Molecular Systematics of the Malagasy Babblers (Passeriformes: Timaliidae) and Warblers (Passeriformes: Sylviidae), Based on Cytochrome b and 16S rRNA Sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy “babblers” are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy “babblers” are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Molecular systematics of the family Mormoopidae (Chiroptera) based on cytochrome b and recombination activating gene 2 sequences

We examined 1140 bp of the mitochondrial cytochrome b gene and 1398 bp of the nuclear RAG2 gene to investigate the systematics of the eight species of bats within the family Mormoopidae. It was concluded that within the genus Pteronotus there were four valid subgenera: Phyllodia, Chilonycteris, Pteronotus, and an undescribed subgenus. Within Pteronotus, P. parnellii either was part of an unresolved tetratomy with the other three subgenera (cytochrome b data) or was basal (RAG2 and combined data). For three species, P. gymnonotus, P. macleayii, and P. quadridens, our sample revealed little geographic variation. In P. davyi and P. parnellii, the magnitude of genetic distance suggests the possibility of two biological species existing within the currently recognized taxa. Within P. personatus, there was substantial geographic variation partitioned in a step-like fashion among our specimens. Neither of the species within the genus Mormoops showed the deep distance nodes present in P. davyi, P. parnellii, and P. personatus. Cytochrome b and RAG2 data indicated that M. megalophylla evolved recently from its common ancestor. Although there was considerable agreement among the branching patterns for the nuclear and mitochondrial genes, both genes failed to provide robust data concerning the evolutionary relationships among the subgenera.     

Molecular systematics and diversification of the Asian scimitar babblers (Timaliidae, Aves) based on mitochondrial and nuclear DNA sequences

The Asian scimitar babblers, including the genus Pomatorhinus and Xiphirhynchus, are a small group of babblers characterized by long down-curved bills and a distribution throughout East and Southeast Asia. To infer the molecular phylogeny of this group and their divergence time, we examined sequences of multiple fragments including two entire mitochondrial genes and four nuclear introns (4352 bp in total) from multiple samples of eight of the nine recognized species of Asian scimitar babblers. The phylogeny resulting from the concatenated multi-locus dataset suggests that Pomatorhinus is paraphyletic. Due to its paraphyly, we propose dividing the traditional genus Pomatorhinus into two morphologically and genetically diagnosable genera: Pomatorhinus and Erythrogenys. Results of the molecular dating based on the conventional mitochondrial DNA divergence rate indicates that the diversification of these babblers is likely congruent with the historical climatic events. Our findings shed light on the diversification of avian species in southern Asia, a poorly studied biodiversity hotspot.     

Molecular systematics of Middle American harvest mice Reithrodontomys (Muridae), estimated from mitochondrial cytochrome b gene sequences

We estimated phylogenetic relationships among 16 species of harvest mice using sequences from the mitochondrial cytochrome b (cyt b) gene. Gene phylogenies constructed using maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) optimality criteria were largely congruent and arranged taxa into two groups corresponding to the two recognized subgenera (Aporodon and Reithrodontomys). All analyses also recovered R. mexicanus and R. microdon as polyphyletic, although greater resolution was obtained using ML and BI approaches. Within R. mexicanus, three clades were identified with high nodal support (MP and ML bootstrap, Bremer decay and Bayesian posterior probabilities). One represented a subspecies of R. mexicanus from Costa Rica (R. m. cherrii) and a second was distributed in the Sierra Madre Oriental of Mexico. The third R. mexicanus clade consisted of mice from southern Mexico southward to South America. Polyphyly between the two moieties of R. microdon corresponded to the Isthmus of Tehuantepec in southern Mexico. Populations of R. microdon microdon to the east of the isthmus (Chiapas, Mexico) grouped with R. tenuirostris, whereas samples of R. m. albilabris to the west in Oaxaca, Mexico, formed a clade with R. bakeri. Within the subgenus Reithrodontomys, all analyses recovered R. montanus and R. raviventris as sister taxa, a finding consistent with earlier studies based on allozymes and cyt b data. There was also strong support (ML and BI criteria) for a clade consisting of ((R. megalotis, R. zacatecae) (R. sumichrasti)). In addition, cytb gene phylogenies (MP, ML, and BI) recovered R. fulvescens and R. hirsutus (ML and BI) as basal taxa within the subgenus Reithrodontomys. Constraint analyses demonstrated that tree topologies treating the two subgenera (Aporodon and Reithrodontomys) as monophyletic (ML criterion) was significantly better (p>0.036) and supported polyphyly of R. mexicanus (both ML and MP criteria - p>0.013) and R. microdon (MP criterion only for certain topologies; p>0.02). Although several species-level taxa were identified based on multiple, independent data sets, we recommended a conservative approach which will involve thorough analyses of museum specimens including material from type localities together with additional sampling and data from multiple, nuclear gene markers.     

Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony,likelihood, and Bayesian approaches

The Carangidae represent a diverse family of marine fishes that include both ecologically and economically important species. Currently, there are four recognized tribes within the family, but phylogenetic relationships among them based on morphology are not resolved. In addition, the tribe Carangini contains species with a variety of body forms and no study has tried to interpret the evolution of this diversity. We used DNA sequences from the mitochondrial cytochrome b gene to reconstruct the phylogenetic history of 50 species from each of the four tribes of Carangidae and four carangoid outgroup taxa. We found support for the monophyly of three tribes within the Carangidae (Carangini, Naucratini, and Trachinotini); however, monophyly of the fourth tribe (Scomberoidini) remains questionable. A sister group relationship between the Carangini and the Naucratini is well supported. This clade is apparently sister to the Trachinotini plus Scomberoidini but there is uncertain support for this relationship. Additionally, we examined the evolution of body form within the tribe Carangini and determined that each of the predominant clades has a distinct evolutionary trend in body form. We tested three methods of phylogenetic inference, parsimony, maximum-likelihood, and Bayesian inference. Whereas the three analyses produced largely congruent hypotheses, they differed in several important relationships. Maximum-likelihood and Bayesian methods produced hypotheses with higher support values for deep branches. The Bayesian analysis was computationally much faster and yet produced phylogenetic hypotheses that were very similar to those of the maximum-likelihood analysis.     

Molecular phylogeny of the genus Oryzomys (Rodentia: Sigmodontinae) based on cytochrome b DNA sequences

The genus Oryzomys comprises 40 species arranged in several species groups. To test the monophyly of three Oryzomys species groups ("capito," nitidus, and subflavus), we analyzed, by distance, parsimony, and maximum-likelihood (ML), 801 bp of the mitochondrial gene cytochrome b. Our results did not sustain the monophyly of Oryzomys nor of the nitidus and subflavus species groups. Within the "capito" species group, O. perenensis appeared as a valid species, as a sister branch of the clade formed by O. megacephalus and O. laticeps. Within the nitidius species group, only the association between O. nitidus and O. lamia was well supported.The subflavus species group split into two clades: one with O. subflavus karyomorphotypes and another grouping O. angouya with species of different genera in the parsimony, distance, and ML trees.     

Molecular systematics of Volvocales (Chlorophyceae, Chlorophyta) based on exhaustive 18S rRNA phylogenetic analyses

The taxonomy of Volvocales (Chlorophyceae, Chlorophyta) was traditionally based solely on morphological characteristics. However, because recent molecular phylogeny largely contradicts the traditional subordinal and familial classifications, no classification system has yet been established that describes the subdivision of Volvocales in a manner consistent with the phylogenetic relationships. Towards development of a natural classification system at and above the generic level, identification and sorting of hundreds of sequences based on subjective phylogenetic definitions is a significant step. We constructed an 18S rRNA gene phylogeny based on 449 volvocalean sequences collected using exhaustive BLAST searches of the GenBank database. Many chimeric sequences, which can cause fallacious phylogenetic trees, were detected and excluded during data collection. The results revealed 21 strongly supported primary clades within phylogenetically redefined Volvocales. Phylogenetic classification following PhyloCode was proposed based on the presented 18S rRNA gene phylogeny along with the results of previous combined 18S and 26S rRNA and chloroplast multigene analyses.     

