Search

Cortesia is a halophytic and monotypic genus endemic to Argentina that belongs to Ehretiaceae (Boraginales). It is morphologically distinct from the other members of the family in having cuneate leaves with a 3-dentate apex, an involucrum of fused bracts, spatulate calyx lobes, and white drupes with a two-parted endocarp. Its single species, Cortesia cuneifolia, is here treated and illustrated based on the study of numerous herbarium collections. Additionally, a lectotype is designated for the name to assure its reliable application. Furthermore, the species is recorded for the first time in Tucumán province. [ABSTRACT FROM AUTHOR]

Micracanthodinium setiferum is a very distinctive but poorly known dinophyte with characteristically delicate, unbranched, filiform and pointed setae. A recent study by Mertens et al. (2022, Palynology 46: 1934908) aims to clarify the taxonomy of the species and to introduce two new formae acknowledging the presence or absence of setae in environmentally collected cells. We assert that the epitype choice of illustrations by these authors is inappropriate, but also not achieved following the rules of the International Code of Nomenclature for algae, fungi, and plants (ICN). Additionally, the two new formae are not described in accordance with the rules of the ICN. A more suitable epitype may therefore be chosen, once corresponding physical material from the type locality off Sicily is at hand. The taxonomic identity of M. setiferum meanwhile remains elusive. [ABSTRACT FROM AUTHOR]

Dinophyte evolution is essentially inferred from the pattern of thecal plates, and two different labelling systems are used for the important subgroups Gonyaulacales and Peridiniales. The partiform hypotheca of cladopyxidoid dinophytes fits into the morphological concepts of neither group, although they are assigned to the Gonyaulacales. Here, we describe the thecate dinophyte Fensomea setacea, gen. & sp. nov., which has a cladopyxidoid tabulation. The cells displayed a Kofoidean plate formula APC, 3′, 4a, 7″, 7C, 6S, 6′′′, 2′′′′, and slender processes were randomly distributed over the echinate or baculate surface. In addition, we obtained rRNA sequences of F. setacea, gen. & sp. nov., but dinophytes that exhibit a partiform hypotheca did not show a close relationship to Gonyaulacales. Character evolution of thecate dinophytes may have progressed from the ancestral state of six postcingular plates, and two more or less symmetrically arranged antapical plates, towards patterns of only five postcingular plates (Peridiniales) or more asymmetrical configurations (Gonyaulacales). Based on our phylogenetic reconsiderations the contact between the posterior sulcal plate and the first postcingular plate, as well as the contact between an antapical plate and the distalmost postcingular plate, do not represent a rare, specialized gonyaulacoid plate configuration (i.e., the partiform hypotheca of cladopyxidoid dinophytes). Instead, these contacts correspond to the common and regular configuration of peridinioid (and other) dinophytes. [ABSTRACT FROM AUTHOR]

Dinophytes are widely distributed in marine‐ and fresh‐waters, but have yet to be conclusively documented in terrestrial environments. Here, we evaluated the presence of these protists from an environmental DNA metabarcoding dataset of Neotropical rainforest soils. Using a phylogenetic placement approach with a reference alignment and tree, we showed that the numerous sequencing reads that were phylogenetically placed as dinophytes did not correlate with taxonomic assignment, environmental preference, nutritional mode, or dormancy. All the dinophytes in the soils are rather windblown dispersal units of aquatic species and are not biologically active residents of terrestrial environments. [ABSTRACT FROM AUTHOR]

Reliable determination of organisms is a prerequisite to explore their spatial and temporal occurrence and to study their evolution, ecology, and dispersal. In Europe, Bavaria (Germany) provides an excellent study system for research on the origin and diversification of freshwater organisms including dinophytes, due to the presence of extensive lake districts and ice age river valleys. Bavarian freshwater environments are ecologically diverse and range from deep nutrient‐poor mountain lakes to shallow nutrient‐rich lakes and ponds.We obtained amplicon sequence data (V4 region of small subunit‐rRNA, c. 410 bp long) from environmental samples collected at 11 sites in Upper Bavaria. We found 186 operational taxonomic units (OTUs) associated with Dinophyceae that were further classified by means of a phylogenetic placement approach.The maximum likelihood tree inferred from a well‐curated reference alignment comprised a systematically representative set of 251 dinophytes, covering the currently known molecular diversity and OTUs linked to type material if possible. Environmental OTUs were scattered across the reference tree, but accumulated mostly in freshwater lineages, with 79% of OTUs placed in either Apocalathium, Ceratium, or Peridinium, the most frequently encountered taxa in Bavaria based on morphology.Twenty‐one Bavarian OTUs showed identical sequences to already known and vouchered accessions, two of which are linked to type material, namely Palatinus apiculatus and Theleodinium calcisporum. Particularly within Peridiniaceae, delimitation of Peridinium species was based on the intraspecific sequence variation.Our approach indicates that high‐throughput sequencing of environmental samples is effective for reliable determination of dinophyte species in Bavarian lakes. We further discuss the importance of well‐curated reference databases that remain to be developed in the future. [ABSTRACT FROM AUTHOR]

• High abundance of Amphidomataceae in Argentinean 2015spring bloom communities at the shelf front. • 31 new Argentinean strains of Azadinium dalianense and Az. spinosum are characterized. • Majority of strains revealed a new non-toxigenic ribotype of Az. spinosum. • A single Argentinean Az. spinosum strain of a different ribotype produced only AZA-2. Azaspiracids (AZA) are the most recently discovered group of lipophilic marine biotoxins of microalgal origin, and associated with human incidents of shellfish poisoning. They are produced by a few species of Amphidomataceae, but diversity and occurrence of the small-sized dinophytes remain poorly explored for many regions of the world. In order to analyze the presence and importance of Amphidomataceae in a highly productive area of Argentinean coastal waters (El Rincón area, SW Atlantic), a scientific cruise was performed in 2015 to sample the early spring bloom. In a multi-method approach, light microscopy was combined with real-time PCR molecular detection of Amphidomataceae, with chemical analysis of AZA, and with the establishment and characterization of amphidomatacean strains. Both light microscopy and PCR revealed that Amphidomataceae were widely present in spring plankton communities along the El Rincón area. They were particularly abundant offshore at the shelf front, reaching peak densities of 2.8 × 105 cells L−1, but no AZA were detected in field samples. In total, 31 new strains were determined as Az. dalianense and Az. spinosum , respectively. All Az. dalianense were non-toxigenic and shared the same rRNA sequences. The large majority of the new Az. spinosum strains revealed for the first time the presence of a non-toxigenic ribotype of this species, which is otherwise the most important AZA producer in European waters. One of the new Az. spinosum strains, with a particular slender shape and some other morphological peculiarities, clustered with toxigenic strains of Az. spinosum from Norway and, exceptionally for the species, produced only AZA-2 but not AZA-1. Results indicate a wide diversity within Az. spinosum, both in terms of sequence data and toxin profiles, which also will affect the qualitative and quantitative performance of the specific qPCR assay for this species. Overall, the new data provide a more differentiated perspective of diversity, toxin productivity and occurrence of Amphidomataceae in a poorly explored region of the global ocean. [ABSTRACT FROM AUTHOR]

