Phylogeny of six oligohymenophoreans (Protozoa, Ciliophora) inferred from small subunit rRNA gene sequences

The small subunit rRNA (SSrRNA) genes of six marine oligohymenophoreans, namely Uronemella filificum , Schizocalyptra sp.-WYG07060701, Schizocalyptra aeschtae , Pleuronema sinica , P. czapikae and Paratetrahymena sp., were sequenced. Phylogenetic trees were constructed with four different methods to assess the inter- and intrageneric relationships among the scuticociliates and the phylogenetic assignment of the order Loxocephalida. The SSrRNA phylogeny indicates that: (i) Paratetrahymena is most closely related to Cardiostomatella ; (ii) the order Loxocephalida and the family Uronematidae both appear to be polyphyletic; (iii) the order Philasterida is a well-defined taxon; (iv) Cyclidium porcatum falls outside the order Pleuronematida in all analyses; (v) the validity of the genus Uronemella is confirmed; (vi) Schizocalyptra is a member of the family Pleuronematidae. Furthermore, the predicted secondary structures of the variable region 4 of the SSrRNA gene sequences show that the size of the terminal bulge in Helix E23–7 is probably different for the orders Philasterida and Pleuronematida. Also, compared to Uronema and Homalogastra , Uronemella has distinct patterns in Helices E23–1, E23–7, E23–8 and E23–9.     

Fossil lice (Insecta: Phthiraptera) reconsidered

Abstract.  Five papers describing fossils considered to be Phthiraptera (lice) by their authors are reviewed. We place the specimens described in three papers in the Acari (mites) and regard them as probably not fossils. A fourth paper describes what appears to be a fossil insect. However, we do not consider it to be a louse. The fifth paper describes a more recent fossil that differs little from extant lice.     

Phylogeny of "Philoceanus complex" seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences

The Philoceanus complex is a large assemblage of lice that parasitise procellariiform seabirds (petrels, albatrosses, and their relatives). We obtained mitochondrial 12S rRNA and cytochrome oxidase I DNA sequences from 39 species from diverse hosts and localities. Resolution of deeper relationships between genera was limited, however there is evidence for two major clades, one hosted by albatrosses, the other by petrels. Based on our results, the genera hosted by albatrosses are excellent candidates for detailed analysis of cospeciation. Our results also suggest that a previous estimate of a 5-fold difference in the relative rate of sequence evolution in lice and their avian hosts is an artefact of limited taxonomic sampling.     

Morphological variation of chewing lice (Insecta: Phthiraptera) from different skua taxa

The lice, Haffneria grandis and Saemundssonia were extracted from their hosts, skuas (Aves: Stercorariidae). Lice were extracted from dead birds by combing feathers, while lice from live birds were extracted using a delousing chamber containing chloroform vapour. Lice were measured and the data analysed by canonical discriminant analysis. Lice show variation in morphology that is useful in identifying some of these hosts. This variation is presumably due to micro-environmental pressure provided by each host. Our interpretation is that these chewing lice have evolved to be adapted to each skua taxon; different sizes and morphologies of skua taxa result in different sizes and morphologies of Haffneria grandis and Saemundssonia.     

虱目裂化线粒体基因组研究进展

虱目是哺乳类和鸟类体表的专性寄生虫。在虱科、阴虱科、长角鸟虱科和兽羽虱科的某些寄生虱种中发现了线粒体基因组裂化现象, 其线粒体基因组裂化成了多个环状的线粒体染色体, 如体虱(Pediculus humanus)、头虱(pediculus capitis)和阴虱(Pthirus pubis)的线粒体基因组分别裂化形成20个、20个和14个微环染色体。微环染色体可能是基因删除和同源重组的结果, 关于线粒体基因组裂化的具体原因和机制, 目前并不清楚, 推测可能是进化选择或随机遗传漂变的结果或与线粒体单链DNA结合蛋白的缺失有关。鉴于线粒体基因组裂化研究对于深入理解线粒体的起源和进化方面具有重要意义, 文章以虱目裂化线粒体基因组为主线, 列举了动物裂化线粒体基因组和裂化特征, 阐述了虱目裂化线粒体基因组的研究现状, 分析了虱目线粒体基因组裂化的类型、原因和机制, 并对该领域未来的研究方向进行了展望。     