Molecular phylogeny of musk deer: a genomic view with mitochondrial 16S rRNA and cytochrome b gene

The phylogenetic status of the infra order Pecora is controversial, even though it is supported by paleontological, morphological, and molecular evidence. We analyzed two mitochondrial genes (i.e., 16S rRNA and cytochrome b) to resolve the phylogenetic position of pecoran species, i.e., the Bovidae, Cervidae, and Moschidae endemic to the Indian subcontinent. We used phylogenetic analysis based on different algorithms, including neighbor joining, maximum parsimony, Bayesian inference, maximum likelihood, minimum evolution, median joining network, along with multidimensional scaling, and DNA word analysis. Our results established the basal position of Tragulidae and the monophyly of the infra order Pecora within the Suborder Ruminantia. Our results also demonstrated that Bovidae, Cervidae, and Moschidae are allied with the placement of musk deer as more closely related to bovids than to cervids. Molecular dating based on sequence analysis shows that the radiation of Pecora occurred during the early Oligocene and that the majority of the pecoran families radiated and dispersed rapidly during the Oligocene/Miocene transition.     

Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences

The family Sisoridae is one of the largest and most diverse Asiatic catfish families, most species occurring in the water systems of the Qinhai-Tibetan Plateau and East Himalayas. To date published morphological and molecular phylogenetics hypotheses of sisorid catfishes are part congruent, and there are some areas of significant disagreement with respect to intergeneric relationships. We used mitochondrial cytochrome b and 16S rRNA gene sequences to clarify existing gaps in phylogenetics and to test conflicting vicariant and dispersal biogeographical hypotheses of Chinese sisorids using dispersal-vicariance analysis and weighted ancestral area analysis in combination with palaeogeographical data as well as molecular clock calibration. Our results suggest that: (1) Chinese sisorid catfishes form a monophyletic group with two distinct clades, one represented by (Gagata (Bagarius, Glyptothorax)) and the other by (glyptosternoids, Pseudecheneis); (2) the glyptosternoid is a monophyletic group and Glyptosternum, Glaridoglanis, and Exostoma are three basal species having a primitive position among it; (3) a hypothesis referring to Pseudecheneis as the sister group of the glyptosternoids, based on morphological evidence, is supported; (4) the genus Pareuchiloglanis, as presently defined, is not monophyletic; (5) congruent with previous hypotheses, the uplift of Qinghai-Tibetan Plateau played a primary role in the speciation and radiation of the Chinese sisorids; and (6) an evolutionary scenario combining aspects of both vicariance and dispersal theory is necessary to explain the distribution pattern of the glyptosternoids. In addition, using a cytochrome b substitution rate of 0.91% per million years and 0.23% for 16S rRNA, we tentatively date that the glyptosternoids most possibly originated in Oligocene-Miocene boundary (19-24Myr), and radiated from Miocene to Pleistocene, along with a center of origin in the Irrawaddy-Tsangpo drainages and several rapid speciation in a relatively short time.     

Molecular phylogeny of gobioid fishes (Perciformes: Gobioidei) based on mitochondrial 12S rRNA sequences

The molecular phylogeny of the gobioid fishes, comprising 33 genera and 43 valid species, was examined by use of complete mitochondrial 12S rRNA and tRNA(VAL)genes. Both parsimony and neighbor-joining analyses revealed comparable results and are generally congruent with those of morphological studies. The Odontobutis, which was always placed at the base of the phylogenetic trees, can be treated as a sister group of all other nonrhyacichthyid gobioids. Within eleotrid fishes, the monophyly of the Eleotrinae is strongly supported by molecular data. The Butinae is closer to fishes with five branchiostegal rays and should be treated as a sister group of the latter. The group with five branchiostegal rays, except for sicydiines, can be divided into two groups according to their epural counts. Fish with one epural, the Gobiinae of Pezold plus Microdesmidae, form a monophyletic group which is sister to those with two epurals, the Oxudercinae and Gobionellinae of Pezold. However, Sicydiinae, which have one epural, are closer to the Oxudercinae and Gobionellinae rather than to the Gobiinae. Since progressive reduction in epural number has been observed along this lineage, the sicydiines should be treated as a derived group within the groups with two epurals.     

