The complete mitochondrial genome of Plesiastrea versipora (Scleractinia,Plesiastreidae) sheds light on its phylogeny and taxonomy of the family Plesiastreidae

The genus Plesiastrea used to be a member of the traditional family Faviidae, falling into the challenging ‘Bigmessidae’ clade, and was re-established until recent molecular phylogenies published. The entire mitogenome of the symbiotic coral Plesiastrea versipora (Lamarck, 1816), the type species of the family Plesiastreidae, was sequenced. The length of the mitochondrial genome is 15,320 bp and it includes thirteen protein-coding genes (PCGs), two rRNAs and two tRNAs. The nucleotide composition of GC is 32%. We perform phylogenetic reconstruction based on maximum likelihood (ML) and Bayesian analysis(BI) using all PCGs. Our result indicates that P. versipora clusters closely with species which belong to Mussidae, Merulinidae and Lobophylliidae. Our phylogenetic analyses provide solid evidence for phylogenetic placement of P. versipora and the evolutionary relationships among different families within the traditional robust clade of Scleractinia. In addition, the mitogenome data provide useful information for further molecular systematic investigations on Plesiastreidae as well as conservation biology research of P. versipora.     

Flower and fruit characters in the early-divergent lamiid family Metteniusaceae, with particular reference to the evolution of pseudomonomery

Evaluating the morphological relationships of angiosperm families that still remain unplaced in the current systems of classification is challenging because it requires comparative data across a broad phylogenetic range. The small neotropical family Metteniusaceae was recently placed within the lamiids, as sister to either the enigmatic Oncothecaceae or the clade (Boraginaceae + Gentianales + Lamiales + Solanales + Vahliaceae). We examined the development of two of the primary diagnostic traits of Metteniusaceae, the moniliform anthers and the unilocular gynoecium. The gynoecium is 5-carpellate, and contains two ovules with a massive, vascularized integument. Late sympetaly and unitegmic ovules support placement of Metteniusaceae in the lamiids. The 5-carpellate gynoecium is consistent with a sister-group relationship between Metteniusaceae and Oncothecaceae. The gynoecium of Metteniusaceae is unusual in that it is monosymmetric throughout ontogeny, which indicates pseudomonomery; the five carpel initials are congenitally fused by their margins and form a single locule; the two ovules develop from the two smallest and most poorly developed lateral carpels. Comparisons with other pseudomonomerous taxa allow us to propose division of the complex processes leading to pseudomonomery into eight characters, including carpel number and fusion, gynoecial symmetry, timing of carpel reduction, and number and position of nonfertile carpels.     

Phylogeny and Reclassification of Hemistasia phaeocysticola (Scherffel) Elbrächter & Schnepf, 1996

Hemistasia phaeocysticola is a marine flagellate that preys on diatoms and dinoflagellates among others. Although its morphology and ultrastructure were previously observed and characterized, its phylogenetic position has not been analyzed using molecular sequence data. This flagellate was classified as a kinetoplastid on the basis of the presence of a kinetoplast in the mitochondrion. However, several morphological characteristics similar to those of diplonemids, a sister group of kinetoplastids, have also been noted. Herein, we report that H. phaeocysticola branches within the diplonemid clade in the phylogenetic tree reconstructed by analyzing 18S rRNA gene sequences. Its systematic placement based on this finding is also discussed.     

Phylogenetic position of the enigmatic myxomycete genus Kelleromyxa revealed by SSU rDNA sequences

The coprophilous myxomycete Kelleromyxa fimicola (Dearn. & Bisby) Eliasson was first described in 1929 as Licea fimicola Dearn. & Bisby. Based on the superficial resemblance of its sporocarps to those of Licea biforis, the species was placed within the Liceales, an order assigned by molecular phylogenies to the bright-spored clade of myxomycetes. However, detailed studies of the morphology and life cycle of K. fimicola revealed several characters of the dark-spored order Physarales. To elucidate the systematic position of Kelleromyxa, we obtained three partial and one complete sequence of the SSU rDNA, which demonstrated a clear relationship of K. fimicola to the order Physarales. However, the obtained sequences are not closely related to any of the two known families of Physarales, supporting the erection of a monotypic family for this species. Along with morphological observations, our data support the exclusion of K. fimicola from the order Liceales and placement among the order Physarales within the dark-spored clade of myxomycetes.     

