Characterization of Fasciola spp. in Myanmar on the basis of spermatogenesis status and nuclear and mitochondrial DNA markers

Fasciola spp. in Myanmar were characterized on the basis of spermatogenesis status and DNA markers of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase subunit 1 (nad1). We collected 88 adult flukes from Yangon, Lashio, and Myitkyina. Spermatogenesis status was analyzed by the presence of sperm in the seminal vesicles, and 8 aspermic and 80 spermic flukes were detected. The flukes were identified on the basis of spermatogenesis status and ITS1 types which were analyzed by a PCR-RFLP method, and 80 spermic flukes were identified as F. gigantica. A very low detection rate of aspermic Fasciola sp. indicated that they are not established in Myanmar. In phylogenetic analyses, the 7 aspermic Fasciola sp. from Myitkyina displayed a haplotype in nad1 sequence, which was identical to that of aspermic Fasciola sp. from other Asian countries including China. Therefore, they were probably introduced from China through an infected domestic ruminant. On the other hand, 17 nad1 haplotypes detected in F. gigantica belonged to 2 clades unique to Myanmar, each with a distinct founder haplotype in a network analysis. This indicated a unique history of F. gigantica introduction into Myanmar involving ancient artificial movements of domestic ruminants.     

Phylogenetic relationships of finches and allies based on nuclear and mitochondrial DNA

The complete mitochondrial gene cytochrome b in combination with a nuclear gene, beta-fibrinogen intron 7, is sequenced for different groups of mostly granivorous species in the superfamily Passeroidea, with a focus on the estrildids and fringillids. From our study we can conclude that within the group of granivorous finches two clades can be distinguished, the estrildid weaver clade and the cardueline, fringillid, emberizid, passerine sparrow clade. In contrast to many other studies the passerine sparrows are not placed within the weavers estrildid clade which is in agreement with other recent studies (e.g., ). Our study also shows that the estrildids do form a monophyletic group, but there is a division based on geographic origin: an African group and an Asian-Australian group. Within the Fringillidae the Fringilla species are the sister group of the carduelines.     

Phylogenetic relationships in European Ceriporiopsis species inferred from nuclear and mitochondrial ribosomal DNA sequences

The aim of this work was to clarify taxonomy and examine evolutionary relationships within European Ceriporiopsis species using a combined analysis of the large subunit (nLSU) nuclear rRNA and small subunit (mtSSU) mitochondrial rRNA gene sequences. Data from the ITS region were applied to enhance the view of the phylogenetic relationships among different species. The studied samples grouped into four complex clades, suggesting that the genus Ceriporiopsis is polyphyletic. The generic type Ceriporiopsis gilvescens formed a separate group together with Ceriporiopsis guidella and Phlebia spp. in the phlebioid clade. In this clade, the closely related species Ceriporiopsis resinascens and Ceriporiopsis pseudogilvescens grouped together with Ceriporiopsis aneirina. C. resinascens and C. pseudogilvescens have identical LSU and SSU sequences but differ in ITS. Ceriporiopsis pannocincta also fell in the phlebioid clade, but showed closer proximity to Gloeoporus dichrous than to C. gilvescens or C. aneirina–C. pseudogilvescens–C. resinascens group. Another clade was composed of a Ceriporiopsis balaenae–Ceriporiopsis consobrina group and was found to be closely related to Antrodiella and Frantisekia, with the overall clade highly reminiscent of the residual polyporoid clade. The monotypic genus Pouzaroporia, erected in the past for Ceriporiopsis subrufa due to its remarkable morphological differences, also fell within the residual polyporoid clade. Ceriporiopsis subvermispora held an isolated position from the other species of the genus. Therefore, the previously proposed name Gelatoporia subvermispora has been adopted for this species. Physisporinus rivulosus appeared unrelated to two other European Physisporinus species. Moreover, Ceriporiopsis (=Skeletocutis) jelicii grouped in a separate clade, distinct from Ceriporiopsis species. Finally, the ITS data demonstrated the proximity of some Ceriporiopsis species (Ceriporiopsis portcrosensis and Ceriporiopsis subsphaerospora) to Skeletocutis amorpha.     

