Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa

Maize streak virus strain A (MSV-A), the causal agent of maize streak disease, is today one of the most serious biotic threats to African food security. Determining where MSV-A originated and how it spread transcontinentally could yield valuable insights into its historical emergence as a crop pathogen. Similarly, determining where the major extant MSV-A lineages arose could identify geographical hot spots of MSV evolution. Here, we use model-based phylogeographic analyses of 353 fully sequenced MSV-A isolates to reconstruct a plausible history of MSV-A movements over the past 150 years. We show that since the probable emergence of MSV-A in southern Africa around 1863, the virus spread transcontinentally at an average rate of 32.5 km/year (95% highest probability density interval, 15.6 to 51.6 km/year). Using distinctive patterns of nucleotide variation caused by 20 unique intra-MSV-A recombination events, we tentatively classified the MSV-A isolates into 24 easily discernible lineages. Despite many of these lineages displaying distinct geographical distributions, it is apparent that almost all have emerged within the past 4 decades from either southern or east-central Africa. Collectively, our results suggest that regular analysis of MSV-A genomes within these diversification hot spots could be used to monitor the emergence of future MSV-A lineages that could affect maize cultivation in Africa. © 2011, American Society for Microbiology.

Spatio-temporal patterns in maturation of the chokka squid (Loligo vulgaris reynaudii) off the coast of South Africa

Knowledge of the temporal and spatial characteristics of chokka squid (Loligo vulgaris reynaudii) biology in South African waters is limited, so the possibility of there being a geographically fragmented stock was examined by investigating the distribution of maturity patterns for the species, covering all known spawning areas and using both historical and recent data. Gonadosomatic indices (GSI) varied between year-round consistency and apparent seasonal peaks in both summer and winter; there was no clear spatial pattern. Monthly percentage maturity provided further evidence for two peak reproductive periods each year, although mature squid were present throughout. Sex ratios demonstrated great variability between different areas and life history stages. Male-biased sex ratios were only apparent on the inshore spawning grounds and ranged between 1.118:1 and 4.267:1. Size at sexual maturity was also seasonal, squid maturing smaller in winter/spring than in summer/autumn. Also, squid in the east matured smaller than squid in the west. Although the results from the present study do not provide conclusive evidence of distinct geographic populations, squid likely spawn over a significantly larger area of the Agulhas Bank than previously estimated, and squid on the west coast of South Africa may return to spawn on the western portion of the Agulhas Bank. It remains likely, however, that the east and west coast populations are a single stock and that migration of juveniles to the west coast and their subsequent return as sub-adults is an integral but non-essential and variable part of the life history.

Spatial patterns in the biology of the chokka squid, Loligo reynaudii on the Agulhas Bank, South Africa

Although migration patterns for various life history stages of the chokka squid (Loligo reynaudii) have been previously presented, there has been limited comparison of spatial variation in biological parameters. Based on data from research surveys; size ranges of juveniles, subadults and adults on the Agulhas Bank were estimated and presented spatially. The bulk of the results appear to largely support the current acceptance of the life cycle with an annual pattern of squid hatching in the east, migrating westwards to offshore feeding grounds on the Central and Western Agulhas Bank and the west coast and subsequent return migration to the eastern inshore areas to spawn. The number of adult animals in deeper water, particularly in autumn in the central study area probably represents squid spawning in deeper waters and over a greater area than is currently targeted by the fishery. The distribution of life history stages and different feeding areas does not rule out the possibility that discrete populations of L. reynaudii with different biological characteristics inhabit the western and eastern regions of the Agulhas Bank. In this hypothesis, some mixing of the populations does occur but generally squid from the western Agulhas Bank may occur in smaller numbers, grow more slowly and mature at a larger size. Spawning occurs on the western portion of the Agulhas Bank, and juveniles grow and mature on the west coast and the central Agulhas Bank. Future research requirements include the elucidation of the age structure of chokka squid both spatially and temporally, and a comparison of the statolith chemistry and genetic characterisation between adults from different spawning areas across the Agulhas Bank.

Molecular Characterization of Viruses Causing the Cassava Brown Streak Disease Epidemic in Eastern Africa

