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Pigeonpea (Cajanus cajan (L.) Millsp.) is a drought tolerant legume of the Fabaceae family in the order Fabales and the only cultivated species in the genus Cajanus. It is mainly cultivated in the semi-arid tropics of Asia and Oceania, Africa and America. In Malawi, one of the top producers of pigeonpea in Africa, it is grown by small scale farmers as a source of food and income and for soil improvement in intercropping systems. However, varietal contamination due to natural outcrossing causes significant yield losses for farmers. In this study, 48 polymorphic SSR markers were used to assess diversity in all pigeonpea varieties cultivated in Malawi with the aim of developing a genetic fingerprint to distinguish the released varieties. SSR alleles were separated by capillary electrophoresis on an ABI 3700 automated sequencer and allele sizes determined using GeneMapper 4.0 software. Allelic data was analysed with PowerMarker. A total of 212 alleles were revealed averaging 5.58 alleles per marker with a maximum number of 14 alleles produced by CCttc019 (Marker 40). Polymorphic information content (PIC) ranged from 0.03 to 0.89 with an average of 0.30. DARwin software was used to generate a neighbour-joining tree that displayed three major clusters with two sub clusters in Cluster I. The released varieties were scattered across all the clusters observed, indicating that they generally represent the genetic diversity available in Malawi, although it was observed that there is substantial variation that can still be exploited through further breeding. Screening of the allelic data associated with five popular pigeonpea varieties for which a DNA fingerprint was to be developed, revealed 6 markers – CCB1 (Marker 1), CCB7 (Marker 2), Ccac035 (Marker 7), CCttc003 (Marker 15), Ccac026 (Marker 37) and CCttc019 (Marker 40)– which gave unique allelic profiles for each of the five varieties. With further tests needed for its robustness, this genetic fingerprint can be used for seed certification to ensure only genetically pure seeds are delivered to Malawi farmers. / Agriculture and  Animal Health / M. Sc. (Agriculture)

Cajanus cajan (L.) Millsp. (Pigeonpea) belongs to the Leguminosae genus Cajanus which is composed of 34 species. Pigeonpea is the only cultivated member of the genus, while the remaining species are wild relatives belonging mainly to the secondary gene pool. DNA sequence data from the nuclear ITS region and the chloroplast trnL-F spacer were utilized to investigate the phylogenetic relationships between Cajanus and five other allied genera in the subtribe Cajaninae. This study revealed the non-monophyly of Cajanus and Rhynchosia and supported the monophyly of Eriosema and Flemingia, but more sampling ,especially from the large genera of Rhynchosia and Eriosema, is recommend to adequately test the hypothesis of generic monophyly. The phylogenetic relationships within the genus Cajanus resolved Cajanus scarabaeoides (L.) Thouars as the most basal species in the Cajanus clade. The study also utilized Single Nucleotide Polymorphism (SNP) markers derived from low copy orthologous genes and genotyped using the high throughput SNP-OPA Illumina golden gate assay. The aim was to understand phylogenetic and domestication history, genetic structure, patterns of genetic diversity, gene flow and historical hybridization between Cajanus cajan (pigeonpea) and wild relatives. The neighbor-joining tree resolved well-supported clusters, which reflect the distinctiveness of species and congruence with their geographical origin. It supported the ITS based phylogeny and resolved C. scarabaeoides as basal to the Cajanus clade. The phylogenetic signal and genetic signatures revealed insights into the domestication history of pigeonpea. Our results supported Cajanus cajanifolius as the presumed progenitor of pigeonpea and we speculate that for pigeonpea there was a single major domestication event in India. Genetic admixture and historical hybridization were evident between pigeonpea and wild relatives. Abundant allelic variation and genetic diversity was found in the wild relatives, with the exception of wild species from Australia, as compared to the domesticated pigeonpea. There was a reduction of about 75% in genetic polymorphism in domesticated pigeonpea as compared to the wild relatives, indicating a severe “domestication bottleneck” during pigeonpea domestication. We discovered SNP markers associated with disease resistance (NBS-LRR) loci. The SNPs were mined in a comparison of BAC-end sequences (BES) of C. cajan and amplicons of the wild species, C. scarabaeoides. A total of ~3000 SNPs were identified from 304 BES. These SNPs could potentially be used in constructing a genetic map and for marker assisted breeding.

Census of the feral pigeon (Columba livia f. domestica) population in the selected localities and flying through the corridor of the Radlické valley in Prague. The diploma thesis is dealing with the research of the number of the pigeons (Columba livia f. domestica) flying through the corridor of the Radlické údolí, with the exploration of the next pigeons' flying routes, with inventorying of the number of pigeons in the localities Smíchovské nádraží and Na Knížecí and with dependece of the number of pigeons on the abiotical conditions, season, day time and the time of the spring seeding and harvest. The food ecology of pigeons was also investigated within the process of inventorying in the locality Na Knížecí. The final chapter is focused on coloring of the individuals in the different Prague localities. The research was realised from July 2012 to November 2013. The folowing methods of research were used: observation, marking with the wing tapes, modified linear method of addition. The results of the diploma thesis indicate that number of pigeons in the observed localities change especially in the time of seeding and harvest. Numerical fluctuations are not so extreme because the group of the resident pigeons always stays in the city. The spectrum of the food offered by local inhabitants doesn't...

