Depositional age, provenance and metamorphic age of metasedimentary rocks from southern Madagascar

Southern Madagascar is the core of a >1 million km(2) Gondwanan metasedimentary belt that forms much of the southern East African Orogen of eastern Africa, Madagascar, southern India and Sri Lanka. Here the Vohibory Series yielded U-Pb isotopic data from detrital zircon cores that indicate that it was deposited in the latest Tonian to late Cryogenian (between -900 and 640 Ma). The deposition of the Graphite and Androyen Series protoliths is poorly constrained to between the late Palaeoproterozoic and the Cambrian (similar to 1830-530 Ma). The Vohibory Series protoliths were sourced from very restricted-aged sources with a maximum age range between 910 and 760 Ma. The Androyen and Graphite Series protoliths were sourced from Palaeoproterozoic rocks ranging in age between 2300 and 1800 Ma. The best evidence of the timing of metamorphism in the Vohibory Series is a weighted mean Pb-206/U-238 age of 642 +/- 8 Ma from 3 analyses of zircon from sample M03-01. A considerably younger Pb-206/U-238 metamorphic age of 531 +/- 7 Ma is produced from 10 analyses of zircon from sample M03-28 in the Androyen Series. This similar to 110 Ma difference in age is correlated with the early East African Orogeny affecting the west of Madagascar along with its type area in East Africa, whereas the Cambrian Malagasy Orogeny affected the east of Madagascar and southern India during the final suturing of the Mozambique Ocean. (C) 2011 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

The igneous charnockite—high-K alkali-calcic I-type granite—incipient charnockite association in Trivandrum Block, southern India

The Pan-African (640 Ma) Chengannoor granite intrudes the NW margin of the Neoproterozoic high-grade metamorphic terrain of the Trivandrum Block (TB), southern India, and is spatially associated with the Cardamom hills igneous charnockite massif (CM). Geochemical features characterize the Chengannoor granite as high-K alkali-calcic I-type granite. Within the constraints imposed by the high temperature, anhydrous, K-rich nature of the magmas, comparison with recent experimental studies on various granitold source compositions, and trace- and rare-earth-element modelling, the distinctive features of the Chengannoor granite reflect a source rock of igneous charnockitic nature. A petrogenetic model is proposed whereby there was a period of basaltic underplating; the partial melting of this basaltic lower crust formed the CM charnockites. The Chengannoor granite was produced by the partial melting of the charnoenderbites from the CM, with subsequent fractionation dominated by feldspars. In a regional context, the Chengannoor I-type granite is considered as a possible heat source for the near-UHT nature of metamorphism in the northern part of the TB. This is different from previous studies, which favoured CM charnockite as the major heat source. The Occurrence of incipient charnockites (both large scale as well as small scale) adjacent to the granite as well as pegmatites (which contain CO2, CO2-H2O, F and other volatiles), suggests that the fluids expelled from the alkaline magma upon solidification generated incipient charnockites through fluid-induced lowering of water activity. Thus the granite and associated alkaline pegmatites acted as conduits for the transfer of heat and volatiles in the Achankovil Shear Zone area, causing pervasive as well as patchy charnockite formation. The transport Of CO2 by felsic melts through the southern Indian middle crust is suggested to be part of a crustal-scale fluid system that linked mantle heat and CO2 input with upward migration of crustally derived felsic melts and incipient charnockite formation, resulting in an igneous charnockite - I-type granite - incipient charnockite association.

