Trochus kotschyi, the first Indian Ocean record of the genus Osilinus (Mollusca: Gastropoda: Trochidae)

The species Trochus kotschyi Philippi, 1849, and Priotrochus obscurus (Wood, 1828) have been much confused in the past. Consistent differences between these taxa in respect of shell morphology, external anatomy and radular and opercular form are demonstrated. The distribution of T. kotschyi and the extent to which it and P. obscurus are sympatric are discussed. T. korschyi is referred to the genus Osilinus Philippi, 1847, a new combination and the first record of the genus from the Indo-West Pacific. The species is thought to be a pre-Miocene relict reflecting a mid-Tethyan origin of the genus. A note on the type species designation of Osilinus is provided.     

Cladogenesis as the result of long-distance rafting events in South Pacific topshells (Gastropoda, Trochidae)

We used DNA sequences of lecithotrophic monodontine topshells, belonging to the genera Diloma, Melagraphia, and Austrocochlea, to ascertain how this group became established over a large area of the South Pacific Ocean. The phylogeny of the topshells was estimated using portions of two mitochondrial genes (16S and cytochrome oxidase 1) and one nuclear gene (actin). A range of divergence rates was used to estimate the approximate timing of cladogenetic events within their phylogenetic tree. These estimates allow us to unambiguously reject vicariant explanations for several major divergence events and to infer several dispersal events across wide stretches of ocean. The first were two initial dispersal events from Australia (1) to an area between Samoa and Japan and (2) to New Zealand. Subsequently, at least one, and possibly two, recent eastward dispersals took place from New Zealand to Chile and the Juan Fernandez Islands, and one further dispersal occurred from somewhere in the tropical Pacific to Samoa. Moreover, owing to the short-lived nature of the topshell larvae, transoceanic larval dispersal is unlikely. The apparent paradox of a short larval phase and broad geographic range suggests that dispersal most probably occurred by rafting of adults on a suitable platform such as macroalgae; indeed, naturally buoyant bull kelp is the natural habitat of the most geographically widespread species in this group. Our molecular phylogenies imply that, despite of being an unlikely event, adult rafting in ocean currents has occurred on several occasions throughout the evolutionary history of topshells, resulting in their wide present-day distribution.     

Host specificity and molecular phylogeny of larval Digenea isolated from New Zealand and Australian topshells (Gastropoda: Trochidae)

The maintenance of strict host specificity by parasites when several closely related host species live in sympatry is poorly understood. Species of intertidal trochid snails in the genera Diloma, Melagraphia and Austrocochlea often occur together and are parasitised by a single digenean morphotype (Platyhelminthes, Trematoda), tentatively placed in Opecoelidae. Of the 10 trochid species (6 from New Zealand, 4 from Australia) we examined, six were found to be infected, and the prevalence of infection was as high as 17.5%. We obtained molecular data (mitochondrial 16S and nuclear rDNA internal transcriber spacer 2 sequences, representing 774 bp), to infer phylogenetic relationships amongst these Digenea. Our phylogeny separated the single morphotype into three clearly defined clades (which are almost certainly separate biological species): (i) those infecting two species of Austrocochlea from Tasmania, (ii) those infecting Diloma subrostrata in Otago and Southland, New Zealand, and (iii) those infecting all the parasitised New Zealand topshells (Melagraphia aethiops, D. subrostrata, Diloma nigerrima and Diloma arida) throughout the country. This last group comprised two subclades, one infecting only D. subrostrata and one infecting the other three species. Two D. subrostrata populations were each found to be infected by genetically distinct parasites, yet sympatric populations of the other snails were not necessarily infected. This study is thus the first to reveal cryptic species of digeneans in a single population of a molluscan first intermediate host. We point out also that the degree of host specificity would have been grossly underestimated if, in the absence of our genetic analysis, we had only considered digenean morphology. Our results shed light on the conditions that may favour switching among intermediate hosts in digeneans, and on the presence/absence of host specificity in these parasites.     

