already available for the two divisions with new data from Sundaic Chiropodomys, Indian Vandeleuria oleracea and the recently described Sulawesian Margaretamys christinae. Using this new phylogenetic framework and molecular dating methodologies, our study allows some more detailed classification of the former Micromys and Pithecheir divisions, while confirming their polyphyletic status. Specifically, the former Micromys division should now be split into four monotypic divisions: Chiropodomys, Hapalomys, Micromys and Vandeleuria divisions. The former Pithecheir division is likely to be refined and restricted to Pithecheir and probably Pithecheirops, whereas Lenothrix and Margaretamys should now be recognized as representatives of the Dacnomys division. Our findings have profound implications with regard to the systematics of Murinae, as well as to the early evolution of murine morphology and dental characters.     

Extensive horizontal transfer of core genome genes between two <Emphasis Type="Italic">Lactobacillus</Emphasis> species found in the gastrointestinal tract

Background  

While genes that are conserved between related bacterial species are usually thought to have evolved along with the species, phylogenetic trees reconstructed for individual genes may contradict this picture and indicate horizontal gene transfer. Individual trees are often not resolved with high confidence, however, and in that case alternative trees are generally not considered as contradicting the species tree, although not confirming it either. Here we conduct an in-depth analysis of 401 protein phylogenetic trees inferred with varying levels of confidence for three lactobacilli from the acidophilus complex. At present the relationship between these bacteria, isolated from environments as diverse as the gastrointestinal tract (Lactobacillus acidophilus and Lactobacillus johnsonii) and yogurt (Lactobacillus delbrueckii ssp. bulgaricus), is ambiguous due to contradictory phenotypical and 16S rRNA based classifications.     

New species of <Emphasis Type="Italic">Moristroma</Emphasis> (Ascomycetes) and phylogenetic position of the genus

The loculoascomycete Moristroma quercinum sp. nov. and Moristroma japonicum sp. nov. are described from Northern Europe (Denmark, Lithuania, Sweden) and Japan, respectively. M. quercinum is reported from wood of Quercus robur and Q. petraea, and M. japonicum is reported from wood of Quercus mongolica var. grossoserrata. Ascostromata of both species were found on hard heartwood of attached or shed branches. The two new species differ from the type species of the genus, M. polysporum, by the presence of pycnidia, and by the size of ascostromata, asci and ascospores. Drawings illustrate ascostromata, pycnidia, asci, hamathecium and ascospores of the two new species. A phylogenetic analysis suggests that Moristroma belongs to the Chaetothyriomycetes, rather than to the Dothideomycetes as previously suggested.