Phylogenetic studies of the rRNA group II pseudomonads based on 16S rRNA gene sequences

Nearly complete sequences of 16S rRNA genes were determined for eight bacterial strains representing five species of the rRNA homology group II pseudomonads that are members of the beta subclass of the class Proteobacteria. Comparative analysis with published sequence data indicated that Pseudomonas andropogonis, Ps. caryophylli, Ps. gladioli pv. gladioli and Ps. cepacia aggregate in one coherent cluster at 94·2% sequence similarity; Ps. solanacearum and Ps. pickettii shared 95·3% and 92·8% similarity with Alcaligenes eutrophus in another cluster. Both clusters joined at 87·8% similarity, which is similar to that for genera in this subclass of Proteobacteria. Based on this study and on comparison with other works we suggest that these species are separated from authentic pseudomonads and constitute a new genus or possibly two related genera accommodating Ps. andropogonis, Ps. caryophylli, Ps. gladioli, Ps. cepacia, and Ps. solanacearum, Ps. pickettii and A. eutrophus, respectively. Four strains of Ps. solanacearum representing Biovars 1, 2, 3 and 4 were subdivided into two clusters at 99·1% sequence similarity, in agreement with other published phenotypic and genotypic studies. The two clusters may be potentially regarded as subspecies.     

Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA genes

Pectinidae is a large bivalve family characterised by almost circular, flat shells. Species are distributed worldwide and fall into three life-styles: swimming, byssally attached to hard substrates, and cemented to rocks with one valve. Despite these very different life strategies, pectinid shells are highly conservative in shape and offer few clues for the unravelling of phylogenetic issues. Consequently, phylogenetic studies based on morphological features have not yielded conclusive results. We thus set out to analyse partial sequences of mitochondrial 12S and 16S rRNA genes from 23 species of 16 genera with molecular techniques. The results are largely in contrast, both at the genus and the subfamily level, with the systematic classifications based on adult morphological characters, whereas they agree with the morphological classifications based on the more conserved non-adaptive features.     

Towards a phylogeny of the clostridia based on 16S rRNA sequences

Abstract The genes hbl3, cpl1 and cpl7 coding for the pneumococcal phage lytic enzymes HBL3, CPL1 and CPL7, respectively, have been cloned into shuttle plasmids that can replicate in Streptococcus pneumoniae and Escherichia coli . All these genes were expressed in E. coli under the control of either the lyt^P promoter of the lytA gene, which codes for the major pneumococcal autolysin, or the promoter of the tetracycline-resistance gene (tet^P). In contrast, cpl1 and cpl7 genes that code for lysozymes were expressed in pneumococcus only under the control of tet^P, whereas the hbl3 gene that codes for an amidase can be expressed using either promoter. The phage lysozymes or amidase expressed in S. pneumoniae M31, a mutant deleted in the lyA gene coding for short chains, were placed under physiological control since these transformed bacteria grew as normal 'diplo' cells during the exponential phase and underwent autolysis only after long incubation at 37°C. The lysis genes appear to be expressed constitutively in the transformed pneumococci, since sharply defined lysis of these cultures could be induced prematurely during the exponential phase of growth by addition of sodium deoxycholate.     

Molecular phylogeny of the crab genus Brachynotus (Brachyura: Varunidae) based on the 16S rRNA gene

The crab genus Brachynotus de Haan, 1833 is restricted to the intertidal and shallow subtidal of the Mediterranean and northeastern Atlantic. It is presently recognized to consist of four species, of which three (B. foresti, B. gemmellari and B. sexdentatus) are endemic to the Mediterranean. The fourth species, B. atlanticus, is found along the Atlantic coasts of northern Africa and southern Europe, but also extends into the western Mediterranean. This high level of endemism suggests that speciation within Brachynotus is strongly correlated with the geography and geology of the Mediterranean Sea. A molecular phylogeny based on the mitochondrial large subunit (16S) rRNA gene indicates that the four species of Brachynotus form a monophyletic group within Atlantic Varunidae. The DNA sequence data also show that the genus Brachynotus can be subdivided into two species groups, one comprising B. atlanticus and B. foresti, and the other one B. gemmellari and B. sexdentatus. While B. atlanticus and B. foresti are clearly genetically distinct, B. gemmellari and B. sexdentatus are identical in the studied region of the 16S rRNA gene, suggesting a recent separation or continuing gene flow.     

Molecular systematics of the order anaspidea based on mitochondrial DNA sequence (12S, 16S, and COI)

Fragments from three mitochondrial genes (12S, 16S, and COI) were sequenced to reconstruct a molecular phylogeny of the opisthobranch order Anaspidea. The molecular phylogeny supports the placement of the genus Akera, a taxon previously regarded by some authors as a cephalaspidean, within the Anaspidea. Incongruence between the molecular data and the classifications based on morphology suggests that some of the taxonomic characters (i.e., shell, parapodia fusion) traditionally used for the classification of sea hares must be reevaluated, since they may be homoplastic. The ancestral nature of Notarchus based on the molecular evidence suggests that homoplasy may be an explanation for the morphological resemblance of this species to the more derived sea hares with highly fused parapodia and concentrated nerve ganglia. Finally, examples are given of how comparative studies of the evolution of learning mechanisms in the anaspidean clade will benefit from the phylogenetic hypothesis presented in this paper.     

