Taxonomic clarification of the dinophyte Rhabdosphaera erinaceus Kamptner, ≡ Scrippsiella erinaceus comb. nov. (Thoracosphaeraceae,Peridiniales)

The Scrippsiella trochoidea species complex (Thoracosphaeraceae, Peridiniales) consists of a cryptic diversity and multiple species, for which established scientific names are not available at present. Previously, the name Scrippsiella trochoidea has been taxonomically clarified, leaving a reliable determination of morphologically similar, but only distantly related species impossible. We isolated and cultivated Scrippsiella erinaceus comb. 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. The Scrippsiella trochoidea species complex was composed of three primary clades, and the Adriatic strains were reliably assigned to one of them being distinct from the true Scrippsiella trochoidea. We designate an epitype for the basionym Rhabdosphaera erinaceus prepared 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.     

Delimitation of the Thoracosphaeraceae (Dinophyceae), including the calcareous dinoflagellates, based on large amounts of ribosomal RNA sequence data

The phylogenetic relationships of the Dinophyceae (Alveolata) are not sufficiently resolved at present. The Thoracosphaeraceae (Peridiniales) are the only group of the Alveolata that include members with calcareous coccoid stages; this trait is considered apomorphic. Although the coccoid stage apparently is not calcareous, Bysmatrum has been assigned to the Thoracosphaeraceae based on thecal morphology. We tested the monophyly of the Thoracosphaeraceae using large sets of ribosomal RNA sequence data of the Alveolata including the Dinophyceae. Phylogenetic analyses were performed using Maximum Likelihood and Bayesian approaches. The Thoracosphaeraceae were monophyletic, but included also a number of non-calcareous dinophytes (such as Pentapharsodinium and Pfiesteria) and even parasites (such as Duboscquodinium and Tintinnophagus). Bysmatrum had an isolated and uncertain phylogenetic position outside the Thoracosphaeraceae. The phylogenetic relationships among calcareous dinophytes appear complex, and the assumption of the single origin of the potential to produce calcareous structures is challenged. The application of concatenated ribosomal RNA sequence data may prove promising for phylogenetic reconstructions of the Dinophyceae in future.     

Morphological delineation and distribution patterns of four newly described species within the Synura petersenii species complex (Chrysophyceae,Stramenopiles)

The Synura petersenii species complex represents a common, cosmopolitan and highly diverse taxon of autotrophic freshwater flagellates. In this paper, we describe and characterize four new species (S. borealis, S. heteropora, S. hibernica and S. laticarina) that have been identified during our extensive sampling of freshwater habitats in 15 European countries. Morphometric analyses of siliceous scales led to the significant phenotypic differentiation of all four newly described species, and their separation from other related species of the S. petersenii complex. Two of these newly described species (S. hibernica and S. borealis) can be clearly distinguished by characteristic large colonies consisting of elongated, lanceolate-shaped cells. Development of strongly elongated, narrow cells in S. hibernica could be explained by the adaptation of this species to oligotrophic conditions. Though morphologically distinct, S. borealis possesses an exceptionally high degree of genetic diversity, possibly indicating recent speciation and evolutionary diversification within this taxon. Three of the four newly described species exhibit restricted biogeographic distribution. The evolutionarily related S. borealis and S. laticarina occur only in Northern Europe, and seem to be adapted to colder areas. The most remarkable distribution pattern was observed for S. hibernica, which has a geographic distribution that is restricted to western Ireland.     

