Diversity In West Africa Research Articles

Garlic (Allium sativum L.): Overview on its Biology and Genetic Markers Available for the Analysis of Its Diversity in West Africa

Garlic belongs to the Allium genus, which includes more than 750 species divided into more than 60 taxonomic groups. It is cultivated in many countries throughout the world for the bulb and used as a spice and functional food. The plant vegetatively propagates. This review will focus on origins, biology, analysis of genetic diversity, pharmacological properties of garlic. It appears from this synthesis that the Allium sativum species is derived from Allium longicuspis and is native to Central Asia. Studies on the analysis of genetic diversity through morphological markers revealed a wide variation in the color, shape and number of cloves and the ability to flower. Biochemical markers such as Esterase (EST), Phosphoglucomutase (PGI), Malate Deshydrogenase (MDH), and Diaphorase (DIA as well as molecular markers such as Random Amplified Polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), Amplified Fragment Length Polymorphism (AFLP), and Simple Sequence Repeats (SSRS) Inter-Simple Sequence Repeat (ISSR) were successfully used. RFLPs or RAPD are the most used for assessing genetic variability within asexually reproducing garlic species. Work using SSRs markers is limited in garlic relative to other crops.

Food diversity in West Africa: Case of the main traditional dishes consumed in Côte d'Ivoire

Objective: According to regional or ethnic affiliation, Ivoirians consume a variety of traditional dishes. This study aimed to discover the dietary diversity and determine the nutritional contribution of the Ivorian traditional dishes. Methodology and results: For that, a family food survey was conducted in forty-four localities in different regions (North, South, East, Center and West). Households from these localities were interviewed using a questionnaire. The interview focused on the preparation of the most commonly consumed traditional dishes, selected based on the consumption frequency. Then, the physico-chemical characteristics of these dishes were determined. The results showed that Ivorian traditional dishes consist mainly of starchy basic dishes and side sauces. The main dishes consist of tubers and roots (yam, cassava, potato) or cereals (rice, corn, millet, sorghum.) and starchy fruits (plantain). The side sauces are cooked from vegetables (eggplants, seeds, tomatoes, okra, leaves, peppers, peanuts, and pistachios), proteins like fish, meat, poultry, molluscs, mushrooms, seafood and spices (salt, pepper). The Ivorian traditional dishes provide a sufficient share of carbohydrates, proteins and lipids with average contents ranging respectively between 45 to 69 %, 10 to 20 % and less than 35 % of dry matter. In addition, these dishes provided sufficient energy (373.33 to 516.78 Kcal / 100 g DM) and had low sodium, calcium and magnesium contents. Their iron contents were relatively good. Conclusion and application of results: The Ivorian population’s diets diversity is real and beneficial to them because the different dishes consumed provide the necessary nutrients for the proper functioning of the consumer’s bodies. However, compliance with the principles of a good diet, particularly in terms of quantity, is essential to avoid pathologies by excess or by default. Keywords: Dietary diversity, traditional dishes, chemical composition, Côte d’Ivoire

Mapping mycological ignorance \u2013 checklists and diversity patterns of fungi known for West Africa

