Systématique évolutive et biogéographie de Angraecum (Orchidaceae, Angraecinae) à Madagascar

Le genre Angraecum est un groupe d’orchidées tropicales qui compte environ 221 espèces réparties en Afrique subsaharienne, dans l’ouest de l’Océan Indien, et au Sri Lanka. Plus de la moitié des espèces se trouvent à Madagascar, dont au moins 90% sont endémiques à l’île. L’étude systématique et taxonomique du genre Angraecum a toujours été problématique à cause de sa grande diversité morphologique. Pour faciliter la classification, des sections ont été établies dont la plus connue est celle de Garay (1973), qui regroupe les espèces sous 19 sections. Plusieurs analyses phylogénétiques avaient montré que le genre Angraecum et les sections de Garay ne sont pas monophylétiques. Cependant, aucune révision systématique n’a été apportée à cause du faible échantillonnage dans ces analyses. En incorporant un plus grand nombre d'espèces et en ajoutant d’autres caractères morphologiques dans l’analyse, nous avons apporté une plus grande résolution à la reconstruction phylogénétique du groupe. Cette résolution concerne surtout les nœuds plus profonds qui représentent les différents clades à l’intérieur d'Angraecum, qui correspondent à des sections naturelles. A partir de ces clades, nous avons redéfini 14 sections monophylétiques toute en reconnaissant cinq nouvelles. Grâce à cette nouvelle phylogénie d'Angraecum, nous avons pu étudier la diversification du genre et de la sous-tribu Angraecinae en utilisant des méthodes macroévolutives, notamment les roles joués par les traits floraux dans la spéciation, tout en l'interprétant grâce aux histoires géologique et paléoclimatique. Le modèle de diversification chez les Angraecinae semble avoir été celui communément rencontré dans les forêts tropicales humides, c’est-à-dire une diversification par accumulation graduelle d’espèces à travers le temps et non pas une radiation adaptative rapide, comme souvent observée chez des lignées animales malgaches. Plusieurs caractères morphologiques jouent un rôle important dans la diversification des espèces d'Angraecum. Le début de la diversification d'Angraecum à Madagascar coïncide avec le mouvement progressif de l’île vers le nord, l’établissement de la mousson dans la partie nord de l’île durant le Miocène, et l’expansion de la forêt tropicale malgache pendant cette période. Notre étude de l’histoire biogéographique des Angraecinae suggère une origine malgache de la sous-tribu et du genre Angraecum. On observe de la dispersion à longue distance à partir de Madagascar vers le reste du monde dans le genre Angraecum. La forêt tropicale humide du Nord Est de Madagascar est le point de départ de la diversification des espèces d'Angraecum. Le premier événement de dispersion a débuté à l’intérieur de l’île vers la fin du Miocène. Cet évènement est marqué par une migration du Nord Est vers le centre de Madagascar. Par ailleurs, la majorité des événements de dispersion à longue distance se sont produits durant le Pliocène-Pléistocène à partir soit du centre, soit du Nord Est de l'île. On assiste à des migrations indépendantes vers l’Afrique de l’est et les Comores d’une part, et vers les Mascareignes d’autre part. Un seul événement fondateur ayant conduit à l’apparition de la section Hadrangis est observé dans les Mascareignes. La saison cyclonique joue un rôle significatif dans la dispersion à longue distance des graines d’orchidées, comparée aux vents dominants qui soufflent dans la région ouest de l’Océan Indien, notamment l’alizé et la mousson. La similarité des niches écologiques a facilité l’expansion des espèces d'Angraecum dans les Comores et les Mascareignes.

Stable oxygen and carbon isotopes ratios of sediment core GeoB9528-3

The carbon isotopic composition of individual plant leaf waxes (a proxy for C3 vs. C4 vegetation) in a marine sediment core collected from beneath the plume of Sahara-derived dust in northwest Africa reveals three periods during the past 192,000 years when the central Sahara/Sahel contained C3 plants (likely trees), indicating substantially wetter conditions than at present. Our data suggest that variability in the strength of Atlantic meridional overturning circulation (AMOC) is a main control on vegetation distribution in central North Africa, and we note expansions of C3 vegetation during the African Humid Period (early Holocene) and within Marine Isotope Stage (MIS) 3 (approx. 50-45 ka) and MIS 5 (approx. 120-110 ka). The wet periods within MIS 3 and 5 coincide with major human migration events out of sub-Saharan Africa. Our results thus suggest that changes in AMOC influenced North African climate and, at times, contributed to amenable conditions in the central Sahara/Sahel, allowing humans to cross this otherwise inhospitable region.