Molecular data illuminate cryptic nudibranch species: the evolution of the Scyllaeidae (Nudibranchia: Dendronotina) with a revision of Notobryon

Scyllaeidae represents a small clade of dendronotoid nudibranchs. Notobryon wardi Odhner, 1936, has been reported to occur in tropical oceans from the Indo‐Pacific and eastern Pacific to temperate South Africa. The systematics of Notobryon has not been reviewed using modern systematic tools. Here, specimens of Notobryon were examined from the eastern Pacific, the Indo‐Pacific, and from temperate South Africa. Additionally, representatives of Scyllaea and Crosslandia were studied. Scyllaeidae was found to be monophyletic. Notobryon was also found to be monophyletic and is the sister group to Crosslandia plus Scyllaea. The molecular data also clearly indicate that within Notobryon, at least three distinct species are present, two of which are here described. Genetic distance data indicate that eastern Pacific and South African exemplars are 10–23% divergent from Indo‐Pacific exemplars of Notobryon wardi. Scyllaea pelagica has been regarded as a single, circumtropical species. Our molecular studies clearly indicate that the Atlantic and Indo‐Pacific populations are distinct and we resurrect Scyllaea fulva Quoy & Gaimard, 1824 for the Indo‐Pacific species. Our morphological studies clearly corroborate our molecular findings and differences in morphology distinguish closely related species. Different species clearly have distinct penial morphology. These studies clearly reinforce the view that eastern Pacific, Indo‐Pacific, and temperate biotas consist largely of distinct faunas, with only a minor degree of faunal overlap. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 311–336.     

Molecular tests of the proposed diploid hybrid originof Gilia achilleifolia (Polemoniaceae)

Gilia achilleifolia is a putative diploid hybrid species. Hybrid origin was hypothesized based on traditional biosystematicevidence (i.e., morphological, cytological, and crossability data),which may be insufficient to establish genealogical history. Here,phylogenetic analysis of sequence data from the internal transcribedspacer (ITS) regions is used to examine the relationship between theputative hybrid species and its proposed parents. Isozyme variation isassayed to test for genetic additivity in the putative hybrid taxon andmorphological data are analyzed cladistically to evaluate the charactersthat led to the original hypothesis of hybrid origin. The ITS-basedgene tree placed G. achilleifolia in two divergent clades, eachsister to one of the putative parental lineages. Little isozymeadditivity was observed and G. achilleifolia possessed sixunique alleles among 42 alleles observed. However, ITS and isozymetrees differed in their placement of the two lineages of G.achilleifolia; both lineages are closer to a third putative parentin the isozyme tree. Also, G. achilleifolia is intermediate orpolymorphic for all nine morphological characteristics differentiatingthe parental species. Sorting of ancestral polymorphisms cannot easilyaccount for expression patterns of seven of these characters. In ourview, these results fail to distinguish between alternative hypothesesof ancient hybrid origin and divergent evolution, belying the difficultyof detecting ancient hybrids.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

Testing monophyly of the freshwater fish Leporinus (Characiformes,Anostomidae) through molecular analysis

Monophyly of the genus Leporinus (Characiformes: Anostomidae) was tested by sequencing and analysing a total of 4732 bp, including two mitochondrial [cytochrome oxidase subunit 1 (CO1) and cytochrome b (Cytb)] and three nuclear [myosin heavy chain 6 cardiac muscle alpha (Myh6), recombination activating gene 1 (RAG1) and recombination activating gene 2 (RAG2)] loci for 22 species of Leporinus, or c. 25% of all described species in the genus. Phylogenetic tree analyses (maximum parsimony, maximum likelihood and Bayesian species tree) indicate Leporinus to be paraphyletic, with monophyly being rejected by both Kishino–Hasegawa and Shimodaira–Hasegawa tests. The sequenced species of Leporinus are distributed across five clades that are interleaved among other anostomid genera. Several taxonomic changes are suggested as being necessary to restore monophyly for the group. The clade containing the type species, Leporinus fasciatus, should be considered Leporinus sensu stricto and at least three new genera should be described for other species currently considered part of Leporinus.     