Halgania (Ehretiaceae, Boraginales) comprises ~20 species of ericoid shrubs endemic to Australia. The current taxonomic concepts based on morphology are confusing and are sometimes based on misidentification or lack of information about the type material. We describe the morphological diversity and infer relationships using molecular phylogenetics. The five petals in all Halgania species are blue to violet (rarely white). The yellow or yellow-purple anthers are connected into a cone surrounding the single style. Differences among the species are mainly found in the indumentum of the plants, the leaf margin (i.e. degree of serration), the sepals (being either of equal or of unequal size) and the length of the beak-like anther appendages.Aphylogenetic tree mainly based on ITS sequences retrieves three highly supported groups. The H. andromedifolia clade uniquely has sepals of unequal size, and the H. anagalloides clade exhibits dolabriform trichomes. The remaining taxa (constituting the H. littoralis clade) lack such diagnostic morphological traits, but are reliably retrieved as sister group to the H. anagalloides clade. As a first step towards the taxonomic revision of Halgania, we have compiled a nomenclatural list of all validly published names (at the species level and below), provide information about herbarium deposition of original material and discuss the current use of the names. [ABSTRACT FROM AUTHOR]

Flowers that release their powdery pollen by being vibrated through buzzing are morphologically diverse and have evolved many times independently. Most prominently, buzz-pollination is known from Solanum (Solanaceae) defining the “solanoid” flower type by Knut Fægri. The flowers of buzz-pollinated, Australian Halgania resemble the actinomorphic Solanum floral architecture: The plants have a yellow anther cone with an apical pore, protruding from a widely funnel-shaped to rotate, blue to violet corolla. However, Fægri rejected the solanoid flower type for some of the Halgania species due to a contracted inflorescence, a funnel-shaped corolla or an ostensible lack of a female stage. Using light and scanning electron microscopy, we investigated traits referring to the floral architecture of Halgania and compared the flowers of different species. In all investigated species the anthers of the cone are connected via long, intertwined trichomes (denoted “capillinection”) both between the individual anthers and in the central stylar channel. The anther opening is functionally reduced to an apical pore by 1) capillinection and spatial compression of the thecal walls, leaving only small apical slits and 2) by anther appendages that unify the ten slits to a single pore. Halgania flowers are morphologically similar to each other and are buzz-pollinated. We conclude that they are all structurally and functionally matching the flowers of tomato, Solanum lycopersicum , and thus the concept of solanoid flowers as defined by Knut Fægri. [ABSTRACT FROM AUTHOR]

Amphidomais an old though poorly studied thecate dinophyte that has attracted attention recently as a potential producer of azaspiracids (AZA), a group of lipophilic phycotoxins. A new species,Amphidoma parvula, sp. nov. is described from the South Atlantic shelf of Argentina. With a Kofoidean thecal plate pattern Po, cp, X, 6′, 6′′, 6C, 5S, 6′′′, 2′′′′, the cultivated strain H-1E9 (from which the type material ofAm. parvula, sp. nov. was prepared) shared the characteristic plate arrangement ofAmphidomaeach with six apical, precingular and postcingular plates.Amphidoma parvula, sp. nov. differs from other species ofAmphidomaby a characteristic combination of small size (10.7–13.6 µm in length), ovoid shape, high length ratio between epitheca and hypotheca, and small length ratio between apical and precingular plates. Other morphological details, such as the number and arrangement of sulcal plates and the fine structure of the apical pore complex support the close relationship betweenAmphidomaand the other known genus of Amphidomataceae,Azadinium. However,Am. parvula, sp. nov. lacks a ventral pore, a characteristically structured pore found in all contemporary electron microscopy studies ofAmphidomaandAzadinium. As inferred from liquid chromatography coupled with tandem mass spectrometry,Am. parvula, sp. nov. did not produce AZA in measurable amounts. Molecular phylogenetics confirmed the systematic placement ofAm. parvula, sp. nov. inAmphidoma(as sister species ofAmphidoma languida) and the Amphidomataceae. The results of this study have improved the knowledge of Amphidomataceae biodiversity. [ABSTRACT FROM AUTHOR]

Two sexual systems are predominant in Catasetinae (Orchidaceae), namely protandry (which has evolved in other orchid lineages as well) and environmental sex determination (ESD) being a unique trait among Orchidaceae. Yet, the lack of a robust phylogenetic framework for Catasetinae has hampered deeper insights in origin and evolution of sexual systems. To investigate the origins of protandry and ESD in Catasetinae, we sequenced nuclear and chloroplast loci from 77 species, providing the most extensive data matrix of Catasetinae available so far with all major lineages represented. We used Maximum Parsimony, Maximum Likelihood and Bayesian methods to infer phylogenetic relationships and evolution of sexual systems. Irrespectively of the methods used, Catasetinae were monophyletic in molecular phylogenies, with all established generic lineages and their relationships resolved and highly supported. According to comparative reconstruction approaches, the last common ancestor of Catasetinae was inferred as having bisexual flowers (i.e., lacking protandry and ESD as well), and protandry originated once in core Catasetinae (comprising Catasetum , Clowesia , Cycnoches , Dressleria and Mormodes ). In addition, three independent gains of ESD are reliably inferred, linked to corresponding loss of protandry within core Catasetinae. Thus, prior gain of protandry appears as the necessary prerequisite for gain of ESD in orchids. Our results contribute to a comprehensive evolutionary scenario for sexual systems in Catasetinae and more generally in orchids as well. [ABSTRACT FROM AUTHOR]

Tiquilia is very different from the other members of the Ehretiaceae ( Boraginales) in many aspects of morphology and ecology. Because detailed knowledge about flower and fruit traits is necessary to reliably infer character evolution of and within Tiquilia, we investigated flower to fruit ontogeny in eight species of Tiquilia using light and electron microscopy. Tiquilia accumulated a number of autapomorphies such as the prostrate growth form, the lack of lateral and ventral bundles in the gynoecium, and the formation of nutlet-like mericarpids as dispersal units instead of more or less succulent drupes. The internal architecture of the superior bicarpellate ovary resulted from the development of several secondary septa including apical, basal and false septa, as it has been reported also from other Boraginales. However, no character found in Tiquilia can be regarded as synapomorphic with any other taxon of the Ehretiaceae. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 520-534. [ABSTRACT FROM AUTHOR]

Highlights: [•] Ehretiaceae including parasitic Lennoaceae as major lineage of the Boraginales. [•] Molecular analysis covering the diversity of Ehretiaceae and using a four-locus data set. [•] Nine lineages to be taxonomically accepted at the generic level. [•] Historical biogeography explained by few colonization events. [•] Fusion of endocarp parts several times independently. [ABSTRACT FROM AUTHOR]

Abstract: Infection by papillomaviruses (PVs) has been linked to different types of neoplasias, in both human and non-human hosts. Knowledge about PV diversity is essential to reliably infer the evolutionary history of these pathogens and to elucidate the link between infection and disease. We cloned and sequenced the complete genome of a novel PV, EhelPV1, isolated from hair bulbs from a captive straw-colored fruit bat Eidolon helvum (Pteropodidae, Chiroptera). We also retrieved partial sequences of the E1 and L1 genes from hair bulbs from a captive Indian flying fox Pteropus giganteus (Pteropodidae, Chiroptera). The detected virus (PgigPV1) presumably corresponded to a novel type as well. Maximum likelihood phylogenetic analyses were conducted using a representative collection of 132 PVs. EhelPV1 belonged to the Lambda+Mu-PV crown group and was most closely related to another bat PV, MschPV2. Both fragments of PgigPV1 were placed alongside with EhelPV1. The novel PVs were phylogenetically distant from other previously described bat PVs, namely MrPV1, MschPV1 and RaPV1. We have further characterized the sequence patterns of the E2-binding sites occurring in the upstream regulatory region of Lambda+Mu-PVs. Common fingerprints within this region are shared by certain PVs. However, there is not a sharp correspondence between the repertoire of transcription factor binding sites in the viral regulatory region and host range, tissue tropism or viral life style. Our results reinforce the hypothesis that PVs have undergone an initial radiation prior to the divergence of the mammalian hosts, giving rise to the present-day PV crown groups. [Copyright &y& Elsevier]