Reduced taxonomic richness of lice (Insecta: Phthiraptera) in diving birds

Avian lice occupy different habitats in the host plumage that the physical environment outside the host body may affect in several ways. Interactions between host plumage and water may be an important source of such effects. Here, we use a comparative approach to examine the effect of a host's diving behavior on the taxonomic richness of its lice. Louse genera richness was significantly lower in clades of diving birds than on their nondiving sister clades. Species richness of host and body mass did not differ significantly between these clades; thus, these factors did not bias our results. This study suggests that the hosts' diving behavior can effectively influence ectoparasite communities.     

Dramatically elevated rate of mitochondrial substitution in lice (Insecta: Phthiraptera)

Few estimates of relative substitution rates, and the underlying mutation rates, exist between mitochondrial and nuclear genes in insects. Previous estimates for insects indicate a 2-9 times faster substitution rate in mitochondrial genes relative to nuclear genes. Here we use novel methods for estimating relative rates of substitution, which incorporate multiple substitutions, and apply these methods to a group of insects (lice, Order: Phthiraptera). First, we use a modification of copath analysis (branch length regression) to construct independent comparisons of rates, consisting of each branch in a phylogenetic tree. The branch length comparisons use maximum likelihood models to correct for multiple substitution. In addition, we estimate codon-specific rates under maximum likelihood for the different genes and compare these values. Estimates of the relative synonymous substitution rates between a mitochondrial (COI) and nuclear (EF-1alpha) gene in lice indicate a relative rate of several 100 to 1. This rapid relative mitochondrial rate (>100 times) is at least an order of magnitude faster than previous estimates for any group of organisms. Comparisons using the same methods for another group of insects (aphids) reveals that this extreme relative rate estimate is not simply attributable to the methods we used, because estimates from aphids are substantially lower. Taxon sampling affects the relative rate estimate, with comparisons involving more closely related taxa resulting in a higher estimate. Relative rate estimates also increase with model complexity, indicating that methods accounting for more multiple substitution estimate higher relative rates.     

Phylogeny of Geomydoecus and Thomomydoecus pocket gopher lice (Phthiraptera: Trichodectidae) inferred from cladistic analysis of adult and first instar morphology

The phylogeny for all 122 species and subspecies of chewing lice of the genera Geomydoecus and Thomomydoecus (Phthiraptera: Trichodectidae) hosted by pocket gophers (Rodentia: Geomyidae) is estimated by a cladistic analysis of fifty-eight morphological characters obtained from adults and first instars. The data set has considerable homoplasy, but still contains phylogenetic information. The phylogeny obtained is moderately resolved and, with some notable exceptions, supports the species complexes proposed by Hellenthal and Price over the the last two decades. The subgenera G. (Thaelerius) and T. (Thomomydoecus) are both shown to be monophyletic, but the monophly of subgenus T. (Jamespattonius) could not be confirmed, perhaps due to the lack of first-instar data for one of its component species. The nominate subgenus of Geomydoecus may be monophyletic, but our cladogram was insufficiently resolved to corroborate this. Mapping the pocket gopher hosts onto the phylogeny reveals a consistent pattern of louse clades being restricted to particular genera or subgenera of gophers, but the history of the host-parasite association appears complex and will require considerable effort to resolve.     

Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences

The phylogenetic relationships among peritrichs remain unresolved. In this study, the complete small subunit rRNA (SSrRNA) gene sequences of seven species (Epistylis galea, Campanella umbellaria, Carchesium polypinum, Zoothamnium arbuscula, Vaginicola crystallina, Ophrydium versatile, and Opercularia microdiscum) were determined. Trees were constructed using distance-matrix, maximum-likelihood and maximum-parsimony methods, all of which strongly supported the monophyly of the subclass Peritrichia. Within the peritrichs, 1) E. galea grouped with Opercularia microdiscum and Campanella umbellaria but not the other Epistylis species, which indicates that the genus Epistylis might not be monophyletic; 2) the topological position of Carchesium and Campanella suggested that Carchesium should be placed in the family Zoothamniidae, or be elevated to a higher taxonomic rank, and that Campanella should be independent of the family Epistylididae, and probably be given a new rank; and 3) Opisthonecta grouped strongly with Astylozoon, which suggested that Opisthonecta species were not the ancestors of the stalked peritrichs.     

