Consistent patterns of common species across tropical tree communities

Trees structure the Earth's most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations1-6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth's 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world's most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.

Resistance of African tropical forests to an extreme climate anomaly

The responses of tropical forests to environmental change are critical uncertainties in predicting the future impacts of climate change. The positive phase of the 2015-2016 El Niño Southern Oscillation resulted in unprecedented heat and low precipitation in the tropics with substantial impacts on the global carbon cycle. The role of African tropical forests is uncertain as their responses to short-term drought and temperature anomalies have yet to be determined using on-the-ground measurements. African tropical forests may be particularly sensitive because they exist in relatively dry conditions compared with Amazonian or Asian forests, or they may be more resistant because of an abundance of drought-adapted species. Here, we report responses of structurally intact old-growth lowland tropical forests inventoried within the African Tropical Rainforest Observatory Network (AfriTRON). We use 100 long-term inventory plots from six countries each measured at least twice prior to and once following the 2015-2016 El Niño event. These plots experienced the highest temperatures and driest conditions on record. The record temperature did not significantly reduce carbon gains from tree growth or significantly increase carbon losses from tree mortality, but the record drought did significantly decrease net carbon uptake. Overall, the long-term biomass increase of these forests was reduced due to the El Niño event, but these plots remained a live biomass carbon sink (0.51 ± 0.40 Mg C ha-1 y-1) despite extreme environmental conditions. Our analyses, while limited to African tropical forests, suggest they may be more resistant to climatic extremes than Amazonian and Asian forests.

A map of African humid tropical forest aboveground biomass derived from management inventories

Forest biomass is key in Earth carbon cycle and climate system, and thus under intense scrutiny in the context of international climate change mitigation initiatives (e.g. REDD+). In tropical forests, the spatial distribution of aboveground biomass (AGB) remains, however, highly uncertain. There is increasing recognition that progress is strongly limited by the lack of field observations over large and remote areas. Here, we introduce the Congo basin Forests AGB (CoFor-AGB) dataset that contains AGB estimations and associated uncertainty for 59,857 1-km pixels aggregated from nearly 100,000 ha of in situ forest management inventories for the 2000 - early 2010s period in five central African countries. A comprehensive error propagation scheme suggests that the uncertainty on AGB estimations derived from c. 0.5-ha inventory plots (8.6-15.0%) is only moderately higher than the error obtained from scientific sampling plots (8.3%). CoFor-AGB provides the first large scale view of forest AGB spatial variation from field data in central Africa, the second largest continuous tropical forest domain of the world.

Miocene Diversification in the Savannahs Precedes Tetraploid Rainforest Radiation in the African Tree Genus Afzelia (Detarioideae, Fabaceae)

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.

Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis reveals no significant past fragmentation of their distribution ranges

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.

Do topography and fruit presence influence occurrence and intensity of crop-raiding by forest elephants (Loxodonta africana cyclotis)?

Crop damage by forest elephants (Loxodonta africana cyclotis) and the resulting human-elephant conflict are issues of great concern for both the conservation of the species and the protection of rural livelihoods in Central Africa. Addressing these problems requires identifying the factors that facilitate or impede crop-raiding by forest elephants. Yet to date, the environmental or anthropogenic factors that influence the occurrence and intensity of crop-raiding by forest elephants are largely unknown. We used a multivariate approach to investigate conditions under which forest elephants raid some fields and not others in the buffer zone of Monts de Cristal National Park (MCNP), Gabon. We first interviewed 121 farmers from 11 villages situated within 10 km of MCNP regarding the occurrence of elephant crop-raiding of their fields. We then collected data on 39 explanatory variables to characterize the agricultural fields. Of these, the most important predictors of elephant raid occurrence of crop damage were presence of fruit trees, elephant deterrents (scarecrows, fire, wire string fences and empty barrels), and field topography. We secondly assessed the effect of stage of crop growth, presence of fruit trees, field topography and presence of elephant deterrents on crop-raiding occurrence and intensity by counting raids and measuring areas of crop damage every week in 17 plantations over 19 weeks in the most elephant-impacted zone of the study area. We found that fruit presence and stage of crop growth led to more intense damage to crops, whereas local deterrents did not inhibit raiding events and crop damage by elephants. We report a tradeoff between non-timber forest products (NTFP) services and crop-raiding by elephants. We show for the first time that steep topography impedes elephant damage to crops with no raids recorded in fields with surrounding slopes greater than 25%. We discuss whether farming on steep fields could be used as a strategy for mitigating crop-raiding to favor human-elephant coexistence and enhance elephant conservation.

