Organogenesis during budding and lophophoral morphology of Hislopia malayensis Annandale, 1916 (Bryozoa, Ctenostomata)

Background  

Bryozoans represent a large lophotrochozoan phylum with controversially discussed phylogenetic position and in group relationships. Developmental processes during the budding of bryozoans are in need for revision. Just recently a study on a phylactolaemate bryozoan gave a comprehensive basis for further comparisons among bryozoans. The aim of this study is to gain more insight into developmental patterns during polypide formation in the budding process of bryozoans. Particular focus is laid upon the lophophore, also its condition in adults. For this purpose we studied organogenesis during budding and lophophoral morphology of the ctenostome bryozoan Hislopia malayensis.     

libcov: A C++ bioinformatic library to manipulate protein structures,sequence alignments and phylogeny

Background  

An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task.     

aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species

Background  

Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny of Escherichia coli. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B₂ variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B₁ variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene.     

Automated group assignment in large phylogenetic trees using GRUNT: GRouping,Ungrouping, Naming Tool

Background  

Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies.     

Evolution of feeding specialization in Tanganyikan scale-eating cichlids: a molecular phylogenetic approach

Background  

Cichlid fishes in Lake Tanganyika exhibit remarkable diversity in their feeding habits. Among them, seven species in the genus Perissodus are known for their unique feeding habit of scale eating with specialized feeding morphology and behaviour. Although the origin of the scale-eating habit has long been questioned, its evolutionary process is still unknown. In the present study, we conducted interspecific phylogenetic analyses for all nine known species in the tribe Perissodini (seven Perissodus and two Haplotaxodon species) using amplified fragment length polymorphism (AFLP) analyses of the nuclear DNA. On the basis of the resultant phylogenetic frameworks, the evolution of their feeding habits was traced using data from analyses of stomach contents, habitat depths, and observations of oral jaw tooth morphology.     

A common origin of complex life cycles in parasitic flatworms: evidence from the complete mitochondrial genome of <Emphasis Type="Italic">Microcotyle sebastis</Emphasis> (Monogenea: Platyhelminthes)

Background  

The parasitic Platyhelminthes (Neodermata) contains three parasitic groups of flatworms, each having a unique morphology, and life style: Monogenea (primarily ectoparasitic), Trematoda (endoparasitic flukes), and Cestoda (endoparasitic tapeworms). The evolutionary origin of complex life cyles (multiple obligate hosts, as found in Trematoda and Cestoda) and of endo-/ecto-parasitism in these groups is still under debate and these questions can be resolved, only if the phylogenetic position of the Monogenea within the Neodermata clade is correctly estimated.     

Multi-character perspectives on the evolution of intraspecific differentiation in a neotropical hylid frog

Background  

Multi-character empirical studies are important contributions to our understanding of the process of speciation. The relatively conserved morphology of, and importance of the mate recognition system in anurans, combined with phylogenetic tools, provide an opportunity to address predictions about the relative role of each in the process of speciation. We examine the relationship among patterns of variation in morphology, call characters, and 16S gene sequences across seven populations of a neotropical hylid frog, Hyla leucophyllata, to infer their relative importance in predicting the early stages of population differentiation.     

PFAAT version 2.0: A tool for editing,annotating, and analyzing multiple sequence alignments

Background  

By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis.     

Three-Dimensional Phylogeny Explorer: Distinguishing paralogs,lateral transfer,and violation of "molecular clock" assumption with 3D visualization

Background  

Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful and insightful tree visualization tools.     

The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA

Background  

The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics. Platysternon was traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis.     

Evolutionary morphology of the rattlesnake style

Background  

The rattlesnake rattling system is an evolutionary novelty that includes anatomical, behavioral, and physiological modifications of the generalized pitviper tail. One such modification, the formation of a bony clublike style at the terminal region of the caudal vertebrae, has not previously been examined in a phylogenetic context. Here we used skeletal material, cleared and stained preparations, and radiographs of whole preserved specimens to examine interspecific variation in style morphology among 34 rattlesnake species.     

