MESHWR / Department of Ecology and Resources Management / The presence of harmful algal blooms (HABs) and cyanobacteria toxins in drinking water sources are known to pose a great threat to humans. The main aim of this study was to use molecular technique to determine the origins of the cyanobacteria species at Musina raw water abstraction point by identifying and comparing the non-toxic and toxic cyanobacteria species in the Limpopo River and some of its tributaries based on the phylogenetic analyses of 16S rRNA gene. The Musina water treatment plant is located downstream of a weir and the Beit bridge on the Limpopo River and the raw water supply is abstracted from 22 boreholes of which 14 are along the Limpopo River and 8 boreholes are inside the Limpopo River channel. The bottom sediments samples were collected from these rivers: Limpopo, Crocodile, Mokolo, Mogalakwena, Nzhelele, Lephalale, Sand rivers (South Africa); Notwane (Botswana), Shashe River and Mzingwane River (Zimbabwe). The physical-chemical analysis of the bottom sediments showed the availability of nutrients, nitrates and phosphates, in excess of 0.5 mg/l for most the of rivers, alkaline pH and salinity in excess of 500 mg/l. Total genomic DNA were extracted from cyanobacteria species on the bottom sediments and Polymerase Chain Reaction (PCR) method was used to detect the genetic profile of the cyanobacteria species. Molecular identification of cyanobacteria was based on PCR amplification and sequencing of the 16S rRNA gene. The 16S rRNA gene was absent from sediments of the Mogalakwena and Lephalale rivers but present in all other selected rivers. The cyanotoxins detection was also based on PCR by amplification of microcystin/nodularin and cylindrospermopsin polyketide synthetase genes. Most of the samples showed no amplification of the toxin genes. While two samples showed the amplification of cylindrospermopsin polyketide synthetase gene (Sand River and Nzhelele River Next to Tshipise) and two samples showed amplification for microcystin/nodularin synthetase gene, Crocodile River and Mzingwane River. The first was the confirmation of similarity of samples from Crocodile River downstream of hartbeespoort Dam and Shashe River to Leptolyngbya boryana with 99% bootstrap confidence. The similarity of sample from Musina borehole to Sand River upstream to Alkalinema pantanalense with 98% bootstrap. Thus, the presence of toxic genes may imply the presence of toxic cyanobacteria species in the river sediments and may be hazardous to humans because rural communities and commercial farmers abstract water from Limpopo River catchment for human consumption, livestock and irrigation. The waters of the Limpopo River basin also provide drinking water to wildlife and a habitant for aquatic organisms/animals.

Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of 'tree quality'. In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignment is low, and (2) there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/.

No description available.