Abstract: Endosymbiotic dinophytes are diverse and are found in a large variety of aquatic partners. They are colloquially coined zooxanthellae, and knowledge about those dinophytes with a coral as partner (i.e., Symbiodinium) is extensive. However, Zooxanthella nutricula has been specifically described based on material isolated from radiolarians, and its phylogenetic position within the dinophyte tree is unclear at present. We isolated genomic DNA and sequenced the ribosomal RNA genes from an endosymbiotic dinophyte found in a radiolarian. In phylogenetic analyses, the endosymbiont was distantly related to Symbiodinium and the Suessiales, but clustered together with members of the Peridiniales. Specifically, it was the sister lineage of a small group, whose members host a diatom as endosymbiont (i.e., the dinotoms). Endosymbiosis is thus of multiple origin within the dinophytes, and more research is necessary to work out ecological and morphological character traits that are congruent to the DNA trees. [Copyright &y& Elsevier]

Despite a growing knowledge about the biological diversity of papillomaviruses (PV), only little is known about non-human PV in general and about PV mice models in particular. We cloned and sequenced the complete genomes of two novel PV types from the Norway rat (Rattus norvegicus; RnPV2) and the wood mouse (Apodemus sylvaticus; AsPV1) as well as a novel variant of the recently described MmuPV1 (originally designated as MusPV) from a house mouse (Mus musculus; MmuPV1 variant). In addition, we conducted phylogenetic analyses using a systematically representative set of 79 PV types, including the novel sequences. As inferred from concatenated amino acid sequences of six proteins, MmuPV1 variant and AsPV1 nested within the Beta+Xi-PV super taxon as members of the Pi-PV. RnPV2 is a member of the Iota-PV that has a distant phylogenetic position from Pi-PV. The phylogenetic results support a complex scenario of PV diversification driven by different evolutionary forces including co-divergence with hosts and adaptive radiations to new environments. PV types particularly isolated from mice and rats are the basis for new animal models, which are valuable to study PV induced tumors and new treatment options. [ABSTRACT FROM AUTHOR]

The origin of Geraniales (approximately 900 species in three families: Geraniaceae, Melianthaceae, and Vivianiaceae) is traced back to the Cretaceous of Gondwana, yet their geotemporal history is largely unknown because of a limited fossil record and incomplete phylogenies. In the present study, we provide the first fossil record of Vivianiaceae and a highly resolved molecular phylogeny for all extant Geraniales genera. Our results support the hypothesis that five (instead of three) families should be recognized in the order Geraniales: Francoaceae A. Juss. ( Francoa, Greyia, Tetilla), Geraniaceae Juss. ( Erodium, Geranium, Monsonia, Pelargonium), Hypseocharitaceae Wedd. (monogeneric), Melianthaceae Horan. ( Bersama, Melianthus), and Vivianiaceae Klotzsch ( Balbisia, Rhynchotheca, Viviania). The four major lineages (i.e. Geraniaceae, Francoaceae + Melianthaceae, Hypseocharitaceae, Vivianiaceae) all originated within a narrow time frame during the Eocene (36.9-49.9 Mya) based on the five fossil calibration points. The divergence of most of the extant genera occurred much later, from the Miocene onwards. The South American-South African disjunction in Francoaceae apparently goes back to long distance dispersal with an estimated divergence time of the lineages in the Middle Miocene [11.2 (5.9-17.7) Mya]. Diversification in Melianthus appears to be much more recent than previously assumed [starting approximately 3.4 (1.9-5.2) Mya rather than approximately 8-20 Mya]. However, divergence of the Andean Hypseocharis lineage [36.9 (31.9-42.8) Mya] significantly predates the main Andean uplift: Current distributions likely go back to northward migrations and subsequent extinctions in Patagonia. Similarly, Rhynchotheca, Balbisia, and Viviania have a current southern distribution limit > 10°N of the fossil finds, indicating a massive northward displacement. The present evidence suggests that niche conservatism likely played a major role in the historical biogeography of Geraniales. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••-••. [ABSTRACT FROM AUTHOR]

SUMMARY: Prorocentrum comprises a unique group of dinophytes with several apomorphic traits, such as an apical insertion of flagella and the presence of two major, large thecal plates. Species delimitation is challenging, especially for morphologically very similar, small planktonic species. Contemporary analyses, including SEM studies and molecular phylogenetics of type material, are not available for many described species. Based on six strains isolated from Antarctic, subarctic and North Atlantic waters, Prorocentrum pervagatum sp. nov. is described. Prorocentrum pervagatum was small (12–16 μm long and deep), oval to round in outline, and moderately compressed. One small, pyrenoid‐like structure was faintly visible in some cells. Rod‐like, long trichocysts were present. Cells had one distinct apical spine (1.1–1.7 μm in length) visible in light microscopy. The plate surface appeared smooth in light microscopy with few pores located close to the plate margin visible in empty thecae. Electron microscopy revealed plates to be densely covered by small projections and two size classes of thecal pores. Cells had a row of mostly four large pores in apical‐ventral position on the right thecal plate. The periflagellar area consisted of eight small platelets. The apical spine was formed by platelet six. In molecular phylogenetics, P. pervagatum was part of a species group generally exhibiting small size and spiny thecal ornamentation, together with Prorocentrum cordatum and Prorocentrum obtusidens. The new species is distinct in DNA trees and differs from the protologues of other small species of Prorocentrum by the unique combination of size, shape (i.e. only moderately compressed or round), presence of a distinct apical spine, and position of thecal pores (i.e. located at the plate margins only). Its clear description and illustration may stimulate similar work of other small species of Prorocentrum, particularly including the re‐investigation of taxa with historical names collected at the corresponding type localities. [ABSTRACT FROM AUTHOR]

Abstract: The phylogenetic position of cetacean papillomaviruses (PVs: Omikron-PVs and Upsilon-PVs) varies depending on the region of the genome analysed. They cluster together with Alpha-PVs when analysing early genes and with Xi-PVs and Phi-PVs when analysing late genes. We cloned and sequenced the complete genomes of five novel PVs, sampled from genital and oesophageal lesions of free-ranging cetaceans: Delphinus delphis (DdPV1), Lagenorhynchus acutus (TtPV3 variant), and Phocoena phocoena (PphPV1, PphPV2, and PphPV3). Using Maximum Likelihood and Bayesian approaches, all cetacean PVs constituted a monophyletic group with Alpha-, Omega-, and Dyodelta-PVs as inferred from E1–E2 early genes analyses, thus matching the shared phenotype of mucosal tropism. However, cetacean PVs, with the exception of PphPV3, were the closest relatives of Xi-PVs and Phi-PVs in L2–L1 late genes analyses, isolated from cow and goat, thus reflecting the close relationship between Cetacea and Artiodactyla. Our results are compatible with a recombination between ancestral PVs infecting the Cetartiodactyla lineage. Our study supports a complex evolutionary scenario with multiple driving forces for PV diversification, possibly including recombination and also interspecies transmission. [Copyright &y& Elsevier]

The article offers information on a study which investigated the phylogenetic relationships of Trigonotideae based on micromorphology and molecular data. It offers information on the tribe Trigonotideae of the family Boragineae. Methods employed include plant microscopy, alignment and comparative sequence analysis, and DNA extraction, amplification and sequencing. A discussion on research findings, including floral morphology, pollen and fruits, is detailed.