Phylogenetic placement of the enigmatic parasite, <Emphasis Type="Italic">Polypodium hydriforme</Emphasis>, within the Phylum Cnidaria

Background  

Polypodium hydriforme is a parasite with an unusual life cycle and peculiar morphology, both of which have made its systematic position uncertain. Polypodium has traditionally been considered a cnidarian because it possesses nematocysts, the stinging structures characteristic of this phylum. However, recent molecular phylogenetic studies using 18S rDNA sequence data have challenged this interpretation, and have shown that Polypodium is a close relative to myxozoans and together they share a closer affinity to bilaterians than cnidarians. Due to the variable rates of 18S rDNA sequences, these results have been suggested to be an artifact of long-branch attraction (LBA). A recent study, using multiple protein coding markers, shows that the myxozoan Buddenbrockia, is nested within cnidarians. Polypodium was not included in this study. To further investigate the phylogenetic placement of Polypodium, we have performed phylogenetic analyses of metazoans with 18S and partial 28S rDNA sequences in a large dataset that includes Polypodium and a comprehensive sampling of cnidarian taxa.     

Morphological evolution in the variable resin-producing Detarieae (Fabaceae): do morphological characters retain a phylogenetic signal?

Background and Aims

Previous molecular phylogenetic studies disagree with the informal generic-level taxonomic groups based on morphology. In this study morphological characters in the caesalpinioid clade Detarieae are evaluated within a phylogenetic framework as a means of better understanding phylogenetic relationships and morphological evolution.

Methods

Morphological characters were observed and scored for representative species of Detarieae focusing on the resin-producing genera. Phylogenetic analyses were carried out with morphological characters alone and then combined with DNA sequences.

Key Results

Despite a high level of homoplasy, morphological data support several clades corresponding to those recovered in molecular phylogenetic analyses. The more strongly supported clades are each defined by at least one morphological synapomorphy. Several characters (e.g. apetaly) previously used to define informal generic groups evolved several times independently, leading to the differences observed with the molecular phylogenetic analyses. Although floral evolution is complex in Detarieae some patterns are recovered.

Conclusions

New informal taxonomic groupings are proposed based on the present findings. Floral evolution in the diverse Detarieae clade is characterized by a repeated tendency toward zygomorphy through the reduction of lateral petals and toward complete loss of petals.Key words: Caesalpinioideae, Detarieae, floral evolution, Leguminosae, morphology, phylogeny, resins, taxonomy     

A new classification of the long-horned caddisflies (Trichoptera: Leptoceridae) based on molecular data

Background  

Leptoceridae are among the three largest families of Trichoptera (caddisflies). The current classification is founded on a phylogenetic work from the 1980's, based on morphological characters from adult males, i.e. wing venation, tibial spur formula and genital morphology. In order to get a new opinion about the relationships within the family, we undertook a molecular study of the family based on sequences from five genes, mitochondrial COI and the four nuclear genes CAD, EF-1α, IDH and POL.     

Martharaptor greenriverensis, a New Theropod Dinosaur from the Lower Cretaceous of Utah

Background

The Yellow Cat Member of the Cedar Mountain Formation (Early Cretaceous, Barremian?) of Utah has yielded a rich dinosaur fauna, including the basal therizinosauroid theropod Falcarius utahensis at its base. Recent excavation uncovered a new possible therizinosauroid taxon from a higher stratigraphic level in the Cedar Mountain Formation than F. utahensis.

Methodology/Principal Findings

Here we describe a fragmentary skeleton of the new theropod and perform a phylogenetic analysis to determine its phylogenetic position. The skeleton includes fragments of vertebrae, a scapula, forelimb and hindlimb bones, and an ischium. It also includes several well-preserved manual unguals. Manual and pedal morphology show that the specimen is distinct from other theropods from the Cedar Mountain Formation and from previously described therizinosauroids. It is here named as the holotype of a new genus and species, Martharaptor greenriverensis. Phylogenetic analysis places M. greenriverensis within Therizinosauroidea as the sister taxon to Alxasaurus + Therizinosauridae, although support for this placement is weak.

