The Structure and Development of the Dorsal Bristle Complex of Oxytricha fallax and Stylonychia pustulata*

SYNOPSIS. Oxytricha fallax and Stylonychia pustulata possess 6 rows of dorsal bristle units. Each dorsal bristle unit consists of a pair of kinetosomes; the anterior kinetosome has a cilium and the posterior kinetosome a ciliary stub. The kinetosome pair, located at the bottom of a cortical pit surrounding the cilium and ciliary stub, is surrounded by an asymmetrical fibrillar mass. Future rows 1-4 are formed from 2 sets of primordia originating within mature dorsal rows 1-3. Rows 5 and 6 originate from the anterior regions of both right marginal cirral primordia. Old dorsal bristle units utilized in formation of primordia are presumably maintained in the new rows of the proter and opisthe; those outside the primordia are resorbed. The morphogenetic pattern of the Oxytrichidae is similar to those of the Urostylidae and Holostichidae, but quite different from that of the Euplotidae.     

Phylogeny of the Stichotrichia (Ciliophora; Spirotrichea) reconstructed with nuclear small subunit rRNA gene sequences: discrepancies and accordances with morphological data

The Stichotrichia, known as an especially various and taxonomically difficult group, were intensely studied with morphological, morphogenetic, and molecular methods in the last years. Nevertheless, a consistent classification is lacking and several important questions about the phylogenetic relationships within this group remain unsolved. In order to gain deeper insights into these relationships, the nuclear small subunit rRNA genes of seven species of the Stichotrichia, representatives of the families Oxytrichidae, Amphisiellidae, and Pseudourostylidae, were phylogenetically analysed. Although our analyses resulted in a poor resolution of the phylogenetic relationships, some conclusions can be drawn. Firstly, following the current classification systems the Oxytrichidae as well as their subfamilies seem to be paraphyletic and the basic 18 FVT cirral pattern has been modified several times independently. Secondly, sequence analyses of several Oxytricha species resulted in a high molecular diversity, which does not support monophyly of this genus. Thirdly, several families of the order Urostylida (Urostylidae, Pseudokeronopsidae, and Pseudourostylidae) also do not form monophyletic groups.     

A molecular approach to the tangled intrageneric relationships underlying phylogeny in Euplotes (Ciliophora, Spirotrichea).

The cosmopolitan genus Euplotes is remarkable among ciliates for its species richness. To understand the still tangled taxonomy and phylogenetic relationships within the genus, small subunit rRNA sequences of 11 morphologically defined species colonizing different habitats were determined. Euplotes 18S rRNA is unique among ciliates for its anomalous length and high evolutionary rate. Phylogenetic reconstruction pointed to a high divergence between this genus and the other Spirotrichea, together with a high variability within the genus. Some of the relationships within the Euplotes group were also resolved. Data from the literature, based on morphological features, habitat, and symbiotic relationships, have been compared with our results and are critically discussed. In many cases, the molecular phylogenetic analysis disagreed with species relatedness established on morphological and ecological grounds. The occurrence of a radiation phenomenon in the evolution of the genus is postulated.     

下毛目纤毛虫的系统修订Ⅲ.散毛亚目:游仆亚目(纤毛动物门)

对散毛亚目Ｓｐｏｒａｄｏｔｒｉｃｈｉｎａ和游仆亚目Ｅｕｐｌｏｔｉｎａ中科属进行了重新修订。散毛亚目的特征为腹面棘毛数目少且分组化,游仆亚目的特征为右缘棘毛均退化。修订后的芨毛亚目有５科２０科,游仆亚目４科１１属。盘头虫科Ｄｉｓｃｏｃｅｐｈａｌｉｄａｅ虫体前端形成明显的头部。侧毛虫科Ｐｌｅｕｒｏｔｒｉｃｈｉｄａｅ缘棘毛至少有一侧为多列;稀毛虫科Ｐｓｉｌｏｔｒｉｃｈｉｄａｅ虫体形状一般不规则,可形成细     

Phylogenetic patterns in populations of Chilean species of the genus Orestias (Teleostei: Cyprinodontidae): results of mitochondrial DNA analysis

Patterns of molecular genetic differentiation among taxa of the "agassii species complex" (Parenti, 1984) were analysed based on partial mtDNA control region sequences. Special attention has been paid to Chilean populations of Orestias agassii and species from isolated lakes of northern Chile, e.g., O. agassii, Orestias chungarensis, Orestias parinacotensis, Orestias laucaensis, and Orestias ascotanensis. Orestias tschudii, Orestias luteus, and Orestias ispi were analysed comparatively. Our findings support the utility of mtDNA control region sequences for phylogenetic studies within the "agassii species complex" and confirmed the monophyly of this particular lineage, excluding O. luteus. However, the monophyly of further morphologically defined lineages within the "agassii complex" appears doubtful. No support was found for the utility of these data sets for inferring phylogenetic relationships between more distantly related taxa originating from Lake Titicaca.     

