Multi-Locus Sequence Typing of Bartonella bacilliformis DNA Performed Directly from Blood of Patients with Oroya's Fever During a Peruvian Outbreak.Pons, Maria J, Silva-Caso, Wilmer, Del Valle Mendoza, Juana, Ruiz, Joaquim 01 February 2016 (has links)
Background Bartonella bacilliformis is the etiological agent of Carrion’s disease, a neglected tropical poverty-linked illness. This infection is endemic of Andean regions and it is estimated that approximately 1.7 million of South Americans are at risk. This bacterium is a fastidious slow growing microorganism, which is difficult and cumbersome to isolate from clinical sources, thereby hindering the availability of phylogenetic relationship of clinical samples. The aim of this study was to perform Multi Locus Sequence Typing of B. bacilliformis directly in blood from patients diagnosed with Oroya fever during an outbreak in Northern Peru. Methodology/Principal Findings DNA extracted among blood samples from patients diagnosed with Oroya’s fever were analyzed with MLST, with the amplification of 7 genetic loci (ftsZ, flaA, ribC, rnpB, rpoB, bvrR and groEL) and a phylogenetic analysis of the different Sequence Types (ST) was performed. A total of 4 different ST were identified. The most frequently found was ST1 present in 66% of samples. Additionally, two samples presented a new allelic profile, belonging to new STs (ST 9 and ST 10), which were closely related to ST1. Conclusions/Significance The present data demonstrate that B. bacilliformis MLST studies may be possible directly from blood samples, being a promising approach for epidemiological studies. During the outbreak the STs of B. bacilliformis were found to be heterogeneous, albeit closely related, probably reflecting the evolution from a common ancestor colonizing the area. Additional studies including new samples and areas are needed, in order to obtain better knowledge of phylogenetic scenario B. bacilliformis
Merz, Clayton, Merz, Clayton
Herein we tested the repeatability of RAD-seq phylogeographic construction by creating a second, independent phylogeography of the pitcher-plant mosquito, Wyeomyia smithii. We sampled 25 populations drawn from different localities nearby previous collection sites and used these new data to construct a second, independent phylogeography to test the reproducibility of phylogenetic patterns. Our previous phylogeography was based on 3,741 phylogenetically informative markers from 21 populations and rooted with mitochondrial COI. The present phylogeography was based on 16,858 informative markers and rooted with RAD-seq. We found correspondence between clades at the extremes of W. smithii's distribution; however, there were several discrepancies between the trees, including the refugium that gave rise to all post-glacial populations. We observed that combining all 46 populations resolved these discrepancies and, equally importantly, that extensive taxon sampling in areas of historical importance is more valuable than increasing the number of informative sites in establishing an accurate, robust phylogeography. This thesis includes unpublished co-authored material.
RESOLVING THE PHYLOGENETIC RELATIONSHIPS OF THREE GENERA OF EPHEMEROPTERA (MAYFLIES); STENONEMA, STENACRON, AND MACCAFFERTIUMZembrzuski, Deanna 01 August 2017 (has links)
Stenonema, Stenacron, and Maccaffertium are three closely related genera of mayflies commonly found across North America. There are currently 22 described species in Maccaffertium, 7 described species in Stenacron, and 1 described species in Stenonema. Their primarily aquatic life history, and sensitivity to aquatic pollutant make these organisms ideal water quality indicators. However, there is little morphological variation within these genera leading to difficulties in identifications. The classifications of many of the species within these genera have been changed multiple times and still little is known about the relationships with in these genera. In an attempt to resolve the phylogenetic relationships of Stenonema, Stenacron, and Maccaffertium, two Mitochondrial genes (Cytochrome oxidase subunit 1 (cox1), and 16s ribosomal RNA (rrnl)) and two Nuclear genes (Wingless (Wg), and Histone H3) were sequenced from 60 individuals from the three genera, and ten individuals from three outgroup genera (Pseudiron, Epeorus, and Heptagenia). Maximum likelihood and Bayesian analysis were conducted on single-gene and concatenated multi-gene data sets, and species tree methods were utilized to resolve the phylogenetic relationships. Molecular analysis resolve Maccaffertium as paraphyletic, with Stenonema femoratum being resolved within Maccaffertium, as sister to M. mexicanum integrum. Stenacron in most cases was also resolved within Maccaffertium, as a close relative of M. lenati. In order to achieve monophyly, Stenonema needs to be expanded to include Maccaffertium and Stenacron, and four subgenera should be erected to name the well supported clades; Stenonema, Maccaffertium, Stenacron, and Lewisa.