On the origin of the Hirudinea and the demise of the Oligochaeta

The phylogenetic relationships of the Clitellata were investigated with a data set of published and new complete 18S rRNA gene sequences of 51 species representing 41 families. Sequences were aligned on the basis of a secondary structure model and analysed with maximum parsimony and maximum likelihood. In contrast to the latter method, parsimony did not recover the monophyly of Clitellata. However, a close scrutiny of the data suggested a spurious attraction between some polychaetes and clitellates. As a rule, molecular trees are closely aligned with morphology-based phylogenies. Acanthobdellida and Euhirudinea were reconciled in their traditional Hirudinea clade and were included in the Oligochaeta with the Branchiobdellida via the Lumbriculidae as a possible link between the two assemblages. While the 18S gene yielded a meaningful historical signal for determining relationships within clitellates, the exact position of Hirudinea and Branchiobdellida within oligochaetes remained unresolved. The lack of phylogenetic signal is interpreted as evidence for a rapid radiation of these taxa. The placement of Clitellata within the Polychaeta remained unresolved. The biological reality of polytomies within annelids is suggested and supports the hypothesis of an extremely ancient radiation of polychaetes and emergence of clitellates.     

THE DELIMITATION OF BIGNONIACEAE AND SCROPHULARIACEAE BASED ON FLORAL ANATOMY,AND THE PLACEMENT OF PROBLEM GENERA

The delimitation of Bignoniaceae and Scrophulariaceae has long been a taxonomic problem. Several genera, including Paulownia, Schlegelia, Gibsoniothamnus, and Synapsis, have been variously placed in one or the other family. Differences between these two families have been noted with regard to the presence of endosperm, embryo and seed morphology, and placentation; however, the lack of comprehensive data on the distribution of such characters within these two families left the delimitation problem unsolved. A comprehensive study of floral anatomy confirmed a basic difference in the placentation of these two families, as well as a basic difference in gynoecial vascularization. Paulownia has a floral anatomy, embryo morphology, and seed morphology consistent with placement in Scrophulariaceae. While reminiscent of Bignoniaceae, Paulownia is not an intermediate genus linking the two families. Schlegelia and Gibsoniothamnus have a floral anatomy consistent with placement in Scrophulariaceae. Schlegelia also has a scrophulariaceous seed morphology. Considered anomalous in the Bignoniaceae, the Schlegelieae similarly are distinct in the Scrophulariaceae.     

Molecular systematics and biogeography of Crawfurdia, Metagentiana and Tripterospermum (Gentianaceae) based on nuclear ribosomal and plastid DNA sequences

BACKGROUND AND AIMS: The systematic position of the genus Metagentiana and its phylogenetic relationships with Crawfurdia, Gentiana and Tripterospermum have not been explicitly addressed. These four genera belong to one of two subtribes (Gentianinae) of Gentianeae. The aim of this paper is to examine the systematic position of Crawfurdia, Metagentiana and Tripterospermum and to clarify their phylogenetic affinities more clearly using ITS and trnL intron sequences. METHODS: Nucleotide sequences from the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the plastid DNA trnL (UAA) intron were analysed phylogenetically. Ten of fourteen Metagentiana species were sampled, together with 40 species of other genera in the subtribe Gentianinae. KEY RESULTS: The data support several previously published conclusions relating to the separation of Metagentiana from Gentiana and its closer relationships to Crawfurdia and Tripterospermum based on studies of gross morphology, floral anatomy, chromosomes, palynology, embryology and previous molecular data. The molecular clock hypothesis for the tested sequences in subtribe Gentianinae was not supported by the data (P < 0.05), so the clock-independent non-parametric rate smoothing method was used to estimate divergence time. This indicates that the separation of Crawfurdia, Metagentiana and Tripterospermum from Gentiana occurred about 11.4-21.4 Mya (million years ago), and the current species of these three genera diverged at times ranging from 0.4 to 6.2 Mya. CONCLUSIONS: The molecular analyses revealed that Crawfurdia, Metagentiana and Tripterospermum do not merit status as three separate genera, because sampled species of Crawfurdia and Tripterospermum are embedded within Metagentiana. The speciation and rapid radiation of these three genera is likely to have occurred in western China as a result of upthrust of the Himalayas during the late Miocene and the Pleistocene.     