Scientific information about biodiversity distribution is indispensable for nature conservation and sustainable management of natural resources. For several groups of animals and plants, such data are available, but for fungi, especially in tropical regions like West Africa, they are mostly missing. Here, information for West African countries about species diversity of fungi and fungus-like organisms (other organisms traditionally studied by mycologists) is compiled from literature and analysed in its historical context for the first time. More than 16,000 records of fungi representing 4843 species and infraspecific taxa were found in 860 publications relating to West Africa. Records from the Global Biodiversity Information Facility (GBIF) database (2395 species), and that of the former International Mycological Institute fungal reference collection (IMI) (2526 species) were also considered. The compilation based on literature is more comprehensive than the GBIF and IMI data, although they include 914 and 679 species names, respectively, which are not present in the checklist based on literature. According to data available in literature, knowledge on fungal richness ranges from 19 species (Guinea Bissau) to 1595 (Sierra Leone). In estimating existing species diversity, richness estimators and the Hawksworth 6:1 fungus to plant species ratio were used. Based on the Hawksworth ratio, known fungal diversity in West Africa represents 11.4% of the expected diversity. For six West African countries, however, known fungal species diversity is less than 2%. Incomplete knowledge of fungal diversity is also evident by species accumulation curves not reaching saturation, by 45.3% of the fungal species in the checklist being cited only once for West Africa, and by 66.5% of the fungal species in the checklist reported only for a single country. The documentation of different systematic groups of fungi is very heterogeneous because historically investigations have been sporadic. Recent opportunistic sampling activities in Benin showed that it is not difficult to find specimens representing new country records. Investigation of fungi in West Africa started just over two centuries ago and it is still in an early pioneer phase. To promote proper exploration, the present checklist is provided as a tool to facilitate fungal identification in this region and to aid conceptualisation and justification of future research projects. Documentation of fungal diversity is urgently needed because natural habitats are being lost on a large scale through altered land use and climate change.

Long-term droughts may drive drier tropical forests towards increased functional, taxonomic and phylogenetic homogeneity

Tropical ecosystems adapted to high water availability may be highly impacted by climatic changes that increase soil and atmospheric moisture deficits. Many tropical regions are experiencing significant changes in climatic conditions, which may induce strong shifts in taxonomic, functional and phylogenetic diversity of forest communities. However, it remains unclear if and to what extent tropical forests are shifting in these facets of diversity along climatic gradients in response to climate change. Here, we show that changes in climate affected all three facets of diversity in West Africa in recent decades. Taxonomic and functional diversity increased in wetter forests but tended to decrease in forests with drier climate. Phylogenetic diversity showed a large decrease along a wet-dry climatic gradient. Notably, we find that all three facets of diversity tended to be higher in wetter forests. Drier forests showed functional, taxonomic and phylogenetic homogenization. Understanding how different facets of diversity respond to a changing environment across climatic gradients is essential for effective long-term conservation of tropical forest ecosystems.

New insights from Gorongosa National Park and Niassa National Reserve of Mozambique increasing the genetic diversity of Trypanosoma vivax and Trypanosoma vivax-like in tsetse flies, wild ungulates and livestock from East Africa

BackgroundTrypanosoma (Duttonella) vivax is a major pathogen of livestock in Africa and South America (SA), and genetic studies limited to small sampling suggest greater diversity in East Africa (EA) compared to both West Africa (WA) and SA.MethodsMultidimensional scaling and phylogenetic analyses of 112 sequences of the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) gene and 263 sequences of the internal transcribed spacer of rDNA (ITS rDNA) were performed to compare trypanosomes from tsetse flies from Gorongosa National Park and Niassa National Reserve of Mozambique (MZ), wild ungulates and livestock from EA, and livestock isolates from WA and SA.ResultsMultidimensional scaling (MDS) supported Tvv (T. vivax) and TvL (T. vivax-like) evolutionary lineages: 1) Tvv comprises two main groups, TvvA/B (all SA and WA isolates plus some isolates from EA) and TvvC/D (exclusively from EA). The network revealed five ITS-genotypes within Tvv: Tvv1 (WA/EA isolates), Tvv2 (SA) and Tvv3–5 (EA). EA genotypes of Tvv ranged from highly related to largely different from WA/SA genotypes. 2) TvL comprises two gGAPDH-groups formed exclusively by EA sequences, TvLA (Tanzania/Kenya) and TvLB-D (MZ). This lineage contains more than 11 ITS-genotypes, seven forming the lineage TvL-Gorongosa that diverged from T. vivax Y486 enough to be identified as another species of the subgenus Duttonella. While gGAPDH sequences were fundamental for classification at the subgenus, major evolutionary lineages and species levels, ITS rDNA sequences permitted identification of known and novel genotypes.ConclusionsOur results corroborate a remarkable diversity of Duttonella trypanosomes in EA, especially in wildlife conservation areas, compared to the moderate diversity in WA. Surveys in wilderness areas in WA may reveal greater diversity. Biogeographical and phylogenetic data point to EA as the place of origin, diversification and spread of Duttonella trypanosomes across Africa, providing relevant insights towards the understanding of T. vivax evolutionary history.

