Major discrepancy between phylogenetic hypotheses based on molecular and morphological criteria within the Order Haplosclerida (Phylum Porifera: Class Demospongiae)

Taxonomy within the sponge Order Haplosclerida remains somewhat contentious. Both morphology and biochemistry have been employed to help unravel the relationships of the Order with limited results perhaps because of the small number of reliable characters. We employed phylogenetic analysis of 750 base pairs of the 5′ end of the 28S rRNA gene to study relationships between 20 taxa within the Order. While preliminary (low number of taxa, one gene region) results suggested strong discrepancy to former phylogenies, there was no support for the monophyly of the Order and almost all morphologically defined genera appeared to be polyphyletic.     

Discopersicus n. gen., a New Member of the Family Tylenchidae ?rley, 1880 with Detailed SEM Study on Two Known Species of the Genus Discotylenchus Siddiqi, 1980 (Nematoda; Tylenchidae) from Iran

Discopersicus iranicus n. gen., n. comb., previously described from Iran as a new species under the genus Discotylenchus, is illustrated using light microscope and scanning electron microscope (SEM) observations and further studied using molecular characters. SEM studies revealed the newly proposed genus has oblique amphidial apertures on the lateral sides of the lip region. SEM images are also provided for two species of Discotylenchus, namely D. discretus and D. brevicaudatus, as the first SEM study of the genus. These results confirmed longitudinal amphidial aperture type on lateral sides of the lip region in genus Discotylenchus, as noted by Siddiqi while erecting the genus with D. discretus as the type species. Molecular phylogenetic analyses using partial small subunit (SSU) and large subunit (LSU) rDNA sequences revealed the affinity of the genus Discopersicus n. gen. with members of the subfamily Boleodorinae, as supported by morphological characters (mainly, the oblique amphidial opening).     

Monophyly of the family Desmoscolecidae (Nematoda,Demoscolecida) and Its Phylogenetic position inferred from 18S rDNA sequences

To infer the monophyletic origin and phylogenetic relationships of the order Desmoscolecida, a unique and puzzling group of mainly free-living marine nematodes, we newly determined nearly complete 18S rDNA sequences for six marine desmoscolecid nematodes belonging to four genera (Desmoscolex, Greeffiella, Tricoma and Paratricoma). Based on the present data and those of 72 nematode species previously reported, the first molecular phylogenetic analysis focusing on Desmoscolecida was done by using neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All four resultant trees consistently and strongly supported that the family Desmoscolecidae forms a monophyletic group with very high node confidence values. The monophyletic clade of desmocolecid nematodes was placed as a sister group of the clade including some members of Monhysterida and Araeolaimida, Cyartonema elegans (Cyartonematidae) and Terschellingia longicaudata (Linhomoeidae) in all the analyses. However, the present phylogenetic trees do not show any direct attraction between the families Desmoscolecidae and Cyartonematidae. Within the monophyletic clade of the family Desmoscolecidae in all of the present phylogenetic trees, there were consistently observed two distinct sub-groups which correspond to the subfamilies Desmoscolecinae [Greeffiella sp. + Desmoscolex sp.] and Tricominae [Paratricoma sp. + Tricoma sp].     

The interrelationships of proseriata (Platyhelminthes: seriata) tested with molecules and morphology

Proseriate flatworms are common members of the interstitial benthic fauna worldwide, predominantly occupying marine environments. As minute animals, having relatively few characters useful for cladistic analysis, they have been difficult to present in a phylogenetic framework using morphology alone. Here we present a new morphological matrix consisting of 16 putatively homologous characters and two molecular data sets to investigate further this major group of free-living members of the Platyhelminthes. Complete 18S rDNA (representing 277 parsimony-informative characters) from 17 ingroup taxa and partial 28S rDNA spanning variable expansion regions D1 to D3 and D1 to D6 (representing 219 and 361 parsimony-informative characters, respectively) from 27 and 14 ingroup taxa, respectively, were determined and aligned as complementary data sets. Morphological and molecular data sets were analyzed separately and together to determine underlying phylogenetic patterns and to resolve conflict between published scenarios based on morphology alone. The monophyly of the Proseriata cannot be confirmed categorically with any of these data sets. However, the constituent taxa are confirmed as basal members of the Neoophora, and a sister group relationship with Tricladida is rejected. Similarly, the monophyly of one of the two subtaxa of the Proseriata, the Lithophora, could not be confirmed with molecules. Concerning intragroup relationships, we could reject one of the two phylogenetic trees formerly proposed, as well as the clade Otoplanidae + Coelogynoporidae. However, a clade Otoplanidae + Archimonocelididae + Monocelididae (to which the Monotoplanidae belong) was supported, and the position of the genus Calviria shifted from the Archimonocelididae to the Coelogynoporidae.     