The complete mitochondrial genome sequence of the little grebe (<Emphasis Type="Italic">Tachybaptus ruficollis</Emphasis>)

Podicipediformes comprises one family (Podicipedidae) including 6 genera, 22 species, and the phylogenetic placement of this order was still in debate. In this study, we sequenced the complete mitochondrial genome (mitogenome) of little grebe (Tachybaptus ruficollis) in Podicipediformes, and explored the phylogenetic position of this order with mitogenome sequences of 21 species from ten families in seven orders. The genome was 16,688 bp in length, and contained 37 genes typical to avian mitogenomes and one control region. The gene organization and characters were similar with other two mitogenomes available in Podicipediformes to date. Phylogenetic tree was constructed with Bayesian method based on mitogenome sequences excluding the control regions. The results supported the closest relationship between Podicipediformes and Phoenicopteriformes, and the topology of our tree was generally similar with the conclusions of previous molecular systematic investigations. Our results furtherly proved the validity of mitogenome data in taxonomic and phylogenetic studies.     

Molecular phylogeny of Diplostomum,Tylodelphys, Austrodiplostomum and Paralaria (Digenea: Diplostomidae) necessitates systematic changes and reveals a history of evolutionary host switching events

The Diplostomidae Poirier, 1886 is a large, globally distributed family of digeneans parasitic in intestines of their definitive hosts. Diplostomum and Tylodelphys spp. are broadly distributed, commonly reported, and the most often sequenced diplostomid genera. The majority of published DNA sequences from these genera originated from larval stages only, which typically cannot be identified to the species level based on morphology alone. We generated partial large ribosomal subunit (28S) rRNA and cytochrome c oxidase subunit 1 (cox1) mtDNA gene sequences from 14 species/species-level lineages of Diplostomum, six species/species-level lineages of Tylodelphys, two species/species-level lineages of Austrodiplostomum, one species previously assigned to Paralaria, two species/species-level lineages of Dolichorchis and one unknown diplostomid. Our DNA sequences of 11 species/species-level lineages of Diplostomum (all identified to species), four species/species-level lineages of Tylodelphys (all identified to species), Austrodiplostomum compactum, Paralaria alarioides and Dolichorchis lacombeensis originated from adult specimens. 28S sequences were used for phylogenetic inference to demonstrate the position of Paralaria alarioides and Dolichorchis spp. within the Diplostomoidea and study the interrelationships of Diplostomum, Tylodelphys and Austrodiplostomum. Our results demonstrate that two diplostomids from the North American river otter (P. alarioides and a likely undescribed taxon) belong within Diplostomum. Further, our results demonstrate the non-monophyly of Tylodelphys due to the position of Austrodiplostomum spp., based on our phylogenetic analyses and morphology. Furthermore, the results of phylogenetic analysis of 28S confirmed the status of Dolichorchis as a separate genus. The phylogenies suggest multiple definitive host-switching events (birds to otters and among major avian groups) and a New World origin of Diplostomum and Tylodelphys spp. Our DNA sequences from adult digeneans revealed identities of 10 previously published lineages of Diplostomum and Tylodelphys, which were previously identified to genus only. The novel DNA data from this work provide opportunities for future comparisons of larval diplostomines collected in ecological studies.     