Rubasinghe, Sumudu Chandima Kumari
Liverworts (Phylum Marchantiophyta) form the earliest diverging lineage of extant land plants and hold a key position in the evolutionary history of land plants. The family Cleveaceae, first defined in 1881 by Leitgeb by its complex thallus anatomy and star-shaped epidermal pores with strongly thickened radial walls, is now included within Marchantiopsida (Complex Thalloid Liverworts). The family is widely distributed in warm temperate to arctic regions throughout the Northern Hemisphere, but very rare in South America and absent from Australia and New Zealand. Since Cleveaceae was described, the number and names of genera and species recognized within the family have changed many times, with three genera currently accepted: Athalamia (12 to 15 species), Sauteria (2 to 5 species) and Peltolepis (1 or 2 species). However, no robust phylogenetic frame work or taxonomic monographs of the family have previously been undertaken and the species diversity within the genera remains uncertain. The study presents the first robust phylogenetic framework for the family, based on three chloroplast genes (psbA, rpoC1 and rps4) and one nuclear ribosomal region (26S) sequenced for 54 ingroup accessions representing a substantial part of the geographic range of the family (except South America) and a large part of its morphological diversity. Samples sequenced include the type species of the three currently accepted genera as well as those of previously synonymised genera; Clevea, Spathysia, Gollaniella and Sauchia. The current circumscription and relationships of the genera were tested using Maximum Parsimony, Bayesian and Likelihood inferences. Cleveaceae was strongly supported as monophyletic with four main lineages resolved within the family, two corresponding to Peltolepis and Sauteria and two composing a polyphyletic Athalamia. The latter is therefore divided into a more narrowly defined Athalamia and a fourth genus, for which Clevea is the earliest published name. Inferred evolutions of twelve morphological characters, that are useful or have been used in classifications of Cleveaceae, were reconstructed using maximum parsimony and maximum likelihood methods. The misleading influence of homoplasy on past morphological classifications and phylogenies is discussed. The study also presents the first worldwide taxonomic revision of Cleveaceae based on around 2300 specimens studied, including all available type specimens. The monographic work is based on morphological and anatomical characters reviewed using dissecting, compound and scanning electron microscopes including both herbarium and fresh material collected on field excursions during the study. Ventral scale morphology, position and aggregation of androecia and shape of receptacle were found to be valuable characters in generic and species delimitation. The traditional definition of genera of Cleveaceae based mainly on two characters (carpocephalum stalk position and anatomy) was rejected. A total of seven species were recognized from 25 formerly described names including one new necessary combination: Clevea hyalina (Sommerf.) Lindb., C. spathysii (Lindenb.) Müll. Frib., C. pusilla (Steph.) Rubasinghe & D.G.Long comb. nov., Athalamia pinguis Falc., Sauteria alpina (Nees) Nees, S. spongiosa (Kashyap) S.Hatt., and Peltolepis quadrata (Saut.) Müll. Frib. Nine excluded and doubtful species are listed along with reasons for their exclusion. Generic and species keys are presented based on vegetative, reproductive and spore morphological characters. For each genus and species, descriptions, illustrations, and distribution maps are given along with ecological, taxonomic and nomenclatural notes.
