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Selfing or mating between related individuals can lead to inbreeding depression (ID), which can influence the survival, growth and evolution of populations of tree species. As selective logging involves a decrease in the density of congeneric partners, it could lead to increasing biparental inbreeding or self-fertilization, exposing the population to higher ID. We assessed the influence of inbreeding on the growth of a commercial timber species, Pericopsis elata (Fabaceae), which produced about 54% of self-fertilized seedlings in a natural population of the Congo basin. We followed the survival and growth of 540 plants raised in a plantation along a gradient of plant density (0.07-15.9 plants per m 2 ). Parentage analysis allowed us distinguishing selfed and outcrossed seedlings. The annual growth was higher for outcrossed than selfed plants, on average by 10.8% for diameter and 12.9% for height growth. Based on the difference in above ground biomass between selfed and outcrossed seedlings after 41 months, we estimated the level of ID at δ = 0.33, while a lifetime estimate of ID based on the proportions of selfed plants at seedling and adult stages led to δ = 0.7. The level of ID on growth rate did not change significantly with age but tended to vanish under high competition. Pericopsis elata is a particularly interesting model because inbreeding depression is partial, with about 26% of reproducing adults resulting from selfing, contrary to most tropical tree species where selfed individuals usually die before reaching adulthood. Hence, the risks of ID must be considered in the management and conservation of the species., (© 2024. The Author(s).)

Premise of the Study: Coula edulis Baill (Coulaceae) is a common tree species in the Guineo-Congolian forests producing an edible fruit known as African walnut, which is an important food and income resource for rural populations. However, the species suffers from a deficit of natural regeneration. We developed here nuclear microsatellite markers for C. edulis to be able to study the genetic structure of its natural populations and gene flow., Methods and Results: A genomic library was obtained using the Illumina platform, and 21 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed eight to 22 alleles per locus (average: 14.2), with a mean expected heterozygosity ranging from 0.33 to 0.72 in five populations from Central and West Africa., Conclusions: The high polymorphism of the nuclear microsatellite markers developed makes them useful to investigate gene flow and the organization of genetic diversity in C. edulis, and to assess whether particular genetic resources require conservation efforts., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

The latitudinal diversity gradient (LDG) is one of the most recognized global patterns of species richness exhibited across a wide range of taxa. Numerous hypotheses have been proposed in the past two centuries to explain LDG, but rigorous tests of the drivers of LDGs have been limited by a lack of high-quality global species richness data. Here we produce a high-resolution (0.025° × 0.025°) map of local tree species richness using a global forest inventory database with individual tree information and local biophysical characteristics from ~1.3 million sample plots. We then quantify drivers of local tree species richness patterns across latitudes. Generally, annual mean temperature was a dominant predictor of tree species richness, which is most consistent with the metabolic theory of biodiversity (MTB). However, MTB underestimated LDG in the tropics, where high species richness was also moderated by topographic, soil and anthropogenic factors operating at local scales. Given that local landscape variables operate synergistically with bioclimatic factors in shaping the global LDG pattern, we suggest that MTB be extended to account for co-limitation by subordinate drivers., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

The dating of diversification events, including transitions between biomes, is key to elucidate the processes that underlie the assembly and evolution of tropical biodiversity. Afzelia is a widespread genus of tropical trees, threatened by exploitation for its valuable timber, that presents an interesting system to investigate diversification events in Africa. Africa hosts diploid Afzelia species in the savannahs north and south of the Guineo-Congolian rainforest and autotetraploid species confined to the rainforest. Species delimitation and phylogenetic relationships among the diploid and tetraploid species remained unresolved in previous studies using small amounts of DNA sequence data. We used genotyping-by-sequencing in the five widespread Afzelia species in Africa, the savannah species A. africana and A. quanzensis and the rainforest species A. bipindensis , A. pachyloba , and A. bella . Maximum likelihood and coalescent approaches resolved all species as monophyletic and placed the savannah and rainforest taxa into two separate clades corresponding to contrasted ploidy levels. Our data are thus compatible with a single biome shift in Afzelia in Africa, although we were unable to conclude on its direction. SNAPP calibrated species trees show that the savannah diploids started to diversify early, at 12 (9.09-14.89) Ma, which contrasts with a recent and rapid diversification of the rainforest tetraploid clade, starting at 4.22 (3.12 - 5.36) Ma. This finding of older diversification in a tropical savannah clade vs. its sister rainforest clade is exceptional; it stands in opposition to the predominant observation of young ages for savannahs lineages in tropical regions during the relatively recent expansion of the savannah biome., (Copyright © 2020 Donkpegan, Doucet, Hardy, Heuertz and Piñeiro.)