The persistence of carbon in the African forest understory

Quantifying carbon dynamics in forests is critical for understanding their role in long-term climate regulation^1-4. Yet little is known about tree longevity in tropical forests^3,5-8, a factor that is vital for estimating carbon persistence^3,4. Here we calculate mean carbon age (the period that carbon is fixed in trees⁷) in different strata of African tropical forests using (1) growth-ring records with a unique timestamp accurately demarcating 66 years of growth in one site and (2) measurements of diameter increments from the African Tropical Rainforest Observation Network (23 sites). We find that in spite of their much smaller size, in understory trees mean carbon age (74 years) is greater than in sub-canopy (54 years) and canopy (57 years) trees and similar to carbon age in emergent trees (66 years). The remarkable carbon longevity in the understory results from slow and aperiodic growth as an adaptation to limited resource availability^9-11. Our analysis also reveals that while the understory represents a small share (11%) of the carbon stock^12,13, it contributes disproportionally to the forest carbon sink (20%). We conclude that accounting for the diversity of carbon age and carbon sequestration among different forest strata is critical for effective conservation management^14-16 and for accurate modelling of carbon cycling⁴.

The limited contribution of large trees to annual biomass production in an old-growth tropical forest

Although the importance of large trees regarding biodiversity and carbon stock in old-growth forests is undeniable, their annual contribution to biomass production and carbon uptake remains poorly studied at the stand level. To clarify the role of large trees in biomass production, we used data of tree growth, mortality, and recruitment monitored during 20 yr in 10 4-ha plots in a species-rich tropical forest (Central African Republic). Using a random block design, three different silvicultural treatments, control, logged, and logged + thinned, were applied in the 10 plots. Annual biomass gains and losses were analyzed in relation to the relative biomass abundance of large trees and by tree size classes using a spatial bootstrap procedure. Although large trees had high individual growth rates and constituted a substantial amount of biomass, stand-level biomass production decreased with the abundance of large trees in all treatments and plots. The contribution of large trees to annual stand-level biomass production appeared limited in comparison to that of small trees. This pattern did not only originate from differences in abundance of small vs. large trees or differences in initial biomass stocks among tree size classes, but also from a reduced relative growth rate of large trees and a relatively constant mortality rate among tree size classes. In a context in which large trees are increasingly gaining attention as being a valuable and a key structural characteristic of natural forests, the present study brought key insights to better gauge the relatively limited role of large trees in annual stand-level biomass production. In terms of carbon uptake, these results suggest, as already demonstrated, a low net carbon uptake of old-growth forests in comparison to that of logged forests. Tropical forests that reach a successional stage with relatively high density of large trees progressively cease to be carbon sinks as large trees contribute sparsely or even negatively to the carbon uptake at the stand level.

History of the fragmentation of the African rain forest in the Dahomey Gap: insight from the demographic history of Terminalia superba

Paleo-environmental reconstructions show that the distribution of tropical African rain forests was affected by Quaternary climate changes. They suggest that the Dahomey Gap (DG)-the savanna corridor that currently separates Upper Guinean (UG, West Africa) and Lower Guinean (LG, western Central Africa) rain forest blocks-was forested during the African Humid Holocene period (from at least 9 ka till 4.5 ka), and possibly during other interglacial periods, while an open vegetation developed in the DG under drier conditions, notably during glacial maxima. Nowadays, relics of semi-deciduous forests containing UG and LG forest species are still present within the DG. We used one of these species, the pioneer tree Terminalia superba (Combretaceae), to study past forest fragmentation in the DG and its impact on infraspecific biodiversity. A Bayesian clustering analysis of 299 individuals genotyped at 14 nuclear microsatellites revealed five parapatric genetic clusters (UG, DG, and three in LG) with low to moderate genetic differentiation (Fst from 0.02 to 0.24). Approximate Bayesian Computation analyses inferred a demographic bottleneck around the penultimate glacial period in all populations. They also supported an origin of the DG population by admixture of UG and LG populations around 54,000 (27,600-161,000) years BP, thus before the Last Glacial Maximum. These results contrast with those obtained on Distemonanthus benthamianus where the DG population seems to originate from the Humid Holocene period. We discuss these differences in light of the ecology of each species. Our results challenge the simplistic view linking population fragmentation/expansion with glacial/interglacial periods in African forest species.