During European settlement, the vast majority of grasslands in Illinois were converted for agricultural purposes. Some of the remaining natural areas in southern Illinois include natural xeric forest openings (i.e., barrens, glades, outcrops), that have transitional community compositions representative of previously extensive grasslands and adjacent hardwood forests. Previous research in these forest openings show that the communities are largely driven by edaphic conditions and vary spatially across southern Illinois. While most of these communities are currently protected and established as nature preserves, threats to these natural xeric forest openings continue to persist, such as climate change and exotic invasion. These threats are capable of altering taxonomic, phylogenetic, and functional diversity and community composition. The overall goals of this research were to 1) determine metapopulations and metacommunity structure in a local group of sandstone outcrop communities (a subset of natural xeric forest opening communities), 2) expand resolution to a regional scale to include natural xeric forest openings with several substrates to investigate changes in taxonomic, phylogenetic, and functional diversity and community composition since surveys conducted in 1988, and 3) include spatial analyses to characterize autocorrelation structure of diversity and environmental variables and biological turnover of natural xeric forest openings at a global scale. Sandstone outcrop communities at Jackson Hollow in Pope County, Illinois had several metapopulation species based on Hanski’s incidence functional model. These metapopulation species were more often members of the Asteraceae and Poaceae than members of other plant families, and were often exotic in origin with short-lived lifecycles. These metapopulation species were also neither dominant species or singletons within sandstone patches. Based on the Elements of Metacommunity (EMS) Framework, positive coherence, species turnover, and boundary clumping indicate that these sandstone outcrop communities are predictable communities where species replace one each other regularly as groups of species and respond similarly to environmental gradients. Furthermore, diversity metrics were all positively correlated with each other, but not with patch characteristics. In addition, total species and metapopulation species were positively associated with phylogenetic and functional diversity, but metapopulation species were positively associated with non-standardized phylogenetic and functional indices. When looking at several natural xeric forest openings across southern Illinois and comparing them based on substrate types and between surveys in 1988 and 2019, taxonomic, phylogenetic, and functional compositions were distinct based on substrates, but were stable and resilient across surveys. Sandstone and shale communities were the most similar based on composition, followed by limestone communities compared to sandstone and shale communities, and then loess communities being the most dissimilar from all other communities. Environmental variables that best explained differences in community composition were canopy cover, soil acidity, photosynthetically active radiation, and soil depth. Diversity variables that best explained differences in community composition were phylogenetic nearest taxon index, Faith’s phylogenetic diversity, and dominant species richness. Ninety-four different species were either significant indicators for specific substrates, or 2019 surveys. While no cases of phylogenetic signal were observed based on functional traits, substrate types, or surveys, three cases of functional signal based on dominant communities were observed in sandstone communities in 2019, shale communities in 2019, and overall shale communities across 1988 and 2019 surveys. When applying spatial analyses to these natural xeric forest openings to understand autocorrelation structure and biological turnover, soil depth was the only environmental variable that exhibited significant spatial autocorrelation, as previous glacial events caused loess hill prairies in the northwestern extent of this study to have deeper soil due to Quaternary loess deposition. However, several diversity metrics exhibited spatial structure based on 1988 and 2019 surveys (1988: dominant species richness, Pielou’s evenness, Shannon-Weiner diversity, Faith’s phylogenetic diversity, and distance-based functional diversity; 2019: dominant species richness, Pielou’s evenness, Shannon-Weiner diversity, Faith’s phylogenetic diversity, and phylogenetic nearest taxon index). In addition, climate variables daily mean temperature and total annual precipitation exhibited spatial structure. Most variables were spatially clustered at local site scales and spatially dispersed at larger scales and spatially over-dispersed at a regional scale. Generalized dissimilarity models constructed based on elevation, soil, and climate variables showed that models based on both functional composition and 2019 surveys best explained biological turnover compared to taxonomic and phylogenetic and 1988 models. Several variables included in models differed based on aspects of biological turnover or surveys, but temperature annual range and soil bulk density variables were common across all models. However, differences between total deviance explained and null deviances show that geographic distance between natural xeric forest openings was overwhelmingly the most influential variable contributing to biological turnover. Given these observations, natural xeric forest openings at local scales persist as distinct habitat patches amidst a landscape that largely constitutes an inhospitable matrix to colonizing species, yet certain species are able to migrate between patches. The resulting community assembly of individual patches is determined by both colonizing species and environmental gradients across the landscape. Despite simultaneous threats to diversity and composition in natural xeric forest openings at a regional scale, substrate continues to drive community assembly, in that certain species are characteristic indicators of these substrates. Furthermore, the most recent surveys in sandstone and shale communities exhibited functional signals. However, these natural xeric forest openings are spatially structured based on soil depth due to glacial history, certain metrics of diversity, and climate variables. Along with these occurrences of spatial autocorrelations, different aspects of biological turnover are best predicated by geographic distance as well as unique combinations of climate and soil variables between different aspects of diversity and surveys.

Members of the Mylagaulidae have been known for over a century to bear nasal horns; the only rodents, extinct or extant, ever to have done so. This striking feature is known from five of the over 30 species of mylagaulid rodents discovered across North America and Eurasia, all relatively large animals that were likely less fossorial than their relatives. We describe herein a sixth new species of horned mylagaulid. This new taxon from Sioux County, Nebraska, offers the opportunity to reassess the phylogenetic relationships of Mylagaulidae and test several evolutionary hypotheses. Our analyses demonstrate that horns evolved only once in Mylagaulidae, in the common ancestor of Ceratogaulus, first as short horns exapted from the thickened nasals of fossorial ancestors, and later as taller horns. The horns evolved following a positive allometric scaling with body mass that suggests a response to predation pressure in these nearly blind animals. The evolution of tall horns also corresponds to a jump in body mass. The largest mylagaulids are not horn-bearing species, however. Additional analyses of the complex pattern of body mass evolution we reveal will be necessary to explain the evolution of the largest head-lift digging rodents in Earth history. https://zoobank.org/urn:lsid:zoobank.org:pub:81FE999A-F79E-4BD4-9A81-2C7D3D5D81CD.

The phylogenetic relationships of Pseudophryne and the closely related monotypic Metacrinia are resolved with the use of morphological characters and comparison with representatives species of Crinia, Uperoleia, and Taudactylus as defined out-groups. Characters describing musculature are not sufficient to resolve the relationships, but do provide support when used in combination with osteological and external characteristics. When all data are considered, parsimony and maximum likelihood analyses yield the same hypothesis of relationships within Pseudophryne + Metacrinia. Thus, a monophyletic lineage of Pseudophryne + Metacrinia is supported by four synapomorphies: (1) the absence of toe fringes, (2) wide frontoparietal fontanelle, (3) m. abductor indicis longus arising from the humerus and radioulna, and (4) neopalatine in contact with the maxilla. The columella is shown as a relatively plastic characteristic, present ancestrally but lost in the common ancestor to Pseudophrye+Metacrinia and then reappearing within that taxon as well as one outgroup species (Crinia riparia). Analyses of size data reveal shape trends among the outgroup taxa that differ from the in-group of Pseudophryne and Metacrinia. Interpretations of shape differences are congruent with the placement of Uperoleia as more closely related to Pseudophrye. This study suggests support for re-synonymy of Metacrinia nichollsi with Pseudophryne, but formal change of status depends on access to more complete data.