基于18S rDNA序列的蝽次目(半翅目：异翅亚目)

利用18SrDNA分子约1 912 bp的序列对蝽次目21个科53个种进行系统发育分析。运用MP法、ML法和NJ法分析后的结果表明:蝽次目的单系性得到很高的支持;扁蝽总科成为毛点类的姐妹群;毛点类基本确定为两大分支:一支包含蝽总科和红蝽总科;另一支主要由长蝽总科、缘蝽总科和南蝽总科组成;长蝽总科和缘蝽总科都是多系;长蝽总科中,跷蝽科和皮蝽科的关系最近,构成姐妹群,位于整个毛点类的基部;与长蝽总科中另外两个科长蝽科和地长蝽科的关系很远。说明利用18SrDNA分子对研究蝽次目的系统发育关系是适合的,能够重建蝽次目;扁蝽总科和蝽总科单系性的结果与形态学的研究以及Li et al (2005)的研究一致;但较Li et al(2005)的研究更进一步把红蝽总科从广义的缘蝽总科中分出来;并建议皮蝽科作为一个独立的总科更合适。     

Molecular systematics of the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera')

Phylogenetic relationships among extant families in the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera') were inferred from partial sequences of the nuclear 18S rDNA and Histone 3 and mitochondrial 16S rDNA genes. Analyses of these data produced trees that largely supported the traditional classification; however, monophyly of the infraorder Psocathropetae (= Psyllipsocidae + Prionoglarididae) was not recovered. Instead, the family Psyllipsocidae was recovered as the sister taxon to the infraorder Atropetae (= Lepidopsocidae + Trogiidae + Psoquillidae), and the Prionoglarididae was recovered as sister to all other families in the suborder. Character states previously used to diagnose Psocathropetae are shown to be plesiomorphic. The sister group relationship between Psyllipsocidae and Atropetae was supported by two morphological apomorphies: the presence of a paraproctal anal spine and an anteriorly opened phallosome. Based on these sequence data and morphological observations, we propose a new classification scheme for the Trogiomorpha as follows: infraorder Prionoglaridetae (Prionoglarididae), infraorder Psyllipsocetae (Psyllipsocidae), infraorder Atropetae (Lepidopsocidae, Trogiidae, Psoquillidae).  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 287–299.     

Evidence supporting the paraphyly of Hucho (Salmonidae) based on ribosomal DNA restriction maps

Relationships among the less derived genera in the subfamily Salmoninae were investigated by phylogenetic analysis of data from restriction maps of the ribosomal DNA using Osmerus mordax (rainbow smelt), Coregonus hoyi (bloater), and Thymattus arcticus (Arctic grayling) as outgroups. Analysis of the results suggests that Hucho h. taimen is more closely related to Brachymystax lenok (lenok) than to Hucho perryi (Sakhalin taimen) and that B. lenok and Hucho h. taimen (Eurasian taimen) form the most ancestral clade of the Salmoninae.     

Phylogeny of Podocarpaceae: comparison of evidence from morphology and 18S rDNA

Maximum parsimony analyses of the genera of Podocarpaceae were conducted using sequence data from 18S ribosomal DNA. Trees from sequence, morphological, and combined data differ in taxon arrangement, but are similar in that Podocarpus sensu lato and Dacrydium s.l. are unnatural, while Podocarpaceae (including Phyllocladus) are monophyletic. The clade Microcachrys + Microstrobos is recognized in all analyses, but its placement differs, i.e., nested among other scale-leaved taxa in the morphological analysis, but associated with Nageia and other tropical genera in the sequence analyses. Trees from combined data reflect this ambiguity. Podocarpus sensu stricto is paraphyletic according to most trees. Inferences of plesiomorphic character states within the family are largely consistent between analyses and support the view that prototypical podocarps had bifacial leaves, cones with several fertile cone scales, and large epimatia (cone scales) that covered the inverted ovules.     

Phylogenetic relationships of Amur sturgeon Acipenser schrenckii Brandt, 1869 based on 18S rDNA sequencing

The phylogenetic relationships of Amur sturgeon A. schrenckii Brandt, 1869 with related species have been analyzed based on sequencing of the 18S rDNA small subunit. The complete sequence (1746 bp) of 18S rDNA has been estimated in seven individual A. schrenckii clones. The results show that the rDNA mutation profile of A. schrenckii 18S is very similar to that of A. fulvescens (Genbank data). Structural-functional and phylogenetic analyses allowed us to identify a presumably expressed variant, as well as taxon-specific mutation (adenine insertion after position 658 bp), for A. schrenckii 18S rDNA. Phylogenetic reconstructions performed with various approaches (NJ, MP, ML and Bayesian) support the monophyly of the genus Acipenser and point (1), based on which, in accordance with the classification based on ecological and morphological data (Artyukhin, 2006), the Amur sturgeon is closer to the sterlet than the Baltic sturgeon and (2) to substantial differentiation between North American (A. fulvescens) and Eurasian (A. schrenckii, A. ruthenus, and A. sturio) species of Acipenseridae.     

