Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger

The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger’s agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976–2003). Global genetic differentiation between the two collections was very low (F _st = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F _st, and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers’ management has globally preserved sorghum genetic diversity in Niger.     

Elosuchus,a new genus of crocodile from the Cretaceous of the North of Africa

‘Thoracosaurus’ cherifiensis Lavocat, 1955, a longirostrine from the late Lower Cretaceous of Morocco and Algeria, is attributed to Elosuchus, n. g., with another species, E. felixi n. sp., from In Abangarit (Niger), of the same age. Stolokrosuchus from the Lower Cretaceous of Niger is also referred to the new family Elosuchidae. Synapomorphies and grades are indicated for the families of ‘mesosuchian’ longirostrine crocodiles, but no synapomorphy has been found to unite the families, except perhaps for the Thalattosuchia.     

Valdosaurus, a hypsilophodontid dinosaur from the Lower Cretaceous of Europe and Africa

Material of the hypsilophodontid dinosaur Valdosauruscanaliculatus (Ornithischia: Ornithopoda) is described from the Lower Cretaceous (Barremian) of southern England and a new species is recognized from the Lower Cretaceous (Aptian) of Niger, West Africa. This occurrence of Valdosaurus in Europe and Africa provides evidence of a land connection between these continents across Tethys sometime in the early Cretaceous.     

Emergence of multi-drug-resistant Mycobacterium tuberculosis in Niger: A snapshot based on whole-genome sequencing

BackgroundAmong other West African countries experiencing the high endemicity of deadly tuberculosis, the situation in Niger is poorly evidenced by microbiological investigations.Methodology/Principal findingsThe study of 42 isolates of Mycobacterium tuberculosis from Niger by whole genome sequencing using Illumina iSeq technology yielded four M. tuberculosis lineages: Indo-Oceanic L1 (n = 1) (2.3%), East-Asian (n = 1) (2.3%), East-African Indian L3 (n = 2) (4.7%) and Euro-American L4 (n = 38) (90.4%). The sub-lineage L4.1.3 comprising 18 isolates (47.3%) was predominant, followed by the L4.6.2.2 sub-lineage (Cameroon genotype, n = 13 isolates) (34.2%). Investigating drug resistance profile for 12 antibiotics found 8/42 (19%) pan-susceptible isolates and 34/42 (81%) resistant isolates; with 40/42 (95.2%) isolates being susceptible to clofazimine-bedaquiline.Conclusions/SignificanceThese unprecedented data from Niger highlight the dynamics of tuberculosis transmission and drug resistance in Niger and may assist tuberculosis control in this country which continues to support a high burden of tuberculosis.     

Toxoplasmosis seroprevalence in urban rodents: a survey in Niamey,Niger

A serological survey of Toxoplasma gondii was conducted on 766 domestic and peridomestic rodents from 46 trapping sites throughout the city of Niamey, Niger. A low seroprevalence was found over the whole town with only 1.96% of the rodents found seropositive. However, differences between species were important, ranging from less than 2% in truly commensal Mastomys natalensis, Rattus rattus and Mus musculus, while garden-associated Arvicanthis niloticus displayed 9.1% of seropositive individuals. This is in line with previous studies on tropical rodents - that we reviewed here - which altogether show that Toxoplasma seroprevalence in rodent is highly variable, depending on many factors such as locality and/or species. Moreover, although we were not able to decipher statistically between habitat or species effect, such a contrast between Nile grass rats and the other rodent species points towards a potentially important role of environmental toxoplasmic infection. This would deserve to be further scrutinised since intra-city irrigated cultures are extending in Niamey, thus potentially increasing Toxoplasma circulation in this yet semi-arid region. As far as we are aware of, our study is one of the rare surveys of its kind performed in Sub-Saharan Africa and the first one ever conducted in the Sahel.     

A massively-constructed iguanodont from Gadoufaoua,lower Cretaceous of Niger

A ponderously constructed ornithischian dinosaur, Lurdusaurus arenatus, nov.g., nov.sp., from the Aptian of Niger resembles extinct giant ground sloths in general body form. Details of its skeletal anatomy indicate a close affinity to European iguanodontids of Early Cretaceous age.     