Diversity and microstructure of quitons (Mollusca: Polyplacophora) from the Caribbean of Costa Rica

Diversity and microstructure of quitons (Mollusca: Polyplacophora) from the Caribbean of Costa Rica. The polyplacophorans of the coral reef on the Caribbean coast of Costa Rica have been insufficiently studied. The examination of coral rubble accumulated in the shallow sublitoral waters on four collection stations in Provincia Limón revealed a higher diversity of chitons than was documented. From the country eight species were previously known: Ischnochiton erythronotus (C.B. Adams 1845); Ischnoplax pectinata (Sowerby 1840); Stenoplax boogii (Haddon 1886); S. purpurascens (C.B. Adams 1845); Acanthopleura granulata (Gmelin 1791); Chiton marmoratus Gmelin 1791; C. tuberculatus Linnaeus 1758 and Acanthochitona rhodea (Pilsbry 1893). This study added five more species that are reported here for the first time: Callistochiton portobelensis Ferreira 1976; Ischnochiton kaasi Ferreira 1987; I. pseudovirgatus Kaas 1972; Acanthochitona balesae Abbott 1954 and Cryptoconchus floridanus (Dall 1889).     

Phylogenomics and rapid diversification of the genus Eutrema on the Qinghai–Tibet Plateau and adjacent regions

Both geographic isolation and polyploidization are assumed to play an important role in driving species diversification. However, this is rarely illustrated through phylogenomic analyses. The genus Eutrema (Brassicaceae), which also includes the salt-resistant species, are distributed mainly in Asia with extensive species diversification in the Qinghai–Tibet Plateau (QTP) and adjacent regions. In this study, we revealed almost fully resolved backbone relationships of the genus with genome re-sequencing data for genomes of 168 individuals from 28 species. Phylogenetic analyses of both plastomes and single-copy nuclear genes from the whole genome recovered six well-supported clades with almost consistent relationships. The first two clades are mainly distributed in central China and central Asia, while the other four in the QTP and adjacent regions. All of them diversified within 12 million years. Within each clade, we recovered numerous conflicts in the interspecific relationships between nuclear and plastome phylogenies, likely suggesting hybridization and incomplete lineage sorting during species diversification. Our estimation of genome size and comparison of the number of the single-copy nuclear genes demonstrated frequent occurrences of polyploids in the genus. Except for an establishment of the backbone phylogeny, our phylogenomic analyses suggest that in addition to strong geographic isolation, polyploidization may have played an important role in species diversification of this genus.     

Wood anatomy of Krameriaceae with comparisons with Zygophyllaceae: phylesis, ecology and systematics

Wood of nine species of Krameria (including all clades proposed within the genus) reveals a few characters related to infrageneric systematics; most relate primarily to ecology and habit. Wood of Krameria closely fits quantitative data reported for desert shrubs. Lack of vessel grouping correlates with the presence of densely pitted tracheids. Wood xeromorphy in Krameria may relate in part to hemiparasitism. Tracheid presence may also account for relatively low vessel density. Wood anatomy of six species of Zygophyllaceae (including both genera of Morkillioideae) is compared with that of Krameriaceae because recent phylogenies propose that these two families comprise the order Zygophyllales. Several wood characters appear to represent synapomorphies reflecting this relationship. Differences in wood anatomy between Krameriaceae and Zygophyllaceae are believed to represent autapomorphies. Notable among these include Paedomorphic Type II rays (Krameriaceae), storying (Zygophyllaceae), presence of vestured pits (Zygophyllaceae), and differentiation into vasicentric tracheids and fibre-tracheids (Zygophyllaceae). The latter feature is referable to the concept of fibre-tracheid dimorphism. Recognition of Krameriaceae as separate from Zygophyllaceae is supported by wood characters. Wood of Zygophyllales does not conflict with the idea that the order belongs to rosids, with Malpighiaceae as the outgroup of Zygophyllales.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 149 , 257–270.     