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.     

Phylogenetic analysis of protozoa in the rumen contents of cow based on the 18S rDNA sequences

AIMS: To examine the diversity of protozoa in the rumen contents of cow. METHODS AND RESULTS: Protozoa that inhabit the rumen were detected by PCR using protozoan-specific primers. Libraries of protozoan rDNA sequences were constructed from rumen fluid, solid tissues and epithelium. Twenty-three clones isolated from rumen fluid fell into two genera identified as Entodinium (69.6% of clones) and Epidinium (31.4% of clones). Of the clones isolated from rumen fluid, a moderate number were unidentifiable (30.4%). CONCLUSIONS: The predominant protozoan genus identified in the whole rumen belonged to the Entodinium group (81.1%). Protozoa were not detected in the rumen epithelium. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings suggest that rumen fluid and solid tissues contain different protozoan populations that may play specific roles in rumen function. Quantitative PCR techniques and a more specific set of phylogenetic probes that distinguish between protozoan species are needed to determine the significance of newly identified groups and to determine the distribution of identified protozoan clusters in rumen microbial communities.     

The mushroom bodies – prominent brain centres of arthropods and annelids with enigmatic evolutionary origin

Loesel, R. and Heuer, C.M. 2010. The mushroom bodies – prominent brain centres of arthropods and annelids with enigmatic evolutionary origin. —Acta Zoologica (Stockholm) 91 : 29–34 Mushroom bodies (MBs) are the most prominent and conspicuous neuropils in the brain of arthropods, onychophorans and vagile polychaete annelids but have not been described in any other animal group with complex brain architecture. Due to a number of unique neuroanatomical characters MBs can easily be identified and distinguished from other brain centres. However, their evolutionary origin and the question whether MBs are homologous structures is still under debate. This paper will briefly summarize the available morphological data and their implications with respect to the molecular evidence on early metazoan radiation. Unraveling the origin of MBs is an example of the challenges neurophylogenists will face in the future, especially so since it will signify a major step towards reconstructing early metazoan brain evolution.     

Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia)

The series Staphyliniformia is one of the mega‐diverse groups of Coleoptera, but the relationships among the main families are still poorly understood. In this paper we address the interrelationships of staphyliniform groups, with special emphasis on Hydrophiloidea and Hydraenidae, based on partial sequences of the ribosomal genes 18S rDNA and 28S rDNA. Sequence data were analysed with parsimony and Bayesian posterior probabilities, in an attempt to overcome the likely effect of some branches longer than the 95% cumulative probability of the estimated normal distribution of the path lengths of the species. The inter‐family relationships in the trees obtained with both methods were in general poorly supported, although most of the results based on the sequence data are in good agreement with morphological studies. In none of our analyses a close relationship between Hydraenidae and Hydrophiloidea was supported, contrary to the traditional view but in agreement with recent morphological investigations. Hydraenidae form a clade with Ptiliidae and Scydmaenidae in the tree obtained with Bayesian probabilities, but are placed as basal group of Staphyliniformia (with Silphidae as subordinate group) in the parsimony tree. Based on the analysed data with a limited set of outgroups Scarabaeoidea are nested within Staphyliniformia. However, this needs further support. Hydrophiloidea s.str., Sphaeridiinae, Histeroidea (Histeridae + Sphaeritidae), and all staphylinoid families included are confirmed as monophyletic, with the exception of Hydraenidae in the parsimony tree. Spercheidae are not a basal group within Hydrophiloidea, as has been previously suggested, but included in a polytomy with other Hydrophilidae in the Bayesian analyses, or its sistergroup (with the inclusion of Epimetopidae) in the parsimony tree. Helophorus is placed at the base of Hydrophiloidea in the parsimony tree. The monophyly of Hydrophiloidea s.l. (including the histeroid families) and Staphylinoidea could not be confirmed by the analysed data. Some results, such as a placement of Silphidae as subordinate group of Hydraenidae (parsimony tree), or a sistergroup relationship between Ptiliidae and Scydmaenidae, appear unlikely from a morphological point of view.     

