The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: An application of One Fungus One Name

Understanding the systematics and evolution of clavicipitoid fungi has been greatly aided by the application of molecular phylogenetics. They are now classified in three families, largely driven by reevaluation of the morphologically and ecologically diverse genus Cordyceps. Although reevaluation of morphological features of both sexual and asexual states were often found to reflect the structure of phylogenies based on molecular data, many species remain of uncertain placement due to a lack of reliable data or conflicting morphological characters. A rigid, darkly pigmented stipe and the production of a Hirsutella-like anamorph in culture were taken as evidence for the transfer of the species Cordyceps cuboidea, Cordyceps prolifica, and Cordyceps ryogamiensis to the genus Ophiocordyceps. Data from ribosomal DNA supported these species as a single group, but were unable to infer deeper relationships in Hypocreales. Here, molecular data for ribosomal and protein coding DNA from specimens of Ophiocordyceps cuboidea, Ophiocordyceps ryogamiensis, Ophiocordyceps paracuboidea, Ophiocordyceps prolifica, Cordyceps ramosopulvinata, Cordyceps nipponica, and isolates of Polycephalomyces were combined with a broadly sampled dataset of Hypocreales. Phylogenetic analyses of these data revealed that these species represent a clade distinct from the other clavicipitoid genera. Applying the recently adopted single system of nomenclature, new taxonomic combinations are proposed for these species in the genus Polycephalomyces, which has been historically reserved for asexual or anamorphic taxa.     

Robust Frankia phylogeny,species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size

Diazotrophic Actinobacteria of the genus Frankia represent a challenge to classical bacterial taxonomy as they include many unculturable strains. As a consequence, we still have a poor understanding of their diversity, evolution and biogeography. In this study, a Multi-Locus Sequence Analysis (MLSA) using atpD, dnaA, ftsZ, pgk, and rpoB loci was done on a large set of cultured and uncultured strains, compared to 16S rRNA and correlated to Average Nucleotide Identity (ANI) from available Frankia genomes. MLSA provided a robust resolution of Frankia genus phylogeny and clarified the status of unresolved species and complex of species.The robustness of single-gene topologies and their congruence with the MLSA tree were tested. Lateral Gene Transfers (LGT) were few and scattered, suggesting they had no impact on the concatenate topology. The pgk marker – providing the longest sequence, highest mean genetic divergence and least occurrence of LGT – was used to survey an unequalled number of Alnus-infective Frankia — mainly uncultured strains from a broad range of host-species and geographic origins. This marker allowed reliable Single-Locus Strain Typing (SLST) below the species level, revealed an undiscovered taxonomical diversity, and highlighted the effect of cultivation, sporulation phenotype and host plant species on symbiont richness, diversity and phylogeny.     

Trilobites Plicatolina lucida Lazarenko from the Upper Cambrian of the Kharaulakh Mountains (Northeastern Siberian Platform)

A collection of trilobites of the genus Plicatolina Shaw, 1951 from the upper Ogon’or Formation, Cambrian Section, Chekurovka Anticline (northeastern Siberian Platform, Kharaulakh Mountains), is studied. It is shown that all specimens of this collection belong to the same species, Plicatolina lucida Lazarenko, 1966, but represent different age stages. It is also shown that species of the genus Plicatolina (P. quadrata Pokrovskaya, 1966 and P. yakutica Pokrovskaya, 1966) described from the Upper Cambrian of the Siberian Platform are probably synonyms of P. lucida.     

A Revision of Australian River Prawns, Macrobrachium (Crustacea: Decapoda: Palaemonidae)

A taxonomic revision of Australian Macrobrachium identified three species new to the Australian fauna – two undescribed species and one new record, viz. M. auratumsp. nov., M. koombooloombasp. nov., and M. mammillodactylus(Thallwitz, 1892). Eight taxa previously described by Riek (1951) are recognised as new junior subjective synonyms, viz. M. adscitum adscitum, M. atactum atactum, M. atactum ischnomorphum, M. atactum sobrinum, M. australiense crassum, M. australiense cristatum, M. australiense eupharum of M. australienseHolthuis, 1950, and M. glypticumof M. handschiniRoux, 1933. Apart from an erroneous type locality for a junior subjective synonym, there were no records to confirm the presence of M. australe(Guérin-Méneville, 1838) on the Australian continent. In total, 13 species of Macrobrachiumare recorded from the Australian continent. Keys to male developmental stages and Australian species are provided. A revised diagnosis is given for the genus. A list of 31 atypical species which do not appear to be based on fully developed males or which require re-evaluation of their generic status is provided. Terminology applied to spines and setae is revised.     

