Polyphyly and two emerging lineages in the rust genera Puccinia and Uromyces

The phylogenetic validity of Puccinia and Uromyces, Pucciniaceae, and closely related genera was evaluated using nucLSU rDNA sequences. Using a wide range of rust species with different life cycles and with different host specificities, Puccinia and Uromyces were shown to be highly polyphyletic and to also include representatives of the genera Aecidium, Cumminsiella, Dietelia, Endophyllum, Miyagia, and Uredo. Furthermore, the structure of the phylogenetic data did not reflect previous sub-generic delimitations based on teliospore pedicel structure, but rather suggests that at least two major lineages have evolved within Puccinia/Uromyces: Rusts with telial states on Poaceae were exclusively found in one of these groupings and those with telial states on Cyperaceae resided in the other lineage. This might suggest that the two lineages evolved in close association with these host groups in different biomes.     

Test of the monophyly of Odostomiinae and Turbonilliinae (Gastropoda, Heterobranchia, Pyramidellidae) based on 16S mtDNA sequences

Schander, C., Halanych, K. M., Dahlgren, T. & Sundberg, P. (2003) Test of the monophyly of Odostomiinae and Turbonilliinae (Gastropoda, Heterobranchia, Pyramidellidae) based on 16S mtDNA sequences. — Zoologica Scripta, 32 , 243−254.
While gastropod phylogeny has received much recent attention, relationships within some major gastropod clades have still not been studied. The Pyramidellidae is one such group, comprising more than 6000 named species in more than 350 genera. We sequenced part of the mitochondrial 16S gene from 32 species in an attempt to clarify pyramidellid phylogeny and employed a successive alignment approach that allowed us to maximize the phylogenetic signal of the data. Neighbour-joining, maximum parsimony and likelihood analyses recovered two distinct clades. One clade consisted of Noemiamea which nested within Odostomia ( sensu stricto ) . The inclusion of Brachystomia , Megastomia , Jordaniella and Liostomia within Odostomia is not supported. The second clade comprised Spiralinella , Brachystomia , Boonea , Jordaniella , Liostomia and Parthenina . Our results further suggest that Turbonilla, as interpreted by most authors, is polyphyletic. This study shows that the 16S gene is useful in unravelling pyramidellid phylogeny but needs to be combined with other data (including molecular, morphological and developmental) to fully clarify the evolutionary relationships.     

Infrafamilial Phylogeny of the Aquatic Angiosperm Podostemaceae Inferred from the Nucleotide Sequences of the matK Gene

Abstract: The infrafamilial relationships of Podostemaceae were deduced from nucleotide sequences of the chloroplast matK gene. The matK phylogenetic analyses show that Podostemaceae are composed of two major clades that correspond to the subfamily Tristichoideae sensu stricto and Weddellina and the subfamily Podostemoideae. Weddellina, which has long been recognized as a member of the Tristichoideae, is sister to the Podostemoideae, supporting the classification that recognized a third subfamily Weddellinoideae. Malaccotristicha malayana and Terniopsis sessilis form a basal clade in Tristichoideae sensu stricto. Tristichoideae show a high morphological diversity and, surprisingly, a close relationship exists between Dalzellia zeylanica and Indotristicha ramosissima, which remarkably differ in their body plans. A few genera defined by particular characters, such as Synstylis and Torrenticola, merge into clades of other larger genera. The Podostemoideae taxa studied are composed of two American clades, an Asian-Australian clade and a Madagascan clade, and may suggest that the subfamily perhaps originated in America and migrated to the Old World.     

Multigene Molecular Phylogeny and Biogeographic Diversification of the Earth Tongue Fungi in the Genera Cudonia and Spathularia (Rhytismatales,Ascomycota)

The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the “earth tongue fungi” in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America.     

