MORPHOLOGICAL SEPARATION OF THE EUGLENOID GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) BASED ON LORICA DEVELOPMENT AND POSTERIOR STRIP REDUCTION1

Since the separation of the Trachelomonas Ehrenberg subgroup “Saccatae” into a new genus, Strombomonas Deflandre (1930) , there has been some question as to its validity. Deflandre's separation was based entirely on characteristics of the lorica, including the shape of the lorica, the lack of a distinctive collar, possession of a tailpiece, lack of ornamentation, and the ability of Strombomonas species to aggregate particles on the surface of the lorica. Recent molecular analyses indicated that the loricate taxa (Trachelomonas and Strombomonas) formed a single monophyletic clade; however, the phylogenetic relationship of Strombomonas to Trachelomonas remains unclear because only two Strombomonas taxa have been sequenced to date. In this study, we evaluated the monophyly of the loricate genera using two sets of morphological characters, lorica development and pellicle strip reduction. Lorica development in Strombomonas occurred from the anterior of the cell to the posterior, forming a shroud over the protoplast. In Trachelomonas, a layer of mucilage was excreted over the entire protoplast, followed by creation of the collar at the anterior end. Taxa from both genera underwent exponential strip reduction at the anterior and posterior poles. In Strombomonas only one reduction was visible in the anterior pole, whereas in most Trachelomonas species two reductions were visible. Likewise, Strombomonas species possessed two whorls of strip reduction in the posterior end compared with a single whorl of strip reduction in Trachelomonas species. These morphological characters support the separation of Trachelomonas and Strombomonas as distinct genera.     

13 Viral control of phytoplankton

Since the separation of the Trachelomonas subgroup "Saccatae" into a new genus, Strombomonas Deflandre (1930), there has been some question as to its validity. Deflandre's separation was based on morphological characteristics such as the shape of the lorica, lack of a distinctive collar, possession of a tailpiece, lack of ornamentation, and ability to aggregate particles on the lorica. Recent molecular analyses indicated that the loricate taxa were monophyletic, but few species have been sampled. The LSU rDNA from eleven Strombomonas and thirty-eight Trachelomonas species was sequenced to evaluate the monophyly of the two genera. Bayesian and maximum-likelihood analyses found one monophyletic clade for each genus. The Trachelomonas clade was weakly supported, but had five strongly supported subclades. Morphological characters, such as lorica development and pellicle strip reduction, also supported separation of the genera. Lorica development in Strombomonas occurred from the anterior of the cell to the posterior, forming a shroud over the protoplast whereas in Trachelomonas , a layer of mucilage was excreted over the entire protoplast, followed by creation of the collar at the anterior end. Taxa from both genera underwent exponential strip reduction at the anterior and posterior poles. In Strombomonas , only one reduction was visible in the anterior pole, while in most Trachelomonas species, two reductions were visible. Likewise, Strombomonas species possessed two whorls of strip reduction in their posterior end compared to a single whorl of strip reduction in Trachelomonas species. The combined morphological and molecular data support the retention of Trachelomonas and Strombomonas as separate genera.     

PHYLOGENY OF THE EUGLENOID LORICATE GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) INFERRED FROM NUCLEAR SSU AND LSU rDNA1

Previous studies using the nuclear SSU rDNA and partial LSU rDNA have demonstrated that the euglenoid loricate taxa form a monophyletic clade within the photosynthetic euglenoid lineage. It was unclear, however, whether the loricate genera Trachelomonas and Strombomonas were monophyletic. In order to determine the relationships among the loricate taxa, SSU and LSU nuclear rDNA sequences were obtained for eight Strombomonas and 25 Trachelomonas strains and combined in a multigene phylogenetic analysis. Conserved regions of the aligned data set were used to generate maximum‐likelihood (ML) and Bayesian phylogenies. Both methods recovered a strongly supported monophyletic loricate clade with Strombomonas and Trachelomonas species separated into two sister clades. Taxa in the genus Strombomonas sorted into three subclades. Within the genus Trachelomonas, five strongly supported subclades were recovered in all analyses. Key morphological features could be attributed to each of the subclades, with the major separation being that all of the spine‐bearing taxa were located in two sister subclades, while the more rounded, spineless taxa formed the remaining three subclades. The separation of genera and subclades was supported by 42 distinct molecular signatures (33 in Trachelomonas and nine in Strombomonas). The morphological and molecular data supported the retention of Trachelomonas and Strombomonas as separate loricate genera.     