基于16S rDNA序列探讨中国剑角蝗科的单系性及其六属的系统发育关系

在中国学者夏凯龄的分类系统中,剑角蝗科Acrididae一直被看作是单系群,包含6个亚科。但是,近年来的研究对其单系性争议较大。为探讨其单系性和剑角蝗属等6属的系统发育关系,我们测定了剑角蝗科14种蝗虫的16S rRNA基因部分序列,并从GenBank中下载了1种蝗虫的同源序列。以蚱科的2个种作外群,用NJ、MP及ML法重建系统发生树。由三棵分子系统树中得出的系统发生关系与中国的分类系统差别较大,都不支持剑角蝗科是单系群,但与国外Kevan的系统相一致,提示我们国内的分类系统亟待修改和完善。长腹蝗亚科与斑腿蝗科的亲缘关系要近于与剑角蝗科的其他种类的关系。另外,尽管所测的红足剑角蝗和上海剑角蝗的16S rDNA的片段序列完全相同,我们仍不能断定二者是同一个物种[动物学报52 (2) : 302 -308 , 2006]。     

Variations and evolution of polyubiquitin genes from ciliates

Polyubiquitin genes from seven ciliate species were amplified, cloned and sequenced. It is estimated that Strombidium sulcatum, Euplotes vannus, E. rariseta and Anteholosticha manca have a polyubiquitin gene of 3 repeats, and A. parawarreni, Paramecium caudatum and Pseudokeronopsis flava 4 repeats. The newly obtained ubiquitins mostly differ from that of humans by 1–5 residues in amino acid sequences. A neighbor-joining tree constructed based on monomeric ubiquitin genes supports the monophyly of an assemblage comprising the litostomateans and some oligohymenophoreans, but not the class Spirotrichea. The monomers from the same species are generally placed together and highly supported for the class Litostomatea, the genera Paramecium and Ichthyophthirius, but not for other species. The non-synonymous/synonymous rate ratio (dN/dS) at the protein level are less than 1, and the synonymous nucleotide differences per synonymous site (p_S) from intraspecific comparisons are fairly high (0.02–0.72). These results indicate that ciliates have not only the conserved, but also some quite divergent, polyubiquitin genes and confirm that the polyubiquitin genes in ciliates evolve according to the birth-and-death mode of evolution under strong purifying selection.     

Molecular systematics of New World suboscine birds

Phylogenetic relationships among New World suboscine birds were studied using nuclear and mitochondrial DNA sequences. New World suboscines were shown to constitute two distinct lineages, one apparently consisting of the single species Sapayoa aenigma, the other made up of the remaining 1000+ species of New World suboscines. With the exception of Sapayoa, monophyly of New World suboscines was strongly corroborated, and monophyly within New World suboscines of a tyrannoid clade and a furnarioid clade was likewise strongly supported. Relationships among families and subfamilies within these clades, however, differed in several respects from current classifications of suboscines. Noteworthy results included: (1) monophyly of the tyrant-flycatchers (traditional family Tyrannidae), but only if the tityrines (see below) are excluded; (2) monophyly of the pipromorphine flycatchers (Pipromorphinae of ) as one of two primary divisions of a monophyletic restricted Tyrannidae; (3) monophyly of the tityrines, consisting of the genus Tityra plus all sampled species of the Schiffornis group (), as sister group to the manakins (traditional family Pipridae); (4) paraphyly of the ovenbirds (traditional family Furnariidae), if woodcreepers (traditional family Dendrocolaptidae) are excluded; and (5) polyphyly of the antbirds (traditional family Formicariidae) and paraphyly of the ground antbirds (Formicariidae sensu stricto). Genus Melanopareia (the crescent-chests), although clearly furnarioid, was found to be distant from other furnarioids and of uncertain affinities within the Furnarii. Likewise, the species Oxyruncus cristatus (the Sharpbill), although clearly tyrannoid, was distantly related to other tyrannoids and of uncertain affinities within the Tyranni. Results of this study provide support for some of the more novel features of the suboscine phylogeny of, but also reveal key differences, especially regarding relationships among suboscine families and subfamilies. The results of this study have potentially important implications for the reconstruction of character evolution in the suboscines, especially because the behavioral evolution of many suboscine groups (e.g., Furnariidae) is of great interest.     