Igniting taxonomic curiosity: The amazing story of Amazonocrinis with the description of a new genus Ahomia gen. nov. and novel species of Ahomia,Amazonocrinis, and Dendronalium from the biodiversity-rich northeast region of India

Five cyanobacterial strains exhibiting Nostoc-like morphology were sampled from the biodiversity hotspots of the northeast region of India and characterized using a polyphasic approach. Molecular and phylogenetic analysis using the 16S rRNA gene indicated that the strains belonged to the genera Amazonocrinis and Dendronalium. In the present investigation, the 16S rRNA gene phylogeny clearly demarcated two separate clades of Amazonocrinis. The strain MEG8-PS clustered along with Amazonocrinis nigriterrae CENA67, which is the type strain of the genus. The other three strains ASM11-PS, RAN-4C-PS, and NP-KLS-5A-PS clustered in a different clade that was phylogenetically distinct from the Amazonocrinis sensu stricto clade. Interestingly, while the 16S rRNA gene phylogeny exhibited two separate clusters, the 16S–23S ITS region analysis did not provide strong support for the phylogenetic observation. Subsequent analyses raised questions regarding the resolving power of the 16S–23S ITS region at the genera level and the associated complexities in cyanobacterial taxonomy. Through this study, we describe a novel genus Ahomia to accommodate the members clustering outside the Amazonocrinis sensu stricto clade. In addition, we describe five novel species, Ahomia kamrupensis, Ahomia purpurea, Ahomia soli, Amazonocrinis meghalayensis, and Dendronalium spirale, in accordance with the International Code of Nomenclature for algae, fungi, and plants (ICN). Apart from further enriching the genera Amazonocrinis and Dendronalium, the current study helps to resolve the taxonomic complexities revolving around the genus Amazonocrinis and aims to attract researchers to the continued exploration of the tropical and subtropical cyanobacteria for interesting taxa and lineages.     

Phylogenetic taxonomy of Hymenochaete and related genera (Hymenochaetales)

Species delimitation in Hymenochaete sensu lato was evaluated based on partial nucLSU rDNA sequences, isoenzyme analyses and morphological data. Analyses of LSU data revealed Hymenochaete sensu stricto and Pseudochaete as distinct monophyletic genera. Transfer of Hydnochaete olivacea into genus Pseudochaete and Dichochaete setosa into genus Hymenochaete (as H. resupinata) was supported by the results of molecular analyses. A new species Hymenochaete koeljalgii from Tanzania was described. The species of genus Hymenochaete sensu stricto were divided into four well-supported clades possessing no distinctive morphological characters.     

Phylogeny of swallows (Aves: Hirundinidae) estimated from nuclear and mitochondrial DNA sequences

The phylogeny of swallows was reconstructed by comparing segments of three genes, nuclear beta-fibrinogen intron 7 (betafib7), mitochondrial cytochrome b (cytb), and mitochondrial ND2, in a variety of combinations using maximum likelihood and Bayesian methods. betafib7 was sequenced for 47 species, cytb for 74 species, and ND2 for 61 species to yield comparisons among 75 of the 84 currently recognized swallow species. The family Hirundinidae was confirmed to consist of two clades, Pseudochelidoninae (river martins) and Hirundininae (typical swallows). The Hirundininae is further divided into mud nesters (Hirundo sensu lato), core martins (Phedina, Riparia, and New World endemic genera), and basal relicts (Psalidoprocne, Cheramoeca, and Pseudhirundo). We did not resolve the hierarchy among these three hirundinine groups, but discovered many relationships within them. Mud-nesting genera have the following relationships: (Hirundo sensu stricto, Ptyonoprogne), (Delichon, (Petrochelidon, Cecropis)). Core martins have the following topology: (Phedina, Riparia cincta), (Riparia sensu stricto, Tachycineta, ((Stelgidopteryx, Progne), (Neotropical endemic genera))). Interspecific relationships among the Neotropical endemics were resolved completely; Atticora and Notiochelidon are paraphyletic, and all Neotropical endemics probably should be lumped into one or two genera. The final group of hirundinines, the basal relicts, consists of a sister pair, the Australian Cheramoeca and African Pseudhirundo. The African saw-wings (Psalidoprocne) are their likely sister group.     

Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows

Phylogenetic relationships and lineage diversification of the family Salicaceae sensu lato (s.l.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, Flacourtia was identified as the most basal and the successive clades comprised both Itoa and Poliothyrsis, Idesia, two genera of the Salicaceae sensu stricto (s.s.) (Populus and Salix). Five major subclades were recovered within the Populus clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the Salix clade. Molecular dating suggested that species diversification of the major subclades in the Populus and Salix clades occurred mainly within the recent Pliocene. In addition, we found that the rpl32 gene was lost and the rps7 gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae s.l. Compared with previous studies, our results provide a well‐resolved phylogeny from the perspective of the plastomes.     

Morphologic and molecular data suggest that Lynnella semiglobulosa n. g., n. sp. represents a new family within the subclass Choreotrichia (Ciliophora, Spirotrichea)

The morphology, morphogenesis, and phylogeny of an undescribed oligotrich sensu lato (s. lat.) ciliate, Lynnella semiglobulosa n. g., n. sp., found in Daya Bay, southern China, were investigated. This species shares some features with both oligotrichs sensu stricto and choreotrichs, but most morphological and morphogenetic characters as well as the phylogenetic analysis suggest that it should be assigned into subclass Choreotrichia temporarily. Lynnella semiglobulosa is distinguished from members of all known genera and families of the subclass Choreotrichia by a unique combination of characteristics of the buccal and somatic ciliatures. Thus, a new family Lynnellidae n. fam. and a new genus Lynnella n. g. are proposed for it. The new family is distinguished by an open adoral zone of membranelles (AZM) in which, however, there are no ventral membranelles; the distal and proximal portions of the new adoral zone lie close to each other forming an open circle in stomatogenesis. The new genus Lynnella is characterized by possessing two longitudinally oriented somatic kineties, one dorsal and one ventral, several proximal membranelles progressively lengthened toward the proximal end of adoral zone, and two macronuclear nodules. In phylogenetic analyses based on small subunit rRNA gene sequences, L. semiglobulosa clustered basally to all choreotrichs, but with relatively weak support; nevertheless, the possibility of a relationship with the subclass Oligotrichia was not rejected by the approximately unbiased nor Shimodaira-Hasegawa test. Based on morphological, morphogenetic, and molecular evidence of L. semiglobulosa, it is confirmed that the open AZM should be a plesiomorphic character of oligotrichs s. lat. as suggested previously.     

Higher‐level phylogeny of diving beetles (Coleoptera: Dytiscidae) based on larval characters

A comprehensive higher‐level phylogeny of diving beetles (Dytiscidae) based on larval characters is presented. Larval morphology and chaetotaxy of a broad range of genera and species was studied, covering all currently recognized subfamilies and tribes except for the small and geographically restricted Hydrodytinae, where the larva is unknown. The results suggest several significant conclusions with respect to the systematics of Dytiscidae including the following: monophyly of all currently recognized subfamilies, although Dytiscinae when considered in a broad context is rendered paraphyletic by Cybistrinae; currently recognized tribes are monophyletic except for Agabini, Hydroporini and Laccornellini; inter‐subfamily and inter‐tribe relationships generally show weak support, except for a few well supported clades; three distinct clades are recognized within Dytiscinae [Dytiscini sensu lato (i.e. including the genera Dytiscus Linnaeus and Hyderodes Hope), Hydaticini sensu lato, and Cybistrini]; and recognition of Pachydrini as a distinct tribe. Other less robust results include: Methlini sister to the rest of Hydroporinae; relative basal position of Laccornini, Hydrovatini and Laccornellini within Hydroporinae; close relationship of Agabinae and Copelatinae; Matinae nested deep within Dytiscidae, as sister to a large clade including Colymbetinae, Coptotominae, Lancetinae and Dytiscinae sensu lato; the sister‐group relationship of Agabetini and Laccophilini is confirmed. The results presented here are discussed and compared with previous phylogenetic hypotheses based on different datasets, and the evolution of some significant morphological features is discussed in light of the proposed phylogeny. All suprageneric taxa are diagnosed, including illustrations of all relevant synapomorphies, and a key to separate subfamilies and tribes is presented, both in traditional (paper) format and as an online Lucid interactive identification key.     