Phylogenetic relationships of the Subclass Peniculia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences

Peniculine ciliates have been recognized as a distinct higher taxon of ciliates for almost 50 years. However, phylogenetic relationships within the Subclass Peniculia are still unsettled. To contribute to our understanding of their phylogeny and provide evidence for the position of Urocentrum turbo, we sequenced its small subunit (SS) rRNA gene and the SSrRNA genes from Lembadion bullinum, Frontonia sp., Paramecium caudatum, Paramecium multimicronucleatum, Paramecium putrinum, and Paramecium woodruffi. Urocentrum turbo was the only one of these species not to exhibit a shortened Helix E10_1, which we conclude characterizes the "higher" peniculines. Except for U. turbo, the peniculines are strongly supported as a monophyletic clade with Lembadion, Frontonia, and Paramecium species forming separate and strongly supported clades by bootstrap analysis using distance matrix, maximum parsimony, and maximum likelihood methods. Urocentrum turbo is associated with different lineages, depending upon the analysis used. The Paramecium species form at least four clades with the Paramecium aurelia subgroup being the most derived. We conclude that the Subclass Peniculia should be divided into two orders, the Order Urocentrida and Order Peniculida, with the latter order having two suborders, the Suborder Frontoniina and Peniculina. We place U. turbo with the peniculines because of shared morphological and stomatogenetic features.     

Phylogenetic relationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA gene sequences

The small subunit rDNAs of five species belonging to the Euplotidae and eight species of the Oxytrichidae were sequenced to obtain a more detailed picture of the phylogenetic relationships within the Spirotrichea (Ciliophora). Various tree reconstruction algorhythms yielded nearly identical topologies. All Euplotidae were separated from the other Spirotrichea by a deep split. Further, a large genetic distance between the marine genus Moneuplotes and the freshwater species of Euplotoides was found. Differences between the methods used occurred only within the Oxytrichidae. Whereas the monophyly of the Stylonychinae was supported in all trees, the monophyly of the Oxytrichinae was not. However, the molecular data support the morphological and ontogenetic evidence that the pattern of 18 frontal-ventral-transversal cirri evolved in the stemline of the Oxytrichidae and was modified several times independently. Our results are also in agreement with taxonomic revisions: the separation of both Sterkiella nova from Oxytricha and Tetmemena pustulata from Stylonychia.     

Phylogeny and classification of the Psocodea, with particular reference to the lice (Psocodea: Phthiraptera)

ABSTRACT. Apomorphies that have been proposed for the Psocodea, Psocoptera, Phthiraptera and superfamilial groups within the Phthiraptera are enumerated and evaluated. The Psocodea and Phthiraptera are considered to be holophyletic, but the sister-group of the Phthiraptera lies within the Psocoptera. Within the Phthiraptera the Anoplura and Rhyncophthirina form a holophyletic group whose sister-group is the Ischnocera, and the Amblycera is the sister-group of this assemblage. The common ancestor of the Phthiraptera is suggested to have been parasitic, and all lice are believed to have evolved under environmental constraints similar to those operating today. On the evidence provided by host relationships the origin of the lice is dated as the Cretaceous, but the host of the ancestor of the order is not identified. The lice of marsupials in South America and Australia are not considered to comprise a holophyletic group.     