Species monophyly

In biological systematics, as well as in the philosophy of biology, species and higher taxa are individuated through their unique evolutionary origin. This is taken by some authors to mean that monophyly is a (relational) property not only of higher taxa, but also of species. A species is said to originate through speciation, and to go extinct when it splits into two daughter species (or through terminal extinction). Its unique evolutionary origin is said to bestow identity on a species through time and change, and to render species names rigid designators. Species names are thus believed to function just like names of supraspecific taxa. However, large parts of the Web of Life are composed of species that do not have a unique evolutionary origin from a single population, lineage or stem-species. Further, monophyly is an ambiguous concept if it is defined simply in terms of 'unique evolutionary origin'. Disambiguating the concept by defining a monophyletic taxon as 'a taxon that includes the ancestor and all, and only, its descendant' renders monophyly inapplicable to species. At the heart of the problem lies a fundamental distinction between species and monophyletic taxa, where species form mutually exclusive reticulated systems, while higher taxa form inclusive hierarchical systems. Examples are given both at the species level and below to illustrate the problems that result from the application of the monophyly criterion to species. The conclusion is that the concepts of exclusivity and monophyly should be treated as non-overlapping: exclusivity marks out a species synchronistically, i.e. in the present time. Monophyly marks out clades (groups of species) diachronistically, i.e. within an historical dimension.     

Evaluation of relationships within the endemic Hawaiian Platynini (Coleoptera: Carabidae) based on molecular and morphological evidence

Relationships among 69 species of Hawaiian Platynini, a monophyletic beetle radiation, was investigated based on evidence from five data partitions, comprising mitochondrial and nuclear DNA sequences (cytochrome oxidase II, 624 bp; cytochrome b, 783 bp; 28S rDNA, 668 bp; wingless; 441 bp) and morphology (206 features of external and internal anatomy). Results from individual and combined data analyses generally support the monophyly of three putative divisions within Platynini in Hawaii: Division 0 (Colpocaccus species group), Division 1 (Blackburnia species group), and Division 2 (Metromenus species group). However, relationships within and among these three divisions differ from previous morphological hypotheses. An extensive series of sensitivity analyses was performed to assess robustness of recovered clades under a variety of weighted parsimony conditions. Sensitivity analyses support the monophyly of Divisions 0 and 1, but were equivocal for the monophyly of Division 2. A phylogeny based on combined data suggests at least four independent losses/reductions of platynine flight wings. The combined analysis provides corroboration for biogeographic hypotheses, including (1) colonization of Kauai by Hawaiian Platynini with subsequent dispersal and colonization along the island chain from Oahu to Maui Nui to Hawaii Island and (2) incongruent area relationships among Eastern Molokai, West Maui, and Haleakala for two species triplets.     

Phylogenetic relationships, biogeography and speciation in the avian genus Saxicola

The avian genus Saxicola is distributed throughout Africa, Asia, Europe and various islands across Oceania. Despite the fact that the group has great potential as a model to test evolutionary hypotheses due to the extensive variability in life history patterns recorded between and within species, the phylogenetic relationships among species and subspecies of this genus are poorly understood. We undertook a systematic investigation of the relationships within this genus with three main objectives in mind, (1) to test the monophyly of the genus; (2) to ascertain geographical origin and dispersal sequence; and (3) to test for monophyly within the most morphologically diverse species, S. torquata and S. caprata. We studied sequence data from the mitochondrial cytochrome b gene from 11 of the 12 recognized species and 15 of the 45 described subspecies. Four clades, two exclusively Asian, one Eurasian, and the fourth encompassing Eurasia and Africa, were identified. Based on our analyses, monophyly of the genus Saxicola is not supported and an Asian origin for the genus can be inferred. Results from DIVA analyses, tree topology and nodal age estimates suggest independent colonisation events from Asia to Africa and from Asia to the Western Palearctic, with the Sahara desert acting as a natural barrier for S. torquata. Subspecies and populations of S. torquata are not monophyletic due to S. tectes, S. dacotiae and S. leucura grouping within this complex. Subspecies and populations of S. caprata are monophyletic. Importantly, within S. torquata and S. caprata, slight morphological traits and plumage colour pattern differences used to recognize subspecies are indicative of the greater cryptic diversification that has occurred within this genus.     