Evolution in the Amphi-Atlantic tropical genus Guibourtia (Fabaceae, Detarioideae), combining NGS phylogeny and morphology

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.

Extensive seed and pollen dispersal and assortative mating in the rain forest tree Entandrophragma cylindricum (Meliaceae) inferred from indirect and direct analyses

Pollen and seed dispersal are key processes affecting the demographic and evolutionary dynamics of plant species and are also important considerations for the sustainable management of timber trees. Through direct and indirect genetic analyses, we studied the mating system and the extent of pollen and seed dispersal in an economically important timber species, Entandrophragma cylindricum (Meliaceae). We genotyped adult trees, seeds and saplings from a 400-ha study plot in a natural forest from East Cameroon using eight nuclear microsatellite markers. The species is mainly outcrossed (t = 0.92), but seeds from the same fruit are often pollinated by the same father (correlated paternity, r_p  = 0.77). An average of 4.76 effective pollen donors (N_ep ) per seed tree contributes to the pollination. Seed dispersal was as extensive as pollen dispersal, with a mean dispersal distance in the study plot approaching 600 m, and immigration rates from outside the plot to the central part of the plot reaching 40% for both pollen and seeds. Extensive pollen- and seed-mediated gene flow is further supported by the weak, fine-scale spatial genetic structure (Sp statistic = 0.0058), corresponding to historical gene dispersal distances (σ_g ) reaching approximately 1,500 m. Using an original approach, we showed that the relatedness between mating individuals (F_ij  = 0.06) was higher than expected by chance, given the extent of pollen dispersal distances (expected F_ij  = 0.02 according to simulations). This remarkable pattern of assortative mating could be a phenomenon of potentially consequential evolutionary and management significance that deserves to be studied in other plant populations.

Characterization of microsatellite markers in the African tropical tree species Guibourtia ehie (Fabaceae, Detarioideae)

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.

Present-day central African forest is a legacy of the 19th century human history

The populations of light-demanding trees that dominate the canopy of central African forests are now aging. Here, we show that the lack of regeneration of these populations began ca. 165 ya (around 1850) after major anthropogenic disturbances ceased. Since 1885, less itinerancy and disturbance in the forest has occurred because the colonial administrations concentrated people and villages along the primary communication axes. Local populations formerly gardened the forest by creating scattered openings, which were sufficiently large for the establishment of light-demanding trees. Currently, common logging operations do not create suitable openings for the regeneration of these species, whereas deforestation degrades landscapes. Using an interdisciplinary approach, which included paleoecological, archaeological, historical, and dendrological data, we highlight the long-term history of human activities across central African forests and assess the contribution of these activities to present-day forest structure and composition. The conclusions of this sobering analysis present challenges to current silvicultural practices and to those of the future.

DOI:http://dx.doi.org/10.7554/eLife.20343.001

The world’s forests contain trillions of trees. Some of those trees require more light than others to mature, and certain species can only grow to reach the forest canopy if they have access to sunlight throughout their whole life.

Central Africa is home to the second largest tropical rainforest in the world. Previous studies showed that few young trees of light-demanding species were growing to replace the old trees in this forest. As a result this population is aging and at risk of disappearing, which is a major concern. Many light-demanding tree species in the Central African forest are cut down for their valuable timber. However, if young trees do not grow to replace the mature ones that are logged, even logging operations that follow national and international environmental rules cannot guarantee the sustainability of these trees.

As such, Morin-Rivat et al. set out to understand what changed in the Central African forest in the past to stop the regeneration of the light-demanding trees. The analyses focused on four species classified as light-demanding trees in part of Central Africa called the northern Congo Basin. Most of the trees in these species were about 165 years old. This was the case even though the different species grow at different rates, and it means that they all grew from young trees that settled in the middle of the 19^th century.

So what was it that changed after this period to stop this population of light-demanding trees in the Central African forest from regenerating? By combining information from a number of datasets and historical records, Morin-Rivat et al. arrived at the following conclusion. Before the mid-19^th century, many people lived in the forest and their activities created clearings that turned the forest into a relatively patchy landscape. However from about 1850 onwards, when Europeans started to colonize the region, people and villages were moved out of the forests and closer to rivers and roads for administrative and commercial purposes. Moreover, many people were killed in conflicts or died because of newly introduced diseases, which also led to fewer people in the forest. As a result, the forest became less disturbed. With fewer clearings, fewer light-demanding trees would have had enough access to sunlight to grow to maturity.

