samuel kiboi - Academia.edu (original) (raw)

Papers by samuel kiboi

African Journal of Ecology, 2011

Although it is clear that the farmlands neighbouring fragmented forests are utilized by some fore... more Although it is clear that the farmlands neighbouring fragmented forests are utilized by some forest birds, it is not clear how birds in general respond to farmland habitat mosaic. An effort was made to determine how bird density and foraging assemblages were influenced by farm structural characteristics and distance from forest edge. Thirty farms up to a distance of 12 km around Kakamega forest in western Kenya were studied. Farm structure entailed size, hedge volume, habitat heterogeneity, woody plant density, plant diversity and crop cover. Birds were surveyed using line transects and DISTANCE analyses and classified into six feeding guilds and three habitat associations. Size of farms increased away from the forest, as woody plant density, plant diversity, indigenous trees and subsistence crop cover declined. The most important farm structure variable was hedge volume, which enhanced bird species richness, richness of shrub-land bird species and insectivorous bird density (R = 0.58, P < 0.01). Bird density increased with tree density while indigenous trees were suitable for insectivores and nectarivores. There were very few forest bird encounters. Agricultural practices incorporating maintenance of hedges and sound selection of agroforestry trees can enhance conservation of birds on farmland, though, not significantly for forest species.

Sexual plant reproduction, 2006

We investigated whether resistant pollen genotypes can be selected for when the maternal plants a... more We investigated whether resistant pollen genotypes can be selected for when the maternal plants are infected and whether infection can result to changes in the pistil nutrient level influencing reproductive outcome. Both resistance and susceptibility come with costs that may affect pre-and post-fertilization reproductive functions. We performed the study by crossing zucchini yellow mosaic virus resistant and susceptible pollen (from a hybrid donor) to infected and healthy maternal plants. We also analysed the pistil nutrient content in both treatments and found an increase of the susceptible and not resistant genotypes when maternal plants were infected. The level of nutrients K, P and S was higher in the pistils of the infected maternal plants than the healthy ones. Pistil nutrient level did not affect pollen tube growth rates, as indicated by seed siring patterns along the fruit. We propose that the effect on the siring ability of pollen carrying the susceptible and resistant alleles occurred at the post-fertilization stage, possibly as an indirect result of different growth rates of the two embryo genotypes under elevated nutrient conditions. We discuss our results with respect to possibilities of differential selection, costs and reproductive implications.

Sustainable Living with Environmental Risks, 2014

Urban green areas not only provide aesthetic qualities but also provide important ecosystem servi... more Urban green areas not only provide aesthetic qualities but also provide important ecosystem services in ever-shrinking habitats, and therefore need sustainable management practices. The western and northwestern parts of Nairobi are within an upland dry forest that stretched from Karura to Ngong forests with a characteristic vegetation composition. Much of that vegetation has been replaced by exotic species and, over time, the original indigenous tree species composition may be lost. No previous studies have profi led the local vegetation structure in Kenya and then used this knowledge to restore the urban green environment. We carried out studies in Karura and Ngong forests and used 16 carefully selected species to recreate a natural forest using the 'Miyawaki method' at the College of Biological and Physical Sciences of the University of Nairobi. In just 16 months the species have established extremely well, with the best performing species ( Ehretia cymosa ) growing to more than 210 cm from just about 43 cm. We expect to recreate a quasinatural forest and use such studies and methods to restore urban green environments in Kenya.

BioMed Research International, 2014

Science is going through two rapidly changing phenomena: one is the increasing capabilities of th... more Science is going through two rapidly changing phenomena: one is the increasing capabilities of the computers and software tools from terabytes to petabytes and beyond, and the other is the advancement in high-throughput molecular biology producing piles of data related to genomes, transcriptomes, proteomes, metabolomes, interactomes, and so on. Biology has become a data intensive science and as a consequence biology and computer science have become complementary to each other bridged by other branches of science such as statistics, mathematics, physics, and chemistry. The combination of versatile knowledge has caused the advent of big-data biology, network biology, and other new branches of biology. Network biology for instance facilitates the system-level understanding of the cell or cellular components and subprocesses. It is often also referred to as systems biology. The purpose of this field is to understand organisms or cells as a whole at various levels of functions and mechanisms. Systems biology is now facing the challenges of analyzing big molecular biological data and huge biological networks. This review gives an overview of the progress in big-data biology, and data handling and also introduces some applications of networks and multivariate analysis in systems biology.