Structure of sweet potato (Ipomoea batatas) diversity in West Africa covaries with a climatic gradient.

Sub-Saharan agriculture has been identified as vulnerable to ongoing climate change. Adaptation of agriculture has been suggested as a way to maintain productivity. Better knowledge of intra-specific diversity of varieties is prerequisites for the successful management of such adaptation. Among crops, root and tubers play important roles in food security and economic growth for the most vulnerable populations in Africa. Here, we focus on the sweet potato. The Sweet potato (Ipomoea batatas) was domesticated in Central and South America and was later introduced into Africa and is now cultivated throughout tropical Africa. We evaluated its diversity in West Africa by sampling a region extending from the coastal area of Togo to the northern Sahelian region of Senegal that represents a range of climatic conditions. Using 12 microsatellite markers, we evaluated 132 varieties along this gradient. Phenotypic data from field trials conducted in three seasons was also obtained. Genetic diversity in West Africa was found to be 18% lower than in America. Genetic diversity in West Africa is structured into five groups, with some groups found in very specific climatic areas, e.g. under a tropical humid climate, or under a Sahelian climate. We also observed genetic groups that occur in a wider range of climates. The genetic groups were also associated with morphological differentiation, mainly the shape of the leaves and the color of the stem or root. This particular structure of diversity along a climatic gradient with association to phenotypic variability can be used for conservation strategies. If such structure is proved to be associated with specific climatic adaptation, it will also allow developing strategies to adapt agriculture to ongoing climate variation in West Africa.

Tree species diversity of three Ghanaian reserves

Among tropical areas, Africa is considered to be poor in terms of biodiversity as compared with Amazon or South-East Asia, especially with respect to forest diversity. Despite this lower diversity, some African tropical zones, such as Ghana, harbour a plethora of species, particularly of trees. Unfortunately, as a result of anthropogenic impacts, biological diversity in West Africa dramatically decreased in the last decades, with very limited reference to evaluate the amount of the loss. Due to these growing pressure, a collection of relevant biodiversity information in this region seems to be urgent. We surveyed 127 temporary plots randomly distributed within 3 protected areas in Ghana and we collected data on tree (dbh>10 cm) species richness and their abundances. We also performed α, and β diversity analyses, and estimated the effective number of species, adopting various indices and approaches to provide further information on each assemblage. The main goals of this research were: (i) to provide a wide tree species database (abundance-based data), together with some biodiversity analyses; (ii) to estimate the sampling effort needed for next biodiversity surveys in the same and similar regions; and (iii) to calculate some indices useful to monitor the future of these protected areas both in terms of conservation and biodiversity research.

Farmers’ contributions to the conservation of tree diversity in the Groundnut Basin, Senegal

Tree diversity in West Africa is threatened by intensified land uses and salinization, and farmers’ role in conservation of tree species is unclear. We hypothesized that farmers contribute to conservation of tree diversity through protection of trees in their agroforestry landscapes and compared the diversity and structure of the tree vegetation across landscape classes. Inventories were carried out in three villages in the Groundnut Basin in Senegal, assessing tree diversity, density and crown cover. Tree diversity as assessed by species accumulation curves was high in forests, but cultivated landscapes had comparable or almost comparable diversity, especially in the cases where the forest was planted or was affected by charcoal production. However, the occurrence of exotic species was higher in cultivated parts of the landscape, and although many species were in common, ordination plots indicated that forests and cultivated landscapes to some degree had different species composition. Salinity had a strong influence on vegetation, not only in the tans (salt marshes) but also across the other landscape classes. In conclusion, agroforestry landscapes in the three villages harbor considerable tree diversity, but insufficient to fully conserve the tree species. We argue that informing and including farmers in tree management in the region will contribute to overall conservation of tree genetic resources.