18S rDNA phylogeny of the Tubificidae (Clitellata) and its constituent taxa: dismissal of the Naididae

The phylogeny of the Tubificidae, and of most of its subfamilies and some of its genera, is revisited, on the basis of sequences of 18S ribosomal DNA in a selection of species. Forty-six new 18S sequences of Naididae (6), Tubificidae (37), Phreodrilidae (1), Lumbriculidae (1), and Enchytraeidae (1) are reported and aligned together with corresponding sequences of 21 previously studied taxa. The 18S gene of Insulodrilus bifidus provides the first molecular evidence that phreodrilids are closely related to tubificids, corroborating previous conclusions based on morphology. The data further support the monophyletic status of Tubificidae, provided that the "Naididae" is regarded a part of this family; "naidids" may not even constitute a monophyletic group. It is thus suggested that the family name Naididae is formally suppressed as a junior synonym of the Tubificidae. The 18S gene also resolves a number of relationships within the tubificids. Among the subfamilies, Tubificinae is supported, Rhyacodrilinae and Phallodrilinae are revealed as nonmonophyletic, and Limnodriloidinae remains unresolved. Most tubificid genera tested for monophyly are corroborated by the data, only one (Tubifex) is refuted, and two (Tubificoides and Limnodriloides) are unresolved from other taxa. It is concluded that it will be valuable to expand the taxonomic sampling for 18S rDNA in clitellates, and in annelids in general, as this is likely to improve the resolution at many levels. However, it will be equally important to combine the annelid 18S data with other gene sequences and nonmolecular characters, to estimate the phylogeny of these common and diverse worms with greater precision.     

堆肥发酵菌种的分离、鉴定及其堆肥发酵效果研究

为获得适应性良好的菌种用于猪粪的堆肥处理,从新鲜猪粪中分离出一株酵母样菌株783,并采用PCR技术扩增其18S rDNA基因,并测定其基因序列.基于18S rDNA序列同源性比对以及系统发育树的分析,发现783是解脂耶罗威亚酵母.菌株783的18S rDNA序列已经被GenBank数据库收录,其序列号为EU434621.对猪粪堆肥发酵效果表明其在提高堆肥质量方面有着较好的效果.     

Genetic diversity and phylogenetic relations of salmon trematode Nanophyetus japonensis

Nanophyetiasis is the severe zoonotic disease caused by parasitic worms from the genus Nanophyetus. Humans and carnivorous animals become infected when they ingest raw fish containing metacercariae, especially Pacific salmonids. Nanophyetiasis is detected in limited geographical areas which include the coastal regions of the North Pacific: the United States of America, Russian Federation and Japan. Despite the epidemiological significance, Nanophyetus species have not been well studied genetically. In this research, we for the first time explored genetic diversity of Nanophyetus japonensis from Japan in comparison with those of related species, N. salmincola from North America and N. schikhobalowi from the Russian Far East, based on sequence variation in the nuclear ribosomal gene family (18S, ITS1–5.8S–ITS2 and 28S) and mitochondrial nad1 gene, encoding subunit I of the respiratory chain NADH dehydrogenase. The results confirmed the independent species status for the compared flukes, demonstrated a greater genetic similarity of Asian species between themselves than each of them with the North American one, suggesting that N. japonensis and N. schikhobalowi are close sister species, and also revealed discrepancy between the levels of morphological and genetic differentiation.     

产紫杉醇内生真菌EFY-21的鉴定与生物学特性研究

利用PCR技术克隆了产紫杉醇内生真菌EFY-21的18S rDNA序列,通过同源性分析,初步确定该菌与拟盘多毛孢属(Pestalotiopsis)有较高的同源性,相似性为99%。为了进一步了解EFY-21的有关生物学特性,分别选用PDA、PSA、查氏、玉米粉琼胶、牛肉膏蛋白胨5种培养基,按照常规方法培养,用十字法测量菌落直径;同时选用查氏培养基为基本培养基,分别观察不同碳源葡萄糖、甘露醇、麦芽糖、果糖、可溶性淀粉,不同氮源KNO3、Ca(N03)2、(NH4)2SO4、NH4N03、(NH4)2HPO4、蛋白胨、尿素,不同培养温度10,15,20,25,28,30,37℃,不同pH值4,5,6,7,8,9对内生真菌菌丝的影响。试验结果表明:EFY-21在PDA培养基上生长最快,生长状况最好;供试的碳氮源中,对EFY-21菌丝生长影响的大小顺序为葡萄糖甘露醇果糖麦芽糖可溶性淀粉;蛋白胨KNO3Ca(N03)2NH4N03(NH4)2HPO4(NH4)2SO4尿素;最适培养温度为25～30℃;最适pH为5～7。