BioMed Research International, 2014

With the data deluge caused by the recent high throughput experiments in molecular biology emerge... more With the data deluge caused by the recent high throughput experiments in molecular biology emerged the popular topics such as big data biology and network biology aiming at understanding life as a system by integrating and applying knowledge and facilities of different branches of science including mathematics, physics, statistics, chemistry, computer science, and information technology. Naturally, the spectrum of topics under big data and network biology is widespread and the present special issue is not an exhaustive representation of the subject. Nonetheless the articles selected for this special issue represent recent trends and versatile knowledge concerning the title topic, that we have the pleasure of sharing with the readers. Data-intensive sciences like contemporary biology consist of three basic activities: capture, curation, and analysis. Being in the bioinformatics domain, this special issue mainly focuses on analysis; that is, it contains articles about novel tools and methodologies for data analysis and mining and review articles describing databases, tools, and algorithms useful for curation and analysis of biological data.

The American Naturalist, 2007

Theory predicts that, during pollen competition, selection may favor a pollen trait that increase... more Theory predicts that, during pollen competition, selection may favor a pollen trait that increases donor competitive ability at the expense of the female reproductive function. One such pollen trait could be manipulation of the onset of stigma receptivity. We evaluated the potential occurrence of this kind of sexual conflict by testing female control of the timing of stigma receptivity in the self-compatible annual Collinsia heterophylla. By performing one-donor crosses in the greenhouse, we found that differences in both recipients and pollen donors influenced when stigmas became receptive. Because we did not detect an interaction effect, our result suggests that some donors were consistently better than others at germinating pollen and siring seeds earlier. Unexpectedly, self-pollen was able to fertilize seeds earlier during floral development compared with outcross pollen. These results suggest that female control on timing of stigma receptivity is not complete in this species. In addition, fertilizations that occurred early during floral development resulted in fewer seeds than later fertilizations, possibly indicating a cost of lost control over the onset of receptivity. The ability of pollen donors to influence the timing of stigma receptivity might reflect a conflict between the sexual functions in C. heterophylla.

Molecular Ecology, 2002

We studied the phylogeny of avian haemosporidian parasites, Haemoproteus and Plasmodium , in a nu... more We studied the phylogeny of avian haemosporidian parasites, Haemoproteus and Plasmodium , in a number of African resident and European migratory songbird species sampled during spring and autumn in northern Nigeria. The phylogeny of the parasites was constructed through sequencing part of their mitochondrial cytochrome b gene. We found eight parasite lineages, five Haemoproteus and three Plasmodium , infecting multiple host species. Thus, 44% of the 18 haemospiridian lineages found in this study were detected in more than one host species, indicating that host sharing is a more common feature than previously thought. Furthermore, one of the Plasmodium lineages infected species from different host families, Sylviidae and Ploceidae, expressing exceptionally large host range. We mapped transmission events, e.g. the occurrence of the parasite lineages in resident bird species in Europe or Africa, onto a phylogenetic tree. This yielded three clades, two Plasmodium and one Haemoproteus , in which transmission seems to occur solely in Africa. One Plasmodium clade showed European transmission, whereas the remaining two Haemoproteus clades contained mixes of lineages of African, European or unknown transmission. The mix of areas of transmission in several branches of the phylogenetic tree suggests that transmission of haemosporidian parasites to songbirds has arisen repeatedly in Africa and Europe. Blood parasites could be viewed as a cost of migration, as migratory species in several cases were infected with parasite lineages from African resident species. This cost of migration could have considerable impact on the evolution of migration and patterns of winter distribution in migrating birds.

