The scrub pythons (Morelia amethistina complex) are revised based on museum specimens and new material recently collected in eastern Indonesia. Morelia kinghorni (formerly M. amethistina kinghorni) and M. amethistina (formerly M. amethistina amethistina) are recognized as species, and three new species are described. The phylogenetic relationships of scrub pythons are resolved using morphological and molecular characters Scrub pythons are most closely related to Morelia boeleni and have undergone both ancient divergences and a relatively recent radiation. The distribution of scrub pythons corresponds well with areas of endemism recognized in earlier studies of other taxa. Their distribution and evolution appears to have been shaped by combined effects of dispersal and vicariance. Scrub python populations exhibit interesting color and pattern polymorphism and ontogenetic change, and these characteristics vary among populations.

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Master of Science / Department of Biology / Jesse B. Nippert / In 1902, President Theodore Roosevelt signed and enacted the Reclamation Act, which would fundamentally alter the lowland hydrology of the arid southwest over the next century. Flow regulations, groundwater pumping, damming, and river channel changes have led to decreases in water table heights and periodic overbank flooding, and subsequently, increased soil salinity in the arid Southwest. During this period, native riparian tree species have declined significantly and an invasive tree species, Tamarix ramosissima, has increased in abundance and distribution. Increases in soil salinity negatively impact the physiology of native riparian tree species, but the impacts of soil salinity on Tamarix physiology are incompletely known. I studied the impact of increasing soil salinities on the physiology of Tamarix in both field and controlled environments. I first studied the impacts of increasing soil salinities on Tamarix physiology at two semi-arid sites in western Kansas. I concluded that physiological functioning in Tamarix was maintained across a soil salinity gradient from 0 to 14,000 ppm illustrating robust physiological responses. Using cuttings from Tamarix trees at both sites, I subjected plants to higher NaCl concentrations (15,000 and 40,000 ppm). Tamarix physiology was decreased at 15,000 ppm and 40,000 ppm. Tamarix physiological functioning was affected at the induction of treatments, but acclimated over 30-40 days. These results reveal a threshold salinity concentration at which Tamarix physiological functioning decreases, but also illustrate the advantageous halophytic nature of Tamarix in these saline environments. Many arid and semi-arid environments are predicted to become more saline, however, results from both studies suggest that increasing salinity will not be a major barrier for Tamarix persistence and range expansion in these environments.