Premise: Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes., Methods: We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals., Results: Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation., Conclusions: These results suggest that populations have remained connected throughout the large, continuous savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees., (© 2020 Botanical Society of America.)

Adaptive evolution is a major driver of organism diversification, but the links between phenotypic traits and environmental niche remain little documented in tropical trees. Moreover, trait-niche relationships are complex because a correlation between the traits and environmental niches displayed by a sample of species may result from (a) convergent evolution if different environmental conditions have selected different sets of traits, and/or (b) phylogenetic inertia if niche and morphological differences between species are simply function of their phylogenetic divergence, in which case the trait-niche correlation does not imply any direct causal link. Here, we aim to assess the respective roles of phylogenetic inertia and convergent evolution in shaping the differences of botanical traits and environmental niches among congeneric African tree species that evolved in different biomes.This issue was addressed with the tree genus Guibourtia Benn. (Leguminosae and Detarioideae), which contains 13 African species occupying various forest habitat types, from rain forest to dry woodlands, with different climate and soil conditions. To this end, we combined morphological data with ecological niche modelling and used a highly resolved plastid phylogeny of the 13 African Guibourtia species.First, we demonstrated phylogenetic signals in both morphological traits (Mantel test between phylogenetic and morphological distances between species: r  = .24, p  = .031) and environmental niches (Mantel test between phylogenetic and niche distances between species: r  = .23, p  = .025). Second, we found a significant correlation between morphology and niche, at least between some of their respective dimensions (Mantel's r  = .32, p  = .013), even after accounting for phylogenetic inertia (Phylogenetic Independent Contrast: r  = .69, p  = .018). This correlation occurred between some leaflet and flower traits and solar radiation, relative humidity, precipitations, and temperature range.Our results demonstrate the convergent evolution of some morphological traits in response to climatic factors in congeneric tree species and highlight the action of selective forces, along with neutral ones, in shaping the divergence between congeneric tropical plants., Competing Interests: None declared., (© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Detarioideae is well known for its high diversity of floral traits, including flower symmetry, number of organs, and petal size and morphology. This diversity has been characterized and studied at higher taxonomic levels, but limited analyses have been performed among closely related genera with contrasting floral traits due to the lack of fully resolved phylogenetic relationships. Here, we used four representative transcriptomes to develop an exome capture (target enrichment) bait for the entire subfamily and applied it to the Anthonotha clade using a complete data set (61 specimens) representing all extant floral diversity. Our phylogenetic analyses recovered congruent topologies using ML and Bayesian methods. Anthonotha was recovered as monophyletic contrary to the remaining three genera (Englerodendron, Isomacrolobium and Pseudomacrolobium), which form a monophyletic group sister to Anthonotha. We inferred a total of 35 transitions for the seven floral traits (pertaining to flower symmetry, petals, stamens and staminodes) that we analyzed, suggesting that at least 30% of the species in this group display transitions from the ancestral condition reconstructed for the Anthonotha clade. The main transitions were towards a reduction in the number of organs (petals, stamens and staminodes). Despite the high number of transitions, our analyses indicate that the seven characters are evolving independently in these lineages. Petal morphology is the most labile floral trait with a total of seven independent transitions in number and seven independent transitions to modification in petal types. The diverse petal morphology along the dorsoventral axis of symmetry within the flower is not associated with differences at the micromorphology of petal surface, suggesting that in this group all petals within the flower might possess the same petal identity at the molecular level. Our results provide a solid evolutionary framework for further detailed analyses of the molecular basis of petal identity., (Copyright © 2019 Elsevier Inc. All rights reserved.)

