Morphological evolution of silica scales in the freshwater genus Synura (Stramenopiles)

A high degree of morphological variability is expressed between the ornately sculptured siliceous scales formed by species in the chrysophycean genus, Synura. In this study, we aimed to uncover the general principles and trends underlying the evolution of scale morphology in this genus. We assessed the relationships among thirty extant Synura species using a robust molecular analysis that included six genes, coupled with morphological characterization of the species‐specific scales. The analysis was further enriched with addition of morphological information from fossil specimens and by including the unique modern species, Synura punctulosa. We inferred the phylogenetic position of the morphologically unique S. punctulosa, to be an ancient Synura lineage related to S. splendida in the section Curtispinae. Some morphological traits, including development of a keel or a labyrinth ribbing pattern on the scale, appeared once in evolution, whereas other structures, such as a hexagonal meshwork pattern, originated independently several times over geologic time. We further uncovered numerous construction principles governing scale morphology and evolution, as follows: (i) scale roundness and pore diameter decreased during evolution; (ii) elongated scales became strengthened by a higher number of struts or ribs; (iii) as a consequence of scale biogenesis, scales with spines possessed smaller basal holes than scales with a keel and; and (iv) the keel area was proportional to scale area, indicating its potential value in strengthening the scale against breakage.     

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.     

Comparing Morphological and Molecular Estimates of Species Diversity in the Freshwater Genus Synura (Stramenopiles): A Model for Understanding Diversity of Eukaryotic Microorganisms

We performed a comparison of molecular and morphological diversity in a freshwater colonial genus Synura (Chrysophyceae, Stramenopiles), using the island of Newfoundland (Canada) as a case study. We examined the morphological species diversity in collections from 79 localities, and compared these findings to diversity based on molecular characters for 150 strains isolated from the same sites. Of 27 species or species-level lineages identified, only one third was recorded by both molecular and morphological techniques, showing both approaches are complementary in estimating species diversity within this genus. Eight taxa, each representing young evolutionary lineages, were recovered only by sequencing of isolated colonies, whereas ten species were recovered only microscopically. Our complex investigation, involving both morphological and molecular examinations, indicates that our knowledge of Synura diversity is still poor, limited only to a few well-studied areas. We revealed considerable cryptic diversity within the core S. petersenii and S. leptorrhabda lineages. We further resolved the phylogenetic position of two previously described taxa, S. kristiansenii and S. petersenii f. praefracta, propose species-level status for S. petersenii f. praefracta, and describe three new species, S. vinlandica, S. fluviatilis, and S. cornuta. Our findings add to the growing body of literature detailing distribution patterns observed in the genus, ranging from cosmopolitan species, to highly restricted taxa, to species such as S. hibernica found along coastal regions on multiple continents. Finally, our study illustrates the usefulness of combining detailed morphological information with gene sequence data to examine species diversity within chrysophyte algae.     

Molecular phylogeny of Punctaria mageshimensis reveals evidence for its transfer to Spatoglossum as S. mageshimense (Dictyotales,Phaeophyceae)

Taxonomy of the little‐studied brown algal species Punctaria mageshimensis (Ectocarpales s.l.) was reexamined by molecular phylogeny and morphology. In the genetic analyses of newly collected specimens using plastid rbcL and psaA gene sequences, the specimens morphologically referable to P. mageshimensis were phylogenetically distant from Ectocarpales s.l. and were included in the clade of Spatoglossum (Dictyotales). Morphological reexamination of the type specimen and newly collected specimens confirmed its systematic position in Dictyotales: Branched thallus; cushion‐shaped rhizoidal holdfast occasionally forming secondary holdfast at the bottom of the thallus; many discoidal plastids without pyrenoid per cell; tetrasporangium‐like reproductive structures with dark, homogeneous cell content; occurrence of hair tufts. Genetically P. mageshimensis was most related to a reported sequence of Spatoglossum asperum, but P. mageshimensis was considerably different from S. asperum as well as other known Spatoglossum species in the deep habitat and in having scarcely‐branched lanceolate and considerably thickened thallus. In conclusion, we propose the transfer of P. mageshimensis to Spatoglossum as S. mageshimense comb. nov.     

