Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid‐Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo‐climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo‐climatic factors impacting the diversification of the sub‐Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

Biodiversity, phylogeography and population genetic studies will be revolutionized by access to large data sets thanks to next-generation sequencing methods. In this study, we develop an easy and cost-effective protocol for in-solution enrichment hybridization capture of complete chloroplast genomes applicable at deep-multiplexed levels. The protocol uses cheap in-house species-specific probes developed via long-range PCR of the entire chloroplast. Barcoded libraries are constructed, and in-solution enrichment of the chloroplasts is carried out using the probes. This protocol was tested and validated on six economically important West African crop species, namely African rice, pearl millet, three African yam species and fonio. For pearl millet, we also demonstrate the effectiveness of this protocol to retrieve 95% of the sequence of the whole chloroplast on 95 multiplexed individuals in a single MiSeq run at a success rate of 95%. This new protocol allows whole chloroplast genomes to be retrieved at a modest cost and will allow unprecedented resolution for closely related species in phylogeography studies using plastomes.

Next-generation sequencing allows access to a large quantity of genomic data. In plants, several studies used whole chloroplast genome sequences for inferring phylogeography or phylogeny. Even though the chloroplast is a haploid organelle, NGS plastome data identified a nonnegligible number of intra-individual polymorphic SNPs. Such observations could have several causes such as sequencing errors, the presence of heteroplasmy or transfer of chloroplast sequences in the nuclear and mitochondrial genomes. The occurrence of allelic diversity has practical important impacts on the identification of diversity, the analysis of the chloroplast data and beyond that, significant evolutionary questions. In this study, we show that the observed intra-individual polymorphism of chloroplast sequence data is probably the result of plastid DNA transferred into the mitochondrial and/or the nuclear genomes. We further assess nine different bioinformatics pipelines' error rates for SNP and genotypes calling using SNPs identified in Sanger sequencing. Specific pipelines are adequate to deal with this issue, optimizing both specificity and sensitivity. Our results will allow a proper use of whole chloroplast NGS sequence and will allow a better handling of NGS chloroplast sequence diversity.

Afin d'optimiser l'usage des mycorhizes en agriculture, douze inoculants commerciaux de champignon mycorhizien arbusculaire (CMA) furent évalués en serres sur le maïs. Dans un premier temps, les inoculants furent propagés en pots sur sable stérilisé afin d'évaluer leur potentiel sur la colonisation racinaire du maïs par rapport à celui d'un sol agricole du Kenya et d'inventorier les espèces CMA contenues dans les inoculants. Trois inoculants augmentèrent le taux de colonisation racinaire comparé au sol agricole. Treize espèces AMF furent isolées des inoculants dont 5 non déclarées. Quatre des 12 espèces annoncées n'ont pas sporulé. Dans une seconde expérience, les inoculants furent utilisés en combinaison avec le sol agricole afin d'évaluer leur impact sur le rendement du maïs. Six semaines après le semis, 7 inoculants augmentèrent le taux de colonisation racinaire par rapport au sol témoin alors que 3 inoculants entraînèrent une légère augmentation de la biomasse aérienne. Ces évaluations démontrent la nécessité d'effectuer une pré-évaluation des inoculants commerciaux sur une culture et un sol donnés avant de les implanter à grande échelle. (Résumé d'auteur

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Even though African rain forests display high levels of local species diversity and endemism, their lower continental species diversity when compared with the Neotropics and Asia is paradoxical. This disparity is mainly thought to be linked to either important extinction events during the Pleistocene or at the Eocene-Oligocene boundary. African rattans or climbing palms are one of the most diverse clades of palms in Africa, representing one-third of all known species. Here, we reconstruct the phylogeny and temporal evolution of African rattans (Arecaceae: Calamoideae: Lepidocaryeae: Ancistrophyllinae) to test the two main hypotheses of palm evolution in Africa. We constructed a near-complete, dated species-level phylogenetic tree for subtribe Ancistrophyllinae using plastid and nuclear markers. The generic relationships between Ancistrophyllinae were fully resolved and species-level relationships are well to weakly supported. Ancistrophyllinae diversified during the Eocene with most species originating during the late Miocene after 10 Mya. This result is in agreement with several other studies suggesting a pre-Pleistocene origin of the extant African flora. Ancistrophyllinae display an anti-sigmoidal lineage-through-time plot with a moderate overall extinction fraction. Our simulations suggest important roles for an ancient extinction event at the Oligocene-Eocene boundary. In contrast, the hypothesis of an important extinction event in palms during the late Pliocene at 3 Mya is not supported. We suggest that the evolutionary history of African rattans has undergone a constant diversification rate punctuated by one or several important extinction events during the first part of the Cenozoic with most species diversity accumulating during the late Miocene and Pliocene.

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The aim of this study was to assess the potential of commercial mycorrhizal inoculants and a rhizobial inoculant to improve soybean yield in Kenya. A promiscuous soybean variety was grown in a greenhouse pot study with two representative soils amended with either water-soluble mineral P or rock P to assess product performance. The performance of selected mycorrhizal inoculants combined with a rhizobial inoculant (Legumefix) was then assessed with farmer groups in three agroecological zones using a small-plot, randomized complete block design to assess soybean root colonization by mycorrhiza, nodulation, and plant biomass production in comparison to rhizobial inoculant alone or with water-soluble mineral P. Greenhouse results showed highly significant root colonization by commercial mycorrhizal inoculant alone (p < 0.001) and in interaction with soil type (p < 0.0001) and P source (p < 0.0001). However, no significant effect was shown in plant P uptake, biomass production, or leaf chlorophyll index. In field conditions, the effects of mycorrhizal and rhizobial inoculants in combination or alone were highly context-specific and may induce either a significant increase or decrease in root mycorrhizal colonization and nodule formation. Mycorrhizal and rhizobial inoculants in combination or alone had limited effect on plant P uptake, biomass production, leaf chlorophyll index, and grain yield. Though some mycorrhizal inoculants induced significant root colonization by mycorrhizal inoculants, this did not lead to higher soybean yield, even in soils with limited P content. Our results are further evidence that inoculant type, soil type, and P source are critical factors to evaluate commercial inoculants on a context-specific basis. However, our results highlight the need for the identification of additional targeting criteria, as inoculant type, soil type, and P source alone were not enough to be predictive of the response. Without the identification of predictive criteria for improved targeting, the economic use of such inoculants will remain elusive.