Patterns of taxonomic diversity among terrestrial isopods

The publication of the world catalog of terrestrial isopods some ten years ago by Schmalfuss has facilitated research on isopod diversity patterns at a global scale. Furthermore, even though we still lack a comprehensive and robust phylogeny of Oniscidea, we do have some useful approaches to phylogenetic relationships among major clades which can offer additional insights into isopod evolutionary dynamics. Taxonomic diversity is one of many approaches to biodiversity and, despite its sensitiveness to biases in taxonomic practice, has proved useful in exploring diversification dynamics of various taxa. In the present work, we attempt an analysis of taxonomic diversity patterns among Oniscidea based on an updated world list of species containing 3,710 species belonging to 527 genera and 37 families (data till April 2014). The analysis explores species diversity at the genus and family level, as well as the relationships between species per genera, species per families, and genera per families. In addition, we consider the structure of isopod taxonomic system under the fractal perspective that has been proposed as a measure of a taxon’s diversification. Finally, we check whether there is any phylogenetic signal behind taxonomic diversity patterns. The results can be useful in a more detailed elaboration of Oniscidea systematics.     

Molecular phylogeny of Sericostomatoidea (Trichoptera) with the establishment of three new families

We inferred the phylogenetic relationships among 58 genera of Sericostomatoidea, representing all previously accepted families as well as genera that were not placed in established families. The analyses were based on five fragments of the protein coding genes carbamoylphosphate synthetase (CPSase of CAD), isocitrate dehydrogenase (IDH), Elongation factor 1a (EF‐1a), RNA polymerase II (POL II) and cytochrome oxidase I (COI). The data set was analysed using Bayesian methods with a mixed model, raxml , and parsimony. The various methods generated slightly different results regarding relationships among families, but the shared results comprise support for: (i) a monophyletic Sericostomatoidea; (ii) a paraphyletic Parasericostoma due to inclusion of Myotrichia murina, leading to synonymization of Myotrichia with Parasericostoma; (iii) a polyphyletic Sericostomatidae, which is divided into two families, Sericostomatidae sensu stricto and Parasericostomatidae fam.n. ; (iv) a polyphyletic Helicophidae which is divided into Helicophidae sensu stricto and Heloccabucidae fam.n. ; (v) hypothesized phylogenetic placement of the former incerta sedis genera Ngoya, Seselpsyche and Karomana; (vi) a paraphyletic Costora (Conoesucidae) that should be divided into several genera after more careful examination of morphological data; (vii) reinstatement of Gyrocarisa as a valid genus within Petrothrincidae. A third family, Ceylanopsychidae fam.n. , is established based on morphological characters alone. A hypothesis of the relationship among 14 of the 15 families in the superfamily is presented. A key to the families is presented based on adults (males). Taxonomic history, diagnosis, habitat preference and distribution data for all sericostomatoid families are presented. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:CF6A6B9F‐6A72‐4265‐BD09‐3A710DFCD7B1 .     

PHYLOGENY OF ZYGNEMOPHYCEAE BASED ON COXIII GENE SEQUENCE DATA

Molecular phylogenetic analysis of the conjugating green algae (Class Zygnemophyceae) using nuclear (SSU rDNA) and chloroplast (rbcL) gene sequences has resolved hypotheses of relationship at the class, order, and family levels, but several key questions will require data from additional genes. Based on SSU and rbcL sequences, the Zygnemophyceae and Desmidiales are monophyletic, and families of placoderm desmids are distinct clades (Desmidiaceae, Peniaceae, Closteriaceae, and Gonatozygaceae). In contrast, the Zygnemataceae and Mesotaeniaceae are paraphyletic, although whether these two traditional families constitute a clade is uncertain. In addition, relationships of genera within families have proven resistant to resolution with these two oft‐used genes. We have sequenced the coxIII gene from the mitochondrial genome to address some of these ambiguous portions of the phylogeny of conjugating green algae. The coxIII gene is more variable than rbcL or SSU rDNA and offers greater resolving power for relationships of genera. We present preliminary analyses of coxIII sequences from each of the traditional families of Zygnemophyceae and contrast the resulting topologies with those derived from nuclear and chloroplast genes.     