What is this thing called Historical Archaeology?

Historical archaeology, in its narrow temporal sense -as an archaeology of the emergence and subsequent evolution of the Modern world- is steadily taking pace in Spanish academia. This paper aims at provoking a more robust debate through understanding how Spanish historical archaeology is placed in the international scene and some of its more relevant particularities. In so doing, the paper also stresses the strong links that have united historical and prehistorical archaeology since its inception, both in relation to the ontological, epistemological and methodological definition of the first as to the influence of socio-political issues in the latter. Such reflection is partly a situated reflection from prehistory as one of the paper’s authors has been a prehistorian for most of her professional life.

Task sharing within a managed clinical network to improve child health in Malawi

BACKGROUND: Eighty per cent of Malawi's 8 million children live in rural areas, and there is an extensive tiered health system infrastructure from village health clinics to district hospitals which refers patients to one of the four central hospitals. The clinics and district hospitals are staffed by nurses, non-physician clinicians and recently qualified doctors. There are 16 paediatric specialists working in two of the four central hospitals which serve the urban population as well as accepting referrals from district hospitals. In order to provide expert paediatric care as close to home as possible, we describe our plan to task share within a managed clinical network and our hypothesis that this will improve paediatric care and child health.

PRESENTATION OF THE HYPOTHESIS: Managed clinical networks have been found to improve equity of care in rural districts and to ensure that the correct care is provided as close to home as possible. A network for paediatric care in Malawi with mentoring of non-physician clinicians based in a district hospital by paediatricians based at the central hospitals will establish and sustain clinical referral pathways in both directions. Ultimately, the plan envisages four managed paediatric clinical networks, each radiating from one of Malawi's four central hospitals and covering the entire country. This model of task sharing within four hub-and-spoke networks may facilitate wider dissemination of scarce expertise and improve child healthcare in Malawi close to the child's home.

TESTING THE HYPOTHESIS: Funding has been secured to train sufficient personnel to staff all central and district hospitals in Malawi with teams of paediatric specialists in the central hospitals and specialist non-physician clinicians in each government district hospital. The hypothesis will be tested using a natural experiment model. Data routinely collected by the Ministry of Health will be corroborated at the district. This will include case fatality rates for common childhood illness, perinatal mortality and process indicators. Data from different districts will be compared at baseline and annually until 2020 as the specialists of both cadres take up posts.

IMPLICATIONS OF THE HYPOTHESIS: If a managed clinical network improves child healthcare in Malawi, it may be a potential model for the other countries in sub-Saharan Africa with similar cadres in their healthcare system and face similar challenges in terms of scarcity of specialists.

Effect of Wealth on Health Care Seeking Behavior And Out of Pocket Health Expenditure in Malawi

Thesis (Master's)--University of Washington, 2016-06

Quantifying Selection Bias from Birth History Estimates of Child Mortality

Thesis (Master's)--University of Washington, 2016-08

Implementation science to expand an mHealth intervention for improving retention in care for women living with HIV and their children

Thesis (Ph.D.)--University of Washington, 2016-08

Children with intellectual disabilities’ perceptions of their participation in activities in everyday life – a pilot study : A minor field study conducted in Ethiopia

Background: Children with disabilities living in low and middle income countries’ perceptions of participation are not shown in research. These perceptions are important for providing appropriate interventions. Aim: To describe how children aged 8-12 with an intellectual disability living in Ethiopia perceive their situation regarding participation in activities in everyday life. Method: A descriptive design with a quantitative approach was used. The sample was gathered using consecutive sampling. Fifteen structured interviews were conducted, using “Picture my participation,” an instrument under development. Analyses were made using SPSS Statistics and Microsoft Excel. Results: The children perceived that they participated in activities in everyday life. There was a broad variation in the activities the children prioritized as most important. On a group level, they were very involved in these activities. The majority did not experience any barriers to perform these activities. Conclusions: The perceptions of the majority of the children were that they were involved in daily activities. They did not experience any barriers to participation. The results should be read with caution and generalization is not possible, due to the sample characteristics and that the instrument is under development.