The findings of Morin-Rivat et al. show that disturbance is needed to maintain certain forest habitats and tree species, including light-demanding species of tree. As common logging operations do not create openings large enough to guarantee that such species will be able to establish themselves naturally, complementary treatments are needed. These might include selectively logging mature trees around young members of light-demanding species, or planting threatened species.

DOI:http://dx.doi.org/10.7554/eLife.20343.002

Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia

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.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0831-9) contains supplementary material, which is available to authorized users.

Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae)

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.

Microsatellite development for the genus Guibourtia (Fabaceae, Caesalpinioideae) reveals diploid and polyploid species

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.

IS THE WESTERN LOWLAND GORILLA A GOOD GARDENER? EVIDENCE FOR DIRECTED DISPERSAL IN SOUTHEAST GABON

Dans les forêts tropicales d’Afrique cen- trale, le gorille des plaines occidentales dépose la plupart des graines qu’il dis- perse dans des nids bien éclairés pro- pices à la croissance de plantules, laquelle est susceptible d’être renforcée par l’effet fertilisant des matières fécales entourant les graines. Cet effet fertilisant n’avait jamais été testé. Notre étude visait ainsi à déterminer si le dépôt de graines par les gorilles (i) dans une matrice fécale et (ii) dans leurs nids présente un avan- tage pour le développement des plan- tules (taux de croissance et de foliation) et pour leur survie (% de plantules survi- vantes). Pour évaluer l’effet de la matrice fécale, des graines de Santiria trimera (Burséracée), Chrysophyllum lacourtia- num (Sapotacée) et Plagiostyles africana (Euphorbiacée) recueillies dans des déjections de gorilles ont été semées en pépinière avec et sans matrice fécale. Des plantules de Santiria trimera et Dacryodes normandii (Burséracées) ont été installées dans des nids et en forêt de terra firme à couvert fermé afin d’évaluer l’impact du dépôt de graines sur le déve- loppement et la survie des plantules. Nos observations montrent une influence positive de la matrice fécale sur le déve- loppement des plantules des essences étudiées, mais aucun effet sur leur survie. Concernant les sites de dépôt, les taux de croissance observés étaient de deux à dix fois plus élevés dans les nids qu’en forêt à couvert fermé. Le développement accru des plantules est corrélé positivement avec l’ouverture du couvert forestier. Des études in situ de la germination et de la croissance et la survie des plantules sont nécessaires pour mieux caractériser le destin des graines dispersées par les gorilles. Cependant, nos résultats tendent à prouver que les gorilles jouent un rôle de dispersion dirigée important dans les forêts à couvert ouvert. 

Microsatellite development and flow cytometry in the African tree genus Afzelia (Fabaceae, Caesalpinioideae) reveal a polyploid complex

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.

Large-scale pattern of genetic differentiation within African rainforest trees: insights on the roles of ecological gradients and past climate changes on the evolution of Erythrophleum spp (Fabaceae)

Background

The evolutionary events that have shaped biodiversity patterns in the African rainforests are still poorly documented. Past forest fragmentation and ecological gradients have been advocated as important drivers of genetic differentiation but their respective roles remain unclear. Using nuclear microsatellites (nSSRs) and chloroplast non-coding sequences (pDNA), we characterised the spatial genetic structure of Erythrophleum (Fabaceae) forest trees in West and Central Africa (Guinea Region, GR). This widespread genus displays a wide ecological amplitude and taxonomists recognize two forest tree species, E. ivorense and E. suaveolens, which are difficult to distinguish in the field and often confused.

Results

Bayesian-clustering applied on nSSRs of a blind sample of 648 specimens identified three major gene pools showing no or very limited introgression. They present parapatric distributions correlated to rainfall gradients and forest types. One gene pool is restricted to coastal evergreen forests and corresponds to E. ivorense; a second one is found in gallery forests from the dry forest zone of West Africa and North-West Cameroon and corresponds to West-African E. suaveolens; the third gene pool occurs in semi-evergreen forests and corresponds to Central African E. suaveolens. These gene pools have mostly unique pDNA haplotypes but they do not form reciprocally monophyletic clades. Nevertheless, pDNA molecular dating indicates that the divergence between E. ivorense and Central African E. suaveolens predates the Pleistocene. Further Bayesian-clustering applied within each major gene pool identified diffuse genetic discontinuities (minor gene pools displaying substantial introgression) at a latitude between 0 and 2°N in Central Africa for both species, and at a longitude between 5° and 8°E for E. ivorense. Moreover, we detected evidence of past population declines which are consistent with historical habitat fragmentation induced by Pleistocene climate changes.