Climate and the distribution of grasses in West Africa

AbstractQuestionsWhich environmental variables influence grass diversity in West Africa? What are the effects of climate and grass functional traits on the spatial patterns (richness and abundance) of the grass clades Andropogoneae, Paniceae and Chloridoideae?LocationWest Africa, demarcated by the Atlantic Ocean in the west and south (20° W and 4° N), the Sahara desert in the north (25° N) and the border between Niger and Chad in the east (20° E).MethodsBased on 38 912 georeferenced occurrence records, we modelled the distribution of 302 grass species (51% of West African grass diversity). We integrated species richness, abundance and functional traits (life cycle, photosynthetic type and height) to determine the contribution of the most speciose grass clades (Andropogoneae, Paniceae and Chloridoideae) to overall grass diversity in West Africa.ResultsPrecipitation is the variable most often influencing the species distribution models of grasses in West Africa. Richness and relative abundance of the tribe Andropogoneae show a centre of diversity in Sudanian savanna regions. The height of Andropogoneae species, generally >150 cm, is driving this ecological dominance. Species richness of the tribe Paniceae is more dispersed and shows two main centres of abundance: The southern regions with higher mean annual precipitation and tree density are dominated by C3 Paniceae species. The Sahelian regions in the north are dominated by short Paniceae species with the C4 NAD‐ME photosynthetic subtype, as well as Chloridoideae possessing the same functional attributes.ConclusionsOur study provides insight into the environmental correlates of grass species richness in West Africa and contributes to the much‐needed research on tropical rangelands. Moreover, the integration of evolutionary history significantly improves our understanding of large‐scale biodiversity patterns.

Evaluation of Elite Rice Varieties Unmasks New Sources of Bacterial Blight and Leaf Streak Resistance for Africa

Background: Bacterial Leaf Blight (BLB) and Bacterial Leaf Streak (BLS) diseases respectively caused by Xanthomonas oryzae pv oryzae (Xoo) and X. oryzae pv oryzicola (Xoc) have become a real threat to rice production in West Africa. Genetic and pathogenicity studies revealed African X. oryzae (Xo) pathovars to be both fairly distant from their Asian counterparts. It is therefore mandatory to evaluate whether available major resistance genes are adapted for an efficient and durable control of BLB in Africa. As to BLS no resistance sources have been identified in rice so far. Results: We screened eleven upland and lowland elite rice varieties cultivated in Burkina Faso for resistance to bacterial blight and bacterial leaf streak. We show that all five upland varieties including three NERICAs are highly resistant to each of the three races of Xoo identified in Africa and generally susceptible to several strains from Asia. We next demonstrated that resistance is occurring independently of the plant developmental stage. Strikingly, phenotyping and in planta growth curves assays showed that the five varieties are also highly resistant to a set of Xoc strains representative of the diversity in West Africa. Finally, we show that resistance of the NERICA varieties to both Xoo and Xoc is likely to be inherited from the O. sativa ssp. japonica rather than the O. glaberrima parental lines. Conclusion: We identified and characterized rice accessions exhibiting new sources of resistance against African Xoo and Xoc strains specifically. These results provide important perspectives for the control of BLB and BLS in West Africa.

Detecting the Paternal Genetic Diversity in West Africa using Y-STRs and Y-SNPs

The pattern of human variation in Africa is the result of a complex series of demographic events. There are few databases related to the peoples of Africa, especially in western and central regions. In this study, 17 Y-STR and 31 Y-SNP loci were genotyped in a sample from Western Africa, which was compared with other representative populations of other African regions. The haplotype diversity observed in this region was 1.0000 (±0.0018) and that is similar to those values obtained in other African samples already studied. The most frequent haplogroup found in our sample belongs to E, showing the M2 derived allele. The haplogroup diversity was 0.6895 (±0.0200), very similar to that observed in countries where the Bantu groups are predominant (0.681 in Angola; 0.753 in Equatorial Guinea). Concerning the Western Africa, significant differences were observed between Guinea–Bissau and the remaining populations of this region. In addition, there was no significant difference between our sample and samples from Eastern and Central Africa. The genetic composition of the population studied was significantly different from that of Guinea–Bissau, although a genetic homogeneity was found among most countries belonging to West Africa.

Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava

The availability of genomic resources can facilitate progress in plant breeding through the application of advanced molecular technologies for crop improvement. This is particularly important in the case of less researched crops such as cassava, a staple and food security crop for more than 800 million people. Here, expressed sequence tags (ESTs) were generated from five drought stressed and well-watered cassava varieties. Two cDNA libraries were developed: one from root tissue (CASR), the other from leaf, stem and stem meristem tissue (CASL). Sequencing generated 706 contigs and 3,430 singletons. These sequences were combined with those from two other EST sequencing initiatives and filtered based on the sequence quality. Quality sequences were aligned using CAP3 and embedded in a Windows browser called HarvEST:Cassava which is made available. HarvEST:Cassava consists of a Unigene set of 22,903 quality sequences. A total of 2,954 putative SNPs were identified. Of these 1,536 SNPs from 1,170 contigs and 53 cassava genotypes were selected for SNP validation using Illumina's GoldenGate assay. As a result 1,190 SNPs were validated technically and biologically. The location of validated SNPs on scaffolds of the cassava genome sequence (v.4.1) is provided. A diversity assessment of 53 cassava varieties reveals some sub-structure based on the geographical origin, greater diversity in the Americas as opposed to Africa, and similar levels of diversity in West Africa and southern, eastern and central Africa. The resources presented allow for improved genetic dissection of economically important traits and the application of modern genomics-based approaches to cassava breeding and conservation.

Past climate changes explain the phylogeography of Vitellaria paradoxa over Africa

The evolution of the savanna biome has been deeply marked by repeated contraction/expansion phases due to climate perturbations during the Quaternary period. In this study, we investigated the impact of the last glacial maximum (LGM) on the present genetic pattern of Vitellaria paradoxa (shea tree), a major African savanna tree. A range-wide sampling of the species enabled us to sample 374 individuals from 71 populations distributed throughout sub-Sahelian Africa. Trees were genotyped using 3 chloroplasts and 12 nuclear microsatellites, and were sequenced for 2 polymorphic chloroplast intergenic spacers. Analyses of genetic diversity and structure were based on frequency-based and Bayesian methods. Potential distributions of V. paradoxa at present, during the LGM and the last interglacial period, were examined using DIVA-GIS ecological niche modelling (ENM). Haplotypic and allelic richness varied significantly across the range according to chloroplast and nuclear microsatellites, which pointed to higher diversity in West Africa. A high but contrasted level of differentiation was revealed among populations with a clear phylogeographic signal, with both nuclear (F(ST) = 0.21; R(ST) = 0.28; R(ST) > R(ST) (permuted)) and chloroplast simple sequence repeats (SSRs) (G(ST) = 0.81; N(ST) = 0.90; N(ST) > N(ST) (permuted)). We identified a strong geographically related structure separating western and eastern populations, and a substructure in the eastern part of the area consistent with subspecies distinction. Using ENM, we deduced that perturbations during the LGM fragmented the potential eastern distribution of shea tree, but not its distribution in West Africa. Our main results suggest that climate variations are the major factor explaining the genetic pattern of V. paradoxa.