First reports of Grania (Clitellata: Enchytraeidae) from Africa and South America: molecular phylogeny and descriptions of nine new species

In this article, our knowledge of the geographic distribution of Grania species is expanded by describing seven new species, G rania bekkouchei sp. nov. , G rania brasiliensis sp. nov. , G rania capensis sp. nov. , G rania chilensis sp. nov. , G rania cryptica sp. nov. , G rania hinojosai sp. nov. , and G rania simonae sp. nov. , from poorly investigated regions of the Southern Hemisphere, plus two new species, G rania carolinensis sp. nov. and G rania unitheca sp. nov. , from off the east coast of the USA. An immature achaetous specimen that we call Grania cf. levis was also included. The newly generated data were combined with a previously published data set in order to update the hypothesis of phylogenetic relationships among Grania species. All new species except G . cryptica sp. nov. are supported by both morphological and molecular data. In addition, we find that G . chilensis sp. nov. is structured in at least four distinct populations along the Chilean coast. The species described from South Africa form a monophyletic clade where two are morphologically indistinguishable but diverging in both mitochondrial and nuclear ribosomal genes, and thus we describe them as different species, G . bekkouchei sp. nov. and G . cryptica sp. nov. Among the North Carolinian species, G . unitheca sp. nov. is indicated as a close relative of Grania monospermatheca Erséus & Lasserre, 1976, and G . carolinensis sp. nov. is indicated as a close relative of G. cf. levis. The updated phylogeny is strongly concordant with geographical species distributions, thus supporting a low level of dispersal within this genus, as has previously been hypothesized. © 2015 The Linnean Society of London     

Molecular phylogeny of Chinese Rubia (Rubiaceae: Rubieae) inferred from nuclear and plastid DNA sequences

Rubia L. is the type genus of the coffee family Rubiaceae and the third largest genus in the tribe Rubieae, comprising ca. 80 species restricted to the Old World. China is an important diversity center for Rubia, where approximately half of its species occur. However, its internal phylogenetic relationships are still poorly understood. The objective of the present study is to contribute to the phylogenetic relationships within Rubia, using the nuclear internal transcribed spacer and six plastid markers and focusing on species from China. Twenty-seven species of Rubia were sampled to infer their phylogeny using Maximum parsimony, Maximum likelihood, and Bayesian analyses. The monophyly of Rubia is supported, provided that R. rezniczenkoana Litv. is excluded from Rubia and transferred to Galium as a new combination: G. rezniczenkoanum (Litv.) L. E Yang & Z. L. Nie. Within Rubia, two clades are clearly supported. They correspond to the traditional sect. Rubias.l. (A) and sect. Oligoneura Pojark. (B), and are morphologically mainly separable by their pinnate (A) versus palmate (B) leaf venation. Plesiomorphic features are the pinnate leaf veining in sect. Rubia s.l. and the occurrence of some species with opposite leaves and true stipules in sect. Oligoneura. In sect. Oligoneura one can assume an evolution from species with opposite leaves and true stipules (as in the R. siamensis Craib group) to those with whorls of two leaves and two leaf-like stipules (as in ser. Chinenses and the R. mandersii Collett & Hemsl. group) and finally with whorls of 6 or even more elements (as in ser. Cordifoliae). The correlation between clades recognized by DNA analyses and available differential morphological features is partly only loose, particularly in the group of R. cordifolia with 2×, 4×, and 6× cytotypes. This may be due to rapid evolutionary divergence and/or hybridization and allopolyploidy.     

Five Cyanophora (Cyanophorales,Glaucophyta) species delineated based on morphological and molecular data

Cyanophora is an important glaucophyte genus of unicellular biflagellates that may have retained ancestral features of photosynthetic eukaryotes. The nuclear genome of Cyanophora was recently sequenced, but taxonomic studies of more than two strains are lacking for this genus. Furthermore, no study has used molecular methods to taxonomically delineate Cyanophora species. Here, we delimited the species of Cyanophora using light and electron microscopy, combined with molecular data from several globally distributed strains, including one newly established. Using a light microscope, we identified two distinct morphological groups: one with ovoid to ellipsoidal vegetative cells and another with dorsoventrally flattened or broad, bean‐shaped vegetative cells containing duplicated plastids. Our light and scanning electron microscopy clearly distinguished three species with ovoid to ellipsoidal cells (C. paradoxa Korshikov, C. cuspidata Tos.Takah. & Nozaki sp. nov., and C. kugrensii Tos.Takah. & Nozaki sp. nov.) and two species with broad, bean‐shaped cells (C. biloba Kugrens, B.L.Clay, C.J.Mey. & R.E.Lee and C. sudae Tos.Takah. & Nozaki sp. nov.) based on differences in cell shape and surface ornamentations of the vegetative cells under the field‐emission scanning electron microscope. Molecular phylogenetic analyses of P700 chl a apoprotein A2 (psaB) genes and internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (rDNA), as well as a comparison of secondary structures of nuclear rDNA ITS‐2 and genetic distances of psaB genes, supported the delineation of five morphological species of Cyanophora.     

