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Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats ( SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability. [ABSTRACT FROM AUTHOR]

Aim We sought to test the refuge hypothesis as a major driver of genetic differentiation to explain the development of distinct phytogeographical domains in tropical Central African rain forest. To address this aim, we studied the phylogeographical pattern of a pair of sister plant species, Haumania danckelmaniana and H. liebrechtsiana (Marantaceae), distributed across the two phytogeographical domains: Lower Guinea and Congolia. Location Tropical Central Africa including the phytogeographical domains Lower Guinea and Congolia. Methods Seven polymorphic microsatellite loci were genotyped in a total of 513 individuals from both species. The dataset was analysed for population genetic structure and demographic change and the results compared to the geographical pattern of plastid DNA sequences from a previous publication and other sympatric species. Results Based on the microsatellite dataset, three distinct homogeneous genetic clusters were detected in H. danckelmaniana and two in H. liebrechtsiana. These clusters corresponded geographically with the patterns found in the plastid DNA sequences. Genetic diversity and endemism were unevenly distributed between clusters in the two species. Most clusters exhibited signals of population expansion. Main conclusions The phylogeographical data based on microsatellites and plastid DNA revealed a complex history involving (1) allopatric differentiation with each species originating in a different phytogeographical domain, potentially resulting from past forest fragmentation, followed by (2) population expansion and interspecific introgression, which probably occurred during a phase of forest expansion. Moreover, phylogeographical patterns within each species provided evidence of (3) past population fragmentation followed by partial population admixture in H. danckelmaniana, and deep differentiation between Lower Guinea and Congolia in H. liebrechtsiana. The observed patterns were globally consistent with the refuge hypothesis and the presented scenario illustrates evolutionary processes that likely have contributed to shaping the African phytogeographical domains. [ABSTRACT FROM AUTHOR]

• Premise of the study: Anthonotha macrophylla (Fabaceae) is a common tree species throughout the Guineo-Congolian forest that is sometimes confounded with other congeneric species; it is expected to be an interesting phylogeographical model to infer the history of the African dense forests. We developed 18 microsatellite markers from this species and tested their transferability in 15 congeneric species. • Methods and Results: A genomic library was obtained using the Illumina platform, and 18 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed two to 24 alleles (average: 11.9 alleles per locus, expected heterozygosity range: 0.18-0.91, mean: 0.64) in three populations of A. macrophylla from Benin, Liberia, and Cameroon. Cross-amplification in one to nine individuals of 15 congeneric Anthonotha species (A. acuminata, A. brieyi, A. cladantha, A. crassifolia, A. ferruginea, A. fragrans, A. gilletii, A. lamprophylla, A. mouandzae, A. noldeae, A. pellegrinii, A. pynaertii, A. stipulacea, A. wijmacampensis, and A. xanderi) showed successful amplification in six to 17 loci, making most of these markers useful at the generic level. • Conclusions: This set of markers will be useful to study species delimitation and the genetic structure of Anthonotha species, and thus to better understand the history of tropical African rainforests. [ABSTRACT FROM AUTHOR]

Background: Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species' divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure. Results: West African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct 'Fields For Recombination' corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance. Conclusions: Our genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species. [ABSTRACT FROM AUTHOR]

Gene dispersal and clonality are important aspects of plant evolution affecting the spatial genetic structure (SGS) and the long-term survival of species. In the tropics these parameters have mostly been investigated in trees and some herbs, but rarely in climbers which frequently: (1) show clonal growth leading to a patchy distribution pattern similar to that of understory herbs; and (2) flower in the canopy where they may have access to long-distance dispersal like canopy trees. We thus hypothesize for climbers an intermediate genetic structure between herbs and trees. The study aims at assessing breeding system and spatial extent of clonality and gene dispersal in Haumania danckelmaniana (Marantaceae), a common climber in the tropical rain forests from western Central Africa. In eastern Cameroon, 330 ramets were sampled at three spatial scales and genotyped at seven microsatellite loci. Clonality was moderate (clonal extend: 15-25 m, clonal diversity 0.4-0.65) indicating the importance of recruitment from seeds at this locality. The low inbreeding ( FIS) suggested predominant outcrossing. The rate of decay of the relatedness between individuals with distance indicated limited gene dispersal distance ( σg = 9-50 m, neighborhood sizes Nb = 23-67) in accordance with narrowly gravity dispersed seeds and restricted pollen transfer distance in densely flowering populations. The marked SGS ( Sp = 0.011-0.026) was similar to that reported in tropical trees, but might increase with augmented clonality as in many herbs, especially under more severe disturbance regimes. [ABSTRACT FROM AUTHOR]

• Premise of the study: To study the genetic structure among three morphotypes of an African rainforest tree species, Santiria trimera , nuclear microsatellite markers were isolated and characterized. • Methods and Results: Seven polymorphic loci were isolated using a pyrosequencing-based protocol and successfully amplified on three different morphotypes of S. trimera . For six of the seven loci, there is at least one private allele for one of the three morphotypes. The mean effective number of alleles is about four for each of the three morphotypes. • Conclusions: These microsatellite markers are promising to explore the genetic delimitation among sympatric morphotypes found in Gabonese forests and to study the spatial genetic structure within each gene pool. [ABSTRACT FROM AUTHOR]

• Premise of the study: Microsatellite loci were developed in the endangered Pericopsis elata using a combination of low-cost procedures. • Methods and Results: Microsatellite isolation was performed simultaneously on three distinct species through a newly available procedure that associates multiplex microsatellite enrichment and next-generation sequencing, allowing the rapid and low-cost development of microsatellite-enriched libraries through the use of a 1/32nd GS-FLX plate. Genotyping using M13-like labeling in multiplexed reactions allowed additional cost savings. From 72 primers selected for initial screening, 21 positively amplified P. elata , and 11 showed polymorphism with two to 11 alleles per locus and a mean value of 5.4 alleles per locus. • Conclusions: These microsatellite loci will be useful to further investigate the level of genetic variation within and between natural populations of P. elata in Africa. [ABSTRACT FROM AUTHOR]