Molecular differences distinguish clonal lineages within East African populations of Fusarium oxysporum f.sp. cubense

Abstract The presence of Early and Middle Stone Age human remains and associated archaeological artefacts from various sites scattered across southern Africa, suggests this geographic region to be one of the first abodes of anatomically modern humans. Although the presence of hunter-gatherer cultures in this region dates back to deep times, the peopling of southern Africa have largely been reshaped by three major sets of migrations over the last 2000 years. These migrations have led to a confluence of four distinct ancestries (San hunter-gatherer, East African pastoralist, Bantu-speaker farmer and Eurasian) in populations from this region. In this review, we have summarized the recent insights into the refinement of timelines and routes of the migration of Bantu-speaking populations to southern Africa and their admixture with resident southern African Khoe-San populations. We highlight two recent studies hinting at the emergence of fine-scale population structure within some South-Eastern Bantu-speaker groups. We also accentuate whole genome sequencing studies (current and ancient) that have both enhanced our understanding of the peopling of southern Africa and demonstrated a huge potential for novel variant discovery in populations from this region. Finally, we identify some of the major gaps and inconsistencies in our understanding and emphasize the importance of more systematic studies of southern African populations from diverse ethnolinguistic groups and geographic locations.

Download Full-text

Genetic diversity of lactase persistence in East African populations

BMC Research Notes ◽

10.1186/s13104-015-1833-1 ◽

2016 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Hisham Y. Hassan ◽

Anke van Erp ◽

Martin Jaeger ◽

Hanan Tahir ◽

Marije Oosting ◽

...

Keyword(s):

Genetic Diversity ◽

Lactase Persistence ◽

East African ◽

African Populations

Download Full-text

The development of a multiplex PCR assay for the detection of Fusarium oxysporum f. sp. cubense lineage VI strains in East and Central Africa

European Journal of Plant Pathology ◽

10.1007/s10658-020-02092-9 ◽

2020 ◽

Vol 158 (2) ◽

pp. 495-509 ◽

Cited By ~ 3

Author(s):

P. Ndayihanzamaso ◽

P. Karangwa ◽

D. Mostert ◽

G. Mahuku ◽

G. Blomme ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Multiplex Pcr ◽

Fusarium Wilt ◽

Central Africa ◽

East African ◽

Pcr Assay ◽

Vegetative Compatibility Groups ◽

Worldwide Population ◽

Multiplex Pcr Assay ◽

Disease Free

Abstract Banana is a staple food and cash crop grown in East and Central Africa (ECA). The main banana varieties grown in ECA are the East African highland bananas (EAHB), although dessert/beer bananas such as Sukari Ndizi, Kayinja (Pisang Awak) and Gros Michel are also produced due to their high value at local markets. The Fusarium wilt fungus Fusarium oxysporum f. sp. cubense (Foc) causes disease of susceptible dessert/beer bananas, which significantly reduces yields. Banana Fusarium wilt is managed by excluding the pathogen from disease-free areas and by planting disease-resistant varieties in infested fields. Six phylogenetically closely-related vegetative compatibility groups (VCGs) of Foc, VCGs 0124, 0125, 0128, 01212, 01220 and 01222 are present in ECA, which all group together in Foc Lineage VI. Rapid and accurate detection of Foc Lineage VI strains is thus important to prevent its spread to disease-free areas. In this study, molecular markers specific to Foc Lineage VI were therefore developed. Primer sets were then combined in a multiplex PCR assay, and validated on a worldwide population of 623 known Foc isolates, other formae speciales and non-pathogenic Fusarium oxysporum isolates. The Foc Lineage VI multiplex PCR was used to identify Foc isolates collected in banana fields at five locations in Uganda and Tanzania. Foc Lineage VI DNA was detected at a concentration as low as 0.1 ng/μl, both in the absence and presence of banana DNA, and can therefore be used as an accurate diagnostic tool for Foc Lineage VI strains.