Molecular phylogeny of interstitial Polycopidae ostracods (Crustacea) and descriptions of a new genus and four new species

Family Polycopidae is one of the more abundant and diverse taxa occurring in marine interstitial environments. Most of the interstitial polycopids are so far known from Japan and belong to the genus Parapolycope Klie, 1936. In this paper we describe another four new species from Japan. A new genus, K liecope gen. nov. is erected to include one new species K liecope mihoensis sp. nov. and one new combination Kliecope oligohalina (Tanaka & Tsukagoshi, 2010) comb. nov. Although the morphology of K liecope is similar to Parapolycope, the new genus has the following diagnostic characters: absence of an inward bulge on the antennular second podomere, presence of two setae bearing a sucker on the antennular third podomere, and absence of a dorsal seta on the basis of mandibula. Another three Parapolycope, P arapolycope setouchiensis sp. nov. , P arapolycope subtidalis sp. nov. , and P arapolycope miurensis sp. nov. are described as well. To test the phylogenetic relationship between the new genus and Parapolycope, we performed phylogenetic analyses based on the 14 18S rDNA sequences of interstitial Polycopidae species, 12 of which were newly obtained from our material. The 18S gene proved to be suitable for phylogenetic analyses in polycopids with high intraspecific or intrageneric resolution. Here we present trees obtained with maximum likelihood, maximum parsimony, and neighbour‐joining methods, and they support the divergence between Kliecope and Parapolycope with high bootstrap values. © 2014 The Linnean Society of London     

Halosarpheia unicellularis sp. nov. (Halosphaeriales, Ascomycota) based on morphological and molecular evidence

Halosarpheia unicellularis sp. nov. is described from decayed attached wood ofAvicennia marina collected from two mangrove sites in the Red Sea, Egypt. The ascomycete is compared with other marine taxa having ascospores with polar unfurling appendages. It is also compared with other marine genera with oval, round or ellipsoid hyaline, unicellular ascospores, but for which appendages have not been reported. Molecular data confirms the assignment of the fungus toHalosarpheia which forms a clade with the type speciesHalosarpheia fibrosa.     

Evolutionary history of two allopatric Terricola species (Arvicolinae, Rodentia) from molecular, morphological, and palaeontological data

To investigate the phylogenetic and phylogeographical relationships of arvicolines, we use several Western European ground voles. More particularly, our study is focused on Microtus ( Terricola ) savii and M. ( T. ) pyrenaicus . These two allopatric species are usually considered as having originated from the same ancestor, possibly M . ( T. ) mariaclaudiae . We propose molecular and morphological approaches: nucleotidic data from the mitochondrial cytochrome b and 12S rRNA genes and global morphological analyses from the first lower molar. Four other Terricola species ( multiplex , lusitanicus , duodecimcostatus , subterraneus ) were added to the data set for both analyses, and two other vole species ( Clethrionomys glareolus and Chionomys nivalis ) as outgroup to the molecular analysis, and five fossil populations to the morphological one. Palaeontological data are also widely taken into account. Both molecular and morphological analyses indicate that intra- Terricola relationships reflect the present-day geographical distribution of our data set species. Our results show that M. ( T. ) savii and M. ( T. ) pyrenaicus are from separate speciation events leading to two different biogeographical groups, respectively the Alpine–Italian group and the French–Iberian group, the latter being much more homogeneous. These speciation events could be related to Quaternary climatic changes, which induced southward migration, leading first to M. ( T. ) savii and second to M. ( T. ) pyrenaicus . The classical hypothesis of a geographical speciation for these two taxa from M. ( T. ) mariaclaudiae is invalid. However, the morphological data suggest a potential phylogenetic relationship between M. ( T. ) mariaclaudiae (ancestor) and M. ( T. ) pyrenaicus (descendant).  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 309–323.     