Molecular phylogeny and biogeography of Honey‐buzzards (genera Pernis and Henicopernis)

A partial sequence of the cytb gene (382 bp) was amplified and sequenced from 35 individuals (mainly museum specimens) of the genus Pernis representing all valid taxa (10) and two taxa (P. p. gurneyi, P. p. japonicus) with questionable validity as well as representatives of the Old World Perninae, namely Henicopernis and Aviceda, to assess their relationships to the genus Pernis. Furthermore, Gypaetus barbatus, Neophron percnopterus, and Buteo buteo were included as outgroup taxa. In the trees derived from the sequence data, Aviceda represents the sister group of the genus Pernis. The genus Henicopernis and the Old World vultures Gypaetus andNeophron appear rather distantly related to Pernis. Within the genus Pernis, two of the described species (Pernis apivorus, Pernis ptilorhyncus) form monophyletic groups, whereas the relationships of the two clades representing three subspecies of Pernis celebensis are still uncertain. Although this study is based on comparatively short DNA‐sections, the trees deduced from these sequences can be considered as a first approach for inferring the phylogenetic relationships of the genus Pernis and related genera and for addressing questions concerning the evolutionary history, biogeography, and systematics of this group.     

A reconsideration of Gallicolumba (Aves: Columbidae) relationships using fresh source material reveals pseudogenes,chimeras, and a novel phylogenetic hypothesis

Phylogenetic analyses of nuclear and mitochondrial DNA sequences were used to test a recent phylogenetic hypothesis for the avian genus Gallicolumba that relied heavily on preserved museum study skins for DNA samples. Our comparisons show that several published gene sequences represent pseudogenes or chimeras of multiple taxa, and these sequences had an adverse influence on phylogeny estimation. A new phylogenetic hypothesis strongly supports the monophyly of Philippine bleeding-hearts, the monophyly of Gallicolumba sensu stricto, and places Leucosarcia as part of an Australasian radiation rather than sister to Alopecoenas. These findings clarify Gallicolumba biogeography and also highlight the need for greater caution in the use of suboptimal source material in molecular systematic studies.     

Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae)

Aim We investigate spatial and temporal patterns of diversification within the Neotropical avifauna using the phylogenetic history of parrots traditionally belonging to the genus Pionopsitta Bonaparte 1854. This genus has long been of interest for those studying Neotropical biogeography and diversity, as it encompasses species that occur in most Neotropical forest areas of endemism. Location The Neotropical lowland forests in South and Central America. Methods Phylogenetic relationships were investigated for all species of the genus Pionopsitta and five other short‐tailed parrot genera using complete sequences of the mitochondrial genes cyt b and ND2 as well as 26 plumage characters. The resulting phylogeny was used to test the monophyly of the genus, investigate species limits, and as a framework for reconstructing their historical biogeography and patterns of diversification. Results We found that the genus Pionopsitta, as previously defined, is not monophyletic and thus the Chocó, Central American and Amazonian species will now have to be placed in the genus Gypopsitta. The molecular and morphological phylogenies are largely congruent, but disagree on the position of one of the Amazon basin taxa. Using molecular sequence data, we estimate that species within Gypopsitta diversified between 8.7 and 0.6 Ma, with the main divergences occurring between 3.3 and 6.4 Ma. These temporal results are compared to other taxa showing similar vicariance patterns. Main conclusions The results suggest that diversification in Gypopsitta was influenced mainly by geotectonic events, marine transgressions and river dynamics, whereas Quaternary glacial cycles of forest change seem to have played a minor role in the origination of the currently recognized species.     