Cassava brown streak disease (CBSD) was described for the first time in Tanganyika (now Tanzania) about seven decades ago. Tanganyika (now Tanzania) about seven decades ago. It was endemic in the lowland areas of East Africa and inland parts of Malawi and caused by Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae). However, in 1990s CBSD was observed at high altitude areas in Uganda. The causes for spread to new locations were not known.The present work was thus initiated to generate information on genetic variability, clarify the taxonomy of the virus or viruses associated with CBSD in Eastern Africa as well as to understand the evolutionary forces acting on their genes. It also sought to develop a molecular based diagnostic tool for detection of CBSD-associated virus isolates. Comparison of the CP-encoding sequences of CBSD-associated virus isolates collected from Uganda and north-western Tanzania in 2007 and the partial sequences available in Genbank revealed occurrence of two genetically distinct groups of isolates. Two isolates were selected to represent the two groups. The complete genomes of isolates MLB3 (TZ:Mlb3:07) and Kor6 (TZ:Kor6:08) obtained from North-Western (Kagera) and North-Eastern (Tanga) Tanzania, respectively, were sequenced. The genomes were 9069 and 8995 nucleotides (nt), respectively. They translated into polyproteins that were predicted to yield ten mature proteins after cleavage. Nine proteins were typical in the family Potyviridae, namely P1, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP, but the viruses did not contain HC-Pro. Interestingly, genomes of both isolates contained a Maf/HAM1-like sequence (HAM1h; 678 nucleotides, 25 kDa) recombined between the NIb and CP domains in the 3’-proximal part of the genomes. HAM1h was also identified in Euphorbia ringspot virus (EuRSV) whose sequence was in GenBank. The HAM1 gene is widely spread in both prokaryotes and eukaryotes. In yeast (Saccharomyces cerevisiae) it is known to be a nucleoside triphosphate (NTP) pyrophosphatase. Novel information was obtained on the structural variation at the N-termini of polyproteins of viruses in the genus Ipomovirus. Cucumber vein yellowing virus (CVYV) and Squash vein yellowing virus (SqVYV) contain a duplicated P1 (P1a and P1b) but lack the HC-Pro. On the other hand, Sweet potato mild mottle virus (SPMMV), has a single but large P1 and has HC-Pro. Both virus isolates (TZ:Mlb3:07 & TZ:Kor6:08) characterized in this study contained a single P1 and lacked the HC-Pro which indicates unique evolution in the family Potyviridae. Comparison of 12 complete genomes of CBSD-associated viruses which included two genomes characterized in this study, revealed genetic identity of 69.0–70.3% (nt) and amino acid (aa) identities of 73.6–74.4% at polyprotein level. Comparison was also made among 68 complete CP sequences, which indicated 69.0-70.3 and 73.6-74.4 % identity at nt and aa levels, respectively. The genetic variation was large enough for dermacation of CBSD-associated virus isolates into two distinct species. The name CBSV was retained for isolates that were related to CBSV isolates available in database whereas the new virus described for the first time in this study was named Ugandan cassava brown streak virus (UCBSV) by the International Committee on Virus Taxonomy (ICTV). The isolates TZ:Mlb3:07 and TZ:Kor6:08 belong to UCBSV and CBSV, respectively. The isolates of CBSV and UCBSV were 79.3-95.5% and 86.3-99.3 % identitical at nt level, respectively, suggesting more variation amongst CBSV isolates. The main sources of variation in plant viruses are mutations and recombination. Signals for recombination events were detected in 50% of isolates of each virus. Recombination events were detected in coding and non-coding (3’-UTR) sequences except in the 5’UTR and P3. There was no evidence for recombination between isolates of CBSV and UCBSV. The non-synonomous (dN) to synonomous (dS) nucleotide substitution ratio (ω) for the HAM1h and CP domains of both viruses were ≤ 0.184 suggesting that most sites of these proteins were evolving under strong purifying selection. However, there were individual amino acid sites that were submitted to adaptive evolution. For instance, adaptive evolution was detected in the HAM1h of UCBSV (n=15) where 12 aa sites were under positive selection (P< 0.05) but not in CBSV (n=12). The CP of CBSV (n=23) contained 12 aa sites (p<0.01) while only 5 aa sites in the CP gene of UCBSV were predicted to be submitted to positive selection pressure (p<0.01). The advantages offered by the aa sites under positive selection could not be established but occurrence of such sites in the terminal ends of UCBSV-HAMIh, for example, was interpreted as a requirement for proteolysis during polyprotein processing. Two different primer pairs that simultaneously detect UCBSV and CBSV isolates were developed in this study. They were used successfully to study distribution of CBSV, UCBSV and their mixed infections in Tanzania and Uganda. It was established that the two viruses co-infect cassava and that incidences of co-infection could be as high as 50% around Lake Victoria on the Tanzanian side. Furthermore, it was revealed for the first time that both UCBSV and CBSV were widely distributed in Eastern Africa. The primer pair was also used to confirm infection in a close relative of cassava, Manihot glaziovii (Müller Arg.) with CBSV. DNA barcoding of M. glaziovii was done by sequencing the matK gene. Two out of seven M. glaziovii from the coastal areas of Korogwe and Kibaha in north eastern Tanzania were shown to be infected by CBSV but not UCBSV isolates. Detection in M. glaziovii has an implication in control and management of CBSD as it is likely to serve as virus reservoir. This study has contributed to the understanding of evolution of CBSV and UCBSV, which cause CBSD epidemic in Eastern Africa. The detection tools developed in this work will be useful in plant breeding, verification of the phytosanitary status of materials in regional and international movement of germplasm, and in all diagnostic activities related to management of CBSD. Whereas there are still many issues to be resolved such as the function and biological significance of HAM1h and its origin, this work has laid a foundation upon which the studies on these aspects can be based.