Forest Ecology and Management, 2011

We examined whether heavy fuelwood collection can cause threshold change in understory forest com... more We examined whether heavy fuelwood collection can cause threshold change in understory forest community and evaluated how selective wood extraction might lead to delayed forest recovery in an urban forest of Nairobi, Kenya. Piecewise regression which represents strongest support for threshold change provided the best fit for the relationships between understory floristic composition (i.e. DCA axis 1) and human disturbance gradients (i.e. canopy cover, and distance from the slum), where threshold changes were detected at c.a. 350 m from the slum and c.a. 30% canopy cover. Only one tree species significantly indicated communities beyond the threshold while an aggressive invasive alien plant (IAP) Lantana camara was strongly represented. Total species diversity along the two human disturbance gradients peaked before the threshold was reached, suggesting that decline in species diversity along the prevailing disturbance gradient might be able to forecast threshold change. Tree species richness in the understory rapidly declined as the threshold was surpassed while other growth forms (i.e. shrubs, herbs and climbers) were relatively unaffected. The effect of selective tree cutting was indirectly impacting the forest understory as species richness pattern of preferred and non-preferred species paralleled that of trees and shrubs, respectively. Thickets of L. camara can negatively affect indigenous flora and its establishment was favored under selective fuelwood extraction removing certain tree species while leaving the IAP untouched. Shading can readily eliminate the IAP, but weak tree regeneration beyond the threshold suggested forest recovery might be delayed for longer than expected because of the interaction between selective fuelwood use and the IAP.

Biological Conservation, 2011

... Author Contact Information , E-mail The Corresponding Author , Kazue Fujiwara b , E-mail The ... more ... Author Contact Information , E-mail The Corresponding Author , Kazue Fujiwara b , E-mail The Corresponding Author , Samuel K. Kiboi c ... Spatial patterns of resource use are strongly correlated with resource accessibility (Boxall and Beckley, 2002), resulting in skewed resource ...

African Journal of Ecology, 2011

Although it is clear that the farmlands neighbouring fragmented forests are utilized by some fore... more Although it is clear that the farmlands neighbouring fragmented forests are utilized by some forest birds, it is not clear how birds in general respond to farmland habitat mosaic. An effort was made to determine how bird density and foraging assemblages were influenced by farm structural characteristics and distance from forest edge. Thirty farms up to a distance of 12 km around Kakamega forest in western Kenya were studied. Farm structure entailed size, hedge volume, habitat heterogeneity, woody plant density, plant diversity and crop cover. Birds were surveyed using line transects and DISTANCE analyses and classified into six feeding guilds and three habitat associations. Size of farms increased away from the forest, as woody plant density, plant diversity, indigenous trees and subsistence crop cover declined. The most important farm structure variable was hedge volume, which enhanced bird species richness, richness of shrub-land bird species and insectivorous bird density (R = 0.58, P < 0.01). Bird density increased with tree density while indigenous trees were suitable for insectivores and nectarivores. There were very few forest bird encounters. Agricultural practices incorporating maintenance of hedges and sound selection of agroforestry trees can enhance conservation of birds on farmland, though, not significantly for forest species.

Sexual plant reproduction, 2006

We investigated whether resistant pollen genotypes can be selected for when the maternal plants a... more We investigated whether resistant pollen genotypes can be selected for when the maternal plants are infected and whether infection can result to changes in the pistil nutrient level influencing reproductive outcome. Both resistance and susceptibility come with costs that may affect pre-and post-fertilization reproductive functions. We performed the study by crossing zucchini yellow mosaic virus resistant and susceptible pollen (from a hybrid donor) to infected and healthy maternal plants. We also analysed the pistil nutrient content in both treatments and found an increase of the susceptible and not resistant genotypes when maternal plants were infected. The level of nutrients K, P and S was higher in the pistils of the infected maternal plants than the healthy ones. Pistil nutrient level did not affect pollen tube growth rates, as indicated by seed siring patterns along the fruit. We propose that the effect on the siring ability of pollen carrying the susceptible and resistant alleles occurred at the post-fertilization stage, possibly as an indirect result of different growth rates of the two embryo genotypes under elevated nutrient conditions. We discuss our results with respect to possibilities of differential selection, costs and reproductive implications.