Molecules,morphology, missing data and the phylogenetic position of a recently extinct madtom catfish (Actinopterygii: Ictaluridae)

Taxa missing large amounts of data pose challenges that may hinder the recovery of a well‐resolved, accurate phylogeny and leave questions surrounding their phylogenetic position. Systematists commonly have to contend with one or two species in a group for which there is little or no material available suitable for recovering molecular data. It is unclear whether these taxa can be better placed using analyses based on morphological data only, or should be included in broader analyses based on both morphological and molecular data. The extinct madtom catfish Noturus trautmani is known from few specimens for which molecular data are unavailable. We included this taxon in parsimony and Bayesian analyses of relationships of madtom catfishes based on a combination of morphological and molecular data. Results indicate that using a combination of morphological and molecular data does a better job at providing a phylogenetic placement for N. trautmani than morphology alone, even though it is missing all of its molecular characters. We provide a novel hypothesis of relationships among Noturus species and recommendations for classification within the group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 60–75.     

Molecular insight into systematics,host associations,life cycles and geographic distribution of the nematode family Rhabdiasidae

Rhabdiasidae Railliet, 1915 is a globally distributed group of up to 100 known species of nematodes parasitic in amphibians and reptiles. This work presents the results of a molecular phylogenetic analysis of 36 species of Rhabdiasidae from reptiles and amphibians from six continents. New DNA sequences encompassing partial 18S rDNA, ITS1, 5.8S rDNA, ITS2 and partial 28S rDNA regions of nuclear ribosomal DNA were obtained from 27 species and pre-existing sequences for nine species were incorporated. The broad taxonomic, host and geographical coverage of the specimens allowed us to address long-standing questions in rhabdiasid systematics, evolution, geographic distribution, and patterns of host association. Our analysis demonstrated that rhabdiasids parasitic in snakes are an independent genus sister to the rest of the Rhabdiasidae, a status supported by life cycle data. Based on the combined evidence of molecular phylogeny, morphology and life cycle characteristics, a new genus Serpentirhabdias gen. nov. with the type species Serpentirhabdias elaphe (Sharpilo, 1976) comb. nov. is established. The phylogeny supports the monophyly of Entomelas Travassos, 1930, Pneumonema Johnston, 1916 and the largest genus of the family, Rhabdias Stiles and Hassall, 1905. DNA sequence comparisons demonstrate the presence of more than one species in the previously monotypic Pneumonema from Australian scincid lizards. The distribution of some morphological characters in the genus Rhabdias shows little consistency within the phylogenetic tree topology, in particular the apical structures widely used in rhabdiasid systematics. Our data suggest that some of the characters, while valuable for species differentiation, are not appropriate for differentiation among higher taxa and are of limited phylogenetic utility. Rhabdias is the only genus with a cosmopolitan distribution, but some of the lineages within Rhabdias are distributed on a single continent or a group of adjacent zoogeographical regions. Serpentirhabdias, Entomelas and Pneumonema show rather strict specificity to their host groups. The evolution of the Rhabdiasidae clearly included multiple host switching events among different orders and families of amphibians as well as switching between amphibians and squamatan reptiles. Only a few smaller lineages of Rhabdias demonstrate relatively strict associations with a certain group of hosts.     

Early Cretaceous Enantiornithine Birds (Aves,Ornithothoraces) and Establishment of the Ornithuromorpha Morphological Type

New data on the taxonomic and morphological diversity of Early Cretaceous Enantiornithes are reviewed. A new hypothesis concerning the phylogenetic position of Pengornithidae is proposed. These birds traditionally treated as primitive enantiornithines may in fact be more closely related to Ornithuromorpha. This phylogenetic placement implies that the fan-shaped tail and modern-type humeral joint was formed once in the early evolution of birds. Hence, the similarity between Pengornithidae and other enantiornithines may be plesiomorphic. The ecology of Early Cretaceous enantiornithines is discussed. The increased mobility of neck in Holbotia is possibly accounted for by the cranioinertial swallowing mechanism, as in modern ratites. The hypotheses of scansorial adaptations in Parapengornis and Fortunguavis are criticized. In addition, the phylogenetic position of Mystiornis is discussed.     