PHYLOGENY OF THE EUGLENALES BASED UPON COMBINED SSU AND LSU RDNA SEQUENCE COMPARISONS AND DESCRIPTION OF DISCOPLASTIS GEN. NOV. (EUGLENOPHYTA)1

A Bayesian analysis, utilizing a combined data set developed from the small subunit (SSU) and large subunit (LSU) rDNA gene sequences, was used to resolve relationships and clarify generic boundaries among 84 strains of plastid‐containing euglenophytes representing 11 genera. The analysis produced a tree with three major clades: a Phacus and Lepocinlis clade, a Discoplastis clade, and a Euglena, Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade. The majority of the species in the genus Euglena formed a well‐supported clade, but two species formed a separate clade near the base of the tree. A new genus, Discoplastis, was erected to accommodate these taxa, thus making the genus Euglena monophyletic. The analysis also supported the monophyly of Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena, which formed two subclades sister to the Euglena clade. Colacium, Trachelomonas, and Strombomonas, all of which produce copious amounts of mucilage to form loricas or mucilaginous stalks, formed a well‐supported lineage. Our analysis supported retaining Strombomonas and Trachelomonas as separate genera. Monomorphina and Cryptoglena formed two well‐supported clades that were sister to the Colacium, Trachelomonas, and Strombomonas clade. Phacus and Lepocinclis, both of which have numerous small discoid chloroplasts without pyrenoids and lack peristaltic euglenoid movement (metaboly), formed a well‐supported monophyletic lineage that was sister to the larger Euglena through Cryptoglena containing clade. This study demonstrated that increased taxon sampling, multiple genes, and combined data sets provided increased support for internal nodes on the euglenoid phylogenetic tree and resolved relationships among the major genera in the photosynthetic euglenoid lineage.     

PHYLOGENY OF THE EUGLENALES INFERRED FROM PLASTID LSU rDNA SEQUENCES1

To gain insights into the phylogeny of the Euglenales, we analyzed the plastid LSU rDNA sequences from 101 strains of the photosynthetic euglenoids belonging to nine ingroup genera (Euglena, Trachelomonas, Strombomonas, Monomorphina, Cryptoglena, Colacium, Discoplastis, Phacus, and Lepocinclis) and two outgroup genera (Eutreptia and Eutreptiella). Bayesian and maximum‐likelihood (ML) analyses resulted in trees of similar topologies and four major clades: a Phacus and Lepocinclis clade; a Colacium clade; a Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade; and a Euglena clade. The Phacus and Lepocinclis clade was the sister group of all other euglenalian genera, followed by Discoplastis spathirhyncha (Skuja) Triemer and the Colacium clade, respectively, which was inconsistent with their placement based on nuclear rDNA genes. The Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade was sister to the Euglena clade. The loricate genera, Trachelomonas and Strombomonas, were closely related to each other, while Monomorphina and Cryptoglena also grouped together. The Euglena clade formed a monophyletic lineage comprising most species from taxa formerly allocated to the subgenera Calliglena and Euglena. However, within this genus, none of the subgenera was monophyletic.     