A molecular phylogeny of Panicum (Poaceae: Paniceae): tests of monophyly and phylogenetic placement within the Panicoideae

Panicum L. is a cosmopolitan genus with approximately 450 species. Although the genus has been considerably reduced in species number with the segregation of many taxa to independent genera in the last two centuries, Panicum remains a heterogeneous assemblage, as has been demonstrated in recent years. The genus is remarkably uniform in its floral characters but exhibits considerable variation in anatomical, physiological, and cytological features. As a result, several classifications, and criteria of what the genus should really include, have been postulated in modern literature. The purpose of this research, based on molecular data of the chloroplast ndhF gene, is to test the monophyly of Panicum, to evaluate infrageneric classifications, and to propose a robust phylogenetic hypothesis. Based on the present results, previous morphological and molecular phylogenetic studies, and inferred diagnostic morphological characters, we restrict Panicum sensu stricto (s.s.) to the former subgenus Panicum and support recognition of Dichanthelium, Phanopyrum, and Steinchisma as distinct genera. We have transfered other species of Panicum to other genera of the Paniceae. Most of the necessary combinations have been made previously, so few nomenclatural changes have been required. The remaining species of Panicum sensu lato (s.l.) are included within Panicum incertae sedis representing isolated species or species grouped within monophyletic clades. Additionally, we explore the performance of the three codon position characters in producing the supported phylogeny.     

Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments

Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1) the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2) three advanced sections (Populus, Aigeiros and Tacamahaca) are of hybrid origin; (3) species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4) many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments.     

Implications of High Molecular Divergence of Nuclear rRNA and Phylogenetic Structure for the Dinoflagellate Prorocentrum (Dinophyceae,Prorocentrales)

The small and large nuclear subunit molecular phylogeny of the genus Prorocentrum demonstrated that the species are dichotomized into two clades. These two clades were significantly different (one‐factor ANOVA, p < 0.01) with patterns compatible for both small and large subunit Bayesian phylogenetic trees, and for a larger taxon sampled dinoflagellate phylogeny. Evaluation of the molecular divergence levels showed that intraspecies genetic variations were significantly low (t‐test, p < 0.05), than those for interspecies variations (> 2.9% and > 26.8% dissimilarity in the small and large subunit [D1/D2], respectively). Based on the calculated molecular divergence, the genus comprises two genetically distinct groups that should be considered as two separate genera, thereby setting the pace for major systematic changes for the genus Prorocentrum sensu Dodge. Moreover, the information presented in this study would be useful for improving species identification, detection of novel clades from environmental samples.     

Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data

Phylogenetic relationships were studied based on DNA sequences obtained from all recognized genera of the family Corvidae sensu stricto . The aligned data set consists 2589 bp obtained from one mitochondrial and two nuclear genes. Maximum parsimony, maximum-likelihood, and Bayesian inference analyses were used to estimate phylogenetic relationships. The analyses were done for each gene separately, as well as for all genes combined. An analysis of a taxonomically expanded data set of cytochrome b sequences was performed in order to infer the phylogenetic positions of six genera for which nuclear genes could not be obtained. Monophyly of the Corvidae is supported by all analyses, as well as by the occurrence of a deletion of 16 bp in the β-fibrinogen intron in all ingroup taxa. Temnurus and Pyrrhocorax are placed as the sister group to all other corvids, while Cissa and Urocissa appear as the next clade inside them. Further up in the tree, two larger and well-supported clades of genera were recovered by the analyses. One has an entirely New World distribution (the New World jays), while the other includes mostly Eurasian (and one African) taxa. Outside these two major clades are Cyanopica and Perisoreus whose phylogenetic positions could not be determined by the present data. A biogeographic analysis of our data suggests that the Corvidae underwent an initial radiation in Southeast Asia. This is consistent with the observation that almost all basal clades in the phylogenetic tree consist of species adapted to tropical and subtropical forest habitats.