Impact of Cryptosporidium spp. interaction with co-occurring microorganisms on moderate-to-severe diarrhea in the developing world

Diarrheal illness is responsible for over a quarter of all deaths in children under 5 years of age in sub-Saharan Africa and South Asia. Recent findings have identified the parasite Cryptosporidium as a contributor to enteric disease. We examined 9,348 cases and 13,128 controls from the Global Enteric Multicenter Study to assess whether Cryptosporidium interacted with co-occurring pathogens based on adjusted odds of moderate-to-severe diarrhea (MSD). Cryptosporidium was found to interact negatively with Shigella spp., with multiplicative interaction score of 0.16 (95% CI: 0.07 to 0.37, p-value=0.000), and an additive interaction score of -9.81 (95% CI: -13.61 to -6.01, p-value=0.000). Cryptosporidium also interacted negatively with Aeromonas spp., Adenovirus, Norovirus, and Astrovirus with marginal significance. Odds of MSD for Cryptosporidium co-infection with Shigella spp., Aeromonas spp., Adenovirus, Norovirus, or Astrovirus are lower than odds of MSD with either organism alone. This may reduce the efficacy of intervention strategies targeted at Cryptosporidium.

Prevalence and associations of Trypanosoma spp. and Sodalis glossinidius with intrinsic factors of tsetse flies

Trypanosomiasis has been identified as a neglected tropical disease in both humans and animals in many regions of sub-Saharan Africa. Whilst assessments of the biology of trypanosomes, vectors, vertebrate hosts and the environment have provided useful information about life cycles, transmission, and pathogenesis of the parasites that could be used for treatment and control, less information is available about the effects of interactions among multiple intrinsic factors on trypanosome presence in tsetse flies from different sites. It is known that multiple species of tsetse flies can transmit trypanosomes but differences in their vector competence has normally been studied in relation to individual factors in isolation, such as: intrinsic factors of the flies (e.g. age, sex); habitat characteristics; presence of endosymbionts (e.g. Wigglesworthia glossinidia, Sodalis glossinidius); feeding pattern; host communities that the flies feed on; and which species of trypanosomes are transmitted. The purpose of this study was to take a more integrated approach to investigate trypanosome prevalence in tsetse flies. In chapter 2, techniques were optimised for using the Polymerase Chain Reaction (PCR) to identify species of trypanosomes (Trypanosoma vivax, T. congolense, T. brucei, T. simiae, and T. godfreyi) present in four species of tsetse flies (Glossina austeni, G. brevipalpis, G. longipennis and G. pallidipes) from two regions of eastern Kenya (the Shimba Hills and Nguruman). Based on universal primers targeting the internal transcribed spacer 1 region (ITS-1), T. vivax was the predominant pathogenic species detected in flies, both singly and in combination with other species of trypanosomes. Using Generalised Linear Models (GLMs) and likelihood ratio tests to choose the best-fitting models, presence of T. vivax was significantly associated with an interaction between subpopulation (a combination between collection sites and species of Glossina) and sex of the flies (X2 = 7.52, df = 21, P-value = 0.0061); prevalence in females overall was higher than in males but this was not consistent across subpopulations. Similarly, T. congolense was significantly associated only with subpopulation (X2 = 18.77, df = 1, P-value = 0.0046); prevalence was higher overall in the Shimba Hills than in Nguruman but this pattern varied by species of tsetse fly. When associations were analysed in individual species of tsetse flies, there were no consistent associations between trypanosome prevalence and any single factor (site, sex, age) and different combinations of interactions were found to be significant for each. The results thus demonstrated complex interactions between vectors and trypanosome prevalence related to both the distribution and intrinsic factors of tsetse flies. The potential influence of the presence of S. glossinidius on trypanosome presence in tsetse flies was studied in chapter 3. A high number of Sodalis positive flies was found in the Shimba Hills, while there were only two positive flies from Nguruman. Presence or absence of Sodalis was significantly associated with subpopulation while trypanosome presence showed a significant association with age (X2 = 4.65, df = 14, P-value = 0.0310) and an interaction between subpopulation and sex (X2 = 18.94, df = 10, P-value = 0.0043). However, the specific associations that were significant varied across species of trypanosomes, with T. congolense and T. brucei but not T. vivax showing significant interactions involving Sodalis. Although it has previously been concluded that presence of Sodalis increases susceptibility to trypanosomes, the results presented here suggest a more complicated relationship, which may be biased by differences in the distribution and intrinsic factors of tsetse flies, as well as which trypanosome species are considered. In chapter 4 trypanosome status was studied in relation to blood meal sources, feeding status and feeding patterns of G. pallidipes (which was the predominant fly species collected for this study) as determined by sequencing the mitochondrial cytochrome B gene using DNA extracted from abdomen samples. African buffalo and African elephants were the main sources of blood meals but antelopes, warthogs, humans, giraffes and hyenas were also identified. Feeding on multiple hosts was common in flies sampled from the Shimba Hills but most flies from Nguruman had fed on single host species. Based on Multiple Correspondence Analysis (MCA), host-feeding patterns showed a correlation with site of sample collection and Sodalis status, while trypanosome status was correlated with sex and age of the flies, suggesting that recent host-feeding patterns from blood meal analysis cannot predict trypanosome status. In conclusion, the complexity of interactions found suggests that strategies of tsetse fly control should be specific to particular epidemic areas. Future studies should include laboratory experiments that use local colonies of tsetse flies, local strains of trypanosomes and local S. glossinidius under controlled environmental conditions to tease out the factors that affect vector competence and the relative influence of external environmental factors on the dynamics of these interactions.