Viruses of banana in East Africa

Bananas are one of the world's most important food crops, providing sustenance and income for millions of people in developing countries and supporting large export industries. Viruses are considered major constraints to banana production, germplasm multiplication and exchange, and to genetic improvement of banana through traditional breeding. In Africa, the two most important virus diseases are bunchy top, caused by Banana bunchy top virus (BBTV), and banana streak disease, caused by Banana streak virus (BSV). BBTV is a serious production constraint in a number of countries within/bordering East Africa, such as Burundi, Democratic Republic of Congo, Malawi, Mozambique, Rwanda and Zambia, but is not present in Kenya, Tanzania and Uganda. Additionally, epidemics of banana streak disease are occurring in Kenya and Uganda. The rapidly growing tissue culture (TC) industry within East Africa, aiming to provide planting material to banana farmers, has stimulated discussion about the need for virus indexing to certify planting material as virus-free. Diagnostic methods for BBTV and BSV have been reported and, for BBTV, PCR-based assays are reliable and relatively straightforward. However for BSV, high levels of serological and genetic variability and the presence of endogenous virus sequences within the banana genome complicate diagnosis. Uganda has been shown to contain the greatest diversity in BSV isolates found anywhere in the world. A broad-spectrum diagnostic test for BSV detection, which can discriminate between endogenous and episomal BSV sequences, is a priority. This PhD project aimed to establish diagnostic methods for banana viruses, with a particular focus on the development of novel methods for BSV detection, and to use these diagnostic methods for the detection and characterisation of banana viruses in East Africa. A novel rolling-circle amplification (RCA) method was developed for the detection of BSV. Using samples of Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV) from Australia, this method was shown to distinguish between endogenous and episomal BSV sequences in banana plants. The RCA assay was used to screen a collection of 56 banana samples from south-west Uganda for BSV. RCA detected at least five distinct BSV isolates in these samples, including BSOLV and Banana streak GF virus (BSGFV) as well as three BSV isolates (Banana streak Uganda-I, -L and -M virus) for which only partial sequences had been previously reported. These latter three BSV had only been detected using immuno-capture (IC)-PCR and thus were possible endogenous sequences. In addition to its ability to detect BSV, the RCA protocol was also demonstrated to detect other viruses within the family Caulimoviridae, including Sugar cane bacilliform virus, and Cauliflower mosaic virus. Using the novel RCA method, three distinct BSV isolates from both Kenya and Uganda were identified and characterised. The complete genome of these isolates was sequenced and annotated. All six isolates were shown to have a characteristic badnavirus genome organisation with three open reading frames (ORFs) and the large polyprotein encoded by ORF 3 was shown to contain conserved amino acid motifs for movement, aspartic protease, reverse transcriptase and ribonuclease H activities. As well, several sequences important for expression and replication of the virus genome were identified including the conserved tRNAmet primer binding site present in the intergenic region of all badnaviruses. Based on the International Committee on Taxonomy of Viruses (ICTV) guidelines for species demarcation in the genus Badnavirus, these six isolates were proposed as distinct species, and named Banana streak UA virus (BSUAV), Banana streak UI virus (BSUIV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), Banana streak CA virus (BSCAV) and Banana streak IM virus (BSIMV). Using PCR with species-specific primers designed to each isolate, a genotypically diverse collection of 12 virus-free banana cultivars were tested for the presence of endogenous sequences. For five of the BSV no amplification was observed in any cultivar tested, while for BSIMV, four positive samples were identified in cultivars with a B-genome component. During field visits to Kenya, Tanzania and Uganda, 143 samples were collected and assayed for BSV. PCR using nine sets of species-specific primers, and RCA, were compared for BSV detection. For five BSV species with no known endogenous counterpart (namely BSCAV, BSUAV, BSUIV, BSULV and BSUMV), PCR was used to detect 30 infections from the 143 samples. Using RCA, 96.4% of these samples were considered positive, with one additional sample detected using RCA which was not positive using PCR. For these five BSV, PCR and RCA were both useful for identifying infected samples, irrespective of the host cultivar genotype (Musa A- or B-genome components). For four additional BSV with known endogenous counterparts in the M. balbisiana genome (BSOLV, BSGFV, BSMYV and BSIMV), PCR was shown to detect 75 infections from the 143 samples. In 30 samples from cultivars with an A-only genome component there was 96.3% agreement between PCR positive samples and detection using RCA, again demonstrating either PCR or RCA are suitable methods for detection. However, in 45 samples from cultivars with some B-genome component, the level of agreement between PCR positive samples and RCA positive samples was 70.5%. This suggests that, in cultivars with some B-genome component, many infections were detected using PCR which were the result of amplification of endogenous sequences. In these latter cases, RCA or another method which discriminates between endogenous and episomal sequences, such as immuno-capture PCR, is needed to diagnose episomal BSV infection. Field visits were made to Malawi and Rwanda to collect local isolates of BBTV for validation of a PCR-based diagnostic assay. The presence of BBTV in samples of bananas with bunchy top disease was confirmed in 28 out of 39 samples from Malawi and all nine samples collected in Rwanda, using PCR and RCA. For three isolates, one from Malawi and two from Rwanda, the complete nucleotide sequences were determined and shown to have a similar genome organisation to previously published BBTV isolates. The two isolates from Rwanda had at least 98.1% nucleotide sequence identity between each of the six DNA components, while the similarity between isolates from Rwanda and Malawi was between 96.2% and 99.4% depending on the DNA component. At the amino acid level, similarities in the putative proteins encoded by DNA-R, -S, -M, - C and -N were found to range between 98.8% to 100%. In a phylogenetic analysis, the three East African isolates clustered together within the South Pacific subgroup of BBTV isolates. Nucleotide sequence comparison to isolates of BBTV from outside Africa identified India as the possible origin of East African isolates of BBTV.