Sustainable Living with Environmental Risks, 2014

Urban green areas not only provide aesthetic qualities but also provide important ecosystem servi... more Urban green areas not only provide aesthetic qualities but also provide important ecosystem services in ever-shrinking habitats, and therefore need sustainable management practices. The western and northwestern parts of Nairobi are within an upland dry forest that stretched from Karura to Ngong forests with a characteristic vegetation composition. Much of that vegetation has been replaced by exotic species and, over time, the original indigenous tree species composition may be lost. No previous studies have profi led the local vegetation structure in Kenya and then used this knowledge to restore the urban green environment. We carried out studies in Karura and Ngong forests and used 16 carefully selected species to recreate a natural forest using the 'Miyawaki method' at the College of Biological and Physical Sciences of the University of Nairobi. In just 16 months the species have established extremely well, with the best performing species ( Ehretia cymosa ) growing to more than 210 cm from just about 43 cm. We expect to recreate a quasinatural forest and use such studies and methods to restore urban green environments in Kenya.

BioMed Research International, 2014

Science is going through two rapidly changing phenomena: one is the increasing capabilities of th... more Science is going through two rapidly changing phenomena: one is the increasing capabilities of the computers and software tools from terabytes to petabytes and beyond, and the other is the advancement in high-throughput molecular biology producing piles of data related to genomes, transcriptomes, proteomes, metabolomes, interactomes, and so on. Biology has become a data intensive science and as a consequence biology and computer science have become complementary to each other bridged by other branches of science such as statistics, mathematics, physics, and chemistry. The combination of versatile knowledge has caused the advent of big-data biology, network biology, and other new branches of biology. Network biology for instance facilitates the system-level understanding of the cell or cellular components and subprocesses. It is often also referred to as systems biology. The purpose of this field is to understand organisms or cells as a whole at various levels of functions and mechanisms. Systems biology is now facing the challenges of analyzing big molecular biological data and huge biological networks. This review gives an overview of the progress in big-data biology, and data handling and also introduces some applications of networks and multivariate analysis in systems biology.

BioMed Research International, 2014

With the data deluge caused by the recent high throughput experiments in molecular biology emerge... more With the data deluge caused by the recent high throughput experiments in molecular biology emerged the popular topics such as big data biology and network biology aiming at understanding life as a system by integrating and applying knowledge and facilities of different branches of science including mathematics, physics, statistics, chemistry, computer science, and information technology. Naturally, the spectrum of topics under big data and network biology is widespread and the present special issue is not an exhaustive representation of the subject. Nonetheless the articles selected for this special issue represent recent trends and versatile knowledge concerning the title topic, that we have the pleasure of sharing with the readers. Data-intensive sciences like contemporary biology consist of three basic activities: capture, curation, and analysis. Being in the bioinformatics domain, this special issue mainly focuses on analysis; that is, it contains articles about novel tools and methodologies for data analysis and mining and review articles describing databases, tools, and algorithms useful for curation and analysis of biological data.

The American Naturalist, 2007

Theory predicts that, during pollen competition, selection may favor a pollen trait that increase... more Theory predicts that, during pollen competition, selection may favor a pollen trait that increases donor competitive ability at the expense of the female reproductive function. One such pollen trait could be manipulation of the onset of stigma receptivity. We evaluated the potential occurrence of this kind of sexual conflict by testing female control of the timing of stigma receptivity in the self-compatible annual Collinsia heterophylla. By performing one-donor crosses in the greenhouse, we found that differences in both recipients and pollen donors influenced when stigmas became receptive. Because we did not detect an interaction effect, our result suggests that some donors were consistently better than others at germinating pollen and siring seeds earlier. Unexpectedly, self-pollen was able to fertilize seeds earlier during floral development compared with outcross pollen. These results suggest that female control on timing of stigma receptivity is not complete in this species. In addition, fertilizations that occurred early during floral development resulted in fewer seeds than later fertilizations, possibly indicating a cost of lost control over the onset of receptivity. The ability of pollen donors to influence the timing of stigma receptivity might reflect a conflict between the sexual functions in C. heterophylla.