Phylogenetic relationships of Sparassis inferred from nuclear and mitochondrial ribosomal DNA and RNA polymerase sequences

Sparassis species show extensive morphological variation, especially when materials from eastern Asia and Australia are compared with collections from North America and Europe. We have been studying the taxonomy of Sparassis from eastern Asia, North America, Australia and Europe, using both morphological and molecular data. DNA was extracted from 32 recent collections of Sparassis from Australia, Canada, China, Finland, France, Germany, Japan, Switzerland, Thailand, the United Kingdom and the United States. The report of a Sparassis taxon from Australia is the first report of this genus from the Southern Hemisphere. Sequences of nuclear and mitochondrial rDNA and the gene encoding RNA polymerase subunit II (RPB2) were used to examine relationships both within the genus Sparassis and between Sparassis species and other members of the polyporoid clade. Equally weighted parsimony analyses and Bayesian analyses were performed using independent datasets and combined datasets of sequences from different regions. Our results suggest that: (i) Polyporoid fungi producing a brown rot may form a clade; (ii) as suggested in a previous study, Sparassis and Phaeolus form a monophyletic group, which is united by the production of a brown rot, the presence of a bipolar mating system and the frequent habit of growing as a root and butt rot on living trees; (iii) at least seven lineages are within Sparassis, represented by S. spathulata, S. brevipes, S. crispa, S. radicata and three taxa that have not been described, which can be distinguished on the basis of fruiting body structure, presence or absence of clamp connections, presence or absence of cystidia and spore size.     

Phylogenetic relationships of Old World Brassicaceae from Iran based on nuclear ribosomal DNA sequences

Phylogenetic analysis of 155 nuclear rDNA ITS sequences among them 19 Iranian endemic genera were used to elucidate phylogenetic relationships of Old World Brassicaceae from Iran in the context of the most recent tribal system suggested by Al-Shehbaz et al. [Al-Shehbaz, I.A., Beilstein, M.A, Kellogg, E.A., 2006. Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview. Plant Syst. Evol. 259, 89–120]. Iranian endemic taxa are assigned to 16 clades, 15 of these correspond to recognized tribes. Our data support the recent tribal recognition of Calepina and relatives and further indicate that the Orychophragmus clade (with Conringia planisiliqua and Orychophragmus) may be recognized as a new tribe. Our data also support the inclusion of 13 genera not previously studied, or with unresolved positions in previous phylogenetic analyses in 10 tribes with the tribal assignment given in parentheses: Acanthocardamum (Aethionemeae), Alyssopsis (Camelineae), Anastatica (Malcolmieae), Asperuginoides (Cochlearieae), Camelinopsis (Thlaspideae), Didymophysa (Thlaspideae), Dielsiocharisi (Camelineae), Lachnoloma (Anchonieae), Micrantha (Anchonieae), Noccidium (Camelineae), Octoceras (Euclidieae), Pseudofortuynia (Sisymbrieae) and Streptoloma (Euclidieae). ITS data and morphological characters further indicate that the remaining five genera, i.e., Acanthocardamum, Olimarabidopsis, Brossardia, Noccidium and Zuvanda may be subsumed under Aethionema, Alyssopsis, Noccaea, Capsella and Conringia, respectively. Alyssum, Chorispora, Fibigia and Goldbachia are paraphyletic and Conringia, Malcolmia, Matthiola are polyphyletic taxa.     