18S ribosomal DNA sequences provide insight into the phylogeny of patellogastropod limpets (Mollusca: Gastropoda)

To investigate the phylogeny of Patellogastropoda, the complete 18S rDNA sequences of nine patellogastropod limpets Cymbula canescens (Gmelin, 1791), Helcion dunkeri (Krauss, 1848), Patella rustica Linnaeus, 1758, Cellana toreuma (Reeve, 1855), Cellana nigrolineata (Reeve, 1854), Nacella magellanica Gmelin, 1791, Nipponacmea concinna (Lischke, 1870), Niveotectura pallida (Gould, 1859), and Lottia dorsuosa Gould, 1859 were determined. These sequences were then analyzed along with the published 18S rDNA sequences of 35 gastropods, one bivalve, and one chiton species. Phylogenetic trees were constructed by maximum parsimony, maximum likelihood, and Bayesian inference. The results of our 18S rDNA sequence analysis strongly support the monophyly of Patellogastropoda and the existence of three subgroups. Of these, two subgroups, the Patelloidea and Acmaeoidea, are closely related, with branching patterns that can be summarized as [(Cymbula + Helcion) + Patella] and [(Nipponacmea + Lottia) + Niveotectura]. The remaining subgroup, Nacelloidea, emerges as basal and paraphyletic, while its genus Cellana is monophyletic. Our analysis also indicates that the Patellogastropoda have a sister relationship with the order Cocculiniformia within the Gastropoda.     

Molecular phylogenetics of the butterflyfishes (Chaetodontidae): taxonomy and biogeography of a global coral reef fish family

Marine butterflyfishes (10 genera, 114 species) are conspicuously beautiful and abundant animals found on coral reefs worldwide, and are well studied due to their ecological importance and commercial value. Several phylogenies based on morphological and molecular data exist, yet a well-supported molecular phylogeny at the species level for a wide range of taxa remains to be resolved. Here we present a molecular phylogeny of the butterflyfishes, including representatives of all genera (except Parachaetodon) and at least one representative of all commonly cited subgenera of Chaetodon (except Roa sensuBlum, 1988). Genetic data were collected for 71 ingroup and 13 outgroup taxa, using two nuclear and three mitochondrial genes that total 3332 nucleotides. Bayesian inference, parsimony, and maximum likelihood methods produced a well-supported phylogeny with strong support for a monophyletic Chaetodontidae. The Chaetodon subgenera Exornator and Chaetodon were found to be polyphyletic, and the genus Amphichaetodon was not the basal sister group to the rest of the family as had been previously proposed. Molecular phylogenetic analysis of data from 5 genes resolved some clades in agreement with previous phylogenetic studies, however the topology of relationships among major butterflyfish groups differed significantly from previous hypotheses. The analysis recovered a clade containing Amphichaetodon, Coradion, Chelmonops, Chelmon, Forcipiger, Hemitaurichthys, Johnrandallia, and Heniochus. Prognathodes was resolved as the sister to all Chaetodon, as in previous hypotheses, although the topology of subgeneric clades differed significantly from hypotheses based on morphology. We use the species-level phylogeny for the butterflyfishes to resolve long-standing questions regarding the use of subgenera in Chaetodon, to reconstruct molecular rates and estimated dates of diversification of major butterflyfish clades, and to examine global biogeographic patterns.     

Phylogeny of the túngara frog genus Engystomops (= Physalaemus pustulosus species group; Anura: Leptodactylidae)

We present a phylogeny of the Neotropical genus Engystomops (= Physalaemus pustulosus species group) based on sequences of approximately 2.4 kb of mtDNA, (12S rRNA, valine-tRNA, and 16S rRNA) and propose a phylogenetic nomenclature. The phylogeny includes all described taxa and two unnamed species. All analyses indicate that Engystomops is monophyletic and contains two basal allopatric clades. Clade I (Edentulus) includes E. pustulosus and the Amazonian E. petersi + E. cf. freibergi. Clade II (Duovox) includes all species distributed in W Ecuador and NW Peru. Brevivox, a clade of small-sized species is strongly supported within Duovox. Populations of Engystomops pustulosus fall into two well-supported clades, each of which occupies two disjunct portions of the species range. Overall, our phylogeny is congruent with most previous hypotheses. This study is among the few published species-level phylogenies of Neotropical amphibians derived from molecular datasets. A review of the proportion of new species detected by similar studies suggests that the increasing use of molecular techniques will lead to the discovery of a vast number of species of Neotropical amphibians.     