Conclusions/Significance

The new specimen adds to the known dinosaurian fauna of the Yellow Cat Member of the Cedar Mountain Formation. If the phylogenetic placement is correct, it also adds to the known diversity of Therizinosauroidea.     

Age-related,interindividual, and right/left differences in anterior-posterior foot pressure ratio in preschool children

Background

This study aimed to examine age-related, interindividual, and right/left differences in anterior-posterior foot pressure ratio in 764 preschool children (364 boys and 400 girls) aged 3.5-6.5 years.

Methods

Subjects maintained an upright standing posture for 10 seconds on the Footview Clinic, an instrument designed to calculate the anterior-posterior foot pressure ratio. The ratio of anterior foot pressure in each subject’s right and left feet was selected as a variable, and the mean of a 10 s measurement was used for analysis.

Results

The ratio of anterior foot pressure was significantly larger in the right foot than in the left foot. With regard to age, the ratio of anterior foot pressure was significantly larger in children aged over 4.5 years than in children aged 3.5 years. It was also larger in children aged 6 and 6.5 years than in children aged 4 years. Interindividual differences in variables were large, and coefficients of variance were highest in children aged 3.5 years and lowest in children aged 6.5 years.

Conclusions

In conclusion, anterior foot pressure increases with age in preschool children. Interindividual differences in anterior foot pressure are large and tend to decrease with age. Furthermore, the anterior foot pressure is slightly higher in the right foot than in the left foot. These results will be useful for various studies, such as examining relationships between the anterior-posterior foot pressure ratio and factors, such as untouched toes, physical fitness, and level of exercise.     

The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation,pelvic fin loss,and craniofacial morphology in Osteichthyes

Background  

The family Polypteridae, commonly known as "bichirs", is a lineage that diverged early in the evolutionary history of Actinopterygii (ray-finned fish), but has been the subject of far less evolutionary study than other members of that clade. Uncovering patterns of morphological change within Polypteridae provides an important opportunity to evaluate if the mechanisms underlying morphological evolution are shared among actinoptyerygians, and in fact, perhaps the entire osteichthyan (bony fish and tetrapods) tree of life. However, the greatest impediment to elucidating these patterns is the lack of a well-resolved, highly-supported phylogenetic tree of Polypteridae. In fact, the interrelationships of polypterid species have never been subject to molecular phylogenetic analysis. Here, we infer the first molecular phylogeny of bichirs, including all 12 recognized species and multiple subspecies using Bayesian analyses of 16S and cyt-b mtDNA. We use this mitochondrial phylogeny, ancestral state reconstruction, and geometric morphometrics to test whether patterns of morphological evolution, including the evolution of body elongation, pelvic fin reduction, and craniofacial morphology, are shared throughout the osteichthyan tree of life.     

Ancestry and evolution of a secretory pathway serpin

Background  

The serpin (serine protease inhibitor) superfamily constitutes a class of functionally highly diverse proteins usually encompassing several dozens of paralogs in mammals. Though phylogenetic classification of vertebrate serpins into six groups based on gene organisation is well established, the evolutionary roots beyond the fish/tetrapod split are unresolved. The aim of this study was to elucidate the phylogenetic relationships of serpins involved in surveying the secretory pathway routes against uncontrolled proteolytic activity.     

Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison

Background  

Protein structure comparison is one of the most important problems in computational biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and protein docking.     

Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

Background  

Phylogenetic analyses of angiosperm relationships have used only a small percentage of available sequence data, but phylogenetic data matrices often can be augmented with existing data, especially if one allows missing characters. We explore the effects on phylogenetic analyses of adding 378 matK sequences and 240 26S rDNA sequences to the complete 3-gene, 567-taxon angiosperm phylogenetic matrix of Soltis et al.