Phylogenetic relationships in Bupleurum (apiaceae) based on nuclear ribosomal DNA its sequence data

BACKGROUND AND AIMS: The genus Bupleurum has long been recognized as a natural group, but its infrageneric classification is controversial and has not yet been studied in the light of sequence data. METHODS: Phylogenetic relationships among 32 species (35 taxa) of the genus Bupleurum were investigated by comparative sequencing of the ITS region of the 18-26S nuclear ribosomal DNA repeat. Exemplar taxa from all currently accepted sections and subsections of the genus were included, along with outgroups from four other early branching Apioideae genera (Anginon, Heteromorpha, Physospermum and Pleurospermum). RESULTS: Phylogenies generated by maximum parsimony, maximum likelihood, and neighbour-joining methods show similar topologies, demonstrating monophyly of Bupleurum and the division of the genus into two major clades. This division is also supported by analysis of the 5.8S coding sequence alone. The first branching clade is formed by all the species of the genus with pinnate-reticulate veined leaves and B. rigidum with a unique type of leaf venation. The other major clade includes the remaining species studied, all of which have more or less parallel-veined leaves. CONCLUSIONS: These phylogenetic results do not agree with any previous classifications of the genus. Molecular data also suggest that the endemic Macaronesian species B. salicifolium is a neoendemic, as the sequence divergence between the populations in Madeira and Canary Islands, and closer mainland relatives in north-west Africa is small. All endemic north-west African taxa are included in a single unresolved but well-supported clade, and the low nucleotide variation of ITS suggests a recent radiation within this group. The only southern hemisphere species, B. mundii (southern Africa), is shown to be a neoendemic, apparently closely related to B. falcatum, a Eurasian species.     

Phylogenetic relationships of living and recently extinct bandicoots based on nuclear and mitochondrial DNA sequences

Bandicoots (Peramelemorphia) are a major order of australidelphian marsupials, which despite a fossil record spanning at least the past 25 million years and a pandemic Australasian range, remain poorly understood in terms of their evolutionary relationships. Many living peramelemorphians are critically endangered, making this group an important focus for biological and conservation research. To establish a phylogenetic framework for the group, we compiled a concatenated alignment of nuclear and mitochondrial DNA sequences, comprising representatives of most living and recently extinct species. Our analysis confirmed the currently recognised deep split between Macrotis (Thylacomyidae), Chaeropus (Chaeropodidae) and all other living bandicoots (Peramelidae). The mainly New Guinean rainforest peramelids were returned as the sister clade of Australian dry-country species. The wholly New Guinean Peroryctinae was sister to Echymiperinae. The poorly known and perhaps recently extinct Seram Bandicoot (Rhynchomeles) is sister to Echymipera. Estimates of divergence times from relaxed-clock Bayesian methods suggest that living bandicoots originated in the late Oligocene or early Miocene, much earlier than currently thought based on fossils. Subsequent radiations within Peramelemorphia probably took place on the Australian mainland during the Miocene, with diversification of rainforest taxa on the newly emergent New Guinean landmasses through the middle-late Miocene and complete establishment of modern lineages by the early Pliocene.     

Molecular characterization of Fasciola spp. from the endemic area of northern Iran based on nuclear ribosomal DNA sequences

Fasciolosis caused by Fasciola spp. (Platyhelminthes: Trematoda: Digenea) is considered as the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. In the endemic regions of the North of Iran, Fasciola hepatica and Fasciola gigantica have been previously characterized on the basis of morphometric differences, but the use of molecular markers is necessary to distinguish exactly between species and intermediate forms. Samples from buffaloes and goats from different localities of northern Iran were identified morphologically and then genetically characterized by sequences of the first (ITS-1) and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA). Comparison of the ITS of the northern Iranian samples with sequences of Fasciola spp. from GenBank showed that the examined specimens had sequences identical to those of the most frequent haplotypes of F. hepatica (n = 25, 48.1%) and F. gigantica (n = 20, 38.45%), which differed from each other in different variable nucleotide positions of ITS region sequences, and their intermediate forms (n = 7, 13.45%), which had nucleotides overlapped between the two Fasciola species in all the positions. The ITS sequences from populations of Fasciola isolates in buffaloes and goats had experienced introgression/hybridization as previously reported in isolates from other ruminants and humans. Based on ITS-1 and ITS-2 sequences, flukes are scattered in pure F. hepatica, F. gigantica and intermediate Fasciola clades, revealing that multiple genotypes of Fasciola are able to infect goats and buffaloes in North of Iran. Furthermore, the phylogenetic trees based upon the ITS-1 and ITS-2 sequences showed a close relationship of the Iranian samples with isolates of F. hepatica and F. gigantica from different localities of Africa and Asia. In the present study, the intergenic transcribed spacers ITS-1 and ITS-2 showed to be reliable approaches for the genetic differentiation of Fasciola spp., providing bases for further studies on F. hepatica, F. gigantica and their intermediate forms in the endemic areas in Asia.     