Scale evolution in Paraphysomonadida (Chrysophyceae): Sequence phylogeny and revised taxonomy of Paraphysomonas,new genus Clathromonas,and 25 new species

Heterotrophic chrysomonads of the genus Paraphysomonas are ubiquitous phagotrophs with diverse silica scale morphology. Over 50 named species have been described by electron microscopy from uncultured environmental samples. Sequence data exist for very few, but the literature reveals misidentification or lumping of most previously sequenced. For critically integrating scale and sequence data, 59 clonal cultures were studied light microscopically, by sequencing 18S ribosomal DNA, and recording scale morphology by transmission electron microscopy. We found strong congruence between variations in scale morphology and rDNA sequences, and unexpectedly deep genetic diversity. We now restrict Paraphysomonas to species with nail-like spine scales, establishing 23 new species and eight subspecies (Paraphysomonadidae). Species having base-plates with dense margins form three distinct subclades; those with a simple margin only two. We move 29 former Paraphysomonas species with basket scales into a new genus, Clathromonas, and describe two new species. Clathromonas belongs to a very distinct rDNA clade (Clathromonadidae fam. n.), possibly distantly sister to Paraphysomonas. Molecular and morphological data are mutually reinforcing; both are needed for evaluating paraphysomonad diversity and confirm excessive past lumping. Former Paraphysomonas species with neither nail-like nor basket scales are here excluded from Paraphysomonas and will be assigned to new genera elsewhere.     

Molecular phylogeny and morphological evolution of the Acantharia (Radiolaria)

Acantharia are ubiquitous and abundant rhizarian protists in the world ocean. The skeleton made of strontium sulphate and the fact that certain harbour microalgal endosymbionts make them key planktonic players for the ecology of marine ecosystems. Based on morphological criteria, the current taxonomy of Acantharia was established by W.T. Schewiakoff in 1926, since when no major revision has been undertaken. Here, we established the first comprehensive molecular phylogeny from single morphologically-identified acantharian cells, isolated from various oceans. Our phylogenetic analyses based on 78 18S rDNA and 107 partial 28S rDNA revealed the existence of 6 main clades, sub-divided into 13 sub-clades. The polyphyletic nature of acantharian families and genera demonstrates the need for revision of the current taxonomy. This molecular phylogeny, which highlights the taxonomic relevance of specific morphological criteria, such as the presence of a shell and the organisation of the central junction, provides a robust phylogenetic framework for future taxonomic emendation. Finally, mapping all the existing environmental sequences available to date from different marine ecosystems onto our reference phylogeny unveiled another 3 clades and improved the understanding of the biogeography and ecology of Acantharia.     

The pitfalls of molecular phylogeny based on four species,as illustrated by the Cetacea/Artiodactyla relationships

We study the reliability of phylogeny based on four taxa, when the internal, ancestral, branch is short. Such a quartet approach has been broadly used for inferring phylogenetic patterns. The question of branching pattern between the suborders Ruminantia and Suiformes (order Artiodactyla) and the order Cetacea is chosen as an example. All the combinations of four taxa were generated by taking on and only one species per group under study (three ingroups and one outgroup). Using real sequences, the analysis of these combinations demonstrates that the quartet approach is seriously misleading. Using both maximum parsimony and distance methods, it is possible to find a quartet of species which provided a high bootstrap proportion for each of the three possible unrooted trees. With the same set of sequences, we used all the available species simultaneously to construct a molecular phylogeny. This approach proved much more reliable than the quartet approach. When the number of informative sites is rather low, the branching patterns are not supported through bootstrap analysis, preventing us from false inference due to the lack of information. The reliable resolution of the phylogenetic relationships among Ruminantia, Suiformes, and Cetacea will therefore require a large number of nucleotides, such as the complete mitochondrial genomes of at least 30 species.     

Systematics and phylogeny of the tribe Paragini (Diptera: Syrphidae) based on molecular and morphological characters

We studied the phylogeny and systematics of the tribe Paragini (Diptera: Syrphidae) using morphological and molecular data. The paper presents separate parsimony analyses of both adult morphological characters and partial DNA sequence data from mitochondrial cytochrome c oxidase I and nuclear ribosomal 28S rRNA gene, as well as a combined analysis of all the data. The data set of morphological characters included some features of the male terminalia (i.e. shape of the ejaculatory apodeme; relative position of elements of the aedeagal complex; shape of surstylar apodeme; shape of the aedeagal apodeme) not previously used in the systematics of the Paragini. The trees obtained from separate parsimony analyses of molecular and morphological data produced almost identical topologies. Four lineages are supported by the combined data set, and we establish two new subgenera, i.e. Serratoparagus Vujić et Radenković subgen. nov., and Afroparagus Vujić et Radenković subgen. nov., and redefine Pandasyopthalmus Stuckenberg, 1954 stat. rev. and Paragus Latreille, 1804, stat. rev. The monophyly of the Pandasyopthalmus clade, including the species fitting neither of the current species groups ( jozanus -group) of Paragini, is established. Diagnoses of all known species groups are presented, including a new arrangement of almost all valid species of Paragini.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 507–536.     