A study on the trend of sports fishery of Mafia Island (Tanzania) along the East African coast from 1961-1972

Mafia waters in the western Indian Ocean on the east coast of Africa is a natural attractive area for fishing. It has extensive coral beds which harbour good fish life and attracts sport fishery in the area. About 12 commercially important fishes listed are caught by sports fishermen. The data indicates that this area can become an attractive centre for sports fishery almost throughout the year with peak season from November to February. Long-term planning of the fishery is necessary. The conservation measures should be evolved and gan fishing, dynamiting or any other kind of distructive fishing should be prohibited. This area has natural potential to become a sports fishing centre in the future and a great attraction for tourists and anglers.

East African Inland Fisheries Research Organization Annual Report for the year 1948

Introduction The laboratory at Jinja is being developed as a centre for hydro-biological research in East Africa, It has been built and is at present wholly financed from a grant from the Central Research allocation of the Colonial Development Fund. The building contains six laboratories in addition to a library, common room and general office. A maximum number of ten research workers could be given laboratory accommodation. However, shortage of living accommodation will limit the numbers who can work here for the next year or two.

The history and research results of the East African Freshwater Fisheries Research Organization from 1946 - 1966.

Continuous research on the freshwater fisheries industry in East Africa, in common with most other African countries, did not commence until the end of the Second World War in 1945. Before the war some work on the fishes and hydrobiology of the lakes of East Africa had been undertaken by a series of scientific expeditions, which were sent out from Europe, between the years 1896 and 1939. These expeditions usually lasted for only a few months, and the collected data were published by young graduates and undergraduates, including such people as Mr. L. C. Beadle, (lately Professor Beadle of Makerere), Mr. V. E. Fuchs (now Sir Vivian Fuchs) and Mr. E. B. Worthington of Gonville and Caius College,Cambridge. Later. Dr. Worthington became Scientific Secretary to the Scientific Council for Africa, Scientific Secretary to the East African High Commission, and played a very large part in the furtherance of fisheries research and management in East Africa.

Annual Report of the East African Agricultural and Fisheries Research Council, 1961

In June, 1961, discussions were held in London to consider the future of the East Africa High Commission Services. It was agreed that the functions of the East Africa High Commission, with the exception of Defence, should be transfered to the East African Common Services Organization, which was subsequently established on 9th December, 1961, on the achievement of independence by Tanganyika. The Common Services Organization is controlled by an Authority, consisting of the principal elected Minister in each of the East African territories, which is responsible for the overall policy and direction of the Organization. The Authority is assisted by four Ministerial Committees, of which one is responsible for the Social and Research Services of the Organization

East African Fisheries Research Organization Annual Report 1955/1956

This report covers the period 1st July, 1955, to 30th June, 1956. As printing has been delayed for various reasons, reference should be made to certain important proposals put forward since the 30th June. Just after the close of the year a meeting of the Lake Victoria Fisheries Board was held at Entebbe on 26th July. At this meeting disagreement arose between the representatives of the three East African Governments on the subject of whether or not existing restrictions on fishing in Lake Victoria should be retained. This organization holds strongly to the view that the existing restrictions on fishing should be retained, Kenya holds similar views, but Uganda and Tanganyika were in favour of a proposal to lift these restrictions. This question was discussed a month earlier by the Director with the Colonial Office Fisheries Advisory Committee and they also advised the Lake Victoria Fisheries Board against lifting the restrictions.

East African Fisheries Research Organization Annual Report 1958

A brief review of work carried out since the laboratory was established ten years ago will put present studies into perspective and show to what extent the aims of this organisation are being fulfilled. These aims can be simply defined under two heads: the maintenance of a watch on the commercial fisheries and original research designed to provide the necessary if these fisheries are to be exploited rationally and managed efficiently. While reference to past results, which cover a wide range of subjects, can best be made in the appropriate sections of this report, a short general statement on the Lake Victoria Fisheries may be useful. From the earliest records contained in Michael Graham's Report it was clear that even before 1929 considerable inroads had been made the stocks of fish in Lake Victoria. Some control measures were subsequently introduced which must have had a moderating effect, but so the Game Department reports continued to express concern regarding the state of the fisheries. During the last war some reduction in fishing effort occurred due to ,a shortage of nets, this afforded some respite to the fisheries, but after this period the fishing effort again increased steadily. At the present time the fishing effort is higher than it has ever been.