Leptospirosis in northern Tanzania: exploring the role of rodents and ruminant livestock in a neglected public health problem

Leptospirosis is an important but neglected zoonotic disease that is often overlooked in Africa. Although comprehensive data on the incidence of human disease are lacking, robust evidence of infection has been demonstrated in people and animals from all regions of the continent. However, to date, there are few examples of direct epidemiological linkages between human disease and animal infection. In East Africa, awareness of the importance of human leptospirosis as a cause of non-malarial febrile illness is growing. In northern Tanzania, acute leptospirosis has been diagnosed in 9% of patients with severe febrile illness compared to only 2% with malaria. However, little is known about the relative importance of different potential animal hosts as sources of human infection in this area. This project was established to investigate the roles of rodents and ruminant livestock, important hosts of Leptospira in other settings, in the epidemiology of leptospirosis in northern Tanzania. A cross-sectional survey of rodents living in and around human settlements was performed alongside an abattoir survey of ruminant livestock. Unusual patterns of animal infection were detected by real-time PCR detection. Renal Leptospira infection was absent from rodents but was detected in cattle from several geographic areas. Infection was demonstrated for the first time in small ruminants sub-Saharan Africa. Two major Leptospira species and a novel Leptospira genotype were detected in livestock. L. borgpetersenii was seen only in cattle but L. kirschneri infection was detected in multiple livestock species (cattle, sheep and goats), suggesting that at least two distinct patterns of Leptospira infection occur in livestock in northern Tanzania. Analysis of samples from acute leptospirosis in febrile human patients could not detect Leptospira DNA by real-time PCR but identified social and behavioural factors that may limit the utility of acute-phase diagnostic tests in this community. Analysis of serological data revealed considerable overlap between serogroups detected in cattle and human leptospirosis cases. Human disease was most commonly attributed to the serogroups Mini and Australis, which were also predominant reactive serogroups in cattle. Collectively, the results of this study led to the hypothesis that livestock are an important reservoir of Leptospira infection for people in northern Tanzania. These results also challenge our understanding of the relationship between Leptospira and common invasive rodent species, which do not appear to maintain infection in this setting. Livestock Leptospira infection has substantial potential to affect the well-being of people in East Africa, through direct transmission of infection or through indirect effects on food production and economic security. Further research is needed to quantify the impact of livestock leptospirosis in Africa and to develop effective interventions for the control of human and animal disease.