Abstract: Warts from immunosuppressed organ transplant recipients (OTR) persist over years and may progress into non-melanoma skin cancer. Human papillomaviruses (HPV) are considered the causal agents for the development of such warts. We isolated the novel type HPV-117 from a persisting wart by rolling circle amplification. One hundred eighteen warts from immunocompetent patients (IC) and 49 warts from OTR were analyzed by HPV-117 E6 type-specific PCR. As inferred from a phylogenetic analysis, the new type HPV-117 belonged to alpha-PV species 2, including the most similar types HPV-10 and HPV-94. The general prevalence of HPV-117 in warts was 2% in IC (2/118), and 12% in OTR (6/49). The high viral load in dysplastic cells of a Verruca vulgaris was shown by in situ hybridization. Our results suggest an active role of the novel type in the development of cutaneous warts of OTR. [Copyright &y& Elsevier]

Several cutaneotropic human papillomavirus (HPV) types seem to be involved in the early onset of cutaneous squamous-cell carcinoma. To test the hypothesis that cutaneotropic HPV infections are facilitated because of close and frequent skin contact (for example, between child and mother), we examined HPV prevalence in hair follicle cells from 134 volunteers (1–89 years of age, median 42 years) from 13 families. We used a high-throughput HPV-typing approach with a sensitive β-/γ-cutaneous PCR method, followed by reverse line blotting, to detect 30 cutaneotropic HPV types. HPV prevalence in all individuals was 42% and increased with age from 5% at 20 years to 27% at 21–40 years, 53% at 41–60 years, and 76% at >60 years. The effect of life age was significant, independent of couples and family members shown by regression analyses (P10−8). A higher similarity of HPV infection patterns was observed in couples versus two randomly chosen individuals (P0.05). However, the same specific HPV type was rarely found within couples or between children and their parents. Cutaneotropic HPV types are occasionally exchanged between family members during the entire lifetime, but other donors should also be considered in viral transmission. [ABSTRACT FROM AUTHOR]

Abstract: Phylogenetic relationships are complex within the Lithospermeae, a large subgroup of the Boraginaceae s.str. The relationships of New World Lasiarrhenum, Macromeria, Nomosa, Onosmodium, Perittostoma, and Psilolaemus to subcosmopolitan and much larger Lithospermum have not been critically investigated in the recent past. No molecular data on the phylogeny of these genera and Lithospermum have so far been published. We investigated the relationships within Lithospermeae using three loci (nuclear ITS plus 5.8S rRNA, chloroplast trnL-F-spacer, and trnS-G-spacer) and micromorphological character traits (pollen, nutlets). Lithospermum s.l. constitutes the sistergroup of Asian Ulugbekia and is monophyletic only when its American segregates “Macromeria”, monotypic Nomosa, and Onosmodium are included. Both the African and the South American species groups of Lithospermum are monophyletic, but North American representatives are not resolved in a single clade. Morphological characters that have been considered as important for generic delimitation in the past (such as large, yellow corollas without faucal scales, particular pollen types, coarsely veined leaves, shrubby habit) have evolved in at least two only distantly related lineages within Lithospermum s.l. The reduction of American “Macromeria”, Nomosa, and Onosmodium as well as Asian Ulugbekia under Lithospermum is proposed to render the latter monophyletic. This redefined Lithospermum s.l. appears to have undergone a type of recent “island radiation” in the Americas, reflected in a morphological diversity far exceeding that found in the Old World. [Copyright &y& Elsevier]

Based on morphological and molecular data, calcareous dinoflagellates (Thoracosphaeraceae, Peridiniales) are a monophyletic group comprising the three major clades Ensiculifera/ Pentapharsodinium, Thoracosphaera/ Pfiesteria, and Scrippsiella sensu lato. We used stratigraphically well-documented first occurrences of particular archeopyle types to constrain relaxed Bayesian molecular clocks applied to nuclear rRNA sequences of 18 representatives of the three main clades. By comparing divergence estimates obtained in differently calibrated clocks with first stratigraphic occurrences of taxa not themselves used as constraints, we identified plausible divergence times for several subclades of calcareous dinoflagellates. The initial diversification of extant calcareous dinoflagellates probably took place in the Late Jurassic, with the three main clades all established by the Cretaceous. The two mesoepicystal operculum types observed in calcareous dinoflagellates probably evolved independently from simple apical archeopyles. Based on our taxon sample, the K/T boundary had relatively little effect on the diversity of the group, with several lineages dating to before 65 mya (million years ago). The first stratigraphic occurrences of key taxa, such as Thoracosphaera and Calciodinellum (not themselves used as constraints), are in agreement with the molecular time estimates. Conflicts that involve “ Calciodinellum” levantinum, Leonella, Pentapharsodinium, Pernambugia, and the Scrippsiella trochoidea species complex may be due to inaccurate assignment of fossils because of high morphological homoplasy and insufficient knowledge of the extant diversity of calcareous dinoflagellates. [ABSTRACT FROM AUTHOR]

Human papillomaviruses (HPV) infect cutaneous and mucosal epithelia and induce benign and malignant lesions. Non-melanoma skin cancer (NMSC), encompassing basal cell carcinoma and squamous cell carcinoma (SCC), is the most frequent cancer in the Caucasian population, and the incidence has increased dramatically worldwide. Ultraviolet (UV) radiation is a major risk factor for NMSC, and cutaneous HPV is also considered to play an active role during the pathogenesis of these cancers. The first evidence for the involvement of HPV in NMSC was reported in patients with Epidermodysplasia verruciformis (EV). HPV types detected in skin tumours of these patients are referred to as EV/cutaneous HPV types belonging to the beta- and gamma-papillomaviruses (PV). Epidemiological studies have shown a higher risk of several EV/cutaneous HPV types for NMSC. Furthermore, in vitro and animal models show transforming properties of some PV types. The anti-apoptotic activities, and the delay of DNA repair mechanism caused by some EV/cutaneous HPV E6 proteins in response to UV-induced mutations, may lead to the persistence of DNA-damaged keratinocytes. Thus, specific EV/cutaneous HPV types as co-factors in association with UV-radiation and the immune system seem to be involved in the early pathogenesis of cutaneous SCC. [ABSTRACT FROM AUTHOR]

Abstract: Human papillomaviruses (HPV) of the β-group seem to be involved in the pathogenesis of non-melanoma skin cancer. Papillomaviruses are host specific and are considered closely co-evolving with their hosts. Evolutionary incongruence between early genes and late genes has been reported among oncogenic genital α-papillomaviruses and considerably challenge phylogenetic reconstructions. We investigated the relationships of 29 β-HPV (25 types plus four putative new types, subtypes, or variants) as inferred from codon aligned and amino acid sequence data of the genes E1, E2, E6, E7, L1, and L2 using likelihood, distance, and parsimony approaches. An analysis of a L1 fragment included additional nucleotide and amino acid sequences from seven non-human β-papillomaviruses. Early genes and late genes evolution did not conflict significantly in β-papillomaviruses based on partition homogeneity tests (p ⩾0.001). As inferred from the complete genome analyses, β-papillomaviruses were monophyletic and segregated into four highly supported monophyletic assemblages corresponding to the species 1, 2, 3, and fused 4/5. They basically split into the species 1 and the remainder of β-papillomaviruses, whose species 3, 4, and 5 constituted the sistergroup of species 2. β-Papillomaviruses have been isolated from humans, apes, and monkeys, and phylogenetic analyses of the L1 fragment showed non-human papillomaviruses highly polyphyletic nesting within the HPV species. Thus, host and virus phylogenies were not congruent in β-papillomaviruses, and multiple invasions across species borders may contribute (additionally to host-linked evolution) to their diversification. [Copyright &y& Elsevier]