Filimban, Faten Zubair Bahnan Bakri
Senna comprises c.300-350 species and is one of the most species-rich and widely distributed genera in the family Leguminosae (Fabaceae). It is most diverse in tropical America, with secondary centres of diversity in tropical Africa, Madagascar and Australia. Only a few species are found in South Eastern Asia and in the Pacific Islands. Several Senna species are used as purgatives or laxatives in medicine, and some species are cultivated for their attractive flowers and foliage. The taxonomic revision of Senna species from Arabia presented here is based principally on herbarium specimens from the Royal Botanic Garden Edinburgh and the Royal Botanic Gardens, Kew and on field observations made in the Kingdom of Saudi Arabia, the Sultanate of Oman and the Republic of Yemen. These materials and observations also formed the basis for a review of the morphological features of the Senna species in Arabia, which was undertaken in the context of the morphological variability of the whole genus. The taxonomic revision recognises nine species that occur in Arabia: Senna alexandrina Mill., S. didymobotrya (Fresen.) H.S. Irwin & Barneby, S. holosericea (Fresen.) Greuter, S. hookeriana Batka, S. italica Mill., S. obtusifolia (L.) H.S. Irwin & Barneby, S. occidentalis (L.) Link, S. sophera (L.) Roxb. and S. tora (L.) Roxb. The study demonstrated that a putative tenth species, S. socotrana (Serrato) Lock, previously thought to be endemic to the region, is morphologically indistinguishable from the widespread Senna sophera. Consequently the study presents S. socotrana (Serrato) Lock as a syn. nov. Four taxa, S. alata (L.) Roxb., S. artemisioides (DC.) Randell subsp. artemisioides, S. auriculata Roxb., and S. multiglandulosa (Jacq.) H.S. Irwin & Barneby, are recorded as or cultivated in the Arabian Peninsula. A phylogeny is presented for the genus Senna, including all nine Arabian species, based upon the chloroplast DNA regions matK and rps16 and analysed in a parsimony and Bayesian framework. Sampling new to this study included 118 accessions of Arabian species representing substantial parts of their geographic range within the Arabian Peninsula. Sequence data newly generated from a further 13 accessions were added to 104 generated in previous studies bringing the number of accessions representing other Senna species from across the range of the genus to 117. The phylogeny is useful in a taxonomic context and is also suggestive of the phylogenetic utility of some features, especially the morphology of the pods. Reconstruction of the morphological diversification of extrafloral nectaries in the context of the phylogeny suggests that it may have been more complex than outlined in previously published work. The phylogeny shows Senna species found in the Arabian Peninsula are placed in three separate clades, suggesting that Senna arrived in the Arabian Peninsula at least three times independently. Dating the phylogeny using a relaxed molecular clock in a Bayesian approach indicates that these arrivals happened at different times over the past c. 20 Mya, suggesting that a common geological explanation is unlikely and that dispersal must have played a key role in developing these biogeographic patterns.
Ni Dhubhghaill, Ciara
The phylogeny of Eumalacostraca (Crustacea) has remained elusive, despite over a century of morphological and more recently molecular studies. Prior to this, no large scale combined evidence analyses of all eumalacostracan orders has been carried out. Evidence from four nuclear ribosomal and mitochondrial loci (18S rRNA, 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I) were combined with a newly synthesized morphological dataset to examine the utility of available data. With an aim to resolve conflict in the morphological dataset, fossils were added to the morphological dataset and their effects examined. The stratigraphic congruence of crustaceans was examined to determine the quality of existing trees. A modified protocol was developed to generate new molecular markers for the investigation of eumalacostracan phylogeny. Finally the effects of the new data on existing datasets were examined in a combined evidence approach. Significant conflict was detected between data partitions, especially between morphology and molecules. The addition of fossil data revealed the morphological dataset to be very sensitive to taxon sampling. Stratigraphic congruence was found to be poor for the five crustacean groups examined. Histone 3 and alanyl-tRNA synthetase were shown to be capable of successfully recovering relationships at the level of genus and above. Glutamyl-prolyl-tRNA synthetase failed to recover monophyletic groupings when analysed alone. Combining all molecular data produced well-supported phylogenies, but significant conflict between data partitions was identified and trees were very sensitive to taxon sampling. Rate heterogeneity and conflict between data partitions mean that the total sum of molecular and morphological evidence as presented here is currently unable to resolve a wellsupported eumalacostracan phylogeny. We recommend additional taxon sampling and further sampling of novel markers using the modified protocol developed here as well as the addition of fossil data and the exploitation of next generation sequencing technologies.