Karyotypic diversification in Hypostomus Lacépède, 1803 (Siluriformes, Loricariidae): biogeographical and phylogenetic perspectives

Hypostomus is a species-rich genus of fish with unclear systematics and phylogenetic relationships. Ten species of Hypostomus (H. albopunctatus, H. ancistroides, H. cochliodon, H. commersoni, H. faveolus, H. hermanni, H. aff. paulinus, H. regani, H. strigaticeps and H. topavae) were cytogenetically analyzed through Giemsa staining and silver nitrate impregnation, and the obtained data were correlated to the available biogeographical and phylogenetic analyses for the genus. Although the silver stained nucleolar organizer regions (AgNORs) were found to vary significantly among the species, the diploid numbers could be correlated to the distribution of the species on northern and southern South America river basins. Species with the lower diploid numbers (2n = 64) were associated to northern hydrographic basins and showed a single AgNORs bearing pair. Diploid numbers of 66–68 chromosomes and of 70–84 chromosomes were correlated to two major clades within Hypostomus and southern hydrographic basins, and showed AgNORs varying on number and position. Our results show that cytogenetic data can be correlated to the phylogeny and biogeography of the genus, helping to clarify its complex evolutionary history.     

Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation

Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted crocodile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial morphology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species delimitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnosing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split ± 6.5–7.5 Ma, which is congruent with intraspecies divergence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of comprehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the community of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group.     

Floral Chemical Signatures in the Genus Ophrys L. (Orchidaceae): A Preliminary Test of a New Tool for Taxonomy and Evolution

Ophrys flowers sexually swindle male insect pollinators that cross-pollinate flowers during acts of pseudocopulation on the labellum. Classification of this species-rich genus into a natural system is difficult, even with the present molecular methods, because of low interspecific genetic variability. We investigated the potential for flower chemical signatures generated from gas chromatography of Ophrys labellum extracts to distinguish taxa and indicate phylogenetic relationships. Labellum extracts of five taxa from southeast France belonging to the sections Araniferae and Pseudophrys were analyzed. We obtained a high variability among all individuals with a good discrimination among all species. We conclude that lipidic compounds on Ophrys labellum represent species-specific chemical signatures, as has proven useful in insect taxonomy. Furthermore, a possible population effect is detected for a poorly described, polytypical species. We conclude that chemical investigations should be continued to clarify the classification of closely related taxa and to better understand the evolutionary processes in this extraordinary genus.     

Old views and new insights: taxonomic revision of the Bukovina blind mole rat,Spalax graecus (Rodentia: Spalacinae)

As a result of their rather uniform external appearance and gross cranial morphology, the systematics of blind mole rats has been hotly debated over the last century; however, the separation of the large‐bodied and small‐bodied blind mole rats at the genus level (Spalax and Nannospalax, respectively), suggested earlier on morphological grounds, is strongly supported by recent molecular biological evidence. The species of Spalax have so far been distinguished from each other by cranial traits only, especially the outline of sutures of the cranium, and the shape and relative size of the nasal and parietal bones. Based on mitochondrial DNA sequences (with the widest taxonomic and geographic coverage so far) and detailed anatomical comparisons of museum specimens, we herewith provide a revision of the taxonomic and phylogenetic status of the westernmost representative of the genus, Spalax graecus s.l. We clarify that antiquus and istricus – presently regarded as synonyms of graecus – are well‐defined species, and they together form a separate clade within Spalax. The robustness of our conclusions is supported by the combined evidence of morphology, multilocus phylogeny, species distribution, and taxon history (species congruence with past tectonic and climate events). © 2013 The Linnean Society of London     

Phylogenetic systematics of the genus Echinococcus (Cestoda: Taeniidae)