The natural regeneration of tree species depends on seed and pollen dispersal. To assess whether limited dispersal could be critical for the sustainability of selective logging practices, we performed parentage analyses in two Central African legume canopy species displaying contrasted floral and fruit traits: Distemonanthus benthamianus and Erythrophleum suaveolens. We also developed new tools linking forward dispersal kernels with backward migration rates to better characterize long-distance dispersal. Much longer pollen dispersal in D. benthamianus (mean distance d p  = 700 m, m p  = 52% immigration rate in 6 km 2 plot, s = 7% selfing rate) than in E. suaveolens (d p  = 294 m, m p  = 22% in 2 km 2 plot, s = 20%) might reflect different insect pollinators. At a local scale, secondary seed dispersal by vertebrates led to larger seed dispersal distances in the barochorous E. suaveolens (d s  = 175 m) than in the wind-dispersed D. benthamianus (d s  = 71 m). Yet, seed dispersal appeared much more fat-tailed in the latter species (15%-25% seeds dispersing >500 m), putatively due to storm winds (papery pods). The reproductive success was correlated to trunk diameter in E. suaveolens and crown dominance in D. benthamianus. Contrary to D. benthamianus, E. suaveolens underwent significant assortative mating, increasing further the already high inbreeding of its juveniles due to selfing, which seems offset by strong inbreeding depression. To achieve sustainable exploitation, seed and pollen dispersal distances did not appear limiting, but the natural regeneration of E. suaveolens might become insufficient if all trees above the minimum legal cutting diameter were exploited. This highlights the importance of assessing the diameter structure of reproductive trees for logged species., (© 2019 John Wiley & Sons Ltd.)

Greenwayodendron (Annonaceae) is a tropical African genus of trees occurring mainly in rain forests. Until recently, Greenwayodendron contained only two species: Greenwayodendronoliveri from West Africa and Greenwayodendronsuaveolens from Central and East Africa. Genetic data, using chloroplast haplotypes and nuclear microsatellites as well as morphometric analyses, provided important information on the delineation of species. Greenwayodendron now contains six species, including two new species ( Greenwayodendronglabrum Lissambou, Hardy & Couvreur, sp. nov. and Greenwayodendronlittorale Lissambou, Dauby & Couvreur, sp. nov. ). Greenwayodendronsuaveolensvar.gabonica and Greenwayodendronsuaveolenssubsp.usambaricum are recognised as distinct species: Greenwayodendrongabonicum and comb. nov. , respectively. A key, detailed descriptions of morphology and geographic distributions, as well as notes on their ecology and uses are presented for all species. Preliminary conservation assessments following IUCN criteria are also provided. Two species are preliminarily identified as threatened, one as Endangered and one as Vulnerable.Greenwayodendronusambaricum comb. nov. , respectively. A key, detailed descriptions of morphology and geographic distributions, as well as notes on their ecology and uses are presented for all species. Preliminary conservation assessments following IUCN criteria are also provided. Two species are preliminarily identified as threatened, one as Endangered and one as Vulnerable.

Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction. All species except G. demeusei and G. copallifera appear monophyletic. Dispersal from Africa to America across the Atlantic Ocean is the most plausible hypothesis to explain the occurrence of Neotropical Guibourtia species, which diverged ca. 11.8 Ma from their closest African relatives. The diversification of the three main clades of African Guibourtia is concomitant to Miocene global climate changes, highlighting pre-Quaternary speciation events. These clades differ by their reproductive characters, which validates the three subgenera previously described: Pseudocopaiva, Guibourtia and Gorskia. Within most monophyletic species, plastid lineages start diverging from each other during the Pliocene or early Pleistocene, suggesting that these species already arose during this period. The multiple transitions between rain forests and dry forests/savannahs inferred here through the plastid phylogeny in each Guibourtia subgenus address thus new questions about the role of phylogenetic relationships in shaping ecological niche and morphological similarity among taxa., (Copyright © 2017 Elsevier Inc. All rights reserved.)