Molecular characterization of Fasciola gigantica from Mauritania based on mitochondrial and nuclear ribosomal DNA sequences

Fasciolosis caused by Fasciola hepatica and Fasciola gigantica (Platyhelminthes: Trematoda: Digenea) is considered the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. From Africa, F. gigantica has been previously characterized from Burkina Faso, Senegal, Kenya, Zambia and Mali, while F. hepatica has been reported from Morocco and Tunisia, and both species have been observed from Ethiopia and Egypt on the basis of morphometric differences, while the use of molecular markers is necessary to distinguish exactly between species. Samples identified morphologically as F. gigantica (n = 60) from sheep and cattle from different geographical localities of Mauritania were genetically characterized by sequences of the first (ITS-1), the 5.8S, and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA) genes and the mitochondrial Cytochrome c Oxidase I (COI) gene.Comparison of the sequences of the Mauritanian samples with sequences of Fasciola spp. from GenBank confirmed that all samples belong to the species F. gigantica. The nucleotide sequencing of ITS rDNA of F. gigantica showed no nucleotide variation in the ITS-1, 5.8S, and ITS-2 rDNA sequences among all samples examined and those from Burkina Faso, Kenya, Egypt and Iran. The phylogenetic trees based on the ITS-1 and ITS-2 sequences showed a close relationship of the Mauritanian samples with isolates of F. gigantica from different localities of Africa and Asia. The COI genotypes of the Mauritanian specimens of F. gigantica had a high level of diversity, and they belonged to the F. gigantica phylogenically distinguishable clade. The present study is the first molecular characterization of F. gigantica in sheep and cattle from Mauritania, allowing a reliable approach for the genetic differentiation of Fasciola spp. and providing basis for further studies on liver flukes in the African countries.     

Identification of conservation units in the European Mergus merganser based on nuclear and mitochondrial DNA markers

The conservation status of small breeding areas of the Goosander (Mergus merganser merganser) in Central Europe is unclear. Geographic isolation of these areas suggests restricted gene flow to and from large North-European populations. On the other hand, migrating Goosanders from northern Europe join the Central European breeding population for wintering. To evaluate the conservation status of the small breeding areas we assessed the genetic structure of M. merganser populations in Europe by examining two nuclear marker systems (microsatellites and Single Nucleotide Polymorphisms, SNP) and mitochondrial (mtDNA) control region sequence variation for Goosanders in 11 sampling areas representing three of five distinct breeding areas and two subspecies (M. m. merganser and M. m. americanus). Overall population differentiation estimates including both subspecies were high, both based on mtDNA () and nuclear markers (θ _ST = 0.219; 95% CI 0.088–0.398, SNP and microsatellites combined). Within Europe, mtDNA revealed a strong overall () and significant pairwise population differentiation between almost all comparisons. In contrast, both nuclear marker systems combined revealed only a small overall genetic differentiation (θ _ST = 0.022; 95% CI 0.003–0.041). The strong genetic differentiation based on female-inherited mtDNA but not on biparentally inherited nuclear markers can be explained by sex-biased dispersal and strong female philopatry. Therefore, small breeding areas in Europe are endangered despite large male-mediated gene-flow, because when these populations decline, only males—but due to strong philopatry not females—can be efficiently supplemented by migration from the large North European populations. We therefore propose to manage the small breeding areas independently and to strengthen conservation efforts for this species in Central Europe.     