Integrative taxonomy of a poorly known Sahelian rodent, Gerbillus nancillus (Muridae,Gerbillinae)

Aridification processes that affected the Sahelian area of West Africa during the last decades have induced significant changes in plant and animal communities of this region. In rodents, the genus Gerbillus characteristic of North African and Asian arid habitats has been affected by this climatic and environmental trends. Several species of this genus showed a southward range expansion in recent years into the Sahelian bioclimatic zone. Recent sampling in several localities of West Africa (Mali, Niger and Senegal) enabled us to collect numerous specimens of small gerbils. An integrative study of these samples using molecular, morphological and cytogenetical methods revealed that many of them were attributable to Gerbillus nancillus, a secretive and poorly known species. Gerbillus nancillus appears characterized by a well differentiated karyotype with 2n = 56 chromosomes, and to represent a unique genetic lineage within this genus. Body and skull measurements of G. nancillus were compared with those of the morphologically similar Gerbillus henleyi, which provided diagnostic clues between them. These new data significantly expand the distribution area of G. nancillus, which now ranges from Sudan in the East to Senegal in the West. G. nancillus is here reported from numerous new localities in Niger and Mali, and for the first time in Senegal, which raises questions about the origin of its presence and the colonization routes it followed to get there. We also show that G. henleyi and G. nancillus are sympatric and apparently often syntopic in the sub-Saharan part of the distribution of G. henleyi.     

Distribution, shape and clonal growth of the rare endemic tree Olea europaea subsp. laperrinei (Oleaceae) in the Saharan mountains of Niger

The populations of the Laperrine’s olive (Olea europaea subsp. laperrinei) are located in three main areas corresponding to the mountains of northern Niger (Aïr), southern Algeria (Hoggar), and north-western Sudan (western Darfur). The populations native of Niger were found to occur in very fragmented patches from 1550 to 1850 m in five isolated mountains with population sizes not exceeding 100 trees each, except in the Tamgak. Samples in the Tamgak and the Bagzane mountains were studied by combining field observations with identification of genets (using highly variable DNA marker analyzes). Trees were relatively small and multi-stemmed like those in the Hoggar, and were associated with some tropical species as in the western Darfur. They were found on borders of “wadis”, i.e., temporary water courses, in ravines and on hillsides. They were unable to rely on sexual reproduction, which was found to be ineffective. In contrast, 28% of the genetic profiles found (n _genet = 98) were represented with two or more trees without aboveground connections. Molecular and morphological data both demonstrated that the populations used clonal growth (CG) to survive in the current unfavorable period of hyper-aridity, and thus are likely to be remnant populations. Signs of human-related disturbances, recorded on 43% of the sampled trees, should be a determining factor of distribution as well. In the Bagzane mountains especially, where human activities are more intense than in the Tamgak mountains, trees developed preferentially on hillsides and ravines with low access rather than on wadi borders with better edaphic conditions but easier access for livestock/people. CG may be therefore, a survival strategy both against aridity and human-related disturbances. Sexual reproduction may be triggered during a less arid period, following the model of multiple demographic strategies, widespread in arid environments. However, survival would be affected by browsing and cuttings. Lastly, the absence of an efficient sexual strategy coupled with the high fragmentation of very small populations and a narrow altitudinal range of distribution indicates that today the populations of O. e. laperrinei in the Aïr mountain range are more endangered than those from southern Algeria and north-western Sudan.     

Exploring stream communities in a tropical biodiversity hotspot: biodiversity,regional occupancy,niche characteristics and environmental correlates