The article examines the taxonomic position of Auxemma, Patagonula and Saccellium (Cordiaceae, Borginales). These species are distinct from Cordia because of their highly specialized fruit morphologies. The article proposes the nomenclature changes necessary to accommodate the species in Cordia. It also notes their distributions as inferred from modern collections

Abstract: The phylogenetic relationships of calcareous dinoflagellates (i.e., Calciodinellaceae and Thoracosphaera) are investigated. Molecular data from the ribosomal 5.8S rRNA and highly conserved motifs of the ITS1 show Calciodinellaceae s.l. to be monophyletic when few non-calcareous taxa are included. They segregate into three monophyletic assemblages in a molecular analysis that considers the 5.8S rRNA and both the Internal Transcribed Spacer regions ITS1 and ITS2: a clade comprising species of Ensiculifera and Pentapharsodinium (E/P-clade), Scrippsiella s.l. (including fossil-based taxa such as Calciodinellum and Calcigonellum), and a heterogeneous group (T/P-clade) of calcareous (e.g., Thoracosphaera) and non-calcareous taxa (e.g., the highly toxic Pfiesteria). The potential to produce calcareous structures is considered as apomorphic within alveolates, and non-calcareous taxa nesting with calcareous dinoflagellates may have reduced calcification secondarily. Molecular results do not contradict general evolutionary scenarios provided by previous morphological (mainly paleontological) investigations. [Copyright &y& Elsevier]

The phylogenetic relationships of Scrippsiella sensu lato (including cyst taxa such as Calcigonellum, Calciodinellum , and Pernambugia ) were investigated based on sequences from the ribosomal 5.8S rRNA and the Internal Transcribed Spacers ITS1 and ITS2, including interpretations on morphology and distribution. To attach importance to the cyst diversity present in calcareous dinoflagellates, a segregation of Scrippsiella sensu lato into four well-recognizable and monophyletic groups is proposed, corresponding to more- or less-established taxonomic units: (i) Calciodinellum (including Calcigonellum and a few species assigned to Scrippsiella ), (ii) Pernambugia (presumptively including Lebessphaera ), (iii) S. precaria and S. ramonii , and (iv) Scrippsiella sensu stricto comprising largely the S. trochoidea species complex. The phylogenetic relationships among these four groups are not sufficiently resolved. Molecular data suggest the existence of numerous cryptic taxa showing molecular, but not morphological, variation (especially in Scrippsiella sensu stricto ). Closely related strains have a wide range of distribution and occur (at least partly) sympatrically in cold through to tropical seas of the world. [ABSTRACT FROM AUTHOR]

Hypotheses on the origin of the current distribution patterns and bicontinental disjunctions of Cordiaceae, Ehretiaceae, and Heliotropiaceae (Primarily Woody Boraginales) are tested by pairwise comparison of Kimura two-parameter distances. Estimated absolute dates of fossils and geological events (plate tectonics, climate changes) were used to calibrate a molecular clock. A mid-Cretaceous origin of the Primarily Woody Boraginales is proposed with an initial diversification in South America. Plate tectonics appear to play a minor role in their phylogeography. Most disjunctions are best explained by the rare events of long-distance dispersal because of the widespread occurrence of drupaceous fruits and their potential for endozoochoria. Furthermore, migrations and extinctions might have played a considerable role in the formation of the current distribution patterns. [ABSTRACT FROM AUTHOR]

Ehretia fruits contain four seeds arranged in an endocarp, which is either four-parted (Ehretia I), two-parted (Ehretia II), or undivided (Ehretia monopyrena). The single parts are called endocarpids, which are one-loculed, two-loculed, or four-loculed respectively. On the basis of its two-loculed endocarp the fossil species Ehretia clausentia from the European Eocene is recognised as a representative of the Ehretia II clade as are also most other fossils of Ehretia. The fossil Ehretia hedericarpa from the European Oligocene and Miocene is the only known fossil of Ehretia with one locule per endocarpid and was therefore placed in the Ehretia I clade. Morphological and anatomical investigations of the fossils demonstrate some syn-apomorphies of the latter with the Ehretia II clade (e.g. diminution of the placenta). In a phylogenetic tree E. hedericarpa is the sister species of the Ehretia II clade. The occurrence of E. hedericarpa in Europe agrees with the assumption that it is closely allied to the Laurasian Ehretia II clade since the representatives of Ehretia I are not known from the former Laurasian Continent. [Copyright &y& Elsevier]

The Prorocentrales are a unique group of dinophytes based on several apomorphic traits, but species delimitation is challenging within the group. Prorocentrum triestinum was described by Josef Schiller in 1918 as an important bloom-forming species from Trieste (Mediterranean, Adriatic Sea) with a conspicuous asymmetric outline and a small, asymmetrically located subapical spine. All subsequent records under this name fail to conform to Schiller's original description. These inconsistencies have their origin in John Dodge's 1975 revision of Prorocentrum, which placed Prorocentrum redfieldii, a more symmetrical, slender species with a long apical spine, into synonymy under P. triestinum. To clarify this confusion, we collected samples at the type locality of P. triestinum in Trieste and established a strain that is morphologically consistent with the protologue and suitable for use in epitypification. Morphology and rRNA sequence data of this strain were compared with four new strains identified as P. redfieldii from the Mediterranean Sea and the North Atlantic Ocean. Cells of P. triestinum had an asymmetric outline in lateral view and a small, dorso-subapical spine. These features, which are readily resolved by light microscopy, were distinct from those of the nearly symmetrical and slender cells of P. redfieldii, which had a long, apically located spine. The species are nevertheless closely related and share an identical architecture of the periflagellar area with a distinctive, largely reduced accessory pore together with a very small platelet 7. This apomorphy clearly differentiates both species from other species of Prorocentrum. Both species differ in their primary rRNA sequences, and ITS and LSU sequence differences will enable them to be distinguished in future meta-barcoding studies. The present study demonstrates that P. triestinum and P. redfieldii are distinct species and thus contributes to a reliable biodiversity assessment of Prorocentrum. HIGHLIGHTS Prorocentrum triestinum is characterised molecularly for the first time and delimited from P. redfieldii. The identity of important bloom-forming species is clarified. Structural details of the periflagellar area are described. [ABSTRACT FROM AUTHOR]

• First dated phylogeny of dinophytes at a global scale. • Molecular phylogenetics based on concatenated rRNA sequences. • Congruence between fossil record and molecular diversification. • Groups including harmful dinophytes predate the Cretaceous–Paleogene boundary. Unicellular dinophytes include a considerable number of harmful algae and potent producers of toxins. The dinophyte fossil record is one of the richest among protists and indicates a geologically old origin of the group dating back to the Triassic. Besides of these records, very few molecular dating studies of dinophytes have been published to date, precluding an understanding of the diversification history of these organisms. In the present study, we used first appearances in the fossil record for the best-represented dinophyte lineages, namely Gonyaulacales and Peridiniales, to calibrate a molecular phylogeny. It is inferred from ribosomal RNA sequence data covering a representative taxon sampling of all currently recognised lineages. Dinophytes may have started diversifying during main tectonic events of the supercontinent Pangaea, witnessing and surviving some of the biggest mass extinction events on Earth. Groups including harmful dinophytes originated at different points in time, but they all predate the Cretaceous–Paleogene boundary. Our chronogram provides a first time frame and may stimulate studies in future bringing molecular phylogenetics of dinophytes and their impressive fossil record together in more detail. [ABSTRACT FROM AUTHOR]