Conclusions

Overall, deep genetic differentiation (major gene pools) follows ecological gradients that may be at the origin of speciation, while diffuse differentiation (minor gene pools) are tentatively interpreted as the signature of past forest fragmentation induced by past climate changes.

Réviser les tarifs de cubage pour mieux gérer les forêts du Cameroun

L'utilisation des tarifs de cubage fait partie du quotidien des aménagistes et gestionnaires forestiers. Toutefois, elle se fait généralement au mépris des conditions d'application (zone géographique, gamme de diamètres), ce qui peut engendrer des erreurs dans les estimations de volume. L'objectif de cette étude est de tester la validité des tarifs de cubage actuellement disponibles pour trois essences des forêts du sud-est du Cameroun, dont ceux utilisés par l'administration nationale et, le cas échéant, de proposer des tarifs adaptés pour la zone d'étude. Trois espèces commerciales sont concernées : le sapelli, Entandrophragma cylindricum, le tali, Erythrophleum suaveolens, et l'assaméla, Pericopsis elata. Les données dendrométriques ont été collectées par échantillonnage destructif de 43 arbres régulièrement répartis sur toute la gamme de diamètres. Le volume du fût a été calculé par la méthode des billons successifs et des tarifs de cubage linéaires et non linéaires ont été ajustés aux données par la méthode des moindres carrés pondérés. Les résultats montrent que le meilleur modèle de cubage est non linéaire pour les trois espèces. Les équations utilisées jusqu'à présent par l'administration forestière sous-estiment significativement le volume des arbres et les erreurs d'estimation sont d'autant plus grandes que la taille de l'arbre est importante. Les tarifs de cubage proposés, une fois validés, devraient pouvoir à l'avenir être utilisés pour une meilleure estimation du volume des arbres dans la zone d'étude. Considérant les enjeux internationaux auxquels adhère le Cameroun (FLEGT et REDD+), il est crucial de disposer d'outils performants d'estimation du volume des arbres. Dans ce contexte, il s'avère important que l'administration forestière camerounaise puisse mener à bien un vaste programme de révision des tarifs de cubage.

Above-ground biomass and structure of 260 African tropical forests

We report above-ground biomass (AGB), basal area, stem density and wood mass density estimates from 260 sample plots (mean size: 1.2 ha) in intact closed-canopy tropical forests across 12 African countries. Mean AGB is 395.7 Mg dry mass ha⁻¹ (95% CI: 14.3), substantially higher than Amazonian values, with the Congo Basin and contiguous forest region attaining AGB values (429 Mg ha⁻¹) similar to those of Bornean forests, and significantly greater than East or West African forests. AGB therefore appears generally higher in palaeo- compared with neotropical forests. However, mean stem density is low (426 ± 11 stems ha⁻¹ greater than or equal to 100 mm diameter) compared with both Amazonian and Bornean forests (cf. approx. 600) and is the signature structural feature of African tropical forests. While spatial autocorrelation complicates analyses, AGB shows a positive relationship with rainfall in the driest nine months of the year, and an opposite association with the wettest three months of the year; a negative relationship with temperature; positive relationship with clay-rich soils; and negative relationships with C : N ratio (suggesting a positive soil phosphorus-AGB relationship), and soil fertility computed as the sum of base cations. The results indicate that AGB is mediated by both climate and soils, and suggest that the AGB of African closed-canopy tropical forests may be particularly sensitive to future precipitation and temperature changes.

Phenological patterns in a natural population of a tropical timber tree species, Milicia excelsa (Moraceae): Evidence of isolation by time and its interaction with feeding strategies of dispersers

PREMISE OF THE STUDY

Population genetic structuring over limited timescales is commonly viewed as a consequence of spatial constraints. Indirect approaches have recently revealed reproductive isolation resulting from flowering time (so-called isolation by time, IBT). Since phenological processes can be subject to selection, the persistence of flowering asynchrony may be due to opposing selective pressures during mating, dispersal, and regeneration phases. Our study aimed to investigate phenology, fruit handling by animals, and their interaction in a timber tree species, Milicia excelsa.

