In this study the composition of the denitrifying bacterial community among constructed wetlands in agricultural areas was investigated. Thirty-two constructed wetlands located in Southern Sweden were surveyed, and biofilm samples from each were analyzed by applying denaturing gradient gel electrophoresis, to investigate the community composition of the three denitrifying bacterial enzyme genes nirK, nirS and nosZ. The DNA sequences of the enzyme genes were compared to known DNA sequences in GeneBank using BLAST. The results of the denitrifying bacterial enzyme genes indicated that these habitats may harbour a heterogeneous denitrifying bacterial community. Individual analysis of the enzyme genes revealed that nirS was more heterogeneous than both nirK and nosZ. Most sequences from the present study clustered with known sequences from species belonging to the group of α-Proteobacteria, and to a lesser extent with β- Proteobacteria and γ-Proteobacteria, and only nirS clustered with a member of gram-positive bacteria. / <p>Included in doctoral thesis: Milenkovski, Susann. Structure and Function of Microbial Communities in Constructed Wetlands - Influence of environmental parameters and pesticides on denitrifying bacteria. Lund University 2009.</p>

The Acentropinae represents a species-rich crambid group with more than 700 species distributed in all the zoogeographic regions except Antarctica, and the highest diversity occurs in the Oriental, Indo-Autralian and Neotropical regions. Most caterpillars of Acentropinae are widely adapted to feed on vegetation in different types of aquatic environments, such as ponds, streams and rivers. However, some of them are known to utilize mosses on land. Therefore the evolutionary relationships between the terrestrial and aquatic lineage become intriguing. The genus Paracymoriza Warren, 1890, is a moderate-sized acentropine genus comprising 39 species ranging throughout southeast and east Asia. Historically the genus was often confused with many unrelated genera due to the superficial resemblance in wing maculation, which is termed the ¡§nymphuliform wing pattern¡¨. The genus is currently divided into 8 species groups, with 5 of them known having aquatic immature stages, while the others having terrestrial immatures. The fact that Paracymoriza includes both truly aquatic and terrestrial species represents a unique case for the Lepidoptera, thus making the monophyly of the genus doubtful. In the present study, a phylogenetic hypothesis Paracymoriza was reconstructed by using morphological characters including wing pattern and immature stage characters obtained from 63 species representing 25 acentropine genera. The results suggest that Paracymoriza is monophyletic. The genus is composed of two major clades: one aquatic, and the other terrestrial. It suggests that Paracymoriza represents a unique example with amphibious immature stage in the Lepidoptera although the tree support values of this phylogenetic hypothesis remains relatively weak due to large amount of homoplasious characters.

Abstract Recent researches have pointed out that most of marine bacteria are uncultivable. However, majority of prior researches about bacteria flora in cultivated ponds used cultivating method to researches. That means those researches ignored uncultivable bacteria in ponds and caused inaccuracy in counting bacteria. Therefore we used analyzing bacteria 16S rDNA sequences to study composition of bacteria in cultivated ponds in place of traditional bacteria taxonomy. The phylogenetic diversity of bacteria examined by analyzing the 16S rDNA sequences permits the characterization of environmental bacteria community without culturing and has been used widely. This research is to adopt both MMA medium cultivation and direct recovery of bacteria 16S rDNA sequences to investigate bacteria flora in a closed Penaeus monodon pond. We sampled from A2 (10¡Ñ8¡Ñ1.5m) test pond at the Department of Marine Resource in Sun Yat-Sen University on August 17, 1999. Then, we adopted AO (Acridine Orange) epifluorescent microscopic technique to count total direct count (TDC) and direct count of viable bacteria cell (DVC). Respective results were 2.846¡Ñ107/ml, 1.029¡Ñ107/ml, and plate count (PC) determined by MPN count method were 1.130¡Ñ105cfu/ml. In the part of cultivable bacteria, they could be separated into 9 groups by their morphologic after culturing in MMA plate at 25¢Jfor 5 days. We isolated 15 strains to analyze their 16S rDNA sequences, and separated respectively into 4 groups after comparing with the genebank. Those four groups are CFB group, low G+C Gram-positive bacteria, Alpha proteobacteria and Gamma proteobacteria. The genus Vibrio (47%) in the Gamma proteobacteria group is the dominant. In the part of uncultivable bacteria, we filtered bacteria from the water in the same pond, amplified the 16S rDNA by the polymerase chain reaction (PCR) and then cloned. After that, we randomly isolated 40 clones for sequence analysis. The bacteria belong to following groups, cyanobacteria, CFB group, Verrucomicrobia, Gram-positive eubacteria, Alpha proteobacterium, Beta proteobacterium, Gamma proteobacterium and Delta proteobacterium.