Translocation involves the movement of organisms, by human intervention, from one area to other suitable (receptor) habitats. In a conservation context, translocation can be employed to support species preservation, population restoration and/or for ecological research. Despite decades of internationally published research, translocation remains a controversial endeavour. However, due to continual degradation and fragmentation of natural habitats in the face of human development, translocation is becoming a vital component of conservation efforts. Prior to the development of an Exxaro coal mine in Mpumalanga, a population of an endangered Highveld succulent species, Frithia humilis Burgoyne (Aizoaceae/Mesembryanthemaceae), was saved from extirpation by means of translocation. Three receptor habitats were identified within the distribution range of the species. The largest part of the donor population was transplanted to sandstone outcrops of the Ecca Group (Karoo Supergroup), resulting in four subpopulations residing on geological substrates typical of the species’ habitat. The remaining portion of the donor population was experimentally translocated to two habitats containing non-native geologies, namely sedimentary outcrops of the Wilge River Formation (Waterberg Group) and (igneous) felsite oucrops of the Rooiberg Group (Transvaal Supergroup). A control population was identified, occupying Ecca and Dwyka Group (Karoo Supergroup) sediments, as a measure to compare the response of translocated populations. A monitoring programme, utilising a plant age classification system, was initiated in February of 2010 to elucidate demographic trends and to gauge the response of translocated populations to novel environments. Plant survival, plant growth, flowering, fruiting (representing reproductive response) and seedling emergence were chosen as indicators to measure translocation success over the short term. Furthermore, quantitative and qualitative entomological investigations into the identity of possible F. humilis pollinators, as well as the presence of pollinator species at receptor habitats, were made. A repeatable methodology for post-translocation monitoring and scientifically sound baseline data for future comparative purposes were successfully established. Initial results showed that F. humilis subpopulations replanted on Ecca standstones had positive responses to translocation: Subpopulations survived and all but one increased in size. Individual plant growth increased, higher reproductive output was evident and seedling emergence was pervasive. Positive responses indicated that F. humilis populations translocated onto typical geologies had the potential to establish and persist over three years. Knowledge of this early success is of immense value to the conservation of the species, as a limited number of known natural populations remain. Coal mining, targeting coal seams underlying typical F. humilis habitats, is also likely to remain a threat. The viability of translocating F. humilis populations to non-typical geological substrates has shown limited efficacy. Poor survival along with inferior reproductive response confirmed Wilge River Formation outcrops as poor receptor sites for translocated F. humilis populations. Rooiberg felsite outcrops also proved to be dubious receptor sites, primarily since there was a downward trend in seedling emergence over time, suggesting inferior germination conditions. Nevertheless, translocation to non-native geological substrates did not have disastrous short-term consequences for these populations, since flowering, fruit production and seedling emergence continued, albeit at reduced (or continually declining) rates. Potential pollinator species of F. humilis were not revealed through quantitative surveys of insect diversity. Qualitative surveys proved more efficient and accurate at pinpointing insect pollinator species. This study provided the first evidence of Apidae, Megachilidae (Hymenoptera) and Bombyliidae (Diptera) insect species pollinating F. humilis. The generalist nature of the plant-pollinator relationship, as well as the presence of generalist pollinator species at some receptor habitats, probably contributed to the initial positive response of F. humilis flowering and fruiting after translocation. Results from this study, however promising, should be viewed as initial indications of translocation success. The literature review revealed a plethora of literature recommending post-translocation monitoring programmes for five years to several decades. This study confirmed that successful establishment of F. humilis can be determined after three years, but that long-term monitoring is required to evaluate persistence. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Translocation involves the movement of organisms, by human intervention, from one area to other suitable (receptor) habitats. In a conservation context, translocation can be employed to support species preservation, population restoration and/or for ecological research. Despite decades of internationally published research, translocation remains a controversial endeavour. However, due to continual degradation and fragmentation of natural habitats in the face of human development, translocation is becoming a vital component of conservation efforts. Prior to the development of an Exxaro coal mine in Mpumalanga, a population of an endangered Highveld succulent species, Frithia humilis Burgoyne (Aizoaceae/Mesembryanthemaceae), was saved from extirpation by means of translocation. Three receptor habitats were identified within the distribution range of the species. The largest part of the donor population was transplanted to sandstone outcrops of the Ecca Group (Karoo Supergroup), resulting in four subpopulations residing on geological substrates typical of the species’ habitat. The remaining portion of the donor population was experimentally translocated to two habitats containing non-native geologies, namely sedimentary outcrops of the Wilge River Formation (Waterberg Group) and (igneous) felsite oucrops of the Rooiberg Group (Transvaal Supergroup). A control population was identified, occupying Ecca and Dwyka Group (Karoo Supergroup) sediments, as a measure to compare the response of translocated populations. A monitoring programme, utilising a plant age classification system, was initiated in February of 2010 to elucidate demographic trends and to gauge the response of translocated populations to novel environments. Plant survival, plant growth, flowering, fruiting (representing reproductive response) and seedling emergence were chosen as indicators to measure translocation success over the short term. Furthermore, quantitative and qualitative entomological investigations into the identity of possible F. humilis pollinators, as well as the presence of pollinator species at receptor habitats, were made. A repeatable methodology for post-translocation monitoring and scientifically sound baseline data for future comparative purposes were successfully established. Initial results showed that F. humilis subpopulations replanted on Ecca standstones had positive responses to translocation: Subpopulations survived and all but one increased in size. Individual plant growth increased, higher reproductive output was evident and seedling emergence was pervasive. Positive responses indicated that F. humilis populations translocated onto typical geologies had the potential to establish and persist over three years. Knowledge of this early success is of immense value to the conservation of the species, as a limited number of known natural populations remain. Coal mining, targeting coal seams underlying typical F. humilis habitats, is also likely to remain a threat. The viability of translocating F. humilis populations to non-typical geological substrates has shown limited efficacy. Poor survival along with inferior reproductive response confirmed Wilge River Formation outcrops as poor receptor sites for translocated F. humilis populations. Rooiberg felsite outcrops also proved to be dubious receptor sites, primarily since there was a downward trend in seedling emergence over time, suggesting inferior germination conditions. Nevertheless, translocation to non-native geological substrates did not have disastrous short-term consequences for these populations, since flowering, fruit production and seedling emergence continued, albeit at reduced (or continually declining) rates. Potential pollinator species of F. humilis were not revealed through quantitative surveys of insect diversity. Qualitative surveys proved more efficient and accurate at pinpointing insect pollinator species. This study provided the first evidence of Apidae, Megachilidae (Hymenoptera) and Bombyliidae (Diptera) insect species pollinating F. humilis. The generalist nature of the plant-pollinator relationship, as well as the presence of generalist pollinator species at some receptor habitats, probably contributed to the initial positive response of F. humilis flowering and fruiting after translocation. Results from this study, however promising, should be viewed as initial indications of translocation success. The literature review revealed a plethora of literature recommending post-translocation monitoring programmes for five years to several decades. This study confirmed that successful establishment of F. humilis can be determined after three years, but that long-term monitoring is required to evaluate persistence. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

BACKGROUND:Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.RESULTS:We developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn's disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn's disease.CONCLUSIONS:By taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.