Borealosuchus (Crocodylia) from the early Campanian Mooreville chalk reveals new insights into the late Cretaceous fauna of Alabama and the origin of Crocodylian lineagesMcCormack, Larkin 01 May 2019 (has links)
Borealosuchus is a significant genus as it is considered either a basal crocodylian or close outgroup. A new species identified from the early Campanian Mooreville Chalk of Alabama is one of the oldest known crocodylians and extends the stratigraphic range of Borealosuchus from the Maastrichtian minimally into the early Campanian. It co-occurs with the giant alligatoroid Deinosuchus in deposits formed in a marginal marine setting with fluvial input. Its age, along with the phylogenetic position of Borealosuchus, renders this material critical for understanding the morphological conditions and relationships at the root of Crocodylia. The most complete specimen consists of partial cranial, mandibular, and postcranial remains preserving a unique combination of characters including a short dentary symphysis, splenial participation in the symphysis, lack of discrete concavity on the angular dorsal margin for an external mandibular fenestra, and bipartite ventral osteoderms. The external mandibular fenestra was either absent or very small, raising questions about the ancestral condition for this structure in Crocodylia. The new species is, surprisingly, closer phylogenetically to more derived species of Borealosuchus, including B. wilsoni, B. threeensis, and B. acutidentatus, than to B. sternbergii and B. formidabilis. This creates many range extensions and ghost lineages in the clade and suggests substantial unsampled diversity within Borealosuchus. Additional mandibular material from the Santonian Eutaw Formation may be referable to this new species, further increasing its stratigraphic range. A specimen consisting of a partial post-cranial skeleton from the Mooreville Chalk is significantly larger than the holotype of the new species, and is referable to Borealosuchus sp., but is too incomplete for more precise referral. These newly described specimens provide additional information about the faunal assemblages of Alabama during the Late Cretaceous and have broader implications because they are some of the earliest crocodylian material known. Indeed, the Eutaw material appears to be the oldest known occurrence of Crocodylia.
Mecham, Jesse Lewis
10 July 2006
Phylogenetic analysis is a central tool in studies of comparative genomics. When a new region of DNA is isolated and sequenced, researchers are often forced to throw away months of computation on an existing phylogeny of homologous sequences in order to incorporate this new sequence. The previously constructed trees are often discarded, and the researcher begins the search again from scratch. The jumpstarting algorithm uses trees from the prior search as a starting point for a new phylogenetic search. This technique drastically decreases search time for large data sets. This kind of analysis is necessary as researchers analyze tree of life size data sets.
Frabotta, Laurence John
12 April 2006
This dissertation has two major sections. In Chapter II, complete mitochondrial (mt DNA) genome sequences were used to construct a hypothesis for affinities of most major lineages of rodents that arose quickly in the Eocene and were well established by the end of the Oligocene. Determining the relationships among extant members of such old lineages can be difficult. Two traditional schemes on subordinal classification of rodents have persisted for over a century, dividing rodents into either two or three suborders, with relationships among families or superfamilies remaining problematic. The mtDNA sequences for four new rodent taxa (Aplodontia, Cratogeomys, Erethizon, and Hystrix), along with previously published Euarchontoglires taxa, were analyzed under parsimony, likelihood, and Bayesian criteria. Likelihood and Bayesian analyses of the protein-coding genes converged on a single topology that weakly supported rodent monophyly and was significantly better than the parsimony trees. Analysis of the tRNAs failed to recover a monophyletic Rodentia and did not reach convergence on a stationary distribution after fifty million generations. Most relationships hypothesized in the likelihood topology have support from previous data. Mt tRNAs have been largely ignored with respect to molecular evolution or phylogenetic utility. In Chapter III, the mt tRNAs from 141 mammals were used to refine secondary structure models and examine their molecular evolution. Both H- and L-encoded tRNAs are AT-rich with different %G and GC-skew and a difference in skew between H- and L-strand stems. Proportion of W-C pairs is higher in the H-strand and GU/UG pairs are higher in the L-strand, suggesting increased mismatch compensation in L-strand tRNAs. Among rodents, the number of variable stem base-pairs was nearly 75% of that observed across all mammals combined. Compensatory base changes were present only at divergences of 4% or greater. Neither loop reduction nor an accumulation of deleterious mutations, both suggestive of mutational meltdown (Muller's ratchet), was observed. Mutations associated with human pathologies are correlated only with the coding strand, with H-strand tRNAs being linked to substantially more of these mutations.