Systematics of the Anopheles barbirostris species complex (Diptera: Culicidae: Anophelinae) in Thailand

This study deals with five species of the Barbirostris Complex of Anopheles subgenus Anopheles that are known to occur in Thailand. Three new species of the complex, A nopheles dissidens sp. nov. , A nopheles saeungae sp. nov. , and A nopheles wejchoochotei sp. nov. , are characterized and compared with Anopheles barbirostris van der Wulp and Anopheles campestris Reid based on specimens of molecularly identified progeny broods. For practical purposes, the five species are essentially isomorphic and can only be unequivocally identified from diagnostic mitochondrial and ribosomal DNA sequences. Based on overall morphological similarity, An. campestris is considered to be a member of the Barbirostris Complex rather than a separate member of the Barbirostris Subgroup. The molecular data, mitotic karyotypes, bionomics, and distributions of the species are reviewed and discussed. It is concluded that integrated molecular epidemiological studies of the complex throughout the Oriental Region are needed to unambiguously elucidate the individual species and their relation to disease. © 2015 The Linnean Society of London     

Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae: Thorius)

The small size and apparent external morphological similarity of the minute salamanders of the genus Thorius have long hindered evolutionary studies of the group. We estimate gene and species trees within the genus using mitochondrial and nuclear DNA from nearly all named and many candidate species and find three main clades. We use this phylogenetic hypothesis to examine patterns of morphological evolution and species coexistence across central and southern Mexico and to test alternative hypotheses of lineage divergence with and without ecomorphological divergence. Sympatric species differ in body size more than expected after accounting for phylogenetic relationship, and morphological traits show no significant phylogenetic signal. Sympatric species tend to differ in a combination of body size, presence or absence of maxillary teeth, and relative limb or tail length, even when they are close relatives. Sister species of Thorius tend to occupy climatically similar environments, which suggests that divergence across climatic gradients does not drive species formation in the genus. Rather than being an example of cryptic species formation, Thorius more closely resembles an adaptive radiation, with ecomorphological divergence that is bounded by organism‐level constraints. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 622–643.     

Untangling the Spurilla neapolitana (Delle Chiaje, 1841) species complex: a review of the genus Spurilla Bergh, 1864 (Mollusca: Nudibranchia: Aeolidiidae)

Spurilla neapolitana (Delle Chiaje, 1823) was considered to be a species with a broad geographic range and substantial colour variability; however, analyses of mitochondrial and nuclear gene data revealed that it is a complex of five distinct species. Further anatomical and morphological examinations determined that coloration is one of the main diagnostic traits for all five species, although some display substantial colour pattern variation. As a result of this study, S. neapolitana is determined to be restricted to the Mediterranean and eastern Atlantic. Spurilla sargassicola Bergh, 1871 from the Caribbean is redescribed and confirmed as a valid species. The name Spurilla braziliana MacFarland, 1909 is retained for western Atlantic and Pacific populations. Two new species are described herein. S purilla onubensis sp. nov. occurs in Europe, with a range overlapping that of S. neapolitana. Finally, S purilla dupontae sp. nov. is found in the Bahamas. © 2014 The Linnean Society of London     

Taxonomic redescriptions of two ciliates, Protogastrostyla pulchra n. g., n. comb. and Hemigastrostyla enigmatica (ciliophora: spirotrichea, stichotrichia), with phylogenetic analyses based on 18S and 28S rRNA gene sequences

The morphology and infraciliature of two stichotrichid ciliates, Gastrostyla pulchra(Perejaslawzewa 1886) Kahl, 1932 and Hemigastrostyla enigmatica(Dragesco and Dragesco-Kernéis 1986) Song & Wilbert, 1997, collected from marine and brackish sediments, were investigated by using living observations and protargol impregnations. Both 18S and 28S rRNA genes of these two species were sequenced. The 18S rDNA show high similarities (98.4%-99.7%) among populations of each species. There is about 94% similarity in 18S rDNA genes between G. pulchra and Gastrostyla steinii, the type species of the genus, which has been confirmed to be an oxytrichid by previous studies. In the phylogenetic trees of 18S, 28S, and combined 18S and 28S rDNA, both G. pulchra and H. enigmatica are consistently placed outside the well-established oxytrichid clade. Based on our analyses and previous ontogenetic data, we conclude that these two species may represent some lower groups in the subclass Stichotrichia, and that G. pulchra should represent a new genus, Protogastrostyla n. g. This new genus, which is morphologically similar to Gastrostyla, differs in its morphogenesis: the apical part of the old AZM is retained combining with the newly built membranelles that develop from the proter's oral primordium; the primary primordia of the dorsal kinety; and marginal primordia commence de novo without a definite contribution from the old structure.     