Phylogenetic relationships of the Dactyloa clade of Anolis lizards based on nuclear and mitochondrial DNA sequence data

The Dactyloa clade, one of two major subgroups of mainland Anolis lizards, is distributed from Costa Rica to Peru, including the Amazon region and the southern Lesser Antilles. We estimated the phylogenetic relationships within Dactyloa based on mitochondrial (ND2, five transfer-RNAs, COI) and nuclear (RAG1) gene regions using likelihood and Bayesian methods under different partition strategies. In addition, we tested the monophyly of five previously recognized groups within Dactyloa. The data strongly support the monophyly of Dactyloa and five major clades: eastern, latifrons, Phenacosaurus, roquet and western, each of which exhibits a coherent geographic range. Relationships among the five major clades are less clear: support for basal nodes within Dactyloa is weak and some contradictory relationships are supported by different datasets and/or phylogenetic methods. Of the previously recognized subgroups within Dactyloa, only the roquet series consistently passed the topology tests applied. The monophyly of the aequatorialis, latifrons (as traditionally circumscribed) and punctatus series was strongly rejected, and the monophyly of Phenacosaurus (as traditionally circumscribed) yielded mixed results. The results of the phylogenetic analyses suggest the need for a revised taxonomy and have implications for the biogeography and tempo of the Dactyloa radiation.     

Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences

The superorder Elopomorpha, a grouping which includes all teleost fishes that possess a specialized leptocephalous larva [true eels (Anguilliformes), gulpers and bobtail snipe eels (Saccopharyngiformes), bonefishes, spiny eels, and halosaurs (Albuliformes, including Notacanthiformes), ladyfishes and tarpons (Elopiformes, including Megalopiformes)] comprises >800 species for which phylogenetic relationships are poorly understood. In the present study, we analyzed mitochondrial DNA sequences in segments of the 12S and 16S rRNA genes in 33 elopomorph taxa encompassing all of the previously proposed orders, and 9 of the 15 currently recognized families of the Anguilliformes, as well as outgroup representatives from the superorders Osteoglossomorpha (nine species) and Clupeomorpha (three species), to develop phylogenetic hypotheses based on distance and parsimony methods. Both methods failed to support the monophyly of the Elopomorpha, casting doubt on the validity of the leptocephalus as an elopomorph synapomorphy. The orders Elopiformes, Albuliformes, and Anguilliformes, however, were resolved as monophyletic assemblages. Parsimony analysis supported the separation of the Anguilliformes into two groups (primitive and advanced) based on the presence of divided versus fused frontal bones. In addition, the molecular data indicated a close affinity of the anguilliform Thalassenchelys coheni (incertae sedis), known only from the leptocephalus, with the family Serrivomeridae. The implications of these data as regards the evolution of the elopomorph assemblage are discussed.     

Isolation and characterization of intraspecific cybrids : Effect of mitochondrial DNA on their cellular properties

Cybrid clones were obtained by fusing whole cells of rat glioma C6BU-1, resistant to 5-bromodeoxyuridine (BrdU), with cytoplasts of embryonic rat 3Y1CAP cells, resistant to chloramphenicol (CAP), in selective medium with BrdU and CAP. The clones resistant to BrdU and CAP were confirmed to be cybrids by chromosome and mtDNA analyses. More than half the mtDNA of all the cybrid clones was from the 3Y1CAP cells. After cultivation of a cybrid clone Y22 for 3 months in the absence of CAP, subclones were isolated. One subclone Y22-22 contained predominantly mitochondrial DNA (mtDNA) from the 3Y1CAP cells. Using this subclone, the effects of the mitochondrial genome on cellular properties were examined. The growth patterns, expression of glioma-specific beta-adrenergic receptor, and composition of the major proteins of C6BU-1 cells were not affected by transmitted mtDNA from the 3Y1CAP cells. This procedure for isolating cells containing predominantly foreign mtDNA will be useful in studies on the interaction between genomes of the mitochondria and nucleus.     