MULTIGENE ANALYSES OF PHOTOSYNTHETIC EUGLENOIDS AND NEW FAMILY,PHACACEAE (EUGLENALES)1

Bayesian and maximum‐likelihood (ML) analyses of the combined multigene data (nuclear SSU rDNA, and plastid SSU and LSU rDNA) were conducted to evaluate the phylogeny of photosynthetic euglenoids. The combined data set consisted of 108 strains of photosynthetic euglenoids including a colorless sister taxon. Bayesian and ML analyses recovered trees of almost identical topology. The results indicated that photosynthetic euglenoids were divided into two major clades, the Euglenaceae clade (Euglena, Euglenaria, Trachelomonas, Strombomonas, Monomorphina, Cryptoglena, Colacium) and the Phacaceae clade (Phacus, Lepocinclis, Discoplastis). The Euglenaceae clade was monophyletic with high support and subdivided into four main clades: the Colacium, the Strombomonas and Trachelomonas, the Cryptoglena and Monomorphina, and the Euglena and Euglenaria clades. The genus Colacium was positioned at the base of the Euglenaceae and was well supported as a monophyletic lineage. The loricate genera (Strombomonas and Trachelomonas) were located at the middle of the Euglenaceae clade and formed a robust monophyletic lineage. The genera Cryptoglena and Monomorphina also formed a well‐supported monophyletic clade. Euglena and the recently erected genus Euglenaria emerged as sister groups. However, Euglena proxima branched off at the base of the Euglenaceae. The Phacaceae clade was also a monophyletic group with high support values and subdivided into three clades, the Discoplastis, Phacus, and Lepocinclis clades. The genus Discoplastis branched first, and then Phacus and Lepocinclis emerged as sister groups. These genera shared a common characteristic, numerous small discoid chloroplasts without pyrenoids. These results clearly separated the Phacaceae clade from the Euglenaceae clade. Therefore, we propose to limit the family Euglenaceae to the members of the Euglena clade and erect a new family, the Phacaceae, to house the genera Phacus, Lepocinclis, and Discoplastis.     

PHYLOGENY OF EUGLENOPHYCEAE BASED ON SMALL SUBUNIT rDNA SEQUENCES: TAXONOMIC IMPLICATIONS1

Small subunit rDNA sequences of 42 taxa belonging to 10 genera were used to infer phylogenetic relationships among euglenoids. Members of the phototrophic genera Euglena, Phacus, Lepocinclis, Colacium, Trachelomonas, and Strombomonas plus the osmotrophs Astasia longa, Khawkinea quartana, and Hyalophacus ocellatus were included. Six major clades were found in most trees using multiple methods. The utility of Bayesian analyses in resolving these clades is demonstrated. The genus Phacus was polyphyletic with taxa sorting into two main clades. The two clades correlated with overall morphology and corresponded in large part to the previously defined sections, Pleur‐ aspis Pochmann and Proterophacus Pochmann. Euglena was also polyphyletic and split into two clades. In Bayesian analyses species with less plastic pellicles and small disk‐like chloroplasts diverged at the base of the tree. They grouped into a single clade which included the two Lepocinclis spp., which also are rigid and bear similar chloroplasts. The metabolic Euglena species with larger plastids bearing pyrenoids and paramylon caps arose near the top of the tree. The loricates Strombomonas and Trachelomonas formed two well‐ supported, but paraphyletic, clades. The strong support for the individual clades confirmed the value of using lorica features as taxonomic criteria. The separation of the osmotrophic species A. longa, K. quartana, and H. ocellatus into different clades suggested that the loss of the photosynthetic ability has occurred multiple times.     

Developmental studies on the loricate choanoflagellateStephanoeca diplocostata ellis

Summary Cells ofStephanoeca diplocostata comprise a colourless, flagellated, protoplast lodged in a lorica made of siliceous costae. The single anterior flagellum creates a water current from which bacteria and other food particles are filtered by the collar and ingested by linguiform pseudopodia that arise from the protoplast at the base of the collar. A waist divides the lorica into two chambers, the anterior of which contains three transverse and 17–20 longitudinal costae whereas the posterior chamber comprises two systems of spirally deflected costae and on some cells a pedicel at the hind end. Between 150–185 costal strips of similar length form the lorica. A thin investment covers the inner surface of the posterior chamber and lower part of the anterior chamber and joins with the protoplast at the level of the waist. Costal strips are produced within membrane-bounded vesicles in the peripheral cytoplasm and, although the origin of these vesicles is unknown, there is usually a close association with the Golgi apparatus. Once complete, strips are apparently released sideways through the plasmalemma into the cavity of the posterior lorica chamber. Later, bundles of strips are transferred to the top of the inner surface of the collar where they collectively form a horizontal ring. When sufficient strips to form a lorica have been accumulated at the top of the collar, cell division proceeds.     