Transfer cells are specialized plant cells that optimize short-distance transport by an extension of the interior surface of the cell walls. Using scanning electron microscopy (SEM), we found transfer cells in the fossil seed coat of Ehretia clausentia (Ehretiaceae, Boraginales) from the London Clay flora (Lower Eocene). This is the first fossil record of transfer cells in angiosperms. [ABSTRACT FROM AUTHOR]

In the microscopy realm, a large body of dark biodiversity still awaits to be uncovered. Unarmoured dinophytes are particularly neglected here, as they only present inconspicuous traits. In a remote German locality, we collected cells, from which a monoclonal strain was established, to study morphology using light and electron microscopy and to gain DNA sequences from the rRNA operon. In parallel, we detected unicellular eukaryotes in ponds of the Botanical Garden Munich‐Nymphenburg by DNA‐metabarcoding (V4 region of the 18S rRNA gene), weekly sampled over the course of a year. Strain GeoK*077 turned out to be a new species of Borghiella with a distinct position in molecular phylogenetics and characteristic coccoid cells of ovoid shape as the most important diagnostic trait. Borghiella ovum, sp. nov., was also present in artificial ponds of the Botanical Garden and was the second most abundant dinophyte detected in the samples. More specifically, Borghiella ovum, sp. nov., shows a clear seasonality, with high frequency during winter months and complete absence during summer months. The study underlines the necessity to assess the biodiversity, particularly of the microscopy realm more ambitiously, if even common species such as formerly Borghiella ovum are yet unknown to science. [ABSTRACT FROM AUTHOR]

To determine the intraspecific variability of microscopic organisms such as dinophytes is challenging, but can be achieved using cultured material. Unusual morphologies of Peridinium tuberosum assigned to the Peridinium cinctum species group have been described as bulges on the posterior end of the cell a hundred years ago and more, but its taxonomic significance is unclear at present. We collected field material in Germany and Poland in order to establish strains to study cell morphology using light and scanning electron microscopy. For the cultured material, DNA sequence data from the rRNA operon was gained as well and included in molecular phylogenetics (including 22 new partial rRNA sequences). Two new, closely related ribotypes were detected, and all strains showed the principle morphology of P. cinctum having an asymmetric epitheca, a large first apical plate and a sulcus extending onto the epitheca. In the single-strain GeoM*979 assigned to one of the two new ribotypes, cells with bulges appeared rarely but consistently, mostly on the hypotheca, but other variations also occurred. Overall, cells of this strain display traits not observed before while studying cultured P. cinctum, and this distinction is further supported by molecular data and additional details of epithecal opening. However, there does not remain enough information to determine strain GeoM*979 as a separate species (namely P. tuberosum) and therefore, it is identified as Peridinium aff. cinctum until further notice. [ABSTRACT FROM AUTHOR]

The taxonomy of Gymnodinium and the Gymnodiniaceae is inconsistent, because the systematic position of the type species, G. fuscum, is elusive at present. Historical names of microscopic species are frequently ambiguous, making reliable determination difficult, although it is crucial to fully explore the biology of the organisms. We collected material at the type locality of a historical variety, namely Gymnodinium fuscum var. rubrum, var. nov., and established a strain for morphological and molecular studies. The motile cells showed a characteristically obovate shape in outline, with acute antapex, and a horseshoe-shaped apical structure complex, which is characteristic for many Gymnodiniaceae. Older cultivated material further exhibited red granules in the cell, being the name-giving diagnostic character of the variety. In a molecular phylogeny, monophyletic Gymnodiniaceae segregated into seven clades at high taxonomic level. The phylogenetic resolution of the molecular DNA-tree provides evidence for a dynamic evolutionary scenario of Gymnodiniaceae and might prove helpful for an improved classification of the group. As the taxonomic result, we validate and epitypify the historical name, G. fuscum var. rubrum, var. nov., showing diagnostic traits such as a descending (but not straight) cingulum and a reciprocal size ratio between episome and hyposome in comparison to the regular form of G. fuscum. [ABSTRACT FROM AUTHOR]

Summary: Dinophytes are one of few protist groups that have an extensive fossil record and are therefore appropriate for time estimations. However, insufficient sequence data and strong rate heterogeneity have been hindering to put dinophyte evolution into a time frame until now. Marine‐to‐freshwater transitions within this group are considered geologically old and evolutionarily exceptional due to strong physiological constraints that prevent such processes. Phylogenies based on concatenated rRNA sequences (including 19 new GenBank entries) of two major dinophyte lineages, Gymnodiniaceae and Peridiniales, were carried out using an uncorrelated molecular clock and five calibration points based on fossils. Contrarily to previous assumptions, marine‐to‐freshwater transitions are more frequent in dinophytes (i.e. five marine‐freshwater transitions in Gymnodiniaceae, up to ten but seven strongly supported transitions in Peridiniales), and none of them occurred as early as 140 MYA. Furthermore, most marine‐to‐freshwater transitions, and the followed diversification, took place after the Cretaceous–Paleogene boundary. Not older than 40 MYA, the youngest transitions within Gymnodiniaceae and Peridiniales occurred under the influence of the Eocene climate shift. Our evolutionary scenario indicates a gradual diversification of dinophytes without noticeable impact of catastrophic events, and their freshwater lineages have originated several times independently at different points in time. [ABSTRACT FROM AUTHOR]

The Prorocentrales are a unique group of dinophytes based on several apomorphic traits, but species delimitation is challenging within the group. The type species of Prorocentrum, namely P. micans, cannot be determined unambiguously, as important characters are not preserved in the original material collected in the first half of the 19th century. Water samples were taken at the type locality of P. micans in the Baltic Sea off Kiel (Germany) and strains with a morphology consistent with the protologue were established. An in-depth morphological analysis was performed, illustrating minute traits such as the periflagellar platelets and three different types of thecal pores. rRNA sequence data allowed for molecular characterization of the species. The newly collected material of P. micans was used for epitypification with the result that the type species of Prorocentrum can now be determined unambiguously. [ABSTRACT FROM AUTHOR]

Tertiary endosymbiosis is proven through dinophytes, some of which (i.e. Kryptoperidiniaceae) have engulfed diatom algae containing a secondary plastid. Chloroplasts are usually inherited together permanently with the host cell, leading to co-phylogeny. We compiled a diatom sequence data matrix of two nuclear and two chloroplast loci. Almost all endosymbionts of Kryptoperidiniaceae found their closest relatives in free-living diatoms and not in other harboured algae, rejecting co-phylogeny and indicating that resident diatoms were taken up by dinophytes multiple times independently. Almost intact ultrastructure and insignificant genome reduction are supportive for young, if not recent events of diatom capture. With their selective specificity on the one hand and extraordinary degree of endosymbiotic flexibility on the other hand, dinophytes hosting diatoms share more traits with lichens or facultatively phototrophic ciliates than with green algae and land plants. Time estimates indicate the dinophyte lineages as consistently older than the hosted diatom lineages, thus also favouring a repeated uptake of endosymbionts. The complex ecological role of dinophytes employing a variety of organismic interactions may explain their high potential and plasticity in acquiring a great diversity of plastids. [ABSTRACT FROM AUTHOR]