METHODS

We analyzed phenological data collected over 6 years on 69 genotyped trees in a Cameroonian natural rainforest complemented by data from germination trials and field observations of dispersers.

KEY RESULTS

Initiation of flowering was correlated with variation in temperature and relative humidity, but was also affected by genetic factors: pairwise differences in flowering time between nearby individuals correlated with kinship coefficient, and earliness of flowering remained stable over time. A decrease in mean seed production per fruit with increasing flowering time suggests selection against late bloomers. However, germination rate was not affected by seed collection date, and the main seed disperser, the bat Eidolon helvum, seemed to increase in abundance at the end of the reproductive season and preferred trees in open habitats where early and late bloomers are expected.

CONCLUSIONS

The pairwise approach performs well in detecting IBT. The persistence of different mating pools in such a case may result from a trade off between selective forces during the mating and seed dispersal processes.

Development and characterization of microsatellite loci in Pericopsis elata (Fabaceae) using a cost-efficient approach

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.

Will elephants soon disappear from West African savannahs?

Precipitous declines in Africa's native fauna and flora are recognized, but few comprehensive records of these changes have been compiled. Here, we present population trends for African elephants in the 6,213,000 km² Sudano-Sahelian range of West and Central Africa assessed through the analysis of aerial and ground surveys conducted over the past 4 decades. These surveys are focused on the best protected areas in the region, and therefore represent the best case scenario for the northern savanna elephants. A minimum of 7,745 elephants currently inhabit the entire region, representing a minimum decline of 50% from estimates four decades ago for these protected areas. Most of the historic range is now devoid of elephants and, therefore, was not surveyed. Of the 23 surveyed elephant populations, half are estimated to number less than 200 individuals. Historically, most populations numbering less than 200 individuals in the region were extirpated within a few decades. Declines differed by region, with Central African populations experiencing much higher declines (-76%) than those in West Africa (-33%). As a result, elephants in West Africa now account for 86% of the total surveyed. Range wide, two refuge zones retain elephants, one in West and the other in Central Africa. These zones are separated by a large distance (∼900 km) of high density human land use, suggesting connectivity between the regions is permanently cut. Within each zone, however, sporadic contacts between populations remain. Retaining such connectivity should be a high priority for conservation of elephants in this region. Specific corridors designed to reduce the isolation of the surveyed populations are proposed. The strong commitment of governments, effective law enforcement to control the illegal ivory trade and the involvement of local communities and private partners are all critical to securing the future of elephants inhabiting Africa's northern savannas.

Forest refugia revisited: nSSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae)

The impact of the Pleistocene climate oscillations on the structure of biodiversity in tropical regions remains poorly understood. In this study, the forest refuge theory is examined at the molecular level in Milicia excelsa, a dioecious tree with a continuous range throughout tropical Africa. Eight nuclear microsatellites (nSSRs) and two sequences and one microsatellite from chloroplast DNA (cpDNA) showed a deep divide between samples from Benin and those from Lower Guinea. This suggests that these populations were isolated in separate geographical regions, probably for several glacial cycles of the Pleistocene, and that the nuclear gene pools were not homogenized despite M. excelsa's wind-pollination syndrome. The divide could also be related to seed dispersal patterns, which should be largely determined by the migration behaviour of M. excelsa's main seed disperser, the frugivorous bat Eidolon helvum. Within Lower Guinea, a north-south divide, observed with both marker types despite weak genetic structure (nSSRs: F(ST) = 0.035, cpDNA: G(ST)  = 0.506), suggested the existence of separate Pleistocene refugia in Cameroon and the Gabon/Congo region. We inferred a pollen-to-seed dispersal distance ratio of c.1.8, consistent with wide-ranging gene dispersal by both wind and bats. Simulations in an Approximate Bayesian Computation framework suggested low nSSR and cpDNA mutation rates, but imprecise estimates of other demographic parameters, probably due to a substantial gene flow between the Lower Guinean gene pools. The decline of genetic diversity detected in some Gabonese populations could be a consequence of the relatively recent establishment of a closed canopy forest, which could negatively affect M. excelsa's reproductive system.