Exploring and describing biodiversity and the mechanisms structuring it is fundamental to advancing ecology. This is particularly pertinent in understudied biogeographical regions, such as the Afrotropics, that are characterised by strong seasonal climatic shifts. We investigated the characteristics of stream biodiversity in the Niger Delta region of Nigeria, a tropical biodiversity hotspot, by examining patterns in 20 stream invertebrate communities across both the wet and dry seasons. For this, we took a multi-faceted approach accounting for the three levels of biodiversity (α, β and γ), including partitioning the nestedness and turnover components of β diversity, regional occupancy-abundance patterns, niche characteristics, and the environmental drivers of community structure. α diversity was low in these streams, with strong turnover between sites leading to high β diversity contributing to regional biodiversity, but there was little variation in communities between seasons. The proportion of sites occupied by taxa declined with increasing niche position, and decreasing niche breadth. Occupancy was predicted well by a combination of these two factors (niche position and breadth), but not mean local abundance, as the abundance-occupancy link was an upper-limit unimodal relationship. On average, community structure was linked more strongly to environmental variables in the wet season. Our findings demonstrate the clear role of spatial, but not temporal, turnover in assemblages, which likely reflects the environmental heterogeneity of this region. This is further supported by the fact that regional occupancy was mostly related to niche characteristics, particularly niche position. We emphasise the importance of continued basic and applied ecological work in this important biogeographic region to enable better protection of its biodiversity.     

Population Genomics Reveals Incipient Speciation,Introgression, and Adaptation in the African Mona Monkey (Cercopithecus mona)

Guenons (tribe Cercopithecini) are the most widely distributed nonhuman primate in the tropical forest belt of Africa and show considerable phenotypic, taxonomic, and ecological diversity. However, genomic information for most species within this group is still lacking. Here, we present a high-quality de novo genome (total 2.90 Gb, contig N50 equal to 22.7 Mb) of the mona monkey (Cercopithecus mona), together with genome resequencing data of 13 individuals sampled across Nigeria. Our results showed differentiation between populations from East and West of the Niger River ∼84 ka and potential ancient introgression in the East population from other mona group species. The PTPRK, FRAS1, BNC2, and EDN3 genes related to pigmentation displayed signals of introgression in the East population. Genomic scans suggest that immunity genes such as AKT3 and IL13 (possibly involved in simian immunodeficiency virus defense), and G6PD, a gene involved in malaria resistance, are under positive natural selection. Our study gives insights into differentiation, natural selection, and introgression in guenons.     

Impact of sublethal doses of Piper guineense (Schum and Thonn) on the biological parameters of Callosobruchus maculatus (F.) (Coleoptera: Chrysomelidae) reared on different cowpea varieties

Cowpea varieties show a wide range of characteristics in their composition that can determine Callosobruchus maculatus (Fabricius) response and survival. Consequently, this work investigated the influence of sublethal doses of Piper guineense on C. maculatus raised on four cowpea varieties: ART-98–12, Niger White, Oloyin, and Ife Brown. Our results demonstrated that C. maculatus from different varieties, despite being reared under the same conditions, responded differently to sublethal doses of P. guineense. Cowpea beetles from ART-98–12 were the most susceptible while those reared on Ife Brown were the least susceptible. Across varieties, survival and reproductive parameters of C. maculatus differed. Furthermore, the ranking for the percentage reduction in the number of eggs laid by C. maculatus was ART-98–12 > Niger White > Oloyin > Ife Brown. According to the log-rank statistic test, the difference observed in C. maculatus’ survival can be explained by variety (log-rank statistic: χ2 [df = 3, N = 16] = 15, p = 0.004). Conversely, the survivability of the chrysomelid beetles reared on Niger white was significantly lower (p = 0.012) compared to the other varieties. This study highlights the role of cowpea variety in dictating the efficacy of a given botanical against C. maculatus.     

Un nouveau gisement Saharien à Amphigenia(Brachiopode Terebratulida Dévonien). Implications paléogéographiques

The occurrence of the genus Amphigenia in the Tassilis 0605 Oua-n-Ahaggar (near the borders Algeria/Niger) is a new evidence of the faunistic relations between the western and the southern Sahara, on the one hand, and the Americas, on the other hand.     