Genetic diversity and phylogenetic position of the subclass Astomatia (Ciliophora) based on a sampling of six genera from West African oligochaetes (Glossoscolecidae, Megascolecidae), including description of the new genus Paraclausilocola n. gen

To more confidently assess phylogenetic relationships among astome ciliates, we obtained small subunit (SSU) rRNA sequences from nine species distributed in six genera and three families: Almophrya bivacuolata, Eudrilophrya complanata, Metaracoelophrya sp. 1, Metaracoelophrya sp. 2, Metaracoelophrya intermedia, Metaradiophrya sp., Njinella prolifera, Paraclausilocola constricta n. gen., n. sp., and Paraclausilocola elongata n. sp. The two new species in the proposed new clausilocolid genus Paraclausilocola n. gen. are astomes with no attachment apparatus, two files of contractile vacuoles, and an arc-like anterior suture that has differentiations of thigmotactic ciliature on the anterior ends of the left kineties of the upper surface. Phylogenetic analyses were undertaken using neighbor-joining, Bayesian inference, maximum likelihood, and maximum parsimony. The nine species of astomes formed a strongly supported clade, showing the subclass Astomatia to be monophyletic and a weakly supported sister clade to the scuticociliates. There were two strongly supported clades within the astomes. However, genera assigned to the same family were found in different clades, and genera assigned to the same order were found in both clades. Thus, astome taxa appear to be paraphyletic when morphology is used to assign species to genera.     

Kakoeca antarctica gen. et sp.n., a loricate choanoflagellate (Acanthoecidae, Choanoflagellida) from Antarctic sea ice with a unique protoplast suspensory membrane

A new genus and species of loricate choanoflagellate, Kakoeca aniarctica Buck & Marchant gen. et sp.n. grown in rough culture from an Antarctic sea ice innoculum is described. This organism has a distinctive lorica morphology consisting of more than 200 costal strips arranged in transverse and longitudinal costae that arc perpendicular to one another in the posterior portion of the lorica. The transverse costae show declination with respect to the lorica axis in the anterior part of the lorica. The cell is suspended in the lorica by a robust protoplast suspensory membrane. This membrane blocks water flow from the posterior of the lorica necessitating water entry through the side of the lorica, an area where the maximum sized apertures in the lorica are found. Terminology (lorica lining and protoplast suspensory) is suggested for the two types of lorica membranes which have been found associated with loricas.     

Developmental studies on the loricate choanoflagellateStephanoeca diplocostata Ellis

Summary Cell division inStephanoeca diplocostata follows the accumulation of a large number of costal strips in horizontal bundles at the top of the parent collar. Prior to nuclear division the flagellum is lost and the protoplast is large and rectangular. Nuclear division takes place whilst the protoplast undergoes vigorous metabolic movements and subsequent cytokinesis is achieved by equatorial constriction. The anterior of the two daughter protoplasts is the juvenile and is inverted with respect to the sister which remains attached to the parent lorica. The two protoplasts are joined by a cytoplasmic strand that consists of two threads both of which are initially attached to the daughter protoplasts at one side of the collar. Cell separation involves elongation of the strand and after each thread has broken contact with one of the daughter cells the two threads slide over each other until the juvenile is released. The juvenile takes the accumulation of supernumerary strips as it leaves the parent lorica and after release of the juvenile the strips are mobilised to form a new lorica. The collar tentacles of the parent are thought to play a significant role in the movement of strips during division and certain selected tentacles on the juvenile are associated with lorica assembly. Cell separation takes between 9–12 minutes and lorica assembly by the juvenile 2–3 minutes.     