Impact of African orography and the Indian summer monsoon on the low-level Somali jet

The low-level jet (LLJ) over the Indian region, which is most prominent during the monsoon (June-September) season, has been studied with a general circulation model (GCM). The role of African orography in modulating this jet is the focus of this article. The presence o African orography intensifies the cross-equatorial flow. Contrary to previous modelling Studies we find that cross-equatorial flow occurs even in the absence of African orography, though this flow is muc weaker even when the Indian monsoon rainfall is high. However, the location of the meridional jet near the equator in the Somali region is linked to the Indian monsoon rainfall rather than to the land-sea contrast over Somalia. Also, the presence of African orography, and not the strength of the Indian monsoon, controls the vertical extent of the equatorial meridional wind. In an aqua-planet simulation, the cross-equatorial flow occurs about 30 to the west of the rainfall maximum. Thus, the longitudinal location of the equatorial Somali jet depends upon the occurrence of monsoon heating, but the vertical structure of the jet is on account of the western boundary current in the atmosphere due to the East African highlands under the influence of monsoonal heat source.

Recent research in the African Great Lakes: fisheries, biodiversity and cichlid evolution

The East African Great Lakes are now well known for (1) their fisheries, of vital importance for their rapidly rising riparian human populations, and (2) as biodiversity hotspots with spectacular endemic faunas, of which the flocks of cichlid fishes unique to each of the three largest lakes, Tanganyika, Malawi and Victoria, offer unique opportunities to investigate how new species evolve and coexist. Since the early 1990s research involving over a hundred scientists, financed by many international bodies, has produced numerous reports and publications in widely scattered journals. This article summarizes their main discoveries and examines the status of, and prospects for, the fisheries, as well as current ideas on how their rich endemic fish faunas have evolved. It first considers fisheries projects in each of the three lakes: the deep rift valley lakes Tanganyika and Malawi and the huge Victoria, all of which share their waters between several East African countries. Secondly it considers the biodiversity surveys of each lake, based on underwater (SCUBA) observations of fish ecology and behaviour which have revealed threats to their fish faunas, and considers what conservation measures are needed. Thirdly, using the lakes as laboratories, what have the international investigations (including DNA techniques and follow-up aquarium experiments) now revealed about the origins and relationships of their cichlid species flocks and mechanisms of evolution?

Coral reef resources of East Africa, Kenya, Tanzania and the Seychelles

Coral reefs are widespread along the east African coast and Seychelle islands. Their roles in island building and coastal protection are often underestimated, they are also important fishery habitats and major tourist attractions. The east African marine fishery production, estimated at 1.4-4.9 tonnes per km super(2), is principally a result of artisanal fishing. Siltation, trampling, and destructive fishing methods are the main cause of coral reef degradation along the east African coast and associated islands. Legislation has been implemented to protect coral reefs by establishing marine parks and reserves. However, poaching and anchor damage are widespread on these protected reefs. Legislative provision to increase the benefit to fishing communities may reduce poaching. The establishment of exclusive nature reserves may be one way to ensure preservation of some coral reefs in the region.

A survey of research and scientific services in East Africa, 1947-56

This "Survey of Research and Scientific Services in East Arica 1947-1956" has been prepared by Dr. E. B. Worthington, who held the post of Scientific Secretary in the Office of the Chief Secretary to the East African Governor's Conference and subsequently in the Administrator's Office of the East Mrica High Commission during the period January, 1947-May, 1951. Dr. Worthington is now Secretary General of the Scientific Council for, Arica South of the Sahara

A review of the fisheries of the Uganda waters of Lake Albert East Africa, 1928-1965/66, with catch data mainly from 1953

An historical account is given of the development of the Lake Albert fisheries since Worthington's survey in 1928. It is noted that the development of the fisheries was related to, and dependent upon, improvements in the type of gear and canoes, an incFease in the number of canoes and outboard engines in use, improved marketing facilities and better road communications. Summarized data, collected mainly since 1954, has been analysed and tabulated to show annual exports to the Congo, total annual catches 'and annual catches of individual species. A change in the relative abundance of the various species in the annual catches is described. It is noted that this change was caused by a change-over from large to small mesh size gill-nets, and that it was associated with an increased demand within Uganda for the smaller species of fish, such as Aleste's baremose and Hydrocynus forskahlii. A brief description of fish processing and marketing in the Lake Albert region is given, which emphasizes the suitability of salt-cured fish to the social and physical environment of the area. Finally, a summary of a recent survey of the potential fish resources of the lake is given in the discussion, and estimates of the 1965 catch at the north and south ends of the lake are compared with the findings of the survey. This showed that there is little danger of overfishing the Alestes baremose stocks of the Wanseko area at the 1965 rate of exploitation of the species, and that the total catch for 1965 at the south end of the lake was well below the estimated annual sustainable yield from the area.