Molecular phylogeny and novel host associations of avian chewing lice (Insecta: Phthiraptera) from South Africa

Compared with Europe and the Americas, the ectoparasites of African birds are poorly understood, despite the avian fauna being relatively well known. Notably, previous studies documenting the host associations and genetic diversity of parasitic chewing lice of southern African birds have been limited in geographic and taxonomic scope. Recent field expeditions exploring the avian diversity in South Africa facilitated an opportunity to obtain louse specimens from a taxonomically diverse host assemblage. This study is the first to investigate avian louse host associations and diversity across a large portion of South Africa encompassing several distinct habitat types, while incorporating molecular genetic data (from portions of the mitochondrial COI and nuclear EF‐1α genes) for ectoparasite phylogenetic analyses. From 1105 South African bird individuals and 170 species examined for lice, a total of 105 new louse–host associations were observed. Morphological and genetic examination of lice with these new host associations reveals a maximum of 66 louse species new to science. Results of this study support the observation that examining museum specimens is a useful way to investigate louse diversity and host associations.     

Phylogeny of the order Tintinnida (Ciliophora, Spirotrichea) inferred from small- and large-subunit rRNA genes

Concatenated sequences of small- and large-subunit rRNA genes were used to infer the phylogeny of 29 species in six genera of Tintinnida. We confirmed previous results on the positions of major clusters and the grouping of various genera, including Stenosemella, the paraphyletic Tintinnopsis, the newly investigated Helicostomella, and some species of the polyphyletic Favella. Tintinnidium and Eutintinnus were found to be monophyletic. This study contributes to tintinnid phylogenetic reconstruction by increasing both the number of species and the range of genetic markers analyzed.     

Phylogenetic relationships of the genus Paramecium inferred from small subunit rRNA gene sequences

The genus Paramecium includes species that are well known and very common in freshwater environments. Species of Paramecium are morphologically divided into two distinct groups: the "bursaria" subgroup (foot-shaped) and the "aurelia" subgroup (cigar-shaped). Their placement within the class Oligohymenophorea has been supported by the analysis of the small subunit rRNA gene sequence of P. tetraurelia. To confirm the stability of this placement and to resolve relationships within the genus, small subunit rRNA gene sequences of P. bursaria, P. calkinsi, P. duboscqui, P. jenningsi, P. nephridiatum, P. primaurelia, and P. polycaryum were determined and aligned. Trees constructed using distance-matrix, maximum-likelihood, and maximum-parsimony methods all depicted the genus as a monophyletic group, clustering with the other oligohymenophorean taxa. Within the Paramecium clade, P. bursaria branches basal to the other species, although the remaining species of the morphologically defined "bursaria" subgroup do not group with P. bursaria, nor do they form a monophyletic subgroup. However, the species of the "aurelia" subgroup are closely related and strongly supported as a monophyletic group.     

Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences,with emphasis on the Devescovinidae and Calonymphidae (Trichomonadea)

Small subunit rRNA sequences were obtained by polymerase chain reaction from trichomonad symbionts of termites that belong to the polymastigont Calonymphidae, including Snyderella tabogae, Calonympha grassii, and Metacoronympha senta. The yet-unidentified sequence Nk9 previously obtained from the termite Neotermes koshunensis, has also been shown to derive from the Devescovinidae Devescovina sp. by in situ hybridization. These new sequences were analyzed by distance, parsimony, and likelihood methods in a broad phylogeny including all identified parabasalid sequences available in databases. All analyses revealed the emergence of a very well supported Devescovinidae/Calonymphidae group but showed an unexpected dichotomy of the Calonymphidae represented by the "Coronympha" and "Calonympha" groups. It strongly suggests that the polymastigont state observed in the Calonymphidae might be explained by at least two independent evolutionary events. In a second phylogenetic analysis, some yet-unidentified parabasalid sequences likely deriving from the Devescovinidae/Calonymphidae taxa, were added to our data set. This analysis confirmed the polyphyly of the Calonymphidae. A tentative identification is proposed for each of these sequences, and hypotheses on the origin of the Devescovinidae and Calonymphidae are discussed. Tritrichomonas foetus or a close relative might be the best candidate for the ancestor of the Devescovinidae, fairly consistent with morphology-based hypotheses. Regarding the Calonymphidae, the origin of the "Coronympha" group might be found within the Devescovinidae, related to Foaina, whereas the "Calonympha" group may directly descend from Tritrichomonas or related species.     

Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Hypermastigea

Small subunit rRNA gene sequences were identified without cultivation from parabasalid symbionts of termites belonging to the hypermastigid orders Trichonymphida (the genera Hoplonympha, Staurojoenina, Teranympha, and Eucomonympha) and Spirotrichonymphida (Spirotrichonymphella), and from four yet-unidentified parabasalid symbionts of the termite Incisitermes minor. All these new sequences were analyzed by Bayesian, likelihood, and parsimony methods in a broad phylogeny including all identified parabasalid sequences available in databases and some as yet unidentified sequences probably derived from hypermastigids. A salient point of our study focused on hypermastigids was the polyphyly of this class. We also noted a clear dichotomy between Trichonymphida and the other parabasalid taxa. However, this hypermastigid order was apparently polyphyletic, probably reflecting its morphological diversity. Among Trichonymphida, Teranympha (Teranymphidae) grouped together with the members of the family Eucomonymphidae, suggesting that its family status is ambiguous. The monophyletic lineage composed by Spirotrichonymphida exhibited a narrower branching pattern than Trichonymphida. The root of parabasalids was examined but could not be discerned accurately.     

The fauna and abundance of chewing lice (Insecta,Phthiraptera) parasitizing sedentary passerine birds (Aves,Passeriformes) in Yakutia

Data on the fauna, abundance and prevalence of chewing lice collected from 360 specimens of 13 sedentary species of passerine birds in Yakutia are given. A total of 3206 specimens of chewing lice belonging to 27 species of 6 genera were collected. Most of the studied bird species were infested with several chewing lice species. Exchange of parasites may take place between some bird species in the study region.     

Molecular phylogenetic study of the heterotrophic dinoflagellate genus Protoperidinium (Dinophyceae) inferred from small subunit rRNA gene sequences

In the present study, we investigated the intrageneric and intergeneric phylogenetic relationships of the heterotrophic marine dinoflagellate genus Protoperidinium. Using single‐cell polymerase chain reaction methods, we determined small subunit ribosomal RNA gene sequences for 10 Protoperidinium species belonging to four sections and two subgenera. Phylogenetic trees were constructed using maximum parsimony, neighbor joining and maximum likelihood methods. We found intraspecific variability of small subunit rDNA sequences in Protoperidinium conicum (Gran) Balech, Protoperidinium crassipes (Kofoid) Balech and Protoperidinium denticulatum (Gran et Braarud) Balech, but not in other species. The small subunit rDNA phylogeny revealed that the genus is monophyletic, but its phylogenetic position within the Dinophyceae could not be determined because of ambiguous basal topologies. Within the genus Protoperidinium, species of the subgenus Archaeperidinium with two anterior intercalary plates (2a) were shown to be monophyletic, but species of the subgenus Protoperidinium with three anterior intercalary plates (3a) were resolved as paraphyletic. The sections Avellana, Divergentia and Protoperidinium were shown to be monophyletic, while the section Conica was paraphyletic. Based on the trees obtained in the present study, most of the traditionally defined sections are supported by molecular phylogeny. It was also indicated that the section Avellana evolved from one of the Conica‐type dinoflagellates.     

Critical evaluation of five methods for quantifying chewing lice (Insecta: Phthiraptera).

Five methods for estimating the abundance of chewing lice (Insecta: Phthiraptera) were tested. To evaluate the methods, feral pigeons (Columba livia) and 2 species of ischnoceran lice were used. The fraction of lice removed by each method was compared, and least squares linear regression was used to determine how well each method predicted total abundance. Total abundance was assessed in most cases using KOH dissolution. The 2 methods involving dead birds (body washing and post-mortem-ruffling) provided better results than 3 methods involving live birds (dust-ruffling, fumigation chambers, and visual examination). Body washing removed the largest fraction of lice (>82%) and was an extremely accurate predictor of total abundance (r2 = 0.99). Post-mortem-ruffling was also an accurate predictor of total abundance (r2 > or = 0.88), even though it removed a smaller proportion of lice (<70%) than body washing. Dust-ruffling and fumigation chambers removed even fewer lice, but were still reasonably accurate predictors of total abundance, except in the case of data sets restricted to birds with relatively few lice. Visual examination, the only method not requiring that lice be removed from the host, was an accurate predictor of louse abundance, except in the case of wing lice on lightly parasitized birds.