East African Fisheries Research Organization Annual Report 1954/1955

This Report covers the period 1st January, 1954, to 30th June, 1955. Scientific work of the organization carried out during the reporting period included the following: Hydrology, Mollusca, Arthropoda , Tilapia, Haplochromis , The Fishes of Uganda , species of fish occurring in Lake Victoria, Analysis of commercial catches, Experimental fishing, The Relative fecundity of Tilapia species, The breeding behaviour of Tilapia, The rings on Tilapia Scales, The Growth of very young fish, The reproductive cycle of non-cichild fishes, The food of fish, some notes on the food of crocodiles, Varanus Lizards and Otters and List of Publications

East African Fisheries Research Organization Annual Report 1950

The annual report presents progress on research activities carried by the organization during the reporting period. The general policy was to integrate the work of every individual on the staff so that all consider themselves members of a scientific team, and so that new problems as they arise could be investigated from more than one aspect. Already some of important findings had arisen as a result of joint studies made by two or more members of the staff working together. As far as possible the work being undertaken was designed to cover the sequence of events which lead from the chemical and physical condition of the water to the ultimate growth of the various populations of fish.

East African Fisheries Research Organization Annual Report 1951

The examination of a considerable amount of data has led to the conclusion that Lake Victoria should be considered as many lakes within a lake. This is not a vague and seemingly obvious remark based on the superficial observation that it is a very large lake containing numerous islands and with a highly indented coastline, and therefore providing variable local conditions. Such local conditions would exist in any lake whose basin departed from a simple geometric form. But evidence has now been collected to show that really significant differences occur between different regions within the lake. These differences are apparent from a variety of data, including the nature of the bottom deposits, the chemical and hydrological condition of the water, the amount and kind of plankton and the distribution and abundance of the fauna. Our findings are as yet somewhat sketchy, and it will be a long time before it will be possible to draw an adequate picture of the various regions of the lake; it is however, of great value to have reached a position enabling us to form this general concept. The most striking and definite evidence is derived, as might be expected, from hydrological data. Details of this work are contained in the hydrological section of this report. Any data recorded below should be considered as applying only to the particular areas mentioned. In other words it would, to draw an obvious example be wrong to suppose that because fish grow at a particular rate in one part of the lake they will grow at the same rate or to the same size in other regions of the lake.

East African Fisheries Research Organization Annual Report 1952

Several important advances have been made in our knowledge both regarding the factors which determine fertility in tropical lakes and the fish that live in them. As a result of our investigations a new theory has been put forward regarding the part played by animals in the bionomics of a lake; this theory, stated somewhat baldly, is that within certain limits the greater the number of animals in a shallow tropical lake, the greater becomes its potential fertility, and therefore the greater the number of animals it can support. The theory arises as a logical conclusion, once we accept the fact that the rate of production in such a lake is determined by the rate at which organic matter is decomposed. Bottom deposits which consist mainly of vegetable matter decompose slowly, whereas deposits which contain a high proportion of matter of animal origin decompose more rapidly. Thus the more animals in a lake, particularly animals which feed on plant material, the faster the biological cycle can proceed and the greater the density of animals it can support. This new concept will have a very profound influence on our ideas concerning the consequences of overfishing tropical waters. It also shows that efforts must be made to encourage and protect all herbivorous and detritus feeding animals, whether they be copepods, fish, or hippopotami, and whether they are of immediate economic importance or not.

Reservoir fishery resources of south-east Asia

Although the reservoir area in south-east Asia is considerable, the fish production is low in the majority of reservoirs. Although high fish production has been recorded in a number of reservoirs in Sri Lanka and Indonesia, high fish production in reservoirs has with few exceptions resulted from the introduction of typical lake species from Africa. Addition of further lake fish species especially into deeper reservoirs will probably increase present fish yields. Diversification of the lake fish fauna can be achieved by introduction of species indigenous to the region like Etroplus suratensis. In this introduction of fish species, three points may be noted with specific reference to Tilapia spp.: (a) Lakes without indigenous cyprinids show marked fluctuation in fish catch with the introduction of Tilapia, and this could be stabilised by the introduction of predators and more diverse species. (b) Lakes with a moderate diversity of fish fauna show a high stabilised production with the introduction of Tilapia, presumably because of the effect of predator pressure on excessive Tilapia breeding. (c) Lowland lakes with a rich diversity of indigenous fish species colonising lakes may not require the introduction of Tilapia. Introduction of invertebrates into reservoirs in south east-Asia has not been done deliberately so far. However, the experience in other parts of the world, notably the Soviet Union, indicates that such introductions are likely to prove beneficial and to increase fish production. The potential for a considerable increase in fish production from reservoirs exists in south-east Asia. Proper management is likely to cost less than what is required for fish culture. Rural areas are likely to benefit most from increased fish production in reservoirs, and this might be a way to provide cheap protein where it is most urgently needed.