Phylogeny, evolution, and taxonomy of vannellid amoebae

We sequenced 18S rRNA genes from 21 vannellid amoebae (Amoebozoa; Vannellidae), including nearly all available type cultures, and performed a comprehensive phylogenetic analysis for 57 Vannellidae sequences. The results show that species of Vannella and Platyamoeba are completely mixed and do not form distinct clades. Several very closely related species pairs exist, each with a Vannella and a Platyamoeba species differing in only a few nucleotides. Therefore, presence (Vannella) or absence (Platyamoeba) of glycostyles in the cell surface coat is an invalid generic distinction; the genera must be merged. As Vannella has priority, we formally transferred Platyamoeba species into Vannella, except for the non-vannellid P. stenopodia, here renamed Stenamoeba stenopodia gen. n. comb. n. and transferred to the family Thecamoebidae. Our trees show that Vannella glycostyles were probably easily and repeatedly evolutionarily lost. We have established a new genus Ripella, with distinct morphology and sequence signatures for Vannella platypodia and morphologically similar species that form a clearly separate clade, very distant from other Vannellidae. Vannellids form four well-separated single-genus clades: Vannella sensu stricto, Ripella, Clydonella, and Lingulamoeba. Species of the revised genus Vannella comprise four closely related, well-supported subclades: one marine and three freshwater. Here, we provide an illustrated checklist for all 40 known Vannellidae species.     

A molecular phylogenetic investigation of zoothamnium (ciliophora, peritrichia, sessilida)

The gene coding for 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in seven free-living, marine species of the sessiline peritrich genus Zoothamnium. These were Zoothamnium niveum, Zoothamnium alternans, Zoothamnium pelagicum, and four unidentified species. The ssu rRNA gene also was sequenced in Vorticella convallaria, Vorticella microstoma, and in an unidentified, freshwater species of Vorticella. Phylogenetic trees were constructed using these new sequences to test a previously published phylogenetic association between Zoothamnium arbuscula, currently in the family Zoothamniidae, and peritrichs in the family Vorticellidae. Trees constructed by means of neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods all had similar topologies. The seven new sequences of Zoothamnium species grouped into three well-supported clades, each of which contained a diversity of morphological types. The three clades formed a poorly supported, larger clade that was deeply divergent from Z. arbuscula, which remained more closely associated with vorticellid peritrichs. It is apparent that Zoothamnium is a richly diverse genus and that a much more intensive investigation, involving both morphological and molecular data and a wider selection of species, will be necessary to resolve its phylogeny. A greater amount of molecular diversity than is predicted by morphological data exists within all major clades of sessiline peritrichs that have been included in molecular phylogenies, indicating that characteristics of stalk and peristomial structure traditionally used to differentiate taxa at the generic level and above may not be uniformly reliable.     

Molecular systematics of Vetigastropoda: Trochidae, Turbinidae and Trochoidea redefined