The Pigeon River was severely impacted beginning in the early 1900s by a paper mill located in Canton, North Carolina. The mill discharged chemical byproducts into the Pigeon River until 1992 when the paper mill modified their processes. As a result, water quality improved but the status of salamander species in the Pigeon River was unknown. Worldwide amphibian declines over the last 20 years have drawn attention to the need for more research and a better understanding of species-specific habitat relationships. There is concern about amphibian population declines because amphibians are critical to the balance of ecosystems and are considered exceptional indicators of environmental health. The objectives of this study were: 1) to conduct a baseline survey of salamander species composition in the Pigeon River watershed, 2) to determine if salamander populations differ above and below the Canton paper mill, and 3) to attempt to explain variance in salamander abundance, richness and diversity by comparing water quality and substrate characteristics among streams. Eight stations were examined on the Pigeon River, with four stations located above the paper mill and four stations below. We also chose three stations on each of four tributaries, Big Creek, Fines Creek, Jonathan Creek and Richland Creek. Snorkel surveys were completed in the summer of 2009. Five of eight species of stream salamanders were found that historically existed in Haywood County, NC: Eastern hellbender, Blue Ridge two-lined salamander, shovel-nosed salamander, black-bellied salamander and spring salamander. No salamanders were found in the main channel of the Pigeon River below the mill. Eastern hellbenders and Blue Ridge two-lined salamanders preferred substrates consisting of rubble and avoided bedrock. Percent rubble was the only variable retained in substrate models and was positively related to salamander abundance, richness and diversity. Conductivity, salinity, and water temperature were higher in the Pigeon River below the mill than at all other sites. Salamander abundance was explained by dissolved oxygen, pH, and stream width in water quality models. The results of this study suggest salamander abundance was negatively associated with the Pigeon River below the mill because of poor water quality and not habitat availability.

The use of environmental geometry as a spatial cue is well established for a range of species. Previous research has focused largely on the use of global geometry (e.g., the shape of a room). Thus, comparatively less is known about how local geometry (e.g., corner angles within a room) is encoded. The purpose of the research presented in this thesis was to examine how angular information is encoded and to determine whether angle size influences encoding, using a discrimination task and a spatial array task. Chapter 2 presents a study during which pigeons were trained to discriminate between a small (60°) and large (120°) angle. Once the birds were accurately choosing the angle associated with reward, they were tested on their ability to discriminate between their training angle and one of a series of novel angles. The pigeons showed an absolute learning pattern for the small training angle, but not the large angle. The significance of this result is that the small angle may have been perceived as more distinctive compared to the large angle. Adopting a comparative approach, Chapter 3 presents a study during which adult humans were trained and tested using a similar paradigm but with different training angles (25°, 50° and 75°). The results of this study also support an absolute learning pattern for the small training angle but not the large. These results are significant in that they suggest that angle size may be an important local geometric cue that is encoded in a similar way by both pigeons and humans. To understand how angular information may be processed during a spatial task, Chapter 4 presents a study during which adult humans were trained and tested on their ability to use local angles (either 50° or 75°) to find a goal location within an object array. The results showed that the smaller angle was used more effectively as a spatial cue than the larger angle. Overall, these results are important as they suggest that small and large angles are encoded differently by pigeons and humans, with small angles perceived as more distinctive than large angles.

The use of environmental geometry as a spatial cue is well established for a range of species. Previous research has focused largely on the use of global geometry (e.g., the shape of a room). Thus, comparatively less is known about how local geometry (e.g., corner angles within a room) is encoded. The purpose of the research presented in this thesis was to examine how angular information is encoded and to determine whether angle size influences encoding, using a discrimination task and a spatial array task. Chapter 2 presents a study during which pigeons were trained to discriminate between a small (60°) and large (120°) angle. Once the birds were accurately choosing the angle associated with reward, they were tested on their ability to discriminate between their training angle and one of a series of novel angles. The pigeons showed an absolute learning pattern for the small training angle, but not the large angle. The significance of this result is that the small angle may have been perceived as more distinctive compared to the large angle. Adopting a comparative approach, Chapter 3 presents a study during which adult humans were trained and tested using a similar paradigm but with different training angles (25°, 50° and 75°). The results of this study also support an absolute learning pattern for the small training angle but not the large. These results are significant in that they suggest that angle size may be an important local geometric cue that is encoded in a similar way by both pigeons and humans. To understand how angular information may be processed during a spatial task, Chapter 4 presents a study during which adult humans were trained and tested on their ability to use local angles (either 50° or 75°) to find a goal location within an object array. The results showed that the smaller angle was used more effectively as a spatial cue than the larger angle. Overall, these results are important as they suggest that small and large angles are encoded differently by pigeons and humans, with small angles perceived as more distinctive than large angles.