The Red List Categories and the accompanying five criteria developed by the International Union for Conservation of Nature (IUCN) provide an authoritative and comprehensive methodology to assess the conservation status of organisms. Red List criterion B, which principally uses distribution data, is the most widely used to assess conservation status, particularly of plant species. No software package has previously been available to perform large-scale multispecies calculations of the three main criterion B parameters [extent of occurrence (EOO), area of occupancy (AOO) and an estimate of the number of locations] and provide preliminary conservation assessments using an automated batch process. We developed ConR , a dedicated R package, as a rapid and efficient tool to conduct large numbers of preliminary assessments, thereby facilitating complete Red List assessment. ConR (1) calculates key geographic range parameters (AOO and EOO) and estimates the number of locations sensu IUCN needed for an assessment under criterion B; (2) uses this information in a batch process to generate preliminary assessments of multiple species; (3) summarize the parameters and preliminary assessments in a spreadsheet; and (4) provides a visualization of the results by generating maps suitable for the submission of full assessments to the IUCN Red List. ConR can be used for any living organism for which reliable georeferenced distribution data are available. As distributional data for taxa become increasingly available via large open access datasets, ConR provides a novel, timely tool to guide and accelerate the work of the conservation and taxonomic communities by enabling practitioners to conduct preliminary assessments simultaneously for hundreds or even thousands of species in an efficient and time-saving way.

Premise of the Study: Microsatellite primers (simple sequence repeats [SSRs]) were developed in Guibourtia ehie (Fabaceae, Detarioideae) to study population genetic structure and the history of African vegetation., Methods and Results: We isolated 18 polymorphic SSRs from a nonenriched genomic library. This set of primer pairs was tested on four populations, and the results showed two to 16 alleles per locus with mean observed and expected heterozygosities of 0.27 ± 0.05 and 0.57 ± 0.05, respectively. Cross-amplification tests in 13 congeneric species were successful for the four taxa belonging to the subgenus Gorskia ., Conclusions: This set of microsatellite markers will be useful to investigate the phylogeography and population genetics of G. ehie , a key representative of African semideciduous moist forests.

Premise of the Study: Multiplexes of nuclear microsatellite primers were developed to investigate population genetic structure and diversity in two exploited African rainforest trees: Entandrophragma candollei and E. utile (Meliaceae)., Methods and Results: Microsatellite isolation was performed simultaneously on two nonenriched genomic libraries after next-generation sequencing. We developed 16 and 22 polymorphic markers for E. candollei and E. utile in three and four multiplexes, respectively. The number of alleles ranged from two to 17 for E. candollei and from three to 19 for E. utile . Mean expected and observed heterozygosity ranged between 0.75 ± 0.13 and 0.55 ± 0.23 for E. candollei and between 0.73 ± 0.10 and 0.49 ± 0.2 for E. utile ., Conclusions: These sets of nuclear microsatellite markers constitute useful tools for exploring gene flow patterns in these two Entandrophragma species.

Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported clade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20Ma while extant tetraploid species started diverging c. 7.0 or 9.4Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics., (Copyright © 2016 Elsevier Inc. All rights reserved.)

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.