Molecular phylogenetics of the Peromyscus boylii species group (Rodentia: muridae) based on mitochondrial cytochrome b sequences

Variation in the mitochondrial cytochrome b gene (1143 bp) was examined to estimate the phylogenetic relationships of taxa within the Peromyscus boylii species group. In addition, phylogenetic relationships among the aztecus, boylii, and truei species groups were addressed. Maximum-likelihood, neighbor-joining, and maximum-parsimony (weighted and equally weighted) analyses produced similar topologies with P. boylii, P. beatae, P. simulus, P. stephani, P. madrensis, P. levipes, and three undescribed taxa from western Mexico forming a monophyletic unit. At least two of the undescribed taxa from western Mexico potentially represent species. Members of the P. aztecus species group formed a clade separate from the P. boylii group and should be recognized as a distinct species group. P. sagax, P. polius, and P. pectoralis, formerly placed in the P. boylii species group, generally formed an unresolved polytomy with the P. truei, P. aztecus, and P. boylii species groups. P. attwateri formed a sister taxon relationship with members of the P. truei species group (P. difficilis and P. nasutus) and should be considered a member of this group. Members of the P. truei species group did not form a monophyletic unit, indicating that this species group is not monophyletic and may be composed of two assemblages.     

Phylogenetic analysis of the genus Microbacterium based on 16S rRNA gene sequences

Abstract 16S rRNA gene (rDNA) studies of the six species of the genus Microbacterium, M. lacticum, M. laevaniformans, M. dextranolyticum, M. imperiale, M. arborescens and M. aurum , were performed and the primary structures were compared with those of 29 representative actinobacteria and related organisms. Phylogenetic analysis indicated that six species of the genus Microbacterium and representative four species of the genus Aureobacterium appear to be phylogenetically coherent as was suggested by Rainey et al., although the peptidoglycan types of these two genera are different (peptidoglycan type B1 or B2). Thus, the phylogenetical analyses revealed that members of actinobacteria with group B-peptidoglycan do not cluster according to their peptidoglycan types, but form compact cluster different from actinobacteria or actinomycetes with group A-peptidoglycan.     

Phylogenetic analysis of the genus Aquaspirillum based on 16S rRNA gene sequences

Phylogenetic analysis of 15 species of the genus Aquaspirillum based on 16S rRNA gene (rDNA) sequences indicated that the genus Aquaspirillum is phylogenetically heterogeneous and the species could be divided into four groups as follows: Aquaspirillum serpens, the type species of this genus, A. dispar and A. putridiconchylium are situated in the family Neisseriaceae; members of the second group, A. gracile, A. delicatum, A. anulus, A. giesbergeri, A. sinuosum, A. metamorphum and A. psychrophilum, are included in the family Comamonadaceae; the two members of the third group, A. arcticum and A. autotrophicum, are included in the family Oxalobacteriaceae; and members of the fourth group, A. polymorphum, A. peregrinum, and A. itersonii, are included in the alpha-subdivision of Proteobacteria. Thus, phylogenetic studies indicated that all the species excepting A. serpens, the type species, should be transferred to distinct genera.     

Phylogenetic analysis of Kineococcus aurantiacus based on 16S rRNA gene sequences

Abstract The DNA of mouse adenovirus strain K87 (MAd-2) was cloned and mapped with restriction endonucleases Bgl II, Cla I, Eco RI, Hin dII and Sph I. Large differences were found the MAd-2 and MAd-1 (strain FL) DNA molecules in terms of number and location of restriction sites. The MAd-2 genome also appeared as larger size than in the MAd-1 genome (34.72 kb vs. 30.14 kb). Our results confirm the existence of two distinct adenovirus species in the mouse. Hybridization experiments, on the other hand, indicate that both MAd-1 and MAd-2 are genetically related to human adenovirus type 2 (HAd-2). Overlapping regions of DNA homology are located in genes coding for HAd-2 structural components which could explain serological relationships observed between the human and the murine adenoviruses.