Reconsideration of anopheline mosquito phylogeny (Diptera: Culicidae: Anophelinae) based on morphological data

The phylogeny of anopheline mosquitoes (Culicidae: Anophelinae) is re‐examined using morphological data derived from adults, fourth‐instar larvae and pupae. Based on the data set of Sallum et al. (2000), we add some previously missing data and simplify and recode characters to eliminate ambiguities and more accurately reflect homologies, with special emphasis on characters of the male genitalia that provide the main criteria for the subgeneric classification of genus Anopheles. The principal aim of the study is to assess objectively the phylogenetic relationships and classification of two taxa not included by Sallum et al. (2000): Anopheles corethroides, a representative of the Australasian Stigmaticus Group, and An. kyondawensis, an unusual Oriental species whose adult and pupal stages were only recently discovered. The revised data set consists of 167 characters for 66 species representing the three traditionally recognised genera of Anophelinae, the six traditionally accepted subgenera of genus Anopheles and all informal series and most species groups of subgenera Anopheles, Cellia and Nyssorhynchus. The data are analysed using equal weighting (EW) and implied weighting (IW). Analysis under EW generates a strict consensus tree with principal lineages consistent with those reported by Sallum et al. (2000). Analysis under IW supports the monophyly of Anophelinae, the basal position of Chagasia, the monophyly of subgenera Cellia, Kerteszia and Nyssorhynchus, and the sister relationship of Kerteszia + Nyssorhynchus, but otherwise yields relationships that differ significantly in one respect or another from those obtained in all previous analyses of both morphological and molecular data. Subgenus Anopheles is arrayed as a polyphyletic lineage basal to a monophyletic clade comprising the Neotropical Kerteszia + Nyssorhynchus and the Old World Cellia in a sister‐group relationship. Bironella, Lophopodomyia and Stethomyia are firmly nested within subgenus Anopheles, which would nevertheless still be paraphyletic if these taxa were subsumed within it. Anopheles kyondawensis is well supported as the sister group of Bironella + all other Anopheles. Bironella, Stethomyia, An. corethroides and several other Anopheles clades are each strongly supported in a pectinate series of relationships, terminating in the clade comprising subgenera Cellia, Kerteszia and Nyssorhynchus. These relationships and other aspects of the phylogeny are discussed in relation to the formal and informal classification of genus Anopheles.     

Aspects of the phylogeny of Platyhelminthes based on 18S ribosomal DNA and protonephridial ultrastructure

DNA studies of 23 taxa (20 platyhelminths, 1 nemertean, Homo and Artemia) and electron-microscopic studies of the protonephridia of many platyhelminths (supported by some additional ultrastructural data) have led to the following conclusions: the Neodermata are monophyletic; Temnocephalida and Dalyelliida form one clade and are not the primitive sister group of the Neodermata; Gyrocotylidea, Amphilinidea and Eucestoda form one monophylum; Pterastericolidae and Umagillidae are dalyelliids and not the sister group of the Neodermata; and Proseriata are unlikely to be closely related with the Tricladida. A large taxon consisting of the Proseriata and some other turbellarians may represent the sister group of the Neodermata.     

Taxonomic revision of Dictyochales (Dictyochophyceae) based on morphological,ultrastructural, biochemical and molecular data

The taxonomy of the siliceous members of Dictyochales has been based exclusively on the structure of their silica skeletons. In this study, other morphological, ultrastructural, pigment and molecular characters, in addition to the silica skeletons, were used in the systematics of the siliceous members of this group. As very little is known about the ultrastructure of Dictyocha octonaria, cells of both the skeleton‐bearing and naked forms were also studied. A cladistic analysis based on morphological data and a molecular phylogeny based on nuclear coded small subunit ribosomal DNA retrieved a well‐supported monophyletic Dictyochales. D. octonaria and D. speculum were resolved together with strong support. There was no support for a clade for the three species currently placed in Dictyocha; D. fibula is clearly distinct from the other two Dictyocha taxa, D. speculum and D. octonaria. It is highly likely there are two or three undescribed species within D. octonaria/D. speculum clade and two undescribed genera within the Dictyochales, based on the positions of sequences from uncultured eukaryotes present in GenBank. These findings necessitate a taxonomic revision of the three siliceous, skeleton‐bearing species. Because D. fibula is the type species of Dictyocha, we propose that D. octonaria and D. speculum be reassigned respectively to the genus Octactis as O. octonaria Hovasse and O. speculum (Ehrenberg) F. H. Chang, J. M. Grieve & J. E. Sutherland, comb. nov.