Relationships of the haematophagous marine snail Colubraria (Rachiglossa: Colubrariidae), within the neogastropod phylogenetic framework

The gastropod genus Colubraria includes marine shallow‐water species from tropical, subtropical, and temperate rocky coral environments. At least six species are known to feed on fish blood. Although there is general consensus in placing Colubraria in the Neogastropoda, the actual relationships and the systematic position of Colubraria and related genera are unknown. This is partly the consequence of the lack of a clear phylogenetic framework for the Neogastropoda. This study attempts to propose a phylogenetic framework for the Neogastropoda, by testing: (1) a preliminary phylogenetic arrangement for a large number of recognized neogastropod families; (2) the position of Colubraria within the neogastropods; and (3) the relationships of Colubraria within one of the major neogastropod lineages. We used two different molecular data sets. The first set included representatives of at least 14 neogastropod families, for points (1) and (2), and was based on mitochondrial (16S, 12S, and cytochrome oxidase subunit I, COI) and nuclear (28S) DNA sequences, giving a total of 3443 aligned positions. The second data set, for point (3), included 30 buccinoid sequences from mitochondrial 16S, giving a total of 1029 aligned positions. We also studied the anatomy of the type species of Colubraria and compared it with other neogastropods within the new phylogenetic framework. The results included the first phylogeny of the neogastropod based on 50% of the recognized families. This clearly indicated that the nematoglossan Cancellariidae represent a basal offshoot of the monophyletic Neogastropoda, and that the toxoglossan Conoidea are the sister group to the Rachiglossa. Within the Rachiglossa, a colubrariid clade, worthy of family ranking, showed clear buccinoid affinities. Most of the anatomy of Colubraria is congruent with a buccinoid model. The peculiar anatomical features that do not conform to the buccinoid model seem to be related to the evolution of haematophagous feeding. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 779–800.     

Aspects of the fossil record and phylogeny of the familyRutaceae (Zanthoxyleae,Toddalioideae)

A comparative analysis of the seed morphology and anatomy of fossil and extantRutaceae (mainlyZanthoxyleae andToddalioideae) is presented. This allows to place the most important fossil taxa in a time-table and on paleogeographical maps. A phylogenetic scheme demonstrates the postulated historical relationships ofEvodia, Zanthoxylum, Fagara, Rutaspermum, Acronychia, Toddalia, Fagaropsis, andPhellodendron.     

Papulosa amerospora accommodated in a new family (papulosaceae, sordariomycetes, ascomycota) inferred from morphological and molecular data

To investigate the systematic position of the unitunicate pyremomycetePapulosa amerospora, we performed phylogenetic analyses of SSU rDNA sequences from 37 ascomycetes. Among these sequences were some new ones from taxa that might be related toPapulosa: Hyponectriaceae (Hyponectria buxi, Monographella nivalis), Phyllachorales (Phyllachora graminis), and Xylariales (Barrmaelia melanotes, Poronia punctata). Our results showed 100% bootstrap support for a clade of all unitunicate pyrenomycetes, the class Sordariomycetes. We also found strong support for recognizing the subclasses Hypocreomycetidae and Xylariomycetidae. The remaining taxa, belonging to subclass Sordariomycetidae, appeared as a polyphyletic group in one analysis, but was monophyletic when shorter SSU sequences were used.Barrmaelia melanotes, Poronia punctata, Hyponectria buxi, andMonographella nivalis are members of Xylariomycetidae, but we could not determine whetherMonographella should be included in Hyponectriaceae. The new family Papulosaceae is erected forPapulosa on molecular and morphological bases, but the exact systematic position ofPapulosa within subclass Sordariomycetidae is still uncertain, since the genus did not cluster consistently with any of the included taxa. Phyllachorales are not closely related to Diaporthales, as previously suggested.     