Molecular Ecology, 2002

We studied the phylogeny of avian haemosporidian parasites, Haemoproteus and Plasmodium , in a nu... more We studied the phylogeny of avian haemosporidian parasites, Haemoproteus and Plasmodium , in a number of African resident and European migratory songbird species sampled during spring and autumn in northern Nigeria. The phylogeny of the parasites was constructed through sequencing part of their mitochondrial cytochrome b gene. We found eight parasite lineages, five Haemoproteus and three Plasmodium , infecting multiple host species. Thus, 44% of the 18 haemospiridian lineages found in this study were detected in more than one host species, indicating that host sharing is a more common feature than previously thought. Furthermore, one of the Plasmodium lineages infected species from different host families, Sylviidae and Ploceidae, expressing exceptionally large host range. We mapped transmission events, e.g. the occurrence of the parasite lineages in resident bird species in Europe or Africa, onto a phylogenetic tree. This yielded three clades, two Plasmodium and one Haemoproteus , in which transmission seems to occur solely in Africa. One Plasmodium clade showed European transmission, whereas the remaining two Haemoproteus clades contained mixes of lineages of African, European or unknown transmission. The mix of areas of transmission in several branches of the phylogenetic tree suggests that transmission of haemosporidian parasites to songbirds has arisen repeatedly in Africa and Europe. Blood parasites could be viewed as a cost of migration, as migratory species in several cases were infected with parasite lineages from African resident species. This cost of migration could have considerable impact on the evolution of migration and patterns of winter distribution in migrating birds.

Forest Ecology and Management, 2011

We examined whether heavy fuelwood collection can cause threshold change in understory forest com... more We examined whether heavy fuelwood collection can cause threshold change in understory forest community and evaluated how selective wood extraction might lead to delayed forest recovery in an urban forest of Nairobi, Kenya. Piecewise regression which represents strongest support for threshold change provided the best fit for the relationships between understory floristic composition (i.e. DCA axis 1) and human disturbance gradients (i.e. canopy cover, and distance from the slum), where threshold changes were detected at c.a. 350 m from the slum and c.a. 30% canopy cover. Only one tree species significantly indicated communities beyond the threshold while an aggressive invasive alien plant (IAP) Lantana camara was strongly represented. Total species diversity along the two human disturbance gradients peaked before the threshold was reached, suggesting that decline in species diversity along the prevailing disturbance gradient might be able to forecast threshold change. Tree species richness in the understory rapidly declined as the threshold was surpassed while other growth forms (i.e. shrubs, herbs and climbers) were relatively unaffected. The effect of selective tree cutting was indirectly impacting the forest understory as species richness pattern of preferred and non-preferred species paralleled that of trees and shrubs, respectively. Thickets of L. camara can negatively affect indigenous flora and its establishment was favored under selective fuelwood extraction removing certain tree species while leaving the IAP untouched. Shading can readily eliminate the IAP, but weak tree regeneration beyond the threshold suggested forest recovery might be delayed for longer than expected because of the interaction between selective fuelwood use and the IAP.

Biological Conservation, 2011

... Author Contact Information , E-mail The Corresponding Author , Kazue Fujiwara b , E-mail The ... more ... Author Contact Information , E-mail The Corresponding Author , Kazue Fujiwara b , E-mail The Corresponding Author , Samuel K. Kiboi c ... Spatial patterns of resource use are strongly correlated with resource accessibility (Boxall and Beckley, 2002), resulting in skewed resource ...