Megachiropteran Evolution Studied with 12S rDNA and c-mos DNA Sequences

Recent studies of mitochondrial DNA sequences have indicated the requirement for substantial revisions of the morphological understanding of the phylogeny of Megachiroptera (Pteropodidae). There is disagreement between studies as to what these revisions might be. This investigation was undertaken to expand the number of studied species and to add the first data from a nuclear gene sequence. For 12S ribosomal DNA (aligned length of 405 positions), 75 Megachiroptera (50 species in 20 genera) and two outgroup species were sequenced. For the oncogene c-mos (aligned length of 488 bases), 56 Megachiroptera (42 species in 19 genera) were sequenced and three eutherians from GenBank used as outgroups.The root of the megachiropteran phylogeny cannot be determined with the present data. Nyctimene, the only studied insectivorous genus (Paranyctimene not being included), plus Notopteris, the only long-tailed megachiropteran, form the sister clade to the other genera in combined analyses. Several alternative rootings are not rejected by the data, suggesting a rapid early radiation. Generic distributions indicate that this may have occurred in Melanesia. The results confirm that the subfamily Macroglossinae is not monophyletic with the long tongued phenoptype arising at least twice and support the existence of a major clade including a monophyletic endemic African component and biogeographically neighboring genera such as Rousettus and Eonycteris. The phylogenetic position of one African genus, Eidolon, remains uncertain.A cynopterine section (excluding Nyctimene and Myonycteris) is supported, albeit weakly, as a monophyletic group. Pteropus and the related, possibly polyphyletic genus Pteralopex, are unexpectedly basal compared to previous molecular studies.     

基于叶绿体16S rRNA的绿色裸藻类系统发育及性状进化研究

该研究基于叶绿体16S rRNA基因序列,构建绿色裸藻类的系统发育树,并对绿色裸藻类植物8个形态性状进行祖先重建分析,以明确绿色裸藻类植物的系统演化关系,为研究该类植物的起源提供理论依据。结果表明：(1)贝叶斯法构建的绿色裸藻类系统发育树显示,双鞭藻属与拟双鞭藻属互为姐妹群,扁裸藻属、鳞孔藻属和盘裸藻属亲缘关系较近,而囊裸藻属和陀螺藻属亲缘关系较近,裸藻属、隐裸藻属、柄裸藻属和旋形藻属亲缘关系较近,表明裸藻属不是一个单系类群。(2)基于形态性状的祖先重建结果显示,绿色裸藻类相对原始的7个性状包括：表质柔软易变形,出现螺旋形线纹,细胞后端渐尖或尖尾刺状,无囊壳,叶绿体为片状、盾状或大盘状,具无鞘蛋白核,副淀粉粒为小颗粒状且数量不定,而鞭毛长度不能推断可能的祖先状态。(3)综合8种性状祖先重建结果发现,裸藻属和眼裸藻属植物具有所有原始性状,可能是最先出现的绿色裸藻类的祖先。     

Phylogenetic relationships within the South American fish family Anostomidae (Teleostei,Ostariophysi, Characiformes)

Analysis of a morphological dataset containing 152 parsimony‐informative characters yielded the first phylogenetic reconstruction spanning the South American characiform family Anostomidae. The reconstruction included 46 ingroup species representing all anostomid genera and subgenera. Outgroup comparisons included members of the sister group to the Anostomidae (the Chilodontidae) as well as members of the families Curimatidae, Characidae, Citharinidae, Distichodontidae, Hemiodontidae, Parodontidae and Prochilodontidae. The results supported a clade containing Anostomus, Gnathodolus, Pseudanos, Sartor and Synaptolaemus (the subfamily Anostominae sensu Winterbottom) albeit with a somewhat different set of relationships among the species within these genera. Anostomus as previously recognized was found to be paraphyletic and is split herein into two monophyletic components, a restricted Anostomus and the new genus Petulanos gen. nov. , described herein. Laemolyta appeared as sister to the clade containing Anostomus, Gnathodolus, Petulanos, Pseudanos, Sartor and Synaptolaemus. Rhytiodus and Schizodon together formed a well‐supported clade that was, in turn, sister to the clade containing Anostomus, Gnathodolus, Laemolyta, Petulanos, Pseudanos, Sartor and Synaptolaemus. Anostomoides was sister to the clade formed by these nine genera. Leporinus as currently defined was not found to be monophyletic, although certain clades within that genus were supported, including the species with subterminal mouths in the former subgenus Hypomasticus which we recognize herein as a genus. Abramites nested in Leporinus, and Leporellus was found to be the most basal anostomid genus. The presence of cis‐ and trans‐Andean species in Abramites, Leporellus, Leporinus and Schizodon, all relatively basal genera, suggests that much of the diversification of anostomid species pre‐dates the uplift of the Andean Cordilleras circa 11.8 million years ago. Several important morphological shifts in anostomid evolution are illustrated and discussed, including instances of convergence and reversal. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 70–210.     