Phylogeny of Veronica in the Southern and Northern Hemispheres based on plastid,nuclear ribosomal and nuclear low-copy DNA

The cosmopolitan and ecologically diverse genus Veronica with approximately 450 species is the largest genus of the newly circumscribed Plantaginaceae. Previous analyses of Veronica DNA sequences were in stark contrast to traditional systematics. However, analyses did not allow many inferences regarding the relationship between major groups identified, hindering further analysis of diversification and evolutionary trends in the genus. To resolve the backbone relationships of Veronica, we added sequences from additional plastid DNA regions to existing data and analyzed matching data sets for 78 taxa and more than 5000 aligned characters from nuclear ribosomal DNA and plastid DNA regions. The results provide the best resolved and supported estimate of relationships among major groups in the Northern (Veronica s. str.) and Southern Hemisphere (hebes). We present new informal names for the five main species groups within the Southern Hemisphere sect. Hebe. Furthermore, in two instances we provide morphological and karyological characters supporting these relationships. Finally, we present the first evidence from nuclear low-copy CYCLOIDEA2-region to compare results from the plastid genome with the nuclear genome.     

Closing the gaps: phylogenetic relationships in the Brassicaceae based on DNA sequence data of nuclear ribosomal ITS region

Sequence data from the nuclear encoded ribosomal internal transcribed spacer (ITS) region were used to determine monophyly of tribes, tribal limits, and tribal relationships of 96 so far unassigned or tentatively assigned genera (represented by 101 taxa/accessions) within the Brassicaceae. Maximum-parsimony and maximum-likelihood analyses of 185 ITS Brassicaceae sequences, which also included representatives of each of the 34 currently recognized tribes, supported the separate phylogenetic distinctness of these tribes and permitted the tribal assignment of all but 12 of the unassigned genera into tribal clades. The data support the recognition of eight new, well-resolved, uni- or oligogeneric tribes recognized herein as the Alyssopsideae [96% bootstrap support (BS); including the central and southwestern Asian Alyssopsis and Calymmatium], Asteae (100% BS; including the Mexican Asta), Eudemeae (97% BS; South American Brayopsis, Eudema, and Xerodraba), Kernereae (96% BS; European Kernera and Rhizobotrya), Notothlaspideae (100% BS; New Zealandic Notothlaspi), Oreophytoneae (100% BS; eastern African Oreophyton and southern European Murbeckiella), and Yinshanieae (100% BS; Chinese Yinshania), as well as the moderately supported Microlepidieae (75% BS; Australian Microlepidium and Carinavalva). Furthermore, the results fully support the recent findings that the tribes Schizopetaleae and Thelypodieae ought to be recognized as two distinct tribes instead of a single tribe, as well as provide some support for the re-establishment of the tribe Cremolobeae, bringing the total number to 44 tribes in the family. Nearly 92% (308) of the 336 genera in the family have been assigned to a tribe. The earlier-published Anastaticeae is taken here to replace the Malcolmieae.     

Molecular phylogeny of North American long-eared bats (Vespertilionidae: Corynorhinus); inter- and intraspecific relationships inferred from mitochondrial and nuclear DNA sequences