Secondary Structure of the ITS1 Transcript and its Application in a Reconstruction of the Phylogeny of Boraginales

Abstract: In this study, we present the possibilities for calculating systematic relationships on higher taxonomical levels based exclusively on ITS1. This is demonstrated for Boraginales (Boraginaceae s.str., Cordiaceae, Ehretiaceae, Heliotropiaceae, Hydrophyllaceae and Lennoaceae). Secondary structure of the ITS1 region is more conserved than the primary structure (i.e., sequence itself) and is therefore a tool for optimizing alignments. It increases the number of structural characters. Information inferred from the secondary structure enables us to construct well-resolved phylogenetic trees at higher taxonomic levels. A general secondary structure of ITS1 for Boraginales, with four major helices, is proposed here. In each subtaxon, derivations from this structure are found. The paraphyly of Boraginaceae s.l. is evident from both a comparison of secondary structures and from bootstrap analysis. Boraginaceae s.str. are the sister group of a clade formed by Hydrophyllaceae, Cordiaceae, Ehretiaceae, Heliotropiaceae and Lennoaceae. The last four taxa constitute a monophyletic group which is the sister group of Hydrophyllaceae. Lennoaceae are closely related to Ehretiaceae, and these two taxa in turn are the sister group of Cordiaceae.     

Observations on the cytology and ultrastructure of Ochromonas tuberculatus sp. nov. (Chrysophyceae), with special reference to the discobolocysts

Ochromonas tuberculatus sp. nov. is described by a combination of light and electron microscopy from material in culture, special attention being given to the structure and ontogeny of the discobolocysts, the cross-banded flagellar root and its relationship with the Golgi body and nucleus, and an unusual type of vesicle associated with the contractile vacuole.     

Towards a new classification of the giant paraphyletic genus Cyperus (Cyperaceae): phylogenetic relationships and generic delimitation in C4 Cyperus

Maximum likelihood and Bayesian inference analyses of nuclear ribosomal DNA (ETS1f) and plastid DNA (rpl32‐trnL, trnH‐psbA) sequence data are presented for ‘C₄ Cyperus’ (Cyperaceae). The term ‘C₄ Cyperus’ encompasses all species of Cyperus s.l. that use C₄ photosynthesis linked with chlorocyperoid vegetative anatomy. Sampling comprises 107 specimens of 104 different taxa, including many of the subdivisions of C₄ Cyperus s.s. and all C₄ segregate genera (Alinula, Ascolepis, Kyllinga, Lipocarpha, Pycreus, Queenslandiella, Remirea, Sphaerocyperus and Volkiella). According to our results, C₄ Cyperus is a well‐supported monophyletic clade nested in C₃ Cyperus. Despite the lack of resolution along the backbone of the C₄ Cyperus clade and for some internal branches, several well‐supported clades can be distinguished. The first clade in C₄ Cyperus is formed by Cyperus cuspidatus and C. waterloti. Other recognizable and well‐supported clades correspond to segregate genera, i.e. Ascolepis, Lipocarpha including Volkiella, and Kyllinga. Species of C₄ Cyperus s.s. form a core grade in which the C₄ segregate genera are embedded. Pycreus, the largest segregate genus composed of c. 120 species, is not monophyletic as it includes several C₄ species of Cyperus s.s. This study establishes a phylogenetic framework for revising the classification and character evolution in Cyperus s.l. © 2013 The Linnean Society of London