Emerging canine tick-borne diseases in Australia and phylogenetic studies of the canine Piroplasmidaryanj@ichr.uwa.edu.au, Ryan Jefferies January 2006 (has links)
Canine tick-borne diseases are an emerging problem within Australia and throughout the world. This thesis investigates Babesia gibsoni and Anaplasma platys infections in dogs in Australia and also explores the evolutionary relationships and taxonomy of the canine piroplasm species and the members of the order Piroplasmida. A nested PCR-RFLP assay was developed for the detection and differentiation of the canine piroplasm species and was found to have a high detection limit, capable of detecting a 2.7 x 10-7 % parasitaemia or the equivalent of 1.2 molecules of target DNA. Detection of piroplasm DNA applied to Whatman FTA classic cards using nested-PCR was found to have a lower detection limit than when using DNA extracted from whole blood but higher than IsoCode Stix or QIAamp extraction from filter paper based techniques. The nested PCR-RFLP assay was further evaluated for the detection of B. gibsoni infection in dogs being exported from Australia to New Zealand and compared to the current screening methods, the Immunofluorescent Antibody Test (IFAT) and microscopy. Of 235 dogs screened, 11 were IFAT positive, 1 was microscopy positive and 3 were PCR positive for B. gibsoni, highlighting the discordance that exists between various detection techniques. Replacing microscopic examination of blood smears with PCR-RFLP is suggested for screening dogs entering New Zealand, in addition to revising the current IFAT cut-off titre to minimize false positive results. The first case of B. gibsoni in New South Wales is also reported. A study was also conducted to further investigate the recent discovery of B. gibsoni in Australia and the association of this infection with American Pit Bull Terriers in an epidemiological study. Both American Pit Bull Terriers (n = 100) and other dog breeds (n = 51) were screened for B. gibsoni using IFAT and PCR-RFLP. A questionnaire was also completed by each dog owner regarding thethe husbandry and habits these dogs. Fourteen dogs were positive for B. gibsoni using IFAT and/or PCR-RFLP and all were American Pit Bull Terriers. Dogs that were male and/or were bitten by or were biters of other American Pit Bull Terriers were statistically more likely to be B. gibsoni positive, thus suggesting that blood-to-blood transmission may contribute to the spread of this disease. Experimental B. gibsoni infections were established in vivo to investigate the efficacy of combined atovaquone and azithromycin therapy and to determine the detection limits of PCR, IFAT and microscopy during various stages of infection. While atovaquone and azithromycin produced a reduction in circulating parasite levels, it did not cause total eradication, and possible drug resistance also developed in one dog. PCR was found to be most useful in detecting early and acute stage infections, while IFAT was most useful during chronic and acute infections. Microscopy is suggested to be only useful for detecting acute stage infections. This study also describes the detection of B. gibsoni in tissue samples during chronic infection for the first time, suggesting possible sequestration of this parasite. Anaplasma platys has also only recently been reported in Australia and the distribution, molecular-charcterisation, pathogenesis, co-infection with Babesia canis vogeli and treatment of infection with doxycycline were investigated. For the first time, A. platys is reported in Western Australia, Queensland and Victoria, with each isolate found to be genetically identical on the basis of the 16S rRNA gene. No correlation could be established between A. platys infection and the development of clinical signs or pathogenesis and definitive treatment using doxycycline could not be determined. Isolates of canine piroplasms from various geographical locations worldwide (n = 46), including Australia were characterised on the basis of multiple gene loci to explore the distribution, genetic variation and possible phylogeographical relationships of these species. Separate genotypes of B. canis vogeli, B. canis canis and B. gibsoni are suggested and may be correlated to different geographical origins. Characterization of B. canis vogeli, B. canis canis and B. canis rossi on the basis of the HSP 70 gene and B. gibsoni on the basis of the ITS 1, 5.8S rRNA gene and ITS 2 is described for the first time. Elevation of each of the B. canis subspecies, with the exclusion of B. canis presentii, to separate species is also proposed. The current paraphyly and taxonomic confusion associated with the members of the order Piroplasmida led to a review of the phylogenetic and taxonomic status of this group of organisms. Phylogenetic relationships are determined using 18S rRNA gene, 5.8S rRNA gene, HSP 70 gene and combined loci analyses. Rearrangement of the Piroplasmida into three families, including the new family Piroplasmiidae is proposed, in addition to the establishment of two new genera, the Piroplasma (Patton, 1895) and the Achromaticus (Dionisi, 1899). Other proposed schemes of classification and the limitations of phenotypic characteristics in taxonomic classification within the Piroplasmida are also discussed.
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