Peridinialean dinophytes include a unique evolutionary group of algae harboring a diatom as an endosymbiont (Kryptoperidiniaceae), whose phylogenetic origin and internal relationships are not fully resolved at present. Several interpretations of the thecal plate pattern present in Durinskia oculata currently compete and lead to considerable taxonomic confusion. Moreover, it is unclear at present whether the species is restricted to freshwater habitats, or occurs in the marine environment as well. We collected material at the type locality of D. oculata in the Czech Republic and established monoclonal strains. Dinophyte cells were studied using light and electron microscopy, and we also determined DNA sequences of several rRNA regions (including the Internal Transcribed Spacers) for molecular characterization and phylogenetics. The morphology of strain GeoM∗662 indicated a plate formula of Po, X, 4′, 2a, 6″, 5c, 5s, 5‴, 2 ⁗ , which was sustained also in form of a microscopic slide serving as an epitype. In the molecular DNA tree based on a matrix composed of concatenated rRNA sequences, strain GeoM∗662 showed a close relationship to other species of Durinskia , and the freshwater species clearly differs from the marine members. Two independent colonization events from the marine into the freshwater environment can be inferred within the Kryptoperidiniaceae. We provide a summarizing cladogram of dinophytes harboring a diatom as endosymbiont with evolutionary novelties indicated as well as a morphological key to the 6 species of Durinskia that are currently accepted. [ABSTRACT FROM AUTHOR]

One of the most common marine dinophytes is a species known as Heterocapsa triquetra. When Stein introduced the taxon Heterocapsa, he formally based the type species H. triquetra on the basionym Glenodinium triquetrum. The latter was described by Ehrenberg and is most likely a species of Kryptoperidinium. In addition to that currently unresolved nomenclatural situation, the thecal plate composition of H. triquetra sensu Stein (1883) was controversial in the past. To clarify the debate, we collected material and established the strain UTKG7 from the Baltic Sea off Kiel (Germany, the same locality as Stein had studied), which was investigated using light and electron microscopy, and whose systematic position was inferred using molecular phylogenetics. The small motile cells (18-26 μm in length) had a biconical through fusiform shape and typically were characterized by a short asymmetrically shaped, horn-like protuberance at the antapex. A large spherical nucleus was located in the episome, whereas a single pyrenoid laid in the lower cingular plane. The predominant plate pattern was identified as apical pore complex (Po, cp?, X), 4′, 2a, 6′′, 6c, 5s, 5′′′, 2′′′′. The triradiate body scales were 254-306 nm in diameter, had 6 ridges radiating from a central spine, 9 peripheral and 3 radiating spines, and 12 peripheral bars as well as a central depression in the basal plate. Our work provides a clarification of morphological characters and a new, validly published name for this important but yet formally undescribed species of Heterocapsa: H. steinii sp. nov. [ABSTRACT FROM AUTHOR]

Detailed anatomical studies of flowers and fruits may render traits of phylogenetic importance, but are still rare in the Boraginales. An Old World clade of Cordia comprises many dioecious species, but the floral anatomy is largely unexplored and, hence, the structural basis for sex separation. Fresh material of buds, functionally unisexual flowers and fruits were studied using a stack shot camera. Fixed such material of Cordia crenata, C. cf. grandicalyx and C. sinensis was sectioned using a microtome and stained with safranin red and astra blue, and the gynoecial surface was studied using SEM. The stamens of the female flowers are largely intact, but do not produce pollen, whereas the gynoecium of the male flowers is highly reduced though develops ovules lacking an embryo sac. The morphologically rather unreduced stamens of the female flower may have undergone a shift of function from producing pollen towards attracting pollinators by optical signals. The outer parenchyma of the gynoecium is strongly stained and after fertilisation, one through three ovules are maturing towards seeds. The presence of more than a single seed enclosed in the undivided endocarp is rare in Cordiaceae. [ABSTRACT FROM AUTHOR]

Aim To examine the historical biogeography of the Boraginales using molecular dating and ancestral area reconstruction. Location World-wide. Methods We constructed data sets that included all major clades of Boraginales and all orders of asterids using previously published sequences of four plastid markers ( trnL -trnF, rps16, ndhF, rbcL). We estimated divergence times using a Bayesian uncorrelated, lognormal relaxed clock approach with four different fossil calibration schemes. Ancestral areas were reconstructed using maximum likelihood methods (Dispersal-Extinction-Cladogenesis). Results Boraginales originated during the Early to Late Cretaceous and started its diversification in the Late Cretaceous. The inferred ancestral area of Boraginales includes the Americas and Africa. The two major clades of Boraginales diversified during the Early Paleogene from African and American ancestors respectively. Early branching families in both clades (Codonaceae and Wellstediaceae in one clade and Hydrophyllacee and Namaceae in the other) may have remained restricted to their areas of origin. The other families started diversifying in several regions of the world during the Eocene (Boraginaceae s.str., Heliotropiaceae, Ehretiaceae) or later (Cordiaceae). Main conclusions Molecular dating and ancestral area reconstruction may be broadly consistent with the idea of a vicariant origin of the two major clades of Boraginales after the break-up of West Gondwana, followed by several independent trans-oceanic dispersal events into most areas of the world. However, uncertainty in both divergence times and ancestral area reconstruction do not rule out the possibility of an origin involving long-distance dispersal. [ABSTRACT FROM AUTHOR]

Character evolution in calcareous dinophytes and their relatives is poorly understood at present, particularly regarding the transformations of the epitheca. The precise taxonomic identity of Chimonodinium lomnickii var. (≡ Peridinium) wierzejskii is unclear, but two different arrangements of the epithecal plate pattern have been reported. We studied dinophyte material collected across Central Europe, including the type localities of Peridinium wierzejskii (Polish Tatra) and Peridinium lomnickii var. punctulatum (Berlin), and investigated the morphology of eight monoclonal strains in detail. We further obtained rRNA sequences of the strains, including 27 new GenBank entries, for a molecular phylogenetic study using a representative taxon sample of the Thoracosphaeroideae. Five ITS ribotypes could be distinguished in Chimonodinium, but neither the distribution nor morphological differentiation seems to correlate with these ribotypes. An evolutionary transformation of the epitheca is inferred from the phylogenetic tree, with the predominant plate pattern found in C. lomnickii var. wierzejskii exemplifying the derived character state. However, the rare epithecal plate pattern of C. lomnickii var. wierzejskii represents the ancestral character state today found in, for example, Peridinium and Scrippsiella. This is an indication of an atavism, of which only very few cases are known from the microbial domain. The name Peridinium wierzejskii is taxonomically clarified by epitypification. HIGHLIGHTS • Rare documentation of atavism in the microbial domain• Deep morphology of strain established from type locality• Molecular phylogenetics inferred from concatenated rRNA sequence data [ABSTRACT FROM AUTHOR]

Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provide valuable information on evolutionary processes such as chloroplast capture following hybridization, incomplete lineage sorting, and horizontal gene transfer. Statistical tools that to date have been used in cophylogenetic studies only also have the potential to test for the degree of topological congruence between organellar and nuclear data sets and reliably detect outlier associations. Two distance-based methods, namely ParaFit and Procrustean Approach to Cophylogeny (PACo), were used in conjunction to detect those outliers contributing to conflicting phylogenies independently derived from chloroplast and nuclear sequence data. We explored their efficiency of retrieving outlier associations, and the impact of input data (unit branch length and additive trees) between data sets, by using several simulation approaches. To test their performance using real data sets, we additionally inferred the phylogenetic relationships within Neotropical Catasetinae (Epidendroideae,Orchidaceae), which is a suitable group to investigate phylogenetic incongruence because of hybridization processes between some of its constituent species. A comparison between trees derived from chloroplast and nuclear sequence data reflected strong, well-supported incongruence within Catasetum, Cycnoches, and Mormodes. As a result, outliers among chloroplast and nuclear data sets, and in experimental simulations, were successfully detected by PACo when using patristic distance matrices obtained from phylograms, but not from unit branch length trees. The performance of ParaFit was overall inferior compared to PACo, using either phylograms or unit branch lengths as input data. Because workflows for applying cophylogenetic analyses are not standardized yet, we provide a pipeline for executing PACo and ParaFit as well as displaying outlier associations in plots and trees by using the software R. The pipeline renders a method to identify outliers with high reliability and to assess the combinability of the independently derived data sets by means of statistical analyses. [ABSTRACT FROM AUTHOR]

Dioecious and thorny Rochefortia Sw. is a poorly known though distinct element of the Ehretiaceae comprising woody plants restricted to the Caribbean and the adjacent American mainland. The approximately ten species display a great morphological variability and overlapping taxonomic boundaries, which makes it difficult to differentiate them (particularly in the Caribbean region). We investigated the phylogenetic relationships of Rochefortia using DNA sequence data from one nuclear locus (Internal Transcribed Spacer) and three chloroplast DNA loci ( rps16, trnL- trnF, trnS- trnG). The monophyly of Rochefortia was confirmed, with a sister group relationship between an American mainland clade and a Caribbean clade. The latter segregates into three, morphologically rather variable lineages, distributed either in the Lesser Antilles or in the eastern Greater Antilles or in the western Greater Antilles. Thus, geographic occurrence rather than morphology is indicative of taxonomic delimitation in Rochefortia. [ABSTRACT FROM AUTHOR]

TheScrippsiella trochoideaspecies complex (Thoracosphaeraceae, Peridiniales) consists of a cryptic diversity and multiple species, for which established scientific names are not available at present. Previously, the nameScrippsiella trochoideahas been taxonomically clarified, leaving a reliable determination of morphologically similar, but only distantly related species impossible. We isolated and cultivatedScrippsiella erinaceuscomb. nov. (strains GeoM*533 and GeoM*534) from material collected near the type locality off Rovinj, Republic of Croatia (Adriatic Sea). We barcoded the species of the Thoracosphaeraceae using rRNA sequences (including 22 new sequences) and investigated the morphology of the strains using light and electron microscopy. TheScrippsiella trochoideaspecies complex was composed of three primary clades, and the Adriatic strains were reliably assigned to one of them being distinct from the trueScrippsiella trochoidea. We designate an epitype for the basionymRhabdosphaera erinaceusprepared from the strain GeoM*534. The unambiguous links between a scientific species name, its protologue, genetic characterization and spatial distribution have particular importance for character-poor, unicellular organisms such as the Dinophyceae. [ABSTRACT FROM PUBLISHER]

Multiple family-level subdivisions of Boraginales have been proposed in the past. The relationships of several constituent genera have been enigmatic, including Codon (Codonaceae), Hoplestigma (Hoplestigmataceae), Pholisma (Lennoaceae), Vahlia (Vahliaceae), and Wellstedia (Wellstediaceae), all of which are included in the present study. We present a molecular analysis with four chloroplast loci, including 89 ingroup taxa and a broad outgroup sampling in the asterids. The genus Vahlia is excluded from Boraginales and appears to represent an early branching lineage of Lamiales. The study provides a well supported topology for the relationships within Boraginales, including all of the genera with previously unclear relationships. Within Boraginales, two major clades are recognized, with "herbaceaous" Boraginales I resolved as [Codonaceae,[Wellstediaceae,[Boraginaceae]]] and "woody" Boraginales II resolved as [Hydrophyllaceae I,[Hydrophyllaceae II,[Heliotropiaceae,[Cordiaceae, [Ehretiaceae,Lennoaceae]]]]. A close relationship between Ehretiaceae and Lennoaceae is well supported, but the exact placement of Lennoaceae remains unresolved. The Cordiaceae lineage includes the monotypic genus Coldenia and the aberrant western and central African genus Hoplestigma. Woody Boraginales II are retrieved in two highly supported clades. Hydrophyllaceae are retrieved in two separate clades, but with poor support. There appear to be clear morphological progressions in vegetative, floral, and fruit morphology in both major Boraginales lineages. Thus capsular fruits are found in the first branching lineages of both clades, whereas reduced seed numbers in indehiscent fruits predominate in the more derived phylogenetic positions. Based on these results, we advocate the recognition of eight morphologically well defined clades in the order, namely Boraginaceae s.str., Codonaceae, Cordiaceae (incl. Coldenia and Hoplestigmataceae), Ehretiaceae (incl. Lennoaceae), Heliotropiaceae, Hydrophyllaceae I and Hydrophyllaceae II, and Wellstediaceae. [ABSTRACT FROM AUTHOR]

Contemporary delimitation of species and populations in the microbial domain relies on an integrative approach combining molecular and morphological techniques. In case of the dinophyte Peridinium volzii, a considerable number of infraspecific taxonomic entities have been reported, but it is unclear at present whether the corresponding traits are stable within reproductively isolated units or refer to intraspecific variability. We established 26 monoclonal strains from Central Europe with a morphology that is consistent for P. volzii and characterised them by sequences gained from the rRNA operon. Ten of such strains, representative for the entire diversity observed, were investigated in detail morphologically using light and electron microscopy. In the molecular tree, P. volzii was monophyletic, sister group of Peridinium willei, and three ITS ribotypes could be distinguished. Some traits corresponding to previously described varieties and forms were found in individual cells across the strains under investigation, but not as stable characters correlating to certain ribotypes. We also observed new morphological variability (e.g., unusual shape of plate 4″). Cell size and displacement of the cingulum were significantly different between certain ribotypes but in turn, such diagnostic traits are impossible to assign to already described taxa due to their ambiguity. Based on the small first apical plate as diagnostic trait and putative apomorphy, P. volzii is a characteristic species but the present data given, we are reserved to accept more than a single reproductive unit. Thus, more research is necessary, including a focus on species delimitation to putative close relatives such as Peridinium maeandricum. [ABSTRACT FROM AUTHOR]

Abstract: All amniotes are probably infected by specific papillomaviruses (PVs), but knowledge about PV diversity remains sparse. An insufficient taxon sampling, and a focus on humans as hosts, may perturb phylogenetic analyses leading to wrong conclusions about PV evolution. We performed a systematic approach to explore the diversity of PVs combining rolling circle amplification with the use of “universal” primers to search for the presence of novel PV sequences in animal samples. We communicate 12 sequences putatively corresponding to novel PVs gained from 10 host species in eight mammal families: Bovidae, Canidae, Cervidae, Equidae, Hominidae, Phocoenidae, Procyonidae and Pteropodidae. The phylogenetic position of the new sequences was inferred with an evolutionary placement algorithm under a Maximum Likelihood framework using a pre-computed, well-resolved tree constructed with the E1–E2–L1 gene sequences as a backbone. The new sequences were phylogenetically diverse and could be respectively placed with confidence within all four PV crown groups. The prevailing presence of sequences from the crown groups Alpha+Omikron-PVs and Beta+Xi-PVs may correspond to an increased viral diversity in these taxa, or rather reflect a combination of anthropocentric bias and preferential amplification from commonly used “universal” primers. Our results combined with literature data support the view that the number and diversity of animal PVs is overwhelmingly large. [Copyright &y& Elsevier]