Download Full-text

Gregariousness, foraging effort, and affiliative interactions in lactating bonobos and chimpanzees

Behavioral Ecology ◽

10.1093/beheco/araa130 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sean M Lee ◽

Gottfried Hohmann ◽

Elizabeth V Lonsdorf ◽

Barbara Fruth ◽

Carson M Murray

Keyword(s):

Social Interaction ◽

Travel Time ◽

Feeding Competition ◽

Wild Populations ◽

East African ◽

Foraging Effort ◽

African Populations ◽

Lactating Females ◽

Term Data

Abstract Fission–fusion dynamics have evolved in a broad range of animal taxa and are thought to allow individuals to mitigate feeding competition. While this is the principal benefit of fission–fusion, few studies have evaluated its costs. We compared gregariousness, foraging budgets, and social budgets between lactating bonobos and chimpanzees from wild populations to evaluate potential costs. Both species exhibit fission–fusion dynamics, but chimpanzees, particularly in East African populations, appear to experience higher feeding competition than bonobos. We expected lactating chimpanzees to be less gregarious than lactating bonobos; reduced gregariousness should allow lactating chimpanzees to mitigate the costs of higher feeding competition without requiring more foraging effort. However, we expected the reduced gregariousness of lactating chimpanzees to limit their time available for affiliative interactions. Using long-term data from LuiKotale bonobos and Gombe chimpanzees, we found that lactating chimpanzees were indeed less gregarious than lactating bonobos, while feeding and travel time did not differ between species. Contrary to our predictions, lactating females did not differ in social interaction time, and lactating chimpanzees spent proportionately more time interacting with individuals other than their immature offspring. Our results indicate that lactating chimpanzees can maintain social budgets comparable to lactating bonobos despite reduced gregariousness and without incurring additional foraging costs. We discuss potential explanations for why lactating bonobos are more gregarious.

Download Full-text

Prediction of peak expiratory flow rate in a Ugandan population

South African Respiratory Journal ◽

10.7196/sarj.2015.v21i4.36 ◽

2015 ◽

Vol 21 (4) ◽

pp. 96

Author(s):

Susan Kiwanuka Nakubulwa ◽

K Baisley ◽

J Levin

Keyword(s):

Lung Function ◽

Reference Values ◽

Regression Equations ◽

East African ◽

Cross Sectional ◽

African Populations ◽

Study Population ◽

Males And Females ◽

Western Uganda ◽

Ugandan Population

Background. Peak expiratory ow rate (PEFR) measurement is one of the commonly used methods for assessing lung function in general practice consultations. e reference values for use by this method are mainly from Caucasian populations; data for African populations are limited. e existence of ethnic and racial dierences in lung function necessitates further generation of PEFR reference values for use in African populations. Objective. To generate equations for predicting PEFR in a Ugandan population. Methods. e PEFR study was cross-sectional and based in rural south-western Uganda. Participants were aged 15 years or more, without respiratory symptoms and were residents of the study area. Multiple regression equations for predicting PEFR were tted separately for males and females. e model used for PEFR prediction was: logePEFR = intercept + a(age, y) + b(logeage) + c(1/height in cm), where a, b and c are the regression coecients. Results. e eligible study population consisted of 774 males and 781 females. Median height was 164 cm (males) and 155 cm (females). e majority of participants had never smoked (males 76.7%; females 98.3%). e equation which gave the best t for males was logePEFR = 6.188 – 0.019age + 0.557logeage – 199.945/height and for females: logePEFR = 5.948 – 0.014 age + 0.317logeage – 85.147/height. Conclusion. e curvilinear model obtained takes into consideration the changing trends of PEFR with increasing age from adolescence to old age. It provides PEFR prediction equations that can be applied in East African populations.

Download Full-text

Differential gene expression in East African highland bananas (Musa spp.): Interactions between non-pathogenic Fusarium oxysporum V5w2 and Radopholus similis

Physiological and Molecular Plant Pathology ◽

10.1016/j.pmpp.2012.10.003 ◽

2013 ◽

Vol 82 ◽

pp. 56-63 ◽

Cited By ~ 3

Author(s):

Pamela Paparu ◽

Thomas Dubois ◽

Daniel Coyne ◽

Altus Viljoen

Keyword(s):

Gene Expression ◽

Fusarium Oxysporum ◽

Differential Gene Expression ◽

Radopholus Similis ◽

East African ◽

Musa Spp ◽

Differential Gene

Download Full-text

Potential Impact of DPYD Variation on Fluoropyrimidine Drug Response in sub-Saharan African Populations

Frontiers in Genetics ◽

10.3389/fgene.2021.626954 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jorge E. B. da Rocha ◽

Zané Lombard ◽

Michèle Ramsay

Keyword(s):