Echinococcosis is a serious helminthic zoonosis in humans, livestock and wildlife. The pathogenic organisms are members of the genus Echinococcus (Cestoda: Taeniidae). Life cycles of Echinococcus spp. are consistently dependent on predator–prey association between two obligate mammalian hosts. Carnivores (canids and felids) serve as definitive hosts for adult tapeworms and their herbivore prey (ungulates, rodents and lagomorphs) as intermediate hosts for metacestode larvae. Humans are involved as an accidental host for metacestode infections. The metacestodes develop in various internal organs, particularly in liver and lungs. Each metacestode of Echinococcus spp. has an organotropism and a characteristic form known as an unilocular (cystic), alveolar or polycystic hydatid. Recent molecular phylogenetic studies have demonstrated that the type species, Echinococcus granulosus, causing cystic echinococcosis is a cryptic species complex. Therefore, the orthodox taxonomy of Echinococcus established from morphological criteria has been revised from the standpoint of phylogenetic systematics. Nine valid species including newly resurrected taxa are recognised as a result of the revision. This review summarises the recent advances in the phylogenetic systematics of Echinococcus, together with the historical backgrounds and molecular epidemiological aspects of each species. A new phylogenetic tree inferred from the mitochondrial genomes of all valid Echinococcus spp. is also presented. The taxonomic nomenclature for Echinococcus oligarthrus is shown to be incorrect and this name should be replaced with Echinococcus oligarthra.     

Numerical analyses of seed morphology and its taxonomic significance in the tribe Nigelleae (Ranunculaceae)

We examined the seed morphology of Nigella, Garidella and Komaroffia to aid systematics and taxonomy. The seeds of 21 taxa in 20 species from Mediterranean and West Asian countries were studied using both zoom stereo and scanning electron microscopy (SEM). Principal coordinate analysis (PCoA) and unweighted average linkage analysis (UPGMA) were performed to assess the contribution of seed characters to the taxonomy of the tribe. Representative pictures from zoom stereo microscopy and SEM studies and measurement of seeds are presented. Most studied species showed unique seed surface sculpturing features, and seed shape, size and surface sculpturing separated the studied taxa into five main groups. However, the variation in seed shape and color were found to be in conflict with the generic taxonomy while macromorphological characters were found more congruent with the sectional taxonomy than with the generic taxonomy. Five main types of seed ornamentations – rugulose + striate, granulate, smooth, rugulose and mucronulate – were identified. Patterns in seed micromorphology strongly supported the sectional level taxonomy of Nigella. Two of the three sections of the genus were found to be well differentiated in terms of seed characters. Furthermore, seed morphology alone provide good support to Garidella as a distinct genus, but shows less taxonomic value for Komaroffia.     

Systematic wood anatomy of the genus Tapirira Aublet (Anacardiaceae)— a numerical approach

A wood anatomical study of the Mexican species ofTapirira was undertaken to uncover evidence to help clarify the systematics of the genus. Three to five individuals of each of 10 populations from throughout the range of the genus in Mexico were studied. For comparative purposes, three Central and South American species were also examined. Cluster analysis showed that the genus in Mexico can be separated into two phenetic units, represented byT. mexicana, a species widely distributed in Mexico, andT. chimalapana, a species endemic to the Isthmus of Tehuantepec. Canonical discriminant and factor analyses indicate that the quantitative wood characters most useful in distinguishing these species are wall thickness of fibers and vessels, diameter of fiber lumen, and diameter and frequency of radial canals. These species also differ in presence/absence of tannins in the fibers and color and specific gravity of the wood. The South American species,Tapirira bethanniana, T. guianensis, andT. obtusa, have wood anatomy similar to that ofT. chimalapana. The differences in the wood anatomical characters betweenT. mexicana and the other taxa suggest that the infrageneric classification ofTapirira should be reevaluated. The results of this study support the utility of sampling of populations in comparative wood anatomy.     