Premise of the Study: Nuclear microsatellites (nSSRs) were designed for Guibourtia tessmannii (Fabaceae, Caesalpinioideae), a highly exploited African timber tree, to study population genetic structure and gene flow., Methods and Results: We developed 16 polymorphic nSSRs from a genomic library tested in three populations of G. tessmannii and two populations of G. coleosperma. These nSSRs display three to 14 alleles per locus (mean 8.94) in G. tessmannii. Cross-amplification tests in nine congeneric species demonstrated that the genus Guibourtia contains diploid and polyploid species. Flow cytometry results combined with nSSR profiles suggest that G. tessmannii is octoploid., Conclusions: nSSRs revealed that African Guibourtia species include both diploid and polyploid species. These markers will provide information on the mating system, patterns of gene flow, and genetic structure of African Guibourtia species.

Premise of the Study: Microsatellites were designed and characterized in the African timber forest tree Terminalia superba (Combretaceae). Due to their high variability, these markers are suitable to investigate gene flow patterns and the structure of genetic diversity., Methods and Results: From a genomic library obtained by next-generation sequencing, seven monomorphic and 14 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed two to 27 alleles (mean 11.4; expected heterozygosity range 0.283-0.940, mean 0.736) in one population from southeastern Cameroon. Genotypes were typical of an outbreeding diploid species, although null alleles explain a significant heterozygote deficit in three loci. Cross-amplification in three congeneric species (T. ivorensis, T. avicennioides, and T. mantaly) failed, suggesting that T. superba is rather divergent., Conclusions: This set of newly developed microsatellite markers will be useful for assessing the genetic diversity, population structure, and demographic history of T. superba in tropical African forests.

Premise of the Study: Microsatellite markers were isolated in the rainforest tree Lophira alata (Ochnaceae), an important timber tree from Central Africa, and cross-amplified on its savannah counterpart, L. lanceolata., Methods and Results: From a microsatellite-enriched library sequenced on a 454 GS FLX platform, 13 primer combinations were identified. Amplification was optimized in two multiplex reactions. The primers amplified di- and trinucelotide repeats, with two to seven alleles per locus. Eleven primers also amplified in L. lanceolata., Conclusions: Microsatellite primers developed for the genus Lophira displayed sufficient variation to investigate hybridization between congeneric species in the rainforest-savannah transition.

Premise of the Study: Microsatellites were developed in the vulnerable African rainforest tree Afzelia bipindensis to investigate gene flow patterns. •, Methods and Results: Using 454 GS-FLX technique, 16 primer sets were identified and optimized, leading to 11 polymorphic and readable markers displaying each six to 25 alleles in a population. Up to four alleles per individual were found in each of the loci, without evidence of fixed heterozygosity, suggesting an autotetraploid genome. Cross-amplification succeeded for all loci in the African rainforest species A. pachyloba and A. bella, which appeared tetraploid, and for most loci in the African woodland species A. africana and A. quanzensis, which appeared diploid, but failed in the Asian species A. xylocarpa. Flow cytometry confirmed the suspected differences in ploidy. •, Conclusions: African Afzelia species are diploid or tetraploid, a situation rarely documented in tropical trees. These newly developed microsatellites will help in the study of their mating system and gene flow patterns.

In macroevolutionary studies, different approaches are commonly used to measure phylogenetic signal--the tendency of related taxa to resemble one another--including the K statistic and the Mantel test. The latter was recently criticized for lacking statistical power. Using new simulations, we show that the power of the Mantel test depends on the metrics used to define trait distances and phylogenetic distances between species. Increasing power is obtained by lowering variance and increasing negative skewness in interspecific distances, as obtained using Euclidean trait distances and the complement of Abouheif proximity as a phylogenetic distance. We show realistic situations involving "measurement error" due to intraspecific variability where the Mantel test is more powerful to detect a phylogenetic signal than a permutation test based on the K statistic. We highlight limitations of the K-statistic (univariate measure) and show that its application should take into account measurement errors using repeated measures per species to avoid estimation bias. Finally, we argue that phylogenetic distograms representing Euclidean trait distance as a function of the square root of patristic distance provide an insightful representation of the phylogenetic signal that can be used to assess both the impact of measurement error and the departure from a Brownian evolution model., (© 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.)

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.