Abstract¡G Athyrioid ferns¡]Athyrioideae, Dryopteridaceae¡^consist of about 700 species with a distribution range from tropical to temperate zone in the world. In Taiwan, the subfamily includes 50 species commonly found from lowland to around 3000 meters in elevation. Phylogenetic relationships and the generic circumscription of athyrioid genera are confused and controversial. In this study, trnL-trnF spacer, which is a nucleotide sequence between genes in the chloroplast, was used to analyze and infer the phylogenetic relationships and evolutionary status of 35 species. Phylogenetic trees produced by neighbor-joining and maximum-parsimony methods are similar in topology. Athyrium and Cornopteris form a clade, and this indicates Cornopteris is more closely related to Athyrium than to Diplazium. Anisogonium nests within Diplazium clade, and it implies these two genera congeneric. Anisocampium is distinct from Athyrium sensu stricto and forms a clade with Athyrium nipponicum. Deparia clade includes Athyriopsis, Lunathyrium, Dryoathyrium, Dictyodroma, Diplazium subsinuatum and Matteuccia. These four clades may be seen as the core part of athyrioid ferns. Woodsia and Thelypteridaceae cluster next to these four clades. Cystopteris and Gymnocarpium occupy a position between Thelypteridaceae and Dryopteridaceae. Rhachidosorus is neither closely related to Athyrium nor Diplazium. Hypodematium is distantly related to athyrioid ferns and forms a clade with Dryopteridaceae. Therefore, Hypodematium may be isolated from athyrioid ferns. Based on the evidences mentioned above, athyrioid ferns are suggested to be closely related to Thelypteriaceae, and are probably members of Woodsiaceae¡]including Thelypteridaceae¡^instead of Dryopteridaceae. In addition, Cystopteris and Gymnocarpium are the most basal lineage of Woodsiaceae sensu lato. The core group of athyrioid ferns probably better treated as a monophyletic tribe or subfamily of Woodsiaceae at current stage.

A unifying goal of plant systematics is in pursuit of a natural system that means phylpgenetic relationships. We can construct it by means of various characters. There are many arguments about generic circumscription of Pteridophyta. It¡¦s worth while to reexamine some characters, such as trichome. Trichomes have long been considered one of the most important characters by pteridologists. However, The study of trichomes in Taiwan is very rare. In the present study, trichome morphology is used to assess phylogenetic relationships among genera of Dryopteridaceae (sensu Kramer et al.) . The observation of trichomes focus on hairs on the lamina and scales on the base of stipes. Lamina surface hairs are classified into unicellular hairs, club-like unicellular glands, uniseriate hairs, spine-like hairs, appressed glandular hairs, uniseriate hairs with a glandular head and verruca. Stipe base scale margins are classified into entire, serrate, unicellular branch, uniseriate branch, multicellular branch with a glandular head, and dorsi-ventral branch. Color distribution and branch dimension of scales were also good differentiation characters. The main taxonomic conclusions are as follows: (1)Trichome characters support the distinctness of Nothoperanema, Peranema, Polystichm, Dryopsis, Ctenitis, Tectaria, Athyrium, Cystopteris, Acystopteris, and Woodsia; (2) Diplazium and Dryopteris are hererogenous and show little correaltion to exist system. The latter two genera need further research.

The central task in phylogenetics is to infer the evolutionary relationships among a given set of species. These relationships are usually represented by a phylogenetic tree with the species of interest at the leaves and where the internal vertices of the tree represent ancestral species. The amount of available molecular data is increasing exponentially and, given the continual advances in sequencing techniques and throughput, this explosive growth will likely continue. These vast amounts of available data mean that biologists are able to assemble large multi-gene datasets for use in phylogenetic analyses, which presents distinct computational challenges. Supertree methods comprise one approach to reconstructing large phylogenies, given estimated trees for overlapping subsets of the entire set of taxa. These source trees are combined into a single supertree on the full set of taxa using various algorithmic techniques. When the data allow, the competing approach is a combined analysis (also known as a “super-matrix” or “total evidence” approach), whereby the different sequence data matrices for each of the different subsets of taxa are put into a single super-matrix, and a tree is estimated on that super-matrix. In this dissertation, I present simulation software I designed to allow users to compare the relative performance of different supertree methods, as well as that of combined analysis, on more realistic data and on a larger scale than has been used up to this point. I present an extensive simulation study that uses this software to compare the performance of supertree methods and combined analysis, and that demonstrates a need for more topologically accurate supertree methods. I also introduce a new supertree method that I have developed that outperforms the most commonly used, and what until now has arguably been the most accurate, supertree method. / text