Although there is a wealth of knowledge on categorization in infancy, there are still many unanswered questions about the nature of category representation in infancy. For example, it is yet unclear whether categories in infancy have well-defined boundaries or what knowledge about species categories young infants have before entering the lab. Using a morphing technique, we linearly altered the proportion of cat versus dog in images and observed how infants reacted to contrasts between pairs of images that either did or did not cross over the categorical boundary. This was done while equating between-category and within-category similarity. Results indicate that infants’ pre-existing categories of cats and dogs are discrete and mutually exclusive. Experiment 2 found that inversion caused a disruption in processing by 6.5- but not 3.5- month-old infants, indicating a developmental change in category representation. These findings demonstrate a propensity to dichotomize early in life that could have implications for social categorizations, such as race and gender. Furthermore, this work extends previous knowledge of infant categorical perception by demonstrating a priori knowledge of familiar species categories and the boundaries between them.

The antelope jackrabbit (Lepus alleni) inhabits the seasonal landscape of the subtropical Sonoran savanna grassland in southern Arizona. Basic ecological information on this understudied lagomorph is lacking beyond historical responses to rangeland conditions. This is the first study to utilize radio collars to assess space use of antelope jackrabbits. In the semidesert grassland of Buenos Aires National Wildlife Refuge, Arizona, we estimated antelope jackrabbit home range size, seasonal ranges, and movement patterns. Home range estimates were comparable to other Lepus species, however, seasonal range sizes did not differ. We analyzed antelope jackrabbit habitat structure, measured vegetation characteristics, and determined whether there was a spatial association between antelope jackrabbits and the endangered Pima pineapple cactus (Coryphantha scheeri var. robustispina). Antelope jackrabbits selected vegetation structure and characteristics similarly to available areas on the refuge. We did not detect a spatial association between antelope jackrabbits and Pima pineapple cacti, however given the importance of understanding endangered species relationships, further investigation is warranted. Our results add to the limited ecological information known about antelope jackrabbits and provide baseline data for future studies. Knowledge about spatial ecology and habitat selection helps managers and biologists make informed recommendations for land and wildlife management.

In the current work, the photophysics and photochemistry of the phototoxic red fluorescent protein (RFP) KillerRed was investigated. KillerRed's phototoxicity makes it useful for studying oxidative stress on cell physiology and for cell killing in photodynamic therapy. Spectroscopic probes were used to show that the phototoxicity of KillerRed stems primarily from a type I photosensitization mechanism producing radicals. The production of radicals was supported by electron paramagnetic resonance (EPR) studies, where a long-lived radical was observed in KillerRed and two other RFPs (mRFP and DsRed) following excitation. Transient absorption spectroscopy, various other spectroscopic techniques, and the published crystal structure of KillerRed indicate that the long-filled water channel is likely responsible for the increased phototoxicity of KillerRed. In the blue fluorescent protein (BFP) mKalama1, some of the same techniques were applied to understand the photophysics and photochemistry on the timescale ranging from femtoseconds to seconds. Transient absorption spectroscopy and previously published results demonstrate that two-photon excitation of mKalama1 likely results in the formation of a radical cation and solvated electrons. This may explain the blinking behavior which has been observed on the single molecule level for many fluorescent proteins, the identity of which has remained elusive. It was also shown that the chromophore, while neutral in the ground state, does not exhibit excited-state proton transfer (ESPT) during its nanosecond excited-state lifetime; however, the chromophore undergoes a deprotonation in the ground state after electronic relaxation. This work plays a key role in our understanding of fluorescent proteins and will help pave the way to developing new ones. The research on the BFPs was extended to improve them for cellular imaging. This was accomplished by identification of dark states in the BFPs which are longer in wavelength than the collected fluorescence. Using dual lasers, it was shown that these dark states could be optically depleted, thereby increasing the overall fluorescence without enhancing the background fluorescence. Rational site-directed mutagenesis was carried out on the BFPs and the mutants were screened for fluorescence enhancement. These proteins were then analyzed using transient absorption spectroscopy to elucidate the identity of the dark state(s) used for fluorescence enhancement.

Contrary to what many scholars hold, a case can be made for human population reduction (the practice of artificially decreasing the number of human beings on the Earth). Robin Attfield's, Paul Taylor's, Arne Næss's and J. Baird Callicott's theories are considered for justifying human population reduction; however, only Næss's actually justifies reduction. Another argument for human population reduction is developed, based on rectification: humans have unjustly harmed other living entities and themselves, and they should provide rectification for the harm done. Human population reduction is a way in which this rectification can be given.