Phylogenetic study of Class Armophorea (Alveolata,Ciliophora) based on 18S-rDNA data

The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree.     

世界今生砂壳纤毛虫名录

砂壳纤毛虫隶属于纤毛门、旋毛纲、环毛亚纲、砂壳目.本文总结了自Kofoid和Campbell(1929)以来的分类学资料,参照Lynn(2008)的分类系统,整理成世界砂壳纤毛虫新名录.厘清砂壳纤毛虫共有15科69属954种,其中海洋种为15科69属925种,淡水种为3科5属29种.在所有属中,以拟铃虫属(Tintinnopsis包含物种最多,为137种,其中海洋种为118种.我国水体共记录有13科36属164种,海洋种13科36属144种,淡水种2科3属20种.除杯形铃壳虫(Codonella cratera)、湖泊领细壳虫(Stenosemella lacustris)、蜉蝣筒壳虫(Tintinnidium ephemeridum)、蝌蚪筒壳虫(Tintinnidium ranunculi)、半缘筒壳虫(Tintinnidium semiciliatum)、纺锤拟铃虫(Tintinnopsis fusiformis)、伊利诺拟铃虫(Tintinnopsis illinoisensis)、卵圆拟铃虫(Tintinnopsis ovalis)、圆柱拟铃虫(Tintinnopsis cylindrata)、这9个种外,其他淡水种在我国都有记录.该名录中,除了已有中文名的159种外,其余的种我们给出了中文译名,并将部分译为似铃虫属(Tintinnopsis)的中文名统一为拟铃虫属,部分译为麻铃虫属(Leprotintinnus)的中文名统一为薄铃虫属,将截短角口虫(Salpingella decurtata)改为截短号角虫,将冰生拟铃壳虫(Codonellopsis glacialis)改为冰生类铃虫.     

AFLPs resolve cytonuclear discordance and increase resolution among barcheek darters (Percidae: Etheostoma: Catonotus)

The use of mitochondrial DNA (mtDNA) sequences in phylogenetic analysis has been the subject of increasing scrutiny. A recent phylogenetic study of barcheek darters (Percidae: Etheostoma: Catonotus) revealed cytonuclear discordance, discordance among mtDNA loci, and discordance between mtDNA and morphometric hypotheses. In particular, mtDNA analyses hypothesized a paraphyletic barcheek darter clade, and a combined mtDNA and nuclear sequence topology was not well resolved. Here, we used amplified fragment length polymorphisms to test the monophyly of barcheek darters and to resolve relationships within the group. By including multiple populations of each species, we were able to generate a highly resolved tree that supports both the monophyly of barcheek darters as well as recently elevated species within the group. Analysis of three mtDNA loci indicates that saturation of highly variable sites best explains the discordant topologies among mtDNA partitions.     

Systematic relationships of Nematomorpha based on molecular and morphological data

Abstract. We sequenced the 18S rRNA gene from 11 nematomorph species from 9 genera and derived hypotheses concerning the sister group of Nematomorpha and relationships within this taxon. The molecular and morphological data are consistent with the monophyly of Nematomorpha, a sister-group relationship between Nematomorpha and Nematoda, and a sister-group relationship between the marine genus Nectonema and all of the freshwater taxa, Gordiida. Hypotheses of relationships within Gordiida support the traditional taxa Gordiidae, Chordodidae, and Chordodinae but reject Parachordodinae and Spinochordodidae. The molecular results differ from those of previous morphological studies by suggesting a reduction of the two tail lobes at the posterior end of males in Chordodinae, monophyly of the genus Paragordionus , and paraphyly of the genus Chordodes .     

Sequences of low-copy nuclear gene support the monophyly of Ostrya and paraphyly of Carpinus (Betulaceae)

Coryloideae consists of four genera: Corylus, Ostryopsis, Carpinus, and Ostrya. While both molecular and non-molecular data support the close relationship of Carpinus and Ostrya, the monophyly of the two genera has remained controversial. In this study, sequences of the nuclear nitrate reductase (Nia) were used to test the naturalness of the two genera. Ostrya species form a robust clade, supporting the monophyly of the genus. The clade, however, is located between Carpinus cordata and the remaining species of Carpinus, indicating that Carpinus is paraphyletic, and Ostrya has evolved from within Carpinus. Within Carpinus, section Distegocarpus is polyphyletic, whereas section Carpinus is a clade where subsections Polyneurae and Carpinus are more closely related to each other than either is to subsection Monbeigianae.