Trochoidea are a large superfamily of morphologically and ecologically diverse marine gastropods. We present here an appraisal of the composition and relationships among trochoidean families based on molecular data, with an especial focus on the family Trochidae. Bayesian analyses of sequences from three genes (18S rRNA, 28S rRNA and COI) including data from 162 vetigastropod species show that the gastropod family Trochidae (sensu  Hickman & McLean (1990 ), Natural History Museum Los Angeles County Science Series, 35, 1–169) is not monophyletic. Recognition of Chilodontidae, Solariellidae and Calliostomatidae at the family level is supported. Our new, more limited, definition of Trochidae includes the subfamilies Stomatellinae, Lirulariinae and Umboniinae and redefined Trochinae, Cantharidinae and Monodontinae. Halistylinae are provisionally retained in the Trochidae based on previous morphological studies. As redefined, Trochidae are a predominantly shallow‐water radiation in the tropics and subtropics. Some subfamilies and genera previously included in Trochidae have been moved to an enlarged family Turbinidae. The family Turbinidae has been redefined to include Turbininae, Skeneinae, Margaritinae, Tegulinae, Prisogasterinae and most surprisingly the commercially important genus Tectus Montfort, 1810. The new definition of Turbinidae means that the family includes both predominantly shallow and deep‐water clades as well as genera that are distributed across the globe from the poles to the tropics. A greater range of habitat is now seen in Turbinidae than in Trochidae. The redefined Trochidae and Turbinidae, together with Solariellidae, Calliostomatidae and Liotiidae, make up the superfamily Trochoidea. Phasianellidae and Colloniidae are recognized as belonging in a new superfamily, Phasianelloidea, and Angaria Röding, 1798 is recognized as belonging in a new superfamily, Angarioidea. Placement of Areneidae into a superfamily awaits further work.     

Contrasting phylogenetic patterns of anther smuts (Pucciniomycotina: Microbotryum) reflect phylogenetic patterns of their caryophyllaceous hosts

Anther smuts in the genus Microbotryum often show very high host specificity toward their caryophyllaceous hosts, but some of the larger host groups such as Dianthus are crucially undersampled for these parasites so that the question of host specificity cannot be answered conclusively. In this study we sequenced the internal transcribed spacer (ITS) region of members of the Microbotryum dianthorum species complex as well as their Dianthus hosts. We compared phylogenetic trees of these parasites including sequences of anther smuts from other Caryophyllaceae, mainly Silene, with phylogenies of Caryophyllaceae that are known to harbor anther smuts. Additionally we tested whether observed patterns in parasites are due to shared ancestry or if geographic separation is a factor that should be taken into consideration in delimitating species. Parasites on Dianthus showed mainly an arbitrary distribution on Dianthus hosts, whereas parasites on other Caryophyllaceae formed well-supported monophyletic clades that corresponded to restricted host groups. The same pattern was observed in the Caryophyllaceae studied: morphologically described Dianthus species did not correspond well with monophyletic clades based on molecular data, whereas other Caryophyllaceae mainly did. We suggest that these different patterns primarily result from different breeding systems and speciation times between different host groups as well as difficulties in species delimitations in the genus Dianthus.     

In search of monophyletic taxa in the family Desmidiaceae (Zygnematophyceae, Viridiplantae): the genus Cosmarium

Nuclear-encoded small subunit (SSU) rDNA, 1506 group I introns, and chloroplast rbcL genes were sequenced from 97 strains representing the largest desmid genus Cosmarium (45 spp.), its putative relatives Actinotaenium (5 spp.), Xanthidium (4 spp.), Euastrum (9 spp.), Staurodesmus (13 spp.), and other Desmidiaceae (Zygnematophyceae, Streptophyta) and used to assess phylogenetic relationships in the family. Analyses of single genes and of a concatenated data set (3260 nt) established 10 well-supported clades in the family with Cosmarium species distributed in six clades and one nonsupported assemblage. Most of the clades contained representatives of at least two genera highlighting the polyphyletic nature of the genera Cosmarium, Euastrum, Staurodesmus, and Actinotaenium. To enhance resolution between clades, we extended the data set by sequencing the slowly evolving chloroplast-encoded large subunit (LSU) rRNA gene from 40 taxa. Phylogenetic analyses of a concatenated data set (5509 nt) suggested a sister relationship between two clades that consisted mainly of Cosmarium species and included C. undulatum, the type species of the genus. We describe molecular signatures in the SSU rRNA for two clades and conclude that more studies involving new isolates, additional molecular markers, and reanalyses of morphological traits are necessary before the taxonomic revision of the genus Cosmarium can be attempted.     

Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses

Species of Saccharomyces, Arxiozyma, Eremothecium, Hanseniaspora (anamorph Kloeckera), Kazachstania, Kluyveromyces, Pachytichospora, Saccharomycodes, Tetrapisispora, Torulaspora, and Zygosaccharomyces, as well as three related anamorphic species assigned to Candida (C. castellii, C. glabrata, C. humilis), were phylogenetically analyzed from divergence in genes of the rDNA repeat (18S, 26S, ITS), single copy nuclear genes (translation elongation factor 1alpha, actin-1, RNA polymerase II) and mitochondrially encoded genes (small-subunit rDNA, cytochrome oxidase II). Single-gene phylogenies were congruent for well-supported terminal lineages but deeper branches were not well resolved. Analysis of combined gene sequences resolved the 75 species compared into 14 clades, many of which differ from currently circumscribed genera.     

Expanding character sampling for the molecular phylogeny of euplotid ciliates (Protozoa, Ciliophora) using three markers, with a focus on the family Uronychiidae

Although euplotida ciliates are widely used as model organisms in multiple fields of biology, details of their phylogenetic relationships remain unresolved despite a rich history of investigation with small subunit (SSU) rDNA sequences and other characters. Here, six genera in Diophrys-like complex and three other euplotid genera are sampled for SSU-rDNA, ITS1-5.8S-ITS2 and LSU-rDNA, and their phylogenies were inferred with unconstrained and constrained analyses. In general, the concatenated analyses infer more reliable, less ambiguous phylogenies with higher node support values. The following conclusions can be made: (1) four well-supported clades are consistently detected in the family Uronychiidae, forming into two subgroups, which challenge the traditional arrangement based on morphological similarities; (2) the subfamily Diophryinae is paraphyletic; (3) the monophyly of Paradiophrys and the establishment of Apodiophrys and Diophryopsis is fully supported by concatenated data; (4) Apodiophrys and Paradiophrys form independent lineages, at the subfamily level, from other Diophrys-like genera; and (5) the highly specialized Pseudodiophrys nests within Diophrys.     

Phylogeny and taxonomy of endangered South and South-east Asian freshwater turtles elucidated by mtDNA sequence variation (Testudines: Geoemydidae: Batagur, Callagur, Hardella, Kachuga, Pangshura)

Using DNA sequences of the mitochondrial cytochrome b gene, we investigated phylogeny and taxonomy of South and South-east Asian turtles of all species and subspecies of the genera Batagur, Callagur, Hardella, Kachuga and Pangshura. We found three major clades: (i) a moderately to well-supported clade containing all large riverine species assigned so far to Batagur, Callagur and Kachuga ; (ii) a well-supported monophylum comprising the four Pangshura species; and (iii) Hardella that could constitute either the sister-taxon of Pangshura or of a clade comprising Batagur, Callagur, Kachuga and Pangshura. The genus Kachuga is clearly polyphyletic. Therefore, we recommend placing all Batagur, Callagur and Kachuga species in one genus. According to the International Code of Zoological Nomenclature Batagur Gray, 1856, being originally erected at higher rank, takes precedence over the simultaneously published name Kachuga Gray, 1856, and the younger name Callagur Gray, 1870, resulting in an expanded genus Batagur. Indonesian and Malaysian Batagur baska proved to be highly distinct from our sequences of this species from the Sundarbans (Bangladesh, adjacent India), suggesting that a previously unidentified species is involved. This finding is of high conservation relevance in the critically endangered B. baska. The currently recognized subspecies within Hardella thurjii , Pangshura smithii and P. tentoria do not correspond well with mtDNA clades. Considering that the two subspecies of H. thurjii are likely to be based only on individual ontogenetic differences, we propose abandoning the usage of subspecies within H. thurjii . In the Ghaghra River, Uttar Pradesh (India) we detected shared haplotypes in P. smithii and P. tentoria, implying that the unusual morphological characters of the Ghaghra River population of P. tentoria could be the result of interspecific hybridization.