The Pigeon River was severely impacted beginning in the early 1900s by a paper mill located in Canton, North Carolina. The mill discharged chemical byproducts into the Pigeon River until 1992 when the paper mill modified their processes. As a result, water quality improved but the status of salamander species in the Pigeon River was unknown. Worldwide amphibian declines over the last 20 years have drawn attention to the need for more research and a better understanding of species-specific habitat relationships. There is concern about amphibian population declines because amphibians are critical to the balance of ecosystems and are considered exceptional indicators of environmental health.The objectives of this study were: 1) to conduct a baseline survey of salamander species composition in the Pigeon River watershed, 2) to determine if salamander populations differ above and below the Canton paper mill, and 3) to attempt to explain variance in salamander abundance, richness and diversity by comparing water quality and substrate characteristics among streams. Eight stations were examined on the Pigeon River, with four stations located above the paper mill and four stations below. We also chose three stations on each of four tributaries, Big Creek, Fines Creek, Jonathan Creek and Richland Creek. Snorkel surveys were completed in the summer of 2009. Five of eight species of stream salamanders were found that historically existed in Haywood County, NC: Eastern hellbender, Blue Ridge two-lined salamander, shovel-nosed salamander, black-bellied salamander and spring salamander. No salamanders were found in the main channel of the Pigeon River below the mill. Eastern hellbenders and Blue Ridge two-lined salamanders preferred substrates consisting of rubble and avoided bedrock. Percent rubble was the only variable retained in substrate models and was positively related to salamander abundance, richness and diversity. Conductivity, salinity, and water temperature were higher in the Pigeon River below the mill than at all other sites. Salamander abundance was explained by dissolved oxygen, pH, and stream width in water quality models. The results of this study suggest salamander abundance was negatively associated with the Pigeon River below the mill because of poor water quality and not habitat availability.

The ability to discriminate relative and absolute number has been researched widely in both human and nonhuman species. However, the full extent of numerical ability in nonhuman animals, and the nature of the underlying numerical representation, on which discriminations are based, is still unclear. The aim of the current research was to examine the performance of pigeons and humans in tasks that require the discrimination of relative number (a bisection procedure), and absolute number (in a reproduction procedure). One of the main research questions was whether numerical control over responding could be obtained, above and beyond control by temporal cues in nonhuman animals, and if so, whether it was possible to quantify the relative influences of number and time on responding. Experiment 1 examines nonhuman performance in a numerical bisection task; subjects were presented with either 2 and 6, 4 and 12, or 8 and 24 keylight flashes across three different conditions, and were required to classify these flash sequences as either a “large” or “small” number, by pecking the blue or white key, respectively. Subjects were then tested with novel values within and 2 values higher and lower than the training values. Experiments 2-4 investigate responding in a novel numerical reproduction procedure, in which pigeons were trained to match the number of responses made during a production phase to the number of keylight flashes (2, 4, or 6) in a recently completed sample phase. Experiments 2 and 2A examined discrimination performance when the temporal variables, flash rate and sample phase duration, were perfectly correlated (Experiment 2) or only weakly correlated (Experiment 2a) with flash number. Acquisition of performance in the numerical reproduction procedure was investigated in Experiment 3. For Experiments 1-3, hierarchical regression analyses showed significant control by number over responding, after controlling for temporal cues. Additionally, positive transfer to novel values both within and outside the training range was obtained when the temporal organization of test sequences was similar to baseline training. Experiment 4 investigated the effects of increasing or decreasing the retention interval (RI) on performance in the reproduction procedure, and found this produced a response bias towards larger numbers, contrary to predictions based on previous RI research, and suggested responding was not affected by memorial decay processes. The structure of the representation of number developed by subjects in the bisection and reproduction procedures was investigated using analyses of responding and response variability in Chapters 2 and 6, respectively. Bisection points obtained in Experiment 1 were located at the arithmetic, not geometric mean of all three scales, and coefficients of variation (CVs) obtained in both the bisection and reproduction experiments tended to decrease as flash number increased. Additionally, analyses of the acquisition data found differences in average response number was better fit by a linear than logarithmic scale. These results show that responding did not conform to scalar variability and is largely inconsistent with previous nonhuman research. Together these results suggest responding appeared to be based on a linear scale of number with constant generalisation between values, similar to that associated with human verbal counting, rather than a logarithmic scale with constant generalisation or a linear scale with scalar generalisation between values. Experiment 5 compared pigeons’ and humans’ verbal and nonverbal discrimination performance with numbers 1-20 in analogous bisection, reproduction and report tasks. Human verbal and nonverbal performance in the three tasks was similar and resembled nonhuman performance, although verbal discriminations were more accurate and less variable. The main findings from Experiments 1 and 2A were replicated with humans; bisection points were located at the arithmetic mean, average response number increased linearly as sample number increased, though there was a tendency to underestimate sample number, and decreasing CVs were also obtained for values less than 8. An additional, interesting finding was that CVs showed scalar variability for values greater than 8, suggesting a less exact representation and discrimination process was being used for these values. Collectively, these five experiments provide new evidence for a nonverbal ability to discriminate relative and absolute number with increasing relative accuracy resembling human verbal counting in both human and nonhumans.