The taxonomy of the North American big-eared bats, genus Corynorhinus, was revised by Handley [Handley, C.O., 1959. A revision of the American bats of the genera Euderma and Plecotus. Proc. U.S. Nat. Mus. 110, 95-246] using a morphological systematics approach. Handley employed 17 morphological characters and identified only four characters that reliably differentiated the three species he recognized, C. townsendii, C. rafinesquii, and C. mexicanus. All three species have been shown to lead relatively sedentary lives and have a wing morphology that limits long-distance dispersal. Further, populations of two species, C. townsendii and C. rafinesquii, are considered to be declining. Handley [Handley, C.O., 1959. A revision of the American bats of the genera Euderma and Plecotus. Proc. U.S. Nat. Mus. 110, 95-246] recognized five subspecies of C. townsendii (C. t. australis, C. t. ingens, C. t. pallescens, C. t. townsendii, and C. t. virginianus) and two of C. rafinesquii (C. r. rafinesquii and C. r. macrotis). Two C. townsendii subspecies, C. t. ingens and C. t. virginianus, are listed as endangered under the Endangered Species Act. These facts and the lack of a thorough molecular systematic examination of this genus were the impetus for this study. Using mitochondrial and nuclear intron DNA sequences, a molecular phylogeny was inferred. The combined DNA phylogeny supports Handley's [Handley, C.O., 1959. A revision of the American bats of the genera Euderma and Plecotus. Proc. U. S. Nat. Mus. 110, 95-246] designation of three species. Further the endangered subspecies, C. t. ingens and C. t. virginianus are corroborated, as were the monophyly of the other subspecies. However, the geographical ranges of two of these subspecies, C. t. pallescens and C. t. townsendii, are revised based on biogeographic distributions as understood from our results. Estimates of timing of divergences indicate that the three species, C. townsendii, C. rafinesquii, and C. mexicanus may have diverged before Pleistocene climatic oscillations began, and therefore their cladogenesis was not the result of those processes. However, subspecific divergences within C. townsendii appear to have occurred during and been driven largely by the climatic processes of the Pleistocene Epoch. We propose new hypotheses of dispersal scenarios that may have led to the current biogeography of these lineages.     

Variation in ribosomal and mitochondrial DNA sequences demonstrates the existence of intraspecific groups in Paramecium multimicronucleatum (Ciliophora, Oligohymenophorea)

This is the first phylogenetic study of the intraspecific variability within Paramecium multimicronucleatum with the application of two-loci analysis (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA) carried out on numerous strains originated from different continents. The species has been shown to have a complex structure of several sibling species within taxonomic species. Our analysis revealed the existence of 10 haplotypes for the rDNA fragment and 15 haplotypes for the COI fragment in the studied material. The mean distance for all of the studied P. multimicronucleatum sequence pairs was p=0.025/0.082 (rDNA/COI). Despite the greater variation of the COI fragment, the COI-derived tree topology is similar to the tree topology constructed on the basis of the rDNA fragment. P. multimicronucleatum strains are divided into three main clades. The tree based on COI fragment analysis presents a greater resolution of the studied P. multimicronucleatum strains. Our results indicate that the strains of P. multimicronucleatum that appear in different clades on the trees could belong to different syngens.     

Phylogenetic relationships of the bulbuls (Aves: Pycnonotidae) based on mitochondrial and nuclear DNA sequence data

Bulbuls (Aves: Pycnonotidae) are a fairly speciose (ca. 130 sp.) bird family restricted to the Old World. Family limits and taxonomy have been revised substantially over the past decade, but a comprehensive molecular phylogeny for the family has not been undertaken. Using nuclear and mitochondrial DNA sequences, we reconstructed a well-supported phylogenetic hypothesis for the bulbuls. Three basal lineages were identified: a large African clade, a large Asian clade that also included African Pycnonotus species, and the monotypic African genus Calyptocichla. The African clade was sister to the other two lineages, but this placement did not have high branch support. The genus Pycnonotus was not monophyletic because three species (eutilotus, melanoleucos, and atriceps) were highly diverged from the other species and sister to all other Asian taxa. Additional taxon sampling is needed to further resolve relationships and taxonomy within the large and variable Hypsipetes complex.     

General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics

To choose one or more appropriate molecular markers or gene regions for resolving a particular systematic question among the organisms at a certain categorical level is still a very difficult process. The primary goal of this review, therefore, is to provide a theoretical information in choosing one or more molecular markers or gene regions by illustrating general properties and phylogenetic utilities of nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) that have been most commonly used for phylogenetic researches. The highly conserved molecular markers and/or gene regions are useful for investigating phylogenetic relationships at higher categorical levels (deep branches of evolutionary history). On the other hand, the hypervariable molecular markers and/or gene regions are useful for elucidating phylogenetic relationships at lower categorical levels (recently diverged branches). In summary, different selective forces have led to the evolution of various molecular markers or gene regions with varying degrees of sequence conservation. Thus, appropriate molecular markers or gene regions should be chosen with even greater caution to deduce true phylogenetic relationships over a broad taxonomic spectrum.