Improved facilities for marine biology in East Africa

In 1967 the then University College of Dar es Salaam built a small laboratory on the shore at Kunduchi, 16 km from the main campus and 24 km north of Dar es Salaam. This was used for undergraduate field courses, and as a base for staff from the University to carry out research. It soon became apparent that the urgent need for studies of the marine environment in the East African area, and the lack of existing facilities, necessitated the development of the Kunduchi Marine Biology station into a research establishment with its own staff of full time scientists. This operation began in 1970: necessary structural modifications have been made to the building, staff have been recruited, and the station has been equipped with an adequate range of field and laboratory apparatus. A varied programme of research is now actively under way.

International Partnering strategy for e-learning provider in emerging economies: Evidence from East Africa learning institutions

International partnership has received growing interest in the literature during the past decades due to globalization, increased technological approaches and rapid changes in competitive environments. The study specifically determines the support provided by international partners on promotion of e-learning in East Africa, assess the motives of partner selection criteria, the determinants of selecting partners, partner models and partner competence of e-learning provider. The study also evaluates obstacles of e-learning partnering strategy in East Africa learning institutions. The research adopts a descriptive survey design. Target population involved East Africa learning institutions with a list of potential institutions generated from the Ministry of Higher Education database. Through a targeted reduction of the initial database, consisting of all learning institutions, both public and private, the study created a target sample base of 200 learning institutions. Structured questionnaires scheduled were used to collect primary data. Study findings showed the approach way East African communities in selecting their e-learning partners depend on international reputation of partners, partner with ability to negotiate with foreign governments, partner with international and local experiences, nationality of foreign partner and partners with local market knowledge.

The competitiveness of domestic rice production in East Africa: A domestic resource cost approach in Uganda

The rapid increase of rice imports in sub-Saharan Africa under the unstable situation in the world rice market during the 2000s has made it an important policy target for the countries in the region to increase self-sufficiency in rice in order to enhance food security. Whether domestic rice production can be competitive with imported rice is a serious question in East African countries that lie close, just across the Arabian Sea, to major rice exporting countries in South Asia. This study investigates the international competitiveness of domestic rice production in Uganda in terms of the domestic resource cost ratio. The results show that rainfed rice cultivation, which accounts for 95% of domestic rice production, does not have a comparative advantage with respect to rice imported from Pakistan, the largest supplier of imported rice to Uganda. However, the degree of non-competitiveness is not serious, and a high possibility exists for Uganda’s rainfed rice cultivation to become internationally competitive by improving yield levels by applying more modern inputs and enhancing labour productivity. Irrigated rice cultivation, though very limited in area, is competitive even under the present input-output structure when the cost of irrigation infrastructure is treated as a sunk cost. If the cost of installing irrigation infrastructure and its operation and maintenance is taken into account, the types of irrigation development that are economically feasible are not large-scale irrigation projects, but are small- and microscale projects for lowland rice cultivation and rain-water harvesting for upland rice cultivation.

The Accumulation of Reproductive Incompatibilities in African Cichlid Fish

The rate at which different components of reproductive isolation accumulate with divergence time between species has only been studied in a limited, but growing, number of species. We measured premating isolation and hybrid inviability at four different ontogenetic stages from zygotes to adults in interspecific hybrids of 26 pairs of African cichlid species, spanning the entire East African haplochromine radiation. We then used multiple relaxed molecular clock calibrations to translate genetic distances into absolute ages to compare evolutionary rates of different components of reproductive isolation. We find that premating isolation accumulates fast initially but then changes little with increasing genetic distance between species. In contrast, postmating isolation between closely related species is negligible but then accumulates rapidly, resulting in complete hybrid inviability after 4.4/8.5/18.4 million years (my). Thus, the rate at which complete intrinsic incompatibilities arise in this system is orders of magnitude lower than rates of speciation within individual lake radiations. Together these results suggest divergent ecological adaptations may prevent populations from interbreeding and help maintain cichlid species diversity, which may be vulnerable to environmental degradation. By quantifying the capacity to produce viable hybrids between allopatric, distantly related lineages our results also provide an upper divergence time limit for the "hybrid swarm origin" model of adaptive radiation.