GENETIC DIVERSITY AMONG SORGHUM LANDRACES OF SOUTHWESTERN HIGHLANDS OF UGANDA

Sorghum ( Sorghum bicolor L. Moench) is an economic and staple crop in sub-Saharan Africa. The genetic diversity in its germplasm is an invaluable aid for its crop improvement. The objective of this study was to assess the existing genetic diversity among sorghum landraces in the southwestern highlands of Uganda. A total of 47 sorghum landraces, collected from southwestern highlands of Uganda, were characterised using 12 qualitative and 13 quantitative traits. The study was conducted at Kachwekano Research Farm in Kabale District, at an altitude of 2,223 m above sea level, during growing season of December 2014 to August 2015. Panicle shape and compactness were the most varied qualitative traits. Grain yield (1.23 to 11.31 t ha-1) and plant height (144.7 to 351.6 cm) were among quantitative traits that showed high variability. Days to 50% flowering (115 to 130 days) showed the least variability. Results of UPGMA cluster analysis generated a dendrogram with three clusters. Panicle weight, leaf width, stem girth, exertion length, peduncle length, panicle shape and compactness, glume colour and threshability were major traits responsible for the observed clustering (P<0.001). Principal Component Analysis revealed the largest variation contributors.

HERITABILITY FOR RESISTANCE TO ROSETTE DISEASE IN EXOTIC VALENCIA GROUNDNUTS

Groundnut rosette disease (GRD) is the most destructive virus disease of Valencia groundnuts ( Arachis hypogaea L.) in sub-Saharan Africa. Cultural, biological and chemical control measures have received limited success due to small scale farmers’ inability to use them. Use of host plant resistance provides the most effective and economically viable management option for the resource poor farmers. This study was conducted to determine heritability for resistance to GRD in Valencia groundnuts. Six crosses; Valencia C (P1) × ICGV-SM 90704 (P2), Valencia C (P1) × ICGV-SM 96801(P2), Valencia C (P1) × ICGV-SM 99566 (P2), NuMex-M3 (P1) × ICGV-SM 90704 (P2), NuMex-M3 × ICGV-SM 96801 (P2), and NuMex-M3 (P1) × ICGV-SM 99566 (P2), were made to generate F1, F2, BC1P1 and BC1P2 populations. Data on GRD severity were collected on a 1-9 score scale. Genetic Advance as a percentage of the mean (GAM) and heritability were estimated using variance components. Phenotypic Coefficient of Variation (PCV) and Genotypic Coefficient of Variation (GCV) estimates were high (20.04-70.1%) in the six crosses, except for Valencia C × ICGV-SM 96801(18.1%) and NuMex-M3 × ICGV-SM 96801(17.1%), which exhibited moderate GCV values. Broad and narrow sense heritability estimates for GRD disease score ranged from 64.1 to 73.7% and 31 to 41.9%, respectively, in all the crosses. GAM was high in all the crosses (21-50.7%), except for Valencia C x ICGV-SM 96801 (14.67), M3 x ICGV-SM 99566 (18%) and NuMex-M3 x ICGV-SM 96801 (13.5%) crosses that exhibited moderate GAM. The study revealed the presence of variability of GRD resistance, implying that genetic improvement of these exotic materials is possible.

Systématique évolutive et biogéographie de Angraecum (Orchidaceae, Angraecinae) à Madagascar