Evidence for the Emergence of New Rice Types of Interspecific Hybrid Origin in West African Farmers' Fields

In West Africa two rice species (Oryza glaberrima Steud. and Oryza sativa L.) co-exist. Although originally it was thought that interspecific hybridization is impossible without biotechnological methods, progenies of hybridization appear to occur in farmer fields.AFLP analysis was used to assess genetic diversity in West Africa (including the countries The Gambia, Senegal, Guinea Bissau, Guinea Conakry, Sierra Leone, Ghana and Togo) using 315 rice samples morphologically classified prior to analysis. We show evidence for farmer interspecific hybrids of African and Asian rice, resulting in a group of novel genotypes, and identify possible mechanisms for in-field hybridization. Spontaneous back-crossing events play a crucial role, resulting in different groups of genetic diversity in different regions developed by natural and cultural selection, often under adverse conditions. These new groups of genotypes may have potential relevance for exploitation by plant breeders. Future advances in crop development could be achieved through co-operation between scientists and marginalized farmer groups in order to address challenges of rapid adaptation in a world of increasing socio-political and climatic uncertainty.

Teaching and Learning Guide for: Africa’s Linguistic Diversity

African languages have played an important role in the development of linguistic theory but their role in the fields of historical linguistics and linguistic typology has been less prominent. Africa’s linguistic diversity has been long underestimated given the dominance of the four-family model proposed by Joseph Greenberg. Criticism of this model has long held among specialists in some of Africa’s smaller and lesser-known language families, but has only recently become more widely acknowledged among linguists. Archaeologists, geneticists, and others continue to model African prehistory based on African linguistic classifications, which are outdated and which have failed to withstand scrutiny. This teaching and learning guide suggests a program to train scholars in recognizing and evaluating the standards by which various African language classifications have been made. Africa’s linguistic diversity will be shown to be far greater than what is suggested by the four-family model.

Diversity is demonstrated in class I HLA-A and HLA-B alleles in Cameroon, Africa: description of HLA-A*03012, *2612, *3006 and HLA-B*1403, *4016, *4703.

To examine the genetic diversity in west Africa, class I HLA-A and HLA-B alleles of 92 unrelated individuals from two areas in the Cameroon, the capital Yaoundé and the village of Etoa, were identified by direct automated DNA sequencing of exons 2 and 3 of the HLA-B locus alleles and sequence-specific oligonucleotide probe (SSOP) and/or sequencing of the HLA-A locus alleles. HLA-A*2301 (18.7%), A*2902 (10.4%), B*5301 (10.9%), and B*5802 (10.9%) were the most frequently detected alleles, present in at least 10% of the population. A total of 30 HLA-A locus and 33 HLA-B locus alleles, including six novel alleles, were detected. The novel alleles were HLA-A*03012, A*2612, A*3006 and HLA-B*1403, B*4016, and B*4703. HLA-B*4703 contains a novel amino acid sequence that is a combination of the first 5 amino acids of the Bw6 epitope and the last 2 residues of the Bw4 epitope. The addition of 6 alleles to the ever-expanding number of known class I HLA alleles supports our hypothesis that extensive genetic diversity, including previously undescribed alleles, would be observed in this African population. In the Yaoundé population, the allele frequency distribution at the HLA-A locus is consistent with distributions indicative of balancing selection. Extensive HLA-A-B haplotypes were observed in this population suggesting that only a fraction of the Cameroon HLA-A-B haplotype diversity has been observed.

Language Diversity in West Africa: An Ecological Approach

Analysis of a linguistic atlas reveals an ecological gradient in the diversity of languages in West Africa. As one moves south from arid into lusher ecoclimatic zones, the average size of ethnolinguistic groups decreases. Various factors are considered which may have contributed to this distribution. I argue that the ethnolinguistic map is primarily a reflection of the systems of generalized exchange and mutual dependence into which people enter. It is hypothesized that such social networks function to reduce subsistence risk due to variations in the food supply. If this hypothesis is correct, the average size of ethnolinguistic groups should be inversely proportional to the degree of ecological variability they face. This prediction is tested and found to hold strongly for a large part of West Africa. There is also limited evidence of a correlation between linguistic diversity and topography. It is concluded that ecological risk has been a key historical force in West Africa and that the ethnolinguistic mosaic can be used as a valuable “fossil record” of people's adaptive social and economic strategies.