Clinical Guidelines ◽

Dihydropyrimidine Dehydrogenase ◽

Whole Genome Sequencing Data ◽

Severe Toxicity ◽

Sequencing Data ◽

East African ◽

Dehydrogenase Enzyme ◽

African Populations ◽

Sub Saharan ◽

Coding Variants

Cancer is a critical health burden in Africa, and mortality rates are rising rapidly. Treatments are expensive and often cause adverse drug reactions (ADRs). Fluoropyrimidine treatments can lead to severe toxicity events which have been linked to variants within the dihydropyrimidine dehydrogenase (DPYD) gene. There are clinical guidelines to improve safety outcomes of treatment, but these are primarily based on variants assessed in non-African populations. Whole genome sequencing data from the 1000 Genomes Project and the African Genome Variation Project were mined to assess variation in DPYD in eight sub-Saharan African populations. Variant functional annotation was performed with a series of bioinformatics tools to assess potential likelihood of deleterious impact. There were 29 DPYD coding variants identified in the datasets assessed, of which 25 are rare, and some of which are known to be deleterious. One African-specific variant (rs115232898-C), is common in sub-Saharan Africans (1–4%) and known to reduce the function of the dihydropyrimidine dehydrogenase enzyme (DPD), having been linked to cases of severe toxicity. This variant, once validated in clinical trials, should be considered for inclusion in clinical guidelines for use in sub-Saharan African populations. The rs2297595-C variant is less well-characterized in terms of effect, but shows significant allele frequency differences between sub-Saharan African populations (0.5–11.5%; p = 1.5 × 10−4), and is more common in East African populations. This study highlights the relevance of African-data informed guidelines for fluorouracil drug safety in sub-Saharan Africans, and the need for region-specific data to ensure that Africans may benefit optimally from a precision medicine approach.

Download Full-text

Morphometric investigation in four populations of S. W. Ethiopia. Comparison with other East African populations

Zeitschrift für Morphologie und Anthropologie ◽

10.1127/zma/70/1979/125 ◽

1979 ◽

Vol 70 (2) ◽

pp. 125-134

Author(s):

F. Vecchi ◽

M. Ricci

Keyword(s):

East African ◽

Morphometric Investigation ◽

African Populations

Download Full-text

Effect of Fusarium oxysporum endophyte inoculation on the activities of phenylpropanoid pathway enzymes and Radopholus similis numbers in susceptible and tolerant East African Highland bananas

Nematology ◽

10.1163/138855409x12571623969646 ◽

2010 ◽

Vol 12 (3) ◽

pp. 469-480 ◽

Cited By ~ 3

Author(s):

Daniel Coyne ◽

Thomas Dubois ◽

Pamela Paparu ◽

Altus Viljoen

Keyword(s):

Wound Healing ◽

Fusarium Oxysporum ◽

Plant Defence ◽

Constitutive Expression ◽

Phenylpropanoid Pathway ◽

Radopholus Similis ◽

East African ◽

Antagonistic Effects ◽

Pal Activity ◽

Burrowing Nematode

AbstractPhenylpropanoid pathway enzymes are involved in plant defence pathways leading to lignification, synthesis of secondary metabolites, such as salicylic acid and phytoalexins, wound healing and the oxidative burst. Endophytic non-pathogenic Fusarium oxysporum isolate V5w2 has been reported to show antagonistic effects against Radopholus similis in the screenhouse. An experiment was designed to study root biochemical changes (PAL, POX and PPO activities) and R. similis numbers in susceptible and tolerant bananas following inoculation with isolate V5w2. Constitutive expression of PAL and PPO were similar between the susceptible and tolerant cultivars, while constitutive POX activity was higher in the tolerant cultivar. PAL activity was suppressed in both cultivars 7 days after endophyte inoculation (7 dai), but was significantly up-regulated in the susceptible cv. Nabusa at 30 days post nematode challenge (dpnc) in endophyte-inoculated plants. In the tolerant cultivar, PAL activity was up-regulated in R. similis-challenged plants at 7 and 30 dpnc, irrespective of endophyte inoculation. POX and PPO were transiently up-regulated in cv. Nabusa 7 dai, exceeding levels observed in non-inoculated plants of the same cultivar. POX activity was up-regulated at 7 dpnc in endophyte-inoculated cv. Nabusa plants challenged with R. similis. In the tolerant cultivar, POX and PPO activities were similarly up-regulated in R. similis-challenged plants at 7 dpnc, irrespective of endophyte inoculation. The findings of this study implicate PAL, POX and PPO in banana defence against the root-burrowing nematode R. similis. Our findings further demonstrate the ability of endophytic F. oxysporum isolate V5w2 directly to induce POX and prime PAL in the susceptible cv. Nabusa for greater up-regulation following R. similis challenge.

Download Full-text