Isozymic classification of pearl millet (Pennisetum glaucum,Poaceae) landraces from Niger (West Africa)

The principal landraces of the pearl millet,Pennisetum glaucum (L.)R. Br., from Niger have been analysed for their genetic structure at eight enzyme systems coded by 12 loci and 46 alleles. Three groups have been identified: (1) early-maturing pearl millets, cultivated between 8° and 13°E longitude, including the oases from Aïr mountains; (2) early-maturing millets situated more to the west (1° and 8°E longitude), and (3) late-maturing millets. Group 1 shows the highest isozyme diversity. The differences between the accessions represent 8.8% of the total diversity and the differences between the three groups 4.5%. The accessions from groups 1 and 3 are the least distant. When considering pearl millets from areas outside Niger, the chadian and sudanese millets are enzymatically close to the Niger group 1. The pearl millets from Niger group 2 are close to millets from east Mali, northern Burkina Faso and Senegal, and the Niger group 3 to the late-maturing millets group from West Africa. This study should help breeders to select the landraces for improvement and parents for crosses from cultivars of Niger and introduced germ plasm.     

Developing and applying a macroinvertebrate‐based multimetric index for urban rivers in the Niger Delta,Nigeria

Urban pollution of riverine ecosystem is a serious concern in the Niger Delta region of Nigeria. No biomonitoring tool exists for the routine monitoring of effects of urban pollution on riverine systems within the region. Therefore, the aim of this study was to develop and apply a macroinvertebrate‐based multimetric index for assessing water quality condition of impacted urban river systems in the Niger Delta region of Nigeria. Macroinvertebrate and physicochemical samples were collected from 11 stations in eight river systems. Based on the physicochemical variables, the stations were categorized into three impact categories namely least impacted stations (LIS), moderately impacted stations (MIS) and heavily impacted stations (HIS). Seventy‐seven (77) candidate metrics were tested and only five: Hemiptera abundance, %Coleoptera + Hemiptera, %Chironomidae + Oligochaeta, Evenness index and Logarithm of relative abundance of very large body size (>40–80 mm) were retained and integrated into the final Niger Delta urban multimetric index (MINDU). The validation dataset showed a correspondence of 83.3% between the index result and the physicochemically‐based classification for the LIS and a 75% correspondence for the MIS. A performance of 22.2% was recorded for the HIS. The newly developed MINDU proved useful as a biomonitoring tool in the Niger Delta region of Nigeria and can thus be used by environmental managers and government officials for routine monitoring of rivers and streams subjected to urban pollution.     

Redescription of Ilyocryptus tuberculatus Brehm, 1913 (Anomopoda,Branchiopoda)

The morphology of Ilyocryptus tuberculatus Brehm, 1913 is redescribed, based on material from the Niger basin, Africa. The species name was given by Brehm erroneously, because under an optical microscope he mistook internal structures (the columns between the outer and inner walls of the valves) for the tubercules on the valve surface. But this species is undoubtedly valid, and `incorrect' species names must be conserved. Differences between I. tuberculatus and the most similar I. agilis (probably absent from the majority of African waters), I. spinifer (common in Africa), and some other species are discussed. Currently, I. tuberculatus is known for the Central African Republic, Mali and Niger.     

Population Size and Migration of Anopheles gambiae in the Bancoumana Region of Mali and Their Significance for Efficient Vector Control

We present results of two intensive mark-release-recapture surveys conducted during the wet and dry seasons of 2008 in the villages of Fourda and Kenieroba, Mali. The former is a small fishing village by the Niger River with a moderate to high densities of Anopheles gambiae Giles s.s. (Diptera: Culicidae) throughout the year, while the latter is a large agricultural community 2 km inland that experiences strong seasonal fluctuation in An. gambiae densities. We estimate the population size of female An. gambiae in Fourda to be in less than 3,000 during the dry season. We found evidence of large population size and migration from Fourda in Kenieroba during the wet season, but very low numbers and no sign of migrants during the dry season. We suggest that malaria vector control measures aimed at adult mosquitoes might be made more efficient in this region and other seasonal riparian habitats by targeting disruption of mosquito populations by the river during the dry season. This would decrease the size of an already small population, and would be likely to delay the explosive growth in vector numbers in the larger inland villages as rainfall increases.     