Aetosaurians are a clade of pseudosuchian archosaurs that were globally dispersed during the Late Triassic Epoch. Aetosaurians are characterized by a suite of osteoderms that covered much of the body. These osteoderms are commonly recovered as fossils and possess characteristic surface ornamentation that can be diagnostic for taxa. The abundance of these osteoderms and the ease of identification have made aetosaurians ideal index taxa for Late Triassic biostratigraphy. Of special interest are specimens from South and North America and Europe that have been assigned to the genus Stagonolepis, which have been utilized for correlation of continental sedimentary units and to approximately date the timing of important biotic events. New finds have called the synonymy of these Stagonolepis-like specimens into question, jeopardizing their ability to serve as biochronological markers. Detailed examination of all of the specimens assigned to Stagonolepis robertsoni demonstrates that all of these specimens do not represent the same species. The South American material is assigned to the genera Aetosauroides, Aetobarbakinoides, and Polesinesuchus; the European material to Stagonolepis; and the North American material to Calyptosuchus, Adamanasuchus, and a newly recognized taxon, Scutarx deltatylus. Scutarx deltatylus can be differentiated from other aetosaurians by the presence of a strongly raised, triangular boss, on the posteromedial corner of the paramedian osteoderms. Scutarx deltatylus also preserves the first good skull material from a Stagonolepis-like aetosaur from North America. A dorsoventrally thickened skull roof and an anteroposteriorly short parabasisphenoid further demonstrate the distinctness of this material from that of South America and Europe. A detailed phylogenetic analysis of all known aetosaurians further demonstrates the distinctness of these taxa. This new expanded analysis of 28 taxa and 83 characters recovers Aetosauroides scagliai as the sister taxon to all other aetosaurians. Stagonolepis robertsoni from Scotland does not clade with Stagonolepis olenkae from Poland. Calyptosuchus wellesi is the sister taxon to a clade consisting of Scutarx deltatylus and Adamanasuchus eisenhardtae. However, distribution of autapomorphies across these taxa precludes them from being synonymized. As a result the Stagonolepis-like aetosaurs cannot be used for global scale correlations of Upper Triassic strata, but do appear to be of utility for regional correlations, in particular those between the Chinle Formation and Dockum Group in the American Southwest. / text

Morphological characters have a long history of use in the estimation of phylogenetic trees. Datasets consisting of morphological characters are most often analyzed using the maximum parsimony criterion, which seeks to minimize the amount of character change across a phylogenetic tree. When combined with molecular data, characters are often analyzed using model-based methods, such as maximum likelihood or, more commonly, Bayesian estimation. The efficacy of likelihood and Bayesian methods using a common model for estimating topology from discrete morphological characters, the Mk model, is poorly-explored. In Chapter One, I explore the efficacy of Bayesian estimation of phylogeny, using the Mk model, under conditions that are commonly encountered in paleontological studies. Using simulated data, I describe the relative performances of parsimony and the Mk model under a range of realistic conditions that include common scenarios of missing data and rate heterogeneity. I further examine the use of the Mk model in Chapter Two. Like any model, the Mk model makes a number of assumptions. One is that transition between character states are symmetric (i.e., there is an equal probability of changing from state 0 to state 1 and from state 1 to state 0). Many characters, including alleged Dollo characters and extremely labile characters, may not fit this assumption. I tested methods for relaxing this assumption in a Bayesian context. Using empirical datasets, I performed model fitting to demonstrate cases in which modelling asymmetric transitions among characters is preferred. I used simulated datasets to demonstrate that choosing the best-fit model of transition state symmetry can improve model fit and phylogenetic estimation. In my final chapter, I looked at the use of partitions to model datasets more appropriately. Common in molecular studies, partitioning breaks up the dataset into pieces that evolve according to similar mechanisms. These pieces, called partitions, are then modeled separately. This practice has not been widely adopted in morphological studies. I extended the PartitionFinder software, which is used in molecular studies to score different possible partition schemes to find the one which best models the dataset. I used empirical datasets to demonstrate the effects of partitioning datasets on model likelihoods and on the phylogenetic trees estimated from those datasets. / text

No description available.

In total 399 samples from three species of squirrels (Sciurus vulgaris, Sciurus carolinensis and Callosciurus finlaysonii) were collected from 2010 to 2013. All samples were examined for the presence of Cryptosporidium using by molecular methods, which demonstrated by presence of Cryptosporidium specific DNA in 18 samples (4.5%). Out of them 12 samples were positive onCryptosporidium ferret genotype, 3 on Cryptosporidium skunk genotype, 1 on Cryptosporidium chipmunk genotype I and 2 samples onCryptosporidium ubiquitum. Statistical analyses did not reveal any influence of gender on the occurrence of Cryptosporidium. Juvenile individuals of squirrels from the family Sciuridae are more often infected by Cryptosporidium than the adult animals.