Le genre Angraecum est un groupe d’orchidées tropicales qui compte environ 221 espèces réparties en Afrique subsaharienne, dans l’ouest de l’Océan Indien, et au Sri Lanka. Plus de la moitié des espèces se trouvent à Madagascar, dont au moins 90% sont endémiques à l’île. L’étude systématique et taxonomique du genre Angraecum a toujours été problématique à cause de sa grande diversité morphologique. Pour faciliter la classification, des sections ont été établies dont la plus connue est celle de Garay (1973), qui regroupe les espèces sous 19 sections. Plusieurs analyses phylogénétiques avaient montré que le genre Angraecum et les sections de Garay ne sont pas monophylétiques. Cependant, aucune révision systématique n’a été apportée à cause du faible échantillonnage dans ces analyses. En incorporant un plus grand nombre d'espèces et en ajoutant d’autres caractères morphologiques dans l’analyse, nous avons apporté une plus grande résolution à la reconstruction phylogénétique du groupe. Cette résolution concerne surtout les nœuds plus profonds qui représentent les différents clades à l’intérieur d'Angraecum, qui correspondent à des sections naturelles. A partir de ces clades, nous avons redéfini 14 sections monophylétiques toute en reconnaissant cinq nouvelles. Grâce à cette nouvelle phylogénie d'Angraecum, nous avons pu étudier la diversification du genre et de la sous-tribu Angraecinae en utilisant des méthodes macroévolutives, notamment les roles joués par les traits floraux dans la spéciation, tout en l'interprétant grâce aux histoires géologique et paléoclimatique. Le modèle de diversification chez les Angraecinae semble avoir été celui communément rencontré dans les forêts tropicales humides, c’est-à-dire une diversification par accumulation graduelle d’espèces à travers le temps et non pas une radiation adaptative rapide, comme souvent observée chez des lignées animales malgaches. Plusieurs caractères morphologiques jouent un rôle important dans la diversification des espèces d'Angraecum. Le début de la diversification d'Angraecum à Madagascar coïncide avec le mouvement progressif de l’île vers le nord, l’établissement de la mousson dans la partie nord de l’île durant le Miocène, et l’expansion de la forêt tropicale malgache pendant cette période. Notre étude de l’histoire biogéographique des Angraecinae suggère une origine malgache de la sous-tribu et du genre Angraecum. On observe de la dispersion à longue distance à partir de Madagascar vers le reste du monde dans le genre Angraecum. La forêt tropicale humide du Nord Est de Madagascar est le point de départ de la diversification des espèces d'Angraecum. Le premier événement de dispersion a débuté à l’intérieur de l’île vers la fin du Miocène. Cet évènement est marqué par une migration du Nord Est vers le centre de Madagascar. Par ailleurs, la majorité des événements de dispersion à longue distance se sont produits durant le Pliocène-Pléistocène à partir soit du centre, soit du Nord Est de l'île. On assiste à des migrations indépendantes vers l’Afrique de l’est et les Comores d’une part, et vers les Mascareignes d’autre part. Un seul événement fondateur ayant conduit à l’apparition de la section Hadrangis est observé dans les Mascareignes. La saison cyclonique joue un rôle significatif dans la dispersion à longue distance des graines d’orchidées, comparée aux vents dominants qui soufflent dans la région ouest de l’Océan Indien, notamment l’alizé et la mousson. La similarité des niches écologiques a facilité l’expansion des espèces d'Angraecum dans les Comores et les Mascareignes.

Hardpan and maize root distribution under conservation and conventional tillage in Agro-Ecological Zone IIA, Zambia

Hardpans (plough/hoe pans) are commonly believed to restrict plant root growth and crop yields under conventional small-scale agriculture in sub-Saharan Africa. This study questions the notion of widespread hardpans in Zambia and their remedy under conservation tillage. Soil penetration resistance was measured in 8x12 grids, covering 80 cm wide and 60 cm deep profiles in 32 soil pits. Large and fine maize roots were counted in 8x6 grids. Soil samples from mid-rows were analysed for pH, exchangeable H+, exchangeable Al3+, cation exchange capacity, total N and extractable P (Bray 1) at six depths from 0-10 to 50-60 cm. Cultivation-induced hardpans were not detected. Soils under conservation tillage were more compact at 5 cm depth than soils under conventional tillage. No differences in root distributions between conservation and conventional tillage were found. Maize ( Zea mays L. ) roots were largely confined to a relatively small soil volume of about 30 cm x 30 cm x 30 cm. Root growth appeared to be restricted by a combination of low concentrations of N and P. Soil acidity and Al saturation appeared to play a minor role in root distribution. L-shaped taproots in soils under manual tillage reported earlier were not necessarily due to hardpans, but may rather be caused by temporarily dry, impenetrable subsoils early in the rain season. There is no scientific basis for the recommendation given to farmers by agricultural extension workers to “break the hardpan” in fields under manual or animal tillage in the study areas.