Genetic diversity and population structure of Chrysichthys nigrodigitatus from Niger Delta based on AFLP analysis

The silver catfish, Chrysichthys nigrodigitatus is an important food fish in the Niger Delta. To understand the genetic variations and population structure in Nigeria’s Niger Delta, eighty-eight individuals collected from 7 locations were analyzed based on amplified fragment length polymorphism (AFLP) analysis. A total of 243 bands were identified using 4 AFLP primer combinations. The average gene diversity was 0.1708 ± 0.1547 and Shannon’s information index was 0.2792 ± 0.2224. The pairwise F_st values ranged from 0.133 to 0.796. The results of AMOVA analysis indicated that 19.03% of the genetic variation was contained among three groups. The gene flow estimates (Nm) demonstrated that different degrees of gene flow existed among populations ranging from 0.064 to 1.630. Two clades were recognized on the UPGMA tree. The results supported that freshwater or brackishwater habitat, limited long-distance dispersal of the adult and juveniles and physical barriers may be responsible for the current genetic structure.     

Ecological comparison of the pre- and post-impoundment macrophyte flora of the river Niger and Lake Kainji,Nigeria

The floristic composition of the macrophyte vegetation of Lake Kainji was investigated and compared with the vegetation of the river Niger before impoundment.Of 18 hydatophytes, 40 tenagophytes and 57 trichophytes listed for the Niger, 18 tenagophytes, 12 trichophytes and 7 hydatophytes were found growing in the lake 17 years after impoundment. Fourteen new tenagophytes, 3 new hydatophytes and 1 new trichophyte were recorded. The hydatophytes which were expected to colonize the lake are limited in number and range.The failure of the hydatophytes to colonize the lake, as predicted by Cook (1968), is discussed in relation to the inflow-to-volume ratio of the lake.Nomenclature follows Hutchinson & Dalziel (1952–1972). Flora of West Tropical Africa.     

Présence du crocodilienPhosphatosaurus (Mesosuchia,Dyrosauridae) dans le paléocène du niger et du Mali

Jaw fragments of the large dyrosaurid crocodilianPhosphatosaurus Bergounioux, 1955, previously known only from the Lower Eocene of Tunisia, are described from the Lower Palaeocene of Niger and Mali. Teeth described by Gemmellaro from the Maastrichtian of Egypt are also referred to a similar form. Although too incomplete to be specifically identified, all these remains indicate that this group of dyrosaurids with a robust snout and large teeth has differentiated early. The evolution of the genusPhosphatosaurus was marked by an elongation of the mandibular symphysis. Résumé Des restes de mâchoires du grand Crocodilien dyrosauridéPhosphatosaurus Bergounioux, 1955, connu jusqu’ici seulement dans l’Eocène inférieur de Tunisie, sont décrits en provenance du Paléocène inférieur du Niger et du Mali. Des dents du Maestrichtien d’Egypte décrites par Gemmellaro sont aussi rapportées à une forme similaire. Bien que trop incomplets pour être identifiés spécifiquement, tous ces restes montrent que ce groupe de Dyrosauridae à museau robuste et à grosses dents s’est différencié de façon précoce. L’évolution du genrePhosphatosaurus a été marquée par une elongation de la symphyse mandibulaire.     

Geographic distribution of phylogenetically-distinct legume pod borer, Maruca vitrata (Lepidoptera: Pyraloidea: Crambidae)

Maruca vitrata Fabricius is a pantropical lepidopteran pest of legumes. Phylogenetic analysis of a mitochondrial cytochrome c oxidase-I gene (cox1) fragment indicates that three Maruca sp. mitochondrial lineages have unique geographic distributions [lineages 1 and 2: Australia, Taiwan, and West Africa (Niger, Nigeria, and Burkina Faso), and lineage 3: Puerto Rico]. The haplotype (T30, T114) is specific to lineages 1&2 and was assayed by NsiI and SacI polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) within population samples; it was not observed in the Puerto Rican samples, but was nearly fixed among samples from West Africa, Australia and Taiwan (85.5?C100%). Re-sequencing and phylogenetic analyses of PCR-RFLP defined cox1 haplotypes indicate that nucleotide diversity is highest among samples from West Africa. Phylogenetic reconstruction based upon ribosomal DNA (rDNA) internal transcribed spacer-2 (ITS-2) sequences provided additional evidence for three Maruca sp. clades. These data suggest that multiple unique Maruca species or subspecies are present worldwide, which has implications for the management of this pest species-complex.