Phylogenetic research on non-model organisms has been hindered by limited marker availability. Next generation sequencing techniques are eliminating that barrier. Using Illumina sequencing technology, Trinity assembly software, custom Perl reciprocal BLAST scripts, and Primer3 primer prediction software, we produced and analyzed 7 Plecopteran transcriptomes, representing 7 of the 16 total families, in an attempt to identify and develop conserved orthologous genetic markers. The transcriptomes were used to reconstruct a gene content phylogeny using a simple distance matrix generated from reciprocal blastn data. By producing and filtering a reciprocal blast network we identified and aligned over 450 putative orthologs. Out of these, 25 primer pairs were selected that showed 100% conserved primer sites across all the transcripts from which they were created. Of those 25, 3 loci (PlecSK1, Perl534, and PvC2190) show very positive phylogenetic potential. These 3 markers may also be suitable and even highly useful in population genetic studies in which the populations have had sufficient time to develop significant genetic separation. The rapid and affordable nature of this study demonstrates the ease by which non-model organism phylogenetics can be expanded and made more robust.

No description available.

<p> Freud's Totem and Taboo was one of the more controversial additions to the literature of religious theory. The two major hypotheses of the work are the parallel between ontogenetic and phylogenetic evolution, and the primal horde parricide. The first hypothesis has rarely been taken seriously. The second, although never verified with anthropological evidence, has generated further hypotheses based upon its value as a symbolic representation rather than an actual occurrence. Paul Roazen has suggested that the primal horde parricide hypothesis possesses characteristics similar to those of most social contract theories. He posited, in light of this, that Totem and Taboo ought to be considered a kind of social contract, although it has never been thought of this way. </p> <p> The major school of philosophical thought which has continued to maintain interest in Totem and Taboo, long after the main anthropological assertions have been dispelled, is the French structuralist movement and its successors. Through the work of Levi-Strauss, carried on with theorists such as Lacan, Bataille, and Derrida, Totem and Taboo has maintained value as important work. The French structuralists have sustained a tradition that began with Rousseau of combining mathematical reasoning and linguistic theory together with anthropological speculation raised in Totem and Taboo. Thus in light of Roazen's hypothesis and the structuralist treatment of Totem and Taboo, together with Bryan Skyrms' s recent work on Rousseau and the mathematics of social contract theory, I posit that Totem and Taboo is comparable to Rousseau's Social Contract, in which human nature, politics, myth and mathematics merge. Implicitly Totem and Taboo contains a novel theory of the political development of society. </p> / Thesis / Doctor of Philosophy (PhD)

Fungi are vital microbes present throughout the biosphere. Many species are essential decomposers in the ecosystem, breaking down organic materials and nourishing other lives. Moreover, some have directly influenced human civilization by providing beneficial products, such as edible mushrooms, brewer's yeast, baker's yeast, and antibiotics. However, it's important to note that this group of organisms can also have a "dark side". Each year, fungal pathogens cause approximately 150 million severe infections and 1.7 million deaths. The high rate of infection is compounded by the limited availability of antifungal drugs and the increasing prevalence of antifungal resistance. In response to the global burden of fungal diseases, the World Health Organization published a list of priority fungal pathogens in 2022 and highlighted strategies such as surveillance, sustainable research investments, and public health interventions to combat the increasing fungal threats. My PhD research has focused on surveillance and genomic analyses of several human fungal pathogens, particularly Candida auris. Candida auris is an emerging multidrug-resistant yeast that causes systemic infections with high mortality rates. While initially recognized as a nosocomial pathogen, our genomic analyses of strains isolated from clinical environments, tropical wetlands, fruit surfaces, and dog ears revealed potential transmission routes between diverse environments and patients, including a potential driver for the prevalence of antifungal resistance. Furthermore, our research indicated limited genetic exchange within and between lineages of Candida auris. Through genome-wide association analyses of global Candida auris strains, several known and novel genomic variants were identified associated with susceptibility to azoles, echinocandins, and amphotericin B. Overall, our studies underscore the importance of continuous surveillance to understand potential routes of Candida auris transmission and the urgent need for innovative approaches to treat multidrug-resistant Candida auris infections. / Thesis / Doctor of Philosophy (PhD)