Origins of Shared Genetic Variation in African Cichlids

Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of approximately 200 genic and nongenic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of 160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic versus nongenic SNPs, as well as for SNPs at putative CpG versus non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for approximately 8% of loci, with contributions from both genic and nongenic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa.

How does the taxonomic status of allopatric populations influence species richness within African cichlid fish assemblages?

Aim  Current estimates of species richness within rapidly evolving species flocks are often highly dependent on the species status of allopatric populations that differ in phenotypic traits. These traits may be unreliable indicators of biological species status and systematists may have inconsistently assigned species among lineages or locations on the basis of these traits, thus hampering comparative studies of regional species richness and speciation rates. Our aim was to develop a method of generating standardized estimates of regional species richness suitable for comparative analysis, and to use these estimates to examine the extent and consistency of species assignment of allopatric populations within rapidly evolving cichlid fish flocks present in three east African lakes. Location  Lakes Malawi, Victoria and Tanganyika. Methods  Using published taxon co-occurrence data, a novel approach was employed to calculate standardized ‘minimum’ estimates of regional species richness for hard substrate associated complexes of cichlids within each of the lakes. Minimum estimates were based on an explicit assumption that if taxa present on equivalent habitats have disjunct distributions, then they are allopatric forms of the same species. These estimates were compared with current observed ‘high-end’ regional species richness estimates for those complexes to determine the consistency of species assignment of allopatric populations between lineages within a lake. A ‘sympatry’ index was developed to enable comparisons of levels of species assignment of allopatric populations between-lakes to be made. Results  Within each lake, the minimum and high-end estimates for species richness were significantly correlated across complexes, indicating that the complexes that contain more recognized species contain the most genuine biological species. However, comparisons of complexes among lakes revealed considerable differences. For equivalent geographical areas, substantially higher proportions of recognized species were totally allopatric within the studied Lake Malawi and Lake Victoria complexes, than those of Lake Tanganyika. Main Conclusions  Among African lakes, levels of assignment to species status of allopatric populations were found to be distinctly different. It is unclear whether the discrepancies are a consequence of differences between the lake faunas in degrees of phenotypic divergence among allopatric populations, or are simply the result of inconsistent taxonomic practices. In either case, these results have considerable wider relevance for they emphasize that quantitative measures of regional and beta diversity are critically dependent on the species status of allopatric populations, an issue usually neglected in comparative studies of species richness. The technique introduced here can be used to standardize measures of regional diversity of lineages for comparative analyses, potentially enabling more accurate identification of processes influencing rates of speciation.

Contrasting long-term records of biomass burning in wet and dry savannas of equatorial East Africa

Rainfall controls fire in tropical savanna ecosystems through impacting both the amount and flammability of plant biomass, and consequently, predicted changes in tropical precipitation over the next century are likely to have contrasting effects on the fire regimes of wet and dry savannas. We reconstructed the long-term dynamics of biomass burning in equatorial East Africa, using fossil charcoal particles from two well-dated lake-sediment records in western Uganda and central Kenya. We compared these high-resolution (5 years/sample) time series of biomass burning, spanning the last 3800 and 1200 years, with independent data on past hydroclimatic variability and vegetation dynamics. In western Uganda, a rapid (<100 years) and permanent increase in burning occurred around 2170 years ago, when climatic drying replaced semideciduous forest by wooded grassland. At the century time scale, biomass burning was inversely related to moisture balance for much of the next two millennia until ca. 1750 ad, when burning increased strongly despite regional climate becoming wetter. A sustained decrease in burning since the mid20th century reflects the intensified modern-day landscape conversion into cropland and plantations. In contrast, in semiarid central Kenya, biomass burning peaked at intermediate moisture-balance levels, whereas it was lower both during the wettest and driest multidecadal periods of the last 1200 years. Here, burning steadily increased since the mid20th century, presumably due to more frequent deliberate ignitions for bush clearing and cattle ranching. Both the observed historical trends and regional contrasts in biomass burning are consistent with spatial variability in fire regimes across the African savanna biome today. They demonstrate the strong dependence of East African fire regimes on both climatic moisture balance and vegetation, and the extent to which this dependence is now being overridden by anthropogenic activity.