Phylogenetic Inferences and the Evolution of Plastid DNA in Campynemataceae and the Mycoheterotrophic <Emphasis Type="Italic">Corsia dispar</Emphasis> D.L Jones &amp; B. Gray (Corsiaceae)

The phylogenetic positions of the families Campynemataceae and Corsiaceae within the order Liliales remains unclear. To date, molecular data from the plastid genome of Corsiaceae has been obtained exclusively from Arachnitis, for which alignment and phylogenetic inference has proved difficult. The extent of gene conservation among mycoheterotrophic species within Corsiaceae remains unknown. To clarify the phylogenetic position of Campynemataceae and Corsiaceae within Liliales, functional plastid-coding genes of species representing both families have been analyzed. Examination of two phylogenetic data sets of plastid genes employing parsimony, maximum-likelihood, and Bayesian inference methods strongly supported both families forming a basal clade to the remaining taxa of Liliales. The first data set consists of five functional plastid-encoded genes (matK, rps7, rps2, rps19, and rpl2) sequenced from Corsia dispar (Corsiaceae). The data set included 31 species representing all families within Liliales, as well as selected orders that are related closely to Liliales (10 outgroup species from Asparagales, Dioscoreales, and Pandanales). The second phylogenetic analysis was based on 75 plastid genes. This data set included 18 species from Liliales, representing major clades within the order, and 10 outgroup species from Asparagales, Dioscoreales, and Pandanales. In this latter data set, Campynemataceae was represented by 60 plastid-encoded genes sequenced from herbarium material of Campynema lineare. A large proportion of the plastid genome of C. dispar was also sequenced and compared to the plastid genomes of photosynthetic plants within Liliales and mycoheterotrophic plants within Asparagales to explore plastid genome reduction. The plastid genome of C. dispar is in the advanced stages of reduction, which signifies its high dependency on mycorrhizal fungi and is suggestive of a loss in photosynthetic ability. Functional plastid genes found in C. dispar may be applicable to other species in Corsiaceae, which will provide a basis for in-depth molecular analyses of interspecies relationships within the family, once molecular data from other members become available.     

Phylogeny and classification of Ranunculales: Evidence from four molecular loci and morphological data

Previous phylogenetic analyses of Ranunculales, which have mostly been focused on an individual family and were based on molecular data alone, have recovered three main clades within the order. However, support for relationships among these three clades was weak. Earlier hypotheses were often hampered by limited taxon sampling; to date less than one-tenth of the genera in the order have been sampled. In this study, we used a greatly enlarged taxon sampling (105 species, representing 99 genera of all seven families in the order). Our study is, furthermore, the first to employ morphology (65 characters) in combination with sequence data from four genomic regions, including plastid rbcL, matK and trnL-F, and nuclear ribosomal 26S rDNA to reconstruct phylogenetic relationships within Ranunculales. Maximum parsimony and Bayesian inference were performed on the individual and combined data sets. Our analyses concur with those of previous studies, but in most cases provide stronger support and better resolution for relationships among the three main clades retrieved. The first, comprised solely of the monogeneric family Eupteleaceae, is the earliest-diverging lineage. The second clade is composed exclusively of taxa of Papaveraceae, which is sister to the third clade, the core Ranunculales, comprising the other five families of the order. Circaeasteraceae and Lardizabalaceae form a strongly supported clade. Pteridophyllum is supported as sister to Hypecoum, contradicting the viewpoint that the former is the earliest-diverging genus in Papaveraceae. Glaucidium is basalmost in Ranunculaceae. Within this phylogenetic framework, the evolution of selected characters is inferred and diagnostic morphological characters at different taxonomic levels are identified and discussed. Based on both morphological and molecular evidence, a classification outline for Ranunculales is presented, including the proposal of two new subfamilies, Menispermoideae and Tinosporoideae in Menispermaceae and a new tribe, Callianthemeae, for the genus Callianthemum (Ranunculaceae).