Additional rDNA ITS sequences and its phylogenetic consequences for the genus Leveillula with emphasis on conidium morphology

Taxonomy of the genus Leveillula has long been considered as a challenge in powdery mildew systematics. The rDNA diversity has recently been used for phylogenetic analysis of several specimens of the genus Leveillula. In the present study, additional rDNA ITS sequences are provided and a new phylogenetic analysis is carried out aiming at a better understanding of the genetic diversity in the genus Leveillula. New analyses confirmed that L. taurica is unique in the genus, as it exhibits an intraspecific gene sequence diversity considerably higher than in other species. In several cases L. taurica s. lat. on a certain host plant species has a sequence different from L. taurica on other host plants. Moreover, DNA data indicated different lineages among L. taurica specimens which were hardly distinguishable by morphology. More than one genotype occurring on a single host is sometimes possible. According to these results, several races such as Leveillula on Artemisia, Acroptilon, Onobrychis, are molecularly well characterized. While there is enough molecular evidence to delimit such races as independent taxa, clear morphological delimitations between these new and already published taxa are very difficult or even impossible. However, ecological features, and above all, host specificity for biotrophic fungi such as powdery mildew, would be a good criterion to discriminate cryptic taxa along with rDNA sequences. In fact, many collections of Leveillula strains on different hosts show their own type of conidial morphology, which is usually consistent for a strain on a single host species. Hence, we have proposed to describe new species for Leveillula on some host plants such as Artemisia, Acroptilon, Echinops and Onobrychis.     

New hyaenodonts (Mammalia) from the late Ypresian locality of Prémontré (France) support a radiation of the hyaenodonts in Europe already at the end of the early Eocene

We describe three new hyaenodonts from the late Ypresian locality of Prémontré (Aisne, France; close to MP 10 reference level). The new species – Lesmesodon gunnelli nov. sp., Cynohyaenodon smithae nov. sp., and Eurotherium mapplethorpei nov. sp. – represent the oldest occurrences of these three European genera. Lesmesodon gunnelli nov. sp. is also reported from the locality of Cuis (Marne, France; Ypresian, ~MP 10). We further present the dentition of two specimens of Lesmesodon edingeri from Messel (Hessia, Germany; type locality of the genus) based on µCT scans. Cynohyaenodon smithae nov. sp. and Lesmesodon gunnelli nov. sp. support the presence of small (300–400 g) hyaenodonts in the late Ypresian of the Paris Basin. Estimates of dental indices indicate that these hyaenodonts had an insectivorous diet. The third species – referred to Eurotherium – may have weighed 4–5 kg and, based on dental indices, likely incorporated more vertebrate prey into its diet. We also performed a phylogenetic analysis in order to test the relationships of these new taxa. These newly discovered species imply that the Proviverra/Allopterodon, Cynohyaenodon, and Eurotherium clades appeared in Europe earlier than previously known (i.e., Lutetian, MP 11). They reinforce the hypothesis that the hyaenodonts radiated during the middle-late Ypresian (MP 8/9–10) in Europe and adapted at that time to diverse ecological niches that they still occupied in the Priabonian (MP 13–14).     

Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)

The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.     

What Can Environmental Sequences Tell Us About the Distribution of Low‐Rank Taxa? The Case of Euplotes (Ciliophora,Spirotrichea), Including a Description of Euplotes enigma sp. nov.

Environmental sequences have become a major source of information. High‐throughput sequencing (HTS) surveys have been used to infer biogeographic patterns and distribution of broad taxa of protists. This approach is, however, more questionable for addressing low‐rank (less inclusive) taxa such as species and genera, because of the increased chance of errors in identification due to blurry taxonomic boundaries, low sequence divergence, or sequencing errors. The specious ciliate genus Euplotes partially escapes these limitations. It is a ubiquitous, monophyletic taxon, clearly differentiated from related genera, and with a relatively well‐developed internal systematics. It has also been the focus of several ecological studies. We present an update on Euplotes biogeography, taking into consideration for the first time environmental sequences, both traditional (Sanger) and HTS. We inferred a comprehensive small subunit rRNA gene phylogeny of the genus including a newly described marine species, Euplotes enigma, characterized by a unique question mark‐shaped macronucleus. We then added available environmental sequences to the tree, mapping associated metadata. The resulting scenario conflicts on many accounts with previously held views, suggesting, for example, that a large diversity of anaerobic Euplotes species exist, and that marine representatives of mainly freshwater lineages (and vice‐versa) might be more common than previously thought.