Phylogenetic evidence for loss of sound production and a shift in sexual recognition signals in Hamadryas butterflies (Nymphalidae: Biblidinae)

The neotropical butterfly genus Hamadryas Hübner comprises 20 species that exhibit an intriguing variation in their natural history traits. Although revised in 1983, no phylogenetic hypothesis was presented: the first phylogenetic hypothesis is estimated here based on 93 characters and including species from the three other genera in the tribe Ageroniini. The phylogeny is used to test the monophyly of the genus, establish the sister group of Hamadryas and identify its apomorphies. The tree allows the inference of patterns of character change in sound production and sexual dimorphism. Implied weights show that Hamadryas is monophyletic and corroborate Ectima Doubleday as a sister genus. Previously suggested subgenera for Hamadryas were non‐monophyletic, with the exception of the laodamia clade, supported by the presence of a complete sterigma. Sound production is inferred to be a derived condition in Hamadryas that has been lost in the laodamia clade. This, plus the presence of androconial organs and sexual dimorphism in the laodamia clade, suggests a shift in sexual recognition signalling. Furthermore, the phylogeny indicates that the colour pattern of males in the laodamia clade is novel, supporting a Darwinian origin of sexual dimorphism.     

New Species of Lagenophrys (Ciliophora,Peritrichia) from New Zealand and Australia1

Lagenophrys novazealandae n. sp. occurs on the gills of Paranephrops zealandicus, a parastacid crayfish from New Zealand. The new species has the hemispheroidal lorica most common among members of its genus and is distinguished by its possession of large tubercles on the thickened edge of the anterior lip of the lorica aperture, a deep cleft in the left side of the lip's edge, and a ovoid to reniform macronucleus located in the right-hand part of the body. It is probable that an as yet unnamed species of Lagenophrys known to occur on another species of Paranephrops in New Zealand is distinct from L. novazealandae but phylogenetically related to it. Lagenophrys petila n. sp. occurs on setae of Parastacoides tasmanicus, a parastacid from Tasmania. The new species has an ovoid lorica tapering to a slender pseudostalk at the posterior end, a type of lorica possessed by only two other members of its genus that also attach to their host's setae. It is distinguished from the other ovoid species by the proportions of the lorica, the extreme shortness of the lips of the lorica aperture, and an ovoid macronucleus located in the right, anterior part of the body. Clefts in the lips of L. novazealandae and other members of Lagenophrys may function as points of flexure to allow the lips to bend in ways that accommodate interspecific differences in the size of the epistomial disk and its operation during suspension feeding.     

Reconciling cladistic and genetic analyses in choreotrichid ciliates (Ciliophora, Spirotricha, Oligotrichea)

Fifty-six features of halteriid, oligotrichid, and choreotrichid ciliates are cladistically analysed, including an updated hypothesis about the evolution of the somatic ciliary patterns. Based on its morphology, Lynnella clusters with Parastrombidinopsis, Parastrombidium, and Strombidinopsis, while it is basal to the other choreotrichids in the molecular phylogenies. The two clusters of Favella species in small subunit rRNA gene trees are supported by morphological features, justifying a separation at genus and family level. The genus Favella has a smooth lorica surface and a somatic ciliary pattern comprising a left and lateral ciliary field as well as two dorsal kineties and a monokinetidal ventral kinety abutting on the right ciliary field. The new genus Schmidingerella n. gen., established for the second Favella cluster, groups with Metacylis and Rhabdonella in the molecular trees. It differs from Favella in (i) a lorica wall with reticulate surface ridges and minute openings and (ii) a ventral kinety that is distinctly apart from the right ciliary field and composed of a monokinetidal anterior and a dikinetidal posterior portion. The genera Codonaria, Codonella, and Codonellopsis are affiliated with the family Dictyocystidae, whose diagnosis is improved to include the lorica sac.